High-throughput analyses of a reconstituted diversity-generating retroelement identify intrinsic and extrinsic determinants of diversification

Abstract

Diversity-Generating Retroelements (DGRs) are specialized genetic systems typically harnessed in nature to evolve new molecular recognition. This mechanism, known as mutagenic retrohoming, relies on an error-prone reverse transcriptase (bRT) that introduces errors at template adenines, followed by the incorporation of the resulting mutagenized complementary DNA (cDNA) into a homologous target gene. Although widely distributed, DGRs are conspicuously absent from key bacterial models, limiting our understanding of their functionality in these hosts and their potential as engineering tools. Here, we demonstrate the ‘plug-and-play’ nature of the Bordetella phage BPP-1 DGR by successfully reconstituting the mutagenic retrohoming mecha nism in Escherichia coli. Using high-throughput tools available in this tractable bacte rium, we identified key regulatory factors that allowed us to enhance DGR efficiency over 1000-fold. Systematic analysis defines how sequence context governs bRT’s fidelity, uncovering a distinct error profile for the AAC motifs prevalent in natural DGR templates. This intrinsic bias prioritizes the sampling of residues essential for antigen recognition, effectively focusing the evolutionary search within the most productive regions of sequence space. Furthermore, a transposon sequencing screen identified the single-stranded DNA exonuclease ExoI as an inhibitor of DGR activity. While removing ExoI enhanced activity by more than ten-fold, we found that its nuclease activity was dispensable for this inhibition, suggesting a non-catalytic mechanism. Finally, a genome-scale survey highlighted enhanced DGR efficiency at targets located near the replication origin and oriented outwardly from it. This bias is clearly linked to replication directionality, suggesting that certain aspects of DNA replication cycles promote mutagenic retrohoming. Collectively, our work reveals previously unappreciated mechanistic features of DGRs and establishes this reconstituted system as a powerful platform for targeted gene diversification and clarifying the molecular mechanism of mutagenic retrohoming.