An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium.
An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium.
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DOI：
10.1073/pnas.2103579118
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发表时间：
2021-06-22
影响因子：
11.1
通讯作者：
Faber F
中科院分区：
文献类型：
--
作者：
Fuchs M;Lamm-Schmidt V;Sulzer J;Ponath F;Jenniches L;Kirk JA;Fagan RP;Barquist L;Vogel J;Faber F
艰难梭状芽胞杆菌是抗生素治疗后全球医疗保健相关腹泻的主要原因。因此，医学上需要对艰难梭菌起作用的新型抗菌剂，使其不会对常驻微生物群造成损害。开发这种窄谱抗生素需要精确了解微调基因表达的机制，以协调基因组中每个基因座的基因组输出。我们通过定义艰难梭菌的全球转录组结构来解决这个问题，其中包括非编码调控元件，其中许多元件在肠道定植期间表达。我们对这些调控因子的分析为HfQ在SRNA结合和革兰氏阳性细菌稳定中的全球功能提供了证据。革兰氏阳性人类病原体艰难梭状芽胞杆菌已成为抗生素相关性腹泻的主要原因。然而，对细菌的转录组结构和转录后控制机制知之甚少。在这里，我们应用转录起始点和终止图来生成艰难梭菌5‘和3’非翻译区、操纵子结构和非编码调节子的单核苷酸分辨RNA图谱，包括42个sRNA。我们的结果表明了许多保守的核糖开关的功能，并预测了多药耐药(MDR)型ATP结合盒(ABC)转运体和转录调节因子上游的顺式调节RNA元件。尽管越来越多的证据表明Hfq在艰难梭菌基于RNA的基因调控中发挥了作用，但在革兰氏阳性病原体中基于Hfq的转录后调控网络的功能仍然存在争议。使用Hfq免疫沉淀和结合RNA物种测序(RIP-seq)，我们鉴定了大量与Hfq结合的转录本，并表明缺少Hfq会影响转录本的稳定性和稳态水平。我们展示了艰难梭菌在肠道定植过程中sRNA的表达，并确定了影响其表达的感染相关信号。作为概念的证明，我们证明了丰富的肠道代谢物乙醇胺的利用受到依赖于Hfq的SRNA CDIF630nc_085的调节。总体而言，我们的研究为理解梭状芽胞杆菌核转录调控与感染过程的关系奠定了基础，并为HfQ在革兰氏阳性细菌转录后调控中的全球作用提供了证据。
Clostridioides difficile is the leading cause of healthcare-associated diarrhea worldwide following antibiotic treatment. Consequently, there is medical need for novel antibacterial agents acting against C. difficile that leave the resident microbiota unharmed. The development of such narrow-spectrum antibiotics requires precise knowledge of the mechanisms that fine-tune gene expression to orchestrate the genomic output at each locus in the genome. We address this issue by defining the global transcriptome architecture of C. difficile including noncoding regulatory elements, many of which are expressed during gut colonization. Our analysis of these regulators provides evidence for the global function of Hfq in sRNA binding and stabilization in a gram-positive bacterium. The gram-positive human pathogen Clostridioides difficile has emerged as the leading cause of antibiotic-associated diarrhea. However, little is known about the bacterium’s transcriptome architecture and mechanisms of posttranscriptional control. Here, we have applied transcription start site and termination mapping to generate a single-nucleotide–resolution RNA map of C. difficile 5′ and 3′ untranslated regions, operon structures, and noncoding regulators, including 42 sRNAs. Our results indicate functionality of many conserved riboswitches and predict cis-regulatory RNA elements upstream of multidrug resistance (MDR)-type ATP-binding cassette (ABC) transporters and transcriptional regulators. Despite growing evidence for a role of Hfq in RNA-based gene regulation in C. difficile, the functions of Hfq-based posttranscriptional regulatory networks in gram-positive pathogens remain controversial. Using Hfq immunoprecipitation followed by sequencing of bound RNA species (RIP-seq), we identify a large cohort of transcripts bound by Hfq and show that absence of Hfq affects transcript stabilities and steady-state levels. We demonstrate sRNA expression during intestinal colonization by C. difficile and identify infection-related signals impacting its expression. As a proof of concept, we show that the utilization of the abundant intestinal metabolite ethanolamine is regulated by the Hfq-dependent sRNA CDIF630nc_085. Overall, our study lays the foundation for understanding clostridial riboregulation with implications for the infection process and provides evidence for a global role of Hfq in posttranscriptional regulation in a gram-positive bacterium.
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核糖开关。含核糖开关的SRNA通过隔离反应调节剂来控制基因表达。
DOI：
10.1126/science.1255091
发表时间：
2014-08-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
DebRoy S;Gebbie M;Ramesh A;Goodson JR;Cruz MR;van Hoof A;Winkler WC;Garsin DA
通讯作者：
Garsin DA
影响因子：
5.1
作者：
Bertin, Yolande;Girardeau, J. P.;Martin, Christine
通讯作者：
Martin, Christine
影响因子：
3.2
作者：
Donnelly, M. Lauren;Fimlaid, Kelly A.;Shen, Aimee
通讯作者：
Shen, Aimee
影响因子：
14.9
作者：
Irnov I;Sharma CM;Vogel J;Winkler WC
通讯作者：
Winkler WC
影响因子：
6.4
作者：
Chen Y;Indurthi DC;Jones SW;Papoutsakis ET
通讯作者：
Papoutsakis ET