title: Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL.
abstract: We report that greA expression is driven by two strong, overlapping P1 and P2 promoters. The P1 promoter is sigma(70)-dependent and P2 is sigma(E)-dependent. Two-thirds of transcripts terminate within the leader region and the remaining third comprises greA mRNA. Termination efficiency seems to be unaffected by growth phase. Two collections of small 40-50 (initiating from P2) and 50-60 nt (from P1) RNA chains, termed GraL, are demonstrable in vivo and in vitro. We document that GraL arrays arise from an intrinsic terminator with an 11 bp stem followed by an AU(7)GCU(2) sequence. Atypical chain termination occurs at multiple sites; the 3'-ends differ by 1 nt over a range of 10 nt. Transcripts observed are shown to be insensitive to Gre factors and physically released from RNAP-DNA complexes. The abundance of individual chains within each cluster displays a characteristic pattern, which can be differentially altered by oligonucleotide probes. Multiple termination sites are particularly sensitive to changes at the bottom of the stem. Evolutionarily conserved GraL stem structures and fitness assays suggest a biological function for the RNA clusters themselves. Although GraL overexpression induces >/=3-fold transcriptional changes of over 100 genes, a direct target remains elusive.
authors.affiliation: Laboratory of Molecular Genetics, Program in Genomics of Development, Eunice Kennedy Shriver NICHD, NIH, Bethesda, MD 20892-2785, USA. potrykuk@mail.nih.gov
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Potrykus
authors.forename: Helen
authors.initials: H
authors.lastname: Murphy
authors.forename: Xiongfong
authors.initials: X
authors.lastname: Chen
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Epstein
authors.forename: Michael
authors.initials: M
authors.lastname: Cashel
mesh_terms: D020121:5' Untranslated Regions; D001483:Base Sequence; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D009876:Operon; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D013728:Terminator Regions, Genetic; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D020121:5' Untranslated Regions; D029968:Escherichia coli Proteins; C079668:GreA protein, E coli; D012329:RNA, Bacterial; D014157:Transcription Factors