PMID:24921646

Citation	Overlöper, A, Kraus, A, Gurski, R, Wright, PR, Georg, J, Hess, WR and Narberhaus, F (2014) Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region. RNA Biol 11:624-40
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.
Links	PubMed PMC4152367
Keywords	ATP-Binding Cassette Transporters/chemistry; ATP-Binding Cassette Transporters/genetics; ATP-Binding Cassette Transporters/metabolism; Alphaproteobacteria/genetics; Alphaproteobacteria/metabolism; Base Pairing; Base Sequence; Binding Sites; Computational Biology; Gene Expression Regulation, Bacterial; Host Factor 1 Protein/genetics; Host Factor 1 Protein/metabolism; Molecular Sequence Data; Mutation; Open Reading Frames; Periplasmic Binding Proteins/genetics; Periplasmic Binding Proteins/metabolism; Proteomics; RNA Stability; RNA, Messenger/chemistry; RNA, Messenger/genetics; RNA, Messenger/metabolism; RNA, Small Untranslated/chemistry; RNA, Small Untranslated/genetics; RNA, Small Untranslated/metabolism; Reproducibility of Results; Sequence Alignment
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
AGRFC:Q7CX36	Contributes to	GO:0006865: amino acid transport	ECO:0000269:		P		14 AbcR1 targets encoding periplasmic transport proteins carrying sugars, amino acids, and opines supports the function of AbcR1 as a key regulator for these transport systems.	complete

References

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