Multisequence comparisons in protein coding genes |
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Authors: | Marcella Attimonelli Cecilia Lanave Elisabetta Sbisa Giuliano Preparata Cecilia Saccone |
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Institution: | (1) Centro Studio sui Mitocondri e Metabolismo Energetico CNR and Istituto di Chimica Biologica, Facoltá di Scienze, Universitá di Bari, Bari, Italia;(2) Dipartimento di Fisica, Universitá di Bari, Bari, Italia |
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Abstract: | A very powerful method for detecting functional constraints operative in biological macromolecules is presented. This method
entails performing a base permanence analysis of protein coding genes at each codon position simultaneously in different species.
It calculates the degree of permanence of subregions of the gene by dividing it into segments,c codons long, counting how many sites remain unchanged in each segment among all species compared. By comparing the base permanence
among several sequences with the expectations based on a stochastic evolutionary process, gene regions showing different degrees
of conservation can be selected. This means that wherever the permanence deviates significantly from the expected value generated
by the simulation, the corresponding regions are considered “constrained” or “hypervariable”.
The constrained regions are of two types: α and β. The α regions result from constraints at the amino acid level, whereas
the β regions are those probably involved in “control” processing. The method has been applied to mitochondrial genes coding
for subunit 6 of the ATPase and subunit 1 of the cytochrome oxidase in four mammalian species: human, rat, mouse, and cow.
In the two mitochondrial genes a few regions that are highly conserved in all codon positions have been identified. Among
these regions a sequence, common to both genes, that is complementary to a strongly conserved region of 12S rRNA has been
found. This method can also be of great help in studying molecular evolution mechanisms. |
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Keywords: | Protein coding genes multisequence comparisons in biological macromolecules functional constraints operative in gene regions selection of different degrees of conservation in constrained regions hypervariable regions mitochondrial genes conservation in cytochrome oxidase molecular evolution mechanisms of |
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