Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions

Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843

The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5 842 795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome.

Evolution of early eukaryotic cells: genomes, proteomes, and compartments

Eukaryotes arose from an endosymbiotic association of an alpha-proteobacterium-like organism (the ancestor of mitochondria) with a host cell (lacking mitochondria or plastids). Plants arose by the addition of a cyanobacterium-like endosymbiont (the ancestor of plastids) to the two-member association. Each member of the association brought a unique internal environment and a unique genome. Analyses of recently acquired genomic sequences with newly developed algorithms have revealed (a) that the number of endosymbiont genes that remain in eukaryotic cells-principally in the nucleus-is surprisingly large, (b) that protein products of a large number of genes (or their descendents) that entered the association in the genome of the host are now directed to an organelle derived from an endosymbiont, and (c) that protein products of genes traceable to endosymbiont genomes are directed to the nucleo-cytoplasmic compartment. Consideration of these remarkable findings has led to the present suggestion that contemporary eukaryotic cells evolved through continual chance relocation and testing of genes as well as combinations of gene products and biochemical processes in each unique cell compartment derived from a member of the eukaryotic association. Most of these events occurred during about 300 million years, or so, before contemporary forms of eukaryotic cells appear in the fossil record; they continue today.

Squalene cyclase and oxidosqualene cyclase from a fern

Ferns are the most primitive vascular plants. The phytosterols of ferns are the same as those of higher plants, but they produce characteristic triterpenes. The most distinct feature is the lack of oxygen functionality at C-3, suggesting that the triterpenes of ferns may be biosynthesized by direct cyclization of squalene. To obtain some insights into the molecular bases for the biosynthesis of triterpenes in ferns, we cloned ACX, an oxidosqualene cyclase homologue, encoding a cycloartenol synthase (CAS) and ACH, a squalene cyclase homologue, encoding a 22-hydroxyhopane synthase from Adiantum capillus-veneris. Phylogenetic analysis revealed that ACH is located in the cluster of bacterial SCs, while ACX is in the cluster of higher plant CASs.

Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek

Many Proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. These filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). This article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. Based on usher amino acid sequence comparisons, our analysis shows that the chaperone/usher assembly class is subdivided into six major phylogenetic clades, which we have termed alpha-, beta-, gamma-, kappa-, pi-, and sigma-fimbriae. Members of each clade share related operon structures and encode fimbrial subunits with similar protein domains. The proposed classification system offers a simple and convenient method for assigning newly discovered chaperone/usher systems to one of the six major phylogenetic groups.

Overproduction and characterization of two distinct aldehyde-oxidizing enzymes from Gluconobacter oxydans 621H

The Gluconobacter oxydans 621H genome contains two genes (gox1122 and gox0499) that encode putative cytosolic NAD(P)-dependent aldehyde dehydrogenases. Each gene was expressed in Escherichia coli, and the recombinant enzymes were purified and characterized. The native protein Gox1122 exhibited an apparent molecular mass of 50.1 kDa, and the subunit mass was 50.5 kDa, indicating a monomeric structure of the native enzyme. The preferred substrates were acetaldehyde and NADP. The enzyme also oxidized other short-chained aliphatic and aromatic aldehydes at lower rates. Recombinant protein Gox0499 was composed of a single subunit and had an apparent molecular mass of 49.5 kDa. The substrate spectrum of Gox0499 was broad with a preference for long-chained aliphatic and aromatic aldehydes. Highest activities were obtained using dodecanal and NAD as substrates. RT real-time PCR showed that genes gox0499 and gox1122 were expressed at an elevated level (about 3-fold) when the cells were exposed to ethanol and dodecanal in comparison to control cells.

Redox of plastoquinone pool regulates the expression and activity of NADPH dehydrogenase supercomplex in Synechocystis sp. strain PCC 6803

A highly active NADPH dehydrogenase supercomplex, which is essential for cyclic electron transport around photosystem I (cyclic PSI) and respiration, was newly identified in cyanobacteria. Synechocystis sp. strain PCC 6803 cells were treated with exogenous glucose (Glc) or 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU); subsequently, active staining of NADPH-nitroblue tetrazolium oxidoreductase, western blot, and the initial rate of P700+ dark reduction were assessed in the cyanobacterium at several time points. The expression and enzyme activity levels of NADPH dehydrogenase supercomplex were gradually inhibited and closely associated with the decrease in the rate of cyclic PSI accompanying the addition of exogenous Glc to the cultures. In contrast, the activity levels were significantly stimulated but did not cause an increase in the rate of cyclic PSI as expected in the presence of DCMU. Since Glc results in the partial reduction of the plastoquinone (PQ) pool while DCMU results in the overoxidation of the PQ pool, the present results demonstrate that the expression and activity of NADPH dehydrogenase supercomplex are under the influence of the redox control of the PQ pool while the operation of cyclic PSI as mediated by this supercomplex requires an appropriate redox poise of the PQ pool.

A large-scale protein protein interaction analysis in Synechocystis sp. PCC6803

Protein-protein interactions (PPIs) play crucial roles in protein function for a variety of biological processes. Data from large-scale PPI screening has contributed to understanding the function of a large number of predicted genes from fully sequenced genomes. Here, we report the systematic identification of protein interactions for the unicellular cyanobacterium Synechocystis sp. strain PCC6803. Using a modified high-throughput yeast two-hybrid assay, we screened 1825 genes selected primarily from (i) genes of two-component signal transducers of Synechocystis, (ii) Synechocystis genes whose homologues are conserved in the genome of Arabidopsis thaliana, and (iii) genes of unknown function on the Synechocystis chromosome. A total of 3236 independent two-hybrid interactions involving 1920 proteins (52% of the total protein coding genes) were identified and each interaction was evaluated using an interaction generality (IG) measure, as well as the general features of interacting partners. The interaction data obtained in this study should provide new insights and novel strategies for functional analyses of genes in Synechocystis, and, additionally, genes in other cyanobacteria and plant genes of cyanobacterial origin.

The Kdp-ATPase system and its regulation

K+, the dominant intracellular cation, is required for various physiological processes like turgor homeostasis, pH regulation etc. Bacterial cells have evolved many diverse K+ transporters to maintain the desired concentration of internal K+. In E.coli, the KdpATPase (comprising of the KdpFABC complex), encoded by the kdpFABC operon, is an inducible high-affinity K+ transporter that is synthesised under conditions of severe K+ limitation or osmotic upshift. The E.coli kdp expression is transcriptionally regulated by the KdpD and KdpE proteins, which together constitute a typical bacterial two-component signal transduction system. The Kdp system is widely dispersed among the different classes of bacteria including the cyanobacteria. The ordering of the kdpA, kdpB and kdpC is relatively fixed but the kdpD/E genes show different arrangements in distantly related bacteria. Our studies have shown that the cyanobacterium Anabaena sp. strain L-31 possesses two kdp operons, kdp1 and kdp2, of which, the later is expressed under K+ deficiency and desiccation. Among the regulatory genes,the kdpD ORF of Anabaena L-31 is truncated when compared to the kdpD of other bacteria, while a kdpE -like gene is absent. The extremely radio-resistant bacterium, Deinococcus radiodurans strain R1, also shows the presence of a naturally short kdpD ORF similar to Anabaena in its kdp operon. The review elaborates the expression of bacterial kdp operons in response to various environmental stress conditions, with special emphasis on Anabaena. The possible mechanism(s)of regulation of the unique kdp operons from Anabaena and Deinococcus are also discussed.

Three different DnaK proteins are functionally expressed in the cyanobacterium Synechocystis sp. PCC 6803

Multiple dnaK genes appear to be common in cyanobacteria; the function of the encoded proteins is, however, still elusive. To characterize the dnaK gene family from the cyanobacterium Synechocystis sp. PCC 6803 in detail, genetic analyses were combined with analyses of the expression and localization patterns of the three encoded proteins. While significant expression of all three genes was found, the results obtained clearly indicate physiological differences of the three proteins in vivo, and DnaK2 seems to have a key function in Synechocystis. Expression of DnaK3 appears also to be as essential as expression of DnaK2, whereas the dnaK1 gene was deleted without resulting in any distorted phenotype. In line with a suggested privileged function, expression of DnaK2 altered most significantly after heat shock.

Global gene expression of a delta PsbO:delta PsbU mutant and a spontaneous revertant in the cyanobacterium Synechocystis sp. strain PCC 6803

The photosystem II (PSII) double mutant delta PsbO:delta PsbU was unable to grow photoautotrophically at pH 7.5, but growth was restored at pH 10. We have isolated a pseudorevertant of this strain, which exhibited photoautotrophic growth at pH 7.5. PSII-specific oxygen evolution and assembled PSII centers in the pseudorevertant and the original delta PsbO:delta PsbU strains were similar at pH 7.5. Comparison of global gene expression of the two strains at pH 7.5 revealed that <4% of genes differed. In the pseudorevertant, up-regulated transcripts included stress-responsive genes, many of which were shown previously to be under the control of Hik34. Elevated transcripts included those encoding heat shock proteins (HspA, DnaK2 and HtpG), two Deg proteases (DegP and DegQ), and the orange carotenoid protein (OCP, Slr1963). Up-regulated genes encoded proteins localized to different cell compartments, including the thylakoid, plasma and outer membranes. We suggest that the cell wide up-regulation of stress response genes in the pseudorevertant may limit the impact of PSII instability that is observed in the delta PsbO:delta PsbU strain. Futhermore, the OCP has a photoprotective role mediating phycobilisome-associated nonphotochemical quenching, such that increased OCP levels in the pseudorevertant may reduce photons reaching these impaired centers. These two responses, in combination with uncharacterized stress responses, are sufficient to permit the growth of pseudorevertant at pH 7.5.

Digalactosyldiacylglycerol is required for better photosynthetic growth of Synechocystis sp. PCC6803 under phosphate limitation

Digalactosyldiacylglycerol (DGDG) is a typical membrane lipid of oxygenic photosynthetic organisms. Although DGDG synthase genes have been isolated from plants, no homologous gene has been annotated in the genomes of cyanobacteria and the unicellular red alga Cyanidioschyzon merolae. Here we used a comparative genomics approach and identified a non-plant-type DGDG synthase gene (designated dgdA) in Synechocystis sp. PCC6803. The enzyme produced DGDG in Escherichia coli when co-expressed with a cucumber monogalactosyldiacylglycerol synthase. A DeltadgdA knock-out mutant showed no obvious phenotype other than loss of DGDG when grown in a BG11 medium, indicating that DGDG is dispensable under optimal conditions. However, the mutant showed reduced growth under phosphate-limited conditions, suggesting that DGDG may be required under phosphate-limited conditions, such as those in natural niches of cyanobacteria.

Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator

Background

Cadmium is a persistent pollutant that threatens most biological organisms, including cyanobacteria that support a large part of the biosphere. Using a multifaceted approach, we have investigated the global responses to Cd and other relevant stresses (H₂O₂ and Fe) in the model cyanobacterium Synechocystis PCC6803.

Results

We found that cells respond to the Cd stress in a two main temporal phases process. In the "early" phase cells mainly limit Cd entry through the negative and positive regulation of numerous genes operating in metal uptake and export, respectively. As time proceeds, the number of responsive genes increases. In this "massive" phase, Cd downregulates most genes operating in (i) photosynthesis (PS) that normally provides ATP and NADPH; (ii) assimilation of carbon, nitrogen and sulfur that requires ATP and NAD(P)H; and (iii) translation machinery, a major consumer of ATP and nutrients. Simultaneously, many genes are upregulated, such as those involved in Fe acquisition, stress tolerance, and protein degradation (crucial to nutrients recycling). The most striking common effect of Cd and H₂O₂ is the disturbance of both light tolerance and Fe homeostasis, which appeared to be interdependent. Our results indicate that cells challenged with H₂O₂ or Cd use different strategies for the same purpose of supplying Fe atoms to Fe-requiring metalloenzymes and the SUF machinery, which synthesizes or repairs Fe-S centers. Cd-stressed cells preferentially breakdown their Fe-rich PS machinery, whereas H₂O₂-challenged cells preferentially accelerate the intake of Fe atoms from the medium.

Conclusion

We view the responses to Cd as an integrated "Yin Yang" reprogramming of the whole metabolism, we found to be controlled by the Slr1738 regulator. As the Yin process, the ATP- and nutrients-sparing downregulation of anabolism limits the poisoning incorporation of Cd into metalloenzymes. As the compensatory Yang process, the PS breakdown liberates nutrient assimilates for the synthesis of Cd-tolerance proteins, among which we found the Slr0946 arsenate reductase enzyme.

Photosynthetic H2 metabolism in Chlamydomonas reinhardtii (unicellular green algae)

Unicellular green algae have the ability to operate in two distinctly different environments (aerobic and anaerobic), and to photosynthetically generate molecular hydrogen (H2). A recently developed metabolic protocol in the green alga Chlamydomonas reinhardtii permitted separation of photosynthetic O2-evolution and carbon accumulation from anaerobic consumption of cellular metabolites and concomitant photosynthetic H2-evolution. The H2 evolution process was induced upon sulfate nutrient deprivation of the cells, which reversibly inhibits photosystem-II and O2-evolution in their chloroplast. In the absence of O2, and in order to generate ATP, green algae resorted to anaerobic photosynthetic metabolism, evolved H2 in the light and consumed endogenous substrate. This study summarizes recent advances on green algal hydrogen metabolism and discusses avenues of research for the further development of this method. Included is the mechanism of a substantial tenfold starch accumulation in the cells, observed promptly upon S-deprivation, and the regulated starch and protein catabolism during the subsequent H2-evolution. Also discussed is the function of a chloroplast envelope-localized sulfate permease, and the photosynthesis-respiration relationship in green algae as potential tools by which to stabilize and enhance H2 metabolism. In addition to potential practical applications of H2, approaches discussed in this work are beginning to address the biochemistry of anaerobic H2 photoproduction, its genes, proteins, regulation, and communication with other metabolic pathways in microalgae. Photosynthetic H2 production by green algae may hold the promise of generating a renewable fuel from nature's most plentiful resources, sunlight and water. The process potentially concerns global warming and the question of energy supply and demand.

Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities

Creating endonucleases with novel sequence specificities provides more possibilities to manipulate DNA. We have created a chimeric endonuclease (CH-endonuclease) consisting of the DNA cleavage domain of BmrI restriction endonuclease and C.BclI, a controller protein of the BclI restriction-modification system. The purified chimeric endonuclease, BmrI198-C.BclI, cleaves DNA at specific sites in the vicinity of the recognition sequence of C.BclI. Double-strand (ds) breaks were observed at two sites: 8 bp upstream and 18 bp within the C-box sequence. Using DNA substrates with deletions of C-box sequence, we show that the chimeric endonuclease requires the 5' half of the C box only for specific cleavage. A schematic model is proposed for the mode of protein-DNA binding and DNA cleavage. The present study demonstrates that the BmrI cleavage domain can be used to create combinatorial endonucleases that cleave DNA at specific sequences dictated by the DNA-binding partner. The resulting endonucleases will be useful in vitro and in vivo to create ds breaks at specific sites and generate deletions.

Fluorescence staining of live cyanobacterial cells suggest non-stringent chromosome segregation and absence of a connection between cytoplasmic and thylakoid membranes

Background

In spite of their abundance and importance, little is known about cyanobacterial cell biology and their cell cycle. During each cell cycle, chromosomes must be separated into future daughter cells, i.e. into both cell halves, which in many bacteria is achieved by an active machinery that operates during DNA replication. Many cyanobacteria contain multiple identical copies of the chromosome, but it is unknown how chromosomes are segregated into future daughter cells, and if an active or passive mechanism is operative. In addition to an outer and an inner cell membrane, cyanobacteria contain internal thylakoid membranes that carry the active photosynthetic machinery. It is unclear whether thylakoid membranes are invaginations of the inner cell membrane, or an independent membrane system.

Results

We have used different fluorescent dyes to study the organization of chromosomes and of cell and thylakoid membranes in live cyanobacterial cells. FM1-43 stained the outer and inner cytoplasmic membranes but did not enter the interior of the cell. In contrast, thylakoid membranes in unicellular Synechocystis cells became visible through a membrane-permeable stain only. Furthermore, continuous supply of the fluorescent dye FM1-43 resulted in the formation of one to four intracellular fluorescent structures in Synechocystis cells, within occurred within 30 to 60 minutes, and may represent membrane vesicles. Using fluorescent DNA stains, we found that Synechocystis genomic DNA is compacted in the cell centre that is devoid of thylakoid membranes. Nucleoids segregated very late in the cell cycle, just before complete closing of the division septum. In striking contrast to Bacillus subtilis, which possesses an active chromosome segregation machinery, fluorescence intensity of stained nucleoids differed considerably between the two Synechocystis daughter cells soon after cell division.

Conclusion

Our experiments strongly support the idea that the cytoplasmic and thylakoid membranes are not directly connected, but separate entities, in unicellular cyanobacteria. Our findings suggest that a transport system may exist between the cytoplasmic membrane and thylakoids, which could mediate the extension of thylakoid membranes and possibly also protein transport from the cytoplasmic membrane to thylakoid membranes. The cell cycle studies in Synechocystis sp. PCC 6803 show that the multiple chromosome copies per cell segregate very late in the cell cycle and in a much less stringent manner than in B. subtilis cells, indicating that chromosomes may become segregated randomly and in a passive fashion, possibly through constriction of the division septum.

Role of sigma factors in controlling global gene expression in light/dark transitions in the cyanobacterium Synechocystis sp. strain PCC 6803

We report on differential gene expression in the cyanobacterium Synechocystis sp. strain PCC 6803 after light-dark transitions in wild-type, DeltasigB, and DeltasigD strains. We also studied the effect of day length in the presence of glucose on a DeltasigB DeltasigE mutant. Our results indicated that the absence of SigB or SigD predominately altered gene expression in the dark or in the light, respectively. In the light, approximately 350 genes displayed transcript levels in the DeltasigD strain that were different from those of the wild type, with over 200 of these up-regulated in the mutant. In the dark, removal of SigB altered more than 150 genes, and the levels of 136 of these were increased in the mutant compared to those in the wild type. The removal of both SigB and SigE had a major impact on gene expression under mixotrophic growth conditions and resulted in the inability of cells to grow in the presence of glucose with 8-h light and 16-h dark cycles. Our results indicated the importance of group II sigma factors in the global regulation of transcription in this organism and are best explained by using the sigma cycle paradigm with the stochastic release model described previously (R. A. Mooney, S. A. Darst, and R. Landick, Mol. Cell 20:335-345, 2005). We combined our results with the total protein levels of the sigma factors in the light and dark as calculated previously (S. Imamura, S. Yoshihara, S. Nakano, N. Shiozaki, A. Yamada, K. Tanaka, H. Takahashi, M. Asayama, and M. Shirai, J. Mol. Biol. 325:857-872, 2003; S. Imamura, M. Asayama, H. Takahashi, K. Tanaka, H. Takahashi, and M. Shirai, FEBS Lett. 554:357-362, 2003). Thus, we concluded that the control of global transcription is based on the amount of the various sigma factors present and able to bind RNA polymerase.

In vitro transposition of ISY100, a bacterial insertion sequence belonging to the Tc1/mariner family

The Synechocystis sp. PCC6803 insertion sequence ISY100 (ISTcSa) belongs to the Tc1/mariner/IS630 family of transposable elements. ISY100 transposase was purified and shown to promote transposition in vitro. Transposase binds specifically to ISY100 terminal inverted repeat sequences via an N-terminal DNA-binding domain containing two helix–turn–helix motifs. Transposase is the only protein required for excision and integration of ISY100. Transposase made double-strand breaks on a supercoiled DNA molecule containing a mini-ISY100 transposon, cleaving exactly at the transposon 3′ ends and two nucleotides inside the 5′ ends. Cleavage of short linear substrates containing a single transposon end was less precise. Transposase also catalysed strand transfer, covalently joining the transposon 3′ end to the target DNA. When a donor plasmid carrying a mini-ISY100 was incubated with a target plasmid and transposase, the most common products were insertions of one transposon end into the target DNA, but insertions of both ends at a single target site could be recovered after transformation into Escherichia coli. Insertions were almost exclusively into TA dinucleotides, and the target TA was duplicated on insertion. Our results demonstrate that there are no fundamental differences between the transposition mechanisms of IS630 family elements in bacteria and Tc1/mariner elements in higher eukaryotes.

Long-term response toward inorganic carbon limitation in wild type and glycolate turnover mutants of the cyanobacterium Synechocystis sp. strain PCC 6803

Concerted changes in the transcriptional pattern and physiological traits that result from long-term (here defined as up to 24 h) limitation of inorganic carbon (C(i)) have been investigated for the cyanobacterium Synechocystis sp. strain PCC 6803. Results from reverse transcription-polymerase chain reaction and genome-wide DNA microarray analyses indicated stable up-regulation of genes for inducible CO(2) and HCO(3)(-) uptake systems and of the rfb cluster that encodes enzymes involved in outer cell wall polysaccharide synthesis. Coordinated up-regulation of photosystem I genes was further found and supported by a higher photosystem I content and activity under low C(i) (LC) conditions. Bacterial-type glycerate pathway genes were induced by LC conditions, in contrast to the genes for the plant-like photorespiratory C2 cycle. Down-regulation was observed for nitrate assimilation genes and surprisingly also for almost all carboxysomal proteins. However, for the latter the observed elongation of the half-life time of the large subunit of Rubisco protein may render compensation. Mutants defective in glycolate turnover (DeltaglcD and DeltagcvT) showed some transcriptional changes under high C(i) conditions that are characteristic for LC conditions in wild-type cells, like a modest down-regulation of carboxysomal genes. Properties under LC conditions were comparable to LC wild type, including the strong response of genes encoding inducible high-affinity C(i) uptake systems. Electron microscopy revealed a conspicuous increase in number of carboxysomes per cell in mutant DeltaglcD already under high C(i) conditions. These data indicate that an increased level of photorespiratory intermediates may affect carboxysomal components but does not intervene with the expression of majority of LC inducible genes.

A transient isotopic labeling methodology for 13C metabolic flux analysis of photoautotrophic microorganisms

Metabolic flux analysis is increasingly recognized as an integral component of systems biology. However, techniques for experimental measurement of system-wide metabolic fluxes in purely photoautotrophic systems (growing on CO(2) as the sole carbon source) have not yet been developed due to the unique problems posed by such systems. In this paper, we demonstrate that an approach that balances positional isotopic distributions transiently is the only route to obtaining system-wide metabolic flux maps for purely autotrophic metabolism. The outlined transient (13)C-MFA methodology enables measurement of fluxes at a metabolic steady-state, while following changes in (13)C-labeling patterns of metabolic intermediates as a function of time, in response to a step-change in (13)C-label input. We use mathematical modeling of the transient isotopic labeling patterns of central intermediates to assess various experimental requirements for photoautotrophic MFA. This includes the need for intracellular metabolite concentration measurements and isotopic labeling measurements as a function of time. We also discuss photobioreactor design and operation in order to measure fluxes under precise environmental conditions. The transient MFA technique can be used to measure and compare fluxes under different conditions of light intensity, nitrogen sources or compare strains with various mutations or gene deletions and additions.

Comparative biochemical and functional studies of family I soluble inorganic pyrophosphatases from photosynthetic bacteria

Soluble inorganic pyrophosphatases (inorganic diphosphatases, EC 3.6.1.1) were isolated and characterized from three phylogenetically diverse cyanobacteria--Synechocystis sp. PCC 6803, Anabaena sp. PCC 7120, and Pseudanabaena sp. PCC 6903--and one anoxygenic photosynthetic bacterium, Rhodopseudomonas viridis (purple nonsulfur). These enzymes were found to be family I soluble inorganic pyrophosphatases with c. 20 kDa subunits with diverse oligomeric structures. The corresponding ppa genes were cloned and functionally validated by heterologous expression. Cyanobacterial family I soluble inorganic pyrophosphatases were strictly Mg(2+)-dependent enzymes. However, diverse cation cofactor dependence was observed for enzymes from other groups of photosynthetic bacteria. Immunochemical studies with antibodies to cyanobacterial soluble inorganic pyrophosphatases showed crossreaction with orthologs of other main groups of phototrophic prokaryotes and suggested a close relationship with the enzyme of heliobacteria, the nearest photosynthetic relatives of cyanobacteria. A slow-growing Escherichia coli JP5 mutant strain, containing a very low level of soluble inorganic pyrophosphatase activity, was functionally complemented up to wild-type growth rates with ppa genes from diverse photosynthetic prokaryotes expressed under their own promoters. Overall, these results suggest that the bacterial family I soluble inorganic pyrophosphatases described here have retained functional similarities despite their genealogies and their adaptations to diverse metabolic scenarios.

Analysis of genome sequences for genes of cyanophycin metabolism: identifying putative cyanophycin metabolizing prokaryotes

CGP, a copolymer of aspartate and arginine, serves as a storage compound for nitrogen, carbon and energy in many cyanobacteria. Analysis of available genome sequences from prokaryotes identified ORFs putatively encoding proteins of high similarity to known cyanophycin synthetases and cyanophycinases from cyanobacteria in various strains of bacteria belonging to different phylogenetic taxa and not closely related to cyanobacteria. Genes of CGP metabolism occur in a wide range of bacteria exhibiting diverse metabolic capabilities, including aerobic and anaerobic respiration, fermentation, phototrophy and chemolithoautotrophy. This study identified different groups of cyanophycin synthetases and cyanophycinases, respectively, and proposes a collective terminology for the putative genes and enzymes of cyanophycin metabolism. Among 570 different microbial strains, whose genomes have been partially or completely sequenced and are publicly accessible, we identified 44 prokaryotes which possess a cyanophycin synthetase and are putatively able to synthesize CGP. From these, 31 prokaryotes harbor also a cyanophycinase enabling them to degrade CGP to dipeptides. From the latter, 24 strains possess in addition a dipeptidase necessary to hydrolyze beta-Asp-Arg dipeptides, thereby enabling them to completely utilize CGP. Therefore, CGP seems to have a much wider distribution among prokaryotes than previously recognized. Genes putatively encoding cyanophycin synthetase homologues were not identified in the genomes of Eukarya and Archaea and are therefore obviously only occurring in Eubacteria. In addition, the outcome of this detailed in silico analysis proposes to distinguish 10 different groups of cyanophycin synthetases.

The serine protease HhoA from Synechocystis sp. strain PCC 6803: substrate specificity and formation of a hexameric complex are regulated by the PDZ domain

Enzymes of the ATP-independent Deg serine endopeptidase family are very flexible with regard to their substrate specificity. Some family members cleave only one substrate, while others act as general proteases on unfolded substrates. The proteolytic activity of Deg proteases is regulated by PDZ protein interaction domains. Here we characterized the HhoA protease from Synechocystis sp. strain PCC 6803 in vitro using several recombinant protein constructs. The proteolytic activity of HhoA was found to increase with temperature and basic pH and was stimulated by the addition of Mg(2+) or Ca(2+). We found that the single PDZ domain of HhoA played a critical role in regulating protease activity and in the assembly of a hexameric complex. Deletion of the PDZ domain strongly reduced proteolysis of a sterically challenging resorufin-labeled casein substrate, but unlabeled beta-casein was still degraded. Reconstitution of the purified HhoA with total membrane proteins isolated from Synechocystis sp. wild-type strain PCC 6803 and a DeltahhoA mutant resulted in specific degradation of selected proteins at elevated temperatures. We concluded that a single PDZ domain of HhoA plays a critical role in defining the protease activity and oligomerization state, combining the functions that are attributed to two PDZ domains in the homologous DegP protease from Escherichia coli. Based on this first enzymatic study of a Deg protease from cyanobacteria, we propose a general role for HhoA in the quality control of extracytoplasmic proteins, including membrane proteins, in Synechocystis sp. strain PCC 6803.

Isolation and characterization of outer and inner envelope membranes of cyanelles from a glaucocystophyte, Cyanophora paradoxa

Envelope membranes were isolated by sucrose density gradient floatation centrifugation from the homogenate of cyanelles prepared from Cyanophora paradoxa. Two yellow bands were separated after 40 h of centrifugation. The buoyant density of one of the two fractions (fraction Y2) coincided with that of inner envelope membranes of spinach or plasma membranes of cyanobacteria. The other yellow fraction (fraction Y1) migrated to top of sucrose-gradient even at 0% sucrose. Pigment analysis revealed that the heavy yellow fraction was rich in zeaxanthin while the light fraction was rich in beta-carotene, and the both fractions contained practically no chlorophylls. Another yellow fraction (fraction Y3) was isolated from the phycobiliprotein fraction, which was the position where the sample was placed for gradient centrifugation. Its buoyant density and absorption spectra were similar to outer membranes of cyanobacteria. We have assigned fractions Y2 and Y3 as inner and outer envelope membrane fractions of cyanelles, respectively. Protein compositions were rather different between the two envelope membranes indicating little cross-contamination among the fractions.

Keeping in touch with PII: PII-interacting proteins in unicellular cyanobacteria

PII protein is conserved among bacteria, archaea and plants, and is thought to function as a carbon/nitrogen balance sensor in these organisms. Recently, several proteins that specifically interact with PII, including a PII phosphatase (PphA), an amino acid biosynthetic enzyme (NAGK), a probable membrane channel (PamA) and a small protein (PipX) that also interacts with the nitrogen transcription factor NtcA, have been identified in the unicellular cyanobacteria Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803. These findings and subsequent analyses have suggested that PII protein controls carbon and nitrogen metabolism at the gene expression level as well as at the protein activity level. In this review, the functions of PII are envisaged based on functional analyses of the PII-interacting proteins identified in cyanobacteria.

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.

The PsbZ subunit of Photosystem II in Synechocystis sp. PCC 6803 modulates electron flow through the photosynthetic electron transfer chain

The psbZ gene of Synechocystis sp. PCC 6803 encodes the approximately 6.6 kDa photosystem II (PSII) subunit. We here report biophysical, biochemical and in vivo characterization of Synechocystis sp. PCC 6803 mutants lacking psbZ. We show that these mutants are able to perform wild-type levels of light-harvesting, energy transfer, PSII oxygen evolution, state transitions and non-photochemical quenching (NPQ) under standard growth conditions. The mutants grow photoautotrophically; however, their growth rate is clearly retarded under low-light conditions and they are not capable of photomixotrophic growth. Further differences exist in the electron transfer properties between the mutants and wild type. In the absence of PsbZ, electron flow potentially increased through photosystem I (PSI) without a change in the maximum electron transfer capacity of PSII. Further, rereduction of P700(+) is much faster, suggesting faster cyclic electron flow around PSI. This implies a role for PsbZ in the regulation of electron transfer, with implication for photoprotection.

Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization

The entire genome of the unicellular cyanobacterium Synechococcus elongatus PCC 6301 (formerly Anacystis nidulans Berkeley strain 6301) was sequenced. The genome consisted of a circular chromosome 2,696,255 bp long. A total of 2,525 potential protein-coding genes, two sets of rRNA genes, 45 tRNA genes representing 42 tRNA species, and several genes for small stable RNAs were assigned to the chromosome by similarity searches and computer predictions. The translated products of 56% of the potential protein-coding genes showed sequence similarities to experimentally identified and predicted proteins of known function, and the products of 35% of the genes showed sequence similarities to the translated products of hypothetical genes. The remaining 9% of genes lacked significant similarities to genes for predicted proteins in the public DNA databases. Some 139 genes coding for photosynthesis-related components were identified. Thirty-seven genes for two-component signal transduction systems were also identified. This is the smallest number of such genes identified in cyanobacteria, except for marine cyanobacteria, suggesting that only simple signal transduction systems are found in this strain. The gene arrangement and nucleotide sequence of Synechococcus elongatus PCC 6301 were nearly identical to those of a closely related strain Synechococcus elongatus PCC 7942, except for the presence of a 188.6 kb inversion. The sequences as well as the gene information shown in this paper are available in the Web database, CYORF (http://www.cyano.genome.jp/).

The presence of multidomain linkers determines the bundle-shape structure of the phycobilisome of the cyanobacterium Gloeobacter violaceus PCC 7421

The complete genome sequence of Gloeobacter violaceus [Nakamura et al. (2003a, b) DNA Res 10:37-45, 181-201] allows us to understand better the structure of the phycobilisomes (PBS) of this cyanobacterium. Genomic analysis revealed peculiarities in these PBS: the presence of genes for two multidomain linker proteins, a core membrane linker with four repetitive sequences (REP domains), the absence of rod core linkers, two sets of phycocyanin (PC) alpha and beta subunits, two copies of a rod PC associated linker (CpcC), and two rod cap associated linkers (CpcD). Also, there is one ferredoxin-NADP(+) oxidoreductase with only two domains. The PBS proteins were investigated by gel electrophoresis, amino acid sequencing and peptide mass fingerprinting (PMF). The two unique multidomain linkers contain three REP domains with high similarity and these were found to be in tandem and were separated by dissimilar Arms. One of these, with a mass of 81 kDa, is found in heavy PBS fragments rich in PC. We propose that it links six PC hexamers in two parallel rows in the rods. The other unique linker has a mass of 91 kDa and is easily released from the heavy fragments of PBS. We propose that this links the rods to the core. The presence of these multidomain linkers could explain the bundle shaped rods of the PBS. The presence of 4 REP domains in the core membrane linker protein (129 kDa) was established by PMF. This core linker may hold together 16 AP trimers of the pentacylindrical core, or alternatively, a tetracylindrical core of the PBS of G. violaceus.

Identification of the start codon for sphS encoding the phosphate-sensing histidine kinase in Synechocystis sp. PCC 6803

In Synechocystis sp. PCC 6803 extracellular phosphate levels are relayed to the pho regulon via the SphS histidine kinase. In this cyanobacterium, the start codon of sphS has been assigned as a GUG, thereby predicting SphS to be a cytosolic protein lacking a putative N-terminal region found in the PhoR orthologue from Escherichia coli. Inspection upstream of sphS located an in-frame AUG positioned 47 codons in front of the putative GUG start. Alterations at either of the putative AUG or GUG start codons did not prevent transcription of sphS; however, up-regulation of alkaline phosphatase mRNA, or alkaline phosphatase activity, was not detected in response to phosphate-limiting conditions when the AUG was mutated. Alkaline phosphatase expression and activity serve as phenotypic markers for activation of the pho regulon. Therefore, the pho regulon had not been induced in these cells, whereas normal up-regulation was observed in strains carrying mutations at the GUG. These results show that the AUG codon, not the GUG codon, is the initiation site for sphS translation in Synechocystis sp. PCC 6803.

Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803

Background

Molecular hydrogen is an environmentally-clean fuel and the reversible (bi-directional) hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 as well as the native Escherichia coli hydrogenase 3 hold great promise for hydrogen generation. These enzymes perform the simple reaction 2H⁺ + 2e^- ↔ H₂ (g).

Results

Hydrogen yields were enhanced up to 41-fold by cloning the bidirectional hydrogenase (encoded by hoxEFUYH) from the cyanobacterium into E. coli. Using an optimized medium, E. coli cells expressing hoxEFUYH also produced twice as much hydrogen as the well-studied Enterobacter aerogenes HU-101, and hydrogen gas bubbles are clearly visible from the cultures. Overexpression of HoxU alone (small diaphorase subunit) accounts for 43% of the additional hydrogen produced by HoxEFUYH. In addition, hydrogen production in E. coli mutants with defects in the native formate hydrogenlyase system show that the cyanobacterial hydrogenase depends on both the native E. coli hydrogenase 3 as well as on its maturation proteins. Hydrogen absorption by cells expressing hoxEFUYH was up to 10 times lower than cells which lack the cloned cyanobacterial hydrogenase; hence, the enhanced hydrogen production in the presence of hoxEFUYH is due to inhibition of hydrogen uptake activity in E. coli. Hydrogen uptake by cells expressing hoxEFUYH was suppressed in three wild-type strains and in two hycE mutants but not in a double mutant defective in hydrogenase 1 and hydrogenase 2; hence, the active cyanobacterial locus suppresses hydrogen uptake by hydrogenase 1 and hydrogenase 2 but not by hydrogenase 3. Differential gene expression indicated that overexpression of HoxEFUYH does not alter expression of the native E. coli hydrogenase system; instead, biofilm-related genes are differentially regulated by expression of the cyanobacterial enzymes which resulted in 2-fold elevated biofilm formation. This appears to be the first enhanced hydrogen production by cloning a cyanobacterial enzyme into a heterologous host.

Conclusion

Enhanced hydrogen production in E. coli cells expressing the cyanobacterial HoxEFUYH is by inhibiting hydrogen uptake of both hydrogenase 1 and hydrogenase 2.

An insight into cyanobacterial genomics--a perspective

At the turn of the millennium, cyanobacteria deserve attention to be reviewed to understand the past, present and future. The advent of post genomic research, which encompasses functional genomics, structural genomics, transcriptomics, pharmacogenomics, proteomics and metabolomics that allows a systematic wide approach for biological system studies. Thus by exploiting genomic and associated protein information through computational analyses, the fledging information that are generated by biotechnological analyses, could be well extrapolated to fill in the lacuna of scarce information on cyanobacteria and as an effort this paper attempts to highlights the perspectives available and awakens researcher to concentrate in the field of cyanobacterial informatics.

Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics

A total of 223 complete bacterial genomes are analyzed, with 281 citations, for the presence of genes encoding modular polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS). We report on the distribution of these systems in different bacterial taxa and, whenever known, the metabolites they synthesize. We also highlight, in the different bacterial lineages, the PKS and NRPS genes and, whenever known, the corresponding products.

Three putative photosensory light, oxygen or voltage (LOV) domains with distinct biochemical properties from the filamentous cyanobacterium Anabaena sp. PCC 7120

Light, oxygen or voltage (LOV) domains function as blue-light sensors in the phototropin family of photoreceptors found in plants, algae and bacteria. We detected putative LOV domains (Alr3170-LOV, All2875-LOV and Alr1229-LOV) in the genome of a filamentous cyanobacterium, Anabaena sp. PCC 7120. These cyanobacterial LOV domains are closely clustered with the known LOV domains. Alr3170-LOV and A112875-LOV carry the conserved cysteine residue unique to the photoactive LOV, whereas Alr1229-LOV does not. We expressed these three LOV domains in Escherichia coli and purified them. In fact, Alr3170-LOV and A112875-LOV that are conserved in Nostoc punctiforme, a related species, bound flavin mononucleotide and showed spectral changes unique to known LOV domains on illumination with blue light. Alr3170-LOV was completely photoreduced and dark reversion was slow, whereas A112875-LOV was slowly photoreduced and dark reversion was rapid. For comparison, AvA112875-LOV in a closely related A. variabilis was also studied as a homolog of A112875-LOV. Finally, we observed that Alr1229-LOV that is not conserved in N. punctiforme showed no flavin binding.

Cooperation of group 2 σ factors, SigD and SigE for light-induced transcription in the cyanobacteriumSynechocystissp. PCC 6803

A light-inducible sigma factor of RNA polymerase, SigD, can contributes to the light-induced transcription of psbA in the cyanobacterium Synechocystis sp. PCC 6803. Here, another light-induced sigma factor, SigE, was characterized together with SigD. Results indicated that SigE also contributes to light-induced transcription on the cpcBACD, psbA, petBD and psaAB promoters whose potential sequences are of the Escherichia coli sigma(70)-type. SigD and SigE interfere with each other's expression. A rhythmic expression, in which the periodic peak of SigE exhibits a 24-h interval according to the upcoming night, was observed at the protein level. The cooperation of group 2 sigma factors, SigD and SigE, for light-induced transcription was discussed.

Large-Scale Analysis of Chlorophyll Fluorescence Kinetics in Synechocystis sp. PCC 6803: Identification of the Factors Involved in the Modulation of Photosystem Stoichiometry

Since chlorophyll fluorescence reflects the redox state of photosynthetic electron transport chain, monitoring of chlorophyll fluorescence has been successfully applied for the screening of photosynthesis-related genes. Here we report that the mutants having a defect in the regulation of photosystem stoichiometry could be identified through the simple comparison of the induction kinetics of chlorophyll fluorescence. We made a library containing 500 mutants in the cyanobacterium Synechocystis sp. PCC 6803 with transposon-mediated gene disruption, and the mutants were used for the measurement of chlorophyll fluorescence kinetics for 45 s. We picked up two genes, pmgA and sll1961, which are involved in the modulation of photosystem stoichiometry. The disruptants of the two genes share common characteristics in their fluorescence kinetics, and we searched for mutants that showed such characteristics. Out of six mutants identified so far, five showed a different photosystem stoichiometry under high-light conditions. Thus, categorization based on the similarity of fluorescence kinetics is an excellent way to identify the function of genes.

Sll1330 controls the expression of glycolytic genes in Synechocystis sp. PCC 6803

In the complete annotated genome sequences of cyanobacterium Synechocystis sp. PCC 6803, one can find many putative genes for two-component response regulators that include a helix-turn-helix DNA-binding domain. The mRNA level of one of the putative genes, sll1330, was increased by glucose, especially in the presence of light. We successfully disrupted the sll1330 gene by targeted mutagenesis with a spectinomycin resistance cassette. Deltasll1330 could not grow well under light-activated heterotrophic growth conditions. Analyses of the expression of glycolytic genes revealed that the mRNA levels of five glycolytic genes, that is, glk (sll0593), pfkA (sll1196), fbaA (sll0018), gpmB (slr1124), and pk (sll0587), were decreased, and were regulated by Sll1330 under light and glucose-supplemented conditions. The Synechocystis sp. PCC 6803 genome each encodes two isozymes for these five glycolytic genes, suggesting that each of the two isozymes is regulated by Sll1330 at the mRNA level.

Genome display tool: visualizing features in complex data sets

Background

The enormity of the information contained in large data sets makes it difficult to develop intuitive understanding. It would be useful to have software that allows visualization of possible correlations between properties that can be associated with a core data set. In the case of bacterial genomes, existing visualization tools focus on either global properties such as variations in composition or detailed local displays of the features that comprise the annotation. It is not easy to visualize other information in the context of this core information.

Results

A Java based software known as the Genome Display Tool (GDT), allows the user to simultaneously view the distribution of multiple attributes pertaining to genes and intragenic regions in a single bacterial genome using different colours and shapes on a single screen. The display represents each gene by small boxes that correlate with physical position in the genome. The size of the boxes is dynamically allocated based on the number of genes and a zoom feature allows close-up inspection of regions of interest. The display is interfaced with a MS-Access relational database and can display any feature in the database that can be represented by discrete values. Data is readily added to the database from an MS-Excel spread sheet. The functionality of GDT is demonstrated by comparing the results of two predictions of recent horizontal transfer events in the genome of Synechocystis PCC-6803. The resulting display allows the user to immediately see how much agreement exists between the two methods and also visualize how genes in various categories (e.g. predicted in both methods, one method etc) are distributed in the genome.

Conclusion

The GDT software provides the user with a powerful tool that allows development of an intuitive understanding of the relative distribution of features in a large data set. As additional features are added to the data set, the number of possible correlations that can be visualized grows rapidly. Although described here for use in bacterial genomics, the principle is general and similar software might be useful in other contexts such as patient studies.

Inhibition of respiration and nitrate assimilation enhances photohydrogen evolution under low oxygen concentrations in Synechocystis sp. PCC 6803

In cyanobacterial membranes photosynthetic light reaction and respiration are intertwined. It was shown that the single hydrogenase of Synechocystis sp. PCC 6803 is connected to the light reaction. We conducted measurements of hydrogenase activity, fermentative hydrogen evolution and photohydrogen production of deletion mutants of respiratory electron transport complexes. All single, double and triple mutants of the three terminal respiratory oxidases and the ndhB-mutant without a functional complex I were studied. After activating the hydrogenase by applying anaerobic conditions in the dark hydrogen production was measured at the onset of light. Under these conditions respiratory capacity and amount of photohydrogen produced were found to be inversely correlated. Especially the absence of the quinol oxidase induced an increased hydrogenase activity and an increased production of hydrogen in the light compared to wild type cells. Our results support that the hydrogenase as well as the quinol oxidase function as electron valves under low oxygen concentrations. When the activities of photosystem II and I (PSII and PSI) are not in equilibrium or in case that the light reaction is working at a higher pace than the dark reaction, the hydrogenase is necessary to prevent an acceptor side limitation of PSI, and the quinol oxidase to prevent an overreduction of the plastoquinone pool (acceptor side of PSII). Besides oxygen, nitrate assimilation was found to be an important electron sink. Inhibition of nitrate reductase resulted in an increased fermentative hydrogen production as well as higher amounts of photohydrogen.

Role of the GlgX protein in glycogen metabolism of the cyanobacterium, Synechococcus elongatus PCC 7942

The putative glgX gene encoding isoamylase-type debranching enzyme was isolated from the cyanobacterium, Synechococcus elongatus PCC 7942. The deduced amino acid sequence indicated that the residues essential to the catalytic activity and substrate binding in bacterial and plant isoamylases and GlgX proteins were all conserved in the GlgX protein of S. elongatus PCC 7942. The role of GlgX in the cyanobacterium was examined by insertional inactivation of the gene. Disruption of the glgX gene resulted in the enhanced fluctuation of glycogen content in the cells during light-dark cycles of the culture, although the effect was marginal. The glycogen of the glgX mutant was enriched with very short chains with degree of polymerization 2 to 4. When the mutant was transformed with putative glgX genes of Synechocystis sp. PCC 6803, the short chains were decreased as compared to the parental mutant strain. The result indicated that GlgX protein contributes to form the branching pattern of polysaccharide in S. elongatus PCC 7942.

Functional characterization of a NapA Na+/H+antiporter fromThermus thermophilus

Na(+)/H(+) antiporters are ubiquitous membrane proteins and play an important role in cell homeostasis. We amplified a gene encoding a member of the monovalent cation:proton antiporter-2 (CPA2) family (TC 2.A.37) from the Thermus thermophilus genome and expressed it in Escherichia coli. The gene product was identified as a member of the NapA subfamily and was found to be an active Na(+)(Li(+))/H(+) antiporter as it conferred resistance to the Na(+) and Li(+) sensitive strain E. coli EP432 (DeltanhaA, DeltanhaB) upon exposure to high concentration of these salts in the growth medium. Fluorescence measurements using the pH sensitive dye 9-amino-6-chloro-2-methoxyacridine in everted membrane vesicles of complemented E. coli EP432 showed high Li(+)/H(+) exchange activity at pH 6, but marginal Na(+)/H(+) antiport activity. Towards more alkaline conditions, Na(+)/H(+) exchange activity increased to a relative maximum at pH 8, where by contrast the Li(+)/H(+) exchange activity reached its relative minimum. Substitution of conserved residues D156 and D157 (located in the putative transmembrane helix 6) with Ala resulted in the complete loss of Na(+)/H(+) activity. Mutation of K305 (putative transmembrane helix 10) to Ala resulted in a compromised phenotype characterized by an increase in apparent K(m) for Na(+) (36 vs. 7.6 mM for the wildtype) and Li(+) (17 vs. 0.22 mM), In summary, the Na(+)/H(+) antiport activity profile of the NapA type transporter of T. thermophilus resembles that of NhaA from E. coli, whereas in contrast to NhaA the T. thermophilus NapA antiporter is characterized by high Li(+)/H(+) antiport activity at acidic pH.

Knock-out of the plastid-encoded PetL subunit results in reduced stability and accelerated leaf age-dependent loss of the cytochrome b6f complex

The cytochrome-b6f complex, a key component of the photosynthetic electron transport chain, contains a number of very small protein subunits whose functions are not well defined. Here we have investigated the function of the 31-amino acid PetL subunit encoded in the chloroplast genome in all higher plants. Chloroplast-transformed petL knock-out tobacco plants display no obvious phenotype, suggesting that PetL is not essential for cytochrome b6f complex biogenesis and function (Fiebig, A., Stegemann, S., and Bock, R. (2004) Nucleic Acids Res. 32, 3615-3622). We show here that, whereas young mutant leaves accumulate comparable amounts of cytochrome b6f complex and have an identical assimilation capacity as wild type leaves, both cytochrome b6f complex contents and assimilation capacities of mature and old leaves are strongly reduced in the mutant, indicating that the cytochrome b6f complex is less stable than in the wild type. Reduced complex stability was also confirmed by in vitro treatments of isolated thylakoids with chaotropic reagents. Adaptive responses observed in the knockout mutants, such as delayed down-regulation of plastocyanin contents, indicate that plants can sense the restricted electron flux to photosystem I yet cannot compensate the reduced stability of the cytochrome b6f complex by adaptive up-regulation of complex synthesis. We propose that efficient cytochrome b6f complex biogenesis occurs only in young leaves and that the capacity for de novo synthesis of the complex is very low in mature and aging leaves. Gene expression analysis indicates that the ontogenetic down-regulation of cytochrome b6f complex biogenesis occurs at the post-transcriptional level.

Identification of novel targets of cyanobacterial glutaredoxin

Glutaredoxins (Grxs) are small ubiquitous glutathione-disulfide oxidoreductase that reduce disulfide bonds of target proteins and maintain the redox homoeostasis of cells. Disruption of ssr2061 reduced the viability of cells indicated Grx2061 has a protective role against oxidative stress in Synechocystis sp. PCC 6803. To understand the function of Grx2061 in cyanobacteria and its difference from plant, Grx targets were retained specifically on an affinity media coupled with a mutated monocysteinic Grx and identified by mass spectra. Among 42 identified targets, 26 of them are novel ones compared with those known in higher plants. These proteins are supposed to be involved in 12 cellular processes including oxidative stress response, Calvin cycle, protein synthesis, and etc. Biochemical tests highlighted four of them which showed a Grx-dependent activation of peroxiredoxin and deactivation of catalase. Oxidized Grx2061 could keep redox equilibrium with another probable Grx and be reduced by thioredoxin reductase, indicating that Grx2061 can accept electrons from either glutathione or thioredoxin reductase. Our studies suggest Grx2061 in cyanobacteria plays an important role in redox network and its targets are as extensive as that in other organisms.

Group 3 sigma factors in the marine cyanobacterium Synechococcus sp. strain PCC 7002 are required for growth at low temperature

Three genes, sigF, sigG and sigH, encoding group 3 sigma factors have been cloned and characterized in the marine cyanobacterium Synechococcus sp. strain PCC 7002. The sigF gene product was similar to sigma factors involved in general stress response and sporulation in other organisms, and the sigG and sigH gene products were similar to extracytoplasmic function (ECF) sigma factors. The sigG and sigH genes were associated with the putative regulatory genes and the sizes of transcripts for sigG and sigH genes were large enough to be cotranscribed with the associated downstream genes. The sigG downstream gene was designated sapG (sigG-associated protein), and yeast two-hybrid analysis demonstrated that SigG and SapG interact when produced in yeast cells. Null mutants of these three group 3 sigma factor genes were created by interposon mutagenesis. The growth of the sigF mutant strain was much slower than the wild-type strain at 15 degrees C, although the growth rates at 22 degrees C and 38 degrees C were identical to those of the wild-type strain. The sigG mutant could not grow continuously at 22 degrees C, and no growth occurred at 15 degrees C. Since SigG and SapG interact in yeast cells and the sigG and sapG mutants showed a similar growth phenotype, SapG is likely to be a regulatory protein for SigG involved in the same pathway in transcriptional regulation in this cyanobacterium.

A membrane-bound FtsH protease is involved in osmoregulation in Synechocystis sp. PCC 6803: the compatible solute synthesizing enzyme GgpS is one of the targets for proteolysis

Protein quality control and proteolysis are involved in cell maintenance and environmental acclimatization in bacteria and eukaryotes. The AAA protease FtsH2 of the cyanobacterium Synechocystis sp. PCC 6803 was identified during a screening for mutants impaired in osmoregulation. The ftsH2(-) mutant was salt sensitive because of a decreased level of the osmoprotectant glucosylglycerol (GG). In spite of wild type-like transcription of the ggpS gene in ftsH2(-) cells the GgpS protein content increased but only low levels of GgpS activity were observed. Consequently, salt tolerance of the ftsH2(-) mutant decreased while addition of external osmolyte complemented the salt sensitivity. The proteolytic degradation of the GgpS protein by FtsH2 was demonstrated by an in vitro assay using inverted membrane vesicles. The GgpS is part of a GG synthesizing complex, because yeast two-hybrid screens identified a close interaction with the GG-phosphate phosphatase. Besides GgpS as the first soluble substrate of a cyanobacterial FtsH protease, several other putative targets were identified by a proteomic approach. We present a novel molecular explanation for the salt-sensitive phenotype of bacterial ftsH(-) mutants as the result of accumulation of inactive enzymes for compatible solute synthesis, in this case GgpS the key enzyme of GG synthesis.