Deep-sea vent ε-proteobacterial genomes provide insights into emergence of pathogens

  1. Satoshi Nakagawa†,‡,
  2. Yoshihiro Takaki§,
  3. Shigeru Shimamura§,
  4. Anna-Louise Reysenbach,
  5. Ken Takai†, and
  6. Koki Horikoshi†,§
  1. †Subground Animalcule Retrieval (SUGAR) Program and
  2. §Extremophiles Research Program, Extremobiosphere Research Center (XBR), Japan Agency for Marine–Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan; and
  3. Department of Biology, Portland State University, Portland, OR 97201

  1. Edited by Rita R. Colwell, University of Maryland, College Park, MD, and approved June 7, 2007 (received for review January 25, 2007)

  1. Fig. 1.
    View larger version:
    Fig. 1.

    Phylogenetic tree of 16S rRNA gene sequences. The deep-sea vent ε-Proteobacteria are shown in red. Branch points conserved with bootstrap values of >75% (filled circles) and bootstrap value of 50 to 74% (open circles) are indicated. Scale bar represents the expected number of changes per position.


  2. Fig. 2.
    View larger version:
    Fig. 2.

    Central metabolism and solute transport in the deep-sea vent ε-Proteobacteria. Pathways for which no predictable enzymes were found in strains SB155-2 and NBC37-1 genomes are shown in blue and red arrows, respectively. Numbers of transport machineries are shown for both strains. The KEGG database was used for the reconstruction of metabolic pathways. Cyt, cytochrome; H2ase, hydrogenase; Sqr, sulfide-quinone oxidoreductases; Nap, periplasmic nitrate reductase; cdNir, cytochrome cd 1 nitrite reductase; Nor, nitric oxide reductase; Nos, nitrous oxide reductase; Mdh, malate dehydrogenase; Sdh, succinate dehydrogenase.


  3. Fig. 3.
    View larger version:
    Fig. 3.

    Virulence genes in ε Proteobacteria. (A) Organization of N-linked glycosylation gene clusters. Cje, C. jejuni NCTC11168; Hpy, H. pylori 26695; Wsu, W. succinogenes DSM1740. Genes are color-coded by the function of encoded protein (essential oligosaccharyltransferase PglB, red; glycosyltransferase, yellow; enzymes involved in sugar biosynthesis, blue). Connecting lines indicate corresponding orthologs. (B) Organization of H2-uptake and -sensing hydrogenase gene clusters. Orthologs are shown in the same colors. hydA, small subunit gene; hydB, large subunit gene; hydC, cytochrome b subunit gene; others, maturation or accessory genes necessary for the assembly of holoenzyme.


  4. Fig. 4.
    View larger version:
    Fig. 4.

    DNA-repair genes in representative Proteobacteria. Blue indicates presence, and yellow indicates absence. Hpy, H. pylori 26695; Cje, C. jejuni NCTC11168; Wsu, W. succinogenes DSM1740; Eco, Escherichia coli K12 (γ-proteobacterium); Hin, Haemophilus influenzae Rd KW20 (γ-proteobacterium); Cvi, Chromobacterium violaceum ATCC12472 (β-proteobacterium); Gsu, Geobacter sulfurreducens PCA (δ-proteobacterium).


Footnotes

  • ‡To whom correspondence should be addressed. E-mail: nakagawas{at}jamstec.go.jp
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  1. Published online before print July 5, 2007, doi: 10.1073/pnas.0700687104 PNAS July 17, 2007 vol. 104 no. 29 12146-12150
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