The standard molecular clock describes a constant rate of molecular evolution and provides a powerful framework for evolutionary timescales. Here, we describe the existence and implications of a molecular clock of folds, a universal recurrence in the discovery of new structures in the world of proteins. Using a phylogenomic structural census in hundreds of proteomes, we build phylogenies and time lines of domains at fold and fold superfamily levels of structural complexity. These time lines correlate approximately linearly with geological timescales and were here used to date two crucial events in life history, planet oxygenation and organism diversification. We first dissected the structures and functions of enzymes in simulated metabolic networks. The placement of anaerobic and aerobic enzymes in the time line revealed that aerobic metabolism emerged about 2.9 billion years (giga-annum; Ga) ago and expanded during a period of about 400 My, reaching what is known as the Great Oxidation Event. During this period, enzymes recruited old and new folds for oxygen-mediated enzymatic activities. Remarkably, the first fold lost by a superkingdom disappeared in Archaea 2.6 Ga ago, within the span of oxygen rise, suggesting that oxygen also triggered diversification of life. The implications of a molecular clock of folds are many and important for the neutral theory of molecular evolution and for understanding the growth and diversity of the protein world. The clock also extends the standard concept that was specific to molecules and their timescales and turns it into a universal timescale-generating tool.

No abstract

No abstract

Chroogomphis rutillus is an ectomycorrhizal edible mushroom available in China. The ethanolic, cold water and hot water extracts were prepared and their antioxidant properties studied. At 4 mg/mL, the ethanolic extract showed a high reducing power of 1.561, whereas those of cold water and hot water extracts were 1.161 and 0.808. With regard to the scavenging ability on 1,1-diphenyl-2-picrylhydrazyl radicals, extracts were effective in the order: ethanolic > cold water > hot water extracts. EC50values for chelating ability on ferrous ions for ethanolic, cold water and hot water extracts were 15.755, 0.059, and 0.067 mg/mL, respectively. Based on EC50values, the various extracts from C. rutillus were effective antioxidants.

Holiota nameko is an edible mushroom widely cultivated in the northeast of China. The cold water, hot water and ethanol extracts were prepared and their antioxidant properties were studied. At 2 mg/mL, the cold water extract showed a high reducing power of 1.502, whereas those of hot water and ethanol extracts were 0.868 and 0.159. With regard to the scavenging ability on DPPH free radicals, extracts were effective in the order: cold water > hot water > ethanol extracts. EC50 values for chelating ability on ferrous ions for cold water, hot water, and ethanol extracts were 1.461, 0.663, and 11.791 mg/mL, respectively. Based on EC50 values, the water extracts of P. nameko were effective antioxidants.