Logo of narLink to Publisher's site
Nucleic Acids Res. 2005; 33(18): 5991–5999.
Published online 2005 Oct 20. doi:  10.1093/nar/gki908
PMCID: PMC1266065

Specific function of a plastid sigma factor for ndhF gene transcription


The complexity of the plastid transcriptional apparatus (two or three different RNA polymerases and numerous regulatory proteins) makes it very difficult to attribute specific function(s) to its individual components. We have characterized an Arabidopsis T-DNA insertion line disrupting the nuclear gene coding for one of the six plastid sigma factors (SIG4) that regulate the activity of the plastid-encoded RNA polymerase PEP. This mutant shows a specific diminution of transcription of the plastid ndhF gene, coding for a subunit of the plastid NDH [NAD(P)H dehydrogenase] complex. The absence of another NDH subunit, i.e. NDHH, and the absence of a chlorophyll fluorescence transient previously attributed to the activity of the plastid NDH complex indicate a strong down-regulation of NDH activity in the mutant plants. Results suggest that plastid NDH activity is regulated on the transcriptional level by an ndhF-specific plastid sigma factor, SIG4.


The plastid genome of higher plants encodes ∼120 genes mostly organized into polycistronic transcription units forming altogether ∼35 transcription units. These few transcription units are transcribed by two different RNA polymerases, named PEP (Plastidial-Encoded RNA Polymerase) and NEP (Nucleus-Encoded RNA Polymerases) [reviewed in (1,2)]. NEP enzymes are monomeric and of the phage-type (35). PEP represents a multimeric, prokaryotic-type enzyme. Its activity is regulated by nucleus-encoded sigma-type transcription initiation factors (6,7).

NEP enzymes are constitutively expressed (8) and perform overall transcription of the whole plastid genome (9). In photosynthetically active tissues this basic overall transcriptional activity is overlaid by PEP transcriptional activity that plays a predominant role in the transcription of photosynthesis-related genes (10). The switch from predominant NEP to predominant PEP activity during plant development might be regulated by glutamyl-tRNA (11). In Arabidopsis, cDNAs encoding six different sigma-like transcription factors that could be involved in the regulation of plastid transcription have been isolated and sequenced (1214).

In adaptation to this multiple polymerase transcription system, many of the plastid genes or transcription units are preceded by NEP as well as PEP promoters thus allowing transcription by NEP as well as PEP enzymes or specific regulation of transcription by NEP/PEP competition for a promoter region containing overlapping promoters. Well-characterized examples for such multiple promoter regions are those directing the psbD-psbC, rrn, atpB, atpI and clpP genes (1521). Single promoters are rare. Two of them, rbcL and psbA, are relatively well characterized. It has been shown that they can be recognized by several sigma factors having overlapping specificity (2224) and by several RNA polymerase forms (2528). In addition to production from heterogeneous promoters, quantitative differences in NEP and PEP transcripts are probably related to quantitative changes between NEP/PEP enzymes and/or enzyme activities (8,21). Differential turnover of NEP and PEP originating transcripts has also been described previously (29).

This complexity of plastid gene expression makes it particularly difficult to recognize and to follow specific events on the transcriptional level and to determine the components that are engaged in specific gene expression on a molecular level. Pools of different transcripts corresponding to each gene have to be dissected and each promoter of a multiple promoter region should be characterized individually.

Break-through in revealing specificity of transcription in plastids came only recently from characterization of Arabidopsis sigma knock-out mutants. Based on these analyses, it could be shown that the transcription of several tRNA genes (trnV, trnM and trnE) is under predominant control of AtSIG2 (30,31) and that transcription initiation at the psbD light-responsive promoter (32,33) is mediated by AtSIG5 (34,35).

In the present paper, we report on the characterization of an Arabidopsis knock-out mutant of the SIG4 gene. We show that AtSIG4 is specifically important for the transcription of the plastid ndhF gene encoding a subunit of the plastid NDH complex.


Isolation of SIG4 knock-out lines

Genomic DNA from 11 000 insertion lines [INRA collection, Versailles, ecotype Wassilewskija (WS) (36)], divided into 11 super pools (SP) of 1000 independent lines each, was screened by PCR. PCR was performed on 50 ng template DNA in a final volume of 50 µl using AdvanTaq Plus™ DNA Polymerase (Clontech) in the presence of 0.2 mM of all four dNTPs and 0.4 µM of each primer. To reduce unspecific hybridization, temperature was decreased for 1 degree/cycle (65–55°C) during the first 10 cycles (30″ denaturation, 30″ hybridization and 3 min elongation), followed by 35 cycles at 55°C and a final elongation of 5 min. Each of the two primers specific to the genomic sequence (1) 5′-AATCTAAGGTGTGGGAAGCTCTGC-3′ and (4) 5′-ACTAAGTACCTGCAATGTCATGC-3′ was combined with each of the two primers specific to the left and right borders of the T-DNA (2) 5′-CTACAAATTGCCTTTTCTTATCGAC-3′ and (3) 5′-CTGCCAGTTCAGTTCGTTGTTCAC-3′, respectively. Amplification products were separated by electrophoresis on 1% agarose gels at 100 V. DNA bands were gel-extracted, purified using GeneClean II kit (Bio101™) and sequenced to determine the flanking sequence of the T-DNA borders and the position of the T-DNA in the SIG4 gene.

Heterozygous SIG4 insertion lines were backcrossed with WT (WS) plants in order to eliminate any other T-DNA insertion. Every generation resulting from self-pollination were analysed for 3:1 kanamycin-resistance segregation and by PCR for the presence of the T-DNA insertion in the SIG4 gene. Five homozygote lines resulting from three successive backcrosses were isolated.

Array analyses

Plant materials and growth conditions

Imbibed seeds of Arabidopsis thaliana were sown on 0.4% gelrite (Wako Co. Ltd) plates of Murashige and Skoog (MS) medium (Wako Co. Ltd) without sucrose and were grown for 7 days at 23°C under continuous white light.

Nucleic acids preparation from plant materials

Plant materials were frozen in liquid nitrogen and ground with Multibeads shocker (Yasui Kikai Co. Ltd). DNA was purified using DNeasy Plant Mini Kit (Qiagen). RNA was first prepared using RNeasy Plant Mini Kit (Qiagen) followed by DNase I (0.1 U/µl; NIPPON GENE) treatment at 37°C for 15 min. After phenol/chloroform/isoamyl alcohol (25:24:1) extraction, the RNA was precipitated with ethanol. Q-RNA was synthesized by Riboprobe System–SP6 (Promega CO. Ltd) and Q-DNA fragment containing a SP6 promoter and a poly(T) tract, which allows us to use this PCR product as templates for the transcription reaction and the reverse transcription reaction, respectively. Q-DNA fragment was prepared by PCR using lambda DNA and following primer sets, QS-plus 5′-TCATTTAGGTGACACTATAGGGCGCATGAGACTCGAAAGCGTAGC-3′ with the SP6 transcription promoter at the 5′ end and QE-plus 5′-TTTTTTTTTTTTTTTTTTCATGCTGCTAACGTGTGACCGCATTC-3′ with the poly(T) tract at the 5′ end.

DNA microarray preparation

The A.thaliana plastid DNA [ecotype Columbia (Col)] microarray was constructed from 81 PCR products that corresponded to 79 plastid-encoded protein genes, and the lambda phage Q-gene as a control as described previously (37). For three intron-containing genes (petB, clpP and rpl2), DNA was obtained by RT–PCR (RT–PCR kit, Toyobo) amplification of total RNA (Col). Each DNA sample was spotted four times on the glass slides.

Microarray analysis

For the fluorescent probe preparation, 20 µg of each RNA sample was mixed with 35 ng of Q-RNA as an external control. This RNA solution was added with the primer mixture containing 0.5 pmol each of gene specific primers [antisense (R) primers for each gene], and the fluorescent-labelling and the purification were performed using Atlas Glass Fluorescent Labelling Kit (Clontech) and Cy3 (wild-type plant) or Cy5 (sig4 plant) Mono-Reactive Dye (Amersham Pharmacia) as described by the supplier. Finally, the purified labelled probe was precipitated with ethanol and dissolved in 5 µl water. For hybridization, 5 µl each of Cy3- and Cy5-labelled probes were mixed with 35 µl of ULTRA hyb hybridization buffer (Ambion), incubated at 95°C for 5 min, cooled at 65°C and applied on the microarray. The array was covered with Spaced Cover Glass L (TaKaRa) and incubated at 50°C for 16 h. Thereafter, the cover glass was slipped from the array in 2× SSC. The slide glass was washed twice with 0.1× SSC containing 0.1% SDS for 5 min, and twice in 0.1× SSC for 5 min. Finally, the slide glass was dipped in water and in 99.5% ethanol, and dried by centrifuging at 2500 g for 2 min at room temperature. Microarrays were scanned with two wavelengths for Cy3 (560 nm) and Cy5 (675 nm) by a laser fluorescent scanner (GeneTAC LS IV, Genomic Solutions). The lambda phage Q-gene spots were used to standardize the two channels with respect to the signal intensity, e.g. the fluorescence ratios of the four control DNA spots were set to 1.00 and the standardization coefficient (0.917) was applied to calculate the values for all other genes. Gene TAC Analyser software version 3.0.1 (Genomic Solutions) was used for the data analysis.


RT–PCR was performed using 2 µg of total RNA as described previously (23). The cDNA synthesis was carried out using poly(dT)18 primer and Superscript RNAse H-Reverse Transcriptase (Life Technologies). For amplification (∼500 bp) of the cDNAs corresponding to the six SIG genes, the following primers were used:

SIG1, 5′-GGCGAAGTATTTAGAAGCTTTAGC-3′ and 5′-ATCAACTTCCTGCGCAACAAGACG-3′; SIG2, 5′-TTGCTTCTACTGAGAGACCTGGC-3′ and 5′-CCGAGATATCTTCAAGATACTGC-3′; SIG3, 5′-TTAGTGCGATCGAGTTTAACATCG-3′ and 5′-TAAGCACGACGTGATTGAGGAACC-3′; SIG4, 5′-ACAATCTCTCCCTTACTCAGAACG-3′ and 5′-AACAACCAACCTACGGTAACAACG-3′; SIG5, 5′-CTGTTCTTTCTTCTACTGAACATGC-3′ and 5′-CTCAAACCATAGCTCAGTCTTTGC-3′; and SIG6, 5′-ACTAGCTCAGAAGGCTTTATCAGC-3′ and 5′-ATGGACTACCAGACGTAGGTTTGC-3′. PCR was performed in 50 µl reaction volumes using the same concentrations of primers and dNTPs as described previously. Thirty cycles of 30″ at 94°C, 30″ at 55°C and 45″ at 72°C were used for SIG1, SIG3, SIG4, SIG5 and SIG6 mRNAs. For SIG2 mRNA, the hybridization temperature was lowered to 48°C. Amplification products were separated by electrophoresis on agarose (1.2%) gels.

For semi-quantitative amplification of ndhF and psbN mRNAs only 1 µg of DNase I-treated total RNA was used. After cDNA synthesis using specific 3′ primers instead of poly(dT)18, the sample was divided into two equal parts for PCR amplification (25 cycles) of either ndhF or psbN cDNA. The following primers have been used:


Complementation of the sig4-1 mutant

Full-length SIG4 cDNA was amplified by RT–PCR using total RNA from 7-day-old Arabidopsis plantlets. The following primers have been used: 5′-cgggatccATGGCGACGACGATTCC-3′ and 5′-gcgtcgacTTATTCACTAGAGGAATAG-3′. The translation start and termination codons are underlined. In order to facilitate cloning, BamHI (5′) and SalI (3′) restriction site (indicated in italics) have been added to the primers. The BamHI–SalI digested PCR product was ligated into BamHI–SalI digested pBluescript II KS(−) (Stratagene) and controlled by sequencing. Later, the SIG4 cDNA was cloned in the binary vector pFP101 (http://www.isv.cnrs-gif.fr/jg/alligator/vectors.html) using the same restriction sites. Stable transformation of Arabidopsis was performed using Agrobacterium tumefaciens-based standard (38). Transformed lines were selected by means of the seed-specific GFP fluorescence.

Primer extension

Using isolated plastid DNA from Arabidopsis as template, the ndhF, ndhG and ycf4 promoter regions have been PCR amplified and cloned into pCRR2.1–TOPOR (Invitrogen) with the following primers:


Primer extension experiments have been performed as described (39) using 10 µg of total RNA. The following primers have been used for primer extension as well to establish the accompanying sequence ladders: 5′-GCACGCGATTTCAAACC-3′ (ndhF); 5′-CATGTATTGGTCCAGGC-3′ (ndhG) and 5′-CCAGCAGAAATTACTTG -3′ (ycf4).

Chlorophyll fluorescence measurements

For chlorophyll fluorescence measurements, Arabidopsis plants were grown in soil in a growth chamber in short day conditions, with a 8-h-light period (150 µmol photons m−2 s−1) at 22°C and a 16-h-dark period at 18°C. Post-illumination chlorophyll fluorescence rises were measured at room temperature on attached leaves using a PAM-2000 modulated fluorometer (Walz Effeltrich, Germany). The basal chlorophyll fluorescence level measured under low non-actinic light was recorded following a 5 min actinic illumination (220 µmol photons m−2 s−1).

Chloroplast subfractionation and protein analyses

All operations were carried out at 0–5°C. Intact chloroplasts were obtained from 2-week-old Arabidopsis plantlets as described (40). Briefly, plantlets were homogenized (0.45 M sorbitol, 20 mM Tricine, 10 mM EDTA, 10 mM NaHCO3, 0.1% BSA w/v, pH 8.4), the homogenate was filtered (50 µm), and crude chloroplasts were obtained by centrifugation at 5000 g for 3 min. Chloroplasts were further purified by short centrifugation (5 min) through a Percoll cushion [40% Percoll in BP (0.3 M sorbitol, 20 mM Tricine, 5 mM MgCl2, 2.5 mM EDTA, pH 7.6)] and three successive washes in the same buffer. After osmotic shock (20 mM Tricine, pH 7.6) chloroplast membranes were pelleted by centrifugation at 5000 g for 5 min and membrane proteins were analysed by western immunoblotting as described previously (23).


Identification of Arabidopsis lines having a T-DNA insertion in the SIG4 gene

To study the function of SIG4, we have isolated a T-DNA tagged line from the INRA collection (Versailles) by PCR-screening of DNA pools (see Materials and Methods). Sequencing of the right and left borders located the insertion to the first exon of the SIG4 gene at position 210 downstream of the ATG initiation start codon (Figure 1A). After cleaning by three successive backcrosses, five homozygous insertion plants were selected. RT–PCR analyses of mRNAs corresponding to all six Arabidopsis sigma factors show complete absence of SIG4 mRNA in all five plants (Figure 1B shows only one of these plants as example). No noticeable phenotype is visible between sig4-1 plants and WT plants independent of plant age (Figure 1C and data not shown). The absence of obvious phenotypic changes in sig4-1 plants might be due to overlapping functions of sigma factors, i.e. other sigma factors can replace SIG4 function(s) in the knock-out mutant (23,24) or to specific, but non-essential, SIG4 function. To learn something more on the function of SIG4, we have analysed the plastid transcriptome of sig4-1 plants and compared it with WT plants.

Figure 1
Characterization of the sig4 knock-out mutant. (A) Schematic presentation of the T-DNA insertion and the location of the primers. The exact position of the T-DNA insertion into the SIG4 gene (210) was determined by sequencing of the DNA fragments amplified ...

Analyses of plastid gene expression in the SIG4 knock-out mutant

To get a rough idea on whether there is replacement of function or specificity of gene transcription of a SIG4/PEP holoenzyme, we performed an overall transcript profiling by microarray hybridization. Transcript levels of 7-day-old SIG4 insertion mutants corresponding to all 79 open reading frames of the A.thaliana plastid genome were compared with that of WT plants by DNA microarray analysis. Analysis was carried out according to Nagashima et al. (37). Two independent experiments have been made using either WS or Col as WT plants. For each analysis, values have been registered from four individual DNA spottings. Normalized average values (sig4/WT) and standard deviations are indicated in Table 1 (Supplementary Table S1). If the commonly used threshold value of 0.66 (1/1.5) is applied (41), only two mRNAs (ndhF and ycf4) are significantly reduced in sig4 plants.

Table 1
Transcript analysis of plastid genes in sig4 compared with WT plants

Next, we have analysed the ndhF, ndhG and ycf4 mRNAs in more detail by primer extension. Upstream regions of ndhF, ndhG and ycf4 genes were cloned and WT and sig4-1 total RNA preparations were analysed by primer extension in order to map the 5′ ends of the corresponding precursor RNAs (Figure 2). The analysis of ndhF mRNA reveals only a single RNA. It has its 5′ end located at position −320 upstream of the ATG translation start codon. This RNA is strongly reduced in sig4-1 plants confirming SIG4-mediated transcription of ndhF (Figure 2A, upper part). The putative transcription start site is preceded by typical prokaryotic-type −35 and −10 consensus sequences (Figure 2D). The strong reduction of ndhF mRNA was verified in addition by semi-quantitative RT–PCR analysis using another RNA as control whose level is not modified in the knock-out mutant (psbN) (Figure 2A, lower part).

Figure 2
Analyses of ndhF, ndhG and ycf4 precursor RNAs. Total RNA was isolated from 7-day-old Arabidopsis plantlets that had been grown under 16 h light/8 h dark cycle. RNA was reverse transcribed and cDNAs were separated on 6% polyacrylamide gels under denaturing ...

The analyses of the ndhG and ycf4 mRNAs show several transcripts (Figure 2B). However, neither of these transcripts is reduced in the sig4-1 plants indicating that these two genes do not depend on SIG4 for transcription. DNA sequences preceding the 5′ ends of the two most abundant transcripts of the ndhG gene are shown in Figure 2D. They are located at positions −138 and −213 relative to the translation initiation codon, respectively. Upstream sequences do not reveal typical prokaryotic-type promoter elements. On the other hand, NEP consensus YRTA sequences are discernable in both cases, suggesting transcription by NEP. The most important transcript of the ycf4 gene is located further than 400 bases upstream of the ATG codon and the sequence is not readable up to that point. The second transcript ends at position −326 relative to the translation start codon. The DNA sequence preceding this 5′ end contains a −35 and −10 consensus element reminiscent for PEP promoters. The minor transcript mapping at position −226 probably corresponds to a processing product since neither PEP nor NEP consensus promoter elements are detectable in the upstream DNA sequence (Figure 2C and D).

The strong decrease of ndhF precursor RNA is due to the lack of SIG4 in sig4-1 plants and leads to a strong decrease of NDH complex amount and activity

To confirm that the strong decrease of ndhF precursor RNA in sig4-1 plants is indeed due to the lack of SIG4 we complemented the mutant by agrobacterium-mediated transformation using the SIG4 cDNA placed under control of the 35S promoter. Figure 3A shows the comparison of ndhF precursor RNAs in WT and sig4-1 plants and after complementation of the sig4-1 plants with 35S-SIG4. Three different complementation lines have been analysed. The expression of SIG4 cDNA under control of the 35S promoter completely restores the level of ndhF precursor RNA in all three lines showing even overexpression of the ndhF gene compared with WT plants. The mRNA levels of another ndh gene, ndhG (only transcript b is shown but both transcripts, a and b, show the same behaviour), are not changed in the three different complemented lines and in the sig4-1 mutant.

Figure 3
Characterization of the sig4 knock-out mutant by complementation and fluorescence induction. (A) An aliquot of 10 µg of total RNA prepared from 7-day-old Arabidopsis WT (lane 1), sig4 (lane 2) and three different 35S-SIG4 complemented lines (lanes ...

To obtain information on the influence of the strong decrease in ndhF gene expression on NDH activity in general, we compared WT, sig4-1 and 35S-SIG4 complemented plants by measuring chlorophyll fluorescence during a light to dark transition. Such an analysis was previously used to characterize plastid ndh knock-out mutants (42), a nuclear mutant affected in a factor that is essential for ndhB expression (43) and, more recently, nuclear knock-out mutants of novel NDH complex subunits (44). It was concluded from these studies that the lack of one subunit of the plastid NDH complex abolishes both, the assembly and the function, of the whole complex resulting in a suppression of the transient increase in chlorophyll fluorescence measured following actinic illumination. The fluorescence induction curve of sig4-1 plants is comparable with that previously reported for ndh mutants (Figure 3B) (41,44), i.e. the transient increase in chlorophyll fluorescence observed in WT plants disappears in the mutants. On the other hand, the fluorescence induction curve of the 35S-SIG4 complemented plants resembles that of the WT. This demonstrates that the lack of SIG4 results in strong down-regulation of NDH activity.

Finally, we also analysed whether the lack of ndhF expression has consequences on the expression of another subunit of the NDH complex on the protein level. For this aim, we analysed the presence of the NDHH subunit (43) in the WT, sig4-1 and 35S-SIG4 plants by western immunoblotting (Figure 3C). The result shows that in the sig4-1 mutant the NDHH protein is not detectable any more, i.e. its level is at least >10-fold decreased compared with the WT dilution analysis (Figure 3C, compare lanes 1–3 with lane 4). On the other hand, in the 35S-SIG4 complemented plants, NDHH is present again in well detectable amount. The amount of plastid terminal oxidase [PTOX (45)], another putative chlororespiratory enzyme, is not affected in the mutants and can be used as a loading control.


We have analysed plastid gene expression in Arabidopsis plants deficient in SIG4 expression. Overall analysis of transcript levels of a 7-day-old sig4 insertion mutant shows up-regulated and down-regulated mRNAs (Table 1). The most down-regulated mRNA corresponds to ndhF and the most up-regulated mRNA is psaJ (Table 1). Up-regulation of mRNAs in a given sigma knock-out mutant could be due to changes in turnover rates or to overexpression of (an)other sigma factor(s). For instance, overexpression of SIG3 in SIG2 antisense plants has recently been shown (23). In order to explain the overexpression of psaJ in sig4 plants, it would be interesting to analyse the expression of all other sigma factors on the protein level in the future.

As a first step towards determination of gene promoters that are specifically recognized by SIG4, we have analysed the three most reduced mRNAs (ndhF > ndhG, ycf4) by primer extension (Figure 2). In addition to quantitative aspects, primer extension also permits to localize 5′ ends of precursor RNAs, i.e. to determine transcription initiation and/or processing sites of mRNAs. These analyses as well as semi-quantitative RT–PCR analysis confirmed the strong underexpression of the ndhF gene in the sig4 mutant (Figure 2A). However, for the two other genes, ndhG and ycf4, equal amounts of precursor RNAs are detected (Figure 2B and C and Figure 3A). The reason for these quantitative differences between primer extension and microarray results is not completely clear. However, ndhF represents a single gene while ndhG and ycf4 are localized within clusters of genes (4648) that give rise to a mixture of monocistronic as well as long polycistronic mRNAs (see below). On double-stranded DNA microarrays, the whole population of monocistronic and polycistronic mRNAs will be analysed including antisense RNAs while primer extension reveals only the mRNAs corresponding to the gene of interest.

A previous transcript analysis of the ndhH-D operon showed a complex pattern of transcripts, including monocistronic transcripts for psaC and ndhD (46,47). NdhG represents the forth ndh gene within the ndhH-D operon and had not been analysed for the presence of monocistronic transcripts. Our study shows the existence of two ndhG RNAs whose 5′ ends locate between ndhG and the preceding ndhI gene suggesting the existence of monocistronic RNAs also for ndhG. These RNAs might arise from processing of longer transcripts or from activation of internal promoters. The DNA sequences preceding the 5′ ends of the two major ndhG mRNAs do reveal YRTA NEP consensus sequences, i.e. the two observed transcripts could be produced by NEP. Prokaryotic-type promoter structures cannot be detected (Figure 2D). This indicates that the ndhG gene is not transcribed by PEP, i.e. precursor RNAs should not be influenced by the lack of a sigma factor that belongs to the PEP transcription system. This is in accordance with our primer extension result that does not show differences between WT and sig4 plants. The ndhG mRNA level is also not influenced by overexpression of ndhF mRNA in 35S-SIG4 plants (Figure 3A), indicating that there is no coordination of expression of different ndh genes on the mRNA level.

The upstream sequence of the −326 ycf4 transcript harbours prokaryotic-type promoter elements (Figure 2D), i.e. it could be transcribed by PEP. However, the two consensus promoter sequences differ from those of the ndhF gene. In addition, all three detectable ycf4 transcripts are present in equal amounts in WT plants and sig4 mutants. Therefore, it is unlikely that one of these transcripts is under control of SIG4. In conclusion, the strong reduction of ndhF RNA observed by microarray as well as primer extension results suggests specific transcription of the ndhF gene by a sigma4/PEP holoenzyme. Although plastid DNA sequences are highly conserved between different plant species, the question of whether this type of ndhF transcriptional regulation by sigma 4 is conserved in other plant species cannot be answered at the moment. Simple alignment of ndhF upstream sequences does not show real sequence conservation (data not shown), and knock-out mutants are not available for other species. Also, only few sigma factor coding genes are actually sequenced in other species.

Disruption of ndh genes in tobacco showed that chloroplast NDH complexes reduce the plastoquinone pool non-photochemically and mediate cyclic electron flow around photosystem I. However, overall electron transport is not affected in ndh knock-out mutants. This was explained by the existence of two parallel pathways of electrons around PSI, one involving the NDH complex and the other an antimycin A-sensitive component (4951). Ndh knock-out plants do not show easily detectable phenotypes (42,49,5255) and, in this respect, these mutants resemble well to our sig4 mutant. In addition, the strong diminution of ndhF expression in sig4 plants seems to provoke the same phenotype as it has been found in ndh knock-out mutants, i.e. it abolishes the transient increase in chlorophyll fluorescence after light to dark transition which is related to the activity of the plastid NDH complex (Figure 3B) (4244). Finally, western blot analysis indicates the absence of other NDH subunits, e.g. NDHH, in sig4 mutants (Figure 3C). This result fits well to previous findings showing that in the absence of one of the NDH proteins the whole NDH complex cannot be assembled (55) and the other subunits disappear (4244,52,56). Our results show that the diminution of ndhF mRNA does not influence the quantity of another ndh mRNA (e.g. ndhG) but it influences the quantity of another NDH subunit on the protein level (e.g. NDHH). It seems therefore likely that NDH complex assembly is regulated on the post-transcriptional level in a way that the quantity of whole NDH complexes could be determined by the quantity of one of its subunits, e.g. NDHF. The PTOX, which might participate in a chloroplast respiratory chain (50) and has been localized to thylakoïd stromal lamellae (57), is not influenced in the different sig4 mutants and is used as loading control (Figure 3C). This result shows that the regulation of the expression of the NDH complex and PTOX is not generally coupled although both components are enhanced in plants with severe defects in photosystem II (58).

NDHF is an important subunit of the NDH complex because the activity of NDH complexes is regulated by phosphorylation of the NDHF polypeptide (59). In addition, NDHF is encoded by a single gene that is not part of a multicistronic transcription unit, i.e. its transcription does not influence the transcription of other, unrelated, genes. Altogether, our results suggest that, via ndhF transcription, SIG4 regulates the overall quantity of NDH complexes and thus influences NDH activity. Future studies will focus on the question of whether SIG4 expression is modulated by environmental and/or developmental parameters, as the NDH complex has been proposed to be involved in plant stress responses [water stress, high light (55,60)] and in leaf senescence (56). Under our presently used growth conditions, we could not detect retardation of senescence of the sig4 mutants as has been published recently for tobacco ndhF knock-out mutants (56).


Supplementary Data are available at NAR Online.

Supplementary Material

[Supplementary Material]


The authors are grateful to H. Pesey for excellent technical assistance throughout the project, to M. Kuntz for providing antibodies against PTOX and to F. Courtois for help in plastid preparation and fractionation. The transformation vector pFP101 was kindly provided by F. Parcy. Part of the work was financed by the European Community (FP6-2002-LifeSciHealth, PLASTOMICS, Proposal No. 503238). Funding to pay the Open Access publication charges for this article was provided by the Centre National de la Recherche Scientifique (CNRS).

Conflict of interest statement. None declared.


1. Hess W.R., Börner T. Organellar RNA polymerases of higher plants. Int. Rev. Cytol. 1999;190:1–59. [PubMed]
2. Liere K., Malliga P. Plastid RNA polymerases in higher plants. In: Aro E.-M., Andersson B., editors. Regulation of Photosynthesis. Netherlands: Kluwer Academic Publishers; 2001. pp. 29–49.
3. Lerbs-Mache S. The 110-kDa polypeptide of spinach plastid DNA-dependent RNA polymerase: Single-subunit enzyme or catalytic core of multimeric enzyme complexes. Proc. Natl Acad. Sci. USA. 1993;90:5509–5513. [PMC free article] [PubMed]
4. Hedtke B., Börner T., Weihe A. Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science. 1997;277:809–811. [PubMed]
5. Hedtke B., Börner T., Weihe A. One RNA polymerase serving two genomes. EMBO Rep. 2000;1:435–440. [PMC free article] [PubMed]
6. Igloi G.L., Kössel H. The transcriptional apparatus of chloroplasts. Crit. Rev. Plant Sci. 1992;10:525–558.
7. Allison L. The role of sigma factors in plastid transcription. Biochimie. 2000;82:537–548. [PubMed]
8. Chang C.-C., Sheen J., Niwa Y., Lerbs-Mache S., Stern D.B. Functional analysis of two Maize cDNAs encoding T7-like RNA polymerases. Plant Cell. 1999;11:911–926. [PMC free article] [PubMed]
9. Legen J., Kemp S., Krause K., Profanter B., Herrmann R.G., Maier R.M. Comparative analysis of plastid transcription profiles of entire chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries. Plant J. 2002;31:171–188. [PubMed]
10. Allison L.A., Simon L.D., Maliga P. Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J. 1996;15:2802–2809. [PMC free article] [PubMed]
11. Hanaoka M., Kanamaru K., Fujiwara M., Takahashi H., Tanaka K. Glutamyl-tRNA mediates a switch in RNA polymerase use during chloroplast biogenesis. EMBO Rep. 2005;6:545–550. [PMC free article] [PubMed]
12. Isono K., Shimizu M., Yoshimoto K., Niwa Y., Satoh K., Yokota A., Kobayashi H. Leaf-specific expressed genes for polypeptides destined for chloroplasts with domains of σ70 factors of bacterial RNA polymerases in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA. 1997;94:14948–14953. [PMC free article] [PubMed]
13. Tanaka K., Tozawa Y., Mochizuki N., Shinozaki K., Nagatani A., Wakasa K., Takahashi H. Characterization of three cDNA species encoding plastid RNA polymerase sigma factors in Arabidopsis thaliana: evidence for the sigma factor heterogeneity in higher plant plastids. FEBS Lett. 1997;413:309–313. [PubMed]
14. Fujiwara M., Nagashima A., Kanamaru K., Tanaka K., Takahashi H. Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid RNA polymerase σ factors in Arabidopsis thaliana. FEBS Lett. 2000;481:47–52. [PubMed]
15. Mullet J.E., Orozco E.M., Chua N.-H. Multiple transcripts for higher plant rbcL and atpB genes and localization of the transcription initiation site of the rbcL gene. Plant Mol. Biol. 1985;4:39–54. [PubMed]
16. Sexton T.B., Christopher D.A., Mullet J.E. Light-induced switch in barley psbD-psbC promoter utilization: A novel mechanism regulating chloroplast gene expression. EMBO J. 1990;9:4485–4494. [PMC free article] [PubMed]
17. Vera A., Sugiura M. Chloroplast rRNA transcription from structurally different tandem promoters: an additional novel-type promoter. Curr. Genet. 1995;27:280–284. [PubMed]
18. Iratni R., Baeza L., Andreeva A., Mache R., Lerbs-Mache S. Regulation of rDNA transcription in chloroplasts: promoter exclusion by constitutive repression. Genes Dev. 1994;8:2928–2938. [PubMed]
19. Hajdukiewicz P.T.J., Allison L., Maliga P. The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J. 1997;16:4041–4048. [PMC free article] [PubMed]
20. Kapoor S., Suzuki J.Y., Sugiura M. Identification and functional significance of a new class of non-consensus-type plastid promoters. Plant J. 1997;11:327–337. [PubMed]
21. Bligny M., Courtois F., Thaminy S., Chang C.C., Lagrange T., Baruah-Wolff J., Stern D., Lerbs-Mache S. Regulation of plastid rDNA transcription by interaction of CDF2 with two different RNA polymerases. EMBO J. 2000;19:1851–1860. [PMC free article] [PubMed]
22. Hakimi M.-A., Privat I., Valay J.-G., Lerbs-Mache S. Evolutionary conservation of C-terminal domains of primary sigma70-type transcription factors between plants and bacteria. J. Biol. Chem. 2000;275:9215–9221. [PubMed]
23. Privat I., Hakimi M.-A., Buhot L., Favory J.-J., Lerbs-Mache S. Characterization of Arabidopsis plastid sigma-like transcription factors SIG1, SIG2 and SIG3. Plant Mol. Biol. 2003;55:385–399. [PubMed]
24. Homann A., Link G. DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression. Eur. J. Biochem. 2003;270:1288–1300. [PubMed]
25. Zaitlin D., Hu J., Bogorad L. Binding and transcription of relaxed DNA templates by fractions of maize chloroplast extracts. Proc. Natl Acad. Sci. USA. 1989;86:876–880. [PMC free article] [PubMed]
26. Eisermann A., Tiller K., Link G. In vitro transcription and DNA binding characteristics of chloroplast and etioplast extracts from mustard (Sinapis alba) indicate differential usage of the psbA promoter. EMBO J. 1990;9:3981–3987. [PMC free article] [PubMed]
27. Pfannschmidt T., Link G. The A and B forms of plastid DNA-dependent RNA polymerase from mustard (Sinapis alba L.) transcribe the same genes in a different developmental context. Mol. Gen. Genet. 1997;257:35–44. [PubMed]
28. Satoh J., Baba K., Nakahira Y., Tsunoyama Y., Shiina T., Toyoshima Y. Developmental stage-specific multi-subunit plastid RNA polymerase (PEP) in wheat. Plant J. 1999;18:407–415. [PubMed]
29. Cahoon A.B., Harris F.M., Stern D.B. Analysis of developing maize plastids reveal two mRNA stability classes correlating with RNA polymerase type. EMBO Rep. 2004;5:801–806. [PMC free article] [PubMed]
30. Kanamaru K., Nagashima A., Fujiwara M., Shimada H., Shirano Y., Nakabayashi K., Shibata D., Tanaka K., Takahashi H. An Arabidopsis sigma factor (SIG2)-dependent expression of plastid-encoded tRNAs in chloroplasts. Plant Cell Physiol. 2001;42:1034–1043. [PubMed]
31. Hanaoka M., Kanamaru K., Takahashi H., Tanaka K. Molecular genetic analysis of chloroplast gene promoters dependent on SIG2, a nucleus-encoded sigma factor for the plastid-encoded RNA polymerase, in Arabisopsis thaliana. Nucleic Acids Res. 2003;31:7090–7098. [PMC free article] [PubMed]
32. Gamble P.E., Mullet J.E. Blue light regulates the accumulation of two psbD–psbC transcripts in barley chloroplasts. EMBO J. 1989;8:2785–2794. [PMC free article] [PubMed]
33. Nakahira Y., Baba K., Yoneda A., Shiina T., Toyoshima Y. Circadian-regulated transcription of the psbD light-responsive promoter in wheat chloroplasts. Plant Physiol. 1998;118:1079–1088. [PMC free article] [PubMed]
34. Tsunoyama Y., Ishizaki Y., Morikawa K., Kobori M., Nakahira Y., Takeba G., Toyoshima Y., Shiina T. Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. Proc. Natl Acad. Sci. USA. 2004;9:3304–3309. [PMC free article] [PubMed]
35. Nagashima A., Hanaoka M., Shikanai T., Fujiwara M., Kanamaru K., Takahashi H., Tanaka K. The Multiple-stress responsive plastid sigma factor, SIG5, directs activation of the psbD blue light-responsive promoter (BLRP) in Arabidopsis thaliana. Plant Cell Physiol. 2004;45:357–368. [PubMed]
36. Bouchet D., Camilleri C., Caboche M. A binary vector based on Bastsa resistance for in planta transformation of Arabidopsis thaliana. C. R. Acad. Sci. Paris, Life sci. 1993;316:1188–1193.
37. Nagashima A., Hanaoka M., Motohashi R., Seki M., Shinozaki K., Kanamaru K., Takahashi H., Tanaka K. DNA microarray analysis of plastid gene expression in an Arabidopsis mutant deficient in a plastid transcription factor sigma, SIG2. Biosci. Biotechnol. Biochem. 2004;68:694–704. [PubMed]
38. Clough S.J., Bent A.F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998;16:735–743. [PubMed]
39. Iratni R., Diederich L., Harrak H., Bligny M., Lerbs-Mache S. Organ-specific transcription of the rrn operon in spinach plastids. J. Biol. Chem. 1997;272:13676–13682. [PubMed]
40. Kunst L. Preparation of physiologically active chloroplasts from Arabidopsis. In: Martinez-Zapater J. M., Salinas J., editors. Arabidopsis protocols. Totowa, NJ: Humana Press; pp. 43–48.
41. Donson J., Fang Y., Espiritu-Santo S.A., Miyamoto S., Armendarez V., Volkmuth W. Comprehensive gene expression analysis by transcript profiling. Plant Mol. Biol. 2002;48:75–97. [PubMed]
42. Burrows P.A., Sazanov L.A., Svab Z., Maliga P., Nixon P.J. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO J. 1998;17:868–876. [PMC free article] [PubMed]
43. Hashimoto M., Endo T., Peltier G., Tasaka M., Shikanai T. A nucleus-encoded factor, CRR2, is essential for the expression of chloroplast ndhB in Arabidopsis. Plant J. 2003;36:541–549. [PubMed]
44. Rumeau D., Bécuwe-Linka N., Beyly A., Louwagie M., Garin J., Peltier G. New Subunits NDH-M, -N, and -O, encoded by nuclear genes, are essential for plastid Ndh complex functioning in higher plants. Plant Cell. 2005;17:219–232. [PMC free article] [PubMed]
45. Josse E.-M., Simkin A.J., Gaffé J., Labouré A.-M., Kuntz M., Carol P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 2000;123:1427–1436. [PMC free article] [PubMed]
46. Del Campo E.M., Sabater B., Martin M. Transcripts of the ndhH-D operon of barley plastids: possible role of unedited site III in splicing of the ndhA intron. Nucleic Acids Res. 2000;28:1092–1098. [PMC free article] [PubMed]
47. Del Campo E.M., Sabater B., Martin M. Post-transcriptional control of chloroplast gene expression. J. Biol. Chem. 2002;277:36457–36464. [PubMed]
48. Barkan A., Walker M., Nolasco M., Johnson D. A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO J. 1994;13:3170–3181. [PMC free article] [PubMed]
49. Joët T., Cournac L., Horvath E.M., Medgyesy P., Peltier G. Increased sensitivity of photosynthesis to antimycin a induced by inactivation of the chloroplast ndhB Gene. Evidence for a participation of the NADH-dehydrogenase complex to cyclic electron flow around photosystem I. Plant Physiol. 2001;125:1919–1929. [PMC free article] [PubMed]
50. Peltier G., Cournac L. Chlororespiration. Annu. Rev. Plant Biol. 2002;53:523–550. [PubMed]
51. Munekage Y., Hashimoto M., Miyake C., Tomizawa K.I., Endo T., Tasaka M., Shikanai T. Cyclic electron flow around photosystem I is essential for photosynthesis. Nature. 2004;429:579–582. [PubMed]
52. Kofer W., Koop H.-U., Wanner G., Steinmüller K. Mutagenesis of the genes encoding subunits A, C, H, I, J and K of the plastid NAD(P)H-plastoquinone-oxidoreductase in tobacco by polyethylene glycol-mediated plastome transformation. Mol. Gen. Genet. 1998;258:166–173. [PubMed]
53. Shikanai T., Endo T., Hashimoto T., Yamada Y., Asada K., Yokota A. Directed disruption of the tobacco ndhB gene impairs cyclic electron flow around photosystem I. Proc. Natl Aad. Sci. USA. 1998;95:9705–9709. [PMC free article] [PubMed]
54. Endo T., Shikanai T., Takabayashi A., Asada K., Sato F. The role of chloroplastic NAD(P)H dehydrogenase in photoprotection. FEBS Lett. 1999;457:5–8. [PubMed]
55. Horvath E.M., Peter S.O., Joët T., Rumeau D., Cournac L., Horvath G.V., Kavanagh T.A., Schäfer C., Peltier G., Medgyesy P. Targeted inactivation of the plastid ndhB gene in tobacco results in an enhanced sensitivity of photosynthesis to moderate stomatal closure. Plant Physiol. 2000;123:1337–1349. [PMC free article] [PubMed]
56. Zapata J.M., Guéra A., Esteban-Carrasco A., Martin M., Sabater B. Chloroplasts regulate leaf senescence: delayed senescence in transgenic ndhF-defective tobacco. Cell Death Differ. 2005;12:1277–1284. [PubMed]
57. Lennon A.M., Prommeenate P., Nixon P.J. Location, expression and orientation of the putative chlororespiratory enzymes, Ndh and IMMUTANS, in higher-plant plastids. Planta. 2003;218:254–260. [PubMed]
58. Baene-Gonzàlez E., Allahverdiyeva Y., Svab Z., Maliga P., Josse E.-M., Kuntz M., Mäenpää P., Aro E.-M. Deletion of the tobacco psbA gene triggers an upregulation of the thylakoid-associated NAD(P)H dehydrogenase complex and the plastid terminal oxidase (PTOX) Plant J. 2003;35:704–716. [PubMed]
59. Lascano H.R., Casano L.M., Martin M., Sabater B. The activity of the chloroplastic Ndh complex is regulated by phosphorylation of the NDH-F subunit. Plant Physiol. 2003;132:256–262. [PMC free article] [PubMed]
60. Casano L.M., Martin M., Sabater B. Hydrogen peroxide mediates the induction of chloroplastic NDH complex under photooxidative stress in barley. Plant Physiol. 2001;125:1450–1458. [PMC free article] [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press
PubReader format: click here to try


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Gene
    Gene records that cite the current articles. Citations in Gene are added manually by NCBI or imported from outside public resources.
  • GEO Profiles
    GEO Profiles
    Gene Expression Omnibus (GEO) Profiles of molecular abundance data. The current articles are references on the Gene record associated with the GEO profile.
  • MedGen
    Related information in MedGen
  • Pathways + GO
    Pathways + GO
    Pathways and biological systems (BioSystems) that cite the current articles. Citations are from the BioSystems source databases (KEGG and BioCyc).
  • Protein
    Protein translation features of primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem chemical substance records that cite the current articles. These references are taken from those provided on submitted PubChem chemical substance records.

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...