The origin and evolution of ribonucleotide reduction

Life
Daniel LundinBritt-Marie Sjöberg

Abstract

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.

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Citations

Jan 23, 2016·Life·Niles Lehman
Jan 7, 2016·Journal of Molecular Evolution·Aaron David GoldmanLaura F Landweber
Oct 4, 2017·The Journal of Biological Chemistry·Christoph LodererBritt-Marie Sjöberg
Sep 1, 2018·The Journal of Biological Chemistry·Inna Rozman GrinbergBritt-Marie Sjöberg
Jul 8, 2017·Beilstein Journal of Organic Chemistry·Antoine Danchin
Jul 31, 2018·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Christopher K Mathews
Apr 18, 2020·Molecular Biology and Evolution·Ashar J MalikJane R Allison
Jun 21, 2019·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Gustav BerggrenBritt-Marie Sjöberg
Aug 16, 2019·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Inna Rozman GrinbergGustav Berggren
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May 15, 2015·The Journal of Biological Chemistry·Venkateswara Rao JonnaAnders Hofer
Nov 19, 2020·Natural Product Reports·Andreas Kirschning
Mar 7, 2021·Biomolecules·Julia FrischChristoph Loderer
Jul 28, 2021·The Journal of Biological Chemistry·Eugen SchellChristoph Loderer
Aug 24, 2021·Journal of the American Chemical Society·JoAnne Stubbe, Daniel G Nocera
Aug 29, 2019·ACS Omega·Laia Miret-CasalsEduard Torrents

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Methods Mentioned

BETA
deamination

Software Mentioned

RNR
GR
urRNR
HMMER
SplitsTree
Align
NeighborNet
protoRNR
LAST

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