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Indole-3-acetic acid in microbial and microorganism-plant signaling Stijn Spaepen, Jos Vanderleyden & Roseline Remans Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Heverlee, Belgium Correspondence: Jos Vanderleyden, Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, K.U. Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium. Tel.: 132 16321631; fax: 132 16321966; e-mail: [email protected] Received 4 December 2006; revised 3 March 2007; accepted 12 March 2007. First published online 18 May 2007. DOI:10.1111/j.1574-6976.2007.00072.x Editor: Fritz Unden Keywords indole-3-acetic acid; plant–microorganism interactions; microbial signaling. Abstract Diverse bacterial species possess the ability to produce the auxin phytohormone indole-3-acetic acid (IAA). Different biosynthesis pathways have been identified and redundancy for IAA biosynthesis is widespread among plant-associated bacteria. Interactions between IAA-producing bacteria and plants lead to diverse outcomes on the plant side, varying from pathogenesis to phytostimulation. Reviewing the role of bacterial IAA in different microorganism–plant interactions highlights the fact that bacteria use this phytohormone to interact with plants as part of their colonization strategy, including phytostimulation and circumvention of basal plant defense mechanisms. Moreover, several recent reports indicate that IAA can also be a signaling molecule in bacteria and therefore can have a direct effect on bacterial physiology. This review discusses past and recent data, and emerging views on IAA, a well-known phytohormone, as a microbial metabolic and signaling molecule. Introduction In 1880 Charles Darwin proposed that some plant growth responses are regulated by ‘a matter which transmits its effects from one part of the plant to another’ (Darwin & Darwin, 1880). Several decades later, this ‘matter,’ termed auxin (from the Greek ‘auxein’ which means ‘to grow’), was identified as indole-3-acetic acid (IAA) (K¨ ogl & Koster- mans, 1934; Went & Thimann, 1937). IAA has since been implicated in virtually all aspects of plant growth and development (reviewed by Woodward & Bartel, 2005 and Teale et al., 2006). Intriguingly, the discovery of IAA as a plant growth regulator coincided with the first indication of the molecular mechanisms involved in tumorigenesis induced by Agrobac- terium. Agrobacterium-induced tumors were shown to be sources of IAA (Link & Eggers, 1941) and capable of growth in the absence of plant growth regulators, which are normally required to incite growth of callus from sterile plant tissues (White & Braun, 1941). It was later found that not only plants but also microorganisms including bacteria and fungi are able to synthesize IAA (Kaper & Veldstra, 1958; Gruen, 1959; Perley & Stowe, 1966; Libbert et al., 1970; Arshad & Frankenberger, 1991; Costacurta & Vanderleyden, 1995). In recent years, advancement in understanding the IAA signaling pathway in plants has been truly spectacular. The role of IAA in bacteria has not thus far been investigated in such detail. Undoubtedly, the advancement in plant IAA signaling has also intensified research on the various aspects of bacterial IAA synthesis, including its role in bacteria– plant interactions. As more bacterial species have been analyzed, the role of auxins in plant–microorganism interactions appears diverse. Molecular studies on the biochemical pathways of bacterial IAA synthesis and their regulation have provided some clues on the possible outcomes of the interactions between plants and IAA-producing bacteria, varying from pathogenesis to phytostimulation. Recently, a number of studies have clearly shown that IAA can be a signaling molecule in microorganisms, in both IAA-producing and IAA-nonproducing species. These findings raise new intri- guing questions on the role of IAA in bacteria and their interaction with plants. IAA biosynthesis pathways in bacteria With the analysis of additional bacterial species, different bacterial pathways to synthesize IAA have been identified. A high degree of similarity between IAA biosynthesis pathways FEMS Microbiol Rev 31 (2007) 425–448 c 2007 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved
Transcript
Page 1: Aia review (1)

Indole-3-acetic acid inmicrobial andmicroorganism-plantsignalingStijn Spaepen, Jos Vanderleyden & Roseline Remans

Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Heverlee, Belgium

Correspondence: Jos Vanderleyden,

Department of Microbial and Molecular

Systems, Centre of Microbial and Plant

Genetics, K.U. Leuven, Kasteelpark Arenberg

20, 3001 Heverlee, Belgium. Tel.: 132

16321631; fax: 132 16321966; e-mail:

[email protected]

Received 4 December 2006; revised 3 March

2007; accepted 12 March 2007.

First published online 18 May 2007.

DOI:10.1111/j.1574-6976.2007.00072.x

Editor: Fritz Unden

Keywords

indole-3-acetic acid; plant–microorganism

interactions; microbial signaling.

Abstract

Diverse bacterial species possess the ability to produce the auxin phytohormone

indole-3-acetic acid (IAA). Different biosynthesis pathways have been identified

and redundancy for IAA biosynthesis is widespread among plant-associated

bacteria. Interactions between IAA-producing bacteria and plants lead to diverse

outcomes on the plant side, varying from pathogenesis to phytostimulation.

Reviewing the role of bacterial IAA in different microorganism–plant interactions

highlights the fact that bacteria use this phytohormone to interact with plants as

part of their colonization strategy, including phytostimulation and circumvention

of basal plant defense mechanisms. Moreover, several recent reports indicate that

IAA can also be a signaling molecule in bacteria and therefore can have a direct

effect on bacterial physiology. This review discusses past and recent data, and

emerging views on IAA, a well-known phytohormone, as a microbial metabolic

and signaling molecule.

Introduction

In 1880 Charles Darwin proposed that some plant growth

responses are regulated by ‘a matter which transmits its

effects from one part of the plant to another’ (Darwin &

Darwin, 1880). Several decades later, this ‘matter,’ termed

auxin (from the Greek ‘auxein’ which means ‘to grow’), was

identified as indole-3-acetic acid (IAA) (Kogl & Koster-

mans, 1934; Went & Thimann, 1937). IAA has since been

implicated in virtually all aspects of plant growth and

development (reviewed by Woodward & Bartel, 2005 and

Teale et al., 2006).

Intriguingly, the discovery of IAA as a plant growth

regulator coincided with the first indication of the molecular

mechanisms involved in tumorigenesis induced by Agrobac-

terium. Agrobacterium-induced tumors were shown to be

sources of IAA (Link & Eggers, 1941) and capable of growth

in the absence of plant growth regulators, which are

normally required to incite growth of callus from sterile

plant tissues (White & Braun, 1941). It was later found that

not only plants but also microorganisms including bacteria

and fungi are able to synthesize IAA (Kaper & Veldstra,

1958; Gruen, 1959; Perley & Stowe, 1966; Libbert et al., 1970;

Arshad & Frankenberger, 1991; Costacurta & Vanderleyden,

1995).

In recent years, advancement in understanding the IAA

signaling pathway in plants has been truly spectacular. The

role of IAA in bacteria has not thus far been investigated in

such detail. Undoubtedly, the advancement in plant IAA

signaling has also intensified research on the various aspects

of bacterial IAA synthesis, including its role in bacteria–

plant interactions.

As more bacterial species have been analyzed, the role

of auxins in plant–microorganism interactions appears

diverse. Molecular studies on the biochemical pathways of

bacterial IAA synthesis and their regulation have provided

some clues on the possible outcomes of the interactions

between plants and IAA-producing bacteria, varying from

pathogenesis to phytostimulation. Recently, a number of

studies have clearly shown that IAA can be a signaling

molecule in microorganisms, in both IAA-producing and

IAA-nonproducing species. These findings raise new intri-

guing questions on the role of IAA in bacteria and their

interaction with plants.

IAA biosynthesis pathways in bacteria

With the analysis of additional bacterial species, different

bacterial pathways to synthesize IAA have been identified. A

high degree of similarity between IAA biosynthesis pathways

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

Page 2: Aia review (1)

in plants and bacteria was observed. Here an overview of

bacterial IAA biosynthesis pathways is given (Fig. 1), and the

current status of related genes, proteins and intermediate

metabolites is discussed. Where relevant, comparisons with

plant IAA biosynthesis are made.

Tryptophan has been identified as a main precursor for

IAA biosynthesis pathways in bacteria. The identification of

intermediates led to the identification of five different path-

ways using tryptophan as a precursor for IAA.

Indole-3-acetamide pathway

The indole-3-acetamide (IAM) pathway is the best charac-

terized pathway in bacteria. In this two-step pathway

tryptophan is first converted to IAM by the enzyme trypto-

phan-2-monooxygenase (IaaM), encoded by the iaaM gene.

In the second step IAM is converted to IAA by an IAM

hydrolase (IaaH), encoded by iaaH. The genes iaaM and

iaaH have been cloned and characterized from various

bacteria, such as Agrobacterium tumefaciens, Pseudomonas

syringae, Pantoea agglomerans, Rhizobium and Bradyrhizo-

bium (Sekine et al., 1989; Clark et al., 1993; Morris, 1995;

Theunis et al., 2004). The IAM-related genes have been

detected on the chromosome in different Pseudomonas

species as well as on plasmids such as pPATH of

Pa. agglomerans (Glickmann et al., 1998; Manulis et al.,

1998).

The IAM pathway was described previously as a bacterial-

specific pathway, as no evidence for this pathway could be

found in plants. However, with an improved, highly sensi-

tive method for the analysis of IAM using a combination of

HPLC and GC-MS/MS techniques it was proven beyond

doubt that IAM is an endogenous compound of Arabidopsis

thaliana (Pollmann et al., 2002). Experiments described by

Piotrowski et al. (2001) and Pollmann et al. (2003) further

support the operation of the IAM pathway in Arabidopsis.

Indole-3-pyruvate pathway

The indole-3-pyruvate (IPyA) pathway is thought to be a

major pathway for IAA biosynthesis in plants. However,

the key genes/enzymes have not been identified yet in plants.

In bacteria, IAA production via the IPyA pathway has

been described in a broad range of bacteria, such as the

pythopathogenic bacterium Pa. agglomerans, the beneficial

bacteria Bradyrhizobium, Azospirillum, Rhizobium and

Enterobacter cloacae, and cyanobacteria. The first step in

this pathway is the conversion of tryptophan to IPyA by

an aminotransferase (transamination). In the rate-limiting

step, IPyA is decarboxylated to indole-3-acetaldehyde

(IAAld) by indole-3-pyruvate decarboxylase (IPDC). In the

last step IAAld is oxidized in IAA (Fig. 1). The gene,

encoding for the key enzyme, IPDC, has been isolated and

characterized from Azospirillum brasilense, En. cloacae,

Fig. 1. Overview of the different pathways to synthesize IAA in bacteria. The intermediate referring to the name of the pathway or the pathway itself is

underlined with a dashed line. IAAld, indole-3-acetaldehyde; IAM, indole-3-acetamide; IPDC, indole-3-pyruvate decarboxylase; Trp, tryptophan.

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

426 S. Spaepen et al.

Page 3: Aia review (1)

Pseudomonas putida and Pa. agglomerans (Koga et al., 1991;

Costacurta et al., 1994; Brandl & Lindow, 1996; Patten &

Glick, 2002b). In Azospirillum lipoferum, the ipdC gene is

located on the chromosome (Blaha et al., 2005) but in most

cases the genome localization of this gene has not been

determined. In these organisms, insertional inactivation of

the pathway resulted in a lower IAA production, up to 90%

reduction in Az. brasilense (Prinsen et al., 1993), indicating

the importance of the IPyA pathway in auxin production.

However, no mutants completely abolished in IAA bio-

synthesis could be constructed, indicating redundancy for

IAA biosynthesis pathways.

Tryptamine pathway

In bacteria, the tryptamine (TAM) pathway has been

identified in Bacillus cereus by identification of tryptophan

decarboxylase activity (Perley & Stowe, 1966) and in Azos-

pirillum by detection of the conversion of exogenous trypta-

mine to IAA (Hartmann et al., 1983). In plants tryptamine

was identified as an endogenous compound and genes

encoding for tryptophan decarboxylases (catalyzing the

decarboxylation of tryptophan to tryptamine) have been

cloned and characterized from different plants, indicating

an IAA biosynthetic pathway via tryptamine in plants. The

rate-limiting step for this pathway in plants is probably

catalyzed by a flavin monooxygenase-like protein (YUCCA)

(conversion of tryptamine to N-hydroxyl-tryptamine). The

presence of the intermediates, which are downstream of

N-hydroxyl-tryptamine (presumably indole-3-acetaldoxime

and indole-3-acetaldehyde), still needs to be confirmed (Bak

et al., 2001; Zhao et al., 2001). The last step of this pathway

in bacteria is different to that in plants: in bacteria TAM is

directly converted to IAAld by an amine oxidase (Hartmann

et al., 1983).

Tryptophan side-chain oxidase pathway

Tryptophan side-chain oxidase (TSO) activity has only been

demonstrated in Pseudomonas fluorescens CHA0. In this

pathway tryptophan is directly converted to IAAld bypass-

ing IPyA, which can be oxidized to IAA (Oberhansli et al.,

1991). There are no indications that this pathway exists in

plants.

Indole-3-acetonitrile pathway

The biosynthesis of IAA via indole-3-acetonitrile (IAN) has

been extensively studied in plants in recent years. The last

step in this pathway – the conversion of IAN to IAA by a

nitrilase – was identified by Bartling et al. (1992); the steps

leading to the formation of IAN from tryptophan are still a

matter of debate. Recently, two pathways were suggested for

this formation: one via indolic glucosinolates (glucobrassi-

cin) and another via indole-3-acetaldoxime (Bak et al., 2001;

Zhao et al., 2001). A tryptophan-independent pathway for

the biosynthesis of IAN in plants has been suggested, but not

further examined (Normanly et al., 1993; Bartling et al.,

1994). In bacteria such as Alcaligenes faecalis (Nagasawa

et al., 1990; Kobayashi et al., 1993) nitrilases have been

detected with specificity for indole-3-acetonitrile. In

Ag. tumefaciens and Rhizobium spp., nitrile hydratase and

amidase activity could be identified, indicating the conver-

sion of IAN to IAA via IAM (Kobayashi et al., 1995).

Tryptophan-independent pathway

Analysis of knock-out mutants of Arabidopsis thaliana for

tryptophan biosynthesis (defective in tryptophan synthase

alpha and beta) revealed increased levels of IAA conjugates,

which led to the proposal of a tryptophan-independent

pathway for the biosynthesis of IAA (Last et al., 1991;

Normanly et al., 1993). This pathway branches from in-

dole-3-glycerolphosphate or indole. However, no enzyme of

this pathway has been characterized. The importance (and

existence) of the tryptophan-independent pathway has been

questioned (Muller & Weiler, 2000).

A bacterial tryptophan-independent pathway could be

demonstrated in Az. brasilense by feeding experiments with

labeled precursors. This pathway is predominant in case no

tryptophan is supplied to the medium: 90% of the IAA is

synthesized via the tryptophan-independent pathway, while

0.1% is produced via the IAM pathway (Prinsen et al., 1993).

As no specific enzymes of this pathway have yet been

identified, the existence of this pathway is currently being

reexamined.

Having described these pathways individually, it should

be noted that some bacteria possess more than one pathway.

In Pa. agglomerans for instance genes for the IAM as well as

for the IPyA pathway have been identified (Manulis et al.,

1998). Our present knowledge on IAA biosynthesis in

bacteria dates back to the end of the last century, as reflected

by the list of references. The use of improved analytical

techniques for the detection and quantitation of intermedi-

ates as well as the rapid progress in functional genomics will

undoubtedly provide a more detailed knowledge on the

different IAA biosynthesis pathways present in bacteria.

IAA conjugation and storage

In plants most IAA is found in a conjugated form; only a

small amount of free IAA is present. The role of these

conjugates is diverse: IAA conjugates are involved in trans-

port, storage and protection of IAA from enzymatic degra-

dation. Furthermore, conjugates can control IAA levels in

the cell (homeostatic mechanism) and these compounds can

allow the catabolism of IAA (Cohen & Bandurski, 1982;

Seidel et al., 2006).

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

427Microbial auxin signaling

Page 4: Aia review (1)

The only characterized bacterial gene involved in IAA

conjugation is the indole-3-acetic acid-lysine synthetase

(iaaL) from Pseudomonas savastanoi pv. savastanoi. The

gene product converts IAA to IAA-lysine via an ATP-

dependent formation of an amide bond between the carbox-

yl group of IAA and the epsilon amino acid group of lysine.

It is presumed that IAA is released through hydrolysis from

its conjugated form inside the plant tissue by plant enzymes

(Glass & Kosuge, 1986).

In bacteria some intermediates of IAA biosynthesis can be

converted to storage compounds, e.g. the reduction of

indole-3-pyruvate and indole-3-acetaldehyde to indole-3-

lactic acid (ILA) and indole-3-ethanol or tryptophol respec-

tively. The physiological function of these compounds

remains unknown. ILA is inactive as a phytohormone but

it can compete for auxin-binding sites in plants with IAA

(Sprunck et al., 1995).

Genome-wide screening for key genes inIAA biosynthesis

It has been suggested that 80% of rhizosphere bacteria

produce IAA (Patten & Glick, 1996; Khalid et al., 2004).

However, studies on the identification and characterization

of the key genes or proteins involved in IAA biosynthesis are

few and have mostly been directed to one specific gene or

protein of a biosynthetic pathway. Although a vast collection

of IAA-producing strains are available, the identification of

genes or proteins is restricted to a small group of ‘model

organisms,’ e.g. Ag. tumefaciens, Azospirillum, Pa. agglomer-

ans and En. cloacae. Even in these model organisms,

attempts to generate mutants, completely impaired in IAA

production, failed, indicating that IAA is synthesized via

multiple pathways present in a single bacterial species.

To extend the overview of bacteria with the capacity to

produce IAA, publicly available genomes were analyzed

in silico for the presence of IAA biosynthetic genes. In a first

stage well-characterized genes or proteins were selected to

function as bait in a BLAST search (see Table 1). The genes or

proteins involved in the tryptophan-independent and TSO

pathway are unknown and therefore these pathways could

not be searched for. Additionally, the IAN pathway was

excluded from the analysis due to the lack of characterized

genes or proteins of this pathway in bacteria. In the second

phase of the BLAST algorithm (Altschul et al., 1997), the

translated nucleotide sequence or protein sequence of the

baits were used to identify similar proteins in the sequenced

genomes. BLAST results are summarized and interpreted in

Table 2, which shows the distribution of the different path-

ways among the annotated genomes. Of the 369 genomes

sequenced (sequences retrieved from NCBI on 12 September

2006), 57 genome sequences (15.4%) contain genes neces-

sary to synthesize IAA from tryptophan. The presence of

IAA biosynthetic genes in the genome does not imply that

the bacterium is capable of producing IAA: functional

analysis of the genes is still needed to confirm a possible role

in IAA production. The uncoupling between the presence of

IAA biosynthetic genes and IAA biosynthesis is illustrated by

the anaerobic aromatic-degrading denitrifying bacterium

Azoarcus strain EbN1. The genome encodes a phenylpyr-

uvate decarboxylase and other genes that form part of the

IPyA pathway (Rabus et al., 2005). The bacterium, however,

does not produce auxins (neither IAA nor phenylacetic acid)

as such. The IAA biosynthesis genes are involved in the

Ehrlich pathway (degradation of amino acids via transami-

nation, decarboxylation and dehydrogenation), leading to

phenylacetic acid, which can be further catalyzed into

benzoyl-coenzyme A (CoA) or into 3-ketoadipyl-CoA via

an aerobic degradation. Benzoyl-CoA is a central molecule

that can be further metabolized (via aerobic b-oxidation to

acetyl-CoA and succinyl-CoA, which can enter the tricar-

boxylic acid cycle; Rabus, 2005).

Among bacteria for which the genome is sequenced and

available at NCBI, genes encoding for the IPyA pathway are

most abundant, present in 89.5% of the putative IAA-

producing strains. Even human pathogens possess genes

encoding for IAA biosynthesis via IPyA. However, as de-

scribed above for Azoarcus, it is likely that the genes in

Table 1. Selected proteins as bait for BLAST search

Pathway Gene Organism Accession no.

Cut-off BLAST

E value

IAM Tryptophan monooxygenase Agrobacterium tumefaciens C58 AAD30489 1e-60

IAM Indole-3-acetamide hydrolase Agrobacterium tumefaciens C58 AAD30488 1e-50

IPyA Indole-3-pyruvate decarboxylase Enterobacter cloacae P23234 1e-75

IPyA Phenylpyruvate decarboxylase Azospirillum brasilense Sp245 P51852 1e-75

IPyA/TAM Indole-3-acetaldehyde dehydrogenase Ustilago maydis FB1� AAC49575 1e-75

TAM Tryptophan decarboxylase Catharanthus roseus� CAA47898 1e-50

TAM Copper amine/tyramine oxidase Klebsiella aerogenes P49250 1e-75

�Member of the Eukaryota; sequence data for the gene/protein are not available from Bacteria.

IAM, indole-3-acetamide; IPyA, indole-3-pyruvate; TAM, tryptamine.

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

428 S. Spaepen et al.

Page 5: Aia review (1)

human pathogenic strains are not involved in IAA produc-

tion. They are part of the Ehrlich pathway, leading to

molecules that can enter different metabolic cycles as energy

source. Similarly, ruminal bacteria and anaerobic bacteria

from the human large intestine are able to metabolize

tryptophan and phenylalanine to indolic and phenolic

compounds such as IAA and phenylacetic acid (Amin &

Onodera, 1997; Smith & Macfarlane, 1997; Mohammed

et al., 2003).

In plant-associated bacteria, both the IAM and the IPyA

pathway are distributed among the sequenced genomes.

Phytopathogenic organisms tend to use the IAM pathway

to produce IAA, whereas beneficial bacteria tend to use the

IPyA pathway. As only five genomic sequences of plant-

associated bacteria that have been annotated encode for one

or more possible IAA biosynthetic pathways, this tendency

needs further confirmation. The capacity to produce IAA is

not as widespread as expected in plant-associated bacteria:

19.2% of the sequenced strains have one or more IAA

biosynthetic pathways encoded in their genome. However,

these data are biased owing to a high number of sequenced

genomes of plant-associated Pseudomonas and Xanthomo-

nas strains (46.2% of the plant-associated bacteria, for

which the genome sequence is publicly available). Only the

genome sequence of Ps. syringae pv. syringae B728a encodes

for a possible IAA biosynthetic pathway.

A remarkable observation is the distribution of the TAM

pathway (identified in 8.8% of the putative IAA-producing

strains): genes encoding enzymes of the TAM pathway were

found in cyanobacteria, and soil and plant-associated bac-

teria (Rhodopseudomonas and Mesorhizobium). Via feeding

experiments, the intermediate TAM was identified in Azos-

pirillum and Bacillus cereus (Hartmann et al., 1983). Pro-

teins similar to tryptophan decarboxylase, involved in the

first step of the TAM pathway, have not yet been identified

and characterized in bacteria.

The production of IAA via IPyA has been described for

cyanobacteria (Sergeeva et al., 2002). As cyanobacteria are

the progenitors of chloroplasts, the evolutionary link be-

tween plant and bacterial IAA biosynthesis becomes rele-

vant. In three cyanobacteria species possible key genes,

involved in IAA biosynthesis, could be determined: both

genes for the IPyA pathway, which is considered as a major

IAA biosynthesis pathway detected in plants, as for the TAM

pathway have been identified.

Factors that influence bacterial IAAbiosynthesis

Reports describing factors that alter the level of IAA

biosynthesis and/or the expression of IAA biosynthesis genes

in bacteria are numerous. However, it is not yet possible to

integrate these factors into a comprehensive regulatory

scheme of IAA biosynthesis in bacteria. This is partly due

to the diversity of IAA expression regulation across IAA

biosynthesis pathways and across bacteria. Furthermore,

there is a lack of integrated studies following IAA expression

in different bacteria and different environments.

This part of the review gives an overview of the different

factors that have been described thus far to modulate IAA

biosynthesis and/or expression of genes involved in IAA

biosynthesis and of the remaining gaps in our understand-

ing of the regulation of IAA biosynthesis in bacteria.

Environmental factors modulating IAAbiosynthesis

A first class of factors influencing IAA biosynthesis in

diverse bacteria is related to environmental stress, including

acidic pH, osmotic and matrix stress, and carbon limitation.

In Az. brasilense IAA production and expression of the key

gene ipdC have been shown to be increased under carbon

limitation, during reduction in growth rate and under acidic

pH (Ona et al., 2003, 2005; Vande Broek et al., 2005).

Interestingly, carbon limitation and reduction in growth

rate are both associated with the entry in the stationary

phase, raising the question of the importance of population

growth status in IAA biosynthesis and, vice versa, the

importance of IAA in cell population behavior. The con-

certed action of these two factors is in agreement with the

observation that overproduction of the stress-related

Table 2. Distribution of IAA biosynthetic pathways in publicly available

annotated genomes of bacteria, including cyanobacteria

Pathway IAM IPyA TAM

Plant-associated bacteria 2/5 2/5 1/5

Plant pathogens 2/2 0/2 0/2

Beneficial bacteria 0/3 2/3 1/3

Soil bacteria� 2/5 3/5 1/5

Human pathogens 0/25 25/25 0/25

Cyanobacteria� 0/3 2/3 2/3

Others� 0/19 19/19 1/19

Total� 4/57 51/57 5/57

The number of publicly available genome sequences was 369 (NCBI

database accession on 12 September 2006). Using the BLAST algorithm,

the baits of Table 1 were used to identify similar genes, using the cut-off

value indicated in Table 1. A biosynthetic pathway was present in a

genome sequence when the E value of all biosynthetic genes leading

from tryptophan to IAA was below the threshold. Using this method,

possible IAA biosynthetic pathways could be identified in 57 bacterial

species.�The total number of IAA biosynthetic pathways is higher than the

number of bacterial species due to redundancy in Burkholderia xenover-

ans LB400, Rhodopseudomonas palustris HaA2 and the cyanobacterium

Anabaena variabilis ATCC 29413. All three organisms have the IPyA

pathway in common, in addition to another pathway.

IAM, indole-3-acetamide; IPyA, indole-3-pyruvate; TAM, tryptamine.

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

429Microbial auxin signaling

Page 6: Aia review (1)

stationary-phase sigma factor RpoS enhanced IAA produc-

tion in En. cloacae and Ps. putida (Saleh & Glick, 2001;

Patten & Glick, 2002a).

The pH inducibility of ipdC gene expression in

Az. brasilense seems to be independent of other regulating

environmental factors. This was shown using different

deletions and mutations in the promoter of ipdC (Vande

Broek et al., 2005). An alternative sigma factor, which is

acid-regulated, was suggested to be responsible in passing on

the pH response to ipdC expression (Ona et al., 2003; Vande

Broek et al., 2005). In contrast to Azospirillum, the expres-

sion of the ipdC gene of Pa. agglomerans is not regulated by

pH. In this bacterial species the ipdC gene was shown to be

under control of other environmental stresses: expression

increased 18-fold under low solute and matrix potentials

(Brandl & Lindow, 1997). This effect was not observed for

the expression of ipdC from Az. brasilense (Vande Broek

et al., 2005).

Despite the diversity in stress factors modulating IAA

expression in different bacteria, a common feature can be

identified. The expression of genes involved in IAA bio-

synthesis is fine-tuned to encounter environmental stresses

associated with the soil and plant environment. An acidic

pH is typical for the rhizosphere environment due to proton

extrusion through membranes of root cells. Matrix potential

may be an important condition encountered in the environ-

ment of epiphytic bacteria on plant surfaces such as

Pa. agglomerans.

A second class of factors altering bacterial IAA produc-

tion contains plant extracts or specific compounds and/or

the presence of plant surfaces. In the symbiotic bacterium

Rhizobium sp. strain NGR234, flavonoids, which are pro-

duced by the host plant and accumulate in the rhizosphere,

stimulate IAA production in a NodD1-, NodD2- and

SyrM2-dependent manner. NodD1, NodD2 and SyrM2

form a regulatory cascade that coordinates the expression

of genes under influence of flavonoids (Prinsen et al., 1991;

Theunis et al., 2004). In Xanthomonas axonopodis IAA

production is increased in the presence of plant leaf extracts

from Citrus cinensis. The question as to which specific

compound is responsible for this induction remains unclear

(Costacurta et al., 1998). Similarly, in the phytopathogenic

gram-positive bacterium Rhodococcus fascians IAA produc-

tion is induced by plant extracts. Interestingly, only extracts

from plant tissue infected with R. fascians, the so-called

leavy galls, could upregulate IAA production in R. fascians.

An extract from a mock-inoculated plant had no effect on

IAA biosynthesis (Vandeputte et al., 2005).

The expression of the ipdC gene of Pa. agglomerans is very

low in broth culture and independent from carbon source,

pH, tryptophan availability and O2 availability, but increases

dramatically when the bacterium is grown on plant surfaces,

indicating that a signal from the plant surface is involved

in transcriptional regulation and subsequent IAA pro-

duction. The environmental cues altering ipdC expression

in Pa. agglomerans allow the bacterium to modify its

habitat and exploit plant surfaces (Brandl & Lindow, 1997).

A later study on the spatial pattern of ipdC expression

on plant leaves revealed a heterogeneous distribution of

expression along the surface environment, suggesting that

the leaf surface significantly varies over a small scale (Brandl

et al., 2001). These results indicate that IAA production

by bacteria can be remarkably different within a micro-

environment.

An important molecule that can alter the level of IAA

synthesis is the amino acid tryptophan, identified as the

main precursor for IAA and thus expected to play a role in

modulating the level of IAA biosynthesis. The application of

exogenous tryptophan was shown to increase strongly the

IAA production in various bacteria, for example Azospir-

illum, Pa. agglomerans, Ps. putida and Rhizobium (Prinsen

et al., 1993; Brandl & Lindow, 1996; Patten & Glick, 2002b;

Theunis et al., 2004). In both Az. brasilense Sp7 as in

Ps. putida GR12-2 the presence of tryptophan increased the

expression level of the key enzyme ipdC, three- to four-fold

and five-fold, respectively (Zimmer et al., 1998; Patten &

Glick, 2002b). In the rhizosphere tryptophan can originate

from two sources: released from degrading root and micro-

bial cells and from root exudates. Support for the first source

is the observation that IAA is produced during the late

exponential and stationary phase in Azospirillum (Omay

et al., 1993). The amount of tryptophan in plant root

exudates can vary strongly among plant species (Kravchen-

ko et al., 2004). Although the amount of tryptophan in root

exudates is rather low (Kravchenko et al., 1991), exogenous

tryptophan can be efficiently absorbed by bacteria. As the

Km value, an indicator of the affinity of the transporter for

tryptophan, is low, the affinity of bacteria for tryptophan is

high, which makes them good scavengers for tryptophan.

This results in efficient transport into the cells, even at low

concentration (Marlow & Kosuge, 1972).

Besides the role of the precursor tryptophan in the

regulation of IAA production, IAA biosynthesis can also be

modulated by the end-product IAA and by its intermediates.

In Ps. savastanoi pv. savastanoi the activity of the first

enzyme in the IAM pathway, IaaM, is controlled through

feedback inhibition by IAM and IAA (Hutcheson & Kosuge,

1985). Curiously, while tryptophan stimulates IAA produc-

tion in Azospirillum, anthranilate, a precursor for trypto-

phan, reduces IAA synthesis. By this mechanism IAA

biosynthesis is fine-tuned because tryptophan inhibits an-

thranilate formation by a negative feedback regulation on

the anthranilate synthase, resulting in an indirect induction

of IAA production (Hartmann & Zimmer, 1994).

Interestingly, nitrile hydratase, which catalyzes the first

step in the conversion of IAN to IAA in Ag. tumefaciens, is

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430 S. Spaepen et al.

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induced by its product IAM, indicating a positive feedback

regulation in IAA biosynthesis (Kobayashi et al., 1995).

Another positive feedback mechanism has been described

for Az. brasilense Sp245 by Vande Broek et al. (1999). The

level of IAA production by Az. brasilense increases during

growth, with highest levels of IAA production during the

stationary phase (Prinsen et al., 1993). The expression of the

key gene for IAA production in the presence of significant

amounts of tryptophan, the indole-3-pyruvate decarboxy-

lase gene, increases with the cell density and reaches its

maximum at stationary phase. Cell density-dependent in-

duction of genes can be mediated by small diffusible signal

molecules. Surprisingly, in Az. brasilense Sp245 IAA itself is

responsible for the increase in expression by induction of the

ipdC gene (Vande Broek et al., 1999). Other auxins such as

naphataleneacetic acid and phenylacetic acid (Somers et al.,

2005) also upregulate the expression. Compounds that had

no effect on the expression were IAA conjugates, indole-3-

butyric acid and tryptophan, although IAA production is

enhanced by tryptophan. In contrast to negative control of

the transcription of biosynthetic genes by the end-product,

the positive feedback regulation or autoinduction by IAA is

rather unusual (Vande Broek et al., 1999). The ipdC gene of

Az. brasilense was the first discovered bacterial gene that is

induced by auxins, indicating that proteins responsible for

IAA perception and signal transduction are present in

bacteria.

Genetic factors

Different genetic factors have been described to affect the

level of IAA biosynthesis in bacteria. Firstly, the location of

auxin biosynthesis genes in the genome, either plasmid or

chromosomal, has been shown to modulate the level of IAA

production. Plasmids are generally present in various copies

in the bacterial cell, providing a higher number of IAA

biosynthesis genes that can be transcribed as compared with

IAA biosynthesis genes that are located on the chromosome

(Brandl & Lindow, 1996; Patten & Glick, 1996). In

Ps. savastanoi pv. savastanoi the biosynthetic genes are

located on a plasmid, whereas in Ps. syringae pv. syringae

the homologous genes are encoded on the chromosomal

DNA. In the latter species, a much smaller amount of IAA is

produced. When this Pseudomonas strain is equipped with a

low-copy plasmid, encoding the IAA operon, IAA produc-

tion is increased four-fold (Mazzola & White, 1994), in-

dicating the importance of either the location or the copy

number or both of the encoding genes.

Secondly, the mode of expression, constitutive vs. in-

duced, of IAA biosynthesis genes was observed to differ

across biosynthesis pathways and across bacterial species. In

Ag. tumefaciens and Agrobacterium rhizogenes the region of

the Ti plasmid containing iaaM and iaaH is transferred and

integrated into the plant genome. The genes are expressed

under control of strong constitutive promoters, resulting

in the production of high levels of IAA inside the plant

tissue (reviewed by Costacurta & Vanderleyden, 1995). In

Ps. fluorescens CHA0 the IPyA pathway is presumably

constitutive, while the TSO pathway is only active during

the stationary phase (Oberhansli et al., 1991).

Furthermore, two transcriptional regulators, RpoS –

which regulates the transcription of genes in response to

stress conditions and starvation – and the two-component

system GacS/GacA – which controls the expression of genes

of which many are induced during a late logarithmic growth

phase and have a role in maintaining the competitiveness of

the bacterium in the rhizosphere – have been shown to

interact with the expression level of IAA biosynthesis genes.

The ipdC genes show a typical stationary-phase-dependent

expression. IAA production starts in the late logarithmic to

early stationary phase and the promoter region of some

ipdC genes contains a sequence similar to the consensus

sequence recognized by RpoS. In Ps. putida GR12-2 and

Pa. agglomerans ipdC expression is regulated by RpoS

(Brandl et al., 2001; Patten & Glick, 2002a): the ipdC

promoter region contains elements similar to the RpoS

recognition sequence, and mutants, carrying constitutively

expressed rpoS on a plasmid, produce IAA earlier at con-

sistently elevated levels as compared with wild-type cells

(Patten & Glick, 2002a). In Azospirillum species RpoS is not

present (RpoS is not detected in Alphaproteobacteria). In

this case alternative sigma factors, RpoN and possibly RpoH,

regulate IAA expression (Gysegom, 2005).

In Pseudomonas chlororaphis, the GacS/GacA two-com-

ponent system acts as a negative regulator of the trypto-

phan-dependent IAA biosynthesis (Haas & Keel, 2003; Kang

et al., 2006). The involvement of RpoS and GacS in IAA

production was further confirmed by overexpression of the

rpoS and gacS genes of Ps. fluorescens in two En. cloacae

strains (Saleh & Glick, 2001).

Bacterial IAA in plant--microorganisminteractions

With the analysis of further bacterial species, the role of

bacterial IAA in plant–microorganism interactions appears

to be diverse. Previously, bacterial auxin production was

mainly associated with pathogenesis, specifically with bac-

terial gall formation. However, it became apparent that

many of the phytopathogenic (not only gall-inducing) as

well as plant growth-promoting bacteria have the ability to

synthesize IAA. The broad distribution of IAA biosynthesis

genes across bacteria, the existence of different metabolic

pathways and the diversity in outcomes on the plant side

when IAA-synthesizing bacteria interact with plants, evoke

the question as to why bacteria produce IAA. Except for a

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431Microbial auxin signaling

Page 8: Aia review (1)

few cases, the link between IAA synthesis and plant, pheno-

type has not been demonstrated or at least remains ambig-

uous. This part of the review aims to give an insight into

bacterial IAA production as one of different strategies to

seduce the plant partner.

Factors steering the outcome of the interactionbetween IAA-producing bacteria and plants

IAA is the main auxin in plants, controlling many important

physiological processes including cell enlargement and

division, tissue differentiation, and responses to light and

gravity (Taiz & Zeiger, 1998; Woodward & Bartel, 2005;

Teale et al., 2006). Bacterial IAA producers interacting with

plants have the potential to interfere with any of these

processes by changing in a spatiotemporal way the plant

auxin pool. The impact of exogenous auxin on plant

development ranges from positive to negative effects. The

consequence for the plant is usually a function of (1) the

amount of IAA produced that is available to the plant and

(2) the sensitivity of the plant tissue to changes in IAA

concentration.

The optimal IAA concentration range for a given plant

phenotype may be extremely narrow, as demonstrated by

the isolation of a plant growth-promoting Ps. putida strain

producing IAA and of a plant growth-inhibiting IAA over-

producer mutant producing only four times the amount of

IAA synthesized by the wild-type strain (Xie et al., 1996;

Persello-Cartieaux et al., 2003). Similarly, inoculation with

Pseudomonas thivervalensis, an IAA-producing strain, re-

sulted in reproducible morphological changes of Arabidopsis

roots without effects on plant growth when inoculated at

a concentration of 105 CFU mL�1, and in inhibition of

plant growth when inoculated at concentrations above

106 CFU mL�1 (Persello-Cartieaux et al., 2001). It cannot,

however, be excluded that other factors (e.g. metabolites)

than auxin production contribute to the inhibitory effect of

highly concentrated inoculants. The use of mutant and

transgenic strains and the analysis of inoculant supernatants

are necessary to distinguish further the role of different

bacterial factors in the diverse outcome on the plant side

upon inoculation with increasing concentrations of bacterial

cells.

The actual concentration of bacterial IAA available to

the plant is, in part, contingent upon the physical relation-

ship between the two organisms. Whereas bacterial phyto-

pathogens infect their host plants and, in the peculiar case

of agrobacteria transform plant cells, beneficial bacteria

(symbionts excepted) appear to exert their effect predomi-

nantly while colonizing the external surface of a plant

(Patten & Glick, 1996). However, as more plant tissues are

analyzed for the presence of bacteria, an increasing number

of IAA-producing plant growth-promoting rhizobacteria

(PGPR) are detected inside the plant tissue (Rosenblueth &

Martinez-Romero, 2006).

The pathway used by the plant-associated bacterial strain

to synthesize IAA may further affect the outcome on the

plant side. Phytopathogenetic symptoms are mostly linked

to the IAM pathway, which is generally believed to be a

specific microbial pathway (see above). However, as men-

tioned above, there is growing evidence for the presence of

an IAM pathway in Arabidopsis thaliana (Piotrowski et al.,

2001; Pollmann et al., 2002, 2003, 2006). As plants may not

generally possess the metabolic intermediates or pools of

this pathway, they may not be able to maintain IAA at

nontoxic or physiologically appropriate levels in their tissues

by feedback regulation (Persello-Cartieaux et al., 2003). In

contrast, the biosynthesis of IAA via indole-3-pyruvic acid

and indole-3-acetaldehyde is predominant in higher plants

and is observed in pathogenic as well as in nonpathogenic

bacteria. Most beneficial bacteria produce IAA via the IPyA

pathway. This view of an IAM route linked to pathogenesis

and an IPyA pathway involved in epiphytic and rhizosphere

fitness of the bacteria has been supported through the

generation of mutants of Pa. agglomerans pv. gypsophilae, a

gall-inducing bacterium, in which the different biosynthetic

pathways were disrupted individually or in combination.

Inactivation of the IAM pathway caused the largest reduc-

tion in gall size whereas inactivation of the IPyA pathway

caused a minor, nonsignificant decrease in pathogenicity.

The reverse effect was observed for epiphytic fitness: inacti-

vation of the IAM pathway did not affect colonization

capacity whereas inactivation of the IPyA pathway did

(Manulis et al., 1998). The difference in function of the two

IAA biosynthesis pathways in Pa. agglomerans was asso-

ciated with differences in expression profiles of the corre-

sponding genes. The ipdC gene showed enhanced expression

during colonization while iaaM was upregulated during

later phases of the plant–microorganism interactions, in-

cluding gall formation. However, it was also reported that

cranberry stem gall is induced by multiple opportunistic

bacteria, including Pa. agglomerans strains, which produce

IAA exclusively through the IPyA pathway. These data

indicate that pathogenesis is not necessarily associated with

the IAM pathway for IAA biosynthesis (Vasanthakumar &

McManus, 2004). Furthermore, some nonpathogenic sym-

biotic bacteria including Rhizobium synthesize IAA mainly

through the IAM pathway (Theunis et al., 2004).

In addition to the amount of bacterial auxin produced,

the contrasting effects of IAA on plant development are

linked to the sensitivity of the host itself. The study of the

effect of auxin-producing bacterial strains on wheat (Kucey,

1988), blackcurrant and sourcherry softwood (Dubeikovsky

et al., 1993) highlights the cultivar specificity of the response

of plants to bacteria. More extremely, auxin-resistant mu-

tants of Arabidopsis are insensitive to Ps. thivervalensis

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432 S. Spaepen et al.

Page 9: Aia review (1)

colonization while the same inoculation on wild-type plants

induces changes in root morphology (Persello-Cartieaux

et al., 2001). The host plant can also take an active part in

the regulation of microbial IAA biosynthesis. Transcription

of ipdC in Pa. agglomerans pv. gypsophilae is induced in

response to bean and tobacco compounds, the structure of

which is not yet known (Brandl & Lindow, 1997). As the

ability to produce auxins from tryptophan is common

among soil organisms, it is tempting to assume that bacterial

auxin is in part dependent upon plant-exuded tryptophan

(Persello-Cartieaux et al., 2003). Bar and Okon proposed

that IAA biosynthesis may contribute to bacterial survival in

the rhizosphere by detoxification of plant-exuded trypto-

phan. They observed that addition of 10 mM (1.4 mg mL�1)

or more of tryptophan strongly inhibited growth of Az.

brasilense Sp7. Instability of tryptophan, variation in exuda-

tion across plant species and environments, and the lack of

comprehensive studies on exudation in the rhizosphere

complicate and currently impede linking this observation

of microbial growth inhibition by tryptophan (Bar & Okon,

1992, 1993) with actual rhizosphere activities.

IAA in gall formation

Tumor- and gall-inducing bacteria were the first plant-

associated bacteria in which IAA biosynthesis pathways were

studied because of the suspected role of microbially released

auxins in disturbing plant morphology and development

(Morris, 1995). Agrobacterium tumefaciens, Ag. rhizogenes,

Ps. savastanoi and Pa. agglomerans pv. gypsophilae all possess

the IAM pathway, and the DNA sequence of the iaaM gene

suggests a common evolutionary origin (Morris, 1995). In

all of these bacteria, IAA is involved in pathogenesis.

However, depending on the bacterial species, the mechan-

ism of either gall or tumor formation and the role of IAA

therein differ. Tumor formation induced by Ag. tumefaciens

involves transfer of T-DNA from the bacteria into the host

genome of infected cells. This T-DNA possesses genes (iaaM

and iaaH) encoding the IAM pathway for IAA biosynthesis

(Zambryski, 1992; Zupan et al., 2000). The overproduction

of auxin and cytokinin by the transformed plant cells results

in the typical crown gall or tumor. Other transferred genes

encode enzymes involved in the synthesis of amino acid and

sugar derivatives, the opines, which the strain of Agrobacter-

ium that induces the tumor can use as a source of carbon,

nitrogen and energy. Removing the Ti phytohormone

biosynthesis genes from Agrobacterium abolishes tumor

formation, demonstrating that the IAA as well as the

cytokinins synthesized by the enzymes encoded by the

transferred bacterial oncogenes are essential for tumor

formation. It was proposed by Aloni et al. (1995) that the

high IAA concentrations induced by the enzymes encoded

by the T-DNA genes iaaM and iaaH stimulate ethylene

synthesis in the crown gall. The tumor-induced ethylene

would be the controlling signal that induces narrowing of

the vessels in the host adjacent to the tumor, which, in turn,

substantially limits water and nutrient supply to the shoot

organs above the tumor (Aloni et al., 1995).

The mechanism of gall formation by Pa. agglomerans

pv. gypsophilae on Gypsophila is fundamentally different

from that by Ag. tumefaciens. Gall formation by Pa. agglom-

erans pv. gypsophilae does not involve transfer of DNA into

host cells (Clark et al., 1989); therefore, it requires the

constant presence of living bacteria, in contrast to the

situation with Ag. tumefaciens. Pathogenic and nonpatho-

genic strains of Pa. agglomerans possess chromosomal genes

encoding the IPyA pathway for IAA biosynthesis, whereas

only pathogenic strains carry the genes encoding the IAM

pathway on the pPATHPag plasmid (Clark et al., 1993;

Brandl & Lindow, 1996; Manulis et al., 1998). Inactivation

of the IPyA pathway in Pa. agglomerans pv. gypsophilae did

not affect gall formation significantly, while mutations in

genes of the IAM pathway substantially reduced the gall size

but did not eliminate gall initiation (Clark et al., 1993;

Manulis et al., 1998). This demonstrates that in Pa. agglom-

erans pv. gypsophilae bacterial IAA synthesized by the IAM

pathway contributes to obtain optimal gall size but is not

essential for gall induction. It has been shown that the

translocation of effectors of the type III secretion system

(TTSS) into the host cells is the key factor for gall induction

by Pa. agglomerans pv. gypsophilae (Mor et al., 2001; Manulis

& Barash, 2003; Nizan-Koren et al., 2003). Similar to tumor

development induced by Ag. tumefaciens, an increase in

ethylene is associated with bacterial IAA production in gall

formation induced by Pa. agglomerans pv. gypsophilae

(Chalupowicz et al., 2006).

IAA in plant growth-promoting rhizobacteria

For various PGPR, it has been demonstrated that enhanced

root proliferation is related to bacterial IAA biosynthesis.

Studies with Azospirillum mutants altered in IAA produc-

tion support the view that increased rooting is caused by

Azospirillum IAA synthesis (Dobbelaere et al., 1999). This

increased rooting enhances plant mineral uptake and root

exudation, which in turn stimulates bacterial colonization

and thus amplifies the inoculation effect (Dobbelaere et al.,

1999; Lambrecht et al., 2000; Steenhoudt & Vanderleyden,

2000). Furthermore, the dose–response curve of roots to

cultures with increasing concentrations of Azospirillum

nicely fits the dose–response curve of roots to increasing

concentrations of IAA (Fallik et al., 1994). However, in

several studies it was shown that Azospirillum IAA

biosynthesis alone cannot account for the overall plant

growth-promoting effect observed. Therefore, the ‘additive

hypothesis’ was suggested to explain growth and yield

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433Microbial auxin signaling

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promotion with Azospirillum, postulating that growth pro-

motion is the result of multiple mechanisms (phytohor-

mone biosynthesis, nitrogen fixation, among others)

working together (Bashan & Holguin, 1997).

Similarly, the capacity of Ps. putida GR12-2 to stimulate

root elongation was shown to be related to its production of

IAA but production of IAA alone does not account for

growth promotion, as evidenced by a study with IAA-

overproducing mutants (Xie et al., 1996). In their study

transposon mutagenesis was used to isolate seven mutants

that overproduced IAA in comparison with the wild-type.

Interestingly, six of the seven mutants, including one which

produced IAA at three times the rate of GR12-2, elicited root

elongation at a level statistically equivalent to GR12-2. This

finding demonstrates that for GR12-2 inoculation there is

not a direct relationship between the level of IAA produced

and the magnitude of root elongation. One mutant that

produced IAA at four times the rate of GR12-2 lost root

elongation activity. This was explained by the interaction of

IAA with the enzyme 1-aminocyclopropane-1-carboxylate

(ACC) synthase. Large amounts of IAA produced by bacter-

ia together with endogenously produced plant IAA activate

ACC synthase, leading to production of ACC, a precursor

for ethylene. Ethylene is an inhibitor of root growth espe-

cially reducing the primary root length (Glick et al., 1998;

Glick, 2005). A key feature of GR12-2 is that the bacterium

produces ACC deaminase that converts ACC to ammonia

and a-ketobutyrate. This conversion lowers the pool of ACC

in the root environment, thereby reducing the amount of

ethylene and consequently its inhibition of root growth. The

bacterium takes advantage of this situation using ACC as a

source of nitrogen. Thus, a balanced interplay of different

factors including bacterial IAA biosynthesis rather than IAA

production per se is needed to stimulate plant growth (Xie

et al., 1996).

IAA in Rhizobium --legume symbiosis

Most Rhizobium species have been shown to produce IAA

via different pathways (Badenochjones et al., 1983; Theunis

et al., 2004), and many studies indicate that changes in auxin

balance in the host plant are a prerequisite for nodule

organogenesis (Mathesius et al., 1998). Auxins are involved

in multiple processes including cell division, differentiation

and vascular bundle formation. These three events are also

necessary for nodule formation as such. It seems likely that

auxins play a role in nodulation. Nevertheless, the exact role

of IAA in the different stages of Rhizobium–plant symbiosis

remains unclear.

A number of experiments suggest that rhizobia, in

particular Rhizobium Nod factors (lipo-chitin oligosacchar-

ides, which are produced by rhizobia upon triggering nod

gene expression by plant-derived flavonoids) interfere with

auxin transport. Moreover, the application of synthetic

polar auxin transport (PAT) inhibitors, which interfere with

the hormone balance in the root, can induce pseudonodule

structures on the root (Allen et al., 1953; Hirsch et al., 1989;

Wu et al., 1996). Direct measurements of auxin transport

using radiolabeled auxin showed that rhizobia locally inhibit

acropetal auxin transport capacity in vetch (Vicia sativa)

roots within 24 h after inoculation (Boot et al., 1999). In

addition, the expression of an auxin-responsive promoter

(GH3) was reduced acropetally from the inoculation site,

between 12 and 24 h following rhizobia inoculation or

addition of Nod factors (Mathesius et al., 1998). This was

followed by an apparent increase in auxin accumulation at

the site of nodule initiation in the inner cortex. By contrast,

in the determinate legume Lotus japonicus, no auxin trans-

port inhibition could be measured after inoculation (Pacios-

Bras et al., 2003). However, an increase of GH3 expression

was still located in the nodule initials, suggesting that high

auxin levels are required for nodule initiation. Moreover, it

has been suggested that the expression of the AUX-1-like

protein LAX in developing Medicago truncatula nodule

primordia is important for a continuous flow of auxin into

the forming primordium (de Billy et al., 2001). It is therefore

likely that auxin transport regulation is part of the process

leading to nodule initiation.

Very recently, it has been demonstrated that a cytokinin

receptor (HIT1 gene in L. japonicus) is involved in the Nod

factor signaling cascade in Lotus as well as in Medicago

(Murray et al., 2007; Tirichine et al., 2007). As the effect of

cytokinins is dependent on the auxin/cytokinin balance,

these findings may give a new dimension to the role of auxin

in nodulation.

Other observations suggest that microbially released IAA

could play a role in rhizobia–plant symbiosis. It was

demonstrated that the specific nod inducers, flavonoids, also

stimulate the production of IAA by Rhizobium (Prinsen

et al., 1991). Moreover, in Rhizobium sp. NGR234 this

flavonoid induction is dependent on the transcriptional

regulators NodD1 and NodD2 and the presence of the nod-

box NB15 upstream of the y4wEFG operon required for IAA

synthesis (Theunis et al., 2004). The link between Nod

factors as symbiotic signaling molecules and rhizobial IAA

biosynthesis points to a role for IAA in the Rhizobium–bean

symbiosis. Knocking-out the flavonoid-dependent IAA bio-

synthesis in NGR234 did not affect nodulation significantly

on Vigna and Tephrosia, although preliminary results with

Lablab have shown NGR234 to be Fix1 while the IAA�

mutants are Fix� (Theunis, 2005).

In addition, root nodules have been shown to contain

more IAA than nonnodulated roots (Dullaart & Duba, 1970;

Badenochjones et al., 1983; Basu & Ghosh, 1998; Theunis,

2005; Ghosh & Basu, 2006), and auxins could be important

for maintaining a functional root nodule (Badenochjones

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434 S. Spaepen et al.

Page 11: Aia review (1)

et al., 1983). In nodules induced by low IAA-producing

mutants of Rhizobium sp. NGR234, the IAA content is

lower than in nodules induced by the wild-type strain,

indicating that at least part of the IAA in nodules derives

from the bacteria (Theunis, 2005). Bacteroids of plants

inoculated with mutant Bradyrhizobium japonicum strains

overproducing IAA contain high amounts of IAA in com-

parison with wild-type bacteroids (Hunter, 1989), support-

ing the hypothesis that increased IAA biosynthesis in

nodules is of prokaryotic origin. Moreover, introduction of

a second synthesis pathway for auxin synthesis in rhizobia

led to larger nodules, an increase in nodule acetylene

reduction ability and a delay in nodule senescence (Camer-

ini et al., 2004). Similarly, a mutant of Br. japonicum that

produces 30-fold more IAA than the wild-type strain

showed higher nodulation efficiency (Kaneshiro & Kwolek,

1985).

The application of exogenous IAA can enhance nodula-

tion on Medicago and Phaseolus vulgaris when added at very

low concentrations (up to 10�8 M) to the medium, while

high concentrations inhibit nodulation (Plazinski & Rolfe,

1985; van Noorden et al., 2006). Combined application of

Rhizobium and Azospirillum can also increase nodulation as

demonstrated in several studies (Okon & Itzigsohn, 1995;

Burdman et al., 1996). Similar to the IAA effect on nodula-

tion, the effect of Azospirillum is dependent on the concen-

tration of the inoculum. Better root development induced

by Azospirillum IAA production could explain the increased

nodulation but also additional factors, such as changes in

flavonoid metabolism, were suggested to be involved (Burd-

man et al., 1996).

IAA in phytopathogenesis, other than gall- ortumor-inducing pathogens

Besides gall- and tumor-inducing plant pathogens, other

phytopathogens like various Ps. syringae species also synthe-

size IAA (Glickmann et al., 1998; Buell et al., 2003).

Infection can result in necrotic lesions often surrounded by

chlorotic halos. Here, the role of IAA in disease development

is not clear. In many bacterial pathogens, the hrp-gene-

encoded type III secretion system that directly translocates

effector proteins into the eukaryotic host cells is key to

pathogenesis and the development of disease symptoms (Jin

et al., 2003; He et al., 2004). Recently, a link between the

TTSS and phytohormone production in the plant pathogen

Ralstonia solanacearum was established through a host

responsive regulator of the TTSS activation cascade, HrpG

(Valls et al., 2006). It was shown that HrpG controls, in

addition to that of the TTSS, the expression of a previously

undescribed TTSS-independent pathway that includes a

number of other virulence determinants and genes probably

involved in adaptation to life in the host and which includes

IAA and ethylene biosynthesis genes. These results provide a

new, integrated view of plant bacterial pathogenicity, in

which a common regulator activates synchronously upon

infection the TTSS, other virulence determinants and a

number of adaptive functions which act cooperatively to

cause disease. In Ps. syringae the presence of a functional

Hrp promoter upstream of the iaaL gene involved in IAA

biosynthesis further supports the role for IAA production in

virulence (Fouts et al., 2002). However, the function of

bacterial IAA in pathogenesis and disease development

remains unclear. New intriguing insights have come from

studies related to plant defense.

IAA in plant defense

Plants respond to bacterial infection using a two-branched

innate immune system. The first branch, the basal defense,

recognizes and responds to molecules common to many

classes of microorganisms, including nonpathogens. The

interaction between pathogen/microbial-associated molecu-

lar patterns (PAMPs/MAMPs) and the plant pathogen

recognition receptors (PRRs) play a key role in activation of

the plant basal defense response (Abramovitch et al., 2006).

The second branch, the hypersensitive response (HR)-based

response, responds to pathogen virulence factors, either

directly or through their effects on host targets. This second,

later response is mediated by plant disease resistance genes

(R genes) (for recent reviews see Abramovitch et al., 2006;

Chisholm et al., 2006; Jones & Dangl, 2006). Navarro et al.

(2006) demonstrated a link between auxin signaling in plants

and resistance to bacterial pathogens. Bacterial PAMPs

downregulate auxin signaling in Arabidopsis by targeting

auxin receptor transcripts, as part of a plant-induced im-

mune response. It has been observed previously that bacterial

quorum sensing (QS) molecules such as N-acylhomoserine

lactones downregulate some auxin-induced genes (Mathe-

sius et al., 2003), raising the question of whether other

bacterial molecules recognized by the plant also decrease

auxin signaling. The results of Navarro et al. (2006) suggest

that lowering plant auxin signaling can increase resistance to

bacterial pathogens. A possible mechanism is the expression

of auxin-repressed plant defense genes (online supplemen-

tary material to Navarro et al., 2006). They further showed

that exogenous application of auxin enhances susceptibility

to the bacterial pathogen. These findings allow us to

hypothesize that bacterial IAA production may contribute

to circumvent the host defense system by derepressing auxin

signaling. In this way, IAA biosynthesis may play an im-

portant role in bacterial resistance and colonization on the

plant (Remans et al., 2006; see Fig. 2).

Different reports supporting this hypothesis for interac-

tions between plants and pathogenic as well as beneficial

bacteria can be cited.

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

435Microbial auxin signaling

Page 12: Aia review (1)

Firstly, it has been observed in various studies, including

high-throughput analyses, that plant-colonizing bacteria

upregulate auxin signaling in plants. An overview of these

reports is given in Table 3. For some of the bacterial strains

used in these studies, it has been described that they possess

IAA biosynthesis genes. However, it has not yet been proven

that bacterial IAA effectively contributes to modulation of

auxin signaling as observed in the plant. Thilmony et al.

(2006) reported that the upregulation of IAA signaling in

Arabidopsis upon colonization of Ps. syringae DC3000 is

partially dependent on the TTSS and the phytotoxin cor-

otanine, which contributes to virulence and disease devel-

opment. This may be linked to the presence of a functional

Hrp promoter upstream of the iaaL gene involved in IAA

production in Ps. syringae, which suggests that expression of

IAA biosynthesis genes is dependent on the Hrp system

(Fouts et al., 2002). However, the use of an IAA mutant

strain is essential to unravel the role of bacterial IAA in

modulating plant IAA signaling upon colonization.

Secondly, it has been observed previously that auxins

interfere with parts of the host defense system. Auxins and

cytokinins are able to block several pathogenesis-related

(PR) enzymes, including b-glucanase (Mohnen et al., 1985;

Jouanneau et al., 1991) and chitinase (Shinshi et al., 1987) at

the mRNA level. Furthermore, comparing gene expression

profiles of Arabidopsis plants treated with IAA vs. nontreated

control plants using the Affymetrix ATH1 Gene Chip

revealed that some proteins of the disease resistance respon-

sive family are downregulated in IAA-treated plants (Red-

man et al., 2004).

Another plant defense strategy is the HR, characterized

by necrosis of plant cells in the inoculated area. In this way,

the bacteria are limited to the area originally inoculated

and do not spread beyond its edges. The HR is thought to

function in the limitation of the growth of the microorgan-

ism and is therefore associated with disease resistance

(Klement, 1982). Robinette & Matthysse (1990) reported

that bacterial auxin of Ps. savastanoi is required to block

the HR in tobacco leaves induced by Ps. syringae pv.

phaseolicola.

Interestingly, the role of bacterial IAA in induced system

resistance (ISR) elicited by some PGPR has been investigated

in several studies but in none of the reported studies did it

appear that IAA was involved in ISR (Oberhansli et al., 1991;

Beyeler et al., 1999; Cartieaux et al., 2003; Suzuki et al.,

2003). Verhagen et al. (2004) showed that ISR in Arabidopsis

Fig. 2. IAA in pathogenic and beneficial microorganism–plant interactions. A model suggested for the role of bacterial IAA production in

microorganism–plant interactions. Signaling taking place in the plant is indicated in gray boxes; signaling taking place in bacterial cells is indicated in

white boxes. Full lines indicate demonstrated links; dashed lines indicate hypothesized links. AHL, N-acyl homoserine lactone; IAA, indole-3-acetic acid;

MAMP, microbial-associated molecular pattern; PAMP, pathogen-associated molecular pattern; QS, quorum sensing; TIR, transport inhibitor response.

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

436 S. Spaepen et al.

Page 13: Aia review (1)

induced by Ps. fluorescens WCS417r is not associated with

changes in the expression of genes encoding PR proteins.

Taking these reports together, they show consistency for the

link between auxin signaling and PR protein expression.

Thirdly, it has been shown that bacterial IAA biosynthesis

contributes to colonization capacity and fitness on the host.

A low IAA-producing mutant of Ps. fluorescens HP72 is

reduced in colonization ability on bentgrass roots as com-

pared with the wild-type (Suzuki et al., 2003). Similarly,

inactivation of the IPyA pathway in Pa. agglomerans

pv. gypsophilae caused a 14-fold reduction in the population

of Pa. agglomerans pv. gypsophilae on bean plants. In-

activation of the IAM pathway did not affect the coloniza-

tion ability (Manulis et al., 1998). An iaaM� mutant of

Ps. syringae pv. syringae retained the ability to colonize the

bean phylloplane but the role of the IPyA pathway in

colonization was not studied in this strain (Mazzola &

White, 1994). Taken these results together, they suggest that

the IPyA biosynthesis pathway rather than the IAM pathway

contributes to colonization capacity.

Studies of bacterial gene expression further support the

importance of bacterial IAA biosynthesis during plant

colonization, demonstrating that the ipdC gene in

Pa. agglomerans pv. gypsophilae is strongly induced during

plant colonization (Manulis et al., 1998; Brandl et al., 2001),

while the iaaM gene is expressed during later stages in the

interaction with the plant (Manulis et al., 1998). Erwinia

chrysanthemi 3937 in interaction with spinach leaves shows

an upregulation of iaaM expression (Yang et al., 2004).

Examining the influence of sugarbeet exudates on the

transcriptome of Ps. aeruginosa PAO1, no specific IAA

biosynthesis genes were found to be induced. However, a

tryptophan permease with tryptophan being a precursor for

IAA was strongly upregulated, independently from the

sugarbeet variety (Mark et al., 2005).

It is logical to postulate that bacteria use IAA as part of

their colonization strategy by stimulating proliferation of

plant tissues and thus enhanced colonization surface and

exudation nutrients for bacterial growth (Fig. 2). The link

between plant defense and auxin signaling gives an extra

dimension to the role of bacterial IAA in colonization

ability.

Taking the reports described above together, auxin signal-

ing seems to interfere with the basal defence (PAMP

recognition) as well as with the R-mediated defence re-

sponse (HR, activation of PR proteins). As proposed by

Abramovitch et al. (2006), the distinctions that are made

between basal and R-protein-mediated defenses might need

to be revised given that the PRR–PAMP interaction shares

many properties with avirulence (Avr)–R protein interac-

tions. In addition, the basal and R-protein-mediated defense

pathways might share some common signaling components

or physical defense mechanisms. For example, HR-likeTab

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FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

437Microbial auxin signaling

Page 14: Aia review (1)

programmed cell death has been reported in response to

PAMPs, and shared mitogen-activated protein kinase

(MAPK) cascades are associated with both PRR and

R-gene-mediated signaling. Further research is needed to

unravel the role of bacterial auxin synthesis in the different

dimensions of plant defense (Abramovitch et al., 2006).

Interestingly, some similarity between auxin signaling in

bacteria–plant interactions, in which IAA is produced by

both partners and seems to play a role in circumvention of

the host defense, can be found with signaling by bacterial QS

molecules in bacteria–host interactions. Well-described QS

signaling molecules such as N-acyl homoserine lactones

(AHLs) exhibit structural similarities to many eukaryotic

hormones and a growing number of reports have documen-

ted apparent biological effects of AHLs on eukaryotic cells.

In bacteria–animal interactions, QS signals appear to be

used by bacteria to prevent the host immune system from

mounting an effective defense and thus from establishing a

productive infection in the host (Shiner et al., 2005). The

reverse communication conduit also appears to be open as

mammalian hormones can interact with components of the

bacterial QS machinery (reviewed by Shiner et al., 2005).

The growing number of examples of interkingdom signaling

molecules evokes the question regarding the role of IAA as a

signaling molecule in bacteria.

IAA as a signaling molecule in bacteria

In addition to the hypothesis that bacterial IAA contributes

to circumvent the host defense by derepressing the auxin

signaling in the plant, IAA also can have a direct effect on

bacterial survival and its resistance to plant defense (Remans

et al., 2006; see Fig. 2). Evidence has been accumulating that

some microorganisms, independent of their ability to pro-

duce IAA, make use of auxin as a signaling molecule steering

microbial behavior.

Examples of IAA as a signaling molecule inmicroorganisms

Research on the regulation of the IAA synthesis in Azospir-

illum resulted in new insights that IAA regulates expression

of genes involved in IAA synthesis by a positive feedback

mechanism (Vande Broek et al., 1999; Lambrecht et al.,

2000), and that a motif known as an auxin responsive

element from plant studies, AuxRe, is present in the up-

stream region of the Azospirillum gene ipdC known to be

regulated by IAA (Lambrecht et al., 1999; Vande Broek et al.,

2005). Comparative analysis shows a striking similarity, in

terms of the mechanism of gene regulation, with indole

signaling in Escherichia coli, postulated to be a mechanism of

QS signaling (Wang et al., 2001; Domka et al., 2006; Walters

& Sperandio, 2006). Wang et al. demonstrated that indole

activates transcription of tnaAB, gabT and astD. Activation

of the tnaAB operon is predicted to induce more indole

production. astD and gabT are involved in pathways that

degrade amino acids to pyruvate or succinate. These results

led the authors to speculate that signaling by indole may

have a role in adaptation of bacterial cells to a nutrient-poor

environment where amino acid catabolism is an important

energy source (Wang et al., 2001). Other targets of indole-

mediated signaling were found recently indicating a role for

indole signaling in biofilm formation (Domka et al., 2006)

and in the stable maintenance of multicopy plasmids (Chant

& Summers, 2007). These findings on indole signaling and

the similarity with IAA signaling in Azospirillum pose

questions regarding targets of IAA signaling in Azospirillum.

The signaling role of IAA has been further demonstrated

in other microbial species. In Ag. tumefaciens IAA inhibits

vir gene expression by competing with the inducing pheno-

lic compound acetosyringone for interaction with VirA (Liu

& Nester, 2006). The authors postulate this vir gene inhibi-

tion by IAA as a putative negative feedback system upon

increased IAA production by transformed plant cells. How-

ever, it is not known whether the amount of exuded IAA

from the transformed plant tissue is within the concentra-

tion range to downregulate vir gene expression.

In Ps. syringae pv. syringae, IAA was shown to be involved

in the expression of syringomycin synthesis which is re-

quired for full virulence of Ps. syringae pv. syringae strains on

stone fruits (Xu & Gross, 1988a, b). IAA� mutants of

Ps. syringae pv. syringae were significantly reduced in

syringomycin production (Mazzola & White, 1994).

Recently, the use of an iaaM deletion mutant of Erwinia

chrysanthemi 3937 indicated a positive role of IAA biosynth-

esis on TTSS and exoenzymes through the Gac-Rsm

posttranscriptional regulatory pathway. Compared with

wild-type Er. chrysanthemi 3937, the expression level of an

oligogalacturonate lyase, ogl, and three endo-pectate lyases,

pelD, pelI and pelL, was reduced in the iaaM mutant. In

addition, the transcription of TTSS genes, dspE (a putative

TTSS effector) and hrpN (TTSS hairpin), was found to be

diminished in the iaaM mutant of Ee. chrysanthemi 3937

(Yang et al., 2007).

Looking at the unicellular eukaryote Saccharomyces cere-

visiae, it is worth mentioning that addition of IAA to the

culture medium provoked invasive growth and differential

gene expression (Prusty et al., 2004). Among the genes

induced by IAA, a gene involved in adhesion, FLO11, was

detected, suggesting that FLO11 activation by elevated con-

centrations of IAA that occur at plant wound sites might be

crucial for feral yeast cells to infect wound sites in plants

(Verstrepen & Klis, 2006). Similarly, activation of adhesins in

animal pathogens occurs when the cells perceive an oppor-

tunity for infection, enabling cells to adhere to the appro-

priate tissue and establish a colony or biofilm of infectious

cells (Verstrepen et al., 2004; Domergue et al., 2005).

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

438 S. Spaepen et al.

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In E. coli evidence that IAA might be a signal able to

coordinate of bacterial behavior enhancing protection

against damage by adverse conditions was recently described

by Bianco et al. (2006a). They showed that IAA induces the

expression of genes related to survival under stress condi-

tions. Here, it has to be taken into account that auxin

molecules can interact with cell-wall peroxidases, inducing

the formation of reactive oxygen species (ROS) within the

cell wall (Kawano et al., 2001). Concerning the differential

gene expression in E. coli upon IAA addition, it is not clear

whether these genes are induced upon IAA as a signaling

molecule or upon IAA as a molecule provoking a stress

condition by induction of ROS. Unfortunately, only indole

and not acetic acid, neither a ROS-inducing compound,

were included as a control to study IAA-altered gene

expression, leaving doubt regarding whether the expression

profile presented is IAA specific. A subsequent report of

Bianco et al. (2006b) further supported the observation that

IAA is able to induce changes in gene expression in E. coli. In

their study, it was observed that genes involved in the central

metabolic pathways such as the tricarboxylic acid cycle

(TCA), glyoxylate shunt and amino acid biosynthesis (leu-

cine, isoleucine, valine and proline) were upregulated by

IAA, whereas the fermentative adhE gene was downregu-

lated. Data on differential gene expression upon addition of

appropriate control metabolites are missing, preventing the

distinction between IAA-specific induced genes and genes

altered in expression by structurally related metabolites.

For cyanobacteria it has been shown that IAA triggers

differentiation of cyanobacterial hormogenia (Bunt, 1961),

although direct evidence for IAA signaling in cyanobacteria

has not been described. In view of the fact that the

progenitors of extant cyanobacteria were ancestors of plas-

tids, the possible evolutionary link between IAA signaling in

plants and cyanobacteria is worth examining. Interestingly,

IAA plays a key role in modulating the level of the bacterial

alarmone guanosine 50-diphosphate 30-diphosphate

(ppGpp) in the chloroplasts of plant cells. In bacteria ppGpp

mediates the ‘stringent control’ upon stress conditions

(reviewed by Braeken et al., 2006). Takahashi et al. (2004)

detected ppGpp for the first time in the chloroplasts of plant

cells. They further showed that plant hormones including

jasmonic acid, abscisic acid and ethylene modulate levels of

ppGpp in plants while IAA blocks the effect of other plant

hormones on ppGpp. These data point towards research

into the role of IAA and other plant hormones in modula-

tion of ppGpp levels in bacterial cells.

Finally, it was reported by Liu & Nester (2006) that high

concentrations of IAA (200 mM) inhibit growth of many

plant-associated bacteria but not the growth of bacteria

that occupy other ecological niches. This emphasizes the

role of IAA as a signaling molecule in microorganism–plant

interactions.

The findings representing IAA as a signaling molecule in

bacteria shed new light on the role of IAA in microorga-

nism–plant interactions.

IAA transport and reception in bacteria

A crucial issue and major challenge in studying IAA as a

signaling molecule in bacteria is the mechanism of IAA

reception and transport in bacteria. As yet, no receptor nor a

membrane transport system for IAA has been described in

bacteria. The search for auxin receptors and transport

systems has mainly focused on plants, with recent break-

throughs including the discovery of the Arabidopsis auxin

receptor TIR1 (Dharmasiri et al., 2005; Kepinski & Leyser,

2005) and mechanisms of auxin transport (for a recent

review see Kramer & Bennett, 2006). Recent discoveries

indicating that IAA can act also as a signaling molecule in

bacteria have given attention to the question of IAA

receptors and transport systems in bacteria. The capacity of

some bacteria such as Pseudomonas and Bradyrhizobium to

degrade IAA (Proctor, 1958; Tsubokura et al., 1961; Mino,

1970; Egebo et al., 1991; Jensen et al., 1995; Olesen &

Jochimsen, 1996; Leveau & Lindow, 2005) indicates that

the uptake of IAA by bacteria does occur. Transport of IAA

over plant cell membranes occurs through a combination of

membrane diffusion and carrier-mediated transport (re-

viewed by Kramer & Bennett, 2006). IAA can enter a plant

cell either in its protonated form (IAAH) by membrane

diffusion or in its anionic form (IAA�) by the action of a

proton-driven auxin influx carrier system. Once inside the

cell, IAA is predominantly in anionic form, necessitating

carrier-mediated transport to exit the plant cell (Delbarre

et al., 1996).

Membrane diffusion of IAAH is often argued to be the

predominant flux of auxin into plant cells (Bean et al., 1968;

Gutknecht & Walter, 1980). Also in bacteria, the ability of

protonated auxin to diffuse across the bacterial lipid mem-

brane needs to be considered. IAA is a weak acid with a

dissociation constant (pK) of 4.8 (Delbarre et al., 1996). It

thus partitions between the anion IAA� and the protonated

IAAH according to the environmental pH. In neutral or

basic conditions, IAA�will dominate (99.4% ionized at pH

7), whereas in strongly acidic compartments IAAH dom-

inates (99.8% protonated at pH 2). The rhizosphere is

generally considered to be a weakly acid environment (Hin-

singer et al., 2003), and therefore it is expected that a

considerable part of IAA is in its protonated form in the

rhizosphere. This leads to the hypothesis that IAA can enter

the bacterial cell by membrane diffusion, dependent on the

permeability of the bacterial membrane and the environ-

mental pH.

Interestingly, studies on IAA degradation report IAA

degradation capacity at a pH of 7.0–7.1. This indicates that

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

439Microbial auxin signaling

Page 16: Aia review (1)

IAA� can enter the bacterial cell, suggesting the existence of

a proton-driven auxin influx carrier (Proctor, 1958; Tsubo-

kura et al., 1961; Mino, 1970; Egebo et al., 1991; Jensen et al.,

1995; Olesen & Jochimsen, 1996; Leveau & Lindow, 2005).

For the synthetic auxin 2,4-dichlorophenoxyacetate (2,4-D)

an active transport system has been described in several

2,4-D-degrading bacteria, for example Ralstonia, Bradyrhi-

zobium and Delftia (Leveau et al., 1998; Kitagawa et al., 2002;

Muller & Hoffmann, 2006). 2,4-D uptake was shown to be

an energy-dependent process involving a transport protein

encoded by a gene (tfdK in Ralstonia and Delftia, cadK in

Bradyrhizobium) that shows similarity to genes encoding the

major facilitator superfamily transporters. In Delftia acid-

ovorans, it was further observed that the presence of the

uncoupler carbonylcyanide m-chlorophenylhydrazone led

to strong inhibition of 2,4-D uptake, suggesting proton

symport as the likely active mechanism (Muller & Hoff-

mann, 2006). This shows analogy to active IAA import in

plant cells, which is driven by proton influx (Li et al., 2005).

Interruption of the gene tdfK encoding a 2,4-D transport

protein in Ralstonia eutropha decimated 2,4-D uptake rates

but did not abolish uptake completely, indicating that

alternative mechanisms for 2,4-D uptake (e.g. membrane

diffusion) exist (Leveau et al., 1998).

Transfer of cadRABKC genes, involved in 2,4-D degrada-

tion in Bradyrhizobium sp. strain HW13, to a nondegrader

Sinorhizobium meliloti Rm1021 enabled this strain to de-

grade 2,4-D. Of note here is the observation that function-

ality of the gene cadK encoding the transport system was not

necessary to turn S. meliloti Rm1021 into a 2,4-D degrader.

These data suggest that the wild-type strain of S. meliloti

Rm1021 possesses a mechanism for 2,4-D uptake despite its

inability to degrade 2,4-D (Kitagawa et al., 2002).

The question as to what extent 2,4-D transport systems

are comparable with IAA transport in bacteria remains

unanswered. Structural differences between 2,4-D and IAA

can limit the extrapolation of the 2,4-D transport system to

IAA transport. Recently, two articles were published tackling

the structure–activity relationships of auxin-like molecules

(Ferro et al., 2006, 2007). Using a computational approach

(Molecular Quantum Similarity Measures) and subsequent

statistical analysis to identify structural similarity groups,

the authors showed that IAA and 2,4-D share the same

quantum spatial regions, indicating structural similarity.

However, differences between IAA and 2,4-D have been

observed in binding activity to plant auxin transporters/

receptors (Venis & Napier, 1995; Napier et al., 2002;

Kepinski & Leyser, 2005; Badescu & Napier, 2006).

Ongoing plant research might provide other relevant

information on putative IAA transporters and receptors in

bacteria. Advancement in understanding IAA signaling

pathways in plants has been truly spectacular over the past

5 years (for recent reviews on auxin receptors see Badescu &

Napier, 2006; Parry & Estelle, 2006; and on auxin transport

see Fleming, 2006; Kramer & Bennett, 2006). Back-to-back

papers identified the F-box protein transport inhibitor

response 1 (TIR1) as a plant receptor for auxin (Dharmasiri

et al., 2005; Kepinski & Leyser, 2005). TIR1 belongs to a

small protein family which is part of the Arabidopsis F-box

family. Currently, three other TIR1-related F-box protein/

receptors (AFB1, AFB2, AFB3) have been identified as auxin

receptors in Arabidopsis (Dharmasiri et al., 2005; Parry &

Estelle, 2006). Exploiting the NCBI database using the BLAST

algorithm to search for homology between the amino acid

sequence of TIR1 (Dharmasiri et al., 2005) and bacterial

proteins, no strong homology was found. However, a

putative F-box-like protein was detected in Candidatus

Protochlamydia amoebophila UWE25 (see supplementary

Table S1).

TIR1 functions as part of a molecular complex SCFTIR1

that attaches the cell’s garbage tag, ubiquitin, to proteins

destined to be recycled. Auxin, by glomming onto TIR1,

helps the SCFTIR1 complex to ubiquitinate Aux/IAA pro-

teins. When the Aux/IAA proteins are broken down, the

genes they repress turn on. Interestingly, similarity for the

functionality of the SCFTIR receptor system can be found

with another indole receptor, the tryptophan receptor of

bacteria. However, the TIR1 pathway has extra layers of

control built in. Tryptophan binds to the bacterial Trp

repressor protein to induce a conformational change that

allows it to bind directly to the trp operator sequence and so

control gene expression (Ramesh et al., 1994). Arguably, a

switching error in such a system will be immediately

amplified. The activity of TIR1 is one step removed from

transcriptional regulation by the ubiquitination system,

allowing small errors to be buffered (Dharmasiri et al.,

2005; Parry & Estelle, 2006).

The TIR1-like signaling cannot account for all auxin

responses in plants (reviewed by Badescu & Napier, 2006).

Regulation through proteolysis and transcriptional activity,

occurring upon TIR1-auxin signaling, takes time; it is

inevitably much slower than membrane depolarization, for

example. Therefore, rapid auxin responses in plants are

unlikely to be TIR1-mediated and another type of auxin

receptor is expected to be involved in rapid auxin-mediated

responses (Badescu & Napier, 2006). Detailed auxin binding

data have been reported for only one other protein, the

auxin-binding protein 1 (ABP1) (Venis & Napier, 1995;

Napier et al., 2002). Besides its strong ability to bind auxin,

the physiological role of ABP1 remains unclear (Napier

et al., 2002). The majority of ABP1 is localized in the

endoplasmatic reticulum, where the pH is too high for

auxin binding. However, some ABP1 is also found on the

plasma membrane, and ABP1 antibody experiments have

implicated this pool in auxin-mediated cell expansion.

Exploiting the NCBI database using BLAST software, some

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

440 S. Spaepen et al.

Page 17: Aia review (1)

homology was found between ABP1 and putative auxin-

binding proteins in various bacteria, for example S. meliloti,

Shewanella amazonensis, Ps. syringae pv. syringae, Ps. syrin-

gae pv. phaseolicola and Ps. syringae pv. tomato (Table S1). It

will be interesting to unravel the role of these putative auxin-

binding-like proteins in bacteria.

In addition, genetic studies in Arabidopsis have led to the

identification of AUX1, pGlycoprotein (PGP, an ABC trans-

porter) and PIN classes as IAA influx and efflux facilitators

(Parry et al., 2001; Paponov et al., 2005; Geisler & Murphy,

2006; see review by Kramer and Bennett, 2006). In a broad

set of bacteria, e.g. various Pseudomonas species (Ps. fluor-

escens, Ps. syringae and Ps. putida), Bradyrhizobium, Mesor-

hizobium, Sinorhizobium and Rhizobium species, proteins

showing strong homology (E values between 4e-90 and 1e-

58) in amino acid sequence with the plant PGP transporter

were detected (Table S1). As PGP is an ABC transporter, the

homology between PGP and bacterial proteins is not

surprising given that ABC transporters are common trans-

port systems in bacteria. Determination of the specificity of

the bacterial ABC transporters that are homologous to the

plant auxin transporter PGP is required to unravel their

putative role in IAA transport in bacteria.

In addition, some degree of homology (Table S1) in

amino acid sequence was found between the plant auxin

transport facilitator PIN and bacterial proteins predicted as

auxin efflux carriers in various species belonging to, among

others, Ralstonia, Burkholderia and Mesorhizobium, which

are 2,4-D degraders (Leveau et al., 1998; Kitagawa et al.,

2002).

Taking these data together, it can be suggested that certain

similarity in IAA reception and transport/IAA signaling

between plants and bacteria may exist.

Conclusions and perspectives

Over 120 years after Darwin’s description of IAA as ‘a matter

which transmits its effects from one part of the plant to

another,’ plant and microbial research results allow us to

identify IAA as a multivalent signaling molecule and as ‘a

matter which transmits its effects within plants and among

plants and bacterial cells.’ Emerging views on IAA as a

common language between bacteria and plants pave the

way for future research on IAA signaling in microorganisms.

A recent editorial in Science (Vogel, 2006) emphasized the

importance of the advancement in unraveling IAA signaling

pathways in plant communication. The moment to extend

this knowledge to other kingdoms seems highly favorable.

Current postgenomic studies already indicate a role for IAA

signaling in bacteria and microorganism–plant interactions.

However, dedicated functional genomic studies are needed

to unravel the function and mechanism of IAA signaling in

bacteria and during the different stages of microorganism–

plant interactions. The increasing amount of genomic data

will further broaden insight into the distribution and

evolution of the capacity to participate in IAA signaling

among organisms. It is clear that not only plants and

bacteria will take part in the IAA conversations, but that

researchers in plant science and microbiology will undoubt-

edly continue talking about this intriguing molecule.

Acknowledgements

S.S. is financed in part by the Fund for Scientific Research

Flanders (G.0085.03) and in part by the Belgian Govern-

ment (IUAP P5/03). R.R. is a recipient of a predoctoral

fellowship from the ‘Vlaamse Interuniversitaire Raad

(VLIR)’. We acknowledge financial support from the K.U.

Leuven (CoE SymBioSys).

References

Abramovitch RB, Anderson JC & Martin GB (2006) Bacterial

elicitation and evasion of plant innate immunity. Nat Rev Mol

Cell Biol 7: 601–611.

Allen EK, Allen ON & Newman AS (1953) Pseudonodulation of

leguminous plants induced by 2-bromo-3,5-dichlorobenzoic

acid. Am J Bot 40: 429–435.

Aloni R, Pradel KS & Ullrich CI (1995) The 3-dimensional

structure of vascular tissues in Agrobacterium tumefaciens-

induced crown galls and in the host stems of Ricinus communis

L. Planta 196: 597–605.

Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller

W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new

generation of protein database search programs. Nucleic Acids

Res 25: 3389–3402.

Amin MR & Onodera R (1997) Synthesis of phenylalanine and

production of other related compounds from phenylpyruvic

acid and phenylacetic acid by ruminal bacteria, protozoa, and

their mixture in vitro. J Gen Appl Microbiol 43: 9–15.

Arshad M & Frankenberger WT (1991) Microbial production of

plant hormones. Plant Soil 133: 1–8.

Badenochjones J, Rolfe BG & Letham DS (1983) Phytohormones,

Rhizobium mutants, and nodulation in legumes. 3. Auxin

metabolism in effective and ineffective pea root nodules. Plant

Physiol 73: 347–352.

Badescu GO & Napier RM (2006) Receptors for auxin: will it all

end in TIRs? Trends Plant Sci 11: 217–223.

Bak S, Tax FE, Feldmann KA, Galbraith DW & Feyereisen R

(2001) CYP83B1, a cytochrome P450 at the metabolic branch

paint in auxin and indole glucosinolate biosynthesis in

Arabidopsis. Plant Cell 13: 101–111.

Bar T & Okon Y (1992) Induction of indole-3-acetic acid

synthesis and possible toxicity of tryptophan in Azospirillum

brasilense Sp7. Symbiosis 13: 191–198.

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

441Microbial auxin signaling

Page 18: Aia review (1)

Bar T & Okon Y (1993) Tryptophan conversion to indole-3-acetic

acid via indole-3-acetamide in Azospirillum brasilense Sp7.

Can J Microbiol 39: 81–86.

Barnett MJ, Toman CJ, Fisher RF & Long SR (2004) A dual-

genome Symbiosis Chip for coordinate study of signal

exchange and development in a prokaryote–host interaction.

Proc Natl Acad Sci USA 101: 16636–16641.

Bartling D, Seedorf M, Mithofer A & Weiler EW (1992) Cloning

and expression of an Arabidopsis nitrilase which can convert

indole-3-acetonitrile to the plant hormone, indole-3-acetic

acid. Eur J Biochem 205: 417–424.

Bartling D, Seedorf M, Schmidt RC & Weiler EW (1994)

Molecular characterization of 2 cloned nitrilases from

Arabidopsis thaliana – key enzymes in biosynthesis of the plant

hormone indole-3-acetic acid. Proc Natl Acad Sci USA 91:

6021–6025.

Bashan Y & Holguin G (1997) Azospirillum–plant relationships:

environmental and physiological advances (1990–1996).

Can J Microbiol 43: 103–121.

Basu PS & Ghosh AC (1998) Indole acetic acid and its

metabolism in root nodules of a monocotyledonous tree

Roystonea regia. Curr Microbiol 37: 137–140.

Bean RC, Shepherd WC & Chan H (1968) Permeability of lipid

bilayer membranes to organic solutes. J Gen Physiol 52:

495–508.

Beyeler M, Keel C, Michaux P & Haas D (1999) Enhanced

production of indole-3-acetic acid by a genetically modified

strain of Pseudomonas fluorescens CHA0 affects root growth of

cucumber, but does not improve protection of the plant

against Pythium root rot. FEMS Microbiol Ecol 28: 225–233.

Bianco C, Imperlini E, Calogero R, Senatore B, Amoresano A,

Carpentieri A, Pucci P & Defez R (2006a) Indole-3-acetic acid

improves Escherichia coli’s defences to stress. Arch Microbiol

185: 373–382.

Bianco C, Imperlini E, Calogero R, Senatore B, Pucci P & Defez R

(2006b) Indole-3-acetic acid regulates the central metabolic

pathways in Escherichia coli. Microbiol-Sgm 152: 2421–2431.

Blaha D, Sanguin H, Robe P, Nalin R, Bally R & Moenne-Loccoz Y

(2005) Physical organization of phytobeneficial genes nifH and

ipdC in the plant growth-promoting rhizobacterium

Azospirillum lipoferum 4V(I). FEMS Microbiol Lett 244:

157–163.

Boot KJM, van Brussel AAN, Tak T, Spaink HP & Kijne JW

(1999) Lipochitin oligosaccharides from Rhizobium

leguminosarum bv. viciae reduce auxin transport capacity in

Vicia sativa subsp nigra roots. Mol Plant–Microbe Interact 12:

839–844.

Braeken K, Moris M, Daniels R, Vanderleyden J & Michiels J

(2006) New horizons for (p)ppGpp in bacterial and plant

physiology. Trends Microbiol 14: 45–54.

Brandl MT & Lindow SE (1996) Cloning and characterization of

a locus encoding an indolepyruvate decarboxylase involved in

indole-3-acetic acid synthesis in Erwinia herbicola.

Appl Environ Microbiol 62: 4121–4128.

Brandl MT & Lindow SE (1997) Environmental signals modulate

the expression of an indole-3-acetic acid biosynthetic gene in

Erwinia herbicola. Mol Plant–Microbe Interact 10: 499–505.

Brandl MT, Quinones B & Lindow SE (2001) Heterogeneous

transcription of an indoleacetic acid biosynthetic gene in

Erwinia herbicola on plant surfaces. Proc Natl Acad Sci USA 98:

3454–3459.

Buell CR, Joardar V, Lindeberg M et al. (2003) The complete

genome sequence of the Arabidopsis and tomato pathogen

Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci

USA 100: 10181–10186.

Bunt JS (1961) Isolation of bacteria-free cultures from

hormogone-producing blue-green algae. Nature 192:

1275–1276.

Burdman S, Volpin H, Kigel J, Kapulnik Y & Okon Y (1996)

Promotion of nod gene inducers and nodulation in common

bean (Phaseolus vulgaris) roots inoculated with Azospirillum

brasilense Cd. Appl Environ Microbiol 62: 3030–3033.

Camerini S, Senatore B, Imperlini E, Bianco C, Miraglia E,

Lonardo E & Defez R (2004) Improve legume yield by

phytohormone release from soil bacteria. Legumes for the

Benefit of Agriculture, Nutrition and the Environment

(European Association for Grain Legume Research, eds),

pp. 127–128. AEP, Dijon.

Cartieaux F, Thibaud MC, Zimmerli L, Lessard P, Sarrobert C,

David P, Gerbaud A, Robaglia C, Somerville S & Nussaume L

(2003) Transcriptome analysis of Arabidopsis colonized by a

plant-growth promoting rhizobacterium reveals a general

effect on disease resistance. Plant J 36: 177–188.

Chalupowicz L, Barash I, Schwartz M, Aloni R & Manulis S

(2006) Comparative anatomy of gall development on

Gypsophila paniculata induced by bacteria with different

mechanisms of pathogenicity. Planta 224: 429–437.

Chant EL & Summers DK (2007) Indole signalling contributes to

the stable maintenance of Escherichia coli multicopy plasmids.

Mol Microbiol 63: 35–43.

Chisholm ST, Coaker G, Day B & Staskawicz BJ (2006)

Host–microbe interactions: shaping the evolution of the plant

immune response. Cell 124: 803–814.

Clark E, Vigodskyhaas H & Gafni Y (1989) Characteristics in

tissue-culture of hyperplasias induced by Erwinia herbicola

pathovar gypsophilae. Physiol Mol Plant Pathol 35: 383–390.

Clark E, Manulis S, Ophir Y, Barash I & Gafni Y (1993) Cloning

and characterization of iaaM and iaaH from Erwinia herbicola

pathovar gypsophilae. Phytopathology 83: 234–240.

Cohen JD & Bandurski RS (1982) Chemistry and physiology of

the bound auxins. Annu Rev Plant Physiol 33: 403–430.

Costacurta A & Vanderleyden J (1995) Synthesis of

phytohormones by plant-associated bacteria. Crit Rev

Microbiol 21: 1–18.

Costacurta A, Keijers V & Vanderleyden J (1994) Molecular

cloning and sequence analysis of an Azospirillum brasilense

indole-3-pyruvate decarboxylase gene. Mol Gen Genet 243:

463–472.

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

442 S. Spaepen et al.

Page 19: Aia review (1)

Costacurta A, Mazzafera P & Rosato YB (1998) Indole-3-acetic

acid biosynthesis by Xanthomonas axonopodis pv. citri is

increased in the presence of plant leaf extracts. FEMS Microbiol

Lett 159: 215–220.

Darwin C & Darwin F (1880) The Power of Movement in Plants.

John Murray, London.

de Billy F, Grosjean C, May S, Bennett M & Cullimore JV (2001)

Expression studies on AUX1-like genes in Medicago truncatula

suggest that auxin is required at two steps in early nodule

development. Mol Plant–Microbe Interact 14: 267–277.

Delbarre A, Muller P, Imhoff V & Guern J (1996) Comparison of

mechanisms controlling uptake and accumulation of 2,4-

dichlorophenoxy acetic acid, naphthalene-1-acetic acid, and

indole-3-acetic acid in suspension-cultured tobacco cells.

Planta 198: 532–541.

Dharmasiri N, Dharmasiri S & Estelle M (2005) The F-box

protein TIR1 is an auxin receptor. Nature 435: 441–445.

Dobbelaere S, Croonenborghs A, Thys A, Vande Broek A &

Vanderleyden J (1999) Phytostimulatory effect of Azospirillum

brasilense wild type and mutant strains altered in IAA

production on wheat. Plant Soil 212: 155–164.

Domergue R, Castano I, las Penas A, Zupancic M, Lockatell V,

Hebel JR, Johnson D & Cormack BP (2005) Nicotinic acid

limitation regulates silecing of Candida adhesins during UTI.

Science 308: 866–870.

Domka J, Lee J & Wood TK (2006) YliH (BssR) and YceP (BssS)

regulate Escherichia coli K-12 biofilm formation by influencing

cell signaling. Appl Environ Microbiol 72: 2449–2459.

Dubeikovsky AN, Mordukhova EA, Kochetkov VV, Polikarpova

FY & Boronin AM (1993) Growth promotion of black currant

softwood cuttings by recombinant strain Pseudomonas

fluorescens Bsp53A synthesizing an increased amount of

indole-3-acetic acid. Soil Biol Biochem 25: 1277–1281.

Dullaart J & Duba L (1970) Presence of gibberellin-like

substances and their possible role in auxin bioproduction in

root nodules and roots of Lupinus luteus L. Acta Bot Neerl 19:

290–297.

Egebo LA, Nielsen SVS & Jochimsen BU (1991) Oxygen

dependent catabolism of indole-3-acetic acid in

Bradyrhizobium japonicum. J Bacteriol 173: 4897–4901.

Fallik E, Sarig S & Okon Y (1994) Morphology and physiology of

plant roots associated with Azospirillum. Azospirillum–Plant

Associations (Okon Y, ed), pp. 77–85. CRC Press, Boca Raton.

Ferro N, Gallegos A, Bultinck P, Jacobsen HJ, Carbo-Dorca R &

Reinard T (2006) Coulomb and overlap self-similarities: a

comparative selectivity analysis of structure–function

relationships for auxin-like molecules. J Chem Inf Model 46:

1751–1762.

Ferro N, Gallegos A, Bultinck P, Jacobsen HJ, Carbo-Dorca R &

Reinard T (2007) Unrevealed structural requirements for

auxin-like molecules by theoretical and experimental

evidences. Phytochemistry 68: 237–250.

Fleming AJ (2006) Plant signalling: the inexorable rise of auxin.

Trends Cell Biol 16: 397–402.

Fouts DE, Abramovitch RB & Alfano JR (2002) Genomewide

identification of Pseudomonas syringae pv. tomato DC3000

promoters controlled by the HrpL alternative sigma factor.

Proc Natl Acad Sci USA 99: 2275–2280.

Geisler M & Murphy AS (2006) The ABC of auxin transport: the

role of p-glycoproteins in plant development. FEBS Lett 580:

1094–1102.

Ghosh S & Basu PS (2006) Production and metabolism of indole

acetic acid in roots and root nodules of Phaseolus mungo.

Microbiol Res 161: 362–366.

Glass NL & Kosuge T (1986) Cloning of the gene for indoleacetic

acid-lysine synthetase from Pseudomonas syringae subsp

savastanoi. J Bacteriol 166: 598–603.

Glick BR (2005) Modulation of plant ethylene levels by the

bacterial enzyme ACC deaminase. FEMS Microbiol Lett 251:

1–7.

Glick BR, Penrose DM & Li JP (1998) A model for the lowering of

plant ethylene concentrations by plant growth-promoting

bacteria. J Theor Biol 190: 63–68.

Glickmann E, Gardan L, Jacquet S, Hussain S, Elasri M, Petit A &

Dessaux Y (1998) Auxin production is a common feature of

most pathovars of Pseudomonas syringae. Mol Plant–Microbe

Interact 11: 156–162.

Gruen HW (1959) Auxin and fungi. Annu Rev Plant Physiol 10:

405–440.

Gutknecht J & Walter A (1980) Transport of auxin (indoleacetic

acid) through lipid bilayer membranes. J Membr Biol 56:

65–72.

Gysegom P (2005) Study of the transcriptional regulation of a key

gene in indole-3-acetic acid biosynthesis in Azospirillum

brasilense. PhD thesis, K.U. Leuven.

Haas D & Keel C (2003) Regulation of antibiotic production in

root-colonizing Pseudomonas spp. and relevance for biological

control of plant disease. Annu Rev Phytopathol 41: 117–153.

Hartmann A & Zimmer W (1994) Physiology of Azospirillum.

Azospirillum/Plant Associations (Okon Y, ed), pp. 15–39. CRC

Press, Boca Raton.

Hartmann A, Singh M & Klingmuller W (1983) Isolation and

characterization of Azospirillum mutants excreting high

amounts of indoleacetic acid. Can J Microbiol 29: 916–923.

He SY, Nomura K & Whittam TS (2004) Type III protein

secretion mechanism in mammalian and plant pathogens.

BBA-Mol Cell Res 1694: 181–206.

Hinsinger P, Plassard C, Tang CX & Jaillard B (2003) Origins of

root-mediated pH changes in the rhizosphere and their

responses to environmental constraints: a review. Plant Soil

248: 43–59.

Hirsch AM, Bhuvaneswari TV, Torrey JG & Bisseling T (1989)

Early nodulin genes are induced in alfalfa root outgrowths

elicited by auxin transport inhibitors. Proc Natl Acad Sci USA

86: 1244–1248.

Hunter WJ (1989) Indole-3-acetic acid production by bacteroids

from soybean root nodules. Physiol Plant 76: 31–36.

Hutcheson SW & Kosuge T (1985) Regulation of 3-indoleacetic

acid production in Pseudomonas syringae pv savastanoi –

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

443Microbial auxin signaling

Page 20: Aia review (1)

purification and properties of tryptophan 2-monooxygenase.

J Biol Chem 260: 6281–6287.

Jensen JB, Egsgaard H, Vanonckelen H & Jochimsen BU (1995)

Catabolism of indole-3-acetic-acid and 4-chloroindole-3-

acetic and 5-chloroindole-3-acetic acid in Bradyrhizobium

japonicum. J Bacteriol 177: 5762–5766.

Jin QL, Thilmony R, Zwiesler-Vollick J & He SY (2003) Type III

protein secretion in Pseudomonas syringae. Microbes Infect 5:

301–310.

Jones JDG & Dangl JL (2006) The plant immune system. Nature

444: 323–329.

Jouanneau JP, Lapous D & Guern J (1991) In plant protoplasts,

the spontaneous expression of defense reactions and the

responsiveness to exogenous elicitors are under auxin control.

Plant Physiol 96: 459–466.

Kaneshiro T & Kwolek WF (1985) Stimulated nodulation of

soybeans by Rhizobium japonicum mutant (B-14075) that

catabolizes the conversion of tryptophan to indol-3yl-acetic

acid. Plant Sci 42: 141–146.

Kang BR, Yang KY, Cho BH, Han TH, Kim IS, Lee MC, Anderson

AJ & Kim YC (2006) Production of indole-3-acetic acid in the

plant-beneficial strain Pseudomonas chlororaphis O6 is

negatively regulated by the global sensor kinase GacS. Curr

Microbiol 52: 473–476.

Kaper JM & Veldstra H (1958) On the metabolism of tryptophan

by Agrobacterium tumefaciens. Biochim Biophys Acta 30:

401–420.

Kawano T, Kawano N, Hosoya H & Lapeyrie F (2001) Fungal

auxin antagonist hypaphorine competitively inhibits indole-3-

acetic acid-dependent superoxide generation by horseradish

peroxidase. Biochem Biophys Res Commun 288: 546–551.

Kepinski S & Leyser O (2005) The Arabidopsis F-box protein TIR1

is an auxin receptor. Nature 435: 446–451.

Khalid A, Tahir S, Arshad M & Zahir ZA (2004) Relative

efficiency of rhizobacteria for auxin biosynthesis in

rhizosphere and non-rhizosphere soils. Aust J Soil Res 42:

921–926.

Kitagawa W, Takami S, Miyauchi K, Masai E, Kamagata Y, Tiedje

JM & Fukuda M (2002) Novel 2,4-dichlorophenoxyacetic acid

degradation genes from oligotrophic Bradyrhizobium sp strain

HW13 isolated from a pristine environment. J Bacteriol 184:

509–518.

Klement Z (1982) Hypersensitivity. Phytopathogenic Prokaryotes

(Mount MS & Lacy GH, eds), pp. 149–177. Academic Press,

New York.

Kobayashi M, Izui H, Nagasawa T & Yamada H (1993) Nitrilase in

biosynthesis of the plant hormone indole-3-acetic acid from

indole-3-acetonitrile – cloning of the Alcaligenes gene and site-

directed mutagenesis of cysteine residues. Proc Natl Acad Sci

USA 90: 247–251.

Kobayashi M, Suzuki T, Fujita T, Masuda M & Shimizu S (1995)

Occurrence of enzymes involved in biosynthesis of indole-3-

acetic acid from indole-3-acetonitrile in plant-associated

bacteria, Agrobacterium and Rhizobium. Proc Natl Acad Sci

USA 92: 714–718.

Koga J, Adachi T & Hidaka H (1991) Molecular cloning of the

gene for indolepyruvate decarboxylase from Enterobacter

cloacae. Mol Gen Genet 226: 10–16.

Kogl F & Kostermans DGFR (1934) Hetero-auxin als

Stoffwechselprodukt niederer pflanzlicher Organismen. XIII.

Isolierung aus Hefe. Z Phys Chem 228: 113–121.

Kramer EM & Bennett MJ (2006) Auxin transport: a field in flux.

Trends Plant Sci 11: 382–386.

Kravchenko LV, Borovkov AV & Pshikril Z (1991) Possibility of

auxin synthesis by association-forming nitrogen-fixing

bacteria in the rhizosphere of wheat. Microbiology 60: 647–650.

Kravchenko LV, Azarova TS, Makarova NM & Tikhonovich IA

(2004) The effect of tryptophan present in plant root exudates

on the phytostimulating activity of rhizobacteria. Microbiology

73: 156–158.

Kucey RMN (1988) Plant growth altering effects of Azospirillum

brasilense and Bacillus C-11-25 on 2 wheat cultivars. J Appl

Bacteriol 64: 187–195.

Lambrecht M, Vande Broek A, Dosselaere F & Vanderleyden J

(1999) The ipdC promoter auxin-responsive element of

Azospirillum brasilense, a prokaryotic ancestral form of the

plant AuxRE? Mol Microbiol 32: 889–891.

Lambrecht M, Okon Y, Vande Broek A & Vanderleyden J (2000)

Indole-3-acetic acid: a reciprocal signalling molecule in

bacteria–plant interactions. Trends Microbiol 8: 298–300.

Last RL, Bissinger PH, Mahoney DJ, Radwanski ER & Fink GR

(1991) Tryptophan mutants in Arabidopsis – the consequences

of duplicated tryptophan synthase beta genes. Plant Cell 3:

345–358.

Leveau JH & Lindow SE (2005) Utilization of the plant hormone

indole-3-acetic acid for growth by Pseudomonas putida strain

1290. Appl Environ Microbiol 71: 2365–2371.

Leveau JHJ, Zehnder AJB & van der Meer JR (1998) The tfdK gene

product facilitates uptake of 2,4-dichlorophenoxyacetate by

Ralstonia eutropha JMP134(pJP4). J Bacteriol 180: 2237–2243.

Li JS, Yang HB, Peer WA et al. (2005) Arabidopsis H1-PPase

AVP1 regulates auxin-mediated organ development. Science

310: 121–125.

Libbert E, Fiscer E, Drawert A & Schrouder R (1970) Pathways of

IAA production from tryptophan by plants and by their

epiphytic bacteria: a comparison II. Establishment of the

tryptophan metabolites, effects of a native inhibitor. Physiol

Plant 23: 278–286.

Link GKK & Eggers V (1941) Hyperauxiny in crown gall of

tomato. Bot Gaz 103: 87–106.

Liu P & Nester EW (2006) Indoleacetic acid, a product of

transferred DNA, inhibits vir gene expression and growth of

Agrobacterium tumefaciens C58. Proc Natl Acad Sci USA 103:

4658–4662.

Manulis S & Barash I (2003) The molecular basis for

transformation of an epiphyte into a gall-forming pathogen as

exemplified by Erwinia herbicola pv. gypsophilae.

Plant–Microbe Interactions (Stacey G & Keen N, eds), pp.

19–52. American Phytopathological Society, St. Paul.

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

444 S. Spaepen et al.

Page 21: Aia review (1)

Manulis S, Haviv-Chesner A, Brandl MT, Lindow SE & Barash I

(1998) Differential involvement of indole-3-acetic acid

biosynthetic pathways in pathogenicity and epiphytic fitness of

Erwinia herbicola pv. gypsophilae. Mol Plant–Microbe Interact

11: 634–642.

Mark GL, Dow JM, Kiely PD et al. (2005) Transcriptome profiling

of bacterial responses to root exudates identifies genes

involved in microbe–plant interactions. Proc Natl Acad Sci

USA 102: 17454–17459.

Marlow JL & Kosuge T (1972) Tryptophan and indoleacetic acid

transport in olive and oleander knot organism Pseudomonas

savastanoi (e F Smith) Stevens. J Gen Microbiol 72: 211.

Mathesius U, Schlaman HRM, Spaink HP, Sautter C, Rolfe BG &

Djordjevic MA (1998) Auxin transport inhibition precedes

root nodule formation in white clover roots and is regulated by

flavonoids and derivatives of chitin oligosaccharides. Plant J

14: 23–34.

Mathesius U, Mulders S, Gao M, Teplitski M, Caetano-Anolles G,

Rolfe BG & Bauer WD (2003) Extensive and specific responses

of a eukaryote to bacterial quorum-sensing signals. Proc Natl

Acad Sci USA 100: 1444–1449.

Mazzola M & White FF (1994) A mutation in the indole-3-acetic-

acid biosynthesis pathway of Pseudomonas syringae pv syringae

affects growth in Phaseolus vulgaris and syringomycin

production. J Bacteriol 176: 1374–1382.

Mino Y (1970) Studies on the destruction of indole-3-acetic acid

by a species of Arthrobacter IV. Decomposition products. Plant

Cell Physiol 11: 129–138.

Mohammed N, Onodera R & Or-Rashid MM (2003)

Degradation of tryptophan and related indolic compounds by

ruminal bacteria, protozoa and their mixture in vitro. Amino

Acids 24: 73–80.

Mohnen D, Shinshi H, Felix G & Meins F (1985) Hormonal

regulation of beta-1,3-glucanase messenger RNA levels in

cultured tobacco tissues. EMBO J 4: 1631–1635.

Mor H, Manulis S, Zuck M, Nizan R, Coplin DL & Barash I

(2001) Genetic organization of the hrp gene cluster and dspAE/

BF operon in Erwinia herbicola pv. gypsophilae. Mol

Plant–Microbe Interact 14: 431–436.

Morris RO (1995) Genes specifying auxin and cytokinin

biosynthesis in prokaryotes. Plant Hormones (Davies PJ, eds),

pp. 318–339. Kluwer Academic Publishers, Dordrecht.

Muller A & Weiler EW (2000) Indolic constituents and indole-3-

acetic acid biosynthesis in the wild-type and a tryptophan

auxotroph mutant of Arabidopsis thaliana. Planta 211:

855–863.

Muller RH & Hoffmann D (2006) Uptake kinetics of 2,4-

dichlorophenoxyacetate by Delftia acidovorans MC1 and

derivative strains: complex characteristics in response to pH

and growth substrate. Biosci Biotechnol Biochem 70:

1642–1654.

Murray JD, Karas BJ, Sato S, Tabata S, Amyot L & Szczyglowski K

(2007) A cytokinin perception mutant colonized by Rhizobium

in the absence of nodule organogenesis. Science 315: 101–104.

Nagasawa T, Mauger J & Yamada H (1990) A novel nitrilase,

arylacetonitrilase, of Alcaligenes faecalis JM3 – purification and

characterization. Eur J Biochem 194: 765–772.

Napier RM, David KM & Perrot-Rechenmann C (2002) A short

history of auxin-binding proteins. Plant Mol Biol 49: 339–348.

Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M,

Voinnet O & Jones JDG (2006) A plant miRNA contributes to

antibacterial resistance by repressing auxin signaling. Science

312: 436–439.

Newman T, Debruijn FJ, Green P et al. (1994) Genes galore – a

summary of methods for accessing results from large-scale

partial sequencing of anonymous Arabidopsis cDNA clones.

Plant Physiol 106: 1241–1255.

Nizan-Koren R, Manulis S, Mor H, Iraki NM & Barash I (2003)

The regulatory cascade that activates the hrp regulon in

Erwinia herbicola pv. gypsophilae. Mol Plant–Microbe Interact

16: 249–260.

Normanly J, Cohen JD & Fink GR (1993) Arabidopsis thaliana

auxotrophs reveal a tryptophan-independent biosynthetic

pathway for indole-3-acetic acid. Proc Natl Acad Sci USA 90:

10355–10359.

Oberhansli T, Defago G & Haas D (1991) Indole-3-acetic-acid

(IAA) synthesis in the biocontrol strain CHA0 of Pseudomonas

fluorescens – role of tryptophan side-chain oxidase. J Gen

Microbiol 137: 2273–2279.

O’Donnell PJ, Schmelz EA, Moussatche P, Lund ST, Jones JB &

Klee HJ (2003) Susceptible to intolerance – a range of

hormonal actions in a susceptible Arabidopsis pathogen

response. Plant J 33: 245–257.

Okon Y & Itzigsohn R (1995) The development of Azospirillum as

a commercial inoculant for improving crop yields. Biotechnol

Adv 13: 415–424.

Olesen MR & Jochimsen BU (1996) Identification of enzymes

involved in indole-3-acetic acid degradation. Plant Soil 186:

143–149.

Omay SH, Schmidt WA & Martin P (1993) Indoleacetic acid

production by the rhizosphere bacterium Azospirillum

brasilense Cd under in vitro conditions. Can J Microbiol 39:

187–192.

Ona O, Smets I, Gysegom P, Bernaerts K, Van Impe J, Prinsen E &

Vanderleyden J (2003) The effect of pH on indole-3-acetic acid

(IAA) biosynthesis of Azospirillum brasilense Sp7. Symbiosis

35: 199–208.

Ona O, Van Impe J, Prinsen E & Vanderleyden J (2005) Growth

and indole-3-acetic acid biosynthesis of Azospirillum brasilense

Sp245 is environmentally controlled. FEMS Microbiol Lett 246:

125–132.

Pacios-Bras C, Schlaman HRM, Boot K, Admiraal P, Langerak

JM, Stougaard J & Spaink HP (2003) Auxin distribution in

Lotus japonicus during root nodule development. Plant Mol

Biol 52: 1169–1180.

Paponov IA, Teale WD, Trebar M, Blilou K & Palme K (2005) The

PIN auxin efflux facilitators: evolutionary and functional

perspectives. Trends Plant Sci 10: 170–177.

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

445Microbial auxin signaling

Page 22: Aia review (1)

Parry G & Estelle M (2006) Auxin receptors: a new role for F-box

proteins. Curr Opin Cell Biol 18: 152–156.

Parry G, Marchant A, May S et al. (2001) Quick on the uptake:

characterization of a family of plant auxin influx carriers.

J Plant Growth Regul 20: 217–225.

Patten CL & Glick BR (1996) Bacterial biosynthesis of indole-3-

acetic acid. Can J Microbiol 42: 207–220.

Patten CL & Glick BR (2002a) Regulation of indoleacetic acid

production in Pseudomonas putida GR12-2 by tryptophan and

the stationary-phase sigma factor RpoS. Can J Microbiol 48:

635–642.

Patten CL & Glick BR (2002b) Role of Pseudomonas putida

indoleacetic acid in development of the host plant root system.

Appl Environ Microbiol 68: 3795–3801.

Perley JW & Stowe BB (1966) On the ability of Taphrina

deformans to produce indoleacetic acid from tryptophan by

way of tryptamine. Plant Physiol 41: 234–237.

Persello-Cartieaux F, David P, Sarrobert C, Thibaud MC,

Achouak W, Robaglia C & Nussaume L (2001) Utilization of

mutants to analyze the interaction between Arabidopsis

thaliana and its naturally root-associated Pseudomonas. Planta

212: 190–198.

Persello-Cartieaux F, Nussaume L & Robaglia C (2003) Tales from

the underground: molecular plant-rhizobacteria interactions.

Plant Cell Environ 26: 189–199.

Piotrowski M, Schonfelder S & Weiler EW (2001) The Arabidopsis

thaliana isogene NIT4 and its orthologs in tobacco encode

beta-cyano-L-alanine hydratase/nitrilase. J Biol Chem 276:

2616–2621.

Plazinski J & Rolfe BG (1985) Azospirillum–Rhizobium

interaction leading to a plant-growth stimulation without

nodule formation. Can J Microbiol 31: 1026–1030.

Pollmann S, Muller A, Piotrowski M & Weiler EW (2002)

Occurrence and formation of indole-3-acetamide in

Arabidopsis thaliana. Planta 216: 155–161.

Pollmann S, Neu D & Weiler EW (2003) Molecular cloning and

characterization of an amidase from Arabidopsis thaliana

capable of converting indole-3-acetamide into the plant

growth hormone, indole-3-acetic acid. Phytochemistry 62:

293–300.

Pollmann S, Muller A & Weiler EW (2006) Many roads lead to

‘‘auxin’’: of nitrilases, synthases, and amidases. Plant Biology 8:

326–333.

Prinsen E, Chauvaux N, Schmidt J, John M, Wieneke U, Degreef J,

Schell J & Vanonckelen H (1991) Stimulation of indole-3-

acetic acid production in Rhizobium by flavonoids. FEBS Lett

282: 53–55.

Prinsen E, Costacurta A, Michiels K, Vanderleyden J & Van

Onckelen H (1993) Azospirillum brasilense indole-3-acetic acid

biosynthesis: evidence for a non-tryptophan dependent

pathway. Mol Plant–Microbe Interact 6: 609–615.

Proctor MH (1958) Bacterial dissimilation of indoleacetic acid: a

new route of breakdown of the indole nucleus. Nature 181:

1345.

Prusty R, Grisafi P & Fink GR (2004) The plant hormone

indoleacetic acid induces invasive growth in Saccharomyces

cerevisiae. Proc Natl Acad Sci USA 101: 4153–4157.

Rabus R (2005) Functional genomics of an anaerobic aromatic-

degrading denitrifying bacterium, strain EbN1. Appl Microbiol

Biot 68: 580–587.

Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F &

Reinhardt R (2005) The genome sequence of an anaerobic

aromatic-degrading denitrifying bacterium, strain EbN1. Arch

Microbiol 183: 27–36.

Ramesh V, Frederick RO, Syed SEH, Gibson CF, Yang JC &

Roberts GCK (1994) The interactions of Escherichia coli Trp

repressor with tryptophan and with an operator

oligonucleotide NMR studies using selectively N-15-labeled

protein. Eur J Biochem 225: 601–608.

Redman JC, Haas BJ, Tanimoto G & Town CD (2004)

Development and evaluation of an Arabidopsis whole genome

Affymetrix probe array. Plant J 38: 545–561.

Remans R, Spaepen S & Vanderleyden J (2006) Auxin signaling in

plant defense. Science 313: 171.

Robinette D & Matthysse AG (1990) Inhibition by Agrobacterium

tumefaciens and Pseudomonas savastanoi of development of

the hypersensitive response elicited by Pseudomonas syringae

pv phaseolicola. J Bacteriol 172: 5742–5749.

Rosenblueth M & Martinez-Romero E (2006) Bacterial

endophytes and their interactions with hosts. Mol

Plant–Microbe Interact 19: 827–837.

Saleh SS & Glick BR (2001) Involvement of gacS and rpoS in

enhancement of the plant growth-promoting capabilities of

Enterobacter cloacae CAL2 and UW4. Can J Microbiol 47:

698–705.

Schenk PM, Kazan K, Wilson I, Anderson JP, Richmond T,

Somerville SC & Manners JM (2000) Coordinated plant

defense responses in Arabidopsis revealed by microarray

analysis. Proc Natl Acad Sci USA 97: 11655–11660.

Schmelz EA, Engelberth J, Alborn HT, O’Donnell P, Sammons M,

Toshima H & Tumlinson JH III (2003) Simultaneous analysis

of phytohormones, phytotoxins, and volatile organic

compounds in plants. Proc Natl Acad Sci USA 100:

10552–10557.

Seidel C, Walz A, Park S, Cohen JD & Ludwig-Muller J (2006)

Indole-3-acetic acid protein conjugates: novel players in auxin

homeostasis. Plant Biol 8: 340–345.

Sekine M, Watanabe K & Syono K (1989) Molecular cloning of a

gene for indole-3-acetamide hydrolase from Bradyrhizobium

japonicum. J Bacteriol 171: 1718–1724.

Sergeeva E, Liaimer A & Bergman B (2002) Evidence for

production of the phytohormone indole-3-acetic acid by

cyanobacteria. Planta 215: 229–238.

Shiner EK, Rumbaugh KP & Williams SC (2005) Interkingdom

signaling: deciphering the language of acyl homoserine

lactones. FEMS Microbiol Rev 29: 935–947.

Shinshi H, Mohnen D & Meins F (1987) Regulation of a plant

pathogenesis-related enzyme – inhibition of chitinase and

chitinase messenger RNA accumulation in cultured tobacco

FEMS Microbiol Rev 31 (2007) 425–448c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

446 S. Spaepen et al.

Page 23: Aia review (1)

tissues by auxin and cytokinin. Proc Natl Acad Sci USA 84:

89–93.

Smith EA & Macfarlane GT (1997) Formation of phenolic and

indolic compounds by anaerobic bacteria in the human large

intestine. Microb Ecol 33: 180–188.

Somers E, Ptacek D, Gysegom P, Srinivasan M & Vanderleyden J

(2005) Azospirillum brasilense produces the auxin-like

phenylacetic acid by using the key enzyme for indole-3-acetic

acid biosynthesis. Appl Environ Microbiol 71: 1803–1810.

Sprunck S, Jacobsen HJ & Reinard T (1995) Indole-3-lactic acid is

a weak auxin analogue but not an anti-auxin. J Plant Growth

Regul 14: 191–197.

Steenhoudt O & Vanderleyden J (2000) Azospirillum a free-living

nitrogen-fixing bacterium closely associated with grasses:

genetic, biochemical and ecological aspects. FEMS Microbiol

Rev 24: 487–506.

Suzuki S, He YX & Oyaizu H (2003) Indole-3-acetic acid

production in Pseudomonas fluorescens HP72 and its

association with suppression of creeping bentgrass brown

patch. Curr Microbiol 47: 138–143.

Taiz L & Zeiger E (1998) Plant Physiology. Sinauer Associates,

Sunderland, MA.

Takahashi K, Kasai K & Ochi K (2004) Identification of the

bacterial alarmone guanosine 50-diphosphate 30-diphosphate

(ppGpp) in plants. Proc Natl Acad Sci USA 101: 4320–4324.

Teale WD, Paponov IA & Palme K (2006) Auxin in action:

signalling, transport and the control of plant growth and

development. Nat Rev Mol Cell Biol 7: 847–859.

Theunis M (2005) IAA biosynthesis in rhizobia and its potential

role in symbiosis. PhD thesis, Universiteit Antwerpen.

Theunis M, Kobayashi H, Broughton WJ & Prinsen E (2004)

Flavonoids, NodD1, NodD2, and nod-box NB15 modulate

expression of the y4wEFG locus that is required for indole-3-

acetic acid synthesis in Rhizobium sp. strain NGR234. Mol

Plant–Microbe Interact 17: 1153–1161.

Thilmony R, Underwood W & He SY (2006) Genome-wide

transcriptional analysis of the Arabidopsis thaliana interaction

with the plant pathogen Pseudomonas syringae pv. tomato

DC3000 and the human pathogen Escherichia coli O157: H7.

Plant J 46: 34–53.

Tirichine L, Sandal N, Madsen LH, Radutoiu S, Albrektsen AS,

Sato S, Asamizu E, Tabata S & Stougaard J (2007) A gain-of-

function mutation in a cytokinin receptor triggers

spontaneous root nodule organogenesis. Science 315: 104–107.

Tsubokura S, Sakamoto Y & Ichihara K (1961) The bacterial

decomposition of indoleacetic acid. J Biochem (Tokyo) 49:

38–42.

Valls M, Genin S & Boucher C (2006) Integrated regulation of the

type III secretion system and other virulence determinants in

Ralstonia solanacearum. PLoS Pathog 2: 798–807.

van Noorden GE, Ross JJ, Reid JB, Rolfe BG & Mathesius U

(2006) Defective long-distance auxin transport regulation in

the Medicago truncatula super numeric nodules mutant. Plant

Physiol 140: 1494–1506.

Vande Broek A, Lambrecht M, Eggermont K & Vanderleyden J

(1999) Auxins upregulate expression of the indole-3-pyruvate

decarboxylase gene in Azospirillum brasilense. J Bacteriol 181:

1338–1342.

Vande Broek A, Gysegom P, Ona O, Hendrickx N, Prinsen E, Van

Impe J & Vanderleyden J (2005) Transcriptional analysis of the

Azospirillum brasilense indole-3-pyruvate decarboxylase gene

and identification of a cis-acting sequence involved in auxin

responsive expression. Mol Plant–Microbe Interact 18:

311–323.

Vandeputte O, Oden S, Mol A, Vereecke D, Goethals K, El Jaziri M

& Prinsen E (2005) Biosynthesis of auxin by the gram-positive

phytopathogen Rhodococcus fascians is controlled by

compounds specific to infected plant tissues. Appl Environ

Microbiol 71: 1169–1177.

Vasanthakumar A & McManus PS (2004) Indole-3-acetic acid-

producing bacteria are associated with cranberry stem gall.

Phytopathology 94: 1164–1171.

Venis MA & Napier RM (1995) Auxin receptors and auxin-

binding proteins. Crit Rev Plant Sci 14: 27–47.

Verhagen BWM, Glazebrook J, Zhu T, Chang HS, van Loon LC &

Pieterse CMJ (2004) The transcriptome of rhizobacteria-

induced systemic resistance in Arabidopsis. Mol Plant–Microbe

Interact 17: 895–908.

Verstrepen KJ & Klis FM (2006) Flocculation, adhesion and

biofilm formation in yeasts. Mol Microbiol 60: 5–15.

Verstrepen KJ, Reynolds TB & Fink GR (2004) Origins of

variation in the fungal cell surface. Nat Rev Microbiol 2:

533–540.

Vogel G (2006) Plant science – auxin begins to give up its secrets.

Science 313: 1230–1231.

Walters M & Sperandio V (2006) Quorum sensing in Escherichia

coli and Salmonella. Int J Med Microbiol 296: 125–131.

Wang D, Ding X & Rather PN (2001) Indole can act as an

extracellular signal in Escherichia coli. J Bacteriol 183:

4210–4216.

Wang YQ, Ohara Y, Nakayashiki H, Tosa Y & Mayama S (2005)

Microarray analysis of the gene expression profile induced by

the endophytic plant growth-promoting rhizobacteria,

Pseudomonas fluorescens FPT9601-T5 in Arabidopsis. Mol

Plant–Microbe Interact 18: 385–396.

Went FW & Thimann KV (1937) Phytohormones. Macmillan,

New York.

White PR & Braun AC (1941) Crown gall production by bacteria-

free tumor tissues. Science 93: 239–241.

White JA, Todd T, Newman T, Focks N, Girke T, de Ilarduya OM,

Jaworski JG, Ohlrogge JB & Benning C (2000) A new set of

Arabidopsis expressed sequence tags from developing seeds.

The metabolic pathway from carbohydrates to seed oil. Plant

Physiol 124: 1582–1594.

Woodward AW & Bartel B (2005) Auxin: regulation, action, and

interaction. Ann Bot (London) 95: 707–735.

Wu CF, Dickstein R, Cary AJ & Norris JH (1996) The auxin

transport inhibitor N-(1-naphthyl)phthalamic acid elicits

FEMS Microbiol Rev 31 (2007) 425–448 c� 2007 Federation of European Microbiological SocietiesPublished by Blackwell Publishing Ltd. All rights reserved

447Microbial auxin signaling

Page 24: Aia review (1)

pseudonodules on nonnodulating mutants of white

sweetclover. Plant Physiol 110: 501–510.

Xie H, Pasternak JJ & Glick BR (1996) Isolation and

characterization of mutants of the plant growth-promoting

rhizobacterium Pseudomonas putida CR12-2 that overproduce

indoleacetic acid. Curr Microbiol 32: 67–71.

Xu GW & Gross DC (1988a) Evaluation of the role of

syringomycin in plant pathogenesis by using Tn5-mutants of

Pseudomonas syringae pv syringae defective in syringomycin

production. Appl Environ Microbiol 54: 1345–1353.

Xu GW & Gross DC (1988b) Physical and functional analyses of

the syrA gene and syrB gene involved in syringomycin

production by Pseudomonas syringae pv syringae. J Bacteriol

170: 5680–5688.

Yang SH, Perna NT, Cooksey DA, Okinaka Y, Lindow SE, Ibekwe

AM, Keen NT & Yang CH (2004) Genome-wide identification

of plant-upregulated genes of Erwinia chrysanthemi 3937 using

a GFP-based IVET leaf array. Mol Plant–Microbe Interact 17:

999–1008.

Yang S, Zhang Q, Guo J, Charkowski AO, Glick BR, Ibekwe AM,

Cooksey DA & Yang CH (2007) Global effect of indole-3-acetic

acid biosynthesis on multiple virulence factors of Erwinia

chrysanthemi 3937. Appl Environ Microbiol 73: 1079–1088.

Zambryski PC (1992) Chronicles from the Agrobacterium – plant

cell DNA transfer story. Annu Rev Plant Physiol 43: 465–490.

Zhao Y, Christensen SK, Fankhauser C, Cashman JR, Cohen JD,

Weigel D & Chory J (2001) A role for flavin monooxygenase-

like enzymes in auxin biosynthesis. Science 291: 306–309.

Zhu T & Wang X (2000) Large-scale profiling of the Arabidopsis

transcriptome. Plant Physiol 124: 1472–1476.

Zimmer W, Wesche M & Timmermans L (1998) Identification

and isolation of the indole-3-pyruvate decarboxylase gene

from Azospirillum brasilense Sp7: sequencing and functional

analysis of the gene locus. Curr Microbiol 36: 327–331.

Zupan J, Muth TR, Draper O & Zambryski P (2000) The transfer

of DNA from Agrobacterium tumefaciens into plants: a feast of

fundamental insights. Plant J 23: 11–28.

Supplementarymaterial

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article online:

Table S1. BLAST homology results: IAA receptor and

transport protein.

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Please note: Blackwell Publishing are not responsible

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448 S. Spaepen et al.


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