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.
ABSTRACT
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