Molecular characterization of cold adaptation based on ortholog protein sequences from Vibrionaceae species.
A set of 298 protein families from psychrophilic Vibrio salmonicida was compiled to identify genotypic characteristics that discern it from orthologous sequences from the mesophilic Vibrio/Photobacterium branch of the gamma-Proteobacteria (Vibrionaceae family). In our comparative exploration we employed alignment based bioinformatical and statistical methods. Interesting information was found in the substitution matrices, and the pattern of asymmetries in the amino acid substitution process. Together with the compositional difference, they identified the amino acids Ile, Asn, Ala and Gln as those having the most psycrophilic involvement. Ile and Asn are enhanced whereas Gln and Ala are suppressed. The inflexible Pro residue is also suppressed in loop regions, as expected in a flexible structure. The dataset were also classified and analysed according to the predicted subcellular location, and we made an additional study of 183 intracellular and 65 membrane proteins. Our results revealed that the psychrophilic proteins have similar hydrophobic and charge contributions in the core of the protein as mesophilic proteins, while the solvent-exposed surface area is significantly more hydrophobic. In addition, the psychrophilic intracellular (but not the membrane) proteins are significantly more negatively charged at the surface. Our analysis supports the hypothesis of preference for more flexible amino acids at the molecular surface. Life in cold climate seems to be obtained through many minor structural modifications rather than certain amino acids substitutions.
Thorvaldsen
Steinar
S
Department of Mathematics and Statistics, Faculty of Science, University of Tromsø, 9037, Tromsø, Norway. steinart@math.uit.no
Hjerde
Erik
E
Fenton
Chris
C
Willassen
Nils P
NP
D000064:Acclimatization; D000409:Alanine / Q000737:chemistry; D044165:Aliivibrio salmonicida / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001216:Asparagine / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D003080:Cold Temperature; D019295:Computational Biology; D030541:Databases, Genetic; D005973:Glutamine / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D007532:Isoleucine / Q000737:chemistry; D011487:Protein Conformation; D016415:Sequence Alignment; D013499:Surface Properties; D014737:Vibrionaceae / Q000737:chemistry* / Q000235:genetics / Q000502:physiology
D001426:Bacterial Proteins; D007532:Isoleucine; D005973:Glutamine; D001216:Asparagine; D000409:Alanine