Research Article Burkholderia contaminans Biofilm...

Research ArticleBurkholderia contaminans Biofilm Regulating Operon andIts Distribution in Bacterial Genomes

Olga L Voronina1 Marina S Kunda1 Natalia N Ryzhova1 Ekaterina I Aksenova1

Andrey N Semenov1 Yulia M Romanova12 and Alexandr L Gintsburg12

1NF Gamaleya Federal Research Center for Epidemiology and Microbiology Ministry of Health of RussiaGamaleya Street 18 Moscow 123098 Russia2IM Sechenov First Moscow State Medical University Moscow 119991 Russia

Correspondence should be addressed to Olga L Voronina olv550gmailcom

Received 24 February 2016 Accepted 8 November 2016

Academic Editor Vassily Lyubetsky

Copyright copy 2016 Olga L Voronina et al This is an open access article distributed under the Creative Commons AttributionLicense which permits unrestricted use distribution and reproduction in any medium provided the original work is properlycited

Biofilm formation by Burkholderia spp is a principal cause of lung chronic infections in cystic fibrosis patients A ldquolacking biofilmproductionrdquo (LBP) strain B contaminans GIMC4587Bct370-19 has been obtained by insertion modification of clinical strain withplasposon mutagenesis It has an interrupted transcriptional response regulator (RR) gene The focus of our investigation wasa two-component signal transduction system determination including this RR B contaminans clinical and LBP strains wereanalyzed by whole genome sequencing and bioinformatics resources A four-component operon (BiofilmReg) has a key role inbiofilm formation The relative location (ie by being separated by another gene) of RR and histidine kinase genes is unique inBiofilmReg Orthologs were found in other members of the Burkholderiales order Phylogenetic analysis of strains containingBiofilmReg operons demonstrated evidence for earlier inheritance of a three-component operon During further evolution onelineage acquired a fourth gene whereas others lost the third component of the operon Mutations in sensor domains have createdbiodiversity which is advantageous for adaptation to various ecological niches Different species Burkholderia and Achromobacterstrains all demonstrated similar BiofilmReg operon structure Therefore there may be an opportunity to develop a common drugwhich is effective for treating all these causative agents

1 Introduction

The Burkholderia cepacia complex (Bcc) bacteria are oppor-tunistic pathogens which cause nosocomial infections andare especially dangerous for cystic fibrosis (CF) patientsAnalysis of Bcc strain diversity in Russian healthcare unitsand in CF patients demonstrated 5 species B cenocepacia Bmultivorans B stabilis B contaminans and B vietnamiensis[1] Among these B cenocepaciawasmore abundant and theRussian epidemic strain ST (sequence type) 709 belonged tothis species However B contaminans ST102 was also isolatedfrom CF and non-CF patients [1] Moreover this strain isknown to have an intercontinental spread across the world[2]

Presently Bcc eradication is complex and in most casesimpossible which leads to chronic infections in the lungs

of CF patients Biofilm formation is the principal reason forbacterial stability in CF patientsrsquo respiratory tracts

The history of biofilm observation is long But in spiteof studies of planktonic and aggregated forms of microbesthat occurred hand in hand the importance of the biofilmphenomena for medicine was first postulated by Hoiby andAxelsen only at the beginning of 1970s based on observationsof CF patients with chronic Pseudomonas aeruginosa lunginfection [3] Later the first biofilm conference in 1996yielded better understanding of the significance of biofilminfection in medicine and marked the beginning of intensivemicrobial biofilm research Many different approaches wereused conventional light microscopy electron microscopyand confocal laser scanning microscopy for biofilm archi-tecture and composition investigation direct and acci-dental mutation of biofilm-forming strains transcriptomic

Hindawi Publishing CorporationBioMed Research InternationalVolume 2016 Article ID 6560534 13 pageshttpdxdoiorg10115520166560534

2 BioMed Research International

analysis and differential measurement of biochemical path-way activity andmetabolite concentrations of planktonic andsessile cells [4] Hence we now know that a large numberof genes are involved in so complicated process of biofilmformation For instance comparison of high- and low-biofilmproducing B pseudomallei strains revealed 563 differentiallyregulated genes [5] It should be noted that upregulated genesrelated to two-component signal transduction systems and adenitrification enzyme pathway [5]

A surprising result came from the work of Romanovaet al [6] on nondirectional insertion mutagenesis of highbiofilm producer (HBP) clinical strain B contaminansGIMC4509Bct370 when just one of 1000 plasposon inser-tions had lost the ability to form biofilm This LBP strainnamed B contaminans GIMC4587Bct370-19 had only oneinterrupted gene DNA sequencing of a fragment adjacent tothe insertion site identified it as the transcriptional regulatorgene ompR which is the part of the two-component signaltransduction system (shortly two-component system TCS)The TCS array consists of a protein histidine kinase (HK) anda response regulator (RR) protein It is now known that TCSsmediate several different bacterial processes chemotaxisaerobicanaerobic regulation sporulation anddifferentiation[7] as well as biofilm response [8]

The purpose of our investigation was the determinationof this key in biofilm formation TCS part of which is foundtranscriptional regulator Detailed study of the BiofilmRegoperon structure and evolution could have significant med-ical applications

2 Materials and Methods

21 Bacterial Strains andTheir Origins All strains used camefrom the Gamaleya Institute Microbial Collection (GIMC)high biofilm producer (HBP) clinical strain B contami-nans GIMC4509Bct370 (ST102 PubMLST id 1264) andlacking biofilm production (LBP) B contaminans strainGIMC4587Bct370-19 The LBP strain was obtained by inser-tion modification of clinical strain with plasposon pTnMod-RKm by Romanova et al [6]

22 DNA Isolation and Genomics Preparation of genomicDNA for the whole genome sequencing was performedas described [9] Whole genome sequencing of B contam-inans strains was performed according to the manufac-turerrsquos (Roche) guidelines for the next generation sequencing(NGS) Two protocols were used for shotgun-sequencinglibrary preparation rapid library and pair-end library

23 Data Acquisition and Processing DNA sequence assem-bly into scaffolds was performedwith 454 Sequencing SystemSoftware v27 and v30 (Roche) To aid in assembling indi-vidual chromosome we used data from reference strains Blata strain Burkholderia sp 383 B contaminans strain MS14B ubonensis strain MSMB22 B cenocepacia strains J2315DDS 22E-1 B cepacia strains DDS 7H-2 ATCC 25416The software Rapid Annotations Subsystems Technology

and SEED [10 11] were used for annotating the genomeof B contaminans strains BioProjects PRJNA349796 andPRJNA349797 were registered in GenBank with BioSam-ple Accessions SAMN05933033 for GIMC4509Bct370 andSAMN05933042 forGIMC4587Bct370-19 Now the genomesare in the process of the chromosomes assembling

24 Bioinformatic Analyses Complementary protein de-scription prediction of domains signal peptides and proteincellular localization have been performed by NCBI BLAST[12] InterPro server [13 14] TMHMM Server v 20 [15]SignalP 41 Server [16] and PSORTb version 302 [17] Pro-moter sequence prediction has been performed by BPROM(Prediction of Bacterial Promoters) [18 19] and NNPP(Neural Network Promoter Prediction) [20] servers Operonborders have been predicted with help of operon predictorPTools04a (BioCyc Database Collection) [21] Searches of theNCBI database for orthologs of operon components and genewas performed with the aid of the KEGG ORTHOLOGY(KO) Database [22 23] and Biocyc Database [24] Multiplealignments of nucleotide sequences were created in a MEGA60 [25] environment using Multiple Sequence Alignmenttools [26] The numbers of nucleotide differences per sitewere counted as pairwise distances Percent similarity anddivergence coefficients have been determined by MegAlign505 [25] Amino acid sequence analysis tools in thesesame software packages were also used Searches usingNCBI BLAST have been performed for identification ofsignificant sequences containing sites of phosphorylationintermolecular recognition polypeptide and DNA bind-ing

25 Phylogenetic Analysis Phylogenetic analyses of polypep-tide sequence data were performed in MEGA 60 [25] Evo-lutionary history was inferred by using the Maximum Like-lihood (ML) method based on the JTT matrix-based model[27]Thepercentage of trees inwhich the associated taxa clus-tered together is shown next to the branches Initial tree forthe heuristic search was obtained automatically by applyingNeighbor-Join and BioNJ algorithms to a matrix of pairwisedistances estimated using a JTT model and then selectingthe topology with superior log likelihood value Trees weredrawn to scale with branch lengths measured as the numberof substitutions per site All positions containing gaps andmissing data were eliminated

Phylogenetic analysis of 16S rDNA nucleotide sequenceswas carried out in MEGA 60 [25] The evolutionary historywas inferred by using ML method based on the general timereversible model GTR+G [28] which was chosen as anoptimal evolution distance model derived from Modeltestbased on theAkaike information criterion [29] Initial tree forthe heuristic search was obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimatedusing theMaximumComposite Likelihood (MCL) approachA discrete Gamma distribution was used tomodel evolution-ary rate differences among sites (6 categories (+G parameter= 03082)) Bootstrap analyses were performed with 500replicates

BioMed Research International 3

Figure 1 BiofilmReg operon location on Burkholderia sp383chromosome 1 (GenBank CP0001511) A4580 1555167 1555871two-component transcriptional regulator winged helix familyA4581 1555868 1557229 peptidoglycan-binding LysM A45821557240 1559627 periplasmic sensor signal transduction histi-dine kinase and A4583 1559665 1560279 hypothetical protein(httpwwwncbinlmnihgov) Blue triangle is in the position ofthe gene interruption by plasposon Blue line marks the genes ofoperon

3 Results and Discussion

31 Localization of Biofilm-Switch Response Regulator (RR)in B contaminans Genomes The clinical HBP strain B con-taminansGIMC4509Bct370 and its modification LBP strainB contaminans GIMC4587Bct370-19 were the objects ofwhole genome sequencing (WGS) Assembling the genomesin scaffolds allowed us to suggest a candidate position forthe interruption position of the plasposon and then tofind the neighbor genes of RR Upstream of the insertsite and on the same sense there were three genes withown promoters The distance between the nearest outsidegene and RR was 269 bp This intergenic region includedpredicted promoter region a transcription start site and a 51015840untranslated region (UTR)The promoter region was locatedat 164ndash213 bp upstream RR gene start codon according toNNPP server The positions of consensus minus10 box and minus35box were detected at minus192 bp and minus212 bp respectively withhelp of BPROM server The 51015840 UTR was surprisingly longfor Prokaryotes 173 bp The suggestion of our predictionwe found in Sass et alrsquos experimental work [30] Authorsanalyzed theRNAextracted fromB cenocepacia J2315 biofilmand revealed 187CDS (coding sequence) which featured long51015840 UTR of gt150 nt for transcriptional regulators nucleotidebinding and membrane proteins Among these 187 CDSwas BCAL1443 (two-component regulatory system responseregulator protein) orthologous to our RR

The three same sense downstream genes are genes ofpeptidoglycan-binding protein (PBP) with additional FecRdomain histidine kinase (HK) and uncharacterized protein(UnP) of DUF4136 superfamily (Figure 1) The next openreading frame (ORF) has been located on the antisensestrandThe start codon of PBP gene was inside the RR codingregion The distance between the PBP and HK genes was10 bp and 27 bp between HK and UnP genes There wasnot any promoter downstream RR gene all the way to thefirst gene on the antisense strand according to promotersequence prediction by BPROM and NNPP servers Sobasing our conclusion on the distances between the fouradjacent genes in the sameDNA strand and on the availabilityof a single transcriptional promoter we predict that theirorganization reflects a common transcriptional operon Sincethe RR interruption by the plasposon had switched off thestrain biofilm formation entirely we had named the operon

ldquoBiofilmRegulatingrdquo (shortly BiofilmReg)The intact operonof HBP strain has been submitted to the NCBI GenBankdatabase with Accession Number KP288492 The LBP strainoperon sequences have Accession Numbers KP288491 andKU252679

As mentioned earlier RR and HK are usually assumedto be a cognate pair because they lie next to one anotherwithin the same operon [31] In contrast here the PBP geneis embedded between the RR and HK genes so they arenot ldquogenomic neighborsrdquo in Sheng et alrsquos [32] interpretationbecause the distance between them is more than 300 bpBecause some researchers who work on bioinformatic analy-sis of TCS in whole genomes might doubt our evidence thatthe HK gene from BiofilmReg operon is part of an operonwith RR we have done further investigations to show thatthese genes form natural functional units within a singleoperon

32 Diversity of Two-Component Transcriptional Regulator(TCTR) Genes in B lata Genome Is this case of a coregulatedgene inserted between RR and HK unique To answer thisquestion we searched for all two-component transcrip-tional regulator (TCTR) genes in the reference B latagenome We found 37 TCTR genes 49 on chromo-some 1 (369Mb NC 0075101) and nearly equal numbers27 versus 24 respectively on chromosome 2 (359MbINSDC NC 0075111) and chromosome 3 (14Mb INSDCNC 0075091) even though the second chromosome is twiceas big as the third Eleven TCTRs were found to be encodedby a single gene the remaining 26 TCTRs were organized inoperons Among these 26 22 operons were two-componenttypes in accordance with the evidence that the averagebacterial operon size is 22 genes [33] The remaining fouroperons included more than two genes The biggest con-tained eight genes whose products participated in phosphatetransport Another one was a three-component type locatedon the second chromosome The last two operons had four-components One of them included genes of the DUF4390family uncharacterized protein and rRNA SAM-dependentmethyltransferase as well as the RR and HK The second onewas the BiofilmReg operon For themajority of these operonsthe gene adjacent to TCTR was HK Only in the BiofilmRegoperon was a PBP gene embedded between the RR and HKgenes Since gene organization in an operon is a means tocoordinate expression functions [34] we next attempted tounderstand the possible functions of proteins encoded byBiofilmReg analyzing there domains

33 Analysis of Proteins Domains in BiofilmReg OperonComponents First we analyzed the domains of the TCTR(Table S1 in Supplementary Material available online athttpdxdoiorg10115520166560534) in reference B latagenome According to the NCBI BLAST results two con-servative domains are present in TCTR receiver and DNAbinding Together they formamultidomain polypeptide hav-ing a Pfam classification [35] Most of the TCTRs examinedabout 70 had a winged helix-turn-helix (wHTH) DNAbinding domain (PF00486) 19 were the representativesof the LuxR family (PF00196) 5 were simple HTH 8


(PF02954) structures and the last 5 belonged to the HTH-AraC (PF00165) family (Table S2) The most abundant groupwas subdivided into eight subgroups according to theirmultidomain characteristics One of the common typesthe CreB family includes RR from the BiofilmReg operonCreB is carbon source responsive response regulator thatbelongs to the CreBC two-component system Investigationof this system in E coli has demonstrated its participationin controlling genes involved in acetate [36] and ribosemetabolism [37] in the maltose regulon [38] and in thepentose phosphate pathway [39] and geneswhich repairDNAdamage associated with the replication fork [40] Avison et al[41] have namedCreBC ldquothe heart ofmetabolic regulationrdquo inE coli [41] RR has localized in cytoplasm of bacterial cell

The next component in the BiofilmReg operon that weexamined is the gene for an uncharacterized conservedprotein containing LysM and FecR domains This is namedaccording to COG4254 (clusters of orthologous groups) [42]The InterPro resource classified this protein as an unchar-acterized conserved protein UCP02964 LysM PA4035Orthologs of this gene were variously named unchar-acterized protein (UniProtKB U2H3R6) peptidase M23B(A0A0J6M8Q8) peptidoglycan-binding LysM (Q39H89)and FecR family protein (A0A088U8M6) The structure ofLysM domain is known and a function in peptidoglycanbinding is predicted for it It is found in a variety of enzymesinvolved in bacterial cell wall degradation [12] The seconddomain is FecR which is involved in regulation of irondicitrate transport and is probably a sensor that recognizesiron dicitrate in the periplasm [12] The InterPro service pre-dicted for the protein product of the second component ofBiofilmReg a signal peptide and the main part of the proteinlocalized outside of the cytoplasm which agrees with putativefunction for this domain

Third gene in BiofilmReg operon is a gene for a histidinekinase or periplasmic sensor signal transductor histidinekinase This HK is a multidomain protein The first domainstarting from the N-terminus is transmembrane the secondis a CHASE2 domain (pfam05226) which is an extracellularsensory domain Environmental factors that are recognizedbyCHASE2 domains are not known at this time [12]Thenextthree HK structural elements are transmembrane domainsThe subsequent PAS domain is a second sensor domainwhich is not present in all HK types [43] This adaptabledomain can monitor changes in light redox potential oxy-gen or small ligands depending on their associated cofactor[7] PAS domain is localized in cytoplasm The next twodomains have the same localization These are (1) dimeriza-tion and phosphotransfer and (2) catalytic and ATP-bindingAll together these last domains formmultidomainAccordingto COG classification (COG3852) the HK from Biofilm-Reg operon is nitrogen specific having multidomain NtrB[12]

The fourth and final component of the operon is thegene for an uncharacterized protein with a DUF4136 domainThis domain has been found in bacterial lipoproteins [12]According to InterPro this polypeptide has a signal peptideand the main part of the protein has external localiza-tion

LysMFecR

DUF4136CHASE2

sensor

ATF-ase

DNAbinding

Receiverdomain

Outer membrane

Peptidoglycan

Periplasm

Cell membrane

Cytoplasm

2

31

4

Figure 2 Components of BiofilmReg operon topology in bacterialcell predicted by InterPro Service (httpwwwebiacukinterpro)The components are as follows (1) two-component transcriptionalregulator (2) uncharacterized conserved protein containing LysMand FecR domains (3) periplasmic sensor signal transductionhistidine kinase and (4) uncharacterized DUF4136 superfamilyprotein

34 AModel of BiofilmReg Protein Localization In summarywe present a proposal for colocalization of the four describedproteins in bacterial cells (Figure 2)

The periplasm contains two proteins and the signalingdomain of HK One is binding to the rigid exoskeleton (pep-tidoglycan) which determines cell shape [44] the secondis bound to the lipids of the outer or inner membranesThe PBP and HK units sense different signals which canbe transmitted to RR in the cytoplasm and alter target geneexpression

The interruption of this operon by plasposon pTnMod-RKm insertion destroyed all four genesrsquo transcription Onlyshort fragment of RR gene (148 bp) rests before plasposonsequence Promoter detected by BPROM and NNPP serversin the end of plasposon is divided by the second part of RRgene (564 bp) from the next ORF and so cannot be activeAs a result Romanova et al detected the absence of biofilmformation in vitro by modified strain [6]

35 Searching of Orthologs of BiofilmReg Operon ComponentsDo such operons occur frequently in other known bacteriaWe searched for orthologs of BiofilmReg operon componentsto answer this question First we analyzed Gram-negativebacteria of classes Beta- and Gammaproteobacteria whichare often recorded among opportunistic microorganismsthat cause nosocomial infections A cohort of 45 genomesbelonging to 21 generawas examined A result was consideredpositive if at least two adjacent components of the operonwere detected together in the panel of genomes we searched(Table 1)

Among Gammaproteobacteria only two Pseudomonasstrains P aeruginosa PAO1 and P fluorescens PCL1751 had acouple of orthologous genesThese appear to be an exceptionIn the class Betaproteobacteria only the Burkholderialesorder had genera containing orthologs of the BiofilmReg


Table1Re

presentativ

esof

BetaproteobacteriaandGam

maproteob

acteria

which

werec

hecked

forp

resenceo

fatleasttwoadjacent

compo

nentso

foperon

Class

Presento

peroncompo

nents

Orderfa

mily

Absent

operon

compo

nents

Betaproteobacteria

Burkholderiacontam

inan

sGIM

C4509Bc

t370B

urkholderia

lata

strB

urkholderia

sp383B

urkholderia

contam

inan

sMS14

Burkholderiadolosa

AU0158B

urkholderia

multiv

oran

sATC

C17616Bu

rkholderiavietna

mien

sisG4Bu

rkholderiacenocepacia

J2315HI2424

Lautropiamira

bilis

ATCC

51599Pa

ndoraeathiooxydan

sDSM

25325

Burkho

lderialesB

urkh

olderia

ceae

Pand

oraeapn

omenusa3k

gm

AlcaligenesfaecalissubspfaecalisNCI

B8687

Achrom

obacterx

ylosoxidan

sNH44

784-1996N

CTC10807M

N001

Achrom

obacterruh

land

iiSC

CH3Ac

hs33-1365ST3

6Ac

hrom

obacterinsuavisA

XX-A

Bordetellabronchise

ptica

MO149Bo

rdetellapertussis

18323

Burkho

lderialesA

lcaligenaceae

mdash

Ralstoniapickettii

12J

Ralstoniapickettii

DTP

0602

Burkho

lderialesR

alsto

niaceae

mdash

mdashBu

rkho

lderialesC

omam

onadaceae

Vario

voraxparadoxu

sS110

Ac

idovorax

avenae

avenae

ATCC

19860

mdashBu

rkho

lderialesS

utterellaceae

Sutte

rella

parviru

braYIT

mdashNeisseriales

Neisseriameningitid

isWUE2594

Gam

maproteob

acteria

Pseudomonas

aeruginosa

PAO1

Pseudomonas

fluorescens

PCL1751

Pseudo

mon

adales

Acinetobacterh

aemolyticu

sATC

C19194

Pseudomonas

fluorescens

A506SB

W25B

RIP3

4879

F113P

f0-1B

Bc6R

8

mdashEn

terobacteriales

Yersiniainterm

ediaAT

CC29909YersiniapestisK

IMD27K

IM10+

Escherich

iacoliK-

12substr

MG1655Shigella

flexneri

2astr2457T2a

str301

Salm

onellaenteric

aenteric

aserovarD

ublin

str

CT02021853

mdashXa

ntho

mon

adales

Xanthomonas

campestr

ispvcam

pestr

isstrA

TCC

33913

mdashLegion

ellales

Legionellapn

eumophilapneumophilaHextuple2q

Hextuple3aTh

underB

aymdash

Vibrionales

Vibriocholerae

CP1030(3)


operon genes Various species of the Burkholderia genusincluded fully sized operons in their genomes (Tables 1 and2) However other genera in the Burkholderiaceae family hadindividual species with orthologs of the operon

Thus Pandoraea thiooxydans contained a couple of thetarget genes (Table 2) but there were no orthologous genes inP pnomenusa (CP0069002) Three genera of Alcaligenaceaeand a single species Ralstonia pickettii from the Ralsto-niaceae family had orthologs of operon genes Representa-tives of two other families of the order BurkholderialesmdashComamonadaceae and Sutterellaceaemdashhad no genomes withorthologs Overall 21 genomes with orthologous genesfor BiofilmReg operon have been identified and analyzed(Table 2) Among them there is the Russian epidemic strainAchromobacter ruhlandii ST36 (GenBank Accession NumberCP0174331) [45] whose operon is submitted in GenBankwith Accession Number KU252680 Almost all Burkholderiagenomes have an identical operon structure RR PBP HKand UnP However in L mirabilis (Burkholderiaceae) andA faecalis (Alcaligenaceae) genome UnP was substituted byglutamyl-tRNA reductase and AraC family transcriptionalregulator respectively Representatives of AchromobacterBordetella and Ralstonia genera had three-component oper-ons without UnP Finally the operon of P thiooxydans DSM25325 was the most divergent in Burkholderiales order andincluded only two genes PBP and HK

In one gammaproteobacterium a related operon wasfound in the P aeruginosa PAO1 genome This consisted ofjust PBP with a truncated LysM domain and an intact FecRdomain plus HK Despite the alteration in PBP it was clas-sified by NCBI BLAST analysis as COG4254 too [12]

Given the interesting distribution of these operons wenow askedWhat is their evolutionary history To reconstructthe original operon structure in their common ancestralbacterium we analyzed the phylogeny of the listed microor-ganisms with help of 16S rDNA gene sequences as a base ofbiosystematics [46]

36 Phylogeny of Burkholderiales Representatives and P aerug-inosa Based on 16S rDNA Gene Sequences A MaximumLikelihood 16S rDNA gene tree (Figure 3) has been createdfor 50 sequences which included all identified 16S rDNAgene copies of 21 representatives of the families Burkholde-riaceae Alcaligenaceae Ralstoniaceae and Pseudomon-adaceae (Table 2) It should be noted that 16S rDNA genecopies of some genomes have differences in the sequence sothe number of 16S rDNA gene copies increases in more thantwo times the number of genomes in the analysis

The phylogenetic tree revealed two main clusters of theBurkholderiales representatives corresponding to the Alcali-genaceae and Burkholderiaceae families Representatives ofRalstoniaceae were embedded inside the Burkholderiaceaecluster as a distinct group The Alcaligenaceae family cluster(Bootstrap Index BI 100) included Achromobacter Borde-tella and Alcaligenes species and the Burkholderiaceae clus-ter (BI 98) included Burkholderia Pandoraea Lautropiaand Ralstonia species It should be noted that representativesof each genus formed separate clades inside the two majorclustersThe P aeruginosa PAO1 operon is the most divergent

2-component operon with an altered PBP and a normalHK In contrast to P aeruginosa PAO1 (PseudomonadaceaeGammaproteobacteria) which is treated as the outgroup allBurkholderiales genomes contain orthologous operons withat least three components RR HK and PBP being thusconsistent with them having a common origin The three-component operon structure was observed in representativesof two families Ralstoniaceae (R pickettii) andAlcaligenaceae(A xylosoxidans A ruhlandii A insuavis B bronchisepticaand B pertussis) And four-component operon was detectedpredominantly in representatives of Burkholderiaceae (Bcontaminans B lata B dolosa B multivorans B vietnam-iensis B cenocepacia and L mirabilis) and only in one Afaecalis strain of Alcaligenaceae So it is clear that thethree-component operon (RR PBP and HK) represents theancestral state for the major clusters

It is interesting to trace the evolution of whole operonand its components across the different taxa For examplein the genome Bordetella pertussis 18323 the damaged HKgene cannot code catalytic domain and remains present in theoperon only as a pseudogene In genus Ralstonia we detectedoperon only in some R pickettii strains

This species differs in chromosome number from othersin the genus Ralstonia Here R solanacearum has only onechromosome R mannitolilytica has two and R pickettiihas three chromosomes as do most representatives of theBurkholderia genus which are dangerous for CF patients andfor patients of the department of reanimation and intensivetherapy as nosocomial infection One strain R pickettii 12Jhad a conventional version of the three-component operon(Table 2) located on chromosome I However in the genomeof R pickettii DTP0602 three-component operon has beenfound on chromosome II indicating the possible transloca-tion of a full-sized operon The PBP structure of this strainhas provided additional support for this suggestionThe PDPsequence had an additional fragment at its C-terminal endwhich was identified as COG4733 phage-related protein tailcomponent [12]

In the P thiooxydansDSM 25325 genome the two operongenes (PBP and HK) lie together on the same sense strandas usual but the orthologous RR gene is duplicated 31015840 andset in the reverse direction on the complementary DNAstrand This arrangement suggests complex recombinationand translocation events

TheBurkholderia speciesLmirabilis (Burkholderiaceae)and A faecalis (Alcaligenaceae) have probably each indepen-dently gained an extra (fourth) operon component duringtheir evolution In contrast to the general similarity of RRHK and PBP between these operons the extra component ofthe A faecalis operon is an AraC family transcriptional regu-lator while the fourth component of the L mirabilis operonis a glutamyl-tRNA reductase [12] The extra componentof all other Burkholderia operons belongs to the DUF4136superfamily whose function is still unknown The variousfunctions of the fourth components may indicate that theseoperons have been recruited in different metabolic pathwaysprobably involving different signal perception and transduc-tion functions depending on bacterial lifestyle The presenceof these components in operons from different phylogenetic


Table2Maindo

mainof

thep

roteinscoding

byBiofi

lmRe

gop

eron

genes

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons

schematicpresentatio

n1

23

4

1112618

30(K

P2884921)

PRK1108

3(C

reB)

18273188

(KP2

884921)

LysM

FecR

12388(K

U252679)

PAS9

NtrB

2426304

0(K

U252679)

DUF4

136

Burkho

lderia

contam

inan

sstrain

GIM

C450

9Bc

t370

(KP2

884921

KU252679)

2BC

EP18194RS

1300

0PR

K1108

3(C

reB)

BCEP

18194RS

13005

LysM

FecR

BCEP

18194RS

13010

PAS9

NtrB

BCEP

18194RS

13015

DUF4

136

Burkho

lderia

lata

strain

Burkho

lderia

sp383

chromosom

e1

completes

equence(

NC

0075101)

3NL3

0RS

08520

PRK1108

3(C

reB)

NL3

0RS

08515

LysM

FecR

NL3

0RS

08510

PAS9

NtrB

NL3

0RS

08505

DUF4

136

Burkho

lderia

contam

inan

sstrain

MS14chromosom

e1com

plete

sequ

ence

(NZCP

009743)

4AK3

4RS

2164

5PR

K1108

3(C

reB)

AK3

4RS

2164

0LysM

FecR

AK3

4RS

21635

PAS9

BaeS

AK3

4RS

21630

DUF4

136

Burkho

lderia

dolosa

AU0158

chromosom

e1com

pletes

equence

(NZCP

009795)

5BM

ULJ

RS06770

PRK1108

3(C

reB)

BMULJ

RS06775

LysM

FecR

BMULJ

RS06780

PAS9

BaeS

BMULJ

RS06785

DUF4

136

Burkho

lderia

multiv

oran

sATC

C17616DNAcom

pleteg

enom

echromosom

e1(N

C0108041)

6BC

EP1808

RS0704

0PR

K1108

3(C

reB)

BCEP

1808

RS07045

LysM

FecR

BCEP

1808

RS07050

PAS9

NtrB

BCEP

1808

RS07055

DUF4

136

Burkho

lderia

vietna

miensisG4

chromosom

e1com

pletes

equence

(NC

0092561)

7QU43

RS43720

PRK1108

3(C

reB)

QU43

RS43725

LysM

FecR

QU43

RS437230

PAS9

NtrB

QU43

RS43735

DUF4

136

Burkho

lderia

ceno

cepa

ciaJ2315

chromosom

e1com

pleteg

enom

e(N

C0110001)

8BC

EN2424

RS07115

PRK1108

3(C

reB)

BCEN

2424

RS07120

LysM

FecR

BCEN

2424

RS07125

PAS9

NtrB

BCEN

2424

RS07130

DUF4

136

Burkho

lderia

ceno

cepa

ciaHI242

4chromosom

e1com

pletes

equence

(NC

0085421)

9HMPR

EF0551

RS12390

PRK1

0643

(BasR)

HMPR

EF0551

RS12385

LysM

FecR

HMPR

EF0551

RS12380

PASabsentB

aeS

HMPR

EF0551

RS12375

glutam

yl-tR

NA

redu

ctase

Lautropiamira

bilis

ATCC5159

9geno

micscaff

oldSC

AFF

OLD

1who

legeno

mes

hotgun

sequ

ence

(NZGL6

360621)

10QWA

RS04

640

PRK1108

3(C

reB)

QWA

RS04

635

LysM

FecR

QWA

RS04

630

PASabsentB

aeS

QWA

RS04

625

AraCfamily

transcrip

tionalregulator

Alcaligenesfaecalissubspfaecalis

NCI

B86

87Con

tig3who

legeno

me

shotgu

nsequ

ence

(NZAKM

R01000

0031)

11NH44

784RS

11280

PRK10336

(QseB)

NH44

784RS

11275

LysM

FecR

NH44

784RS

11270

PAS4B

aeS

mdashAc

hrom

obacterx

ylosoxidan

sNH44

784-1996

completeg

enom

e(N

C0212851)

12ER

S45141506153

PRK1108

3(C

reB)

ERS45141506154

LysM

FecR

ERS45141506155

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sNCT

C108

07(LN8310291)

13Axylo

5268

PRK1108

3(C

reB)

Axylo

5269

LysM

FecR

Axylo

5270

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sstrain

MN00

1completeg

enom

e(C

P01204

61)


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33

phage-relatedprotein

tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)

lowastDifferencesindo

mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55

Bcon MS14Blat Bsp383 2Bcon GIMC4587Bct370-19Blat Bsp383 4Blat Bsp383 1Blat Bsp383 3Bcen J2315 1Bcen J2315 2Bcen J2315 3Bcen J2315 4Bcen HI2424 2Bcen HI2424 1Bcen HI2424 3Bcen HI2424 4Bvie G4 2Bvie G4 3Bvie G4 1Bvie G4 4Bdol AU0158 2Bdol AU0158 3Bdol AU0158 1Bmul ATCC17616 1Bmul ATCC17616 2Bmul ATCC17616 3Pthi DSM25325 1Pthi DSM25325 2Rpic DTP0602 1Rpic DTP0602 2Rpi 12J 2Rpi 12J 1Lmir ATCC51599Afae NCIB8687Bbro MO149 1Bbro MO149 3Bbro MO149 2Bper 18323 1Bper 18323 2Bper 18323 3Axyl MN001 2Axyl MN001 3Axyl MN001 1Aruh SCCH3Ach33-1365Axyl NH44784-1996Axyl NCTC10807 1Axyl NCTC10807 2Axyl NCTC10807 3Paer PAO1 1Paer PAO1 2Paer PAO1 3Paer PAO1 4

Figure 3 ML phylogenetic tree of Burkholderiaceae representatives and P aeruginosa based on 16S rDNA gene sequences Dark blueBurkholderiaceae blue Ralstoniaceae green Alcaligenaceae and grey Pseudomonas aeruginosaOperons schematic representation is givenon the branch nodes according to Table 1 symbols

lineages among Burkholderiaceae and Alcaligenaceae repre-sentatives also supports the view that these were gained bythem rather than lost from all other phylogenetic lineages

If the conventional version of the three-componentoperon has an ancient origin then we can ask How muchgenetic distinction has accumulated in operon genes duringevolution along different phylogenetic lineages To answerthis question we analyzed the polypeptides encoded by aselection of these operons

37 Analysis of the Sequence Diversity in Individual OperonComponents Our first proteins comparison was done atthe level of domains identified by NCBI BLAST Most RRproteins belonged to the CreB subfamily (Table 2) except forthree strains L mirabilis with an RR of the BasR subfamily(PRK10643) and A xylosoxidans NH44784-1996 plus AinsuavisAXX-Awith RRs of theQseB subfamily (PRK10336)The second component PBP includes two domains LysMand FecR in most cases Characteristics of the L mirabilis


Bdol AU0158 Bvie G4

Bmul ATCC17616 Blat Bsp383 Bcon GIMC4509Bct370 Bcon MS14 Bcen J2315 Bcen HI2424

Lmir ATCC51599 Pthi DSM25325

Rpic 12J Rpic DTP0602

Aruh SCCH3Ach33-1365 Axyl MN001 Axyl NCTC10807 Axyl NH44784-1996

Ains AXX-A Bper 18323 Bbro MO149

Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)

Bmul ATCC17616 Bdol AU0158 Bcen J2315 Bcen HI2424 Bcon MS14 Bcon GIMC4587Bct370-19 Blat Bsp383

Bvie G4 Rpic DTP0602

Rpi 12J Aruh SCCH3Ach33-1365 Axyl MN001 Axyl NCTC10807 Axyl NH44784-1996 Ains AXX-A

Bbro MO149 Bper 18323

Afae NCIB8687 Pthi DSM25325 Lmir ATCC51599

Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)

Paer PAO1 Pthi DSM25325

Bcon MS14 Blat Bsp383

Bcon GIMC4587Bct370-19 Bcen J2315 Bcen HI2424 Bmul ATCC17616

Bdol AU0158 Bvie G4


Bbro MO149 Axyl NH44784-1996 Axyl NCTC10807

Ains AXX-A Aruh SCCH3Ach33-1365 Axyl MN001

Lmir ATCC51599 Afae NCIB8687

100

100

9998

69

100

5951

89

71

9564

01(c)

Paer PAO1 Bcen J2315 Bcen HI2424 Bdol AU0158

Bmul ATCC17616 Blat Bsp338 Bcon MS14 Bcon GIMC4587Bct370-19

Bvie G4 Pthi DSM25325


Axyl NH44784-1996 Axyl NCTC10807 Aruh SCCH3Ach33-1365 Axyl MN001

Ains AXX-A Bbro MO149

Afae NCIB8687 Lmir ATCC51599

100

99100

89

79

62

100

93

8067

55

87

02(d)

Figure 4 ML phylogenetic trees based on aligned amino acid characters of (a) response regulator (REC signal receiver domain andtrans reg C effector domain) (b) uncharacterized conserved protein containing LysM and FecR domains (c) histidine kinase PAS + HisKA+ HATPase c domains and (d) histidine kinase CHASE2 domain Dark blue Burkholderiaceae blue Ralstoniaceae green Alcaligenaceaeand grey Pseudomonas aeruginosa 228 aligned characters of response regulator (REC signal receiver domain + trans reg C effector) (a)213 and 199 aligned characters of histidine kinase (PAS + HisKA + HATPase c and CHASE2 resp) (b c) and 113 aligned characters ofpeptidoglycan-binding protein (LysM and FecR domain) (d) were taken for phylogeny reconstruction

and P aeruginosa PBP components were discussed earlier inSection 36 The third component HK has an extracellularsensory CHASE2 domain (pfam05226) in all strains How-ever the cytoplasmic domains are variableThe second sensordomain PAS9 was replaced by PAS4 in six strains fromdifferent phylogenetic lineages and absent in L mirabilis andin A faecalis The next two domains forming multidomainof NtrB subfamily (COG3852) in BiofilmReg operon HKof LBP strain belong in most cases to the BaeS subfamily(COG0642) even in genus Burkholderia (Table 2)

The second level of proteins comparison consisted ofevaluating phylogenetic relatedness for individual operoncomponents based on the most conservative protein regionsFour resulting alignments are shown in Figure 4 The fourresulting ML phylogenetic trees had slightly different topolo-gies

In general the trees included two clusters a Burkholderiaspecies cluster and anAchromobacter +Bordetella clusterThepositions of P aeruginosa L mirabilis A faecalis R pickettiiand P thiooxydans were variable and sometimes unconven-tional For instance R pickettii strains and P thiooxydansDSM 25325 were not merged with Burkholderiaceae speciesin contrast to the more generally accepted phylogeny of thesetaxa Most RRs exhibited greater similarity than HKs 382to 100 compared with 318ndash100 and 249ndash100 percentsimilarity for PAS + HisKA + HATPase c and CHASE2domains of HKs respectively It can be elucidated by variablespecificity of the HK sensor domains

The Burkholderia genus was more representative in ouranalysis so we compared proteins similarities inside thisgenus alone Most variable among them were the CHASEdomains of HK (differences 12ndash13) PBP (37ndash241)


and UnP (24ndash234) sequences All these protein domainsare localized in the periplasm and have first contactedwith signal molecules Five strains (Burkholderia sp 383MS14 G4 HI2424 and ATCC 17616) in our cohort wereenvironment from different ecological niches and threestrains (GIMC4509Bct370 AU0158 and J2315) were host-associated CF or non-CF patients We suggest that thevariability sequences as revealed here may reflect specialadaptive characteristics of the Burkholderia strains

38 Horizontal Gene Transfer versus Foreign DNA Con-tamination The Burkholderia species themselves and otherBurkholderiales representatives are the primary soil-dwellingbacteria successfully specialized to different ecological nicheincluding host-associations The presence of P aeruginosahas been observed in all these niches which could explainthe acquisition of the BiofilmReg operon by an ancestral Paeruginosa strain Moreover Burkholderia AchromobacterRalstonia and Pseudomonas species were previously includedtogether in one genus Pseudomonas Only the advent ofmolecular-genetic methods allowed microbiological system-atics to split this huge assemblage

Surprisingly we found an orthologs of full-size Biofilm-Reg operon in single genome fromGram-positive bacteriumthe actinobacterium Mumia flava strain MUSC 201 This isa new genus in the family Nocardioidaceae which was firstapproved in 2014 [47] This strain was originally isolatedfrom mangrove soil in Malaysia Because horizontal genetransfer (HGT) is a well-known contributor to gene exchangebetween bacteria Archaea and Eukarya we considered thatthis might be an example of this process Orthologs of theBiofilmReg operon have been found in contig 65 of wholeshotgun genome Mumia flava MUSC 201 (JTDJ01000001ndashJTDJ01000923) with similarity for RR PBP HK and UnPgenes 1000 951 970 and 966 respectively How-ever some observations were highly enigmatic For examplethe Mumia flava genome was unexpectedly big 164Mb incontrast to the few other Nocardioidaceae genomes that havebeen assembled into chromosomes with sizes from 31 to76Mb Second contig 65 was very similar in sequence to thereference B lata genome not only within the borders of theoperon but along a 180 kb stretch Third inM flavia contigs1 12 134 150 and 229 we found sequences similar to thoseof Burkholderia cenocepacia J2315 Burkholderia contaminansMS14 and Ralstonia pickettii 12D including their 16S rDNAsequences So we obtained the evidence for foreign DNApollution in M flava strain MUSC 201 genome and madesure exclusively chromosome assembled genomes are verifiedmaterial for gene analysis

This means only some Gram-negative bacteria haveorthologs of BiofilmReg operon

4 Conclusion

The four-component operon of Burkholderia contaminansstrain GIMC4509Bct370 named BiofilmReg was intriguingby biofilm switching ability and structure organization It wasshown to be unique with respect to the relative locations RRand HK in its operon Exact orthologs of this operon were

found only in the Burkholderiales order of Gram-negativebacteria and not in two Pseudomonas strains Phylogeneticanalysis base of 16S rDNA gene sequences and in accordancewith the operon structure demonstrated the evidence ofthree-component operon inherence from an ancestral bac-terium During evolution one lineage acquired a fourth geneand others lost the third component Mutations especiallyin sensor domains helped to increase biodiversity and allowfor adaptation to various ecological niches So now we canobserve Burkholderia Achromobacter and Ralstonia speciesas emerging pathogens This is a result of shift from livingfree in a natural habitant to adoption of a host-associatedpathogen lifestyle [48] Multiple antibiotic resistance andbiofilm formation help these strains avoid therapeutic drugsBecause Burkholderia andAchromobacter strains from differ-ent species all demonstrated a similar operon structure thereis an opportunity to develop a common drug for all thesecausative agents

Abbreviations

Bcc Burkholderia cepacia complexCF Cystic fibrosisGIMC The Gamaleya Institute Microbial

CollectionST Sequence typeHBP High biofilm producerLBP Lacking biofilm productionNGS Next generation sequencingWGS Whole genome sequencingNCBI The National Center for

Biotechnology InformationUTR Untranslated regionCDS Coding sequenceTCS Two-component signal

transduction system (shortlytwo-component system)

RR Response regulatorHK Histidine kinasePBP Peptidoglycan-binding proteinUnP Uncharacterized proteinML Maximum LikelihoodORF Open reading frameBiofilmReg Biofilm RegulatingTCTR Two-component transcriptional

regulatorwHTH Winged helix-turn-helixCOG Clusters of orthologous groupsBI Bootstrap IndexBlat Bsp383 Burkholderia lata strain

Burkholderia sp 383Bcon MS14 Burkholderia contaminans strain

MS14Bdol AU0158 Burkholderia dolosa AU0158Bmul ATCC17616 Burkholderia multivorans ATCC

17616Bvie G4 Burkholderia vietnamiensis G4Bcen J2315 Burkholderia cenocepacia J2315Bcen HI2424 Burkholderia cenocepaciaHI2424


Lmir ATCC51599 Lautropia mirabilis ATCC 51599Afae NCIB8687 Alcaligenes faecalis subsp faecalis

NCIB 8687Axyl NH44784-1996 Achromobacter xylosoxidans

NH44784-1996Axyl NCTC10807 Achromobacter xylosoxidans

NCTC10807Axyl MN001 Achromobacter xylosoxidans

MN001Aruh SCCH3Ach33-1365

Achromobacter ruhlandiiSCCH3Ach33-1365

Ains AXX-A Achromobacter insuavis AXX-ABbro MO149 Bordetella bronchisepticaMO149Bper 18323 Bordetella pertussis 18323Rpic 12J Ralstonia pickettii 12JRpic DTP0602 Ralstonia pickettii DTP0602Pthi DSM25325 Pandoraea thiooxydans DSM

25325Paer PAO1 Pseudomonas aeruginosa PAO1

Competing Interests

The authors declare that there is no conflict of interestsregarding the publication of this paper

Acknowledgments

This work was supported by Grant 14-04-00116 of the RussianFoundation for Basic Research ldquoTwo-Component SignalTransduction System OmpREnvZ is a Target for DirectedSearch Antibacterial Drugs against Biofilm Infectionrdquo

References

[1] O L VoroninaM S Kunda N N Ryzhova et al ldquoThe variabil-ity of the order burkholderiales representatives in the healthcareunitsrdquo BioMed Research International vol 2015 Article ID680210 9 pages 2015

[2] The Main Site PubMLST hosted at The Department of ZoologyUniversity of Oxford Oxford UK 2016 httppubmlstorg

[3] N Hoiby and N H Axelsen ldquoIdentification and quantitationof precipitins against Pseudomonas aeruginosa in patients withcystic fibrosis bymeans of crossed immunoelectrophoresis withintermediate gelrdquoActa Pathologica etMicrobiologica Scandinav-ica Section B Microbiology vol 81 pp 298ndash308 1973

[4] N Hoslashiby ldquoA personal history of research on microbial biofilmsand biofilm infectionsrdquo Pathogens andDisease vol 70 no 3 pp205ndash211 2014

[5] C-Y Chin Y Hara A-K Ghazali et al ldquoGlobal transcriptionalanalysis of Burkholderia pseudomallei high and low biofilm pro-ducers reveals insights into biofilm production and virulencerdquoBMC Genomics vol 16 no 1 article 471 2015

[6] Y M Romanova I G Tiganova I A Khmel et al ldquoBiofilmsof burkholderia cepacia characteristics of mutants with modi-fied formation capacityrdquo Molecular Genetics Microbiology andVirology vol 26 no 3 pp 93ndash101 2011

[7] A M Stock V L Robinson and P N Goudreau ldquoTwo-compo-nent signal transductionrdquo Annual Review of Biochemistry vol69 pp 183ndash215 2000

[8] E Karatan and P Watnick ldquoSignals regulatory networks andmaterials that build and break bacterial biofilmsrdquoMicrobiologyand Molecular Biology Reviews vol 73 no 2 pp 310ndash347 2009

[9] K Wilson UNIT 24 Preparation of Genomic DNA from Bac-teria Current Protocols in Molecular Biology Wiley OnlineLibrary Hoboken NJ USA 2001

[10] R K Aziz D Bartels A Best et al ldquoThe RAST Server rapidannotations using subsystems technologyrdquo BMCGenomics vol9 article 75 2008

[11] R Overbeek T Begley R M Butler et al ldquoThe subsystemsapproach to genome annotation and its use in the project toannotate 1000 genomesrdquo Nucleic Acids Research vol 33 no 17pp 5691ndash5702 2005

[12] A Marchler-Bauer M K Derbyshire N R Gonzales et alldquoCDD NCBIrsquos conserved domain databaserdquo Nucleic AcidsResearch vol 43 no 1 pp D222ndashD226 2015

[13] AMitchell H Y Chang L Daugherty et al ldquoThe InterPro pro-tein families database the classification resource after 15 yearsrdquoNucleic Acids Research vol 43 no 1 pp D213ndashD221 2015

[14] P Jones D Binns H-Y Chang et al ldquoInterProScan 5 genome-scale protein function classificationrdquo Bioinformatics vol 30 no9 pp 1236ndash1240 2014

[15] Center for Biological Sequence Analysis Server Hosted inTechnical University of Denmark httpwwwcbsdtudkser-vicesTMHMM

[16] T N Petersen S Brunak G von Heijne and H Nielsen ldquoSig-nalP 40 discriminating signal peptides from transmembraneregionsrdquo Nature Methods vol 8 no 10 pp 785ndash786 2011

[17] N Y Yu J RWagnerM R Laird et al ldquoPSORTb 30 improvedprotein subcellular localization prediction with refined local-ization subcategories and predictive capabilities for all prokary-otesrdquo Bioinformatics vol 26 no 13 pp 1608ndash1615 2010

[18] V Solovyev and A Salamov ldquoAutomatic annotation of micro-bial genomes and metagenomic sequencesrdquo in Metagenomicsand its Applications in Agriculture Biomedicine and Environ-mental Studies R W Li Ed pp 61ndash78 Nova Science 2011

[19] Site Softberry Inc Mount Kisco NY USA httpwwwsoft-berrycomberryphtmltopic=bpromampgroup=programsampsub-group=gfindb

[20] Site UC BerkeleyUniversity of Hohenheim Berkeley UCStuttgart Germany httpwwwfruitflyorgseq toolspromoterhtml

[21] P R Romero and P D Karp ldquoUsing functional and organi-zational information to improve genome-wide computation-al prediction of transcription units on pathway-genome data-basesrdquo Bioinformatics vol 20 no 5 pp 709ndash717 2004

[22] KEGG Orthology (KO) Database Hosted in Kanehisa Labo-ratories Kyoto University and University of Tokyo Japanesehttpwwwkeggjpkeggkohtml

[23] M Kanehisa Post-Genome Informatics Oxford UniversityPress 2000

[24] R Caspi T Altman R Billington et al ldquoTheMetaCyc databaseof metabolic pathways and enzymes and the BioCyc collectionof PathwayGenomeDatabasesrdquoNucleic Acids Research vol 42no 1 pp D459ndashD471 2014

[25] K Tamura G Stecher D Peterson A Filipski and S KumarldquoMEGA6molecular evolutionary genetics analysis version 60rdquoMolecular Biology and Evolution vol 30 no 12 pp 2725ndash27292013

[26] The Main Site EMBL-EBI European Bioinformatics Institute2016 httpwwwebiacukToolsmsaclustalw2


[27] D T Jones W R Taylor and J M Thornton ldquoThe rapidgeneration of mutation data matrices from protein sequencesrdquoComputer Applications in the Biosciences vol 8 no 3 pp 275ndash282 1992

[28] M Nei and S Kumar Molecular Evolution and PhylogeneticsOxford University Press New York NY USA 2000

[29] D Posada andK A Crandall ldquoMODELTEST testing themodelof DNA substitutionrdquo Bioinformatics vol 14 no 9 pp 817ndash8181998

[30] A M Sass H Van Acker K U Forstner et al ldquoGenome-widetranscription start site profiling in biofilm-grown Burkholderiacenocepacia J2315rdquo BMC Genomics vol 16 article 775 2015

[31] L Burger and E van Nimwegen ldquoAccurate prediction ofprotein-protein interactions from sequence alignments using aBayesian methodrdquoMolecular Systems Biology vol 4 article 1652008

[32] X Sheng M Huvet J W Pinney and M P Stumpf ldquoEvolu-tionary characteristics of bacterial two-component systemsrdquo inEvolutionary Systems Biology vol 751 ofAdvances in Experimen-talMedicine and Biology chapter 6 pp 121ndash137 Springer BerlinGermany 2012

[33] M Madan Babu Ed Bacterial Gene Regulation and Transcrip-tional Networks Caister Academic Press Poole UK 2013

[34] F Jacob and J Monod ldquoGenetic regulatory mechanisms in thesynthesis of proteinsrdquo Journal of Molecular Biology vol 3 pp318ndash356 1961

[35] R D Finn A Bateman J Clements et al ldquoPfam the proteinfamilies databaserdquo Nucleic Acids Research vol 42 no 1 ppD222ndashD230 2014

[36] H Kakuda K Hosono K Shiroishi and S Ichihara ldquoIden-tification and characterization of the ackA (acetate kinaseA)-pta (phosphotransacetylase) operon and complementationanalysis of acetate utilization by an ackA-pta deletion mutantof Escherichia colirdquo Journal of Biochemistry vol 116 no 4 pp916ndash922 1994

[37] C A Dunn S F OrsquoHandley D N Frick and M J BessmanldquoStudies on the ADP-ribose pyrophosphatase subfamily ofthe Nudix hydrolases and tentative identification of trgB agene associated with tellurite resistancerdquo Journal of BiologicalChemistry vol 274 no 45 pp 32318ndash32324 1999

[38] E Richet ldquoOn the role of the multiple regulatory elementsinvolved in the activation of the Escherichia coli malEp pro-moterrdquo Journal ofMolecular Biology vol 264 no 5 pp 852ndash8621996

[39] G A Sprenger ldquoGenetics of pentose-phosphate pathway en-zymes of Escherichia coli K-12rdquo Archives of Microbiology vol164 no 5 pp 324ndash330 1995

[40] C J Saveson and S T Lovett ldquoTandem repeat recombinationinduced by replication fork defects in Escherichia coli requiresa novel factor RadCrdquo Genetics vol 152 no 1 pp 5ndash13 1999

[41] M B Avison R E Horton T R Walsh and P M BennettldquoEscherichia coli CreBC is a global regulator of gene expressionthat responds to growth in minimal mediardquo The Journal ofBiological Chemistry vol 276 no 29 pp 26955ndash26961 2001

[42] R L Tatusov E V Koonin and D J Lipman ldquoA genomic per-spective on protein familiesrdquo Science vol 278 no 5338 pp 631ndash637 1997

[43] A E Bem N Velikova M T Pellicer P V Baarlen A Marinaand J M Wells ldquoBacterial histidine kinases as novel antibacte-rial drug targetsrdquo ACS Chemical Biology vol 10 no 1 pp 213ndash224 2015

[44] T J Silhavy D Kahne and S Walker ldquoThe bacterial cellenveloperdquo Cold Spring Harbor Perspectives in Biology vol 2 no5 Article ID a000414 2010

[45] O LVoroninaM S KundaNN Ryzhova et al ldquoDiversity andhazard of respiratory infection of Achromobacter spp in cysticfibrosis patientsrdquo Pulmonology vol 25 no 4 pp 389ndash402 2015(Russian)

[46] C RWoese ldquoBacterial evolutionrdquoMicrobiological Reviews vol51 no 2 pp 221ndash271 1987

[47] L-H Lee N Zainal A-S Azman N-S Ab Mutalib K Hongand K-G Chan ldquoMumia flava gen nov sp nov an actinobac-terium of the family Nocardioidaceaerdquo International Journal ofSystematic and Evolutionary Microbiology vol 64 no 5 pp1461ndash1467 2014

[48] B Zhu M Ibrahim Z Cui et al ldquoMulti-omics analysis of nichespecificity provides new insights into ecological adaptation inbacteriardquoThe ISME Journal vol 10 pp 2072ndash2075 2016

Submit your manuscripts athttpwwwhindawicom

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Anatomy Research International

PeptidesInternational Journal of


Hindawi Publishing Corporation httpwwwhindawicom

International Journal of

Volume 2014

Zoology


Molecular Biology International

GenomicsInternational Journal of


The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014


BioinformaticsAdvances in

Marine BiologyJournal of



Signal TransductionJournal of


BioMed Research International

Evolutionary BiologyInternational Journal of



Biochemistry Research International

ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014


Genetics Research International


Advances in

Virolog y

Hindawi Publishing Corporationhttpwwwhindawicom

Nucleic AcidsJournal of

Volume 2014

Stem CellsInternational



Enzyme Research



Microbiology


analysis and differential measurement of biochemical path-way activity andmetabolite concentrations of planktonic andsessile cells [4] Hence we now know that a large numberof genes are involved in so complicated process of biofilmformation For instance comparison of high- and low-biofilmproducing B pseudomallei strains revealed 563 differentiallyregulated genes [5] It should be noted that upregulated genesrelated to two-component signal transduction systems and adenitrification enzyme pathway [5]

A surprising result came from the work of Romanovaet al [6] on nondirectional insertion mutagenesis of highbiofilm producer (HBP) clinical strain B contaminansGIMC4509Bct370 when just one of 1000 plasposon inser-tions had lost the ability to form biofilm This LBP strainnamed B contaminans GIMC4587Bct370-19 had only oneinterrupted gene DNA sequencing of a fragment adjacent tothe insertion site identified it as the transcriptional regulatorgene ompR which is the part of the two-component signaltransduction system (shortly two-component system TCS)The TCS array consists of a protein histidine kinase (HK) anda response regulator (RR) protein It is now known that TCSsmediate several different bacterial processes chemotaxisaerobicanaerobic regulation sporulation anddifferentiation[7] as well as biofilm response [8]

The purpose of our investigation was the determinationof this key in biofilm formation TCS part of which is foundtranscriptional regulator Detailed study of the BiofilmRegoperon structure and evolution could have significant med-ical applications

2 Materials and Methods

21 Bacterial Strains andTheir Origins All strains used camefrom the Gamaleya Institute Microbial Collection (GIMC)high biofilm producer (HBP) clinical strain B contami-nans GIMC4509Bct370 (ST102 PubMLST id 1264) andlacking biofilm production (LBP) B contaminans strainGIMC4587Bct370-19 The LBP strain was obtained by inser-tion modification of clinical strain with plasposon pTnMod-RKm by Romanova et al [6]

22 DNA Isolation and Genomics Preparation of genomicDNA for the whole genome sequencing was performedas described [9] Whole genome sequencing of B contam-inans strains was performed according to the manufac-turerrsquos (Roche) guidelines for the next generation sequencing(NGS) Two protocols were used for shotgun-sequencinglibrary preparation rapid library and pair-end library

23 Data Acquisition and Processing DNA sequence assem-bly into scaffolds was performedwith 454 Sequencing SystemSoftware v27 and v30 (Roche) To aid in assembling indi-vidual chromosome we used data from reference strains Blata strain Burkholderia sp 383 B contaminans strain MS14B ubonensis strain MSMB22 B cenocepacia strains J2315DDS 22E-1 B cepacia strains DDS 7H-2 ATCC 25416The software Rapid Annotations Subsystems Technology

and SEED [10 11] were used for annotating the genomeof B contaminans strains BioProjects PRJNA349796 andPRJNA349797 were registered in GenBank with BioSam-ple Accessions SAMN05933033 for GIMC4509Bct370 andSAMN05933042 forGIMC4587Bct370-19 Now the genomesare in the process of the chromosomes assembling

24 Bioinformatic Analyses Complementary protein de-scription prediction of domains signal peptides and proteincellular localization have been performed by NCBI BLAST[12] InterPro server [13 14] TMHMM Server v 20 [15]SignalP 41 Server [16] and PSORTb version 302 [17] Pro-moter sequence prediction has been performed by BPROM(Prediction of Bacterial Promoters) [18 19] and NNPP(Neural Network Promoter Prediction) [20] servers Operonborders have been predicted with help of operon predictorPTools04a (BioCyc Database Collection) [21] Searches of theNCBI database for orthologs of operon components and genewas performed with the aid of the KEGG ORTHOLOGY(KO) Database [22 23] and Biocyc Database [24] Multiplealignments of nucleotide sequences were created in a MEGA60 [25] environment using Multiple Sequence Alignmenttools [26] The numbers of nucleotide differences per sitewere counted as pairwise distances Percent similarity anddivergence coefficients have been determined by MegAlign505 [25] Amino acid sequence analysis tools in thesesame software packages were also used Searches usingNCBI BLAST have been performed for identification ofsignificant sequences containing sites of phosphorylationintermolecular recognition polypeptide and DNA bind-ing

25 Phylogenetic Analysis Phylogenetic analyses of polypep-tide sequence data were performed in MEGA 60 [25] Evo-lutionary history was inferred by using the Maximum Like-lihood (ML) method based on the JTT matrix-based model[27]Thepercentage of trees inwhich the associated taxa clus-tered together is shown next to the branches Initial tree forthe heuristic search was obtained automatically by applyingNeighbor-Join and BioNJ algorithms to a matrix of pairwisedistances estimated using a JTT model and then selectingthe topology with superior log likelihood value Trees weredrawn to scale with branch lengths measured as the numberof substitutions per site All positions containing gaps andmissing data were eliminated

Phylogenetic analysis of 16S rDNA nucleotide sequenceswas carried out in MEGA 60 [25] The evolutionary historywas inferred by using ML method based on the general timereversible model GTR+G [28] which was chosen as anoptimal evolution distance model derived from Modeltestbased on theAkaike information criterion [29] Initial tree forthe heuristic search was obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimatedusing theMaximumComposite Likelihood (MCL) approachA discrete Gamma distribution was used tomodel evolution-ary rate differences among sites (6 categories (+G parameter= 03082)) Bootstrap analyses were performed with 500replicates















LysMFecR

DUF4136CHASE2

sensor

ATF-ase

DNAbinding

Receiverdomain

Outer membrane

Peptidoglycan

Periplasm

Cell membrane

Cytoplasm

2

31

4








Table1Re

presentativ

esof


maproteob

acteria

which

werec

hecked

forp

resenceo

fatleasttwoadjacent

compo

nentso

foperon

Class

Presento

peroncompo

nents

Orderfa

mily

Absent

operon

compo

nents

Betaproteobacteria

Burkholderiacontam

inan

sGIM

C4509Bc

t370B

urkholderia

lata

strB

urkholderia

sp383B

urkholderia

contam

inan

sMS14

Burkholderiadolosa

AU0158B

urkholderia

multiv

oran

sATC

C17616Bu

rkholderiavietna

mien

sisG4Bu


J2315HI2424

Lautropiamira

bilis

ATCC

51599Pa

ndoraeathiooxydan

sDSM

25325

Burkho

lderialesB

urkh

olderia

ceae

Pand

oraeapn

omenusa3k

gm


B8687

Achrom

obacterx

ylosoxidan

sNH44

784-1996N

CTC10807M

N001

Achrom

obacterruh

land

iiSC

CH3Ac

hs33-1365ST3

6Ac

hrom

obacterinsuavisA

XX-A

Bordetellabronchise

ptica

MO149Bo

rdetellapertussis

18323

Burkho

lderialesA

lcaligenaceae

mdash

Ralstoniapickettii

12J

Ralstoniapickettii

DTP

0602

Burkho

lderialesR

alsto

niaceae

mdash

mdashBu

rkho

lderialesC

omam

onadaceae

Vario

voraxparadoxu

sS110

Ac

idovorax

avenae

avenae

ATCC

19860

mdashBu

rkho

lderialesS

utterellaceae

Sutte

rella

parviru

braYIT

mdashNeisseriales

Neisseriameningitid

isWUE2594

Gam

maproteob

acteria

Pseudomonas

aeruginosa

PAO1

Pseudomonas

fluorescens

PCL1751

Pseudo

mon

adales

Acinetobacterh

aemolyticu

sATC

C19194

Pseudomonas

fluorescens

A506SB

W25B

RIP3

4879

F113P

f0-1B

Bc6R

8

mdashEn

terobacteriales

Yersiniainterm

ediaAT


IMD27K

IM10+

Escherich

iacoliK-

12substr

MG1655Shigella

flexneri

2astr2457T2a

str301

Salm

onellaenteric

aenteric

aserovarD

ublin

str

CT02021853

mdashXa

ntho

mon

adales

Xanthomonas

campestr

ispvcam

pestr

isstrA

TCC

33913

mdashLegion

ellales

Legionellapn


Hextuple3aTh

underB

aymdash

Vibrionales

Vibriocholerae

CP1030(3)














Table2Maindo

mainof

thep

roteinscoding

byBiofi

lmRe

gop

eron

genes

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

1112618

30(K

P2884921)

PRK1108

3(C

reB)

18273188

(KP2

884921)

LysM

FecR

12388(K

U252679)

PAS9

NtrB

2426304

0(K

U252679)

DUF4

136

Burkho

lderia

contam

inan

sstrain

GIM

C450

9Bc

t370

(KP2

884921

KU252679)

2BC

EP18194RS

1300

0PR

K1108

3(C

reB)

BCEP

18194RS

13005

LysM

FecR

BCEP

18194RS

13010

PAS9

NtrB

BCEP

18194RS

13015

DUF4

136

Burkho

lderia

lata

strain

Burkho

lderia

sp383

chromosom

e1

completes

equence(

NC

0075101)

3NL3

0RS

08520

PRK1108

3(C

reB)

NL3

0RS

08515

LysM

FecR

NL3

0RS

08510

PAS9

NtrB

NL3

0RS

08505

DUF4

136

Burkho

lderia

contam

inan

sstrain

MS14chromosom

e1com

plete

sequ

ence

(NZCP

009743)

4AK3

4RS

2164

5PR

K1108

3(C

reB)

AK3

4RS

2164

0LysM

FecR

AK3

4RS

21635

PAS9

BaeS

AK3

4RS

21630

DUF4

136

Burkho

lderia

dolosa

AU0158

chromosom

e1com

pletes

equence

(NZCP

009795)

5BM

ULJ

RS06770

PRK1108

3(C

reB)

BMULJ

RS06775

LysM

FecR

BMULJ

RS06780

PAS9

BaeS

BMULJ

RS06785

DUF4

136

Burkho

lderia

multiv

oran

sATC

C17616DNAcom

pleteg

enom

echromosom

e1(N

C0108041)

6BC

EP1808

RS0704

0PR

K1108

3(C

reB)

BCEP

1808

RS07045

LysM

FecR

BCEP

1808

RS07050

PAS9

NtrB

BCEP

1808

RS07055

DUF4

136

Burkho

lderia

vietna

miensisG4

chromosom

e1com

pletes

equence

(NC

0092561)

7QU43

RS43720

PRK1108

3(C

reB)

QU43

RS43725

LysM

FecR

QU43

RS437230

PAS9

NtrB

QU43

RS43735

DUF4

136

Burkho

lderia

ceno

cepa

ciaJ2315

chromosom

e1com

pleteg

enom

e(N

C0110001)

8BC

EN2424

RS07115

PRK1108

3(C

reB)

BCEN

2424

RS07120

LysM

FecR

BCEN

2424

RS07125

PAS9

NtrB

BCEN

2424

RS07130

DUF4

136

Burkho

lderia

ceno

cepa

ciaHI242

4chromosom

e1com

pletes

equence

(NC

0085421)

9HMPR

EF0551

RS12390

PRK1

0643

(BasR)

HMPR

EF0551

RS12385

LysM

FecR

HMPR

EF0551

RS12380

PASabsentB

aeS

HMPR

EF0551

RS12375

glutam

yl-tR

NA

redu

ctase

Lautropiamira

bilis

ATCC5159

9geno

micscaff

oldSC

AFF

OLD

1who

legeno

mes

hotgun

sequ

ence

(NZGL6

360621)

10QWA

RS04

640

PRK1108

3(C

reB)

QWA

RS04

635

LysM

FecR

QWA

RS04

630

PASabsentB

aeS

QWA

RS04

625

AraCfamily

transcrip

tionalregulator


NCI

B86

87Con

tig3who

legeno

me

shotgu

nsequ

ence

(NZAKM

R01000

0031)

11NH44

784RS

11280

PRK10336

(QseB)

NH44

784RS

11275

LysM

FecR

NH44

784RS

11270

PAS4B

aeS

mdashAc

hrom

obacterx

ylosoxidan

sNH44

784-1996

completeg

enom

e(N

C0212851)

12ER

S45141506153

PRK1108

3(C

reB)

ERS45141506154

LysM

FecR

ERS45141506155

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sNCT

C108

07(LN8310291)

13Axylo

5268

PRK1108

3(C

reB)

Axylo

5269

LysM

FecR

Axylo

5270

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sstrain

MN00

1completeg

enom

e(C

P01204

61)


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33


tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)


mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology















LysMFecR

DUF4136CHASE2

sensor

ATF-ase

DNAbinding

Receiverdomain

Outer membrane

Peptidoglycan

Periplasm

Cell membrane

Cytoplasm

2

31

4








Table1Re

presentativ

esof


maproteob

acteria

which

werec

hecked

forp

resenceo

fatleasttwoadjacent

compo

nentso

foperon

Class

Presento

peroncompo

nents

Orderfa

mily

Absent

operon

compo

nents

Betaproteobacteria

Burkholderiacontam

inan

sGIM

C4509Bc

t370B

urkholderia

lata

strB

urkholderia

sp383B

urkholderia

contam

inan

sMS14

Burkholderiadolosa

AU0158B

urkholderia

multiv

oran

sATC

C17616Bu

rkholderiavietna

mien

sisG4Bu


J2315HI2424

Lautropiamira

bilis

ATCC

51599Pa

ndoraeathiooxydan

sDSM

25325

Burkho

lderialesB

urkh

olderia

ceae

Pand

oraeapn

omenusa3k

gm


B8687

Achrom

obacterx

ylosoxidan

sNH44

784-1996N

CTC10807M

N001

Achrom

obacterruh

land

iiSC

CH3Ac

hs33-1365ST3

6Ac

hrom

obacterinsuavisA

XX-A

Bordetellabronchise

ptica

MO149Bo

rdetellapertussis

18323

Burkho

lderialesA

lcaligenaceae

mdash

Ralstoniapickettii

12J

Ralstoniapickettii

DTP

0602

Burkho

lderialesR

alsto

niaceae

mdash

mdashBu

rkho

lderialesC

omam

onadaceae

Vario

voraxparadoxu

sS110

Ac

idovorax

avenae

avenae

ATCC

19860

mdashBu

rkho

lderialesS

utterellaceae

Sutte

rella

parviru

braYIT

mdashNeisseriales

Neisseriameningitid

isWUE2594

Gam

maproteob

acteria

Pseudomonas

aeruginosa

PAO1

Pseudomonas

fluorescens

PCL1751

Pseudo

mon

adales

Acinetobacterh

aemolyticu

sATC

C19194

Pseudomonas

fluorescens

A506SB

W25B

RIP3

4879

F113P

f0-1B

Bc6R

8

mdashEn

terobacteriales

Yersiniainterm

ediaAT


IMD27K

IM10+

Escherich

iacoliK-

12substr

MG1655Shigella

flexneri

2astr2457T2a

str301

Salm

onellaenteric

aenteric

aserovarD

ublin

str

CT02021853

mdashXa

ntho

mon

adales

Xanthomonas

campestr

ispvcam

pestr

isstrA

TCC

33913

mdashLegion

ellales

Legionellapn


Hextuple3aTh

underB

aymdash

Vibrionales

Vibriocholerae

CP1030(3)














Table2Maindo

mainof

thep

roteinscoding

byBiofi

lmRe

gop

eron

genes

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

1112618

30(K

P2884921)

PRK1108

3(C

reB)

18273188

(KP2

884921)

LysM

FecR

12388(K

U252679)

PAS9

NtrB

2426304

0(K

U252679)

DUF4

136

Burkho

lderia

contam

inan

sstrain

GIM

C450

9Bc

t370

(KP2

884921

KU252679)

2BC

EP18194RS

1300

0PR

K1108

3(C

reB)

BCEP

18194RS

13005

LysM

FecR

BCEP

18194RS

13010

PAS9

NtrB

BCEP

18194RS

13015

DUF4

136

Burkho

lderia

lata

strain

Burkho

lderia

sp383

chromosom

e1

completes

equence(

NC

0075101)

3NL3

0RS

08520

PRK1108

3(C

reB)

NL3

0RS

08515

LysM

FecR

NL3

0RS

08510

PAS9

NtrB

NL3

0RS

08505

DUF4

136

Burkho

lderia

contam

inan

sstrain

MS14chromosom

e1com

plete

sequ

ence

(NZCP

009743)

4AK3

4RS

2164

5PR

K1108

3(C

reB)

AK3

4RS

2164

0LysM

FecR

AK3

4RS

21635

PAS9

BaeS

AK3

4RS

21630

DUF4

136

Burkho

lderia

dolosa

AU0158

chromosom

e1com

pletes

equence

(NZCP

009795)

5BM

ULJ

RS06770

PRK1108

3(C

reB)

BMULJ

RS06775

LysM

FecR

BMULJ

RS06780

PAS9

BaeS

BMULJ

RS06785

DUF4

136

Burkho

lderia

multiv

oran

sATC

C17616DNAcom

pleteg

enom

echromosom

e1(N

C0108041)

6BC

EP1808

RS0704

0PR

K1108

3(C

reB)

BCEP

1808

RS07045

LysM

FecR

BCEP

1808

RS07050

PAS9

NtrB

BCEP

1808

RS07055

DUF4

136

Burkho

lderia

vietna

miensisG4

chromosom

e1com

pletes

equence

(NC

0092561)

7QU43

RS43720

PRK1108

3(C

reB)

QU43

RS43725

LysM

FecR

QU43

RS437230

PAS9

NtrB

QU43

RS43735

DUF4

136

Burkho

lderia

ceno

cepa

ciaJ2315

chromosom

e1com

pleteg

enom

e(N

C0110001)

8BC

EN2424

RS07115

PRK1108

3(C

reB)

BCEN

2424

RS07120

LysM

FecR

BCEN

2424

RS07125

PAS9

NtrB

BCEN

2424

RS07130

DUF4

136

Burkho

lderia

ceno

cepa

ciaHI242

4chromosom

e1com

pletes

equence

(NC

0085421)

9HMPR

EF0551

RS12390

PRK1

0643

(BasR)

HMPR

EF0551

RS12385

LysM

FecR

HMPR

EF0551

RS12380

PASabsentB

aeS

HMPR

EF0551

RS12375

glutam

yl-tR

NA

redu

ctase

Lautropiamira

bilis

ATCC5159

9geno

micscaff

oldSC

AFF

OLD

1who

legeno

mes

hotgun

sequ

ence

(NZGL6

360621)

10QWA

RS04

640

PRK1108

3(C

reB)

QWA

RS04

635

LysM

FecR

QWA

RS04

630

PASabsentB

aeS

QWA

RS04

625

AraCfamily

transcrip

tionalregulator


NCI

B86

87Con

tig3who

legeno

me

shotgu

nsequ

ence

(NZAKM

R01000

0031)

11NH44

784RS

11280

PRK10336

(QseB)

NH44

784RS

11275

LysM

FecR

NH44

784RS

11270

PAS4B

aeS

mdashAc

hrom

obacterx

ylosoxidan

sNH44

784-1996

completeg

enom

e(N

C0212851)

12ER

S45141506153

PRK1108

3(C

reB)

ERS45141506154

LysM

FecR

ERS45141506155

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sNCT

C108

07(LN8310291)

13Axylo

5268

PRK1108

3(C

reB)

Axylo

5269

LysM

FecR

Axylo

5270

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sstrain

MN00

1completeg

enom

e(C

P01204

61)


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33


tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)


mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology






LysMFecR

DUF4136CHASE2

sensor

ATF-ase

DNAbinding

Receiverdomain

Outer membrane

Peptidoglycan

Periplasm

Cell membrane

Cytoplasm

2

31

4








Table1Re

presentativ

esof


maproteob

acteria

which

werec

hecked

forp

resenceo

fatleasttwoadjacent

compo

nentso

foperon

Class

Presento

peroncompo

nents

Orderfa

mily

Absent

operon

compo

nents

Betaproteobacteria

Burkholderiacontam

inan

sGIM

C4509Bc

t370B

urkholderia

lata

strB

urkholderia

sp383B

urkholderia

contam

inan

sMS14

Burkholderiadolosa

AU0158B

urkholderia

multiv

oran

sATC

C17616Bu

rkholderiavietna

mien

sisG4Bu


J2315HI2424

Lautropiamira

bilis

ATCC

51599Pa

ndoraeathiooxydan

sDSM

25325

Burkho

lderialesB

urkh

olderia

ceae

Pand

oraeapn

omenusa3k

gm


B8687

Achrom

obacterx

ylosoxidan

sNH44

784-1996N

CTC10807M

N001

Achrom

obacterruh

land

iiSC

CH3Ac

hs33-1365ST3

6Ac

hrom

obacterinsuavisA

XX-A

Bordetellabronchise

ptica

MO149Bo

rdetellapertussis

18323

Burkho

lderialesA

lcaligenaceae

mdash

Ralstoniapickettii

12J

Ralstoniapickettii

DTP

0602

Burkho

lderialesR

alsto

niaceae

mdash

mdashBu

rkho

lderialesC

omam

onadaceae

Vario

voraxparadoxu

sS110

Ac

idovorax

avenae

avenae

ATCC

19860

mdashBu

rkho

lderialesS

utterellaceae

Sutte

rella

parviru

braYIT

mdashNeisseriales

Neisseriameningitid

isWUE2594

Gam

maproteob

acteria

Pseudomonas

aeruginosa

PAO1

Pseudomonas

fluorescens

PCL1751

Pseudo

mon

adales

Acinetobacterh

aemolyticu

sATC

C19194

Pseudomonas

fluorescens

A506SB

W25B

RIP3

4879

F113P

f0-1B

Bc6R

8

mdashEn

terobacteriales

Yersiniainterm

ediaAT


IMD27K

IM10+

Escherich

iacoliK-

12substr

MG1655Shigella

flexneri

2astr2457T2a

str301

Salm

onellaenteric

aenteric

aserovarD

ublin

str

CT02021853

mdashXa

ntho

mon

adales

Xanthomonas

campestr

ispvcam

pestr

isstrA

TCC

33913

mdashLegion

ellales

Legionellapn


Hextuple3aTh

underB

aymdash

Vibrionales

Vibriocholerae

CP1030(3)














Table2Maindo

mainof

thep

roteinscoding

byBiofi

lmRe

gop

eron

genes

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

1112618

30(K

P2884921)

PRK1108

3(C

reB)

18273188

(KP2

884921)

LysM

FecR

12388(K

U252679)

PAS9

NtrB

2426304

0(K

U252679)

DUF4

136

Burkho

lderia

contam

inan

sstrain

GIM

C450

9Bc

t370

(KP2

884921

KU252679)

2BC

EP18194RS

1300

0PR

K1108

3(C

reB)

BCEP

18194RS

13005

LysM

FecR

BCEP

18194RS

13010

PAS9

NtrB

BCEP

18194RS

13015

DUF4

136

Burkho

lderia

lata

strain

Burkho

lderia

sp383

chromosom

e1

completes

equence(

NC

0075101)

3NL3

0RS

08520

PRK1108

3(C

reB)

NL3

0RS

08515

LysM

FecR

NL3

0RS

08510

PAS9

NtrB

NL3

0RS

08505

DUF4

136

Burkho

lderia

contam

inan

sstrain

MS14chromosom

e1com

plete

sequ

ence

(NZCP

009743)

4AK3

4RS

2164

5PR

K1108

3(C

reB)

AK3

4RS

2164

0LysM

FecR

AK3

4RS

21635

PAS9

BaeS

AK3

4RS

21630

DUF4

136

Burkho

lderia

dolosa

AU0158

chromosom

e1com

pletes

equence

(NZCP

009795)

5BM

ULJ

RS06770

PRK1108

3(C

reB)

BMULJ

RS06775

LysM

FecR

BMULJ

RS06780

PAS9

BaeS

BMULJ

RS06785

DUF4

136

Burkho

lderia

multiv

oran

sATC

C17616DNAcom

pleteg

enom

echromosom

e1(N

C0108041)

6BC

EP1808

RS0704

0PR

K1108

3(C

reB)

BCEP

1808

RS07045

LysM

FecR

BCEP

1808

RS07050

PAS9

NtrB

BCEP

1808

RS07055

DUF4

136

Burkho

lderia

vietna

miensisG4

chromosom

e1com

pletes

equence

(NC

0092561)

7QU43

RS43720

PRK1108

3(C

reB)

QU43

RS43725

LysM

FecR

QU43

RS437230

PAS9

NtrB

QU43

RS43735

DUF4

136

Burkho

lderia

ceno

cepa

ciaJ2315

chromosom

e1com

pleteg

enom

e(N

C0110001)

8BC

EN2424

RS07115

PRK1108

3(C

reB)

BCEN

2424

RS07120

LysM

FecR

BCEN

2424

RS07125

PAS9

NtrB

BCEN

2424

RS07130

DUF4

136

Burkho

lderia

ceno

cepa

ciaHI242

4chromosom

e1com

pletes

equence

(NC

0085421)

9HMPR

EF0551

RS12390

PRK1

0643

(BasR)

HMPR

EF0551

RS12385

LysM

FecR

HMPR

EF0551

RS12380

PASabsentB

aeS

HMPR

EF0551

RS12375

glutam

yl-tR

NA

redu

ctase

Lautropiamira

bilis

ATCC5159

9geno

micscaff

oldSC

AFF

OLD

1who

legeno

mes

hotgun

sequ

ence

(NZGL6

360621)

10QWA

RS04

640

PRK1108

3(C

reB)

QWA

RS04

635

LysM

FecR

QWA

RS04

630

PASabsentB

aeS

QWA

RS04

625

AraCfamily

transcrip

tionalregulator


NCI

B86

87Con

tig3who

legeno

me

shotgu

nsequ

ence

(NZAKM

R01000

0031)

11NH44

784RS

11280

PRK10336

(QseB)

NH44

784RS

11275

LysM

FecR

NH44

784RS

11270

PAS4B

aeS

mdashAc

hrom

obacterx

ylosoxidan

sNH44

784-1996

completeg

enom

e(N

C0212851)

12ER

S45141506153

PRK1108

3(C

reB)

ERS45141506154

LysM

FecR

ERS45141506155

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sNCT

C108

07(LN8310291)

13Axylo

5268

PRK1108

3(C

reB)

Axylo

5269

LysM

FecR

Axylo

5270

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sstrain

MN00

1completeg

enom

e(C

P01204

61)


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33


tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)


mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Table1Re

presentativ

esof


maproteob

acteria

which

werec

hecked

forp

resenceo

fatleasttwoadjacent

compo

nentso

foperon

Class

Presento

peroncompo

nents

Orderfa

mily

Absent

operon

compo

nents

Betaproteobacteria

Burkholderiacontam

inan

sGIM

C4509Bc

t370B

urkholderia

lata

strB

urkholderia

sp383B

urkholderia

contam

inan

sMS14

Burkholderiadolosa

AU0158B

urkholderia

multiv

oran

sATC

C17616Bu

rkholderiavietna

mien

sisG4Bu


J2315HI2424

Lautropiamira

bilis

ATCC

51599Pa

ndoraeathiooxydan

sDSM

25325

Burkho

lderialesB

urkh

olderia

ceae

Pand

oraeapn

omenusa3k

gm


B8687

Achrom

obacterx

ylosoxidan

sNH44

784-1996N

CTC10807M

N001

Achrom

obacterruh

land

iiSC

CH3Ac

hs33-1365ST3

6Ac

hrom

obacterinsuavisA

XX-A

Bordetellabronchise

ptica

MO149Bo

rdetellapertussis

18323

Burkho

lderialesA

lcaligenaceae

mdash

Ralstoniapickettii

12J

Ralstoniapickettii

DTP

0602

Burkho

lderialesR

alsto

niaceae

mdash

mdashBu

rkho

lderialesC

omam

onadaceae

Vario

voraxparadoxu

sS110

Ac

idovorax

avenae

avenae

ATCC

19860

mdashBu

rkho

lderialesS

utterellaceae

Sutte

rella

parviru

braYIT

mdashNeisseriales

Neisseriameningitid

isWUE2594

Gam

maproteob

acteria

Pseudomonas

aeruginosa

PAO1

Pseudomonas

fluorescens

PCL1751

Pseudo

mon

adales

Acinetobacterh

aemolyticu

sATC

C19194

Pseudomonas

fluorescens

A506SB

W25B

RIP3

4879

F113P

f0-1B

Bc6R

8

mdashEn

terobacteriales

Yersiniainterm

ediaAT


IMD27K

IM10+

Escherich

iacoliK-

12substr

MG1655Shigella

flexneri

2astr2457T2a

str301

Salm

onellaenteric

aenteric

aserovarD

ublin

str

CT02021853

mdashXa

ntho

mon

adales

Xanthomonas

campestr

ispvcam

pestr

isstrA

TCC

33913

mdashLegion

ellales

Legionellapn


Hextuple3aTh

underB

aymdash

Vibrionales

Vibriocholerae

CP1030(3)














Table2Maindo

mainof

thep

roteinscoding

byBiofi

lmRe

gop

eron

genes

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

1112618

30(K

P2884921)

PRK1108

3(C

reB)

18273188

(KP2

884921)

LysM

FecR

12388(K

U252679)

PAS9

NtrB

2426304

0(K

U252679)

DUF4

136

Burkho

lderia

contam

inan

sstrain

GIM

C450

9Bc

t370

(KP2

884921

KU252679)

2BC

EP18194RS

1300

0PR

K1108

3(C

reB)

BCEP

18194RS

13005

LysM

FecR

BCEP

18194RS

13010

PAS9

NtrB

BCEP

18194RS

13015

DUF4

136

Burkho

lderia

lata

strain

Burkho

lderia

sp383

chromosom

e1

completes

equence(

NC

0075101)

3NL3

0RS

08520

PRK1108

3(C

reB)

NL3

0RS

08515

LysM

FecR

NL3

0RS

08510

PAS9

NtrB

NL3

0RS

08505

DUF4

136

Burkho

lderia

contam

inan

sstrain

MS14chromosom

e1com

plete

sequ

ence

(NZCP

009743)

4AK3

4RS

2164

5PR

K1108

3(C

reB)

AK3

4RS

2164

0LysM

FecR

AK3

4RS

21635

PAS9

BaeS

AK3

4RS

21630

DUF4

136

Burkho

lderia

dolosa

AU0158

chromosom

e1com

pletes

equence

(NZCP

009795)

5BM

ULJ

RS06770

PRK1108

3(C

reB)

BMULJ

RS06775

LysM

FecR

BMULJ

RS06780

PAS9

BaeS

BMULJ

RS06785

DUF4

136

Burkho

lderia

multiv

oran

sATC

C17616DNAcom

pleteg

enom

echromosom

e1(N

C0108041)

6BC

EP1808

RS0704

0PR

K1108

3(C

reB)

BCEP

1808

RS07045

LysM

FecR

BCEP

1808

RS07050

PAS9

NtrB

BCEP

1808

RS07055

DUF4

136

Burkho

lderia

vietna

miensisG4

chromosom

e1com

pletes

equence

(NC

0092561)

7QU43

RS43720

PRK1108

3(C

reB)

QU43

RS43725

LysM

FecR

QU43

RS437230

PAS9

NtrB

QU43

RS43735

DUF4

136

Burkho

lderia

ceno

cepa

ciaJ2315

chromosom

e1com

pleteg

enom

e(N

C0110001)

8BC

EN2424

RS07115

PRK1108

3(C

reB)

BCEN

2424

RS07120

LysM

FecR

BCEN

2424

RS07125

PAS9

NtrB

BCEN

2424

RS07130

DUF4

136

Burkho

lderia

ceno

cepa

ciaHI242

4chromosom

e1com

pletes

equence

(NC

0085421)

9HMPR

EF0551

RS12390

PRK1

0643

(BasR)

HMPR

EF0551

RS12385

LysM

FecR

HMPR

EF0551

RS12380

PASabsentB

aeS

HMPR

EF0551

RS12375

glutam

yl-tR

NA

redu

ctase

Lautropiamira

bilis

ATCC5159

9geno

micscaff

oldSC

AFF

OLD

1who

legeno

mes

hotgun

sequ

ence

(NZGL6

360621)

10QWA

RS04

640

PRK1108

3(C

reB)

QWA

RS04

635

LysM

FecR

QWA

RS04

630

PASabsentB

aeS

QWA

RS04

625

AraCfamily

transcrip

tionalregulator


NCI

B86

87Con

tig3who

legeno

me

shotgu

nsequ

ence

(NZAKM

R01000

0031)

11NH44

784RS

11280

PRK10336

(QseB)

NH44

784RS

11275

LysM

FecR

NH44

784RS

11270

PAS4B

aeS

mdashAc

hrom

obacterx

ylosoxidan

sNH44

784-1996

completeg

enom

e(N

C0212851)

12ER

S45141506153

PRK1108

3(C

reB)

ERS45141506154

LysM

FecR

ERS45141506155

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sNCT

C108

07(LN8310291)

13Axylo

5268

PRK1108

3(C

reB)

Axylo

5269

LysM

FecR

Axylo

5270

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sstrain

MN00

1completeg

enom

e(C

P01204

61)


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33


tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)


mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology














Table2Maindo

mainof

thep

roteinscoding

byBiofi

lmRe

gop

eron

genes

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

1112618

30(K

P2884921)

PRK1108

3(C

reB)

18273188

(KP2

884921)

LysM

FecR

12388(K

U252679)

PAS9

NtrB

2426304

0(K

U252679)

DUF4

136

Burkho

lderia

contam

inan

sstrain

GIM

C450

9Bc

t370

(KP2

884921

KU252679)

2BC

EP18194RS

1300

0PR

K1108

3(C

reB)

BCEP

18194RS

13005

LysM

FecR

BCEP

18194RS

13010

PAS9

NtrB

BCEP

18194RS

13015

DUF4

136

Burkho

lderia

lata

strain

Burkho

lderia

sp383

chromosom

e1

completes

equence(

NC

0075101)

3NL3

0RS

08520

PRK1108

3(C

reB)

NL3

0RS

08515

LysM

FecR

NL3

0RS

08510

PAS9

NtrB

NL3

0RS

08505

DUF4

136

Burkho

lderia

contam

inan

sstrain

MS14chromosom

e1com

plete

sequ

ence

(NZCP

009743)

4AK3

4RS

2164

5PR

K1108

3(C

reB)

AK3

4RS

2164

0LysM

FecR

AK3

4RS

21635

PAS9

BaeS

AK3

4RS

21630

DUF4

136

Burkho

lderia

dolosa

AU0158

chromosom

e1com

pletes

equence

(NZCP

009795)

5BM

ULJ

RS06770

PRK1108

3(C

reB)

BMULJ

RS06775

LysM

FecR

BMULJ

RS06780

PAS9

BaeS

BMULJ

RS06785

DUF4

136

Burkho

lderia

multiv

oran

sATC

C17616DNAcom

pleteg

enom

echromosom

e1(N

C0108041)

6BC

EP1808

RS0704

0PR

K1108

3(C

reB)

BCEP

1808

RS07045

LysM

FecR

BCEP

1808

RS07050

PAS9

NtrB

BCEP

1808

RS07055

DUF4

136

Burkho

lderia

vietna

miensisG4

chromosom

e1com

pletes

equence

(NC

0092561)

7QU43

RS43720

PRK1108

3(C

reB)

QU43

RS43725

LysM

FecR

QU43

RS437230

PAS9

NtrB

QU43

RS43735

DUF4

136

Burkho

lderia

ceno

cepa

ciaJ2315

chromosom

e1com

pleteg

enom

e(N

C0110001)

8BC

EN2424

RS07115

PRK1108

3(C

reB)

BCEN

2424

RS07120

LysM

FecR

BCEN

2424

RS07125

PAS9

NtrB

BCEN

2424

RS07130

DUF4

136

Burkho

lderia

ceno

cepa

ciaHI242

4chromosom

e1com

pletes

equence

(NC

0085421)

9HMPR

EF0551

RS12390

PRK1

0643

(BasR)

HMPR

EF0551

RS12385

LysM

FecR

HMPR

EF0551

RS12380

PASabsentB

aeS

HMPR

EF0551

RS12375

glutam

yl-tR

NA

redu

ctase

Lautropiamira

bilis

ATCC5159

9geno

micscaff

oldSC

AFF

OLD

1who

legeno

mes

hotgun

sequ

ence

(NZGL6

360621)

10QWA

RS04

640

PRK1108

3(C

reB)

QWA

RS04

635

LysM

FecR

QWA

RS04

630

PASabsentB

aeS

QWA

RS04

625

AraCfamily

transcrip

tionalregulator


NCI

B86

87Con

tig3who

legeno

me

shotgu

nsequ

ence

(NZAKM

R01000

0031)

11NH44

784RS

11280

PRK10336

(QseB)

NH44

784RS

11275

LysM

FecR

NH44

784RS

11270

PAS4B

aeS

mdashAc

hrom

obacterx

ylosoxidan

sNH44

784-1996

completeg

enom

e(N

C0212851)

12ER

S45141506153

PRK1108

3(C

reB)

ERS45141506154

LysM

FecR

ERS45141506155

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sNCT

C108

07(LN8310291)

13Axylo

5268

PRK1108

3(C

reB)

Axylo

5269

LysM

FecR

Axylo

5270

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sstrain

MN00

1completeg

enom

e(C

P01204

61)


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33


tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)


mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Table2Maindo

mainof

thep

roteinscoding

byBiofi

lmRe

gop

eron

genes

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

1112618

30(K

P2884921)

PRK1108

3(C

reB)

18273188

(KP2

884921)

LysM

FecR

12388(K

U252679)

PAS9

NtrB

2426304

0(K

U252679)

DUF4

136

Burkho

lderia

contam

inan

sstrain

GIM

C450

9Bc

t370

(KP2

884921

KU252679)

2BC

EP18194RS

1300

0PR

K1108

3(C

reB)

BCEP

18194RS

13005

LysM

FecR

BCEP

18194RS

13010

PAS9

NtrB

BCEP

18194RS

13015

DUF4

136

Burkho

lderia

lata

strain

Burkho

lderia

sp383

chromosom

e1

completes

equence(

NC

0075101)

3NL3

0RS

08520

PRK1108

3(C

reB)

NL3

0RS

08515

LysM

FecR

NL3

0RS

08510

PAS9

NtrB

NL3

0RS

08505

DUF4

136

Burkho

lderia

contam

inan

sstrain

MS14chromosom

e1com

plete

sequ

ence

(NZCP

009743)

4AK3

4RS

2164

5PR

K1108

3(C

reB)

AK3

4RS

2164

0LysM

FecR

AK3

4RS

21635

PAS9

BaeS

AK3

4RS

21630

DUF4

136

Burkho

lderia

dolosa

AU0158

chromosom

e1com

pletes

equence

(NZCP

009795)

5BM

ULJ

RS06770

PRK1108

3(C

reB)

BMULJ

RS06775

LysM

FecR

BMULJ

RS06780

PAS9

BaeS

BMULJ

RS06785

DUF4

136

Burkho

lderia

multiv

oran

sATC

C17616DNAcom

pleteg

enom

echromosom

e1(N

C0108041)

6BC

EP1808

RS0704

0PR

K1108

3(C

reB)

BCEP

1808

RS07045

LysM

FecR

BCEP

1808

RS07050

PAS9

NtrB

BCEP

1808

RS07055

DUF4

136

Burkho

lderia

vietna

miensisG4

chromosom

e1com

pletes

equence

(NC

0092561)

7QU43

RS43720

PRK1108

3(C

reB)

QU43

RS43725

LysM

FecR

QU43

RS437230

PAS9

NtrB

QU43

RS43735

DUF4

136

Burkho

lderia

ceno

cepa

ciaJ2315

chromosom

e1com

pleteg

enom

e(N

C0110001)

8BC

EN2424

RS07115

PRK1108

3(C

reB)

BCEN

2424

RS07120

LysM

FecR

BCEN

2424

RS07125

PAS9

NtrB

BCEN

2424

RS07130

DUF4

136

Burkho

lderia

ceno

cepa

ciaHI242

4chromosom

e1com

pletes

equence

(NC

0085421)

9HMPR

EF0551

RS12390

PRK1

0643

(BasR)

HMPR

EF0551

RS12385

LysM

FecR

HMPR

EF0551

RS12380

PASabsentB

aeS

HMPR

EF0551

RS12375

glutam

yl-tR

NA

redu

ctase

Lautropiamira

bilis

ATCC5159

9geno

micscaff

oldSC

AFF

OLD

1who

legeno

mes

hotgun

sequ

ence

(NZGL6

360621)

10QWA

RS04

640

PRK1108

3(C

reB)

QWA

RS04

635

LysM

FecR

QWA

RS04

630

PASabsentB

aeS

QWA

RS04

625

AraCfamily

transcrip

tionalregulator


NCI

B86

87Con

tig3who

legeno

me

shotgu

nsequ

ence

(NZAKM

R01000

0031)

11NH44

784RS

11280

PRK10336

(QseB)

NH44

784RS

11275

LysM

FecR

NH44

784RS

11270

PAS4B

aeS

mdashAc

hrom

obacterx

ylosoxidan

sNH44

784-1996

completeg

enom

e(N

C0212851)

12ER

S45141506153

PRK1108

3(C

reB)

ERS45141506154

LysM

FecR

ERS45141506155

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sNCT

C108

07(LN8310291)

13Axylo

5268

PRK1108

3(C

reB)

Axylo

5269

LysM

FecR

Axylo

5270

PAS9

BaeS

mdashAc

hrom

obacterx

ylosoxidan

sstrain

MN00

1completeg

enom

e(C

P01204

61)


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33


tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)


mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Table2Con

tinued

NOperongene

locustagprotein

domains

name

Strain

name(

GenBa

nkA

ccessio

nNum

ber)

Operons


n1

23

4

14Com

plem

ent

(126935

39)

PRK1108

3(C

reB)

Com

plem

ent

(36014710)

LysM

FecR

Com

plem

ent

(4744546

0)

PAS9

BaeS

mdashAc

hrom

obacterr

uhland

iiSC

CH3Ac

h33-136

5ST

36(K

U252680)

15AXXA

RS10090

PRK10336

(QseB)

AXXA

RS10095

LysM

FecR

AXXA

RS10100

PAS4B

aeS

mdash

Achrom

obacterinsua

visA

XX-A

geno

micscaff

oldscaff

old0

0003

who

legeno

mes

hotgun

sequ

ence

(NZGL9

824531)

16BN

115RS

00125

PRK1108

3(C

reB)

BN115RS

00120

LysM

FecR

BN115RS

00115

PAS9

BaeS

mdashBo

rdetellabron

chise

ptica

MO149

completeg

enom

e(NC

0188291)

17BN

118RS

00125

PRK1108

3(C

reB)

BN118

RS00120

LysM

FecR

BN118

RS00115

PAS9

BaeS

nocataliticdamain

mdashBo

rdetellapertussis

18323complete

geno

me(

NC

0185181)

18RP

ICRS

04635

PRK1108

3(C

reB)

RPIC

RS04

640

LysM

FecR

RPIC

RS04

645

PAS4B

aeS

mdashRa

lston

iapickettii

12Jc

hrom

osom

e1

completes

equence(

NC

0106

821)

19N234RS

31485

PRK1108

3(C

reB)

N234RS

31480

LysM

FecR

COG47

33


tailcompo

nent

N234RS

31475

PAS4B

aeS

mdashRa

lston

iapickettii

DTP

0602

chromosom

e2com

pletes

equence

(NC

0225141)

20mdash

ABW

99RS

09030

LysM

FecR

ABW

99RS

09035

PAS4B

aeS

mdashPa

ndoraeathiooxyd

ansD

SM25325

completeg

enom

e(NZCP

0115681)

21mdash

PA4035

LysM

trun

catedFecR

PA4036

PAS4B

aeS

mdashPseudo

mon

asaerugino

saPA

O1

chromosom

ecompleteg

enom

e(N

C0025162)

(1) T

wo-

com

pone

nt tr

ansc

riptio

nal r

egul

ator

win

ged

helix

fam

ily

(2) U

ncha

ract

eriz

ed co

nser

ved

prot

ein

cont

aini

ng L

ysM

and

FecR

dom

ains

(3) P

erip

lasm

ic se

nsor

sign

al tr

ansd

uctio

n hi

stidi

ne k

inas

e

(4) U

ncha

ract

eriz

ed D

UF4

136

supe

rfam

ily p

rote

in

Pseu

doge

ne

Unc

hara

cter

ized

cons

erve

d pr

otei

n w

ith tr

unca

ted

LysM

and

inta

ct F

ecR

dom

ains

(2

) G

luta

myl

-tRN

A re

duct

ase

(4)

Ara

C fa

mily

tran

scrip

tiona

l reg

ulat

or

(4)


mainop

eron

organizatio

nor

localizationareu

nderlin

ed


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


70100

100

100

8481

92

100

97

6299

99

100

100

10098

84

100

100

5397

79

8969

100

68

66

64

82

69

51

55







Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Bdol AU0158 Bvie G4






Afae NCIB8687100

100

10066

10099

99

90

87

100

100

70

01(a)






Paer PAO1

99

6666

94

84

66

77

100

6172

64

02(b)




Bdol AU0158 Bvie G4





100

100

9998

69

100

5951

89

71

9564

01(c)








100

99100

89

79

62

100

93

8067

55

87

02(d)











4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology






4 Conclusion



Abbreviations



















Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology










Competing Interests


Acknowledgments


References

























































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology








Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology

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Research Article Burkholderia contaminans Biofilm...

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