RNA-templated DNA synthesis in antiviral immunity and genome evolution

Abstract

The conventional flow of genetic information proceeds from DNA to RNA to protein, and yet reverse transcriptase (RT) enzymes that reverse this flow are widespread across all three domains of life. Many RTs are associated with RNA-based mobile genetic elements (MGEs), promoting their maintenance and propagation by copying them for long-term storage in DNA genomes. However, expanded surveys of RT diversity have revealed that a substantial fraction of these enzymes lack any apparent connection to MGE mobility, implying that they have been repurposed for distinct cellular roles. In this work, I investigate the mechanisms and biological functions of an enigmatic bacterial RT family, termed defense-associated RTs (DRTs), and uncover a remarkable diversity of pathways through which reverse transcription mediates immunity against bacteriophages. By integrating high-throughput sequencing, genetics, biochemistry, microbiology, and bioinformatics approaches, I demonstrate that DRT enzymes catalyze the synthesis of de novo genes, DNA homopolymers, and tandem-repeat products — each functioning in unique ways to confer phage defense. Furthermore, elucidation of the repetitive DNA synthesis mechanism employed by DRT enzymes reveals an evolutionary link between this bacterial RT family and eukaryotic telomerase. This finding points to an ancient bacterial origin for the DNA repeat addition mechanism that safeguards genome integrity across nearly all eukaryotes. Collectively, this work expands the conceptual boundaries of the genome, highlights novel noncoding functions of DNA, and uncovers a striking diversity of previously unrecognized cellular roles for RNA-templated DNA synthesis