Systematic Investigation of Anti-Defense Function and Regulation in Bacterial Conjugation

Objective

The microbial world's genomic arms race spurred a remarkable diversity of defense and anti-defense mechanisms, with CRISPR-Cas and anti-CRISPR systems as prime examples that revolutionized genome editing. Recent years have seen a surge in the discovery of bacterial anti-phage systems and their viral countermeasures, yet little is known about how plasmids—key vectors of antibiotic resistance—overcome host defenses. Our lab recently found that plasmids' leading regions, the first to enter recipient cells, harbor diverse anti-defense systems vital for efficient conjugation. This sets the stage for in-depth studies of plasmid-encoded anti-defenses (PEADs), significantly advancing our understanding of conjugation, with far-reaching implications for clinical and biotechnological applications. Here, we will explore PEADs through three interconnected aims. In Aim 1 we will develop machine-learning and language model approaches, complemented by structural analyses, to identify and characterize putative PEADs from extensive genomic and metagenomic databases. This will be followed by functional testing in both targeted and high-throughput assays. In Aim 2 we will elucidate PEAD regulation, including early expression from single-stranded promoters and unique mechanisms for transient expression, integrating state-of-the-art computational approaches with in vitro transcription and conjugation efficiency assays. In Aim 3 we will determine how multiple PEADs function in concert to counteract multilayered defenses, informing the design of tailored plasmid-leading regions for efficient DNA transfer to targeted bacteria. DEFCONJ tackles a fundamental question: how do plasmids achieve efficient conjugation despite host defenses? Beyond transforming our understanding of the plasmid-host arms race, this research will advance our comprehension of antimicrobial resistance dissemination, while paving the way for powerful new tools for clinical and synthetic biology applications.