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Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, Stark M, Bauer M, Zibat A, Lombardot T, Becker I, Amann J, Gellner K, Teeling H, Leuschner WD, Glöckner FO, Lupas AN, Amann R, Klenk HP. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol 2004; 6:887-902. [PMID: 15305914 DOI: 10.1111/j.1462-2920.2004.00665.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C(4)-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a beta-oxidation complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and ncc. D. psychrophila encodes more than 30 two-component regulatory systems, including a new Ntr subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.
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Affiliation(s)
- R Rabus
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
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Glöckner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K, Rabus R, Schlesner H, Amann R, Reinhardt R. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc Natl Acad Sci U S A 2003; 100:8298-303. [PMID: 12835416 PMCID: PMC166223 DOI: 10.1073/pnas.1431443100] [Citation(s) in RCA: 327] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pirellula sp. strain 1 ("Rhodopirellula baltica") is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales. Here we report the complete genome sequence of a member of this independent phylum. With 7.145 megabases, Pirellula sp. strain 1 has the largest circular bacterial genome sequenced so far. The presence of all genes required for heterolactic acid fermentation, key genes for the interconversion of C1 compounds, and 110 sulfatases were unexpected for this aerobic heterotrophic isolate. Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of genes for peptidoglycan synthesis were found. Genes for lipid A biosynthesis and homologues to the flagellar L- and P-ring protein indicate a former Gram-negative type of cell wall. Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses.
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Affiliation(s)
- F. O. Glöckner
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
- To whom correspondence may be addressed. E-mail:
or
.
Requests for sequencing details, sequences, and clones should go directly to
R. Reinhardt. E-mail:
| | - M. Kube
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - M. Bauer
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
- To whom correspondence may be addressed. E-mail:
or
.
Requests for sequencing details, sequences, and clones should go directly to
R. Reinhardt. E-mail:
| | - H. Teeling
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - T. Lombardot
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - W. Ludwig
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - D. Gade
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - A. Beck
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - K. Borzym
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - K. Heitmann
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - R. Rabus
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - H. Schlesner
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - R. Amann
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - R. Reinhardt
- Max Planck Institute for Marine Microbiology,
Celsiusstrasse 1, D-28359 Bremen, Germany; Max
Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin,
Germany; Department of Microbiology, Technical
University Munich, Am Hochanger 4, D-85350 Freising, Germany; and
Department for General Microbiology, University
of Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
- To whom correspondence may be addressed. E-mail:
or
.
Requests for sequencing details, sequences, and clones should go directly to
R. Reinhardt. E-mail:
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