RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3'UTR required for intermediate vancomycin resistance.
RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3'UTR required for intermediate vancomycin resistance.
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DOI：
10.1038/s41467-022-31177-8
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发表时间：
2022-06-22
影响因子：
16.6
通讯作者：
中科院分区：
文献类型：
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对耐甲氧西林金黄色葡萄球菌感染的治疗依赖于包括万古霉素在内的最后一线抗生素的疗效。治疗失败通常与具有中等万古霉素耐药性(称为VISA)的菌株有关。这些分离株积累了点突变，通常通过加厚细胞壁来共同降低万古霉素的敏感性。在VISA分离株中，调节性小RNA表达的变化与抗生素应激有关，然而大多数RNA调节因子的功能尚不清楚。在这里，我们使用Clash捕获与RNaseIII相关的RNA-RNA相互作用。RNaseIII-Clash在体内发现了数百种新的RNA-RNA相互作用，从而首次能够对许多sRNA进行功能表征。令人惊讶的是，许多mRNA-mRNA的相互作用被恢复，我们发现编码一个长3‘非翻译区(UTR)(称为VigR 3’UTR)的mRNA在RNA-RNA相互作用网络中起着调节‘枢纽’的作用。我们证明了VigR3‘UTR通过直接的m RNA-m RNA碱基配对促进了折叠和细胞壁裂解转糖基酶ISAA的表达。对糖肽处理再敏感的VISA以及IsaA和VigR 3‘UTR的缺失都会影响细胞壁厚度。我们的结果证明了RNaseIII-Clash的实用性，并表明金黄色葡萄球菌利用mRNA-mRNA相互作用来协调基因表达的范围比以前估计的更广泛。调节性小RNA(SRNA)通过多种机制与mRNAs相互作用，调节其稳定性、转录和翻译。在这里，Mediati等人。将RNaseIII-Clash应用于多药耐药金黄色葡萄球菌，以表征与RNaseIII相关的RNA-RNA相互作用网络，并鉴定与万古霉素敏感性相关的基因调控相关的3‘非编码区，称为VigR-3’非编码区。
Treatment of methicillin-resistant Staphylococcus aureus infections is dependent on the efficacy of last-line antibiotics including vancomycin. Treatment failure is commonly linked to isolates with intermediate vancomycin resistance (termed VISA). These isolates have accumulated point mutations that collectively reduce vancomycin sensitivity, often by thickening the cell wall. Changes in regulatory small RNA expression have been correlated with antibiotic stress in VISA isolates however the functions of most RNA regulators is unknown. Here we capture RNA–RNA interactions associated with RNase III using CLASH. RNase III-CLASH uncovers hundreds of novel RNA–RNA interactions in vivo allowing functional characterisation of many sRNAs for the first time. Surprisingly, many mRNA–mRNA interactions are recovered and we find that an mRNA encoding a long 3′ untranslated region (UTR) (termed vigR 3′UTR) functions as a regulatory ‘hub’ within the RNA–RNA interaction network. We demonstrate that the vigR 3′UTR promotes expression of folD and the cell wall lytic transglycosylase isaA through direct mRNA–mRNA base-pairing. Deletion of the vigR 3′UTR re-sensitised VISA to glycopeptide treatment and both isaA and vigR 3′UTR deletions impact cell wall thickness. Our results demonstrate the utility of RNase III-CLASH and indicate that S. aureus uses mRNA-mRNA interactions to co-ordinate gene expression more widely than previously appreciated. Regulatory small RNA (sRNA) interact with mRNAs to regulate their stability, transcription, and translation via diverse mechanisms. Here, Mediati et al. apply RNase III-CLASH to multidrug-resistant Staphylococcus aureus to characterise the network of RNA–RNA interactions associated with RNase III and identify a regulatory mRNA 3′UTR, named vigR-3′UTR, involved in the regulation of genes relevant for vancomycin sensitivity.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
4.6
作者：
Choe D;Szubin R;Dahesh S;Cho S;Nizet V;Palsson B;Cho BK
通讯作者：
Cho BK
DOI：
10.1126/science.aad9822
发表时间：
2016-04-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Dar D;Shamir M;Mellin JR;Koutero M;Stern-Ginossar N;Cossart P;Sorek R
通讯作者：
Sorek R
影响因子：
14.9
作者：
Dar D;Sorek R
通讯作者：
Sorek R
影响因子：
28.3
作者：
Dar, Daniel;Prasse, Daniela;Sorek, Rotem
通讯作者：
Sorek, Rotem