Computer system for analysis of molecular evolution modes of genes and proteins: a case study of the cyclin B molecular evolution
The evolution of protein-coding genes is characterized by two types of single-nucleotide substitutions: non-synonymous, altering protein structure, and synonymous, that does not change the protein. Natural selection of proteins is manifested through various non-synonymous fixations. Protein function, structure and folding are all determined by the combination of physicochemical properties of amino acids. To analyze the protein evolution mode two main approaches were previously introduced: (1) based on the calculation of the radical (large changes in certain physicochemical property) to conservative (small changes in certain physicochemical property) codon substitutions rate ratio (KR/KC), and (2) based on analysis of variance of rate changes of various physicochemical amino acid properties (VPC) in the course of protein evolution. The essential drawback of these approaches is the need to know in advance "positive change" of certain amino acid properties.Our novel computer system for protein evolution mode analysis is also based on the KR/KC and VPC, but has two crucial differences which allow us to overcome the drawback: (1) we take into account all the known properties of amino acids, and (2) we calculate the statistical relation of properties changes with certain adaptive phenotypical features of organisms. The opportunity to match evolutionary change of all amino acid properties with positively selected phenotypical features of organisms permits direct attribution of certain protein changes to selection events. On this basis, a computer system for analyzing of molecular evolution mode of genes and proteins was developed (http://pixie.bionet.nsc.ru/samem/). Our computer system consists of two main pipelines, analyzing the evolutionary modes of genes (I) and proteins (II), and two supplementary pipelines, collecting a sample of genes and proteins (III) and producing their primary analysis (IV). An essential feature of the gene analysis pipeline is a possibility to study gene evolution modes using different KR/KC calculation methods. Pipeline for protein analysis implements a novel algorithm for detection of atypical amino acids fixations on phylogenetic tree branches. This algorithm is based on Markov simulation of protein sequence evolution, and uses the permutation test for comparison of the simulated protein molecular evolution with real one.To test the capabilities of our computer system and performance of our novel algorithm for detection of atypical amino acids fixations on tree branches the molecular evolution of cyclin B protein family was analyzed. It was shown that the fixation of atypical amino acid substitutions is frequent to both cyclin paralogs B1 and B2 after cyclin B duplication in the vertebrate evolution. In contrast, only one of the duplicated cyclin B copies possessed of atypical amino acid fixations in a series of successive cyclin B duplications in the fungal evolution. Moreover, it was shown that the evolution of cyclins B3 subfamily, in contrast with cyclin B1 and B2 subfamilies, was strictly associated with increasing of animal's complexity. This association can be explained by the important role of cyclin B3 in the meiosis and, hence, in the mechanisms of reproductive isolation.
Keywords
молекулярная эволюция,
консервативные и радикальные аминокислотные замены,
система «клиент-сервер»,
статистический анализ,
циклины B,
molecular evolution,
conservative and radical amino acid substitutions,
client-server system,
statistical analysis,
cyclin BAuthors
| Gunbin Konstantin V. | Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk | genkvg@bionet.nsc.ru |
| Genaev Mikhail A. | Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk | mag@bionet.nsc.ru |
| Turnaev Igor I. | Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk | turn@bionet.nsc.ru |
| Afonnikov Dmitry A. | Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk | ada@bionet.nsc.ru |
Всего: 4
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