title: Nascent RNA in transcription complexes interacts with CspE, a small protein in E. coli implicated in chromatin condensation.
abstract: Proteins in a partially fractionated Escherichia coli extract that interact with the nascent RNA in active transcription complexes from several promoters were detected using the photocrosslinking ribonucleotide analogs 5-(azidophenacyl)thio-UTP or 5-(azidophenacyl)thio-CTP as transcription substrates. Upon irradiation of ternary transcription complexes, several extract proteins were crosslinked to the RNA. Most notably, a small protein was crosslinked to the RNA in complexes on seven of nine templates tested. This protein was purified and sequenced and found to match a hypothetical protein, MsmC/CspE, recently shown to be involved in chromatin partitioning. CspE has 69% amino acid sequence identity with the major cold shock protein in E. coli, CspA, which has been shown to bind to a DNA sequence designated the Y box, with the sequence 5'-ATTGG. Of the nine templates tested, CspE was found to be most heavily crosslinked to RNA from the lambda PR' promoter, which is modified by the Q antiterminator protein. CspE was very heavily crosslinked to RNA only ten nucleotides long in initial ternary complexes on this promoter, but not to this same RNA after it had been released from the transcription complex. However, even when present from the start of transcription, CspE did not crosslink to the RNA 82 nucleotides long in elongation complexes from this same promoter. Despite the loss of interaction with the RNA after polymerase had left the promoter, CspE inhibited Q-mediated transcriptional antitermination from PR' in vitro almost 200 nucleotides downstream from the promoter, presumably by interaction with the Y box DNA upstream from PR', which overlaps with the binding site for the Q. A potential role for CspE and transcription in chromosome condensation and nucleoid structure is discussed.
authors.affiliation: Department of Chemistry and Biochemistry, The University of Oklahoma, Norman 73019, USA. mhanna@ou.edu
authors.forename: M M
authors.initials: MM
authors.lastname: Hanna
authors.forename: K
authors.initials: K
authors.lastname: Liu
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D002843:Chromatin / Q000378:metabolism*; D003432:Cross-Linking Reagents; D004269:DNA, Bacterial / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism; D004926:Escherichia coli; D029968:Escherichia coli Proteins; D006360:Heat-Shock Proteins / Q000302:isolation & purification / Q000378:metabolism* / Q000502:physiology; D008969:Molecular Sequence Data; D010441:Peptide Chain Elongation, Translational / Q000235:genetics; D012329:RNA, Bacterial / Q000378:metabolism*; D013698:Templates, Genetic; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D002843:Chromatin; D003432:Cross-Linking Reagents; C088097:CspE protein, E coli; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D006360:Heat-Shock Proteins; D012329:RNA, Bacterial