Abstract
There is a desire for increasing use of statistical methods in analysing the growing amounts of bio-sequences. We present statistical methods that are useful when a protein alignment can be divided into two groups based on known features or traits. The approach is based on stratification of the data, and to show the applicability of the methods we present analysis of genomic data from proteobacteria orders. A dataset of 25 periplasmic/extracellular bacterial enzyme endonuclease I proteins was compiled to identify genotypic characteristics that separate the cold adapted proteins from ortholog sequences with a higher optimal growth temperature. Our results reveal that the cold adapted protein has a significantly more positively charged exterior. Life in a cold climate seems to be enabled by many minor structural modifications rather than a particular amino acid substitution. Redistribution of charge might be one of the most important signatures for cold adaptation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Committee on Frontiers in Polar Biology (CB): Frontiers in polar biology in the genomics era. National Academies Press, Washington (2003)
Sohail, K., Cavicchioli, R.: Cold-adapted enzymes. Annu. Rev. Biochem. 75, 403–433 (2006)
Saunders, N.F.W., Thomas, T., Curmi, P.M.G., et al.: Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13(7), 1580–1588 (2003)
Karlin, S., et al.: Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes. Theor. Popul. Biol. 61, 367–390 (2002)
Pe’er, I., et al.: Proteomic signatures: Amino acid and oligopeptide compositions differentiate among phyla. Proteins-Structure Function and Genetics 54(1), 20–40 (2004)
Jekel, M., Wackernagel, W.: The periplasmic endonuclease I of Escherichia coli has amino-acid sequence homology to the extracellular DNases of Vibrio cholerae and Aeromonas hydrophila. Gene 154(1), 55–59 (1995)
Li, C.L., et al.: DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. Embo J. 22(15), 4014–4025 (2003)
Hall, T.A.: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41, 95–98 (1999)
Lambros, R.J., Mortimer, J.R., Forsdyke, D.R.: Optimum growth temperature and the base composition of open reading frames in prokaryotes. Extremophiles 7, 443–450 (2003)
Bendtsen, J.D., et al.: Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783–795 (2004)
Huang, S.L., et al.: PGTdb: a database providing growth temperatures of prokaryotes. Bioinformatics 20, 276–278 (2004)
Garrity, G.M.: Bergey’s Manual of Systematic Bacteriology, vol. 2B, 2nd edn. Plenum, New York (2005)
Fraczkiewicz, R., Braun, W.: Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comp. Chem. 19(3), 319–333 (1998)
Haney, P.J., Badger, J.H., Buldak, G.L., et al.: Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. PNAS 96(7), 3578–3583 (1999)
McDonald, J.H., Grasso, A.M., Rejto, L.K.: Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Molecular Biology and Evolution 16(12), 1785–1790 (1999)
Smith, N.G.C., Eyre-Walker, A.: A test of amino acid reversibility. J. Mol. Evol. 52, 467–469 (2001)
Chakravarty, S., Varadarajan, R.: Elucidation of factors responsible for enhanced thermal stability of proteins: A structural genomics based study. Biochemistry 41(25), 8152–8161 (2002)
Mantel, N., Fliss, J.L.: Minimum expected cell-size requirements for the Mantel-Haenszel one-degree-of-freedom chi-square test and a related rapid procedure. American Journal of Epidemiology 112, 129–134 (1980)
Parshall, C.G., Miller, T.R.: Exact versus asymptotic Mantel-Haenszel DIF statistics - A comparison of performance under small-sample conditions. Journal of Educational Measurement 32(3), 302–316 (1995)
Benjamini, Y., Yekutieli, D.: The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29(4), 1165–1188 (2001)
Koen, J.F., et al.: Implementing false discovery rate control: increasing your power. OIKOS 108, 643–647 (2005)
Nakashima, H., Fukuchi, S., Nishikawa, K.: Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. Journal of Biochemistry 133(4), 507–513 (2003)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Thorvaldsen, S., Ytterstad, E., Flå, T. (2007). Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices. In: Măndoiu, I., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2007. Lecture Notes in Computer Science(), vol 4463. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72031-7_35
Download citation
DOI: https://doi.org/10.1007/978-3-540-72031-7_35
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-72030-0
Online ISBN: 978-3-540-72031-7
eBook Packages: Computer ScienceComputer Science (R0)