www.sciencemag.org/cgi/content/full/339/6125/1316/DC1
Supplementary Materials for
Circadian Control of Chloroplast Transcription by a Nuclear-Encoded Timing Signal
Zeenat B. Noordally, Kenyu Ishii, Kelly A. Atkins, Sarah J. Wetherill, Jelena Kusakina,
Eleanor J. Walton, Maiko Kato, Miyuki Azuma, Kan Tanaka, Mitsumasa Hanaoka, Antony N. Dodd*
*To whom correspondence should be addressed. E-mail: [email protected]
Published 15 March 2013, Science 339, 1316 (2013)
DOI: 10.1126/science.1230397
This PDF file includes
Materials and Methods Figs. S1 to S9 Tables S1 to S5 Full References
Other Supplementary Material for this manuscript includes the following: (available at www.sciencemag.org/cgi/content/full/339/6125/1316/DC1)
Spreadsheet S1 as an Excel file
1
Supplementary Materials for
Circadian Control of Chloroplast Transcription by a Nuclear-Encoded Timing Signal
Zeenat B. Noordally, Kenyu Ishii, Kelly A. Atkins, Sarah J. Wetherill, Jelena Kusakina, Eleanor J.
Walton, Maiko Kato, Miyuki Azuma, Kan Tanaka, Mitsumasa Hanaoka, Antony N. Dodd.
Correspondence to: [email protected]
This PDF file includes:
Materials and Methods
Figs. S1 to S9
Tables S1 to S5
Other Supplementary Materials for this manuscript includes the following:
Spreadsheet S1
2
Materials and Methods
Arabidopsis cultivation and germplasm
Arabidopsis thaliana was cultivated under sterile conditions using Sanyo MLR-352 growth
chambers as described previously (22). Seedlings were entrained to cycles of 12 h white light/12 h
darkness at 19 °C before transfer to continuous white light after 11 days for bioluminescence
imaging, 12 days for RNA timecourses and 16 days for delayed fluorescence (DF) imaging.
Custom-built LED panels supplied red (660 nm) or blue (440 nm) light for experiments involving
colored light treatments. sig5-2 is a homozygous T-DNA insertion (SAIL Garlic 1232 H11)
characterized elsewhere (4). sig5-3 is a homozygous T-DNA insertion line (SALK 141383C,
obtained from NASC) and is a new allele that we genotyped (Fig. S9). Genomic DNA PCR
confirmed the presence and location of the T-DNA insert and homozygous nature of the line using
the primers 5’-TCTCATACCCGCTTGACAAAG-3’ (LP), 5’-GTTCAGCTGCAAGATCTCCAC-
3’ (RP) and ATTTTGCCGATTTCGGAAC (SALK LBb1.3). We also confirmed that full-length
SIG5 transcripts and psbD BLRP transcripts were absent in sig5-3.
Real-time PCR and Northern analysis
For real-time PCR and Northern analysis, aerial tissue was harvested using 10 seedlings per
timepoint that comprised 5 seedlings from each of two Petri dishes. Two independent biological
repeats were performed for every experiment. Total RNA for real-time PCR was extracted from
frozen tissue using Macherey-Nagel Nucleospin RNAII kits. cDNA was synthesized as previously
(22). 1/200 cDNA dilutions were analyzed using an ABI Prism 7300, ABI SybrGreen Power Mix
and primers in Table S4, with default reaction conditions for all transcripts except psbD BLRP,
which used conditions described previously (27). Data were processed using ABI SDS v1.2.
Rhythmic data were analyzed using the cosine wave fitting package COSOPT (14). Northern
analysis was performed as described previously (4).
3
Bioluminescence imaging of promoter-luciferase reporters and delayed fluorescence
Homogyzous sig5-3 mutants expressing CCA1::LUCIFERASE, TOC1::LUCIFERASE and
CCR2::LUCIFERASE were generated by crossing and backcrossing luciferase reporter lines into
homozygous sig5-3. Bioluminescent F2 seedlings were PCR screened using primers flanking the T-
DNA insert within the SIG5 coding sequence to identify seedlings homozygous for the T-DNA
insertion. F3 seed collected from homozygous sig5-3 seedlings was used for imaging. The
promoter-luciferase background used for crossing was the imaging control. Bioluminescence
imaging was performed as described previously (22), using a Photek HRPCS intensified CCD
photon counting camera (Photek Ltd., UK). Data were analyzed using Image32 (Photek) and
BRASS (www.amillar.org). For DF experiments, images were captured hourly using 60 s
integrations with the camera driven in binary slice mode. DF data were analyzed as elsewhere (12).
Generation of TOC1::SIG5 and SIG5::LUCIFERASE transgenic plants
To create the TOC1::SIG5 construct, the TOC1 -1000 upstream sequence was ligated between
HindIII and PstI sites in the binary vector pGREENII0229 (www.pgreen.ac.uk). The SIG5 coding
sequence was positioned downstream of the TOC1 promoter and upstream of a CaMV 35S
terminator using flanking BamHI sites. To create SIG5::LUCIFERASE, the SIG5 -2460 bp
upstream sequence was ligated between the PstI and BamHI restriction sites in pGREENII0229, and
the luciferase+ coding sequence was ligated between the BamHI and SacI sites in this vector, before
of a NOS terminator. The T-DNA was transformed into sig5-3 (TOC1::SIG5) and Col-0 wild type
(SIG5::LUCIFERASE) Arabidopsis using Agrobacterium-mediated transformation. Transformants
were identified by BASTA resistance screening and validated with genomic DNA PCR and RT-
PCR. Homozygous T3 lines were used for experimentation. Two independent transgenic lines
expressing TOC1::SIG5 were investigated.
Chloroplast ChIP-qPCR
4
Chloroplast chromatin immunoprecipitation followed by qPCR analysis (Chloroplast ChIP-qPCR)
was performed as elsewhere (29), using the primer sets in Table S5 to detect potential SIG5 binding
to chloroplast gene promoters.
Meta-analysis of circadian regulation of chloroplast genome
Chloroplast-encoded genes with circadian oscillations in transcript abundance were identified using
the HAYSTACK pattern-matching algorithm and DIURNAL interface (diurnal.mocklerlab.org).
We analysed transcriptome studies using HAYSTACK rather than with cosinor analysis because we
wished to identify the maximum number of chloroplast transcripts with the potential for circadian
regulation. HAYSTACK compares transcript profiles against a variety of waveforms and has been
demonstrated to identify the widest range of oscillating transcripts (2). We found that the default
DIURNAL correlation threshold of 0.8 suggested for nuclear-encoded genes excluded chloroplast
transcripts demonstrated previously to be rhythmic (e.g. psbDC), so titrated the threshold to 0.65 in
order to capture these transcripts within the analysis (Spreadsheet S1).
5
Fig. S1. Circadian rhythms of delayed fluorescence in wild type and sig5 mutant seedlings. Data are
means from five clusters of between 10 and 15 16-day old seedlings ± S.E.M., from (A)
experimental repeat 1 and (B) experimental repeat 3 in Fig. 1B. Vertical gray lines indicate the
timing of each delayed fluorescence peak in the wild type, to allow direct comparison with the
timing of each peak in sig5-2 and sig5-3 mutants. Hatched bars on x axes indicate subjective dark
period.
Time in constant light (h)
24 36 48 60 72 84 96
-2000
-1500
-1000
-500
0
500
1000
1500
Mea
n n
orm
aliz
ed d
ela
yed f
luore
scen
ce
inte
nsity
-1500
-1000
-500
0
500
1000
-1500
-1000
-500
0
500
1000
1500
2000
-3000
-2000
-1000
0
1000
2000
3000
Mea
n n
orm
aliz
ed d
ela
yed f
luore
scen
ce
inte
nsity
-3000
-2000
-1000
0
1000
2000
Time in constant light (h)
24 36 48 60 72 84 96 108 120
-3000
-1000
1000
3000
Col-0 wild type
sig5-2
sig5-3
sig5-2
sig5-3
Col-0 wild typeA B
6
Fig. S2. SIG5 is required for circadian oscillations in abundance of psbD BLRP mRNA and does
not modulate overall chloroplast transcription. Col-0 wild type blots are from Fig. 1A and
reproduced alongside sig5-2 blots to allow direct comparison. Northern blot analysis shows
abundance of mRNAs for both nuclear (SIG1, SIG5, CAB3) and plastid (psbA, psbD BLRP, rbcL)
encoded transcripts in (A) Col-0 wild type and (B) sig5-2 mutant. Seedlings were grown and
harvested as for qRT-PCR experiments. The positions of RNA markers are indicated as nucleotides
(nt) on the right.
7
Fig. S3. (A) Circadian oscillations of SIG5 promoter activity in Col-0 wild type seedlings measured
using a SIG5::LUCIFERASE transcriptional fusion reporter. Seedlings were entrained previously to
light/dark cycles and luciferase bioluminescence was integrated for 900 s at 2 h intervals under
constant light. (B) Three types of known circadian-regulated cis element occur within the region
upstream of the SIG5 gene coding region. Gene promoters containing the CACGTG (ABA response
element /ABRE) motif are frequently phased to the subjective day, those containing the GATAA
motif are frequently phased to late subjective day, and those with the CCACA (‘morning element’)
are frequently phased to early subjective day (35). In (B), the SIG5 upstream and coding regions are
indicated in green and orange respectively, the precise location of cis elements indicated by black
vertical lines, and the identity of cis elements by black symbols.
ABRE (CACGTG)-like
GATAA late day motif-like
‘Morning element’ CCACA
SIG5 upstream region SIG5 coding sequence
ATG-2000
A
B
Time in constant light (h)
24 36 48 60 72 84 96 108120132144
Mea
n S
IG5::LU
CIF
ER
AS
Eb
iolu
min
escence
(cou
nts
in 9
00 s
)5000
10000
15000
20000
25000
30000
35000
8
Fig. S4. (A, B) psbD BLRP transcripts were arrhythmic in TOC1::SIG5 line 2 that had low
amplitude oscillations of SIG5 transcripts; (C) Circadian oscillations of LHY transcripts are
unaltered in two independent transgenic lines expressing TOC1::SIG5 in the sig5-3 mutant.
Relative abundance of SIG5 and psbD BLRP transcripts quantified as ACT2-normalized mean RQ ±
S.E.M.
Time in constant light (h)
24 36 48 60 72 84 96
Re
lative
tra
nscri
pt
ab
und
ance
0.0
0.2
0.4
0.6
0.8
1.0
1.2SIG5 psbD BLRP
A
LHY
Time in constant light (h)
24 36 48 60 72 84 96
Re
lative
tra
nscri
pt
abun
dan
ce
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Col-0 wild type
sig5-3 TOC1::SIG5 Line 1
sig5-3 TOC1::SIG5 Line 2
C
sig
5-3
TO
C1::S
IG5 re
lativ
etra
nscrip
t abu
nda
nce0.1
0.2
0.3
0.4
0.5
Time in constant light (h)
24 36 48 60 72 84 96
Co
l-0 r
ela
tive tra
nscrip
tab
und
ance
0.0
0.5
1.0
1.5
2.0
2.5 B
9
Fig. S5. The period of the circadian oscillator controls the period of SIG5 and psbD BLRP
transcripts. (A) For wild type, toc1-1 and ztl-1, comparison for LHY of estimated circadian period
and pMMC-β from COSOPT cosinor analysis. (B) Relative abundance of LHY transcripts in C24
wild type, toc1-1 and ztl-1. (C, D) Circadian oscillations of SIG5 and psbD BLRP transcripts in
C24, toc1-1 and ztl1. Relative transcript abundance is ACT2-normalized mean RQ ± S.E.M.
Time in constant light (h)48 60 72 84 96
02468
101214
Rela
tive tra
nscri
pt a
bund
ance
0
4
8
12toc1-1
ztl-1
0
5
10
15
20
25
30C24 wild type
Period estimate (h)
21 22 23 24 25 26 27 28 29
pM
MC
- β
0.0
0.1
0.2
0.3
0.4
0.5
B
A
toc1-1 C24 ztl-1
48 60 72 84 96
0
1
2
3
4
5
0123456
01234567
48 60 72 84 96
0.5
1.0
1.5
1.0
1.5
2.0
2.5
0.4
0.8
1.2
1.6
2.0C24 wild type
toc1-1
ztl-1
Time in constant light (h) Time in constant light (h)
Rela
tive tra
nscript abu
ndan
ce
Rela
tive
tra
nscri
pt abund
ance
C DC24 wild type
toc1-1
ztl-1
LHY SIG5 psbD BLRP
LHY
10
Fig. S6. Blue light regulation of SIG5 and psbD BLRP transcripts. (A) SIG5 transcripts are induced
rapidly by BL but not RL. (B) psbD BLRP are induced by BL but not RL, and this is SIG5-
dependent. (C) Blue light-induced SIG5 transcripts degrade rapidly in darkness. In all experiments,
seedlings were placed in constant darkness and temperature for 24 h prior to induction with 1 h of
10 µmol m-2
s-1
RL or BL. Relative abundance of SIG5 and psbD BLRP transcripts quantified as
ACT2-normalized mean RQ ± S.E.M.
Time after 1 h light pulse (minutes)
0 20 40 60 80
Rela
tive
tra
nscri
pt ab
und
ance
0
20
40
60
80
100
Blue light
Red light
Time after 1 h light pulse (h)
0 1 2 3 4 5 6 7
Re
lative
tra
nscript a
bun
dan
ce
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
Blue light, Col-0 wild type
Red light, Col-0 wild type
Blue light, sig5-2 mutant
Time after transfer to darknessfollowing 1 h light pulse (h)
0 1 2 3 4 5 6 7
Rela
tive
tra
nscri
pt ab
und
ance
0
40
80
120
160
Blue light
Red light
SIG5
psbD BLRP
SIG5
A
B
C
11
Figure S7. A screen for additional targets of SIG5. ChIP-qPCR (29) was performed to detect
potential SIG5 binding with DNA. The quantity of immunoprecipitated DNA of promoter regions
listed was calculated, and shown as percent recovery against total input DNA. Genes with
significantly increased DNA recovery, identified by one-way ANOVA and post-hoc Tukey
analysis, were selected for further study. rps15 was excluded because its promoter is NEP-
dependent (36, 37). p-values indicated when DNA recovery was significantly different, other
promoters not significant (p > 0.025). Data are means from two experiments ± standard deviation.
Broken horizontal line indicates mean DNA recovery across promoters.
psb
A
psb
KI
atp
FA
rpo
BC
trn
EY
D
psb
DC
psa
AB
nd
hC
atp
B
rbcL
accD
psb
EF
LJ
pe
tLG
clp
P
psb
BT
psb
N
trn
I-rp
l23
ycf2
rps1
2-7
trn
V
ycf1
rps1
5
rpl3
2
DN
A r
eco
very
(%
)
0.00
0.02
0.04
0.06
0.08p
< 0
.00
1
p =
0.0
08
p <
0.0
01
p <
0.0
01
p =
0.0
06
Chloroplast promoter
12
Fig. S8. SIG5 modulates the amplitude of circadian oscillations of several chloroplast genes
identified by ChIP-PCR. (A) The abundance of psaAB and psbA transcripts is increased
significantly by SIG5 during the subjective light period, and psbBT may be increased slightly. (B)
rbcL and psbDC formed negative and positive controls respectively; psbDC is SIG5-regulated (Fig.
1A, C), whereas rbcL was not identified during a ChIP screen for potential SIG5-binding
promoters. rbcL transcript abundance was unaltered in sig5-2 and psbDC transcripts abundance was
reduced at many timepoints. Relative transcript abundance quantified as ACT2-normalized mean
RQ ± S.E.M. Statistically-significant differences between wild type and sig5-2 mutant are indicated
by asterisks (* p < 5%, ** p < 1%, *** p < 0.1% from two-sample t-tests; unmarked data points not
significantly different between sig5-2 and wild type).
rbcL
Time in constant light (h)
24 36 48 60
0.6
0.8
1.0
1.2
1.4
1.6
1.8
2.0
Col-0
sig5-2
psbBT
Time in constant light (h)
24 36 48 60
0.4
0.8
1.2
1.6
2.0
2.4
psbA
Rela
tive
tra
nscrip
t ab
und
an
ce
0.5
1.0
1.5
2.0
2.5
psbDC
Re
lative tra
nscript a
bu
nd
ance
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
psaAB
0.4
0.8
1.2
1.6
2.0
***
*
**
*
****
*
**
*
*
*** ***
*
****
**
A
B
13
Fig. S9. The sig5-3 mutant is a homozygous T-DNA insertion mutant. (A) Genomic DNA PCR to
verify location of T-DNA insert within genome. Individual seedlings are homozygous and contain
an inverted repeat of T-DNAs. LP and RP are primers that anneal with genomic DNA flanking the
T-DNA, and LB is a primer that anneals within the T-DNA insert. (B) Real-time PCR
demonstrating that SIG5 and psbD BLRP transcript abundance is reduced by comparable magnitude
in sig5-2 and sig5-3.
14
Col-0 sig5-2 sig5-3
Experiment 1 24.6 ± 0.6 h 24.5 ± 0.9 h 25.4 ± 0.3 h
Experiment 2 24.2 ± 0.6 h 24.6 ± 0.3 h 24.9 ± 0.2 h
Experiment 3 24.0 ± 0.8 h 25.2 ± 0.4 h 24.7 ± 0.6 h
Table S1. Period estimates of circadian oscillations of delayed chlorophyll fluorescence in Col-0
wild type, and sig5-2 and sig5-3 mutants for three independent experiments, ± S.E.M. Of three
experiments, Experiment 3 was experimenter-blind throughout experimentation and analysis.
15
COSOPT period estimate
(h) ± s.e.m.
COSOPT relative phase
(h) ± s.e.m.
Transcript Col-0 sig5-2 Col-0 sig5-2
CCA1 23.8 ± 0 23.6 ± 0.2 -5.3 ± 0.2 -4.8 ± 0.4
CHE 23.4 ± 0.6 24.0 ± 0.1 -10.6 ± 0.3 -10.1 ± 0.2
GI 23.5 ± 0.2 23.8 ± 0.4 10.6 ± 0.3 11.6 ± 0.3
PRR7 23.2 ± 0.2 22.9 ± 0 -11.5 ± 0.1 -11.4 ± 0.1
TOC1 23.7 ± 0.2 23.5 ± 0.2 7.7 ± 0.2 7.8 ± 0.3
LHY 25.6 ± 0.1 25.6 ± .01 -2.7 ± 0.4 -2.2 ± 0.1
COSOPT mean expression
level ± s.e.m.
Transcript Col-0 sig5-2
CCA1 0.3 ± 0.1 0.3 ± 0.0
CHE 1.3 ± 0.1 1.2 ± 0.1
GI 6.0 ± 0.1 4.8 ± 0.4
PRR7 4.9 ± 0.1 4.6 ± 0.4
TOC1 3.1 ± 0.1 2.8 ± 0.1
LHY 0.4 ± 0.1 0.5 ± 0.0
Table S2. The period, phase and mean expression level of transcripts encoding circadian oscillator
components was unaltered in sig5-2 relative to wild type. Period, phase and mean expression levels
16
of CCA1, CHE, GI, PRR7, TOC1 and LHY was calculated from real time PCR data (Fig. 3A) using
COSOPT cosinor analysis.
Reporter Period (h ± s.e.m.) Phase (h ± s.e.m.) Amplitude (counts ±
s.e.m.)
Genotype Col-0 sig5-3 Col-0 sig5-3 Col-0 sig5-3
CCA1::LUC 24.9 ± 0.1 25.2 ± 0.1 3.8 ± 0.4 3.8 ± 0.4 3.7 ± 0.3 3.4 ± 0.2
TOC1::LUC 25.6 ± 0.1 25.4 ± 0.1 16.8 ± 0.4 17.3 ± 0.4 9.1 ± 0.7 8.5 ± 0.4
CCR2::LUC 23.8 ± 0.2 24.3 ± 0.2 6.4 ± 0.4 7.8 ± 0.7 5.4 ± 1.0 4.1 ± 1.1
Table S3. Period, phase and amplitude of circadian oscillations of CCA1::LUCIFERASE,
TOC1::LUCIFERASE and CCR2::LUCIFERASE bioluminescence in Col-0 and sig5-3. Parameters
were calculated using BRASS. CCA1::LUC amplitude is expressed as x104 bioluminescence
counts, TOC1::LUC as x103 counts, and CCR2::LUC as x10
2 counts.
17
Primer Sequence (5’ to 3’)
ACT2 Forward TGAGAGATTCAGATGCCCAGAA
ACT2 Reverse TGGATTCCAGCAGCTTCCAT
psbD BLRP Forward GGAAATCCGTCGATATCTCT
psbD BLRP Reverse CTCTCTTTCTCTAGGCAGGAAC
CCA1 Forward GCACTTTCCGCGAGTTCTTG
CCA1 Reverse TGACTCCTTTCTTACCCTGTTATTCTG
CHE Forward TCCACCGGAAATGGTTTTTG
CHE Reverse GGCGGAAGCTTGCTGTTG
GI Forward ATGGTGTAGTGGTGTAATGGGTAAATAT
GI Reverse CAGATCCTCGAGAAGCAATGG
LHY Forward ACGAAACAGGTAAGTGGCGACA
LHY Reverse TGGGAACATCTTGAACCGCGTT
PRR7 Forward CCACGAGCGGTATCTCTATGG
PRR7 Reverse ACTGATTACTTGGAAACTCAGGGTTAG
psbD Forward AGATGGTGATGGTGCAAATACATT
psbD Reverse AGCGGTGACCATTGAATAAGTTTC
18
psaAB Forward TGCTCGTAGCTCGCGTTTAA
psaAB Reverse CATCACAAGGGAAACGAAAACC
psbA Forward GGGTCGTGAGTGGGAACTTAGT
psbA Reverse GCTGAATATGCAACAGCAATCC
psbB Forward TGGGTATCCGACCCTTATGG
psbB Reverse CCCCACGCCGGGTTTA
rbcL Forward GATGGGCTTACCAGCCTTGA
rbcL Reverse CTGGAACGGGCTCGATGT
SIG5 Forward GTGTTGGAGCTAATAACAGCAGACA
SIG5 Reverse TGTCGAATAACCAGACTCTCTTTCG
TOC1 Forward TCTTCGCAGAATCCCTGTGAT
TOC1 Reverse GCTGCACCTAGCTTCAAGCA
Table S4. Primer sets used for real time PCR experiments. psbD BLRP primers above are as
described elsewhere (27).
19
Promoter Forward (5' to 3') Reverse (5' to 3')
psbKI TTGATCATTACATAGAAT AACAAAAATTGGTGTTCT
psbDC AATAAAATCAAAAATTTTG AGCGATCCTCCTATTCA
rbcL ATGAAAGAATATACAATAA AAGTCCCTCCCTACAAG
accD ATCCTTCTTTTCATTTAG AGAGCTTCTGGCCTCTA
petLG TGAATTGAGTTCTTTTTA GAAGGGACTCAATAAAA
psbBT TTGGTACTTATCGGATAT GGAAATACCCCTTTATCA
ycf2 GCCAATTCCAATAGACTT TGATTCCTCCTAAATTGC
trnV ATGGCTCGAATCCGTAGT TCCCCCATCAAGAAATAG
rpl32 ATTATTTAAATGAGTACT TCAAAAATGAAAAAAAAT
ycf1 TTTAATAGGGAACCTCAA AAACCTCCCTTTTTTCTT
rps15 GATACCAATTATAGCGGA AAAAAGAAATCCTTCCCC
rps12-7 GTATGGATATGTAAAATACA TTGTAGGGTGGATCTCG
trnI-rpl23 ATCCCACTGAATTGAATTG TTAGTGGGGATCCTCGT
psbN TTTACCATATTCGGAATT TATTATAGAATTGAAAGA
clpP TAGTTTTATTCATTCTCT GAAATGAAAAAAAAAGAG
psbEFLJ ATTATGTAACACCCCATT ACTGAACTCCAGATATTC
atpB AGGTTTCAGTTAGTTGA AATAAAAAAAATATGTTAAA
ndhC CTATTAAGTAATAAGTGTA AGACGAACTCCTATGAA
psaAB CATAATAGATCCGAACACT TGAGTCCTCCTCTTTCC
trnEYD AATATAAAAAGAAAGTATAT ATACTTGCTCAACCGC
rpoBC TTCCAATTGAATATAGTC CTTTTTTGAATTTCCCAT
20
atpFA ATAAGTCTCATTATTATTA ATAATCTCCTCTTCTAG
psbA GTGGATTCGCTTCTAATT GGTAAAATCCTTGGTTTA
Table S5. Primer sets used for ChIP-qPCR analysis, as described previously (29).
21
References and Notes 1. A. N. Dodd et al., Plant circadian clocks increase photosynthesis, growth, survival, and
competitive advantage. Science 309, 630 (2005).
2. T. P. Michael et al., Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet. 4, e14 (2008).
3. K. Kanamaru, K. Tanaka, Roles of chloroplast RNA polymerase sigma factors in chloroplast development and stress response in higher plants. Biosci. Biotechnol. Biochem. 68, 2215 (2004).
4. A. Nagashima et al., The multiple-stress responsive plastid sigma factor, SIG5, directs activation of the psbD blue light-responsive promoter (BLRP) in Arabidopsis thaliana. Plant Cell Physiol. 45, 357 (2004).
5. K. Kanamaru et al., An Arabidopsis sigma factor (SIG2)-dependent expression of plastid-encoded tRNAs in chloroplasts. Plant Cell Physiol. 42, 1034 (2001).
6. Y. Ishizaki et al., A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J. 42, 133 (2005).
7. M. Shimizu et al., Sigma factor phosphorylation in the photosynthetic control of photosystem stoichiometry. Proc. Natl. Acad. Sci. U.S.A. 107, 10760 (2010).
8. J.-J. Favory et al., Specific function of a plastid sigma factor for ndhF gene transcription. Nucleic Acids Res. 33, 5991 (2005).
9. P. H. Hoffer, D. A. Christopher, Structure and blue-light-responsive transcription of a chloroplast psbD promoter from Arabidopsis thaliana. Plant Physiol. 115, 213 (1997).
10. Y. Tsunoyama et al., Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. Proc. Natl. Acad. Sci. U.S.A. 101, 3304 (2004).
11. Materials and methods are available as supplementary material on Science Online.
12. P. D. Gould et al., Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants. Plant J. 58, 893 (2009).
13. B. L. Strehler, W. Arnold, Light production by green plants. J. Gen. Physiol. 34, 809 (1951).
14. S. Panda et al., Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307 (2002).
15. S. L. Harmer et al., Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110 (2000).
16. N. F. Tsinoremas et al., A sigma factor that modifies the circadian expression of a subset of genes in cyanobacteria. EMBO J. 15, 2488 (1996).
17. J. Tomita, M. Nakajima, T. Kondo, H. Iwasaki, No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science 307, 251 (2005).
22
18. J. S. O’Neill et al., Circadian rhythms persist without transcription in a eukaryote. Nature 469, 554 (2011).
19. A. J. Millar, I. A. Carré, C. A. Strayer, N. H. Chua, S. A. Kay, Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267, 1161 (1995).
20. D. E. Somers, T. F. Schultz, M. Milnamow, S. A. Kay, ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis. Cell 101, 319 (2000).
21. S. Hanano, M. A. Domagalska, F. Nagy, S. J. Davis, Multiple phytohormones influence distinct parameters of the plant circadian clock. Genes Cells 11, 1381 (2006).
22. A. N. Dodd et al., The Arabidopsis circadian clock incorporates a cADPR-based feedback loop. Science 318, 1789 (2007).
23. N. Dalchau et al., The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose. Proc. Natl. Acad. Sci. U.S.A. 108, 5104 (2011).
24. P. Más, Circadian clock function in Arabidopsis thaliana: Time beyond transcription. Trends Cell Biol. 18, 273 (2008).
25. S. Sugano, C. Andronis, M. S. Ong, R. M. Green, E. M. Tobin, The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 96, 12362 (1999).
26. C. T. Hotta et al., Modulation of environmental responses of plants by circadian clocks. Plant Cell Environ. 30, 333 (2007).
27. T. Mochizuki, Y. Onda, E. Fujiwara, M. Wada, Y. Toyoshima, Two independent light signals cooperate in the activation of the plastid psbD blue light-responsive promoter in Arabidopsis. FEBS Lett. 571, 26 (2004).
28. Y. Onda, Y. Yagi, Y. Saito, N. Takenaka, Y. Toyoshima, Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: Differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters. Plant J. 55, 968 (2008).
29. M. Hanaoka, M. Kato, M. Anma, K. Tanaka, SIG1, a sigma factor for the chloroplast RNA polymerase, differently associates with multiple DNA regions in the chloroplast chromosomes in vivo. Int. J. Mol. Sci. 13, 12182 (2012).
30. C. H. Johnson et al., Circadian oscillations of cytosolic and chloroplastic free calcium in plants. Science 269, 1863 (1995).
31. J. Yao, S. Roy-Chowdhury, L. A. Allison, AtSig5 is an essential nucleus-encoded Arabidopsis σ-like factor. Plant Physiol. 132, 739 (2003).
32. M. Hassidim et al., Mutations in CHLOROPLAST RNA BINDING provide evidence for the involvement of the chloroplast in the regulation of the circadian clock in Arabidopsis. Plant J. 51, 551 (2007).
23
33. K. Ichikawa, A. Shimizu, R. Okada, S. B. Satbhai, S. Aoki, The plastid sigma factor SIG5 is involved in the diurnal regulation of the chloroplast gene psbD in the moss Physcomitrella patens. FEBS Lett. 582, 405 (2008).
34. M. Hanaoka et al., RpaB, another response regulator operating circadian clock-dependent transcriptional regulation in Synechococcus elongatus PCC 7942. J. Biol. Chem. 287, 26321 (2012).
35. M. F. Covington, J. N. Maloof, M. Straume, S. A. Kay, S. L. Harmer, Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol. 9, R130 (2008).
36. W. R. Hess, A. Prombona, B. Fieder, A. R. Subramanian, T. Börner, Chloroplast rps15 and the rpoB/C1/C2 gene cluster are strongly transcribed in ribosome-deficient plastids: Evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J. 12, 563 (1993).
37. M. Swiatecka-Hagenbruch, K. Liere, T. Börner, High diversity of plastidial promoters in Arabidopsis thaliana. Mol. Genet. Genomics 277, 725 (2007).