Cyanobacterial hydrogenases: diversity, regulation and applications

Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria

Background

The validity and reproducibility of gene expression studies depend on the quality of extracted RNA and the degree of genomic DNA contamination. Cyanobacteria are gram-negative prokaryotes that synthesize chlorophyll a and carry out photosynthetic water oxidation. These organisms possess an extended array of secondary metabolites that impair cell lysis, presenting particular challenges when it comes to nucleic acid isolation. Therefore, we used the NHM5 strain of Nostoc punctiforme ATCC 29133 to compare and improve existing phenol based chemistry and procedures for RNA extraction.

Results

With this work we identify and explore strategies for improved and lower cost high quality RNA isolation from cyanobacteria. All the methods studied are suitable for RNA isolation and its use for downstream applications. We analyse different Trizol based protocols, introduce procedural changes and describe an alternative RNA extraction solution.

Conclusion

It was possible to improve purity of isolated RNA by modifying protocol procedures. Further improvements, both in RNA purity and experimental cost, were achieved by using a new extraction solution, PGTX.

THE RELATION BETWEEN N2 FIXATION AND H2 METABOLISM IN THE MARINE FILAMENTOUS NONHETEROCYSTOUS CYANOBACTERIUM LYNGBYA AESTUARII CCY 9616(1)

The marine filamentous nonheterocystous nitrogen-fixing cyanobacterium Lyngbya aestuarii (F. K. Mert.) Liebman ex Gomont CCY 9616 was grown under diazotrophic and nondiazotrophic conditions and under an alternating 16:8 light:dark (L:D) regime. Nitrogenase activity appeared just before the onset of the dark period, reaching its maximum 1-2 h in the dark, subsequently decreasing to zero at the beginning of the following light period. Nitrogenase activity was only detected at low levels of O2 (5%) and when the culture was grown in the absence of combined nitrogen. Quantitative reverse transcriptase-PCR (RT-PCR) analysis of one of the structural genes encoding nitrogenase, nifK, showed that the highest levels of transcription preceded the maximum activity of nitrogenase by 2-4 h. nifK transcription was not completely abolished during the remaining time of the 24 h cycle. Even in the presence of nitrate, when nitrogenase activity was undetectable, nifK was still transcribed. The H2 -uptake activity seemed to follow the nitrogenase, but the transcription of hupL (gene encoding the large subunit of uptake hydrogenase) preceded the nifK transcription. However, H2 -uptake and hupL transcription occurred throughout the 24 h cycle as well as under nondiazotrophic conditions, albeit at much lower levels. The hoxH transcript levels (a structural gene coding for the bidirectional hydrogenase) were similar under diazotrophic or nondiazotrophic conditions but slightly higher during the dark period. All three enzymes investigated are involved in H2 metabolism. It is concluded that the uptake hydrogenase is mainly responsible for H2 uptake. Nevertheless, uptake hydrogenase and nitrogenase do not seem to be coregulated.

Energy biotechnology with cyanobacteria

The world's future energy demand calls for a sustainable alternative for the use of fossil fuels, to restrict further global warming. Harvesting solar energy via photosynthesis is one of Nature's remarkable achievements. Existing technologies exploit this process for energy 'production' via processing of, for example, part of plant biomass into ethanol, and of algal biomass into biodiesel. Fortifying photosynthetic organisms with the ability to produce biofuels directly would bypass the need to synthesize all the complex chemicals of 'biomass'. A promising way to achieve this is to redirect cyanobacterial intermediary metabolism by channeling (Calvin cycle) intermediates into fermentative metabolic pathways. This review describes this approach via the biosynthesis of fermentation end products, like alcohols and hydrogen, driven by solar energy, from water (and CO2).

TRANSCRIPTIONAL ANALYSIS OF THE UNICELLULAR, DIAZOTROPHIC CYANOBACTERIUM CYANOTHECE SP. ATCC 51142 GROWN UNDER SHORT DAY/NIGHT CYCLES(1)

Cyanothece sp. strain ATCC 51142 is a unicellular, diazotrophic cyanobacterium that demonstrates extensive metabolic periodicities of photosynthesis, respiration, and nitrogen fixation when grown under N2 -fixing conditions. We have performed a global transcription analysis of this organism using 6 h light:dark (L:D) cycles in order to determine the response of the cell to these conditions and to differentiate between diurnal and circadian-regulated genes. In addition, we used a context-likelihood of relatedness (CLR) analysis with these data and those from 2 d L:D and L:D plus continuous light experiments to better differentiate between diurnal and circadian-regulated genes. Cyanothece sp. acclimated in several ways to growth under short L:D conditions. Nitrogen was fixed in every second dark period and only once in each 24 h period. Nitrogen fixation was strongly correlated to the energy status of the cells and glycogen breakdown, and high respiration rates were necessary to provide appropriate energy and anoxic conditions for this process. We conclude that glycogen breakdown is a key regulatory step within these complex processes. Our results demonstrated that the main metabolic genes involved in photosynthesis, respiration, nitrogen fixation, and central carbohydrate metabolism have strong (or total) circadian-regulated components. The short L:D cycles enable us to identify transcriptional differences among the family of psbA genes, as well as the differing patterns of the hup genes, which follow the same pattern as nitrogenase genes, relative to the hox genes, which displayed a diurnal, dark-dependent gene expression.

Effect of continuous light on diurnal rhythms in Cyanothece sp. ATCC 51142

Background

Life on earth is strongly affected by alternating day and night cycles. Accordingly, many organisms have evolved an internal timekeeping system with a period of approximately 24 hours. Cyanobacteria are the only known prokaryotes with robust rhythms under control of a central clock. Numerous studies have been conducted to elucidate components of the circadian clock and to identify circadian-controlled genes. However, the complex interactions between endogenous circadian rhythms and external cues are currently not well understood, and a direct and mathematical based comparison between light-mediated and circadian-controlled gene expression is still outstanding. Therefore, we combined and analyzed data from two independent microarray experiments, previously performed under alternating light-dark and continuous light conditions in Cyanothece sp. ATCC 51142, and sought to classify light responsive and circadian controlled genes.

Results

Fourier Score-based methods together with random permutations and False Discovery Rates were used to identify genes with oscillatory expression patterns, and an angular distance based criterion was applied to recognize transient behaviors in gene expression under constant light conditions. Compared to previously reported mathematical approaches, the combination of these methods also facilitated the detection of modified amplitudes and phase-shifts of gene expression. Our analysis showed that the majority of diurnally regulated genes, essentially those genes that are maximally expressed during the middle of the light and dark period, are in fact light responsive. In contrast, most of the circadian controlled genes are up-regulated during the beginning of the dark or subjective dark, and are greatly enriched for genes associated with energy metabolism. Many of the circadian controlled and light responsive genes are found in gene clusters within the Cyanothece sp. ATCC 51142 genome. Interestingly, in addition to cyclic expression patterns with a period of 24 hours, we also found several genes that oscillate with an ultradian period of 12 hours, a novel finding among cyanobacteria.

Conclusion

We demonstrate that a combination of different analytical methods significantly improved the identification of cyclic and transient gene expression in Cyanothece sp. ATCC 51142. Our analyses provide an adaptable and novel analytical tool to study gene expression in a variety of organisms with diurnal, circadian and ultradian behavior.

Survey of the distribution of different types of nitrogenases and hydrogenases in heterocyst-forming cyanobacteria

As a first step toward developing the methodology for screening large numbers of heterocyst-forming freshwater cyanobacteria strains for the presence of various types of nitrogenases and hydrogenases, we surveyed the distribution of these genes and their activities in 14 strains from culture collections. The nitrogenase genes include nif1 encoding a Mo-type nitrogenase expressed in heterocysts, nif2 expressed in vegetative cells and heterocysts under anaerobic conditions, and vnf encoding a V-type nitrogenase expressed in heterocysts. Two methods proved to be valuable in surveying the distribution of nitrogenase types. The first method was Southern blot hybridization of DNA digested with two different endonucleases and hybridized with nifD1, nifD2, and vnfD probes. The second method was ethane formation from acetylene to detect the presence of active V-nitrogenase. We found that all 14 strains have nifD1 genes, and eight strains also have nifD2 genes. Four of the strains have vnfD genes, in addition to nifD2 genes. It is curious that three of these four strains had similar hybridization patterns with all of the nifD1, nifD2, and vnfD probes, suggesting that there could be some bias in strains used in the present study or in strains held in culture collections. This point will need to be assessed in the future. For surveying the distribution of hydrogenases, Southern blot hybridization was an effective method. All strains surveyed had hup genes, with the majority of them also having hox genes.

Transcription profiles of hydrogenases related genes in the cyanobacterium Lyngbya majuscula CCAP 1446/4

BACKGROUND

Lyngbya majuscula CCAP 1446/4 is a N2-fixing filamentous nonheterocystous strain that contains two NiFe-hydrogenases: an uptake (encoded by hupSL) and a bidirectional enzyme (encoded by hoxEFUYH). The biosynthesis/maturation of NiFe-hydrogenases is a complex process requiring several accessory proteins for e.g. for the incorporation of metals and ligands in the active center (large subunit), and the insertion of the FeS clusters (small subunit). The last step in the maturation of the large subunit is the cleavage of a C-terminal peptide from its precursor by a specific endopeptidase. Subsequently, the mature large and small subunits can assemble forming a functional enzyme.

RESULTS

In this work we demonstrated that, in L. majuscula, the structural genes encoding the bidirectional hydrogenase are cotranscribed, and that hoxW (the gene encoding its putative specific endopeptidase) is in the same chromosomal region but transcribed from a different promoter. The gene encoding the putative specific uptake hydrogenase endopeptidase, hupW, can be cotranscribed with the structural genes but it has its own promoter. hoxH, hupL, hoxW and hupW transcription was followed in L. majuscula cells grown under N2-fixing and non-N2-fixing conditions over a 12 h light/12 h dark cycle. The transcription of hoxH, hoxW and hupW did not vary remarkably in the conditions tested, while the hupL transcript levels are significantly higher under N2-fixing conditions with a peak occurring in the transition between the light and the dark phase. Furthermore, the putative endopeptidases transcript levels, in particular hoxW, are lower than those of the respective hydrogenase structural genes.

CONCLUSION

The data presented here indicate that in L. majuscula the genes encoding the putative hydrogenases specific endopeptidases, hoxW and hupW, are transcribed from their own promoters. Their transcript levels do not vary notably in the conditions tested, suggesting that HoxW and HupW are probably constantly present and available in the cells. These results, together with the fact that the putative endopeptidases transcript levels, in particular for hoxW, are lower than those of the structural genes, imply that the activity of the hydrogenases is mainly correlated to the transcription levels of the structural genes. The analysis of the promoter regions indicates that hupL and hupW might be under the control of different transcription factor(s), while both hoxH and xisH (hoxW) promoters could be under the control of LexA.

Immunolocalization of the uptake hydrogenase in the marine cyanobacterium Lyngbya majuscula CCAP 1446/4 and two Nostoc strains

In N(2)-fixing cyanobacteria, the reduction of N(2) to NH(3) is coupled with the production of molecular hydrogen, which is rapidly consumed by an uptake hydrogenase, an enzyme that is present in almost all diazotrophic cyanobacteria. The cellular and subcellular localization of the cyanobacterial uptake hydrogenase remains uncertain, and it is definitely strain dependent. Previous studies focused mainly on heterocystous cyanobacteria and used heterologous antisera. The present work represents the first effort to establish the subcellular localization of the uptake hydrogenase in a N(2)-fixing filamentous nonheterocystous cyanobacterium, Lyngbya majuscula CCAP 1446/4, using the first antiserum produced against a cyanobacterial uptake hydrogenase. The data obtained revealed higher specific labelling associated with the thylakoid membranes of L. majuscula, reinforcing the idea that the cyanobacterial uptake hydrogenase is indeed a membrane-bound protein. For comparative purposes, the localization of the uptake hydrogenase was also investigated in two distinct heterocystous cyanobacterial strains, and while in Nostoc sp. PCC 7120 the labelling was only observed in the heterocysts, in Nostoc punctiforme, the presence of uptake hydrogenase antigens was detected in both the vegetative cells and heterocysts, corresponding most probably to an inactive and an active form of the enzyme.

Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120

BACKGROUND

The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively.

RESULTS

In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW) and LexA (hoxW). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase.

CONCLUSION

Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co-evolution could be the result of a close interaction between the protease and the large subunit of the [NiFe]-hydrogenases, a theory supported by protein-protein docking experiments performed with 3D-models. Finally we present data that may explain the specificity seen among hydrogenase specific proteases, the so called "HOXBOX"; an amino acid sequence specific for proteases of Hox-type. This opens the door for more detailed studies of the specificity found among hydrogenase specific proteases and the structural properties behind it.

Characterization of the hupSL promoter activity in Nostoc punctiforme ATCC 29133

Background

In cyanobacteria three enzymes are directly involved in the hydrogen metabolism; a nitrogenase that produces molecular hydrogen, H₂, as a by-product of nitrogen fixation, an uptake hydrogenase that recaptures H₂ and oxidize it, and a bidirectional hydrogenase that can both oxidize and produce H₂.Nostoc punctiforme ATCC 29133 is a filamentous dinitrogen fixing cyanobacterium containing a nitrogenase and an uptake hydrogenase but no bidirectional hydrogenase. Generally, little is known about the transcriptional regulation of the cyanobacterial uptake hydrogenases. In this study gel shift assays showed that NtcA has a specific affinity to a region of the hupSL promoter containing a predicted NtcA binding site. The predicted NtcA binding site is centred at 258.5 bp upstream the transcription start point (tsp). To further investigate the hupSL promoter, truncated versions of the hupSL promoter were fused to either gfp or luxAB, encoding the reporter proteins Green Fluorescent Protein and Luciferase, respectively.

Results

Interestingly, all hupsSL promoter deletion constructs showed heterocyst specific expression. Unexpectedly the shortest promoter fragment, a fragment covering 57 bp upstream and 258 bp downstream the tsp, exhibited the highest promoter activity. Deletion of the NtcA binding site neither affected the expression to any larger extent nor the heterocyst specificity.

Conclusion

Obtained data suggest that the hupSL promoter in N. punctiforme is not strictly dependent on the upstream NtcA cis element and that the shortest promoter fragment (-57 to tsp) is enough for a high and heterocyst specific expression of hupSL. This is highly interesting because it indicates that the information that determines heterocyst specific gene expression might be confined to this short sequence or in the downstream untranslated leader sequence.

Quantitative overview of N2 fixation in Nostoc punctiforme ATCC 29133 through cellular enrichments and iTRAQ shotgun proteomics

Nostoc punctiforme ATCC 29133 is a photoautotrophic cyanobacterium with the capacity to fix atmospheric N 2. Its ability to mediate this process is similar to that described for Nostoc sp. PCC 7120, where vegetative cells differentiate into heterocysts. Quantitative proteomic investigations at both the filament level and the heterocyst level are presented using isobaric tagging technology (iTRAQ), with 721 proteins at the 95% confidence interval quantified across both studies. Observations from both experiments yielded findings confirmatory of both transcriptional studies, and published Nostoc sp. PCC 7120 iTRAQ data. N. punctiforme exhibits similar metabolic trends, though changes in a number of metabolic pathways are less pronounced than in Nostoc sp. PCC 7120. Results also suggest a number of proteins that may benefit from future investigations. These include ATP dependent Zn-proteases, N-reserve degraders and also redox balance proteins. Complementary proteomic data sets from both organisms present key precursor knowledge that is important for future cyanobacterial biohydrogen research.

Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120

BACKGROUND

The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120.

RESULTS

RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome.

CONCLUSION

This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme.

Transcription of hupSL in Anabaena variabilis ATCC 29413 is regulated by NtcA and not by hydrogen

Nitrogen-fixing cyanobacteria such as Anabaena variabilis ATCC 29413 use an uptake hydrogenase, encoded by hupSL, to recycle hydrogen gas that is produced as an obligate by-product of nitrogen fixation. The regulation of hupSL in A. variabilis is likely to differ from that of the closely related Anabaena sp. strain PCC 7120 because A. variabilis lacks the excision element-mediated regulation that characterizes hupSL regulation in strain PCC 7120. An analysis of the hupSL transcript in a nitrogenase mutant of A. variabilis that does not produce any detectable hydrogen indicated that neither nitrogen fixation nor hydrogen gas was required for the induction of hupSL. Furthermore, exogenous addition of hydrogen gas did not stimulate hupSL transcription. Transcriptional reporter constructs indicated that the accumulation of hupSL transcript after nitrogen step-down was restricted primarily to the microaerobic heterocysts. Anoxic conditions were not sufficient to induce hupSL transcription. The induction of hupSL after nitrogen step-down was reduced in a mutant in the global nitrogen regulator NtcA, but was not reduced in a mutant unable to form heterocysts. A consensus NtcA-binding site was identified upstream of hupSL, and NtcA was found to bind to this region. Thus, while neither hydrogen gas nor anoxia controlled the expression of hupSL, its expression was controlled by NtcA. Heterocyst differentiation was not required for hupSL induction in response to nitrogen step-down, but heterocyst-localized cues may add an additional level of regulation to hupSL.

An AbrB-Like protein regulates the expression of the bidirectional hydrogenase in Synechocystis sp. strain PCC 6803

In the unicellular cyanobacterium Synechocystis sp. strain PCC 6803, the pentameric bidirectional Ni-Fe hydrogenase (HoxEFUYH) is the sole enzyme involved in hydrogen metabolism. Recent investigations implicated the transcription factor LexA in the regulation of the hox genes in this cyanobacterium, suggesting the factor to work as an activator. In this work, we show evidence that LexA cannot account exclusively for the regulation of the hox genes in this cyanobacterium. Therefore, we investigated which additional transcription factors interact in and may regulate the expression of the hox genes in Synechocystis sp. strain PCC 6803. By using DNA affinity assays, a transcription factor with similarity to the transition state regulator AbrB from Bacillus subtilis was isolated. Electrophoretic mobility shift assays showed that the AbrB-like protein specifically interacts with the promoter region of the hox genes as well as with its own promoter region. In addition, results obtained with two genetically modified strains of Synechocystis sp. strain PCC 6803, one with a not fully segregated inactivation mutation of the abrB-like gene and the other overexpressing the same abrB-like gene, suggest that this transcription factor functions as a regulator of hox gene expression.