Genome-based metabolic and phylogenomic analysis of three Terrisporobacter species.

Acetogenic bacteria are of high interest for biotechnological applications as industrial platform organisms, however, acetogenic strains from the genus Terrisporobacter have hitherto been neglected. To date, three published type strains of the genus Terrisporobacter are only covered by draft genome sequences, and the genes and pathway responsible for acetogenesis have not been analyzed. Here, we report complete genome sequences of the bacterial type strains Terrisporobacter petrolearius JCM 19845T, Terrisporobacter mayombei DSM 6539T and Terrisporobacter glycolicus DSM 1288T. Functional annotation, KEGG pathway module reconstructions and screening for virulence factors were performed. Various species-specific vitamin, cofactor and amino acid auxotrophies were identified and a model for acetogenesis of Terrisporobacter was constructed. The complete genomes harbored a gene cluster for the reductive proline-dependent branch of the Stickland reaction located on an approximately 21 kb plasmid, which is exclusively found in the Terrisporobacter genus. Phylogenomic analysis of available Terrisporobacter genomes suggested a reclassification of most isolates as T. glycolicus into T. petrolearius

Virulence factor screen for three <i>Terrisporobacter</i> type strains with VFanalyzer using the VFDB.

Virulence factor screen for three Terrisporobacter type strains with VFanalyzer using the VFDB.</p

Functional annotation of genes from the <i>Terrisporobacter</i> type strain genomes into KEGG categories.

The y-axis shows the different functional KEGG categories and the x-axis the number of genes assigned to each category by BlastKOALA. The bar color indicates the number of genes assigned for the three Terrisporobacter type strains T. mayombei (green), T. petrolearius (blue) and T. glycolicus (red).</p

Reconstruction of the Wood-Ljungdahl pathway in <i>Terrisporobacter</i>.

A: Genome-based reconstruction of the Wood-Ljungdahl pathway for the three type strains of the Terrisporobacter genus. Genome locus tags (black) of the catalyzing enzymes (red) and the required genes (blue) are shown for the three type strains of the Terrisporobacter genus (TEMA, T. mayombei DSM 6539T; TEPE, T. petrolearius JCM 19845T; TEGL, T. glycolicus DSM 1288T). B: Genomic organization of the HDCR-complex gene cluster in the three Terrisporobacter type strains in comparison to the type strain of C. difficile DSM 1269T. The following gene abbreviations were used: fdhF, formate dehydrogenase H; hyfA, hydrogenase-4 component A; hndD, NADP-reducing hydrogenase; focA, putative formate transporter; fdhD, sulfur carrier protein. C: Genomic organization of the Wood-Ljungdahl gene cluster in the three Terrisporobacter type strains in comparison to the type strain of C. difficile DSM 1269T. The following gene abbreviations were used: acsA, anaerobic carbon-monoxide dehydrogenase catalytic subunit; acsF, carbon monoxide dehydrogenase accessory protein; fhs, formyl THF synthetase; fchA, methenyl THF cyclohydrolase; folD, bifunctional cyclohydrolase/dehydrogenase; metV, methylene THF reductase C-terminal catalytic subunit; metF, methylene THF reductase large subunit; lpdA, dihydrolipoyl dehydrogenase; cooC, carbon monoxide dehydrogenase accessory protein; acsD, CoFeSP small subunit; acsC, CoFeSP large subunit; acsE, methyl THF CoFeSP methyltransferase; acsB, carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta; gcvH, glycine cleavage system H protein; acsV, corrinoid activation/regeneration protein. The following enzyme abbreviations were used: HDCR, hydrogen-dependent CO2 reductase; FTS, formyl-THF synthetase; MTC, methenyl-THF cyclohydrolase; MTD, methylene-THF dehydrogenase; MTR, methylene-THF reductase; MT, methyl-transferase; CODH, carbon monoxide dehydrogenase; ACS, acetyl-CoA synthetase; PTA, phosphotransacetylase, ACK, acetate kinase. The legend for size and sequence identity of translated genes are shown at the bottom of B and C in kilobases (kb) and from 0% (white) to 100% (black).</p

Phylogenomic analysis of <i>Terrisporobacter</i> genome sequences.

The legend for sequence identities is shown in the top left corner. Sequence identities higher than 95% are shown in red, while lower values are colored grey to blue. The three type strains of the genomes sequenced from the Terrisporobacter genus in this study are highlighted in green. Genome sequences derived from metagenomic assemblies are indicated by MAG in parentheses.</p

Distribution of IS elements and classification into IS families.

The y-axis shows the different IS families and the x-axis the number of IS elements assigned to each IS family by ISESCAN. The bar color indicates the number of genes assigned for the three Terrisporobacter type strains T. mayombei (green), T. petrolearius (blue) and T. glycolicus (red).</p

Completeness of KEGG pathway modules for KEGG categories.

The completeness of KEGG modules is given in percentage from the total amount of required blocks and the amount of detected blocks in a pathway module for the three Terrisporobacter type strains T. mayombei (1), T. petrolearius (2) and T. glycolicus (3). For metabolites with multiple KEGG modules only the most complete modules detected are shown. The legend for the color gradient is shown in the bottom right.</p

Comparison of the circular plasmids in the three <i>Terrisporobacter</i> type strains.

The plasmids encode a proline-dependent gene cluster for the reductive branch of the Stickland reaction. The legend for the size and the sequence identity of translated genes is shown at the bottom in kilobases (kb) and from 0% (white) to 100% (black). The following genes are encoded: selC, tRNA-Sec; prdD, proline reductase cluster protein PrdD; prdE; proline reductase cluster protein PrdE; csd, putative cysteine desulfurase; lysR, lysR family transcriptional regulator; selB, selenocysteine-specific elongation factor; selA, L-seryl-tRNA (Sec) selenium transferase; selD, selenide water dikinase; parA, parA family protein; hin, DNA-invertase; csp, cold shock protein; parB, DNA primase; prdB, D-proline reductase subunit gamma; prdA, D-proline reductase proprotein PrdA; prdC, proline reductase-associated electron transfer protein; hyp, hypothetical protein.</p