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 journal of 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