title: Nascent peptides that block protein synthesis in bacteria.
abstract: Although the ribosome is a very general catalyst, it cannot synthesize all protein sequences equally well. For example, ribosomes stall on the secretion monitor (SecM) leader peptide to regulate expression of a downstream gene. Using a genetic selection in Escherichia coli, we identified additional nascent peptide motifs that stall ribosomes. Kinetic studies show that some nascent peptides dramatically inhibit rates of peptide release by release factors. We find that residues upstream of the minimal stalling motif can either enhance or suppress this effect. In other stalling motifs, peptidyl transfer to certain aminoacyl-tRNAs is inhibited. In particular, three consecutive Pro codons pose a challenge for elongating ribosomes. The translation factor elongation factor P, which alleviates pausing at polyproline sequences, has little or no effect on other stalling peptides. The motifs that we identified are underrepresented in bacterial proteomes and show evidence of stalling on endogenous E. coli proteins.
authors: Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
authors: Christopher J
authors: CJ
authors: Woolstenhulme
authors: Shankar
authors: S
authors: Parajuli
authors: David W
authors: DW
authors: Healey
authors: Diana P
authors: DP
authors: Valverde
authors: E Nicholas
authors: EN
authors: Petersen
authors: Agata L
authors: AL
authors: Starosta
authors: Nicholas R
authors: NR
authors: Guydosh
authors: W Evan
authors: WE
authors: Johnson
authors: Daniel N
authors: DN
authors: Wilson
authors: Allen R
authors: AR
authors: Buskirk
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics; D017930:Genes, Reporter; D008954:Models, Biological; D008969:Molecular Sequence Data; D010441:Peptide Chain Elongation, Translational; D010443:Peptide Chain Termination, Translational; D010445:Peptide Elongation Factors / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011500:Protein Synthesis Inhibitors / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism; D020798:Two-Hybrid System Techniques
chemical_list: D029968:Escherichia coli Proteins; D010445:Peptide Elongation Factors; D010455:Peptides; D011500:Protein Synthesis Inhibitors; C020746:factor EF-P; C011083:polyproline