title: Nascentome analysis uncovers futile protein synthesis in Escherichia coli.
abstract: Although co-translational biological processes attract much attention, no general and easy method has been available to detect cellular nascent polypeptide chains, which we propose to call collectively a "nascentome." We developed a method to selectively detect polypeptide portions of cellular polypeptidyl-tRNAs and used it to study the generality of the quality control reactions that rescue dead-end translation complexes. To detect nascent polypeptides, having their growing ends covalently attached to a tRNA, cellular extracts are separated by SDS-PAGE in two dimensions, first with the peptidyl-tRNA ester bonds preserved and subsequently after their in-gel cleavage. Pulse-labeled nascent polypeptides of Escherichia coli form a characteristic line below the main diagonal line, because each of them had contained a tRNA of nearly uniform size in the first-dimension electrophoresis but not in the second-dimension. The detection of nascent polypeptides, separately from any translation-completed polypeptides or degradation products thereof, allows us to follow their fates to gain deeper insights into protein biogenesis and quality control pathways. It was revealed that polypeptidyl-tRNAs were significantly stabilized in E. coli upon dysfunction of the tmRNA-ArfA ribosome-rescuing system, whose function had only been studied previously using model constructs. Our results suggest that E. coli cells are intrinsically producing aberrant translation products, which are normally eliminated by the ribosome-rescuing mechanisms.
authors.affiliation: Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan. kito@cc.kyoto-su.ac.jp
authors.forename: Koreaki
authors.initials: K
authors.lastname: Ito
authors.forename: Yuhei
authors.initials: Y
authors.lastname: Chadani
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakamori
authors.forename: Shinobu
authors.initials: S
authors.lastname: Chiba
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Akiyama
authors.forename: Tatsuhiko
authors.initials: T
authors.lastname: Abo
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D001671:Biochemistry / Q000379:methods; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D008954:Models, Biological; D009154:Mutation; D010455:Peptides / Q000737:chemistry; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D040901:Proteomics / Q000379:methods; D012343:RNA, Transfer / Q000737:chemistry; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism; D013997:Time Factors
chemical_list: D001425:Bacterial Outer Membrane Proteins; D010455:Peptides; D012346:RNA, Transfer, Amino Acyl; C019037:tRNA, peptidyl-; C078167:OMPA outer membrane proteins; D012343:RNA, Transfer