1. Evolutionary dynamics of Polynucelotide phosphorylases
- Author
-
Paul B. Fisher, Santanu Dasgupta, Upneet K. Sokhi, Rob DeSalle, Devanand Sarkar, Manny D. Bacolod, and Swadesh K. Das
- Subjects
Polyribonucleotide Nucleotidyltransferase ,Genetics ,Phylogenetic tree ,Lineage (evolution) ,Protein domain ,Sequence Analysis, DNA ,Biology ,RNase PH ,Protein Structure, Secondary ,Evolution, Molecular ,Sister group ,Catalytic Domain ,Gene duplication ,Animals ,Polynucleotide phosphorylase ,Selection, Genetic ,Codon ,Molecular Biology ,Conserved Sequence ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Sequence (medicine) - Abstract
Polynucleotide phosphorylase (PNPase) is an evolutionarily conserved 3′ → 5′ phosphate-dependent exoribonucease belonging to the PDX family of proteins. It consists of two catalytic RNase PH domains (PNP1 and PNP2), an α-helical domain and two RNA-binding domains. The PNP1 and PNP2 domains share substantial sequence and structural homology with RNase PH (RPH), which is another PDX family member found in all the three major kingdoms of life, suggesting that these three domains originated from a common ancestor. Phylogenetic analysis (based on the PNPase/RNase PH sequence information for 43 vertebrate taxa) shows that PNP2 and RPH are sister taxa which arose through duplication of the ancestral PNP1 domain. Also, all three domains (PNP1, PNP2 and RPH), along with the KH and S1 domains have undergone significant and directional sequence change, as determined by branch and site-specific d N /d S analyses. In general, codons that show d N /d S ratios that are significantly greater than 1.0 are outside the ordered regions (α-helices and β-sheets) of these protein domains. In addition, sites that have been selected for mutagenesis in these proteins lie embedded in regions where there is a preponderance of codons with d N /d S values that are not significantly different from 0.0. Overall, this report is an attempt to further our understanding of the evolutionary history of these three protein domains, and define the evolutionary events that led to their refinement in the vertebrate lineage leading to mammals.
- Published
- 2014
- Full Text
- View/download PDF