A diverse single- stranded DNA-annealing protein library enables efficient genome editing across bacterial phyla

• 成果类型: Article
• 署名作者: Filsinger, Gabriel T.; Mychack, Aaron; Lyerly, Evan; Henriksen, Camilla; Bartlett, Thomas M.; Kuchwara, Helene; Eitzinger, Simon; Bernhardt, Thomas G.; Walker, Suzanne; Church, George M.; Wannier, Timothy M.
• 署名单位: Harvard University; Harvard Medical School; Stanford University; Harvard University; University of Copenhagen; Wadsworth Center; State University of New York (SUNY) System; Harvard University; Harvard Medical School; Harvard University; Harvard University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-10125
• DOI: 10.1073/pnas.2414342122
• 发表日期: 2025-04-29
• 关键词: escherichia-coli; recombination; repair; beta; mycobacteria; replacement; mutagenesis; chromosome; selection; SYSTEM

摘要

Genome modification is essential for studying and engineering bacteria, yet making efficient modifications to most species remains challenging. Bacteriophage-encoded single-stranded DNA-annealing proteins (SSAPs) can facilitate efficient genome editing by homologous recombination, but their typically narrow host range limits broad application. Here, we demonstrate that a single library of 227 SSAPs enables efficient genome-editing across six diverse bacteria from three divergent classes: Actinomycetia (Mycobacterium smegmatis and Corynebacterium glutamicum), Alphaproteobacteria (Agrobacterium tumefaciens and Caulobacter crescentus), and Bacilli (Lactococcus lactis and Staphylococcus aureus). Surprisingly, the most effective SSAPs frequently originated from phyla distinct from their bacterial hosts, challenging the assumption that phylogenetic relatedness is necessary for recombination efficiency, and supporting the value of a large unbiased library. Across these hosts, the identified SSAPs enable genome modifications requiring efficient homologous recombination, demonstrated through three examples. First, we use SSAPs with Cas9 in C. crescentus to introduce single amino acid mutations with >70% efficiency. Second, we adapt SSAPs for dsDNA editing in C. glutamicum and S. aureus, enabling one-step gene knockouts using PCR products. Finally, we apply SSAPs for multiplexed editing in S. aureus to precisely map the interaction between a conserved protein and a small-molecule inhibitor. Overall, this library-based SSAP screen expands engineering capabilities across diverse, previously recalcitrant microbes, enabling efficient genetic manipulation for both fundamental research and biotechnological applications.