Genomics of an extreme psychrophile, Psychromonas ingrahamii

Riley, Monica; Staley, James T; Danchin, Antoine; Wang, Ting Zhang; Brettin, Thomas S; Hauser, Loren J; Land, Miriam L; Thompson, Linda S

doi:10.1186/1471-2164-9-210

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

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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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: Staley, James T
Danchin, Antoine
Brettin, Thomas S
Land, Miriam L
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: gold
doi.org
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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