Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade

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Abstract

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.

Data availability

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.

The following data sets were generated

1. Xu D
2. Burnim AA
3. Ando N
(2022) cryo-EM structure of ribonucleotide reductase from Synechoccus phage S-CBP4 bound with TTP
EM DataBank, EMD- 26712.

https://www.ebi.ac.uk/emdb/EMD- 26712
1. Xu D
2. Burnim AA
3. Ando N
(2022) cryo-EM structure of ribonucleotide reductase from Synechoccus phage S-CBP4 bound with TTP
PDB, 7URG.

https://www.rcsb.org/structure/7URG

Article and author information

Author details

Audrey A Burnim

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9962-1397
Matthew A Spence

Research School of Chemistry, Australian National University, Canberra, Australia

Competing interests
The authors declare that no competing interests exist.
Da Xu

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States

Competing interests
The authors declare that no competing interests exist.
Colin J Jackson

Research School of Chemistry, Australian National University, Canberra, Australia

For correspondence
colin.jackson@anu.edu.au

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6150-3822
Nozomi Ando

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States

For correspondence
nozomi.ando@cornell.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7062-1644

Funding

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

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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.