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

Burenina, Olga Y.; Elkina, Daria A.; Migur, Anzhela; Oretskaya, Tatiana S.; Evguenieva‐Hackenberg, Elena; Hartmann, Roland K.; Кубарева, Е. А.

doi:10.1007/s12275-020-0283-1

Cited by 6 publications

(3 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The intracellular levels of 6S RNAs are high, similar to those of essential non-coding RNAs, such as rRNAs, tRNAs, RNAse P, tmRNA or SRP RNA. Furthermore, 6S RNAs have been found in many bacterial species and are widespread in the bacterial kingdom ( Trotochaud and Wassarman, 2005 ; Faucher et al, 2010 ; Sharma et al, 2010 ; Rediger et al, 2012 ; Wehner et al, 2014 ; Köhler et al, 2015 ; Jones et al, 2016 ; Elkina et al, 2017 ; Burenina et al, 2020 ) with one exception—the group of Actinobacteria . This phylum includes serious human pathogens ( Mycobacterium tuberculosis , Mycobacterium leprae , and Corynebacterium diphtheria ), industrially important producers of amino acids ( Corynebacterium glutamicum ) and antibiotics ( Streptomyces) , bacteria involved in symbiotic nitrogen fixation ( Frankia ), bacteria utilized for bioremediation ( Rhodococcus ), probiotic bacteria ( Bifidobacterium ), and numerous other genera ( Nocardia , Micrococcus , Gardnerella ).…”

Section: Introductionmentioning

confidence: 99%

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

et al. 2022

View full text Add to dashboard Cite

Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that binds to a different form of RNAP, the holoenzyme bearing the primary sigma factor. 6S RNAs are widespread in the bacterial kingdom except for the industrially and medicinally important Actinobacteria. While Ms1 RNA was identified in Mycobacterium, it is not clear whether Ms1 RNA is present also in other Actinobacteria species. Here, using a computational search based on secondary structure similarities combined with a linguistic gene synteny approach, we identified Ms1 RNA in Streptomyces. In S. coelicolor, Ms1 RNA overlaps with the previously annotated scr3559 sRNA with an unknown function. We experimentally confirmed that Ms1 RNA/scr3559 associates with the RNAP core without the primary sigma factor HrdB in vivo. Subsequently, we applied the computational approach to other Actinobacteria and identified Ms1 RNA candidates in 824 Actinobacteria species, revealing Ms1 RNA as a widespread class of RNAP binding sRNAs, and demonstrating the ability of our multifactorial computational approach to identify weakly conserved sRNAs in evolutionarily distant genomes.

show abstract

Section: Introductionmentioning

confidence: 99%

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

et al. 2022

View full text Add to dashboard Cite

show abstract

“…The biological importance of 6S RNA can be illustrated using the example of the hyperthermophilic bacterium Aquifex aeolicus [9] that encodes and expresses a 6S RNA, although it has a parsimonious, highly condensed genome and it abandoned another prominent bacterial ncRNA, the catalytic RNA of RNase P [10]. Phenotypic analyses of 6S RNA-deficient bacterial strains revealed dysregulations under various stress conditions (reviewed in [5,7,11]). subtilis 6S-1 RNA in its free state (top) and (B) after the structural rearrangement (bottom) induced by transcription of a pRNA 14-mer (orange) that remains stably bound to 6S-1 RNA.…”

Section: Introductionmentioning

confidence: 99%

Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase

Ganapathy

Hoch

Lechner

et al. 2022

ncRNA

Self Cite

View full text Add to dashboard Cite

Here we investigated the refolding of Bacillus subtilis 6S-1 RNA and its release from σA-RNA polymerase (σA-RNAP) in vitro using truncated and mutated 6S-1 RNA variants. Truncated 6S-1 RNAs, only consisting of the central bubble (CB) flanked by two short helical arms, can still traverse the mechanistic 6S RNA cycle in vitro despite ~10-fold reduced σA-RNAP affinity. This indicates that the RNA’s extended helical arms including the ‘−35′-like region are not required for basic 6S-1 RNA functionality. The role of the ‘central bubble collapse helix’ (CBCH) in pRNA-induced refolding and release of 6S-1 RNA from σA-RNAP was studied by stabilizing mutations. This also revealed base identities in the 5’-part of the CB (5’-CB), upstream of the pRNA transcription start site (nt 40), that impact ground state binding of 6S-1 RNA to σA-RNAP. Stabilization of the CBCH by the C44/45 double mutation shifted the pRNA length pattern to shorter pRNAs and, combined with a weakened P2 helix, resulted in more effective release from RNAP. We conclude that formation of the CBCH supports pRNA-induced 6S-1 RNA refolding and release. Our mutational analysis also unveiled that formation of a second short hairpin in the 3′-CB is detrimental to 6S-1 RNA release. Furthermore, an LNA mimic of a pRNA as short as 6 nt, when annealed to 6S-1 RNA, retarded the RNA’s gel mobility and interfered with σA-RNAP binding. This effect incrementally increased with pLNA 7- and 8-mers, suggesting that restricted conformational flexibility introduced into the 5’-CB by base pairing with pRNAs prevents 6S-1 RNA from adopting an elongated shape. Accordingly, atomic force microscopy of free 6S-1 RNA versus 6S-1:pLNA 8- and 14-mer complexes revealed that 6S-1:pRNA hybrid structures, on average, adopt a more compact structure than 6S-1 RNA alone. Overall, our findings also illustrate that the wild-type 6S-1 RNA sequence and structure ensures an optimal balance of the different functional aspects involved in the mechanistic cycle of 6S-1 RNA.

show abstract

“…Expression levels of 6S RNA in the WT and complementation Δ ssrS+S and WT+ S E. coli strains were estimated by Northern blot analysis (both in standard conditions and in the presence of 2 mM, 5 mM or 20 mM H 2 O 2 ) following the protocols described in [ 66 , 67 ]. For more details see Supplementary Materials, Sections S3 and S4 .…”

Section: Methodsmentioning

confidence: 99%

Involvement of E. coli 6S RNA in Oxidative Stress Response

Burenina

Elkina

Ovcharenko

et al. 2022

IJMS

Self Cite

View full text Add to dashboard Cite

6S RNA, a small non-coding RNA present in almost all bacteria, inhibits transcription via direct binding to RNA polymerase holoenzymes. The mechanism of 6S RNA action was investigated to a large extent in E. coli, however, lack of 6S RNA (ΔssrS) was demonstrated to be unfavorable but not essential for cell survival under various growth conditions. In the present study, we revealed, for the first time, a lethal phenotype of the ΔssrS strain in the presence of high concentrations of H2O2. This phenotype was rescued by complementation of the ssrS gene on a plasmid. We performed comparative qRT-PCR analyses on an enlarged set of mRNAs of genes associated with the oxidative stress response, allowing us to identify four genes known to be involved in this pathway (soxS, ahpC, sodA and tpx) that had decreased mRNA levels in the ΔssrS strain. Finally, we performed comparative proteomic analyses of the wild-type and ΔssrS strains, confirming that ΔssrS bacteria have reduced levels of the proteins AhpC and Tpx involved in H2O2 reduction. Our findings substantiate the crucial role of the riboregulator 6S RNA for bacterial coping with extreme stresses.

show abstract

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

Cited by 6 publications

References 54 publications

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase

Involvement of E. coli 6S RNA in Oxidative Stress Response

Contact Info

Product

Resources

About