Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti
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eISSN 1976-3794 pISSN 1225-8873
Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti§ Olga Y. Burenina1,2†*, Daria A. Elkina2†, Anzhela Y. Migur2,3, Tatiana S. Oretskaya2, Elena Evguenieva-Hackenberg4, Roland K. Hartmann5, and Elena A. Kubareva2
Keywords: small non-coding RNA, 6S RNA, transcription, pRNA transcript
1
Non-coding RNAs (ncRNAs) play an important role in the regulation of gene expression not only in eukaryotes but also in bacteria. For a long time, these molecules have been considered transcriptional noise (Jose et al., 2019). Yet, already in 2013, more than 2,400 ncRNAs with assigned functions and expressed in > 1,000 different prokaryotic organisms were reported (Li et al., 2013). Many of these are involved in stress responses (Gottesman, 2019), activation or repression of transcription and translation (Repoila and Darfeuille, 2009; Waters and Storz, 2009), and in the control of invasion properties of pathogenic species (Ahmed et al., 2016) and their resistance to antibiotics (Dar and Sorek, 2017). Most bacterial ncRNAs act via binding to their target mRNAs, but several molecules were reported to interact with proteins. An example of the latter type is the ncRNA-based regulatory system Csr (carbon storage regulator) in E. coli and its analog Rsm (repressor of stationary phase metabolites) in some other species. In brief, CsrB and CsrC ncRNAs (or RsmX/RsmY) bind the global translational regulator CsrA (RsmA) to prevent its interaction with target mRNAs (Romeo and Babitzke, 2018). A similar mechanism was discovered for small ncRNA RirA (RfaH interacting RNA) in E. coli; this ncRNA binds and blocks lipopolysaccharide regulator RfaH, thereby causing several changes in transcription including upregulation of σE factor (Klein et al., 2016). Interestingly, some ncRNAs also act on protein function in toxin-antitoxin (TA) systems: the type III TA system uses an ncRNA as an antitoxin component (Kang et al., 2018). The most prominent bacterial ncRNA interacting with a protein is 6S RNA that binds to RNA polymerase (RNAP) holoenzymes and inhibits their transcriptional activity (Wassarman and Storz, 2000). A specific feature of 6S RNA is its ability to act as a template for RNA-dependent transcription of short RNA products (pRNAs), thus converting the DNA-dependent RNAP into an RNA-dependent RNAP (Wassarman and Saecker, 2006). The secondary structure of 6S RNA perfectly mimics a DNA promoter bound to RNAP in its open conformation (Chen et al., 2017). This property not only blocks the enzyme’s active site but also prompts RNAP to transcribe pRNAs whose abundance and length pattern depend on cellular NTP concentrations (Beckmann et al., 2011, 2012). Production of pRNAs can rearrange the 6S RNA structure to trigger an RNAP release from 6S RNA, thus serving as a mechanism of escape from the transcriptional block (Wurm et al., 2010; Beckmann et al., 2012).
Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia Lomonosov Moscow State University, Chemist
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