title: Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins.
abstract: The widely conserved protein CsrA (carbon storage regulator A) globally regulates bacterial gene expression at the post-transcriptional level. In many species, CsrA activity is governed by untranslated sRNAs, CsrB and CsrC in Escherichia coli, which bind to multiple CsrA dimers, sequestering them from lower affinity mRNA targets. Both the synthesis and turnover of CsrB/C are regulated. Their turnover requires the housekeeping endonuclease RNase E and is activated by the presence of a preferred carbon source via the binding of EIIA(Glc) of the glucose transport system to the GGDEF-EAL domain protein CsrD. We demonstrate that the CsrB 3' segment contains the features necessary for CsrD-mediated decay. RNase E cleavage in an unstructured segment located immediately upstream from the intrinsic terminator is necessary for subsequent degradation to occur. CsrA stabilizes CsrB against RNase E cleavage by binding to two canonical sites adjacent to the necessary cleavage site, while CsrD acts by overcoming CsrA-mediated protection. Our genetic, biochemical and structural studies establish a molecular framework for sRNA turnover by the CsrD-RNase E pathway. We propose that CsrD evolution was driven by the selective advantage of decoupling Csr sRNA decay from CsrA binding, connecting it instead to the availability of a preferred carbon source.
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Vakulskas
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Leng
authors.affiliation: Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
authors.forename: Hazuki
authors.initials: H
authors.lastname: Abe
authors.affiliation: Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
authors.forename: Takumi
authors.initials: T
authors.lastname: Amaki
authors.affiliation: Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Okayama
authors.affiliation: Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
authors.forename: Paul
authors.initials: P
authors.lastname: Babitzke
authors.affiliation: Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA ksuzuki@agr.niigata-u.ac.jp.
authors.forename: Kazushi
authors.initials: K
authors.lastname: Suzuki
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA tromeo@ufl.edu.
authors.forename: Tony
authors.initials: T
authors.lastname: Romeo
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004722:Endoribonucleases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D008565:Membrane Proteins / Q000378:metabolism*; D009154:Mutation / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism*; D013728:Terminator Regions, Genetic
chemical_list: C093587:CsrA protein, E coli; C107123:CsrB RNA, E coli; C516590:CsrD protein, E coli; D029968:Escherichia coli Proteins; D008565:Membrane Proteins; D012329:RNA, Bacterial; D062085:RNA, Long Noncoding; D016601:RNA-Binding Proteins; D012097:Repressor Proteins; D004722:Endoribonucleases; C022537:ribonuclease E