The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

John F. Heidelberg; Rekha Seshadri; Shelley A. Haveman; Christopher L. Hemme; Ian T. Paulsen; James F. Kolonay; Jonathan A Eisen; Naomi Ward; Barbara Methe; Lauren M. Brinkac; Sean C. Daugherty; Robert T. Deboy; Robert J. Dodson; A. Scott Durkin; Ramana Madupu; William C. Nelson; Steven A. Sullivan; Derrick Fouts; Daniel H. Haft; Jeremy Selengut; Jeremy D. Peterson; Tanja M. Davidsen; Nikhat Zafar; Liwei Zhou; Diana Radune; George Dimitrov; Mark Hance; Kevin Tran; Hoda Khouri; John Gill; Terry R. Utterback; Tamara V. Feldblyum; Judy D. Wall; Gerrit Voordouw; Claire M. Fraser

doi:10.1038/nbt959

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

John F. Heidelberg, Rekha Seshadri, Shelley A. Haveman, Christopher L. Hemme, Ian T. Paulsen, James F. Kolonay, Jonathan A Eisen, Naomi Ward, Barbara Methe, Lauren M. Brinkac, Sean C. Daugherty, Robert T. Deboy, Robert J. Dodson, A. Scott Durkin, Ramana Madupu, William C. Nelson, Steven A. Sullivan, Derrick Fouts, Daniel H. Haft, Jeremy SelengutJeremy D. Peterson, Tanja M. Davidsen, Nikhat Zafar, Liwei Zhou, Diana Radune, George Dimitrov, Mark Hance, Kevin Tran, Hoda Khouri, John Gill, Terry R. Utterback, Tamara V. Feldblyum, Judy D. Wall, Gerrit Voordouw, Claire M. Fraser

Research output: Contribution to journal › Article › peer-review

447 Scopus citations

Abstract

Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.

Original language	English (US)
Pages (from-to)	554-559
Number of pages	6
Journal	Nature Biotechnology
Volume	22
Issue number	5
DOIs	https://doi.org/10.1038/nbt959
State	Published - May 2004
Externally published	Yes

ASJC Scopus subject areas

Microbiology

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10.1038/nbt959

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Heidelberg, J. F., Seshadri, R., Haveman, S. A., Hemme, C. L., Paulsen, I. T., Kolonay, J. F., Eisen, J. A., Ward, N., Methe, B., Brinkac, L. M., Daugherty, S. C., Deboy, R. T., Dodson, R. J., Durkin, A. S., Madupu, R., Nelson, W. C., Sullivan, S. A., Fouts, D., Haft, D. H., ... Fraser, C. M. (2004). The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature Biotechnology, 22(5), 554-559. https://doi.org/10.1038/nbt959

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. / Heidelberg, John F.; Seshadri, Rekha; Haveman, Shelley A.; Hemme, Christopher L.; Paulsen, Ian T.; Kolonay, James F.; Eisen, Jonathan A; Ward, Naomi; Methe, Barbara; Brinkac, Lauren M.; Daugherty, Sean C.; Deboy, Robert T.; Dodson, Robert J.; Durkin, A. Scott; Madupu, Ramana; Nelson, William C.; Sullivan, Steven A.; Fouts, Derrick; Haft, Daniel H.; Selengut, Jeremy; Peterson, Jeremy D.; Davidsen, Tanja M.; Zafar, Nikhat; Zhou, Liwei; Radune, Diana; Dimitrov, George; Hance, Mark; Tran, Kevin; Khouri, Hoda; Gill, John; Utterback, Terry R.; Feldblyum, Tamara V.; Wall, Judy D.; Voordouw, Gerrit; Fraser, Claire M.

In: Nature Biotechnology, Vol. 22, No. 5, 05.2004, p. 554-559.

Research output: Contribution to journal › Article › peer-review

Heidelberg, JF, Seshadri, R, Haveman, SA, Hemme, CL, Paulsen, IT, Kolonay, JF, Eisen, JA, Ward, N, Methe, B, Brinkac, LM, Daugherty, SC, Deboy, RT, Dodson, RJ, Durkin, AS, Madupu, R, Nelson, WC, Sullivan, SA, Fouts, D, Haft, DH, Selengut, J, Peterson, JD, Davidsen, TM, Zafar, N, Zhou, L, Radune, D, Dimitrov, G, Hance, M, Tran, K, Khouri, H, Gill, J, Utterback, TR, Feldblyum, TV, Wall, JD, Voordouw, G & Fraser, CM 2004, 'The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough', Nature Biotechnology, vol. 22, no. 5, pp. 554-559. https://doi.org/10.1038/nbt959

Heidelberg, John F. ; Seshadri, Rekha ; Haveman, Shelley A. ; Hemme, Christopher L. ; Paulsen, Ian T. ; Kolonay, James F. ; Eisen, Jonathan A ; Ward, Naomi ; Methe, Barbara ; Brinkac, Lauren M. ; Daugherty, Sean C. ; Deboy, Robert T. ; Dodson, Robert J. ; Durkin, A. Scott ; Madupu, Ramana ; Nelson, William C. ; Sullivan, Steven A. ; Fouts, Derrick ; Haft, Daniel H. ; Selengut, Jeremy ; Peterson, Jeremy D. ; Davidsen, Tanja M. ; Zafar, Nikhat ; Zhou, Liwei ; Radune, Diana ; Dimitrov, George ; Hance, Mark ; Tran, Kevin ; Khouri, Hoda ; Gill, John ; Utterback, Terry R. ; Feldblyum, Tamara V. ; Wall, Judy D. ; Voordouw, Gerrit ; Fraser, Claire M. / The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. In: Nature Biotechnology. 2004 ; Vol. 22, No. 5. pp. 554-559.

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abstract = "Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.",

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The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

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