Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen

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Title
Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen
Author(s)
Kyung Mo Kim; T Qin; Y Y Jiang; L L Chen; M Xiong; D Caetano-Anolles; H Y Zhang; G Caetano-Anolles
Bibliographic Citation
Structure, vol. 20, no. 1, pp. 67-76
Publication Year
2012
Abstract
The origin and evolution of modern biochemistry remain a mystery despite advances in evolutionary bioinformatics. Here, we use a structural census in nearly 1,000 genomes and a molecular clock of folds to define a timeline of appearance of protein families linked to single-domain enzymes. The timeline sorts out enzymatic recruitment, validates patterns in metabolic history, and reveals that the most ancient reaction of aerobic metabolism involved the synthesis of pyridoxal 5′-phosphate or pyridoxal and appeared 2.9 Gyr ago. The oxygen source for this primordial reaction was probably Mn catalase, which appeared at the same time and could have generated oxygen as a side product of hydrogen peroxide detoxification. Finally, evolutionary analysis of transferred groups and metabolite fragments revealed that oxidized sulfur did not participate in metabolism until the rise of oxygen. The evolutionary patterns we uncover in molecules and chemistries provide strong support for the coevolution of biochemistry and geochemistry.
ISSN
0969-2126
Publisher
Elsevier-Cell Press
DOI
http://dx.doi.org/10.1016/j.str.2011.11.003
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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