title: Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome.
abstract: In Escherichia coli the initial step in the processing or decay of many messenger and structural RNAs is mediated by the endonuclease RNase E, which forms the core of a large RNA-catalysis machine termed the degradosome. Previous experiments have identified a protein that globally modulates RNA abundance by binding to RNase E and regulating its endonucleolytic activity. Here we report the discovery of RraB, which interacts with a different site on RNase E and interferes with cleavage of a different set of transcripts. We show that expression of RraA or RraB in vivo is accompanied by dramatic, distinct, and inhibitor-specific changes in degradosome composition--and that these are in turn associated with alterations in RNA decay and global transcript abundance profiles that are dissimilar to the profile observed during simple RNase E deficiency. Our results reveal the existence of endonuclease binding proteins that modulate the remodelling of degradosome composition in bacteria and argue that such degradosome remodelling is a mechanism for the differential regulation of RNA cleavages in E. coli.
authors.affiliation: Institute for Cell and Molecular Biology, University of Texas, TX 78712, USA.
authors.forename: Junjun
authors.initials: J
authors.lastname: Gao
authors.forename: Kangseok
authors.initials: K
authors.lastname: Lee
authors.forename: Meng
authors.initials: M
authors.lastname: Zhao
authors.forename: Ji
authors.initials: J
authors.lastname: Qiu
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Zhan
authors.forename: Ankur
authors.initials: A
authors.lastname: Saxena
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Moore
authors.forename: Stanley N
authors.initials: SN
authors.lastname: Cohen
authors.forename: George
authors.initials: G
authors.lastname: Georgiou
mesh_terms: D004722:Endoribonucleases / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D009097:Multienzyme Complexes / Q000235:genetics / Q000378:metabolism*; D011117:Polyribonucleotide Nucleotidyltransferase / Q000235:genetics / Q000378:metabolism*; D019704:Protein Disulfide-Isomerases / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism*; D020349:Surface Plasmon Resonance
chemical_list: D029968:Escherichia coli Proteins; D009097:Multienzyme Complexes; D012333:RNA, Messenger; C477942:RraA protein, E coli; C513922:RraB protein, E coli; C111244:degradosome; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; C022537:ribonuclease E; D020365:RNA Helicases; D019704:Protein Disulfide-Isomerases