title: Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region.
abstract: The small RNA AbcR1 regulates the expression of ABC transporters in the plant pathogen Agrobacterium tumefaciens, the plant symbiont Sinorhizobium meliloti, and the human pathogen Brucella abortus. A combination of proteomic and bioinformatic approaches suggested dozens of AbcR1 targets in A. tumefaciens. Several of these newly discovered targets are involved in the uptake of amino acids, their derivatives, and sugars. Among the latter is the periplasmic sugar-binding protein ChvE, a component of the virulence signal transduction system. We examined 16 targets and their interaction with AbcR1 in close detail. In addition to the previously described mRNA interaction site of AbcR1 (M1), the CopraRNA program predicted a second functional module (M2) as target-binding site. Both M1 and M2 contain single-stranded anti-SD motifs. Using mutated AbcR1 variants, we systematically tested by band shift experiments, which sRNA region is responsible for mRNA binding and gene regulation. On the target site, we find that AbcR1 interacts with some mRNAs in the translation initiation region and with others far into their coding sequence. Our data show that AbcR1 is a versatile master regulator of nutrient uptake systems in A. tumefaciens and related bacteria.
authors.affiliation: Microbial Biology; Ruhr University Bochum; Germany.
authors.forename: Aaron
authors.initials: A
authors.lastname: Overlöper
authors.affiliation: Microbial Biology; Ruhr University Bochum; Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kraus
authors.affiliation: Microbial Biology; Ruhr University Bochum; Germany.
authors.forename: Rosemarie
authors.initials: R
authors.lastname: Gurski
authors.affiliation: Genetics and Experimental Bioinformatics; University of Freiburg; Germany.
authors.forename: Patrick R
authors.initials: PR
authors.lastname: Wright
authors.affiliation: Genetics and Experimental Bioinformatics; University of Freiburg; Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Georg
authors.affiliation: Genetics and Experimental Bioinformatics; University of Freiburg; Germany.
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
authors.affiliation: Microbial Biology; Ruhr University Bochum; Germany.
authors.forename: Franz
authors.initials: F
authors.lastname: Narberhaus
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020561:Alphaproteobacteria / Q000235:genetics* / Q000378:metabolism; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D016366:Open Reading Frames; D033902:Periplasmic Binding Proteins / Q000235:genetics / Q000378:metabolism; D040901:Proteomics; D020871:RNA Stability; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D016415:Sequence Alignment
chemical_list: D018528:ATP-Binding Cassette Transporters; D035001:Host Factor 1 Protein; D033902:Periplasmic Binding Proteins; D012333:RNA, Messenger; D058727:RNA, Small Untranslated
keywords: ABC transporter; Agrobacterium; RNA-RNA interaction; alpha-proteobacteria; regulatory RNA; small RNA