title: Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro.
abstract: Transcription elongation factor GreA induces nucleolytic activity of bacterial RNA polymerase (RNAP). In vitro, transcript cleavage by GreA contributes to transcription efficiency by (i) suppressing pauses and arrests, (ii) stimulating RNAP promoter escape, and (iii) enhancing transcription fidelity. However, it is unclear which of these functions is (are) most relevant in vivo. By comparing global gene expression profiles of Escherichia coli strains lacking Gre factors and strains expressing either the wild type (wt) or a functionally inactive GreA mutant, we identified genes that are potential targets of GreA action. Data analysis revealed that in the presence of chromosomally expressed GreA, 19 genes are upregulated; an additional 105 genes are activated upon overexpression of the wt but not the mutant GreA. Primer extension reactions with selected transcription units confirmed the gene array data. The most prominent stimulatory effect (threefold to about sixfold) of GreA was observed for genes of ribosomal protein operons and the tna operon, suggesting that transcript cleavage by GreA contributes to optimal expression levels of these genes in vivo. In vitro transcription assays indicated that the stimulatory effect of GreA upon the transcription of these genes is mostly due to increased RNAP recycling due to facilitated promoter escape. We propose that transcript cleavage during early stages of initiation is thus the main in vivo function of GreA. Surprisingly, the presence of the wt GreA also led to the decreased transcription of many genes. The mechanism of this effect is unknown and may be indirect.
authors.affiliation: Department of Cell Biology, UMDNJ-SOM at Stratford, 2 Medical Center Drive, Stratford, NJ 08084-1489, USA.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Stepanova
authors.forename: Jookyung
authors.initials: J
authors.lastname: Lee
authors.forename: Maria
authors.initials: M
authors.lastname: Ozerova
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Semenova
authors.forename: Kirill
authors.initials: K
authors.lastname: Datsenko
authors.forename: Barry L
authors.initials: BL
authors.lastname: Wanner
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
authors.forename: Sergei
authors.initials: S
authors.lastname: Borukhov
mesh_terms: D026905:Amino Acid Transport Systems / Q000096:biosynthesis / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000502:physiology*; D017353:Gene Deletion; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012269:Ribosomal Proteins / Q000096:biosynthesis / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*
chemical_list: D026905:Amino Acid Transport Systems; D029968:Escherichia coli Proteins; C079668:GreA protein, E coli; D012269:Ribosomal Proteins; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases