# Selective infidelity in diversity-generating retroelements

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2022 · $316,000

## Abstract

Diversity-generating retroelements (DGRs) are unique and unparalleled generators of massive protein
sequence diversity. These elements are prevalent in the microbial ‘dark matter’, which appear to comprise a
major fraction of microbial life, and are widespread in the human virome and microbiome. The only other
example in the natural world of massive protein sequence variation occurs in the vertebrate adaptive immune
system, in which variation enables the recognition of novel targets and consequent adaptation to dynamic
environments. A similar benefit appears to be provided by DGRs. DGRs diversify proteins through a
fundamentally different mechanism than the vertebrate immune system. In DGRs, diversification arises from
genetic information being transmitted unfaithfully for one specific base, adenine, and faithfully for the others.
This occurs during reverse transcription of genetic information from RNA to cDNA, and the specificity to
adenine shapes the pattern of protein functional variation. This selective infidelity to adenines is the central
hallmark feature of DGRs. Selectivity infidelity is unique in biology and how it occurs unknown. We have made
a significant breakthrough on this problem by reconstituting specific infidelity in vitro for the prototypical
Bordetella bacteriophage DGR. We have found that the DGR reverse transcriptase bRT in complex with the
DGR accessory variability determinant (Avd) protein is necessary and sufficient to synthesize adenine-
mutagenized cDNA. Our results indicate that bRT-Avd and the DGR RNA combine to form a functional and
structured ribonucleoprotein (RNP) particle. We are on the verge of uncovering the molecular and atomic
details underlying selective infidelity through the following specific aims: (1) Visualize bRT-Avd/RNA
complexes in different functional states by cryo-electron microscopy; (2) Identify the nucleobase and
protein determinants responsible for selective infidelity; and (3) Determine the basis for position-
specific modulation of specific infidelity. Our proposed studies will provide fundamental advances in
understanding DGRs. Additionally, because of the uniqueness of selective infidelity, these studies will also
likely provide novel insights into mechanisms that control fidelity in other reverse transcriptases (e.g., HIV RT)
and nucleotide polymerases in general.

## Key facts

- **NIH application ID:** 10305645
- **Project number:** 5R01GM132720-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** PARTHO GHOSH
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $316,000
- **Award type:** 5
- **Project period:** 2019-12-01 → 2023-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10305645

## Citation

> US National Institutes of Health, RePORTER application 10305645, Selective infidelity in diversity-generating retroelements (5R01GM132720-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10305645. Licensed CC0.

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