Abstract
Repeated domains in proteins that have undergone duplication or loss, and sequence divergence, are especially informative about phylogenetic relationships. We have exploited divergent repeats of the highly structured, 50-amino acid WHEP domains that join the catalytic subunits of bifunctional glutamyl-prolyl tRNA synthetase (EPRS) as a sequence-informed repeat (SIR) to trace the origin and evolution of EPRS in holozoa. EPRS is the only fused tRNA synthetase, with two distinct aminoacylation activities, and a non-canonical translation regulatory function mediated by the WHEP domains in the linker. Investigating the duplications, deletions and divergence of WHEP domains, we traced the bifunctional EPRS to choanozoans and identified the fusion event leading to its origin at the divergence of ichthyosporea and emergence of filozoa nearly a billion years ago. Distribution of WHEP domains from a single species in two or more distinct clades suggested common descent, allowing the identification of linking organisms. The discrete assortment of choanoflagellate WHEP domains with choanozoan domains as well as with those in metazoans supported the phylogenetic position of choanoflagellates as the closest sister group to metazoans. Analysis of clustering and assortment of WHEP domains provided unexpected insights into phylogenetic relationships amongst holozoan taxa. Furthermore, observed gaps in the transition between WHEP domain groupings in distant taxa allowed the prediction of undiscovered or extinct evolutionary intermediates. Analysis based on SIR domains can provide a phylogenetic counterpart to palaentological approaches of discovering “missing links” in the tree of life.
Highlights
An increasing amount of whole genome sequence information from diverse organisms offers much promise for determining phylogenetic relationships between known taxa, and resolving the tree of life
EPRS belongs to an ancient family of enzymes conserved from bacteria to vertebrates, the aminoacyl tRNA synthetases (AARS), that catalyze the attachment of amino acids to cognate tRNAs essential for establishing the genetic code [10]
Identification as 50amino acid WHEP domains was confirmed by Pustell dot matrix analysis against human WHEP domains [17]
Summary
An increasing amount of whole genome sequence information from diverse organisms offers much promise for determining phylogenetic relationships between known taxa, and resolving the tree of life. Large-scale changes in discrete regions of the genome, which give rise to genome-level characters such as intron indels, retroposons, signature sequences, and duplications ( referred to as rare genomic changes) that occur relatively infrequently and are transmitted between taxa in the course of evolution, constitute quanta of genomic information that can be especially useful in determining phylogenetic relationships [5]. The glutamyl-prolyl tRNA synthetase (EPRS) is one such protein, with defined, 50-amino acid, helix-turn-helix domains referred to as WHEP-TRS (or WHEP) domains present in a variable number of repeats in diverse metazoan taxa [7,8,9]. The functional importance of EPRS WHEP repeats is suggested by their conservation, albeit in variable numbers and amino acid sequence, in diverse bilaterian taxa. An analysis based on intron positions has suggested that the domain was acquired by HRS and GRS early in eukaryote evolution and later spread to EPRS [15]
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