Acetomicrobium hydrogeniformans, an obligate anaerobe of the phylum Synergistetes, was isolated from oil production water. It has the unusual ability to produce almost 4 molecules H2/molecule glucose. The draft genome of A. hydrogeniformans OS1 (DSM 22491T) is 2,123,925 bp, with 2,068 coding sequences and 60 RNA genes

Cook, Lauren E

Gang, Spencer S

Gunsalus, Robert P

Ihlan, Alicia

Lobos, Elizabeth A

Maune, Matthew

McInerney, Michael J

Tanner, Ralph S

Weinstock, George

English

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Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2018Genome sequence of Acetomicrobiumhydrogeniformans OS1Lauren E. CookUniversity of California, Los AngelesSpencer S. GangUniversity of California, Los AngelesAlicia IhlanUniversity of California, Los AngelesMatthew MauneUniversity of OklahomaRalph S. TannerUniversity of OklahomaSee next page for additional authorsFollow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubsThis Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in OpenAccess Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact engeszer@wustl.edu.Recommended CitationCook, Lauren E.; Gang, Spencer S.; Ihlan, Alicia; Maune, Matthew; Tanner, Ralph S.; McInerney, Michael J.; Weinstock, George;Lobos, Elizabeth A.; and Gunsalus, Robert P., ,"Genome sequence of Acetomicrobium hydrogeniformans OS1." GenomeAnnouncements.6,26. e00581-18. (2018).https://digitalcommons.wustl.edu/open_access_pubs/7042AuthorsLauren E. Cook, Spencer S. Gang, Alicia Ihlan, Matthew Maune, Ralph S. Tanner, Michael J. McInerney,George Weinstock, Elizabeth A. Lobos, and Robert P. GunsalusThis open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/7042Genome Sequence of Acetomicrobium hydrogeniformans OS1Lauren E. Cook,a Spencer S. Gang,a Alicia Ihlan,a Matthew Maune,b Ralph S. Tanner,b Michael J. McInerney,bGeorge Weinstock,c Elizabeth A. Lobos,c Robert P. Gunsalusa,daDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles,California, USAbDepartment of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USAcThe Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USAdUCLA DOE Institute, University of California, Los Angeles, California, USAABSTRACT Acetomicrobium hydrogeniformans, an obligate anaerobe of the phylumSynergistetes, was isolated from oil production water. It has the unusual ability toproduce almost 4 molecules H2/molecule glucose. The draft genome of A. hydrogeni-formans OS1 (DSM 22491T) is 2,123,925 bp, with 2,068 coding sequences and 60RNA genes.Acetomicrobium hydrogeniformans strain OS1T, until recently known as Anaerobacu-lum hydrogeniformans (1), of the phylum Synergistetes, is capable of producingalmost four molecules of hydrogen per glucose molecule, the theoretical maximum (2,3). It ferments other substrates, including amino acids, dicarboxylic acids, and othersugars, and can respire using several sulfur compounds. NaCl is an absolute require-ment for growth, which suggests a sodium-based energy strategy (2, 4, 5). Although itcan reduce elemental sulfur, thiosulfate, and L-cysteine to sulﬁde, the pathways areunknown. The genome is currently divided among eight scaffolds, one of whichcontains 2,103,414 bp and seven of which are small scaffolds ranging from 507 bp to7,345 bp. The genome lacks genes needed for respiration of sulfate and nitrate andgenes for b- and c-type cytochromes. The metabolic strategy appears to be limitedprimarily to fermentation of simple sugars, amino acids, and certain dicarboxylic acidsin addition to an as-yet undescribed respiratory mode for elemental sulfur or thiosul-fate. Despite the ability to ferment sugars, the Embden-Meyerhof-Parnas, pentosephosphate, and Entner-Doudoroff pathways appear to be incomplete. It also lacks acomplete set of trichloroacetic acid (TCA) genes. OS1T possesses two gene clusters withhydrogenase-related functions to form molecular hydrogen. It also possesses genes fortwo putative formate dehydrogenases and a formate hydrogenlyase complex. It hasmultiple genes for stress adaptation, including those for motility, pili, osmotic adapta-tion, heavy-metal resistance, multidrug export, and toxin/antitoxin synthesis. It has a21-gene cassette for the synthesis of a carboxysome-like shell structure. Althoughmotility was not previously reported (2), motility can be observed in wet mounts ofcultures, and negative-stained cells exhibit polar ﬂagella (R. S. Tanner, personal com-munication). The genome contains a complete inventory of genes needed to make ﬂagellaand multiple genes for chemoreception and chemotaxis. The genome also contains acomplement of 10 pil/pul genes needed for synthesis and assembly of a type IV pilusapparatus. It has a relatively small number of primary transcription factors (43 genes) andsix predicted two-component regulatory systems, including the aforementioned che-motaxis signaling systems. Thus, OS1 appears to have adopted a minimal regulatorystrategy, although the substrate range is considerable with respect to the variety of sugars,amino acids, and dicarboxylates used (2). Little is known about translational or posttrans-lational control operating in this or other Synergistetes species. Strikingly, the genomeReceived 30 May 2018 Accepted 30 May2018 Published 28 June 2018Citation Cook LE, Gang SS, Ihlan A, Maune M,Tanner RS, McInerney MJ, Weinstock G, LobosEA, Gunsalus RP. 2018. Genome sequence ofAcetomicrobium hydrogeniformansOS1.Genome Announc 6:e00581-18. https://doi.org/10.1128/genomeA.00581-18.Copyright © 2018 Cook et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Robert P. Gunsalus,robg@microbio.ucla.edu.PROKARYOTEScrossmVolume 6 Issue 26 e00581-18 genomea.asm.org 1 on September 6, 2018 by guesthttp://mra.asm.org/Downloaded from lacks genes for the prototypical bacterial FoF1-type ATP synthase but possessesinstead three clusters of genes encoding either archaeal-like or vacuolar-like A/VATP synthases. It also has other archaeal-like annotated genes, including thoseacting in glycolysis; of note, we found four putative candidates for glyceraldehyde-3-phosphate oxidoreductase, a ferredoxin-utilizing enzyme with archaeal properties.Other genes with archaeal properties include those related to formyl methanofurandehydrogenase A, B, C, D, and E subunits, methanyltetrahydromethanopterin cyclo-hydrolase; and Formylmethanofuran-tetrahydromethanopterin N-formyltransferase.These genes may have been acquired by lateral gene transfer (6–8).Accession number(s). This whole-genome shotgun project has been deposited inGenBank under the accession no. ACJX00000000.ACKNOWLEDGMENTSThese sequence data were produced by the US Department of Energy Joint GenomeInstitute (http://www.jgi.doe.gov) in collaboration with the user community.This work was supported by Department of Energy contract DE-FG02-08ER64689 (toR.P.G., R.S.T., and M.J.M.), UCLA-DOE Institute award DE-FC02-02ER63421 (to R.P.G.), andNational Science Foundation grant NSF 1515843 (to R.P.G. and M.J.M.).REFERENCES1. Hania WB, Bouanane-Darenfed A, Cayol J-L, Ollivier B, Fardeau M-L. 2016.Reclassiﬁcation of Anaerobaculum mobile, Anaerobaculum thermoterre-num, Anaerobaculum hydrogeniformans as Acetomicrobium mobilecomb. nov., Acetomicrobium thermoterrenum comb. nov. and Acetomi-crobium hydrogeniformans comb. nov., respectively, and emendation ofthe genus Acetomicrobium. Int J Syst Evol Microbiol 66:1506–1509.https://doi.org/10.1099/ijsem.0.000910.2. Maune MW, Tanner RS. 2012. Description of Anaerobaculum hydrogeni-formans sp. nov., an anaerobe that produces hydrogen from glucose, andemended description of the genus Anaerobaculum. Int J Syst Evol Micro-biol 62:832–838. https://doi.org/10.1099/ijs.0.024349-0.3. Thauer RK, Jungermann K, Decker K. 1977. Energy conservation in che-motrophic anaerobic bacteria. Bacteriol Rev 41:100–180.4. Menes RJ, Muxi L. 2002. Anaerobaculum mobile sp. nov., a novel anaero-bic, moderately thermophilic, peptide-fermenting bacterium that usescrotonate as an electron acceptor, and emended description of the genusAnaerobaculum. Int J Syst Evol Microbiol 52:157–164. https://doi.org/10.1099/00207713-52-1-157.5. Buss KA, Sanders DA, Hasson MS, Ingram-Smith C, Ferry JG. 1997. Crys-tallization of acetate kinase from Methanosarcina thermophila and pre-diction of its fold. Protein Sci 6:2659–2662. https://doi.org/10.1002/pro.5560061222.6. Garcia-Vallvé S, Romeu A, Palau J. 2000. Horizontal gene transfer inbacterial and archaeal complete genomes. Genome Res 10:1719–1725.https://doi.org/10.1101/gr.130000.7. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK,Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, MalekJA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA,Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, WhiteO, Salzberg SL, Smith HO, Venter JC, Fraser CM. 1999. Evidence forlateral gene transfer between Archaea and Bacteria from genome se-quence of Thermotoga maritima. Nature 399:323–329. https://doi.org/10.1038/20601.8. Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-AriasR, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard T,Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, OverbeekR, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G. 2002. The genome ofMethanosarcina mazei: evidence for lateral gene transfer between bacte-ria and archaea. 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Genome sequence of Acetomicrobium hydrogeniformans OS1

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Genome sequence of Acetomicrobium hydrogeniformans OS1

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