Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
mBio. 2024 Aug 14;15(8):e0084024. doi: 10.1128/mbio.00840-24. Epub 2024 Jul 2.
UNLABELLED: While genome-wide transposon mutagenesis screens have identified numerous essential genes in the significant human pathogen (group A or GAS), many of their functions remain elusive. This knowledge gap is attributed in part to the limited molecular toolbox for controlling GAS gene expression and the bacterium's poor genetic transformability. CRISPR interference (CRISPRi), using catalytically inactive GAS Cas9 (dCas9), is a powerful approach to specifically repress gene expression in both bacteria and eukaryotes, but ironically, it has never been harnessed for controlled gene expression in GAS. In this study, we present a highly transformable and fully virulent serotype M1T1 GAS strain and introduce a doxycycline-inducible CRISPRi system for efficient repression of bacterial gene expression. We demonstrate highly efficient, oligo-based single guide RNA cloning directly to GAS, enabling the construction of a gene knockdown strain in just 2 days, in contrast to the several weeks typically required. The system is shown to be titratable and functional both and using a murine model of GAS infection. Furthermore, we provide direct evidence that the expression of the conserved cell division gene is essential for GAS virulence, highlighting its promise as a target for emerging FtsZ inhibitors. Finally, we introduce SpyBrowse (https://veeninglab.com/SpyBrowse), a comprehensive and user-friendly online resource for visually inspecting and exploring GAS genetic features. The tools and methodologies described in this work are poised to facilitate fundamental research in GAS, contribute to vaccine development, and aid in the discovery of antibiotic targets. IMPORTANCE: While group A (GAS) remains a predominant cause of bacterial infections worldwide, there are limited genetic tools available to study its basic cell biology. Here, we bridge this gap by creating a highly transformable, fully virulent M1T1 GAS strain. In addition, we established a tight and titratable doxycycline-inducible system and developed CRISPR interference (CRISPRi) for controlled gene expression in GAS. We show that CRISPRi is functional in a mouse infection model. Additionally, we present SpyBrowse, an intuitive and accessible genome browser (https://veeninglab.com/SpyBrowse). Overall, this work overcomes significant technical challenges of working with GAS and, together with SpyBrowse, represents a valuable resource for researchers in the GAS field.
未加标签:虽然全基因组转座子诱变筛选已经确定了重要人类病原体(A 组或 GAS)中的许多必需基因,但它们的许多功能仍然难以捉摸。造成这种知识差距的部分原因是用于控制 GAS 基因表达的分子工具包有限,以及细菌的遗传转化能力差。CRISPR 干扰(CRISPRi)使用无催化活性的 GAS Cas9(dCas9),是一种在细菌和真核生物中特异性抑制基因表达的强大方法,但具有讽刺意味的是,它从未被用于 GAS 中控制基因表达。在这项研究中,我们展示了一种高度可转化和完全毒力的 M1T1 GAS 血清型菌株,并引入了一种强力霉素诱导的 CRISPRi 系统,用于高效抑制细菌基因表达。我们证明了高效、基于寡核苷酸的单指导 RNA 克隆直接到 GAS,仅用 2 天即可构建基因敲低菌株,而传统方法通常需要数周时间。该系统在使用 GAS 感染的小鼠模型时表现出可滴定性和功能性。此外,我们提供了直接证据表明保守的细胞分裂基因 的表达对于 GAS 毒力是必需的,这突出了它作为新兴 FtsZ 抑制剂靶标的潜力。最后,我们引入了 SpyBrowse(https://veeninglab.com/SpyBrowse),这是一个全面且用户友好的在线资源,用于直观地检查和探索 GAS 遗传特征。本文所述的工具和方法有望促进 GAS 的基础研究,有助于疫苗开发,并有助于发现抗生素靶标。
重要性:虽然 A 组(GAS)仍然是全球细菌性感染的主要原因,但用于研究其基本细胞生物学的遗传工具有限。在这里,我们通过创建一种高度可转化、完全毒力的 M1T1 GAS 菌株来弥补这一差距。此外,我们建立了一个紧密且可滴定的强力霉素诱导系统,并为 GAS 中的受控基因表达开发了 CRISPR 干扰(CRISPRi)。我们表明 CRISPRi 在小鼠感染模型中具有功能性。此外,我们介绍了 SpyBrowse,这是一个直观且易于访问的基因组浏览器(https://veeninglab.com/SpyBrowse)。总的来说,这项工作克服了 GAS 研究中的重大技术挑战,与 SpyBrowse 一起,为 GAS 领域的研究人员提供了宝贵的资源。
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