Sequence comparison and environmental adaptation of a bacterial endonuclease

• Published in: Computational biology and chemistry 2007-06, Vol.31 (3), p.163-172
• Main Authors: Altermark, Bjørn, Thorvaldsen, Steinar, Moe, Elin, Smalås, Arne O., Willassen, Nils P.
• Format: Article
• Language: English
• Subjects: Adaptation, Physiological - genetics; Amino acid property; Amino Acid Substitution; Bacteria - drug effects; Bacteria - enzymology; Bacteria - genetics; Cold adaptation; Cold Temperature; Computational Biology - methods; Databases, Protein; Deoxyribonuclease I - chemistry; Deoxyribonuclease I - genetics; Endonuclease I; Evolution, Molecular; Halophilic enzymes; Hydrophobic and Hydrophilic Interactions; Isoelectric Point; Osmolar Concentration; Protein Conformation; Protein Structure, Secondary; Salts - pharmacology; Sequence Alignment - methods; Sequence analysis; Sequence Analysis, DNA; Surface Properties; Temperature
• ISSN: 1476-9271; 1476-928X
• DOI: 10.1016/j.compbiolchem.2007.03.003

The periplasmic/extracellular bacterial enzyme endonuclease I was chosen as a model system to identify features that might be responsible for temperature- and salt adaptation. A statistical study of amino acid sequence properties belonging to endonuclease I enzymes from three mesophilic habitats (non-marine, brackish water and marine), and three marine temperature groups (psychrophile, intermediate and mesophile) has been conducted. Ten new endonuclease I genes have been sequenced in order to increase the sample size. A bioinformatical method of property dependent statistical analysis of alignments has been applied. To our knowledge this is the first time these methods have been used in order to investigate environmental adaptation of enzymes. Adaptation to low temperature seems to involve increased surface isoelectric point and hydrophobicity in contrast to salt adaptation in which the isoelectric point and hydrophobicity at the surface decreases. Redistribution of charge and hydrophobicity might be the most important signature for cold adaptation and salt adaptation of this enzyme class. The results indicate that general trends of adaptation are possible to elucidate from the amino acid sequences. Also in this paper a new scale of stratified B-factors, derived from the Protein Data Bank, is presented.