title: A role for REP sequences in regulating translation.
abstract: Repetitive extragenic palindromic (REP) sequences are highly structured elements found downstream of ∼500 genes in Escherichia coli that result in extensive stem-loop structures in their mRNAs. However, their physiological role has remained elusive. Here, we show that REP sequences can downregulate translation, but only if they are within 15 nt of a termination codon; a spacing of 16 nt has no effect, suggesting that the REP element acts to stall ribosome movement. Ribosome stalling leads to cleavage of the mRNA and induction of the trans-translation process. Using nrdAB as a model, we find that its regulation can be partially reversed by overexpression of RNA helicases and can be fully overcome upon UV stress, emphasizing the importance of this regulatory process. Since 50% of REP-associated genes have these elements within the critical 15 nt, these findings identify a regulatory mechanism with the potential to affect translation from a large number of genes.
authors.affiliation: Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA; The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Wenxing
authors.initials: W
authors.lastname: Liang
authors.affiliation: Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA.
authors.forename: Kenneth E
authors.initials: KE
authors.lastname: Rudd
authors.affiliation: Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA. Electronic address: mdeutsch@med.miami.edu.
authors.forename: Murray P
authors.initials: MP
authors.lastname: Deutscher
mesh_terms: D015152:Blotting, Northern; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics*; D008957:Models, Genetic; D014176:Protein Biosynthesis; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012262:Ribonucleoside Diphosphate Reductase / Q000235:genetics; D012264:Ribonucleotide Reductases / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins; D012333:RNA, Messenger; C571544:NrdB protein, E coli; D012264:Ribonucleotide Reductases; C449642:NrdA protein, E coli; D012262:Ribonucleoside Diphosphate Reductase