ArticleNucleic acids research2026
ETfinder: harnessing conserved C-terminal tails of single-stranded DNA-binding proteins for mining and engineering RecET systems in non-model microbial chassis.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Nonmodel microorganisms offer substantial potential as next-generation microbial chassis (NGMCs), yet most lack efficient and broadly transferable genome-editing systems. Here we present ETfinder, a framework that uses the conserved C-terminal tail of host single-stranded DNA-binding proteins (SSB-Ct) as a biochemical constraint to guide the discovery of RecET recombineering systems. Applied to Rhodobacter sphaeroides, ETfinder identified 91 candidates from 18 841 α-proteobacterial genomes, and all five experimentally tested RecT homologs supported measurable double-stranded DNA (dsDNA) recombineering, with the Paracoccaceae SJ630 system reaching 8.9 × 10² colony-forming units (CFU) per μg of dsDNA and 100% editing accuracy. Testing in Halomonas further showed that RecT proteins from evolutionarily distant taxa remain functional within the same halophilic chassis, indicating that SSB-Ct-guided selection enriches for portable recombination modules beyond phylogenetic proximity. To facilitate broad adoption, we compiled 25 529 RecT-SSB pairs into a curated database and implemented ETfinder as a standalone, locally deployable toolkit for mining, ranking, and phylogenetic visualization. This framework prioritizes high-compatibility homologs, reduces experimental screening burden, and expands the accessible genome-editing toolbox for NGMCs. ETfinder is freely available at https://github.com/lvdongyuan/ETfinder.
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