Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins

Ji, Hong‐Fang; Chen, Lei; Zhang, Hongyu

doi:10.1002/bies.20788

Cited by 15 publications

(12 citation statements)

References 32 publications

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“…However, a recent analysis revealed that the primitive redox proteins depended more on organic redox coenzymes than on metallic cofactors. (30) This opinion is supported by the present finding, because most of the primordial redox proteins belong to NAD(P)-binding Rossmann-fold domains (c.2, no. 3) or TIM beta/alpha-barrel (c.1, no.…”

Section: Introductionsupporting

confidence: 75%

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Evolutionary formation of new protein folds is linked to metallic cofactor recruitment

Chen

Jiang

et al. 2009

BioEssays

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To explore whether the generation of new protein folds could be linked to metallic cofactor recruitment, we identified the oldest examples of folds for manganese, iron, zinc, and copper proteins by analyzing their fold-domain mapping patterns. We discovered that the generation of these folds was tightly coupled to corresponding metals. We found that the emerging order for these folds, i.e., manganese and iron protein folds appeared earlier than zinc and copper counterparts, coincides with the putative bioavailability of the corresponding metals in the ancient anoxic ocean. Therefore, we conclude that metallic cofactors, like organic cofactors, play an evolutionary role in the formation of new protein folds. This link could be explained by the emergence of protein structures with novel folds that could fulfill the new protein functions introduced by the metallic cofactors. These findings not only have important implications for understanding the evolutionary mechanisms of protein architectures, but also provide a further interpretation for the evolutionary story of superoxide dismutases.

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Section: Introductionsupporting

confidence: 75%

“…3) or TIM beta/alpha-barrel (c.1, no. 4) folds (30,31) , and these folds appeared much earlier than the oldest folds for manganese, iron, and copper proteins (i.e., c.68, a.1 and b.6).…”

Section: Introductionmentioning

confidence: 96%

Evolutionary formation of new protein folds is linked to metallic cofactor recruitment

Chen

Jiang

et al. 2009

BioEssays

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“…, iron, copper and molybdenum), while in aerobic enzymes, metallic redox cofactors were more popular. This mirrors the poor bioavailability of copper and molybdenum in the anaerobic world [20]–[22] and also agrees with prior conclusions that primitive redox enzymes (which are anaerobic enzymes) mainly used organic cofactors in catalysis [23]. Moreover, while NAD(H) is more common than NADP(H) in anaerobic enzymes, the opposite is true for aerobic enzymes (Table 1).…”

Section: Resultssupporting

confidence: 90%

The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation

et al. 2012

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The appearance of planetary oxygen likely transformed the chemical and biochemical makeup of life and probably triggered episodes of organismal diversification. Here we use chemoinformatic methods to explore the impact of the rise of oxygen on metabolic evolution. We undertake a comprehensive comparative analysis of structures, chemical properties and chemical reactions of anaerobic and aerobic metabolites. The results indicate that aerobic metabolism has expanded the structural and chemical space of metabolites considerably, including the appearance of 130 novel molecular scaffolds. The molecular functions of these metabolites are mainly associated with derived aspects of cellular life, such as signal transfer, defense against biotic factors, and protection of organisms from oxidation. Moreover, aerobic metabolites are more hydrophobic and rigid than anaerobic compounds, suggesting they are better fit to modulate membrane functions and to serve as transmembrane signaling factors. Since higher organisms depend largely on sophisticated membrane-enabled functions and intercellular signaling systems, the metabolic developments brought about by oxygen benefit the diversity of cellular makeup and the complexity of cellular organization as well. These findings enhance our understanding of the molecular link between oxygen and evolution. They also show the significance of chemoinformatics in addressing basic biological questions.

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“…The hypothesis that a functional metal homeostasis system would be necessary for the first steps in akaryotic evolution has been argued using transitional arguments (3), and the concomitant appearances of structures involved in metal homeostasis, metal-specific architectures, and the diversification of the akaryotic lineages provides the first genomic evidence of this. Before this coordinated evolution, organic cofactors able to transport protons had already evolved (28), yet when coupled with metal-binding electron transport proteins, redox transformations become possible. The earliest evolving Fe-, Mo-, and Cu-binding protein architectures are intrinsically involved in electron transfer and the transformations of C, N, S, and O (Table S3).…”

Section: Emergence Of the Akaryotes Metal Homeostasis And Biogeochementioning

confidence: 99%

History of biological metal utilization inferred through phylogenomic analysis of protein structures

Dupont

Butcher

Valas³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

286

248

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The fundamental chemistry of trace elements dictates the molecular speciation and reactivity both within cells and the environment at large. Using protein structure and comparative genomics, we elucidate several major influences this chemistry has had upon biology. All of life exhibits the same proteome size-dependent scaling for the number of metal-binding proteins within a proteome. This fundamental evolutionary constant shows that the selection of one element occurs at the exclusion of another, with the eschewal of Fe for Zn and Ca being a defining feature of eukaryotic proteomes. Early life lacked both the structures required to control intracellular metal concentrations and the metal-binding proteins that catalyze electron transport and redox transformations. The development of protein structures for metal homeostasis coincided with the emergence of metal-specific structures, which predominantly bound metals abundant in the Archean ocean. Potentially, this promoted the diversification of emerging lineages of Archaea and Bacteria through the establishment of biogeochemical cycles. In contrast, structures binding Cu and Zn evolved much later, providing further evidence that environmental availability influenced the selection of the elements. The late evolving Zn-binding proteins are fundamental to eukaryotic cellular biology, and Zn bioavailability may have been a limiting factor in eukaryotic evolution. The results presented here provide an evolutionary timeline based on genomic characteristics, and key hypotheses can be tested by alternative geochemical methods.Archean-Proterozoic | biogeochemistry | bioinorganic chemistry | evolution | metal homeostasis M etalloproteins contain one or more ions of an inorganic element in their 3D structure and are said to comprise 30% of all proteins (1). Many biological pathways contain at least one metalloenzyme (2) and consequently require Mg, K, Ca, Fe, Mn, and Zn to sustain life (3). Other elements, like Cu, Mo, Ni, Se, and Co, are required by many-though not all-organismal lineages, and the utilization of trace elements varies greatly between species (3). The different elements have a range of affinities for most coordinating environments in the order Mg +2 /Ca +2 < Mn +2 < Fe +2 < Co +2 < Ni +2 < Cu +2 ∼Zn +2 , an equilibrium series known as the Irving-Williams Series (4). This array of outer-sphere chemistry provides significant catalytic diversity, yet has consequences for both biological and environmental chemistry. Within the cell, metals compete for protein binding sites; hence, extensive protein networks involving transporters and metalsensing regulatory proteins are required to maintain the proper subcellular concentrations of each element, and in some cases directly shuttle each metal to its requisite metalloprotein in the proper cellular compartment (1, 5, 6). It has been hypothesized that the establishment of a metal homeostasis system is required for distinct phylotypes of cells to develop (7).Environmentally, for similar fundamental chemical reasons, the...

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Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins

Cited by 15 publications

References 32 publications

Evolutionary formation of new protein folds is linked to metallic cofactor recruitment

Evolutionary formation of new protein folds is linked to metallic cofactor recruitment

The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation

History of biological metal utilization inferred through phylogenomic analysis of protein structures

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