title: Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.
abstract: BACKGROUND
  The rTS gene (ENOSF1), first identified in Homo sapiens as a gene complementary to the thymidylate synthase (TYMS) mRNA, is known to encode two protein isoforms, rTSalpha and rTSbeta. The rTSbeta isoform appears to be an enzyme responsible for the synthesis of signaling molecules involved in the down-regulation of thymidylate synthase, but the exact cellular functions of rTS genes are largely unknown.
  
  
  RESULTS
  Through comparative genomic sequence analysis, we predicted the existence of a novel protein isoform, rTS, which has a 27 residue longer N-terminus by virtue of utilizing an alternative start codon located upstream of the start codon in rTSbeta. We observed that a similar extended N-terminus could be predicted in all rTS genes for which genomic sequences are available and the extended regions are conserved from bacteria to human. Therefore, we reasoned that the protein with the extended N-terminus might represent an ancestral form of the rTS protein. Sequence analysis strongly predicts a mitochondrial signal sequence in the extended N-terminal of human rTSgamma, which is absent in rTSbeta. We confirmed the existence of rTS in human mitochondria experimentally by demonstrating the presence of both rTSgamma and rTSbeta proteins in mitochondria isolated by subcellular fractionation. In addition, our comprehensive analysis of rTS orthologous sequences reveals an unusual phylogenetic distribution of this gene, which suggests the occurrence of one or more horizontal gene transfer events.
  
  
  CONCLUSIONS
  The presence of two rTS isoforms in mitochondria suggests that the rTS signaling pathway may be active within mitochondria. Our report also presents an example of identifying novel protein isoforms and for improving gene annotation through comparative genomic analysis.
authors.affiliation: Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, USA. Ping.Liang@roswellpark.org
authors.forename: Ping
authors.initials: P
authors.lastname: Liang
authors.forename: Jayakumar R
authors.initials: JR
authors.lastname: Nair
authors.forename: Lei
authors.initials: L
authors.lastname: Song
authors.forename: John J
authors.initials: JJ
authors.lastname: McGuire
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Dolnick
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D015153:Blotting, Western; D002460:Cell Line; D003062:Codon; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D008928:Mitochondria / Q000378:metabolism*; D008954:Models, Biological; D008969:Molecular Sequence Data; D010802:Phylogeny; D020033:Protein Isoforms; D017434:Protein Structure, Tertiary; D013347:Subcellular Fractions; D013940:Thymidylate Synthase / Q000235:genetics* / Q000378:metabolism
chemical_list: D003062:Codon; D020033:Protein Isoforms; D013940:Thymidylate Synthase