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Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL


Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL



Nucleic Acids Research 38(5): 1636-1651



ISSN/ISBN: 0305-1048

PMID: 20008510

DOI: 10.1093/nar/gkp1150

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.

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Accession: 053741959

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