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Cited by 126Polar Research and EcologyBacterial Genetics and BiotechnologyGenomics and Phylogenetic Studies

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Genomics of an extreme psychrophile, Psychromonas ingrahamii

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Riley, Monica, Staley, James T, Danchin, Antoine, Wang, Ting Zhang, Brettin, Thomas S, Hauser, Loren J, Land, Miriam L, Thompson, Linda S·2008·BMC Genomics
DOI 10.1186/1471-2164-9-210PMC PMC2405808
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Abstract

BACKGROUND: The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. RESULTS: Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. CONCLUSION: The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.

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Figure 1 Distribution of lengths of 916 orthologous proteins in four bacteria. Distribution of lengths of proteins as numbers of amino acid residues, ranging from 83 to 1501, in increments of 30. Black diamond = E. coli, red square = S. oneidensis, yellow triangle = V. cholerae, blue cross = P. ingrahamii.
Figure 1 Distribution of lengths of 916 orthologous proteins in four bacteria. Distribution of lengths of proteins as numbers of amino acid residues, ranging from 83 to 1501, in increments of 30. Black diamond = E. coli, red square = S. oneidensis, yellow triangle = V. cholerae, blue cross = P. ingrahamii.CC BY · PubMed Central
Figure 2 Correspondence analysis of amino acid content of P. ingrahamii proteins. Proteins over 100 residues were subjected to correspondence anlysis by amino acid content, clustered and plotted on first three most informative axes. Amino acid frequencies are superimposed. (See Methods).
Figure 2 Correspondence analysis of amino acid content of P. ingrahamii proteins. Proteins over 100 residues were subjected to correspondence anlysis by amino acid content, clustered and plotted on first three most informative axes. Amino acid frequencies are superimposed. (See Methods).CC BY · PubMed Central

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Metadata

Authors
Riley, M., Staley, J. T., Danchin, A., Wang, T. Z., Brettin, T. S., Hauser, L. J., Land, M. L., & Thompson, L. S.
Affiliations
  • Marine Biological Laboratory (US)
  • University of Washington (US)
  • Centre National de la Recherche Scientifique (FR)
  • Los Alamos National Laboratory (US)
  • Oak Ridge National Laboratory (US)
Corresponding author
Riley, Monica
ORCID
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2008
Volume
9
Issue
1
Pages
210
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/1471-2164-9-210
PMC
PMC2405808
OpenAlex
W1970019238
Cited by
126
References
39
Citations by year
2026: 2 · 2025: 3 · 2024: 2 · 2023: 3 · 2022: 7 · 2021: 8 · 2020: 2 · 2019: 5 · 2018: 9 · 2017: 12 · 2016: 7 · 2015: 6 · 2014: 10 · 2013: 12 · 2012: 11
FWCI
7.79
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Open Access Server of the Woods Hole Scientific Community (Woods Hole Scientific Community) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Science Foundation (DEAC02-05CH11231, DEAC05- 00OR22725, 00OR22725, W-7405-ENG-36)
  • U.S. Department of Energy (-AC02-05CH11231, AC05-00OR22725, W-7405, Contract No. DE-AC02-05-CH11231, DE--AC05--00OR22725, DE‐FG02‐, DE-AC05?, Contract No. DE-AC05-00OR22725, 05CH11231, FG02-04ER63940, No. DE-AC02-05-CH11231, DE AC02 05CH11231, -7405-ENG-48, W‐7405‐ENG‐48, No. DE-AC05-00OR22725, W-7405-ENG-36, 00OR22725, DE-AC02-)
  • National Aeronautics and Space Administration (DE-AC02-05CH11231, DE-AC05-00OR22725)
  • University of Washington
  • European Commission (DE-AC05-00OR22725, DE-AC02-05CH11231)
  • Office of Science (DEAC05- 00OR22725, No. DE-AC02- 05-CH11231, No. DE-AC05-00OR22725, DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231, Contract No. DE-AC02-05CH11231, AC05-00OR22725)
  • Biological and Environmental Research (W-7405-Eng-48, 05CH11231, No. DE-AC02-05CH11231, DE-AC02 − 05CH11231, 00OR22725, Contract No. DE-AC02-05CH11231, DE‐AC05–00OR22725, AC02-05CH11231)
  • Lawrence Livermore National Laboratory (W-7405-ENG 48, -7405-Eng-48, DE-AC05-00OR22725, W-7405-ENG-36, W-7405-ENG, DE-AC02-05CH11231)
  • Oak Ridge National Laboratory (AC05-00OR22725, Contract No. DE-AC05-00OR22725, DE-AC0205CH11231, DE-AC05-00OR22725)
  • Lawrence Berkeley National Laboratory (AC02‐05CH11231, DE-AC02-05CH11231, No. DE-AC02-05CH11231, DE-AC05-00OR22725, Contract No. DE-AC02-05CH11231, 05CH11231)
  • Los Alamos National Laboratory (W‐7405‐ENG‐36, DE-AC05-00OR22725, W-7405-Eng-48, DE-AC02-05CH11231)
Topics
  • Physical Sciences › Environmental Science › Ecology › Polar Research and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
sea ice bacteria, cold adaptation, protein composition, exopolysaccharides, osmolytes, nutrient transport, molecular chaperones, stress proteins, genome annotation
MeSH terms
Amino Acids, Bacterial Proteins, Base Composition, Cold Climate, DNA, Bacterial, Energy Metabolism, Fatty Acids, Genes, Bacterial, Multigene Family, Glucose, Heat-Shock Proteins, Ice, Molecular Weight, Seawater, Genome, Bacterial, Molecular Chaperones, Gammaproteobacteria, GC Rich Sequence, Genomics

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