The complex evolutionary history of aminoacyl-tRNA synthetases.
Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. In the course of this analysis, highly conserved protein motifs and domains within each of the AARS loci were identified and used to build a web-based computational tool for the genome-wide detection of AARS coding sequences. This is based on hidden Markov models (HMMs) and is available together with a cognate database that may be used for specific analyses. The bioinformatics tools that we have developed may also help to identify new antibiotic agents and targets using these essential enzymes. These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code.
Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
Anargyros
A
Chaliotis
Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
Panayotis
P
Vlastaridis
Molecular Microbiology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
Dimitris
D
Mossialos
Department of Microbiology, The Ohio State University, Columbus, OH, USA.
Michael
M
Ibba
Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, 4 allée Konrad Röntgen, Strasbourg Cedex, France.
Hubert D
HD
Becker
Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece.
Constantinos
C
Stathopoulos
Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
Grigorios D
GD
Amoutzias
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D001419:Bacteria / Q000187:drug effects / Q000201:enzymology / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D030562:Databases, Protein; D019143:Evolution, Molecular; D008390:Markov Chains; D010802:Phylogeny; D000072417:Protein Domains
D000604:Amino Acyl-tRNA Synthetases