RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

Broglia, Laura; Materne, Solange Lise; Lécrivain, Anne-Laure; Hahnke, Karin; Rhun, Anaïs Le; Charpentier, Emmanuelle

doi:10.1080/15476286.2018.1532253

Cited by 10 publications

(14 citation statements)

References 58 publications

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“…Some of the missing TSS might correspond to genes expressed at low levels under our growth conditions or to serotype-specific differences in gene expression. Alternatively, some of the previously determined 5′ ends, associated with poor promoter sequences, might have been generated through RNase processing such as recently shown for one of the spe B transcript 5′ ends [40]. Indeed we also observed a transcript 5′ end at this position but with a TAP+/TAP- ratio close to 1.…”

Section: Discussionsupporting

confidence: 72%

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Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes

et al. 2019

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BackgroundThe human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adaptation of this pathogen to its different environments and their evolution, we have determined the primary transcriptome of a serotype M1 S. pyogenes strain at single-nucleotide resolution and compared it with that of Streptococcus agalactiae, also from the pyogenic group of streptococci.ResultsBy using a combination of differential RNA-sequencing and oriented RNA-sequencing we have identified 892 transcription start sites (TSS) and 885 promoters in the S. pyogenes M1 strain S119. 8.6% of S. pyogenes mRNAs were leaderless, among which 81% were also classified as leaderless in S. agalactiae. 26% of S. pyogenes transcript 5′ untranslated regions (UTRs) were longer than 60 nt. Conservation of long 5′ UTRs with S. agalactiae allowed us to predict new potential regulatory sequences. In addition, based on the mapping of 643 transcript ends in the S. pyogenes strain S119, we constructed an operon map of 401 monocistrons and 349 operons covering 81.5% of the genome. One hundred fifty-six operons and 254 monocistrons retained the same organization, despite multiple genomic reorganizations between S. pyogenes and S. agalactiae. Genomic reorganization was found to more often go along with variable promoter sequences and 5′ UTR lengths. Finally, we identified 117 putative regulatory RNAs, among which nine were regulated in response to magnesium concentration.ConclusionsOur data provide insights into transcriptome evolution in pyogenic streptococci and will facilitate the analysis of genetic polymorphisms identified by comparative genomics in S. pyogenes.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5613-5) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 72%

“…3 c). Differential expression analysis of the 5′ UTR associated with the two speB TSS (this work and [ 40 , 41 ]) showed that both promoters were likely affected by Mg 2+ status. These 5′ UTR overlap in antisense orientation the 5′ end of the rop B transcript.…”

Section: Resultsmentioning

confidence: 78%

Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes

et al. 2019

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“…The preference of RNase Y for this nucleotide at the processing site was first described in S. aureus, in which 58% of the processing sites were identified to be located upstream of a G 10 . A recent study from our laboratory demonstrated that RNase Y also requires a G to process speB mRNA, encoding a major virulence factor in S. pyogenes 11 . In light of the RNase Y cleavage signature identified in this study, it is likely that the G is required for the processing of substrates other than speB mRNA.…”

Section: Discussionmentioning

confidence: 99%

“…For the long RNAs (Fig. 8), 20 µg of RNA was separated on a 1% agarose gel (1X MOPS (20 mM MOPS free acid, 5 mM sodium acetate, 1 mM EDTA, pH 7.0), 6.6% formaldehyde) in 1X MOPS buffer with 0.7% formaldehyde for 2 h at 80 V. The separated RNAs were transferred onto a Nylon Hybond N + membrane (GE Healthcare) using a capillarity system overnight at room temperature in 20X SSC 11 . The RNAs were crosslinked to the membranes using UV (2X autocrosslinking, UV Stratalinker 1800).…”

Section: Methodsmentioning

confidence: 99%

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An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3′-to-5′ exoRNases and RNase Y

et al. 2020

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RNA degradation is an essential process that allows bacteria to control gene expression and adapt to various environmental conditions. It is usually initiated by endoribonucleases (endoRNases), which produce intermediate fragments that are subsequently degraded by exoribonucleases (exoRNases). However, global studies of the coordinated action of these enzymes are lacking. Here, we compare the targetome of endoRNase Y with the targetomes of 3′-to-5′ exoRNases from Streptococcus pyogenes, namely, PNPase, YhaM, and RNase R. We observe that RNase Y preferentially cleaves after guanosine, generating substrate RNAs for the 3′-to-5′ exoRNases. We demonstrate that RNase Y processing is followed by trimming of the newly generated 3′ ends by PNPase and YhaM. Conversely, the RNA 5′ ends produced by RNase Y are rarely further trimmed. Our strategy enables the identification of processing events that are otherwise undetectable. Importantly, this approach allows investigation of the intricate interplay between endo-and exoRNases on a genome-wide scale.

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Study of key RNA metabolism proteins in Enterococcus faecalis

et al. 2020

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The control of mRNA turnover is essential in bacteria to allow rapid adaptation, especially in opportunistic pathogen like Enterococcus faecalis. This mechanism involves RNase and DEAD-box helicases that are key elements in RNA processing and their associations form the degradosome with accessory proteins. In this study, we investigated the function of four RNases (J1, J2, Y and III) and three DEADbox helicases (CshA, CshB, CshC) present in most Enterococci. The interactions of all these RNA metabolism actors were investigated in vitro, and the results are in accordance with a degradosome structure close to the one of Bacillus subtilis. At the physiological level, we showed that RNase J1 is essential, whereas RNases J2 and III have a role in cold, oxidative and bile salts stress response, and RNase Y in general fitness. Furthermore, RNases J2, Y and III mutants are affected in virulence in the Galleria mellonella infection model. Concerning DEAD-box helicases, all of them are involved in cold shock response. Since the ΔcshA mutant was the most stress impacted strain, we studied this DEAD-box helicase CshA in more detail. This showed that CshA autoregulates its own expression by binding to its mRNA 5ʹUnstranslated Region. Interestingly, CshC is also involved in the expression control of CshA by a hitherto unprecedented mechanism.

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RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

Cited by 10 publications

References 58 publications

Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes

Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes

An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3′-to-5′ exoRNases and RNase Y

Study of key RNA metabolism proteins in Enterococcus faecalis

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