Abstract
BackgroundThe ribosome translates mRNA to protein with the aid of a number of accessory protein factors. Translational GTPases (trGTPases) are an integral part of the ‘core set’ of essential translational factors, and are some of the most conserved proteins across life. This study takes advantage of the wealth of available genomic data, along with novel functional information that has come to light for a number of trGTPases to address the full evolutionary and functional diversity of this superfamily across all domains of life.ResultsThrough sensitive sequence searching combined with phylogenetic analysis, 57 distinct subfamilies of trGTPases are identified: 14 bacterial, 7 archaeal and 35 eukaryotic (of which 21 are known or predicted to be organellar). The results uncover the functional evolution of trGTPases from before the last common ancestor of life on earth to the current day.ConclusionsWhile some trGTPases are universal, others are limited to certain taxa, suggesting lineage-specific translational control mechanisms that exist on a base of core factors. These lineage-specific features may give organisms the ability to tune their translation machinery to respond to their environment. Only a fraction of the diversity of the trGTPase superfamily has been subjected to experimental analyses; this comprehensive classification brings to light novel and overlooked translation factors that are worthy of further investigation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1289-7) contains supplementary material, which is available to authorized users.
Highlights
The ribosome translates mRNA to protein with the aid of a number of accessory protein factors
This was followed by subsequent rounds of phylogenetic analysis to identify clusters representing subfamilies, and sequence searching with Hidden Markov Model (HMM) profiles of trGTPase subfamily alignments against a set of 1483 genomes
The complement of trGTPases that can be found in each of the genomes considered here is recorded in the additional files available online: all identified trGTPases and their sequence identifiers (Additional file 1) and lists of trGTPases found in each genome, sorted by taxonomy (Additional file 2)
Summary
The ribosome translates mRNA to protein with the aid of a number of accessory protein factors. Translational GTPases (trGTPases) are an integral part of the ‘core set’ of essential translational factors, and are some of the most conserved proteins across life. The translational GTPases (trGTPases) are an ancient superfamily of proteins, predating the last common ancestor of life (LUCA). IF2 in bacteria, which is known as eIF5B in eukaryotes and aIF5B in archaea, is an essential initiation factor, promoting initiator tRNA binding to the small ribosomal subunit, and subsequent subunit joining. Previous sequence analysis of the P-loop superclass to which the trGTPases belong identified four families that are found in all domains of life, suggesting their presence in the last universal common ancestor of all life on earth (LUCA): EF1, EF2, IF2 and SelB, a specialized EF1-like factor for the delivery of selenocystyl-tRNA to the ribosome [8]
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