Megascale recombination generates millions of catalytically competent PETases

Abstract

Engineering proteins at the scale of modern high-throughput screening technologies remains challenging because most experimental libraries sample only limited regions of sequence space while maintaining relatively low levels of functional diversity. Although recombination-based strategies can introduce substantially larger sequence changes than conventional mutagenesis approaches, it is unclear whether highly recombined enzymes can retain catalytic competence when library sizes approach millions to billions of variants. To investigate this question, we constructed a recombination library by combining ten sequence blocks from ten bacterial PETases, generating a theoretical diversity of 10^8 chimeric enzymes. Screening of yeast-displayed libraries using a fluorophosphonate probe for catalytic-serine reactivity identified substantial populations of catalytically competent variants despite extensive sequence recombination and dozens of amino acid substitutions per chimera. Approximately 2% of sampled variants possessed active-site serine reactivity, corresponding to an estimated 10 catalytically competent enzymes within the full theoretical library. Deep sequencing showed that functional populations remained broadly distributed across sequence space following selection and contained multiple enriched recombination patterns spanning the PETase structure. Secondary lysate screening and enzyme-normalized activity measurements further identified multiple purified PETase chimeras with soluble esterase activity comparable to or greater than the wild type Ideonella sakaiensis PETase on a chromogenic surrogate substrate. Together, these results demonstrate that large-scale recombination can generate millions of diverse and catalytically competent enzymes while remaining compatible with modern high-throughput screening workflows. More broadly, this work establishes recombination-based diversity generation as a scalable strategy for protein engineering and large-scale sequence-function data generation.