Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009

Abstract

BackgroundMolecular hydrogen, given its pollution-free combustion, has great potential to replace fossil fuels in future transportation and energy production. However, current industrial hydrogen production processes, such as steam reforming of methane, contribute significantly to the greenhouse effect. Therefore alternative methods, in particular the use of fermentative microorganisms, have attracted scientific interest in recent years. However the low overall yield obtained is a major challenge in biological H2 production. Thus, a thorough and detailed understanding of the relationships between genome content, gene expression patterns, pathway utilisation and metabolite synthesis is required to optimise the yield of biohydrogen production pathways.ResultsIn this study transcriptomic and proteomic analyses of the hydrogen-producing bacterium Clostridium butyricum CWBI 1009 were carried out to provide a biomolecular overview of the changes that occur when the metabolism shifts to H2 production. The growth, H2-production, and glucose-fermentation profiles were monitored in 20 L batch bioreactors under unregulated-pH and fixed-pH conditions (pH 7.3 and 5.2). Conspicuous differences were observed in the bioreactor performances and cellular metabolisms for all the tested metabolites, and they were pH dependent. During unregulated-pH glucose fermentation increased H2 production was associated with concurrent strong up-regulation of the nitrogenase coding genes. However, no such concurrent up-regulation of the [FeFe] hydrogenase genes was observed. During the fixed pH 5.2 fermentation, by contrast, the expression levels for the [FeFe] hydrogenase coding genes were higher than during the unregulated-pH fermentation, while the nitrogenase transcripts were less abundant. The overall results suggest, for the first time, that environmental factors may determine whether H2 production in C. butyricum CWBI 1009 is mediated by the hydrogenases and/or the nitrogenase.ConclusionsThis work, contributing to the field of dark fermentative hydrogen production, provides a multidisciplinary approach for the investigation of the processes involved in the molecular H2 metabolism of clostridia. In addition, it lays the groundwork for further optimisation of biohydrogen production pathways based on genetic engineering techniques.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0203-5) contains supplementary material, which is available to authorized users.

Biotechnological and bioinformatics approaches for augmentation of biohydrogen production: A review

“…The novel transcriptomic analysis technique on C. moewusii was reported to be the first to be applied to a potential H 2 producing green alga [77]. In an another study, transcriptomic, metabolite and proteomic analyses were carried out in the H 2 -producing bacterium Clostridium butyricum to investigate the changes at the molecular level that occur when the metabolism shifts to H 2 production [78].…”

Effect of the nitrogen source on the hydrogen production metabolism and hydrogenases of Clostridium butyricum CWBI1009

“…RNA was extracted using a RiboPure TM -Bacteria (Ambion) and cDNA was prepared as described in the Reverse Transcription System manual (Promega); as previously described [19]. Specific primers and probes for the 4 [FeFe]hydrogenases of Clostridium butyricum CWBI1009, i.e.…”

“…Hydrogen is produced via pyruvate-ferredoxin oxidoreductase (PFOR) and, at a lower extent, via NADH-ferredoxin oxidoreductase (NFOR) [18,19]. Both enzymatic complexes transfer electrons to [FeFe]-hydrogenases which generate hydrogen by a reversible reduction of protons accumulated during fermentation.…”

“…However, little is known about the physiological and biochemical properties of clostridial [FeFe]-hydrogenases and their role in the hydrogen metabolism [19,20] since most of the investigations focussed on the commonly known CpI (HydA) from Clostridium pasteurianum [21]. Clostridium butyricum CWBI1009 possesses four different [FeFe]-hydrogenases, three of which (hydA2, hydB2, hydB3) are monomeric intracellular enzymes and one (hydA8) is associated with the heterotrimeric hydrogenase cluster [19,20].…”

“…In addition, particularly relevant conditions were selected for amino acid fingerprinting (HPLC-UV) and expression pattern analysis (RT-qPCR) of the four [FeFe]-hydrogenase genes using specifically designed primers [22,23]. The same was done for the nitrogenase gene since its role in hydrogen production by Clostridium butyricum CWBI1009 appears to depend on the environmental conditions [19].…”