Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265

Alexiev, Alexandra; Coil, David A.; Badger, Jonathan H.; Enticknap, Julie; Ward, Naomi; Robb, Frank T.; Eisen, Jonathan A.

doi:10.1128/genomea.00470-14

Cited by 8 publications

(2 citation statements)

References 14 publications

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“…It is therefore likely that Syn8 was syntrophically associated with Met2 and other hydrogenotrophic methanogens by producing hydrogen from acetate (i.e., SAO). Cop3 and Cop4 were closely related to Coprothermobacter proteolyticus , an anaerobic proteolytic bacterium that is frequently found in thermophilic digesters 45 , 46 , suggesting that these bacteria also contributed to syntrophic methanogenesis by producing hydrogen from organics that were present in the reactor (e.g., proteins released from dead cells). Clo6 and Lut10 were the most closely related to Clostridium ( Ruminiclostridium ) thermocellum and Lutispora thermophila , respectively, which are both thermophilic fermentative bacteria that utilize yeast extract as a growth factor 47 , 48 .…”

Section: Resultsmentioning

confidence: 99%

Non-autotrophic methanogens dominate in anaerobic digesters

Kouzuma

Tsutsumi

Ishii

et al. 2017

Sci Rep

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Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO 2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.Methanogenic archaea (methanogens) are ubiquitously present in anaerobic environments, such as digestive tracts, paddy fields, and aquatic sediments, and play an important role in anaerobic degradation of organic matter and the global cycle of carbon 1, 2 . Additionally, they contribute to human society via their ability to produce methane gas in anaerobic digesters 3 . In methanogenic ecosystems, methane is produced via syntrophic associations between methanogens and anaerobic bacteria, including fermenters and syntrophs 4,5 . Fermenters and syntrophs degrade organic substances and produce acetate, formate, methanol, CO 2 , and H 2 , which serve as carbon and/or energy sources for acetoclastic, methylotrophic, and hydrogenotrophic methanogenesis 6,7 . Among them, acetate serves as the key intermediate metabolite, from which methane is produced by syntrophic acetate oxidation (SAO) coupled to hydrogenotrophic methanogenesis, in addition to acetoclastic methanogenesis [8][9][10] . Thus far, a number of microbes have been isolated from methanogenic microbial communities, and their genomic and metabolic features have been characterized [11][12][13][14] . Furthermore, recent metagenomic and metatranscriptomic studies have provided insights into uncultured members of methanogenic communities [15][16][17][18][19][20][21] . For example, Nobu et al. reported that anaerobic degradation of terephthalate in a methanogenic bioreactor was supported by complex synergistic networks comprised of many uncultivat...

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Section: Resultsmentioning

confidence: 99%

Non-autotrophic methanogens dominate in anaerobic digesters

Kouzuma

Tsutsumi

Ishii

et al. 2017

Sci Rep

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“…The following references are cited in the Supporting Information for this article: Alexiev et al (2014), Beesley et al (2010), Di Franco et al (2002), Gilad (2007) and Mesbah et al (2007).…”

Section: Related Literaturementioning

confidence: 99%

Structural basis for amino-acid recognition and transmembrane signalling by tandem Per–Arnt–Sim (tandem PAS) chemoreceptor sensory domains

Liu

Machuca

Beckham

et al. 2015

Acta Cryst D Biol Crystallogr

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Chemotaxis, mediated by methyl-accepting chemotaxis protein (MCP) receptors, plays an important role in the ecology of bacterial populations. This paper presents the first crystallographic analysis of the structure and ligand-induced conformational changes of the periplasmic tandem Per-Arnt-Sim (PAS) sensing domain (PTPSD) of a characterized MCP chemoreceptor. Analysis of the complex of the Campylobacter jejuni Tlp3 PTPSD with isoleucine (a chemoattractant) revealed that the PTPSD is a dimer in the crystal. The two ligand-binding sites are located in the membrane-distal PAS domains on the faces opposite to the dimer interface. Mutagenesis experiments show that the five strongly conserved residues that stabilize the main-chain moiety of isoleucine are essential for binding, suggesting that the mechanism by which this family of chemoreceptors recognizes amino acids is highly conserved. Although the fold and mode of ligand binding of the PTPSD are different from the aspartic acid receptor Tar, the structural analysis suggests that the PTPSDs of amino-acid chemoreceptors are also likely to signal by a piston displacement mechanism. The PTPSD fluctuates between piston (C-terminal helix) `up' and piston `down' states. Binding of an attractant to the distal PAS domain locks it in the closed form, weakening its association with the proximal domain and resulting in the transition of the latter into an open form, concomitant with a downward (towards the membrane) 4 Å piston displacement of the C-terminal helix. In vivo, this movement would generate a transmembrane signal by driving a downward displacement of the transmembrane helix 2 towards the cytoplasm.

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C oprothermobacter

Paván¹,

Pavan²,

Kämpfer³

et al. 2019

Bergey's Manual of Systematics of Archaea and Bacteria

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Co.pro.ther.mo.bac'ter. Gr. fem. n. kopros manure; Gr. adj. thermos warm; N.L. masc. n. bacter a rod; N.L. masc. n. Coprothermobacter a thermophilic rod from manure. Coprothermobacterota / Coprothermobacteria / Coprothermobacterales / Coprothermobacteraceae / Coprothermobacter Rod‐shaped cells, 0.5 × 1.0–6.0 µm; occur singly or in pairs in young cultures; pleomorphic in old cultures. Colonies are white, circular (diameter 1–2 mm), convex, and smooth with entire edges. Stains Gram‐negative. Non‐spore‐forming. Nonmotile. Strictly anaerobic. Thermophilic. Optimum growth temperature, 55–70°C. Neutrophilic. Chemoorganotrophic. Proteolytic, uses gelatin and peptones. Sugars are used poorly unless yeast extract or rumen fluid is added. Trypticase peptone stimulates glucose utilization. The main end products of sugar or protein fermentation are acetic acid, H 2 , and CO 2 . Thiosulfate, but not sulfate, is used as electron acceptor for growth. Dominant in thermophilic anaerobic digesters, also present in marine and terrestrial environments. The microorganisms of the genus Coprothermobacter represent one of the primary lines of descent in the bacterial domain. DNA G + C content (mol%) : 42.5–44.8 (genome analysis). Type species : Coprothermobacter proteolyticus (Ollivier, Mah, Ferguson, Boone, Garcia and Robinson 1985) Rainey and Stackebrandt 1993a, 858 VP ( Thermobacteroides proteolyticus Ollivier, Mah, Ferguson, Boone, Garcia and Robinson 1985, 427).

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Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265

Abstract: Here we present the complete 1,424,912-bp genome sequence of Coprothermobacter proteolyticus DSM 5265, isolated from a thermophilic digester fermenting tannery wastes and cattle manure.

Cited by 8 publications

References 14 publications

Non-autotrophic methanogens dominate in anaerobic digesters

Non-autotrophic methanogens dominate in anaerobic digesters

Structural basis for amino-acid recognition and transmembrane signalling by tandem Per–Arnt–Sim (tandem PAS) chemoreceptor sensory domains

C oprothermobacter

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