Discovery of bacterial defense and phage counter-defense strategies

细菌防御和噬菌体反防御策略的发现

• 批准号: 10439572
• 负责人: Kevin J Forsberg
• 金额: $ 49.2万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10439572
• 关键词: Antibiotic Resistance; Antibiotics; Bacteria; Bacterial Infections; Bacteriophage lambda; Bacteriophages; Basic Science; Biological Assay; Biology; CRISPR/Cas technology; Cell Survival; DNA; Data; Databases; Drug resistance; Ecosystem; Escherichia coli; Evolution; Genes; Genetic; Genome; Genomic Islands; Genomics; Horizontal Gene Transfer; Human; Human Microbiome; Immune; Immunity; Infection; Knowledge; Libraries; Link; Metagenomics; Methods; Modification; Molecular; Multi-Drug Resistance; Mutation; Nature; Open Reading Frames; Outcome; Pathogenesis; Phenotype; Plasmids; Prophages; Proteins; Resistance; Resources; Scheme; Source; Surveys; System; Techniques; Testing; Therapeutic; Time; Toxin; Virulence; Virulence Factors; alpha Toxin; arms race; base; conventional therapy; flexibility; gain of function; human pathogen; infectious disease treatment; inhibitor; insight; metagenome; microbial; molecular array; novel; novel strategies; pathogen; receptor; resistance gene; response; success

PROJECT SUMMARY Bacteria encode a diverse array of molecular systems to defend against infecting phages. In response, phages have devised many counter-defense strategies to overcome this immunity and re-establish infection. Mounting evidence suggests that most bacterial defense systems and phage counter-defenses in nature have not been identified. This is a major knowledge gap because the interplay between these systems often determines whether a phage successfully infects its bacterial host. These phage infections, in turn, have major impacts on the evolution and treatment of infectious disease. For instance, pathogenesis in bacteria often evolves due to the integration of a prophage that expresses a toxin or other virulence factor. At the same time, phages are increasingly viewed as potential therapeutics to treat bacterial infections, especially in cases where multi-drug resistance renders conventional treatments unsuccessful. Thus, it is important to better understand the natural diversity of bacterial defense and phage counter-defense systems. To meet this need, we will devise new high-throughput functional selections to find defense and counter-defense systems in microbial ecosystems and in libraries of synthesized phage open reading frames. This functional approach does not rely on sequence similarity to predict defense and counter-defense systems, so overcomes the limitations of conventional, homology-based discovery methods. This strategy, therefore, is expected to identify many new defense and counter-defense genes beyond what is known currently. It is especially valuable for examining functions encoded in phage genomes and bacterial genomic islands, as most genes from these sources are of unknown function. Since nearly all bacteria should encode anti-phage defense systems, and almost all phages will encode counter- defense strategies, we expect to make many new discoveries. Because these discoveries are predicted to be novel, we will use a combination of genetic and functional assays to describe their mechanisms of action. We will use Escherichia coli as a host for our functional selections, not only because this will allow us to construct large functional libraries, but also because virulence in this pathogen is driven by prophage-expressed toxins and because its phages are among those used most commonly to develop phage therapies. Thus, our findings will not only be broadly relevant to pathogenesis and phage therapy across bacteria, but also will yield these insights specifically in the context of this important human pathogen.

项目摘要 细菌编码了一系列不同的分子系统来抵御细菌的感染。在答复中， 免疫系统已经设计了许多反防御策略来克服这种免疫力并重新建立感染。 越来越多的证据表明，自然界中大多数细菌防御系统和噬菌体反防御系统都具有 未被确认。这是一个重大的知识差距，因为这些系统之间的相互作用往往 决定了噬菌体是否能成功感染宿主细菌。这些噬菌体感染，反过来，有重大的 对传染病的演变和治疗的影响。例如，细菌的致病机理通常 由于表达毒素或其它毒力因子的原噬菌体的整合而进化。与此同时， 抗生素越来越被视为治疗细菌感染的潜在疗法，特别是在以下情况下， 多重抗药性使得常规治疗不成功。因此，更好地理解 细菌防御和噬菌体反防御系统的天然多样性。为了满足这一需求，我们将 新的高通量功能选择，以发现微生物生态系统中的防御和反防御系统 和在合成噬菌体开放阅读框的文库中。这种功能方法不依赖于顺序 预测防御和反防御系统的相似性，因此克服了传统的局限性， 基于同源性的发现方法因此，这一战略预计将确定许多新的防御措施， 反防御基因超出了目前已知的。它对于检查编码的函数特别有价值 在噬菌体基因组和细菌基因组岛中，因为来自这些来源的大多数基因的功能未知。 由于几乎所有的细菌都应该编码抗噬菌体防御系统，而且几乎所有的噬菌体都将编码反噬菌体防御系统， 防御策略，我们期待有许多新的发现。因为这些发现被预测为 新的，我们将使用遗传和功能测定的组合来描述其作用机制。我们 我们将使用大肠杆菌作为我们功能选择的宿主，不仅因为这将使我们能够构建 大的功能文库，而且还因为这种病原体的毒力是由原噬菌体表达的毒素驱动的 并且因为它的噬菌体是最常用于开发噬菌体疗法的噬菌体。因此，我们的发现 不仅与细菌的发病机制和噬菌体治疗广泛相关，而且还将产生这些 特别是在这种重要的人类病原体的背景下。