RNase II binds to RNase E and modulates its endoribonucleolytic activity in the cyanobacterium Anabaena PCC 7120

Zhou, Cong; Zhang, Ju‐Yuan; Hu, Xinyu; Li, Changchang; Wang, Li; Huang, Qiaoyun; Chen, Wenli

doi:10.1093/nar/gkaa092

Cited by 15 publications

(30 citation statements)

References 59 publications

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“…Notably, protein-protein interaction sites with DEAD-box helicase CrhB and RNase II were mapped to the N-terminal, catalytic domain of RNase E of the cyanobacterium Anabaena (Nostoc) sp. PCC 7120 (77, 78). In E. coli , the analogous binding site of helicase RhlB is located within the C-terminal domain (31).…”

Section: Discussionmentioning

confidence: 99%

The role of the 5’ sensing function of ribonuclease E in cyanobacteria

Hoffmann

Lichtenberg

Rogh

et al. 2023

Preprint

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RNA degradation is crucial for many processes in pro- and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y towards 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing. Cyanobacteria, such as Synechocystis sp. PCC 6803 (Synechocystis), encode RNase E and RNase J homologs. Here, we constructed a Synechocystis strain lacking the 5' sensing function of RNase E and mapped on a transcriptome-wide level 292 5'-sensing-dependent cleavage sites. These included so far unknown targets such as the 5' untranslated region of the response regulator gene lsiR; trxA, apcE and atpI mRNAs, encoding proteins related to energy metabolism; as well as sbtB and rbcLXS encoding proteins relevant for carbon fixation. Cyanobacterial 5' sensing is important for the maturation of rRNA and several tRNAs, including tRNAGluUUC. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and most prokaryotes. We found that increased RNase activities leads to a higher copy number of the major Synechocystis plasmids pSYSA and pSYSM. The results provide a first step towards understanding the relative importance of different target mechanisms of RNase E outside Escherichia coli.

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Section: Discussionmentioning

confidence: 99%

The role of the 5’ sensing function of ribonuclease E in cyanobacteria

Hoffmann

Lichtenberg

Rogh

et al. 2023

Preprint

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“…RebA does not contain any domains or motifs that may confer the activities for RNA cleavage or binding, consistent with our results tested with synthetic RNAs in the presence of RebA (Figures 2A, 2B and S2A). However, with 5' p-LU13-FAM, a 13-nt oligoribonucleotide with a 5'-monophosphate and a 3' FAM modification that has been used as an RNase E substrate previously (Zhou et al, 2020), we found that RebA when present at more than 2-fold molar excess could strongly interfere with the substrate binding activity of RNase E (Figure 2C), suggesting that it may function as a regulator of the RNase E activity. We thus further tested the RNase E activity in the presence of RebA.…”

Section: Reba Inhibits the Binding And The Cleavage Activities Of Rna...mentioning

confidence: 75%

“…pKT25a and pUT18Ca have identical cloning site, thus allowing the same fragment to be cloned into both vectors. All the two hybrid plasmids were constructed by seamlessly cloning as previously described (Zhou et al, 2020).…”

Section: Construction Of Plasmidsmentioning

confidence: 99%

“…The non-catalytic region shows no detectable similarity to that of E. coli RNase E, but contains several subregions well conserved in cyanobacteria. In the filamentous cyanobacterium Anabaena PCC 7120 ( Anabaena hereafter), RNase E can interact with the exoribonuclease PNPase, the exoribonuclease RNase II, and the RNA helicase CrhB, suggesting the presence of an RNase E-based RNA degradosome in this organism (Zhang et al, 2014; Zhou et al, 2020; Yan et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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A conserved protein inhibitor brings under check the activity of RNase E in cyanobacteria

Liu

Lin

Yuan

et al. 2023

Preprint

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RNase E is a major ribonuclease for RNA metabolism in bacteria. Because it has a large substrate spectrum and poor substrate specificity, its activity must be well controlled under different conditions. Only a few regulators of RNase E are known in bacteria, limiting our understanding on the posttranscriptional regulatory mechanisms operating in these organisms. Here we show that, RebA, a protein universally present in cyanobacteria, interacts with RNase E in the filamentous cyanobacterium Anabaena PCC 7120. Distinct from those known regulators of RNase E, RebA interacts with the 5' sensor domain in the catalytic region of RNase E, and suppresses the cleavage activities of RNase E for all tested RNA substrates irrespective of their 5'-end status. Consistent with the inhibitory function of RebA on RNase E, conditional depletion of RNase E and overproduction of RebA caused formation of elongated cells, whereas the absence of RebA and overproduction of RNase E resulted in a shorter-cell phenotype. We further showed that the morphological changes caused by altered levels of RNase E or RebA are dependent on their physical interaction. The action of RebA represents a new mechanism, highly conserved in cyanobacteria, for RNase E regulation. Our findings provide insights into the regulation and the function of RNase E, and demonstrate the importance of balanced RNA metabolism in bacteria.

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“…However, a recent study shows that an RNase II/R protein (identified here as Zam) from Anabaena sp. PCC 7120 interacts with and enhances the activity of RNase E, the major degradosome enzyme, via its cold-shock and S1 domains [ 47 ]. This finding prompts us to propose a different model in which Zam binding to RNase E under oxidizing, but not reducing, conditions increases RNA turnover rates.…”

Section: Discussionmentioning

confidence: 99%

Zam Is a Redox-Regulated Member of the RNB-Family Required for Optimal Photosynthesis in Cyanobacteria

et al. 2022

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The zam gene mediating resistance to acetazolamide in cyanobacteria was discovered thirty years ago during a drug tolerance screen. We use phylogenetics to show that Zam proteins are distributed across cyanobacteria and that they form their own unique clade of the ribonuclease II/R (RNB) family. Despite being RNB family members, multiple sequence alignments reveal that Zam proteins lack conservation and exhibit extreme degeneracy in the canonical active site—raising questions about their cellular function(s). Several known phenotypes arise from the deletion of zam, including drug resistance, slower growth, and altered pigmentation. Using room-temperature and low-temperature fluorescence and absorption spectroscopy, we show that deletion of zam results in decreased phycocyanin synthesis rates, altered PSI:PSII ratios, and an increase in coupling between the phycobilisome and PSII. Conserved cysteines within Zam are identified and assayed for function using in vitro and in vivo methods. We show that these cysteines are essential for Zam function, with mutation of either residue to serine causing phenotypes identical to the deletion of Zam. Redox regulation of Zam activity based on the reversible oxidation-reduction of a disulfide bond involving these cysteine residues could provide a mechanism to integrate the ‘central dogma’ with photosynthesis in cyanobacteria.

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RNase II binds to RNase E and modulates its endoribonucleolytic activity in the cyanobacterium Anabaena PCC 7120

Cited by 15 publications

References 59 publications

The role of the 5’ sensing function of ribonuclease E in cyanobacteria

The role of the 5’ sensing function of ribonuclease E in cyanobacteria

A conserved protein inhibitor brings under check the activity of RNase E in cyanobacteria

Zam Is a Redox-Regulated Member of the RNB-Family Required for Optimal Photosynthesis in Cyanobacteria

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