Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti

Olga Y. Burenina; Daria A. Elkina; Anzhela Y. Migur; Tatiana S. Oretskaya; Elena Evguenieva-Hackenberg; RolK. Hartmann; Elena A. Kubareva

doi:10.1007/s12275-020-0283-1

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Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti: Olga Y. Burenina ^1,2, Daria A. Elkina ², Anzhela Y. Migur ^2,3, Tatiana S. Oretskaya ², Elena Evguenieva-Hackenberg ⁴, RolK. Hartmann ⁵, Elena A. Kubareva ²; Journal of Microbiology 2020;58(11):945-956.
DOI: https://doi.org/10.1007/s12275-020-0283-1
Published online: October 30, 2020

¹Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia, ²Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Moscow 119991, Russia, ³Albert Ludwig University of Freiburg, Freiburg 79085, Germany, ⁴Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen 35390, Germany, ⁵Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg 35037, Germany¹Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia, ²Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Moscow 119991, Russia, ³Albert Ludwig University of Freiburg, Freiburg 79085, Germany, ⁴Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen 35390, Germany, ⁵Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg 35037, Germany

Corresponding author: Olga Y. Burenina , Tel: +7-495-280-1481,

Received: 29 May 2020 • Revised: 3 August 2020 • Accepted: 3 August 2020

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Abstract

6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobiales and are typical nitrogen-fixing symbionts of legumes, their 6S RNA expression profiles were found to differ: B. japonicum 6S RNA accumulated in the stationary phase, thus being reminiscent of Escherichia coli 6S RNA, whereas S. meliloti 6S RNA level peaked at the transition to the stationary phase, similarly to Rhodobacter sphaeroides 6S RNA. We demonstrated in vitro that both RNAs have hallmarks of 6S RNAs: they bind to the σ70-type RNAP holoenzyme and serve as templates for de novo transcription of so-called product RNAs (pRNAs) ranging in length from ~13 to 24 nucleotides, with further evidence of the synthesis of even longer pRNAs. Likewise, stably bound pRNAs were found to rearrange the 6S RNA structure to induce its dissociation from RNAP. Compared with B. japonicum 6S RNA, considerable conformational heterogeneity was observed for S. meliloti 6S RNA and its complexes with pRNAs, even though the two 6S RNAs share ~75% sequence identity. Overall, our findings suggest that the two rhizobial 6S RNAs have diverged with respect to their regulatory impact on gene expression throughout the bacterial life cycle.

Keywords: biodegradation;metagenomics;plastic

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Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti

J. Microbiol. 2020;58(11):945-956. Published online October 30, 2020

DOI: https://doi.org/10.1007/s12275-020-0283-1

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