title: Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms.
abstract: BACKGROUND
  While the premise that lateral gene transfer (LGT) is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA synthetases (aaRS) is no longer contentious. aaRSs are ancient enzymes, guarding the fidelity of the genetic code. They are clustered in two structurally unrelated classes. Only lysine aminoacyl-tRNA synthetase (LysRS) is found both as a class 1 and a class 2 enzyme (LysRS1-2). Remarkably, in several extant prokaryotes both classes of the enzyme coexist, a unique phenomenon that has yet to receive its due attention.
  
  
  RESULTS
  We applied a phylogenetic approach for determining the extent and origin of LGT in prokaryotic LysRS. Reconstructing species trees for Archaea and Bacteria, and inferring that their last common ancestors encoded LysRS1 and LysRS2, respectively, we studied the gains and losses of both classes. A complex pattern of LGT events emerged. In specific groups of organisms LysRS1 was replaced by LysRS2 (and vice versa). In one occasion, within the alpha proteobacteria, a LysRS2 to LysRS1 LGT was followed by reversal to LysRS2. After establishing the most likely LGT paths, we studied the possible origins of the laterally transferred genes. To this end, we reconstructed LysRS gene trees and evaluated the likely origins of the laterally transferred genes. While the sources of LysRS1 LGTs were readily identified, those for LysRS2 remain, for now, uncertain. The replacement of one LysRS by another apparently transits through a stage simultaneously coding for both synthetases, probably conferring a selective advantage to the affected organisms.
  
  
  CONCLUSIONS
  The family of LysRSs features complex LGT events. The currently available data were sufficient for identifying unambiguously the origins of LysRS1 but not of LysRS2 gene transfers. A selective advantage is suggested to organisms encoding simultaneously LysRS1-2.
authors.affiliation: Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel. sshaul@netvision.net.il
authors.forename: Shaul
authors.initials: S
authors.lastname: Shaul
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.forename: Tal
authors.initials: T
authors.lastname: Pupko
mesh_terms: D020561:Alphaproteobacteria / Q000201:enzymology / Q000235:genetics; D001105:Archaea / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D019843:Archaeal Proteins / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D005075:Biological Evolution; D019615:Crenarchaeota / Q000201:enzymology / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics / Q000502:physiology; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D007527:Isoenzymes / Q000235:genetics; D008250:Lysine-tRNA Ligase / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000201:enzymology*; D013045:Species Specificity
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D007527:Isoenzymes; D008250:Lysine-tRNA Ligase