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: 10049809
• 负责人: Kevin J Forsberg
• 金额: $ 49.18万
• 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/10049809
• 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; Race; Resistance; Resources; Scheme; Source; Surveys; System; Techniques; Testing; Therapeutic; Time; Toxin; Virulence; Virulence Factors; alpha Toxin; arm; base; conventional therapy; flexibility; gain of function; human pathogen; infectious disease treatment; inhibitor/antagonist; 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 细菌编码各种分子系统来防御感染噬菌体。作为回应， 噬菌体制定了许多反防卫策略，以克服这种免疫力并重新建立感染。 越来越多的证据表明，大多数细菌防御系统和噬菌体的反防御性质 未被确定。这是一个主要的知识差距，因为这些系统之间的相互作用经常 确定噬菌体是否成功感染了细菌宿主。这些噬菌体感染反过 影响传染病的进化和治疗。例如，细菌的发病机理经常 由于表达毒素或其他毒力因子的预言的整合而发展。同时， 噬菌体越来越被视为治疗细菌感染的潜在疗法，尤其是在 多药抵抗会使常规治疗失败。因此，重要的是要更好地理解 细菌防御和噬菌体反防御系统的自然多样性。为了满足这种需求，我们将设计 新的高通量功能选择，以在微生物生态系统中找到防御和防御系统 并在合成的噬菌体开放式阅读框的库中。这种功能性方法不依赖于序列 与预测防御和防御系统相似，因此克服了常规的局限性， 基于同源的发现方法。因此，预计该策略将确定许多新的辩护和 反防御基因超出了目前已知的。它对于检查编码功能特别有价值 在噬菌体基因组和细菌基因组岛中，这些来源的大多数基因都是未知的功能。 由于几乎所有细菌都应编码防水防御系统，并且几乎所有噬菌体都将编码反式防御系统 国防策略，我们期望有许多新发现。因为这些发现被预测为 小说，我们将使用遗传和功能测定的组合来描述其作用机理。我们 将使用Escherichia Coli作为我们功能选择的主机，不仅因为这将使我们能够构建 大型功能库，也是因为该病原体中的毒力是由预言表达的毒素驱动的 而且因为它的噬菌体是最常用的噬菌体疗法的噬菌体之一。因此，我们的发现 不仅将与细菌的发病机理和噬菌体疗法广泛相关，而且还将产生这些 在这种重要的人类病原体的背景下，特别是见解。