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Comparative Physiology and Genomics of Hydrogen-Producing Vibrios

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Abstract

The Hyf-type formate hydrogen lyase (FHL) complex was first proposed based on sequence comparisons in Escherichia coli in 1997 (Andrews et al. in Microbiology 143:3633–3647, 1997). The hydrogenase in the Hyf-type FHL was estimated to be a proton-translocating energy-conserving [NiFe]-hydrogenase. Although the structure of FHL is similar to that of complex I, silent gene expression in E. coli has caused delays in unveiling the genetic and biochemical features of the FHL. The entire set of genes required for Hyf-type FHL synthesis has also been found in the genome sequences of Vibrio tritonius in 2015 (Matsumura et al. in Int J Hydrog Energy 40:9137–9146, 2015), which produces more hydrogen (H2) than E. coli. Here we investigate the physiological characteristics, genome comparisons, and gene expressions to elucidate the genetic backgrounds of Hyf-type FHL, and how Hyf-type FHL correlates with the higher H2 production of V. tritonius. Physiological comparisons among the seven H2-producing vibrios reveal that V. porteresiae and V. tritonius, grouped in the Porteresiae clade, show greater capacity for H2 production than the other species. The structures of FHL-Hyp gene clusters were closely related in both Porteresiae species, but differed from those of the other species with the presence of hupE, a possible nickel permease gene. Interestingly, deeper genome comparisons revealed the co-presence of nickel ABC transporter genes (nik) with the Hyf-type FHL gene only on the genome of the Porteresiae clade species. Therefore, active primary Ni transport might be one of the key factors characterizing higher H2 production in V. tritonius. Furthermore, the expression of FHL gene cluster was significantly up-regulated in V. tritonius cells stimulated with formate, indicating that formate is likely to be a control factor for the gene expression of V. tritonius FHL in a similar way to the formate regulon encoding the E. coli FHL.

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Data Availability

RNA-Seq reads were deposited DBJ/GenBank/ENA under accession number DRA014595.

Code Availability

Not applicable.

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Acknowledgements

We would like to thank Professor Suzuki (The Tokyo University), and Mr. Mizukoshi (Hokkaido University) for technical supports.

Funding

This work was supported by the MEXT Kaken 25292122, 16H04976, and 19H03041.

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  1. Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan

    Yuta Matsumura, Kazumich Sato, Chunqi Jiang, Sayaka Mino & Tomoo Swabe

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Conceptualization: TS; Research and Data analysis: YM, KS, and TS; Writing—original draft preparation: YM, KS, and TS; Writing—review and editing: YM, KS, JC, SM, and TS; Resources: TS. All authors contributed to the article and approved the submitted version.

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Correspondence to Tomoo Swabe.

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284_2022_3065_MOESM1_ESM.pptx

Supplementary file1 (PPTX 899 kb) Fig. S1. Codon usage of CDSs on FHL-Hyp gene cluster and on chromosome 1 in Vibrio tritonius. All codon including stop codon was shown. The values indicated abundance ratio of each codon. Fig. S2. Schematic of nikABCDE and nikR genes on genomes. The genes responsible for synthesis nickel ABC transporter in genomes of E. coli, V. tritonius, V. porteresiae, and V. aerogenes are shown. Fig. S3. Effect of extracellular formate on H2 production of Vibrio tritonius. (A) Kinetic formate consumption for 96 h of V. tritonius is shown. Error bars represent standard error (N = 3). H2 (B) Kinetic H2 production derived from extracellular formate for 96 h of V. tritonius was shown. Error bars represent standard error (N = 3). Fig. S4. Coverage of RNA-Seq reads mapping to FHL-Hyp gene cluster in Vibrio tritonius. Arrows indicate the predicted discontinuity sites of transcripts of FHL-Hyp gene cluster. Fig. S5. Schematic of nif gene cluster in Vibrio tritonius, Vibrio porteresiae, and Vibrio aerogenes genomes. Table S1. Summary of the genome sequences of seven hydrogen-producing vibrios. Table S2. Genes showing differential expression by mannitol supplementation. Table S3. Genes showing differential expression by formate supplementation.

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Matsumura, Y., Sato, K., Jiang, C. et al. Comparative Physiology and Genomics of Hydrogen-Producing Vibrios. Curr Microbiol 79, 360 (2022). https://doi.org/10.1007/s00284-022-03065-3

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