Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade
Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6,779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from Synechococcus phage S-CBP4 and report the most minimal RNR architecture to-date. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study.
The cryo-EM map has been deposited in the Electron Microscopy Data Bank under accession code EMD-26712, and the model has been deposited in the Protein Data Bank under accession code 7urg. The phylogeny shown in Figure 2 is available at (https://itol.embl.de/shared/yFvz6aVgum9z). The structure-guided sequence alignment and all twenty inferred phylogenies are available for download as supplementary materials.
Article and author information
National Science Foundation (MCB-1942668)
- Nozomi Ando
SAXS was conducted at the Center for High Energy X-ray Sciences (CHEXS), which is supported by the National Science Foundation (NSF) under award DMR-1829070, and the Macromolecular Diffraction at CHESS (MacCHESS) facility, which is supported by award 1-P30-GM124166-01A1 from the National Institute of General Medical Sciences (NIGMS), National Institutes of Health (NIH), and by New York States Empire State Development Corporation (NYSTAR). Cryo-EM work was done using the Cornell Center for Materials Research (CCMR) Shared Facilities
- Nir Ben-Tal, Tel Aviv University, Israel
- Preprint posted: April 23, 2022 (view preprint)
- Received: April 26, 2022
- Accepted: August 31, 2022
- Accepted Manuscript published: September 1, 2022 (version 1)
- Version of Record published: October 4, 2022 (version 2)
© 2022, Burnim et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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