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PMID:12368813

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Citation

Heidelberg, JF, Paulsen, IT, Nelson, KE, Gaidos, EJ, Nelson, WC, Read, TD, Eisen, JA, Seshadri, R, Ward, N, Methe, B, Clayton, RA, Meyer, T, Tsapin, A, Scott, J, Beanan, M, Brinkac, L, Daugherty, S, DeBoy, RT, Dodson, RJ, Durkin, AS, Haft, DH, Kolonay, JF, Madupu, R, Peterson, JD, Umayam, LA, White, O, Wolf, AM, Vamathevan, J, Weidman, J, Impraim, M, Lee, K, Berry, K, Lee, C, Mueller, J, Khouri, H, Gill, J, Utterback, TR, McDonald, LA, Feldblyum, TV, Smith, HO, Venter, JC, Nealson, KH and Fraser, CM (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-23

Abstract

Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion-reducing capabilities.

Links

PubMed Online version:10.1038/nbt749

Keywords

Amino Acid Sequence; Biodegradation, Environmental; Cell Respiration; Electron Transport; Gene Expression; Gene Expression Regulation, Bacterial; Genome, Bacterial; Metals/metabolism; Molecular Sequence Data; Open Reading Frames/genetics; Organic Chemicals/metabolism; Oxidation-Reduction; Plasmids; Proteomics/methods; Sequence Alignment/methods; Sequence Analysis, DNA; Sequence Analysis, Protein; Shewanella/classification; Shewanella/genetics; Shewanella/metabolism; Shewanella/pathogenicity; Species Specificity; Water Pollutants, Chemical/metabolism; Water Purification/methods

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

SHEON:Q8E8A6

enables

GO:0015666: restriction endodeoxyribonuclease activity

ECO:0000304: author statement supported by traceable reference used in manual assertion

F

Seeded From UniProt

complete

SHEON:Q8E8A6

involved_in

GO:0009307: DNA restriction-modification system

ECO:0000304: author statement supported by traceable reference used in manual assertion

P

Seeded From UniProt

complete

SHEON:Q8EBG2

enables

GO:0004721: phosphoprotein phosphatase activity

ECO:0000304: author statement supported by traceable reference used in manual assertion

F

Seeded From UniProt

complete

SHEON:Q8EBG2

involved_in

GO:0006470: protein dephosphorylation

ECO:0000304: author statement supported by traceable reference used in manual assertion

P

Seeded From UniProt

complete

SHEON:Q8EF28

enables

GO:0004721: phosphoprotein phosphatase activity

ECO:0000304: author statement supported by traceable reference used in manual assertion

F

Seeded From UniProt

complete

SHEON:Q8EF28

involved_in

GO:0006470: protein dephosphorylation

ECO:0000304: author statement supported by traceable reference used in manual assertion

P

Seeded From UniProt

complete

SHEON:Q8EGX8

enables

GO:0003677: DNA binding

ECO:0000304: author statement supported by traceable reference used in manual assertion

F

Seeded From UniProt

complete

SHEON:Q8EGX8

part_of

GO:0019812: type I site-specific deoxyribonuclease complex

ECO:0000304: author statement supported by traceable reference used in manual assertion

C

Seeded From UniProt

complete

SHEON:Q8EGX8

involved_in

GO:0009307: DNA restriction-modification system

ECO:0000304: author statement supported by traceable reference used in manual assertion

P

Seeded From UniProt

complete

SHEON:Q8EGX8

involved_in

GO:0006304: DNA modification

ECO:0000304: author statement supported by traceable reference used in manual assertion

P

Seeded From UniProt

complete

SHEON:Q8EG33

enables

GO:0009055: electron transfer activity

ECO:0000250: sequence similarity evidence used in manual assertion

NCBI_gi:3628770

F

Seeded From UniProt

complete

SHEON:Q8EAI2

enables

GO:0009055: electron transfer activity

ECO:0000250: sequence similarity evidence used in manual assertion

UniProtKB:P07598

F

Seeded From UniProt

complete

SHEON:Q8EAI2

enables

GO:0016730: oxidoreductase activity, acting on iron-sulfur proteins as donors

ECO:0000250: sequence similarity evidence used in manual assertion

UniProtKB:P07598

F

Seeded From UniProt

complete

See also

References

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