Draft Genome Sequence of Cytophaga fermentans JCM 21142
 T
 , a Facultative Anaerobe Isolated from Marine Mud

Starns, David; Oshima, Koichiro; Suda, Wataru; Iino, Takao; Yuki, Masahiro; Inoue, Jun; Kitamura, Keiko; Iida, Toshiya; Darby, Alistair C.; Hattori, Masahira; Ohkuma, Moriya

doi:10.1128/genomea.00206-14

Cited by 4 publications

(2 citation statements)

References 11 publications

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“…In addition to ‘ Ca. A. pseudotrichonymphae’ and P. propionicigenes WB4 T , homologous genes were detected in the genomes of Dysgonomonas gadei ATCC BAA-286 T (ADLV00000000, unpublished), Saccharicrinis fermentans JCM 21142 T (BAMD00000000 [ 43 ]; recently renamed from Cytophaga fermentans [ 47 ]), Bacteroides graminisolvens JCM 15093 T , and Geofilum rubicundum JCM 15548 T . The homologous genes were also detected in the very recently appeared genomes of Dysgonomonas capnocytophagoides DSM 22835 T (NZ_AUFL00000000; unpublished) and Alkaliflexus imshenetskii DSM 15055 T (AJUM00000000, unpublished); these two strains were analyzed phylogenetically with their nif genes, but were not assayed for acetylene reduction.…”

Section: Resultsmentioning

confidence: 99%

Distribution and Evolution of Nitrogen Fixation Genes in the Phylum Bacteroidetes

et al. 2015

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Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 15093T and Geofilum rubicundum JCM 15548T. In addition to these and previously reported ‘Candidatus Azobacteroides pseudotrichonymphae’ and Paludibacter propionicigenes, an extensive survey of the genome sequences of diverse Bacteroidetes members revealed the presence of a set of nif genes (nifHDKENB) in strains of Dysgonomonas gadei, Dysgonomonas capnocytophagoides, Saccharicrinis fermentans, and Alkaliflexus imshenetskii. These eight species belonged to and were distributed sporadically within the order Bacteroidales. Acetylene reduction activity was detected in the five species examined, strongly suggesting their diazotrophic nature. Phylogenetic analyses showed monophyletic clustering of the six Nif protein sequences in the eight Bacteroidales species, implying that nitrogen fixation is ancestral to Bacteroidales and has been retained in these species, but lost in many other lineages. The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.

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Section: Resultsmentioning

confidence: 99%

Distribution and Evolution of Nitrogen Fixation Genes in the Phylum Bacteroidetes

et al. 2015

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“…Formosa agariphila [ 24 ], Zobellia galactanivorans [ 25 ] and Sphingomonas sp. A1 [ 18 ] are known as alginate-assimilating bacteria, while Cellulophaga algicola [ 26 ], Cytophaga fermentans [ 27 ] Flavobacterium frigidarium (GenBank accession number, WP_026707247) and Lewinella cohaerens (GenBank accession number, WP_020539555) have not been identified as alginolytic bacteria. Specific sequence motifs of SDR-family enzymes, i.e.…”

Section: Resultsmentioning

confidence: 99%

Identification of a 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid Reductase, FlRed, in an Alginolytic Bacterium Flavobacterium sp. Strain UMI-01

et al. 2015

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In alginate-assimilating bacteria, alginate is depolymerized to unsaturated monosaccharide by the actions of endolytic and exolytic alginate lyases (EC 4.2.2.3 and EC 4.2.2.11). The monosaccharide is non-enzymatically converted to 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH), then reduced to 2-keto-3-deoxy-d-gluconate (KDG) by a specific reductase, and metabolized through the Entner–Doudoroff pathway. Recently, the NADPH-dependent reductase A1-R that belongs to short-chain dehydrogenases/reductases (SDR) superfamily was identified as the DEH-reductase in Sphingomonas sp. A1. We have subsequently noticed that an SDR-like enzyme gene, flred, occurred in the genome of an alginolytic bacterium Flavobacterium sp. strain UMI-01. In the present study, we report on the deduced amino-acid sequence of flred and DEH-reducing activity of recombinant FlRed. The deduced amino-acid sequence of flred comprised 254 residues and showed 34% amino-acid identities to that of A1-R from Sphingomonas sp. A1 and 80%–88% to those of SDR-like enzymes from several alginolytic bacteria. Common sequence motifs of SDR-superfamily enzymes, e.g., the catalytic tetrad Asn-Lys-Tyr-Ser and the cofactor-binding sequence Thr-Gly-x-x-x-Gly-x-Gly in Rossmann fold, were completely conserved in FlRed. On the other hand, an Arg residue that determined the NADPH-specificity of Sphingomonas A1-R was replaced by Glu in FlRed. Thus, we investigated cofactor-preference of FlRed using a recombinant enzyme. As a result, the recombinant FlRed (recFlRed) was found to show high specificity to NADH. recFlRed exhibited practically no activity toward variety of aldehyde, ketone, keto ester, keto acid and aldose substrates except for DEH. On the basis of these results, we conclude that FlRed is the NADH-dependent DEH-specific SDR of Flavobacterium sp. strain UMI-01.

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Effects of micro-aeration on microbial niches and antimicrobial resistances in blackwater anaerobic digesters

Guo

Weissbrodt

et al. 2021

Water Research

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Draft Genome Sequence of Cytophaga fermentans JCM 21142 ^T , a Facultative Anaerobe Isolated from Marine Mud

Cited by 4 publications

References 11 publications

Distribution and Evolution of Nitrogen Fixation Genes in the Phylum <i>Bacteroidetes</i>

Distribution and Evolution of Nitrogen Fixation Genes in the Phylum <i>Bacteroidetes</i>

Identification of a 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid Reductase, FlRed, in an Alginolytic Bacterium Flavobacterium sp. Strain UMI-01

Effects of micro-aeration on microbial niches and antimicrobial resistances in blackwater anaerobic digesters

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Draft Genome Sequence of Cytophaga fermentans JCM 21142 T , a Facultative Anaerobe Isolated from Marine Mud

Cited by 4 publications

References 11 publications

Distribution and Evolution of Nitrogen Fixation Genes in the Phylum <i>Bacteroidetes</i>

Distribution and Evolution of Nitrogen Fixation Genes in the Phylum <i>Bacteroidetes</i>

Identification of a 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid Reductase, FlRed, in an Alginolytic Bacterium Flavobacterium sp. Strain UMI-01

Effects of micro-aeration on microbial niches and antimicrobial resistances in blackwater anaerobic digesters

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Draft Genome Sequence of Cytophaga fermentans JCM 21142 ^T , a Facultative Anaerobe Isolated from Marine Mud