title: Structure based hypothesis of a mitochondrial ribosome rescue mechanism.
abstract: BACKGROUND
  mtRF1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtRF1a. To elucidate the function of mtRF1, we determined the positions that are conserved among mtRF1 sequences but that are different in their mtRF1a paralogs. We subsequently modeled the 3D structure of mtRF1a and mtRF1 bound to the ribosome, highlighting the structural implications of these differences to derive a hypothesis for the function of mtRF1.
  
  
  RESULTS
  Our model predicts, in agreement with the experimental data, that the 3D structure of mtRF1a allows it to recognize the stop codons UAA and UAG in the A-site of the ribosome. In contrast, we show that mtRF1 likely can only bind the ribosome when the A-site is devoid of mRNA. Furthermore, while mtRF1a will adopt its catalytic conformation, in which it functions as a peptidyl-tRNA hydrolase in the ribosome, only upon binding of a stop codon in the A-site, mtRF1 appears specifically adapted to assume this extended, peptidyl-tRNA hydrolyzing conformation in the absence of mRNA in the A-site.
  
  
  CONCLUSIONS
  We predict that mtRF1 specifically recognizes ribosomes with an empty A-site and is able to function as a peptidyl-tRNA hydrolase in those situations. Stalled ribosomes with empty A-sites that still contain a tRNA bound to a peptide chain can result from the translation of truncated, stop-codon less mRNAs. We hypothesize that mtRF1 recycles such stalled ribosomes, performing a function that is analogous to that of tmRNA in bacteria.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P,O, Box 9101, 6400, HB Nijmegen, The Netherlands. huynen@cmbi.ru.nl
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
authors.forename: Isabel
authors.initials: I
authors.lastname: Duarte
authors.forename: Zofia M A
authors.initials: ZM
authors.lastname: Chrzanowska-Lightowlers
authors.forename: Sander B
authors.initials: SB
authors.lastname: Nabuurs
mesh_terms: D000818:Animals; D002265:Carboxylic Ester Hydrolases / Q000378:metabolism; D018388:Codon, Terminator; D017124:Conserved Sequence; D006801:Humans; D008928:Mitochondria / Q000235:genetics; D024101:Mitochondrial Proteins / Q000235:genetics*; D008954:Models, Biological; D010443:Peptide Chain Termination, Translational; D010454:Peptide Termination Factors / Q000235:genetics*; D010802:Phylogeny; D014176:Protein Biosynthesis; D012329:RNA, Bacterial / Q000235:genetics; D012346:RNA, Transfer, Amino Acyl / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D016963:Thermus thermophilus / Q000235:genetics; D014714:Vertebrates / Q000235:genetics*
chemical_list: D018388:Codon, Terminator; C523958:MTRF1L protein, human; D024101:Mitochondrial Proteins; D010454:Peptide Termination Factors; D012329:RNA, Bacterial; D012346:RNA, Transfer, Amino Acyl; C019037:tRNA, peptidyl-; C096222:tmRNA; D002265:Carboxylic Ester Hydrolases; C019674:aminoacyl-tRNA hydrolase