title: Common peptides study of aminoacyl-tRNA synthetases.
abstract: BACKGROUND
  Aminoacyl tRNA synthetases (aaRSs) constitute an essential enzyme super-family, providing fidelity of the translation process of mRNA to proteins in living cells. They are common to all kingdoms and are of utmost importance to all organisms. It is thus of great interest to understand the evolutionary relationships among them and underline signature motifs defining their common domains.
  
  
  RESULTS
  We utilized the Common Peptides (CPs) framework, based on extracted deterministic motifs from all aaRSs, to study family-specific properties. We identified novel aaRS-class related signatures that may supplement the current classification methods and provide a basis for identifying functional regions specific to each aaRS class. We exploited the space spanned by the CPs in order to identify similarities between aaRS families that are not observed using sequence alignment methods, identifying different inter-aaRS associations across different kingdom of life. We explored the evolutionary history of the aaRS families and evolutionary origins of the mitochondrial aaRSs. Lastly, we showed that prevalent CPs significantly overlap known catalytic and binding sites, suggesting that they have meaningful functional roles, as well as identifying a motif shared between aaRSs and a the Biotin-[acetyl-CoA carboxylase] synthetase (birA) enzyme overlapping binding sites in both families.
  
  
  CONCLUSIONS
  The study presents the multitude of ways to exploit the CP framework in order to extract meaningful patterns from the aaRS super-family. Specific CPs, discovered in this study, may play important roles in the functionality of these enzymes. We explored the evolutionary patterns in each aaRS family and tracked remote evolutionary links between these families.
authors.affiliation: The Balvatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel. assafgot@tau.ac.il
authors.forename: Assaf
authors.initials: A
authors.lastname: Gottlieb
authors.forename: Milana
authors.initials: M
authors.lastname: Frenkel-Morgenstern
authors.forename: Mark
authors.initials: M
authors.lastname: Safro
authors.forename: David
authors.initials: D
authors.lastname: Horn
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D019731:Carbon-Nitrogen Ligases / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D008928:Mitochondria / Q000201:enzymology; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D010446:Peptide Fragments; D000604:Amino Acyl-tRNA Synthetases; D019731:Carbon-Nitrogen Ligases; C027739:biotin-(acetyl-CoA carboxylase)synthetase