Genome‐wide screening of potential <scp>RN</scp>ase Y‐processed <scp>mRNA</scp>s in the M49 serotype <i>Streptococcus pyogenes </i><scp>NZ</scp>131

Chen, Zhiyun; Raghavan, Rahul; Qi, Fengxia; Merritt, Justin; Kreth, Jens

doi:10.1002/mbo3.671

Cited by 4 publications

(2 citation statements)

References 45 publications

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“…Although previous reports proposed that RNase Y processes the speB transcript [11,30], this has never been validated. In addition, it has been hypothesized that several RNases target the speB mRNA 5′ UTR, but their identities and their effects on speB transcript abundance and stability are currently unknown [27].…”

Section: Introductionmentioning

confidence: 99%

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

et al. 2018

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Endoribonuclease Y (RNase Y) is a crucial regulator of virulence in Gram-positive bacteria. In the human pathogen Streptococcus pyogenes, RNase Y is required for the expression of the major secreted virulence factor streptococcal pyrogenic exotoxin B (SpeB), but the mechanism involved in this regulation remains elusive. Here, we demonstrate that the 5′ untranslated region of speB mRNA is processed by several RNases including RNase Y. In particular, we identify two RNase Y cleavage sites located downstream of a guanosine (G) residue. To assess whether this nucleotide is required for RNase Y activity in vivo, we mutated it and demonstrate that the presence of this G residue is essential for the processing of the speB mRNA 5′ UTR by RNase Y. Although RNase Y directly targets and processes speB, we show that RNase Y-mediated regulation of speB expression occurs primarily at the transcriptional level and independently of the processing in the speB mRNA 5′ UTR. To conclude, we demonstrate for the first time that RNase Y processing of an mRNA target requires the presence of a G. We also provide new insights on the speB 5′ UTR and on the role of RNase Y in speB regulation.

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Section: Introductionmentioning

confidence: 99%

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

et al. 2018

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“…For visualisation of changes in editing levels, editing z scores were calculated for each target site with enough coverage support in at least two out of three replicates and a mean editing level of at least 3%. Publicly available RNA-seq datasets from other strains of S. pyogenes (40)(41)(42) were processed as described but with whole-genome sequencing data simulated using Mason (v0.1.2; 1 million reads in paired-end mode, 150 bp) (43) due to the lack of matched experimental data. Editing sites with a frequency of at least 0.01 were then compared to sites experimentally identified in S. pyogenes SF370.…”

Section: Ngs Data Analysis and Conservation Of Editing Sitementioning

confidence: 99%

Dynamics of diversified A-to-I editing inStreptococcus pyogenesis governed by changes in mRNA stability

Wulff,

Hahnke,

Lécrivain

et al. 2023

Preprint

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Adenosine-to-inosine (A-to-I) RNA editing plays an important role in the post-transcriptional regulation of eukaryotic cell physiology. However, our understanding of the occurrence, function and regulation of A-to-I editing in bacteria remains limited. Bacterial mRNA editing is catalysed by the deaminase TadA, which was originally described to modify a single tRNA inE. coli. Intriguingly, several bacterial species appear to perform A-to-I editing on more than one tRNA. Here, we provide evidence that in the human pathogenStreptococcus pyogenes, tRNA editing has expanded to an additional tRNA substrate. Using RNA sequencing, we identified more than 27 editing sites in the transcriptome ofS. pyogenesSF370 and demonstrate that the adaptation ofS. pyogenesTadA to a second tRNA substrate has also diversified the sequence context and recoding scope of mRNA editing. Based on the observation that editing is dynamically regulated in response to several infection-relevant stimuli, such as oxidative stress, we further investigated the underlying determinants of editing dynamics and identified mRNA stability as a key modulator of A-to-I editing. Overall, our findings reveal the presence and diversification of A-to-I editing inS. pyogenesand provide novel insights into the plasticity of the editome and its regulation in bacteria.

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Genome‐wide screening of potential RNase Y‐processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131

Chen

Raghavan

et al. 2018

MicrobiologyOpen

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RNase Y is a major endoribonuclease in Group A streptococcus (GAS) and other Gram-positive bacteria. Our previous study showed that RNase Y was involved in mRNA degradation and processing in GAS. We hypothesized that mRNA processing regulated the expression of important GAS virulence factors via altering their mRNA stabilities and that RNase Y mediated at least some of the mRNA-processing events.The aims of this study were to (1) identify mRNAs that were processed by RNase Y and (2) confirm the mRNA-processing events. The transcriptomes of Streptococcus pyogenes NZ131 wild type and its RNase Y mutant (Δrny) were examined with RNAseq. The data were further analyzed to define GAS operons. The mRNA stabilities of the wild type and Δrny at subgene level were determined with tiling array analysis.Operons displaying segmental stability in the wild type but not in the Δrny were predicted to be RNase Y processed. Overall 865 operons were defined and their boundaries predicted. Further analysis narrowed down 15 mRNAs potentially processed by RNase Y. A selection of four candidates including folC1 (folylpolyglutamate synthetase), prtF (fibronectin-binding protein), speG (streptococcal exotoxin G), ropB (transcriptional regulator of speB), and ypaA (riboflavin transporter) mRNAs was examined with Northern blot analysis. However, only folC1 was confirmed to be processed, but it is unlikely that RNase Y is responsible. We conclude that GAS use RNase Y to selectively process mRNA, but the overall impact is confined to selected virulence factors. K E Y W O R D Sgenomics, RNA processing, RNase Y, Streptococcus pyogenes

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Genome‐wide screening of potential RNase Y‐processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131

Cited by 4 publications

References 45 publications

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

Dynamics of diversified A-to-I editing inStreptococcus pyogenesis governed by changes in mRNA stability

Genome‐wide screening of potential RNase Y‐processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131

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