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.

Keywords: :

• regulatory RNA
• small RNA
• ABC transporter
• RNA-RNA interaction
• alpha-proteobacteria
• Agrobacterium

10.4161/rna.29145

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

We thank Rosemarie Gurski for excellent technical assistance, Nicole Frankenberg-Dinkel and Julia Bandow for sharing proteomic infrastructure and expertise; Knut Büttner (Greifswald, Germany) for MALDI-MS analysis and Philip Möller for critical reading of the manuscript. Parts of this study were conducted in the Central Unit for Ion beams and Radionucleotides (RUBION). This work was supported by a grant from the German Research Foundation (DFG priority program SPP 1258: Sensory and regulatory RNAs in Prokaryotes) to F.N. and W.R.H. and by the Bundesministerium für Bildung und Forschung (BMBF) Grant 0316165 to W.R.H.