Jeff Miller

– Abstract –

Diversity-Generating Retroelements in Phage, Microbes, and Microbiomes

Diversity-generating retroelements (DGRs) have evolved to increase host fitness by diversifying ligand-binding domains of variable proteins in bacteria, archaea, and their viruses. DGRs function through a mutagenic retrohoming mechanism in which an RNA intermediate serves as both the primer and template for a unique form of reverse transcriptase-dependent cDNA synthesis in which adenines are specifically miscopied, producing adenine-mutagenized cDNA that replaces parental sequences in genes that encode variable proteins. Naturally-occurring DGRs have the potential to generate astronomical levels of diversity, corresponding in many cases to >1026 unique DNA sequences in diversified genes. DGRs focus their vast mutagenic potential to evolve protein function by positioning variable nucleotides at sites that encode solvent exposed resides in ligand-binding domains. We have discovered an enrichment of DGRs in prominent members of the human microbiome, including numerous Bacteroides species. Bacteroides DGRs are encoded on distinct yet related integrative and conjugative elements that undergo chromosomal excision and transfer in the GI tracts of gnotobiotic mice, and recent evidence suggests they diversify a family of proteins that function as tip adhesins on a newly discovered pilus family with highly modular components. Our results demonstrate the horizontal transfer of accelerated evolvability, highlighting the dynamic nature of host-associated microbial communities.