Characterization and analysis of an NAD(P)H dehydrogenase transcriptional regulator critical for the survival of cyanobacteria facing inorganic carbon starvation and osmotic stress

Cyanobacterial NDH-1 complexes: multiplicity in function and subunit composition

In cyanobacteria, the NAD(P)H:quinone oxidoreductase (NDH-1) is involved in a variety of functions like respiration, cyclic electron flow around PSI and CO(2) uptake. Several types of NDH-1 complexes, which differ in structure and are responsible for these functions, exist in cyanobacterial membranes. This minireview is based on data obtained by reverse genetics and proteomics studies and focuses on the structural and functional differences of the two types of cyanobacterial NDH-1 complexes: NDH-1L, important for respiration and PSI cyclic electron flow, and NDH-1MS, the low-CO(2) inducible complex participating in CO(2) uptake. The NDH-1 complexes in cyanobacteria share a common NDH-1M 'core' complex and differ in the composition of the distal membrane domain composed of specific NdhD and NdhF proteins, which in complexes involved in CO(2) uptake is further associated with the hydrophilic carbon uptake (CUP) domain. At present, however, very important questions concerning the nature of catalytically active subunits that constitute the electron input device (like NADH dehydrogenase module of the eubacterial 'model' NDH-1 analogs), the substrate specificity and reaction mechanisms of cyanobacterial complexes remain unanswered and are shortly discussed here.

Cyanobacterial NADPH dehydrogenase complexes

Cyanobacteria possess functionally distinct multiple NADPH dehydrogenase (NDH-1) complexes that are essential to CO(2) uptake, photosystem-1 cyclic electron transport and respiration. The unique nature of cyanobacterial NDH-1 complexes is the presence of subunits involved in CO(2) uptake. Other than CO(2) uptake, chloroplastic NDH-1 complex has a similar role as cyanobacterial NDH-1 complexes in photosystem-1 cyclic electron transport and respiration (chlororespiration). In this mini-review we focus on the structure and function of cyanobacterial NDH-1 complexes and their phylogeny. The function of chloroplastic NDH-1 complex and characteristics of plants defective in NDH-1 are also described for comparison.

FtsH protease is required for induction of inorganic carbon acquisition complexes in Synechocystis sp. PCC 6803

Cyanobacteria possess a complex CO(2)-concentrating mechanism (CCM), which is induced by low inorganic carbon conditions. To investigate the involvement of proteases in the processes of induction and degradation of the CCM complexes, we studied the FtsH2 (DeltaSlr0228) and Deg-G (DeltaSlr1204/DeltaSll1679/DeltaSll1427) protease mutants of Synechocystis sp. PCC 6803. WT and protease mutant cells were grown under high CO(2) and then shifted to low CO(2), followed by a proteome analysis of the membrane protein complexes. Interestingly, in the FtsH2 protease mutant, inducible CCM complexes were not detected upon shift to low CO(2), whereas the Deg-G mutant behaved like WT. Also the transcripts of the inducible CCM genes and their regulator ndhR failed to accumulate upon shift of FtsH2 mutant cells from high to low CO(2), indicating that the regulation by the FtsH2 protease is upstream of NdhR. Moreover, functional photosynthesis was shown a prerequisite for induction of CCM in WT at low CO(2), possibly via generation of oxidative stress, which was shown here to enhance the expression of inducible CCM genes even at high CO(2) conditions. Once synthesized, the CCM complexes were not subject to proteolytic degradation, even when dispensable upon a shift of cells to high CO(2).

Transcriptional regulation of the CO2-concentrating mechanism in a euryhaline, coastal marine cyanobacterium, Synechococcus sp. Strain PCC 7002: role of NdhR/CcmR

Cyanobacterial photosynthesis occurs in radically diverse habitats and utilizes various forms of a CO(2)-concentrating mechanism (CCM) featuring multiple inorganic carbon (C(i)) transporters. Cyanobacteria from dynamic environments can transform CCM activity depending on C(i) availability, and yet the molecular basis for this regulation is unclear, especially in coastal strains. LysR family transcription factors resembling the Calvin cycle regulator CbbR from proteobacteria have been implicated in the expression of C(i) transporter genes in freshwater cyanobacteria. Our survey of related factors revealed a group of divergent CbbR-like sequences confined to freshwater and coastal or offshore cyanobacteria. Inactivation of the single gene (termed ccmR) from this variable cluster in the euryhaline (coastal) strain Synechococcus sp. strain PCC 7002 led to constitutive expression of a high-affinity CCM. Derepression of HCO(3)(-) transporter gene transcription, including that of BicA, a recently discovered HCO(3)(-) transporter (G. D. Price et al., Proc. Natl. Acad. Sci. USA 101:18228-18233, 2004), was observed. A unique CcmR-regulated operon containing bicA plus 9 open reading frames encoding likely Na(+)/H(+) antiporters from the CPA1 and Mnh families was defined that is essential for maximal HCO(3)(-)-dependent oxygen evolution. The promoter region required for C(i)-regulated transcription of this operon was defined. We propose that CcmR (and its associated regulon) represents a specialization for species inhabiting environments subject to fluctuating C(i) concentrations.

Coordinated high-light response of genes encoding subunits of photosystem I is achieved by AT-rich upstream sequences in the cyanobacterium Synechocystis sp. strain PCC 6803

Genes encoding subunits of photosystem I (PSI genes) in the cyanobacterium Synechocystis sp. strain PCC 6803 are actively transcribed under low-light conditions, whereas their transcription is coordinately and rapidly down-regulated upon the shift to high-light conditions. In order to identify the molecular mechanism of the coordinated high-light response, we searched for common light-responsive elements in the promoter region of PSI genes. First, the precise architecture of the psaD promoter was determined and compared with the previously identified structure of the psaAB promoter. One of two promoters of the psaAB genes (P1) and of the psaD gene (P2) possessed an AT-rich light-responsive element located just upstream of the basal promoter region. These sequences enhanced the basal promoter activity under low-light conditions, and their activity was transiently suppressed upon the shift to high-light conditions. Subsequent analysis of psaC, psaE, psaK1, and psaLI promoters revealed that their light response was also achieved by AT-rich sequences located at the -70 to -46 region. These results clearly show that AT-rich upstream elements are responsible for the coordinated high-light response of PSI genes dispersed throughout Synechocystis genome.

Isolation, subunit composition and interaction of the NDH-1 complexes from Thermosynechococcus elongatus BP-1

NDH (NADH-quinone oxidoreductase)-1 complexes in cyanobacteria have specific functions in respiration and cyclic electron flow as well as in active CO2 uptake. In order to isolate NDH-1 complexes and to study complex-complex interactions, several strains of Thermosynechococcus elongatus were constructed by adding a His-tag (histidine tag) to different subunits of NDH-1. Two strains with His-tag on CupA and NdhL were successfully used to isolate NDH-1 complexes by one-step Ni2+ column chromatography. BN (blue-native)/SDS/PAGE analysis of the proteins eluted from the Ni2+ column revealed the presence of three complexes with molecular masses of about 450, 300 and 190 kDa, which were identified by MS to be NDH-1L, NDH-1M and NDH-1S respectively, previously found in Synechocystis sp. PCC 6803. A larger complex of about 490 kDa was also isolated from the NdhL-His strain. This complex, designated 'NDH-1MS', was composed of NDH-1M and NDH-1S. NDH-1L complex was recovered from WT (wild-type) cells of T. elongatus by Ni2+ column chromatography. NdhF1 subunit present only in NDH-1L has a sequence of -HHDHHSHH- internally, which appears to have an affinity for the Ni2+ column. NDH-1S or NDH-1M was not recovered from WT cells by chromatography of this kind. The BN/SDS/PAGE analysis of membranes solubilized by a low concentration of detergent indicated the presence of abundant NDH-1MS, but not NDH-1M or NDH-1S. These results clearly demonstrated that NDH-1S is associated with NDH-1M in vivo.

LexA regulates the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803 as a transcription activator

The bidirectional NiFe-hydrogenase of Synechocystis sp. PCC 6803 is encoded by five genes (hoxEFUYH) which are transcribed as one unit. The transcription of the hox-operon is regulated by a promoter situated upstream of hoxE. The transcription start point was located at -168 by 5'Race. Several promoter probe vectors carrying different promoter fragments revealed two regions to be essential for the promoter activity. One is situated in the untranslated 5'leader region and the other is found -569 to -690 nucleotides upstream of the ATG. The region further upstream was shown to bind a protein. Even though an imperfect NtcA binding site was identified, NtcA did not bind to this region. The protein binding to the DNA was purified and found to be LexA by MALDI-TOF. The complete LexA and its DNA binding domain were overexpressed in Escherichia coli. Both were able to bind to two sites in the examined region in band-shift-assays. Accordingly, the hydrogenase activity of a LexA-depleted mutant was reduced. This is the first report on LexA acting not as a repressor but as a transcriptional activator. Furthermore, LexA is the first transcription factor identified so far for the expression of bidirectional hydrogenases in cyanobacteria.

Sensing of inorganic carbon limitation in Synechococcus PCC7942 is correlated with the size of the internal inorganic carbon pool and involves oxygen

Freshwater cyanobacteria are subjected to large seasonal fluctuations in the availability of nutrients, including inorganic carbon (Ci). We are interested in the regulation of the CO2-concentrating mechanism (CCM) in the model freshwater cyanobacterium Synechococcus sp. strain PCC7942 in response to Ci limitation; however, the nature of Ci sensing is poorly understood. We monitored the expression of high-affinity Ci-transporter genes and the corresponding induction of a high-affinity CCM in Ci-limited wild-type cells and a number of CCM mutants. These genotypes were subjected to a variety of physiological and pharmacological treatments to assess whether Ci sensing might involve monitoring of fluctuations in the size of the internal Ci pool or, alternatively, the activity of the photorespiratory pathway. These modes of Ci sensing are congruent with previous results. We found that induction of a high-affinity CCM correlates most closely with a depletion of the internal Ci pool, but that full induction of this mechanism also requires some unresolved oxygen-dependent process.

mrpA, a gene with roles in resistance to Na+ and adaptation to alkaline pH in the cyanobacterium Anabaena sp. PCC7120

Transposon mutagenesis of Anabaena sp. PCC7120 led to the isolation of a mutant strain, PHB11, which grew poorly at pH values above 10. The mutant strain exhibited pronounced Na+ sensitivity; this sensitivity was higher under basic conditions. Mutant PHB11 also showed an inhibition of photosynthesis that was much more pronounced at alkaline pH. Reconstruction of the transposon mutation of PHB11 in the wild-type strain reproduced the phenotype of the original mutant. The wild-type version of the mutated gene was cloned and the mutation complemented. In mutant strain PHB11, the transposon had inserted within an ORF that is part of a seven-ORF operon with significant sequence similarity to a family of bacterial operons that are believed to code for a novel multiprotein cation/proton antiporter primarily involved in resistance to salt stress and adaptation to alkaline pH. The Anabaena operon was denoted mrp (multiple resistance and pH adaptation) following the nomenclature of the Bacillus subtilis operon; the ORF mutated in PHB11 corresponded to mrpA. Computer analysis suggested that all seven predicted Anabaena Mrp proteins were highly hydrophobic with several transmembrane domains; in fact, the predicted protein sequences encoded by mrpA, mrpB and mrpC showed significant similarity to hydrophobic subunits of the proton pumping NADH : ubiquinone oxidoreductase. In vivo expression studies indicated that mrpA is induced with increasing external Na+ concentrations and alkaline pH; mrpA is also upregulated under inorganic carbon (Ci) limitation. The biological significance of a putative cyanobacterial Mrp complex is discussed.

Light is required for low-CO2-mediated induction of transcripts encoding components of the CO2-concentrating mechanism in the cyanobacterium Synechococcus elongatus: analysis by quantitative reverse transcription - polymerase chain reaction

Photosynthetic efficiency in cyanobacteria is improved under conditions of inorganic carbon (Ci) limitation by the induction of a CO2-concentrating mechanism (CCM) that elevates the CO2 concentration around the primary carboxylase ribulose-1,5-bisphosphate carboxylase–oxygenase (Rubisco) in the carboxysome. The molecular details of low-Ci sensing in relation to regulation of CCM induction in cyanobacteria are not presently known. We have applied a quantitative reverse transcription – polymerase chain reaction technique to monitor the abundance of key CCM-related transcripts in Synechococcus elongatus under a variety of experimental conditions with the aim of probing the conditions required for CCM induction. Despite preliminary evidence for strong induction of cmpA, sbtA, and chpY transcripts in the dark under low Ci in Synechococcus elongatus, subsequent experiments in which contaminating levels of room light during harvest were eliminated demonstrated that light is required for induction of these transcripts. However, the requirement for light for significant accumulation of CCM-related transcripts was very modest and well below the light level required to induce measurable net photosynthetic electron transport. Brief treatments with weak monochromatic light under low Ci were sufficient to cause significant accumulation of transcripts in Synechococcus elongatus relative to cells held in continuous darkness.Key words: CO2-concentrating mechanism, cyanobacteria, photosynthesis.

Regulation of cyanobacterial CO2-concentrating mechanisms through transcriptional induction of high-affinity Ci-transport systems

Approximately 50% of global CO2-based productivity is now attributed to the activity of phytoplankton, including ocean-dwelling cyanobacteria. In response to inherent restrictions on the rate of CO2 supply in the aquatic environment, cyanobacteria have evolved a very efficient means of capturing inorganic carbon (Ci), as either CO2 or HCO3–. for photosynthetic carbon fixation. This capturing mechanism, known as a CO2-concentrating mechanism (CCM), involves the operation of active CO2 and HCO3– transporters and results in the concentration of CO2 around RuBisCO, in a unique microcompartment called the carboxysome. The CCM exhibits two basic physiological states: a constitutive, low-affinity state; and a high-affinity state, which is induced in response to Ci limitation. Many of the genetic components of the CCM, including genes encoding Ci transporters, have been identified. It is apparent that the expression of genes encoding the inducible, high-affinity Ci transporters is particularly sensitive to Ci availability, and we are now interested in defining how cyanobacterial cells sense and respond to Ci limitation at the transcriptional level. Current theories include direct sensing of external Ci; sensing of internal Ci-pool fluctuations; and detection of changes in photorespiratory intermediates, carbon metabolites, or redox potential. At present, there is no consensual view. We have investigated the physiological and transcriptional responses of CCM mutants and wildtype strains to pharmacological treatments and various light, O2, and Ci regimes. Our data suggest that perception of Ci limitation by a cyanobacterial cell is either directly or indirectly related to the size of the internal Ci pool within the cell, in an oxygen-dependent manner.Key words: CO2-concentrating mechanisms, CO2 sensing, Ci transporters, Synechococcus PCC7942.

Identical Hik-Rre Systems Are Involved in Perception and Transduction of Salt Signals and Hyperosmotic Signals but Regulate the Expression of Individual Genes to Different Extents in Synechocystis

In previous studies, we characterized five histidine kinases (Hiks) and the cognate response regulators (Rres) that control the expression of approximately 70% of the hyperosmotic stress-inducible genes in the cyanobacterium Synechocystis sp. PCC 6803. In the present study, we screened a gene knock-out library of Rres by RNA slot-blot hybridization and with a genome-wide DNA microarray and identified three Hik-Rre systems, namely, Hik33-Rre31, Hik10-Rre3, and Hik16-Hik41-Rre17, as well as another system that included Rre1, that were involved in perception of salt stress and transduction of the signal. We found that these Hik-Rre systems were identical to those that were involved in perception and transduction of the hyperosmotic stress signal. We compared the induction factors of the salt stress- and hyperosmotic stress-inducible genes that are located downstream of each system and found that these genes responded to the two kinds of stress to different respective extents. In addition, the Hik33-Rre31 system regulated the expression of genes that were specifically induced by hyperosmotic stress, whereas the system that included Rre1 regulated the expression of one or two genes that were specifically induced either by salt stress or by hyperosmotic stress. Our observations suggest that the perception of salt and hyperosmotic stress by the Hik-Rre systems is complex and that salt stress and hyperosmotic stress are perceived as distinct signals by the Hik-Rre systems.

Function and regulation of the cyanobacterial genes lexA, recA and ruvB: LexA is critical to the survival of cells facing inorganic carbon starvation

The cyanobacterial genes lexA, recA and ruvB were analysed in Synechocystis PCC6803, which is shown here to be more radiation resistant than the other unicellular model strain Synechococcus PCC7942. We found that cyanobacteria do not have an Escherichia coli-type SOS regulon. The Synechocystis lexA and recA promoters were found to be strong and UV insensitive, unlike the ruvB promoter, which is weak and UV-C inducible. Yet, lexA and recA are regulated by UV-C, but the control is negative and occurs at the post-transcriptional level. Two novel conserved elements were characterized in the lexA promoter: (i) an unusually long crucial box 5'-TAAAATTTTGTATCTTTT-3' (-64, -47); and (ii) a negatively acting motif 5'-TAT GAT-3' (-42, -37). These elements were not found in the recA promoter, which appeared to be unusually simple in harbouring only a single crucial element (i.e. the canonical -10 box). RuvB, operating in recombination-dependent cellular processes, was found to be dispensable to cell growth, whereas LexA and RecA appeared to be critical to cell viability. Using DNA microarrays, we have identified 57 genes with expression that is altered, at least twofold, in response to LexA depletion. None of these genes is predicted to operate in DNA metabolism, arguing against the involvement of LexA in the regulation of DNA repair. Instead, most of the LexA-responsive genes were known to be involved in carbon assimilation or controlled by carbon availability. Consistently, the growth of the LexA-depleted strain was found to be strongly dependent on the availability of inorganic carbon.

A cyanobacterial gene encoding an ortholog of Pirin is induced under stress conditions

Pirin is a recently identified protein in eukaryotes as a transcription cofactor or as an apoptosis-related protein. Although Pirin is highly conserved from bacteria to human, there have been no reports on prokaryotic Pirin orthologs. We show here that pirA (sll1773) encoding an ortholog of Pirin together with an adjacent gene, pirB (ssl3389), was upregulated under high salinity and some other stress conditions in a cyanobacterium Synechocystis sp. PCC 6803. Induction of the pirAB genes was not related to cell death and disruption of pirA did not affect the gene expression profile. Expression of the pirAB genes was negatively regulated by a LysR family transcriptional regulator encoded by pirR (slr1871) located immediately upstream of pirAB in the divergent direction. DNA microarray analysis indicated that PirR repressed expression of closely located ORFs, slr1870 and mutS (sll1772), in addition to pirAB and pirR itself.

The novel Myb transcription factor LCR1 regulates the CO2-responsive gene Cah1, encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii

Chlamydomonas reinhardtii acclimates to CO2-limiting stress by inducing a set of genes for a carbon-concentrating mechanism (CCM). This set includes the gene Cah1, which encodes a periplasmic carbonic anhydrase. Although physiological aspects of CO2response have been extensively studied, regulatory components, such as transcription factors involved in the acclimation, have not been well described in eukaryotic microalgae. Using an arylsulfatase gene driven by the Cah1 promoter, a regulatory mutant of Cah1 was isolated and named lcr1 (for low-CO2 stress response). The photosynthetic affinity for inorganic carbon of lcr1 was reduced compared with that of wild-type cells. Expression of three low-CO2-inducible genes, Cah1, Lci1, and Lci6, were regulated by LCR1 as shown by cDNA array and RNA gel blot analyses. The Lcr1 gene encodes a protein of 602 amino acids containing a single Myb domain, which binds to the Cah1-promoter region. Expression of Lcr1 was induced by lowering CO2 levels and controlled by the regulatory factor CCM1. These results suggest that LCR1 transmits the low CO2 signal to at least three CO2-responsive genes and then fully induces CCM.

Roles of CmpR, a LysR family transcriptional regulator, in acclimation of the cyanobacterium Synechococcus sp. strain PCC 7942 to low-CO2 and high-light conditions

The cmp operon of Synechococcus sp. strain PCC 7942, encoding a high-affinity bicarbonate transporter, is induced under low CO(2) conditions by a LysR family protein CmpR. CmpR was found to be required also for induction of the operon by transfer of the cells from low-light to high-light conditions, indicating involvement of a common mechanism in the high-light- and low-CO(2)-responsive regulation. Expression of the high-light inducible genes psbAII and psbAIII, on the other hand, was found to be induced also by low-CO(2) conditions. A single promoter was responsible for the high-light and low-CO(2) induction of each of psbAII and psbAIII, suggesting involvement of a common regulatory mechanism in the light and CO(2) responses of the psbA genes. CmpR was, however, not required for the induction of psbAII and psbAIII, indicating the presence of multiple mechanisms for induction of genes under high-light and low-CO(2) conditions. The CmpR-deficient mutant nevertheless showed lower levels of the psbAII and psbAIII transcripts than the wild-type strain under all the light and CO(2) conditions examined. Gel shift assays showed that CmpR binds to the enhancer elements of psbAII and psbAIII, through specific interaction with a sequence signature conforming to the binding motif of similar LysR family proteins. These findings showed that CmpR acts as a trans-acting factor that enhances transcription of the photosystem II genes involved in acclimation to high light, revealing a complex network of gene regulation in the cyanobacterium.

Towards functional proteomics of membrane protein complexes in Synechocystis sp. PCC 6803

The composition and dynamics of membrane protein complexes were studied in the cyanobacterium Synechocystis sp. PCC 6803 by two-dimensional blue native/SDS-PAGE followed by matrix-assisted laser-desorption ionization time of flight mass spectrometry. Approximately 20 distinct membrane protein complexes could be resolved from photoautotrophically grown wild-type cells. Besides the protein complexes involved in linear photosynthetic electron flow and ATP synthesis (photosystem [PS] I, PSII, cytochrome b6f, and ATP synthase), four distinct complexes containing type I NAD(P)H dehydrogenase (NDH-1) subunits were identified, as well as several novel, still uncharacterized protein complexes. The dynamics of the protein complexes was studied by culturing the wild type and several mutant strains under various growth modes (photoautotrophic, mixotrophic, or photoheterotrophic) or in the presence of different concentrations of CO2, iron, or salt. The most distinct modulation observed in PSs occurred in iron-depleted conditions, which induced an accumulation of CP43' protein associated with PSI trimers. The NDH-1 complexes, on the other hand, responded readily to changes in the CO2 concentration and the growth mode of the cells and represented an extremely dynamic group of membrane protein complexes. Our results give the first direct evidence, to our knowledge, that the NdhF3, NdhD3, and CupA proteins assemble together to form a small low CO2-induced protein complex and further demonstrate the presence of a fourth subunit, Sll1735, in this complex. The two bigger NDH-1 complexes contained a different set of NDH-1 polypeptides and are likely to function in respiratory and cyclic electron transfer. Pulse labeling experiments demonstrated the requirement of PSII activity for de novo synthesis of the NDH-1 complexes.

Inorganic carbon limitation induces transcripts encoding components of the CO(2)-concentrating mechanism in Synechococcus sp. PCC7942 through a redox-independent pathway

The cyanobacterial CO2-concentrating mechanism (CCM) allows photosynthesis to proceed in CO2-limited aquatic environments, and its activity is modulated in response to inorganic carbon (Ci) availability. Real-time reverse transcriptase-PCR analysis was used to examine the transcriptional regulation of more than 30 CCM-related genes in Synechococcus sp. strain PCC7942 with an emphasis on genes encoding high-affinity Ci transporters and carboxysome-associated proteins. This approach was also used to test hypotheses about sensing of Ci limitation in cyanobacteria. The transcriptional response of Synechococcus sp. to severe Ci limitation occurs rapidly, being maximal within 30 to 60 min, and three distinct temporal responses were detected: (a). a rapid, transient induction for genes encoding carboxysome-associated proteins (ccmKLMNO, rbcLS, and icfA) and the transcriptional regulator, cmpR; (b). a slow sustained induction of psbAII; and (c). a rapid sustained induction of genes encoding the inducible Ci transporters cmpABCD, sbtA, and ndhF3-D3-chpY. The Ci-responsive transcripts investigated had half-lives of 15 min or less and were equally stable at high and low Ci. Through the use of a range of physiological conditions (light and Ci levels) and inhibitors such as 3-(3,4-dichlorophenyl)-1,1dimethylurea, glycolaldehyde, dithiothreitol, and ethoxyzolamide, we found that no strict correlation exists between expression of genes known to be induced under redox stress, such as psbAII, and the expression of the Ci-responsive CCM genes. We argue that redox stress, such as that which occurs under high-light stress, is unlikely to be a primary signal for sensing of Ci limitation in cyanobacteria. We discuss the data in relation to current theories of CO2 sensing in cyanobacteria.

Alterations in global patterns of gene expression in Synechocystis sp. PCC 6803 in response to inorganic carbon limitation and the inactivation of ndhR, a LysR family regulator

The cyanobacterium Synechocystis sp. PCC 6803 possesses multiple inorganic carbon (Ci) uptake systems that are regulated by Ci availability. The control mechanisms of these systems and their integration with other cell functions remain to be clarified. An analysis of the changes in global gene expression in response to Ci downshift and the inactivation of ndhR (sll1594), a LysR family regulator of Ci uptake is presented in this report. Mild Ci limitation (3% CO2 (v/v) in air to air alone) induced a dramatic up-regulation of genes encoding both inducible CO2 and HCO3- uptake systems. An induction of ndhD5/ndhD6 and other genes in a probable transcriptional unit was observed, suggesting a function in inducible Ci uptake. The expression of slr1513 and sll1735, physically clustered with sbtA and ndhF3/ndhD3/cupA, respectively, were also coordinated with upstream genes encoding the essential components for HCO3- and CO2 uptake. Ci limitation induced the regulatory genes slr1214, sll1292, slr1594, sigD, sigG, and sigH, among which slr1214, a two-component response regulator, showed the earliest induction, implying a role for the early response to Ci limitation. Opposite regulation of genes encoding the assimilation of carbon and nitrogen demonstrated a striking coordination of expression to balance C- and N-fluxes. The analyses revealed that ndhR inactivation up-regulated the expression of sbtA/sbtB, ndhF3/ndhD3/cupA/sll1735, and slr2006-13 including ndhD5 and ndhD6, indicating a vital role of this regulatory gene in both CO2 and HCO3- acquisition of the cyanobacterium. We therefore suggest that ndhR be renamed ccmR to better represent its broader regulatory characteristics.

Cis-acting elements and DNA-binding proteins involved in CO2-responsive transcriptional activation of Cah1 encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii

Expression of Cah1, encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii Dangeard, is activated when cells are exposed to low-CO2 conditions (0.04% [v/v]) in light. By using an arylsulfatase reporter gene, a regulatory region essential for the transcriptional activation of Cah1 was delimited to a 63-bp fragment between -293 and -231 relative to the transcription start site. Linker-scan analysis of the 63-bp region identified two enhancer elements, EE-1 (AGATTTTCACCGGTTGGAAGGAGGT) and EE-2 (CGACTTACGAA). Gel mobility shift assays indicated that nuclear extracts purified from cells grown under low-CO2 conditions in light contained DNA-binding proteins specifically interacting with EE-1 and EE-2. Gel mobility shift assays using mutant oligonucleotide probes revealed that the protein binding to EE-1 preferentially recognized a 9-bp sequence stretch (AGATTTTCA) of EE-1, containing a conserved sequence motif named EEC, GANTTNC, which is also present in EE-2. The EE-1- and EE-2-binding proteins interacted with the EECs contained in both of the two enhancer elements in vitro. Four EECs in the 5'-upstream region from -651 to -231 of Cah1 played a central role in the transcriptional activation of Cah1 under low-CO2 conditions. These EEC-binding proteins were present even in cells grown under high-CO2 conditions (5% [v/v]) or in the dark when Cah1 is not activated. On the basis of these results, the relationship between the transcriptional regulation of Cah1 and protein-binding to the enhancer elements in the 5'-upstream region of Cah1 is discussed.

Expression and regulation of the crucial plant-like ferredoxin of cyanobacteria

The Synechocystis fedI gene (petF, ssl0020) was found to be strongly expressed under the negative control of H2O2 or heavy metals, and the positive control of light fluence (regulation dependent on active photosynthesis) or carbon availability [under the control of NdhR, the regulator of the ndh3 operon encoding NAD(P)H dehydrogenase subunits]. The basic and constitutive promoter (BP) of fedI extending from -62 to +25 (relative to the transcription start point) is weakly active, presumably because it harbours a long (30 bp) spacer between the two crucial motifs: the -10 box (5'-TAgtAT-3', -13 to -8) and the '-35' box (5'-TTGctA-3', -49 to -44). BP strength is strongly enhanced by the two upstream regions, -113 to -82 and -151 to -114, mediating the 30-fold constitutive stimulation and the fourfold light activation respectively. Three well-conserved transcriptional elements were characterized for the first time, namely the -19 box (5'-TTTT-3') that is essential to transcription, and the two twice repeated elements that are both critical to light induction: the TTGyCA-3' box (-35 to -30, and -125 to -120) and the 5'-ATTTyA-3' box (-55 to -50, and -134 to -129). That two of these light induction motifs (5'-TTGtCA-3', -35 to -30; 5'-ATTTcA-3', -55 to -50) occur in the constitutive BP promoter indicate that in the fedI gene light activation and transcription per se are closely interacting. Interestingly, the fedI gene from marine strains was found to lack the three transcriptional elements presently described, as well as the 5'-AGGA-3' Shine-Dalgarno sequence, which are all conserved among the fedI from non-marine strains.

Response of NAD(P)H dehydrogenase complex to the alteration of CO2 concentration in the cyanobacterium Synechocystis PCC6803

An NADPH-specific NDH-1 sub-complex was separated by native-polyacrylamide gel electrophoresis and detected by activity staining from the whole cell extracts of Synechocystis PCC6803. Low CO2 caused an increase in the activity of this sub-complex quickly, accompanied by an evident increase in the expression of NdhK and PSI-driven NADPH oxidation activity that can reflect the activity of NDH-1-mediated cyclic electron transport. During incubation with high CO2, the activities of NDH-1 sub-complex and PSI-driven NADPH oxidation as well as the protein level of NdhK slightly increased at the beginning, but decreased evidently in various degrees along with incubation time. These results suggest that CO2 concentration in vitro as a signal can control the activity of NDH-1 complex, and NDH-1 complex may in turn function in the regulation of CO2 uptake.

Inorganic carbon limitation and light control the expression of transcripts related to the CO2-concentrating mechanism in the cyanobacterium Synechocystis sp. strain PCC6803

The cyanobacterium Synechocystis sp. strain PCC6803 possesses three modes of inorganic carbon (Ci) uptake that are inducible under Ci stress and that dramatically enhance the efficiency of the CO(2)-concentrating mechanism (CCM). The effects of Ci limitation on the mRNA transcript abundance of these inducible uptake systems and on the physiological expression of the CCM were investigated in detail in this cyanobacterium. Transcript abundance was assessed with semiquantitative and real-time reverse transcriptase-polymerase chain reaction techniques. Cells aerated with CO(2)-free air for 30 min in the light, but not in the dark, depleted the total [Ci] to near zero levels. Under these conditions, the full physiological expression of the CCM was apparent within 2 h. Transcripts for the three inducible Ci uptake systems, ndhF3, sbtA, and cmpA, showed near-maximal abundance at 15 min under Ci limitation. The transcriptional regulators, cmpR and ndhR, were more moderately expressed, whereas the rbcLXS and ccmK-N operons and ndhF4/ndhD4/chpX and ccaA genes were insensitive to the low-Ci treatment. The combined requirement of low Ci and light for the expression of several CCM-related transcripts was examined using real-time reverse transcriptase-polymerase chain reaction. CmpA, ndhF3, and sbtA were strongly expressed in the light, but not in the dark, under low-Ci conditions. We could find no evidence for induction of these or other CCM-related genes by a high-light treatment under high-CO(2) conditions. This provided evidence that high-light stress alone could not trigger the expression of CCM-related transcripts in Synechocystis sp. PCC6803. Potential signals triggering induction of the high-affinity state of the CCM are discussed.

Effects of low CO2 on NAD(P)H dehydrogenase, a mediator of cyclic electron transport around photosystem I in the cyanobacterium synechocystis PCC6803

The expression and activity of type-1 NAD(P)H dehydrogenase (NDH-1) was compared between cells of Synechocystis PCC6803 grown in high (H-cells) and low (L-cells) CO(2) conditions. Western analysis indicated that L-cells contain higher amounts of the NDH-1 subunits, NdhH, NdhI and NdhK. An NADPH-specific subcomplex of NDH-1 showed higher NADPH-nitroblue tetrazolium oxidoreductase activity in L-cells. The activities of both NADPH-menadione oxidoreductase and light-dependent NADPH oxidation driven by photosystem I were much higher in L-cells than in H-cells. The initial rate of re-reduction of P700(+) following actinic light illumination in the presence of DCMU under background far-red light was enhanced in L-cells. In addition, rotenone, a specific inhibitor of NDH-1, suppressed the relative rate of post-illumination increase in Chl fluorescence of L-cells more than that of H-cells, suggesting that the involvement of NDH-1 in cyclic electron flow around photosystem I was enhanced by low CO(2). Taken together, these results suggest that NDH-1 complex and NDH-1-mediated cyclic electron transport are stimulated by low CO(2) and function in the acclimation of cyanobacteria to low CO(2).

QscR, a LysR-type transcriptional regulator and CbbR homolog, is involved in regulation of the serine cycle genes in Methylobacterium extorquens AM1

A new gene, qscR, encoding a LysR-type transcriptional regulator that is a homolog of CbbR, has been characterized from the facultative methylotroph Methylobacterium extorquens AM1 and shown to be the major regulator of the serine cycle, the specific C1 assimilation pathway. The qscR mutant was shown to be unable to grow on C1 compounds, and it lacked the activity of serine-glyoxylate aminotransferase, a key enzyme of the serine cycle. Activities of other serine cycle enzymes were decreased during growth on C1 compounds compared to the activities found in wild-type M. extorquens AM1. Promoter fusion assays, as well as reverse transcription-PCR assays, have indicated that the serine cycle genes belong to three separate transcriptional units, sga-hpr-mtdA-fch, mtkA-mtkB-ppc-mcl, and gly. Gel retardation assays involving the purified QscR have demonstrated the specific binding of QscR to the DNA regions upstream of sga, mtkA, gly, and qscR. We conclude that QscR acts as a positive transcriptional regulator of most of the serine cycle enzymes and also as an autorepressor.

Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp. PCC 6803

Acclimation of microorganisms to environmental stress is closely related to the expression of various genes. We report here that salt stress and hyperosmotic stress have different effects on the cytoplasmic volume and gene expression in Synechocystis sp. PCC 6803. DNA microarray analysis indicated that salt stress strongly induced the genes for some ribosomal proteins. Hyperosmotic stress strongly induced the genes for 3-ketoacyl-acyl carrier protein reductase and rare lipoprotein A. Genes whose expression was induced both by salt stress and by hyperosmotic stress included those for heat-shock proteins and the enzymes for the synthesis of glucosylglycerol. We also found that each kind of stress induced a number of genes for proteins of unknown function. Our findings suggest that Synechocystis recognizes salt stress and hyperosmotic stress as different stimuli, although mechanisms common to the responses to each form of stress might also contribute to gene expression.

Distinct constitutive and low-CO2-induced CO2 uptake systems in cyanobacteria: genes involved and their phylogenetic relationship with homologous genes in other organisms

Cyanobacteria possess a CO(2)-concentrating mechanism that involves active CO(2) uptake and HCO(3)(-) transport. For CO(2) uptake, we have identified two systems in the cyanobacterium Synechocystis sp. strain PCC 6803, one induced at low CO(2) and one constitutive. The low CO(2)-induced system showed higher maximal activity and higher affinity for CO(2) than the constitutive system. On the basis of speculation that separate NAD(P)H dehydrogenase complexes were essential for each of these systems, we reasoned that inactivation of one system would allow selection of mutants defective in the other. Thus, mutants unable to grow at pH 7.0 in air were recovered after transformation of a DeltandhD3 mutant with a transposon-bearing library. Four of them had tags within slr1302 (designated cupB), a homologue of sll1734 (cupA), which is cotranscribed with ndhF3 and ndhD3. The DeltacupB, DeltandhD4, and DeltandhF4 mutants showed CO(2)-uptake characteristics of the low CO(2)induced system observed in wild type. In contrast, mutants DeltacupA, DeltandhD3, and DeltandhF3 showed characteristics of the constitutive CO(2)-uptake system. Double mutants impaired in one component of each of the systems were unable to take up CO(2) and required high CO(2) for growth. Phylogenetic analysis indicated that the ndhD3/ndhD4-, ndhF3/ndhF4-, and cupA/cupB-type genes are present only in cyanobacteria. Most of the cyanobacterial strains studied possess the ndhD3/ndhD4-, ndhF3/ndhF4-, and cupA/cupB-type genes in pairs. Thus, the two types of NAD(P)H dehydrogenase complexes essential for low CO(2)-induced and constitutive CO(2)-uptake systems associated with the NdhD3/NdhF3/CupA-homologues and NdhD4/NdhF4/CupB-homologues, respectively, appear to be present in these cyanobacterial strains but not in other organisms.