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Online Journal of Bioinformatics©
Volume 9 (1): 1-11, 2008
In silico analysis of P5CS gene evolution in plants
Kumari A1, Patade VY, Suprasanna P
Plant Cell Culture Technology Section,
Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay,
Mumbai 400 084.
Kumari A, Patade VY, Suprasanna P., In Silico analysis of P5CS gene evolution in plants, Online J Bioinformatics, 9 (1): 1-11, 2008. Proline is a ubiquitous osmoprotectant and plants synthesize proline mainly through glutamate pathway under abiotic stress. The bifunctional enzyme, P5CS catalyses the first and rate limiting step in proline biosynthesis. In this study, the molecular evolution of the P5CS gene of higher plants was investigated. The PUA domain was found to be completely removed during evolution, so as to increase the efficiency of the bifunctional P5CS enzyme. Comparative analysis of the domain architectures combined with sequence-based phylogenetic analysis of the γ Glutamyl kinase and L Glutamate γ- semialdehyde dehydrogenase of the enzyme revealed conservation of the domains, from bacteria to plants, with minor variations. The β4-αE loop of G5K is found to be conserved throught the plants, which play an important role in feedback inhibition. Codon substitution analysis revealed 0.508 as ratio of non-synonymous to synonymous substitution (ω) for the entire coding region, suggesting the purifying selection of the gene sequence in nature. However, for few coding sites ω values were significantly higher indicating the presence of buffer sites for mutations in coding sequence.
Keywords: proline, P5CS, GK, GSA dehydrogenase, molecular evolution, Ka/Ks Abbreviations: CDS-Coding Sequence; P5CS- delta1-pyrolline-5-carboxylate synthetase; ENC-Effective Number of Codons; G5K- γ Glutamyl kinase; GSA- L Glutamate γ- semialdehyde; PUA- Pseudouridine synthases. Authors contribution was equal