title: The N-terminus of GalE induces tmRNA activity in Escherichia coli.
abstract: BACKGROUND
  The tmRNA quality control system recognizes stalled translation complexes and facilitates ribosome recycling in a process termed 'ribosome rescue'. During ribosome rescue, nascent chains are tagged with the tmRNA-encoded SsrA peptide, which targets tagged proteins for degradation. In Escherichia coli, tmRNA rescues ribosomes arrested on truncated messages, as well as ribosomes that are paused during elongation and termination.
  
  
  RESULTS
  Here, we describe a new translational pausing determinant that leads to SsrA peptide tagging of the E. coli GalE protein (UDP-galactose 4-epimerase). GalE chains are tagged at more than 150 sites, primarily within distinct clusters throughout the C-terminal domain. These tagging sites do not correspond to rare codon clusters and synonymous recoding of the galE gene had little effect on tagging. Moreover, tagging was largely unaffected by perturbations that either stabilize or destabilize the galE transcript. Examination of GalE-thioredoxin (TrxA) fusion proteins showed that the GalE C-terminal domain is no longer tagged when fused to an N-terminal TrxA domain. Conversely, the N-terminus of GalE induced tagging within the fused C-terminal TrxA domain.
  
  
  CONCLUSIONS
  These findings suggest that translation of the GalE N-terminus induces subsequent tagging of the C-terminal domain. We propose that co-translational maturation of the GalE N-terminal domain influences ribosome pausing and subsequent tmRNA activity.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America.
authors.forename: Zachary C
authors.initials: ZC
authors.lastname: Ruhe
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Hayes
mesh_terms: D003062:Codon; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry; D017353:Gene Deletion; D013058:Mass Spectrometry / Q000379:methods; D009841:Oligonucleotides / Q000737:chemistry; D016366:Open Reading Frames; D010957:Plasmids / Q000378:metabolism; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000737:chemistry; D012270:Ribosomes / Q000378:metabolism; D013879:Thioredoxins / Q000737:chemistry; D014534:UDPglucose 4-Epimerase / Q000737:chemistry* / Q000378:metabolism
chemical_list: D003062:Codon; D029968:Escherichia coli Proteins; D009841:Oligonucleotides; D012329:RNA, Bacterial; D012333:RNA, Messenger; D011993:Recombinant Fusion Proteins; C517609:TrxA protein, E coli; C096222:tmRNA; D013879:Thioredoxins; D014534:UDPglucose 4-Epimerase; C020551:galactose epimerase