Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is a completed genome sequence. Preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. Here, we briefly report the completed and annotated genome sequence of strain TPSY

Bose, Saumyaditya

Byrne-Bailey, Kathryne G.

Chair, Antinea H.

Chertkov, Olga

Coates, John D.

Knox, Traci

Spanbauer, Trisha L.

Weber, Karrie A.

English

DigitalCommons@University of Nebraska

University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in the Biological Sciences Papers in the Biological Sciences 3-2010 Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY Kathryne G. Byrne-Bailey University of California, Berkeley Karrie A. Weber University of Nebraska-Lincoln, kweber@unl.edu Antinea H. Chair University of California, Berkeley Saumyaditya Bose University of California, Berkeley Traci Knox University of California, Berkeley See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/bioscifacpub  Part of the Life Sciences Commons Byrne-Bailey, Kathryne G.; Weber, Karrie A.; Chair, Antinea H.; Bose, Saumyaditya; Knox, Traci; Spanbauer, Trisha L.; Chertkov, Olga; and Coates, John D., "Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY" (2010). Faculty Publications in the Biological Sciences. 193. https://digitalcommons.unl.edu/bioscifacpub/193 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Kathryne G. Byrne-Bailey, Karrie A. Weber, Antinea H. Chair, Saumyaditya Bose, Traci Knox, Trisha L. Spanbauer, Olga Chertkov, and John D. Coates This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/bioscifacpub/193 JOURNAL OF BACTERIOLOGY, Mar. 2010, p. 1475–1476 Vol. 192, No. 50021-9193/10/$12.00 doi:10.1128/JB.01449-09Copyright © 2010, American Society for Microbiology. All Rights Reserved.Completed Genome Sequence of the Anaerobic Iron-OxidizingBacterium Acidovorax ebreus Strain TPSYKathryne G. Byrne-Bailey,1† Karrie A. Weber,1,3† Antinea H. Chair,1 Saumyaditya Bose,1 Traci Knox,1Trisha L. Spanbauer,3 Olga Chertkov,2 and John D. Coates1*Department of Plant and Microbiology, University of California, Berkeley, California 947201; Los Alamos National Laboratory,Los Alamos, New Mexico 875452; and School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 685883Received 4 November 2009/Accepted 25 November 2009Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is acompleted genome sequence. Preliminary protein annotation revealed an organism optimized for survival in acomplex environmental system. Here, we briefly report the completed and annotated genome sequence of strainTPSY.Microorganisms from diverse anoxic environments are ca-pable of nitrate-dependent Fe(II) oxidation at circumneutralpH (4, 11, 17, 18, 20, 21). Despite their geochemical impor-tance (22), little is known of the underlying biochemical andgenetic mechanisms. Genome sequencing of several nitrate-dependent Fe(II) oxidizers will provide insight into this pro-cess. By comparing Fe(II) oxidation mechanisms in variousorganisms, we hope to identify both the conserved and dispar-ate aspects of the metabolism. The genome of Acidovoraxebreus strain TPSY is the first of these to be sequenced.Strain TPSY is a motile, Gram-negative facultative anaerobeisolated from groundwater collected from the U.S. Departmentof Energy Integrated Field Research Challenge site at OakRidge, TN. Growth experiments performed as previously de-scribed (21) revealed TPSY’s incapacity for lithoautotrophicgrowth, which was supported by a lack of genes in the genomeencoding any known CO2 fixation pathways. TPSY did grow mixo-trophically with Fe(II) as the electron donor and a 0.1 mM ace-tate carbon source. 16S rRNA gene sequence analysis placedTPSY in the class Betaproteobacteria with 99.8% similarity toAcidovorax sp. strain JS42 in the family Comamonadaceae.The completed genome consisted of a single circular chro-mosome of 3,796,573 bp with an average 66.8% GC content.A total of 3,479 protein-encoding genes were predicted, and 34(0.98%) had no similarity to public database sequences. Se-quencing performed at the Department of Energy JointGenome Institute (JGI) used Sanger sequencing and 454pyrosequencing to a depth of 20 coverage. All JGI libraryconstruction and sequencing techniques can be found athttp://www.jgi.doe.gov/. Sequence assembly, quality assess-ment, and annotation were performed using the softwarePhred/Phrap/Consed (www.phrap.com) (6–8), Dupfinisher(10), CRITICA (2), GLIMMER, and GENERATION (5)and the JGI Integrated Microbial Genomes site (12). Thecompleted genome sequence contained 33,341 reads andhad an average of ninefold coverage per base and an errorrate of 1 in 100,000.TPSY was named in part for its meandering motility, and itsgenome confirmed the twitching phenotype with the presenceof pilT, pilU, and a complete set of flagellar and chemotaxisgenes. The ability of TPSY to oxidize simple alcohols andacids with oxygen or nitrate respiration was confirmed by thegenome. In addition, biosynthetic pathways for all aminoacids except tyrosine and phenylalanine were present. Nohomologues of chorismate mutase (EC 5.4.99.5), an enzymerequired for tyrosine and phenylalanine anabolism, wereidentified. The genome contained both intact Embden-Mey-erhof-Parnas and Entner-Doudoroff pathways, in addition to apentose phosphate pathway and a trichloroacetic acid cycle.In support of its facultative anaerobicity, a complete set ofgenes for denitrification and three different terminal oxidases(cytochrome aa3, cbb3, and cytochrome d quinol oxidase) werepresent. The cbb3 and cytochrome d oxidases, with their highoxygen affinity, putatively enable survival in microaerobic en-vironments (14).TPSY had sequences encoding 30 transposases, 11 integrases,and 11 phage/prophage-related genes. A region of particular in-terest putatively conferred resistance to lead, arsenate, and mer-cury: pbrRATARTBC, arsRDAB, and merRPCADE. Evidencesuggests horizontal transfer and insertion of this region, as it wasflanked on the 5 end by  prophage-related genes and the 3 endencoded a putative Tn21 transposase. Phenotypic studies by themethod of Wang et al. (19) revealed MICs of 16 M phenylmer-curic acetate and 250 M MgCl2. TPSY was also capable ofgrowth in the presence of arsenate (10 mM) but did not use it asan electron acceptor.Related to phage infection, one CRISPR (clustered, regu-larly interspaced, short palindromic repeats) region (3, 16) waspredicted. The core proteins, the cas1 and cas2 genes, and acsn1 gene formed the CRISPR subtype Nmeni, which is asso-ciated with vertebrate pathogens and commensals (9). How-ever, the lack of typical pathogenic type I or III secretionsystems such as the hec cluster of Dickeya chrysanthemi (15) orthe inv/spa system of Salmonella enterica serovar Typhimurium* Corresponding author. Mailing address: Department of Plant andMicrobiology, University of California, Berkeley, CA 94720. Phone:(510) 643-8455. Fax: (510) 642-4995. E-mail: jdcoates@berkeley.edu.† The first two authors contributed equally to this work and arelisted alphabetically. Published ahead of print on 18 December 2009.1475  (13) indicated that TPSY would probably not exhibit a patho-genic lifestyle.Nucleotide sequence accession number. The genome se-quence of Acidovorax ebreus strain TPSY (formerly Diaphoro-bacter sp. strain TPSY) reported in this paper has been depos-ited in the GenBank database under accession numberNC_011992.We thank Lynne Goodwin for her management of the sequencingproject at the JGI.This research was supported by Office of Science (BER), U.S. De-partment of Energy, grant DE-FG02-07ER64390 to J.D.C. at UCBand by the Nebraska Tobacco Settlement Biomedical Research De-velopment Fund to K.A.W. at the University of Nebraska, Lincoln.The sequencing work on behalf of J.D.C. was performed through theCommunity Sequencing Project 2008 for the JGI under the auspices ofthe U.S. Department of Energy Office of Science, Biological and En-vironmental Research Program, and by the University of CaliforniaLawrence Berkeley National Laboratory under contract DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contractDE-AC52-07NA27344, and Los Alamos National Laboratory undercontract DE AC02-06NA25396.REFERENCES1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990.Basic local alignment search tool. J. Mol. Biol. 215:403–410.2. Badger, J. H., and G. J. Olsen. 1999. CRITICA: coding region identificationtool invoking comparative analysis. Mol. Biol. Evol. 16:512–524.3. Barrangou, R., C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S.Moineau, D. A. Romero, and P. Horvath. 2007. CRISPR provides acquiredresistance against viruses in prokaryotes. Science 315:1709–1712.4. Chaudhuri, S. K., J. G. Lack, and J. D. Coates. 2001. Biogenic magnetiteformation through anaerobic biooxidation of Fe(II). Appl. Environ. Micro-biol. 67:2844–2848.5. Delcher, A. L., D. Harmon, S. Kasif, O. White, and S. L. Salzberg. 1999.Improved microbial gene identification with GLIMMER. Nucleic Acids Res.27:4636–4641.6. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer tracesusing Phred. II. Error probabilities. Genome Res. 8:186–194.7. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling ofautomated sequencer traces using Phred. I. Accuracy assessment. GenomeRes. 8:175–185.8. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool forsequence finishing. Genome Res. 8:195–202.9. Haft, D. H., J. Selengut, E. F. Mongodin, and K. E. Nelson. 2005. A guild of45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cassubtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1:e60.10. Han, C. S., and P. Chain. 2006. Finishing repeat regions automatically withDupfinisher, p. 141–146. In H. R. Arabnia and H. Valafar (ed.), Proc. 2006Int. Conf. Bioinformatics Comput. Biol. CSREA Press, Las Vegas, NV.11. Lack, J. G., S. K. Chaudhuri, R. Chakraborty, L. A. Achenbach, and J. D.Coates. 2002. Anaerobic biooxidation of Fe(II) by Dechlorosoma suillum.Microb. Ecol. 43:424–431.12. Markowitz, V. M., E. Szeto, K. Palaniappan, Y. Grechkin, K. Chu, I. M.Chen, I. Dubchak, I. Anderson, A. Lykidis, K. Mavromatis, N. N. Ivanova,and N. C. Kyrpides. 2008. The Integrated Microbial Genomes (IMG) systemin 2007: data content and analysis tool extensions. Nucleic Acids Res. 36:D528–D533.13. Nies, D. H. 1995. The cobalt, zinc, and cadmium efflux system CzcABC fromAlcaligenes eutrophus functions as a cation-proton antiporter in Escherichiacoli. J. Bacteriol. 177:2707–2712.14. Preisig, O., D. Anthamatten, and H. Hennecke. 1993. Genes for a microaero-bically induced oxidase complex in Bradyrhizobium japonicum are essentialfor a nitrogen-fixing endosymbiosis. Proc. Natl. Acad. Sci. U. S. A. 90:3309–3313.15. Rojas, C. M., J. H. Ham, W. L. Deng, J. J. Doyle, and A. Collmer. 2002.HecA, a member of a class of adhesins produced by diverse pathogenicbacteria, contributes to the attachment, aggregation, epidermal cell killing,and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana cleve-landii seedlings. Proc. Natl. Acad. Sci. U. S. A. 99:13142–13147.16. Sorek, R., V. Kunin, and P. Hugenholtz. 2008. CRISPR—a widespreadsystem that provides acquired resistance against phages in bacteria andarchaea. Nat. Rev. Microbiol. 6:181–186.17. Straub, K. L., M. Benz, B. Schink, and F. Widdel. 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl. Environ. Microbiol.62:1458–1460.18. Straub, K. L., and B. E. E. Buchholz-Cleven. 1998. Enumeration and detec-tion of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from di-verse European sediments. Appl. Environ. Microbiol. 64:4846–4856.19. Wang, Y., M. Moore, H. S. Levinson, S. Silver, C. Walsh, and I. Mahler.1989. Nucleotide sequence of a chromosomal mercury resistance determi-nant from a Bacillus sp. with broad-spectrum mercury resistance. J. Bacte-riol. 171:83–92.20. Weber, K. A., D. B. Hedrick, A. D. Peacock, J. C. Thrash, D. C. White, L. A.Achenbach, and J. D. Coates. 2009. Physiological and taxonomic descriptionof the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp.strain 2002. Appl. Microbiol. Biotechnol. 83:555–565.21. Weber, K. A., J. Pollock, K. A. Cole, S. M. O’Connor, L. A. Achenbach, andJ. D. Coates. 2006. Anaerobic nitrate-dependent iron(II) bio-oxidation by anovel lithoautotrophic betaproteobacterium, strain 2002. Appl. Environ. Mi-crobiol. 72:686–694.22. Weber, K. A., M. M. Urrutia, P. F. Churchill, R. K. Kukkadapu, and E. E.Roden. 2006. Anaerobic redox cycling of iron by freshwater sediment micro-organisms. Environ. Microbiol. 8:100–113.1476 GENOME ANNOUNCEMENTS J. BACTERIOL.

Completed Genome Sequence of the Anaerobic Iron-Oxidizing
Bacterium \u3ci\u3eAcidovorax ebreus\u3c/i\u3e Strain TPSY

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Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium \u3ci\u3eAcidovorax ebreus\u3c/i\u3e Strain TPSY

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