Analysis of the Intermediary Metabolism of a Reductive Chemoautotroph

Srinivasan, Vijayasarathy; Morowitz, Harold J.

doi:10.1086/bblv217n3p222

Cited by 38 publications

(43 citation statements)

References 24 publications

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“…We can argue for the existence of a universal anabolic, autotrophic network [50,51] that comprises the chemistry essential to life. We can then separate the structural requirements and evolutionary history of the universal network from secondary complexities, which we will argue originate in the diversification of species and the concurrent processes of assembly of ecological communities.…”

Section: Hierarchy In Metabolism and The Role Of Individuals And Ecomentioning

confidence: 99%

“…Figure 2 illustrates schematically the relation of the three classes. Both catabolic and anabolic pathways may be large and somewhat diversified; the core itself constitutes no more than a few hundred small metabolites [50,51], most of which have functions that are universal throughout the biosphere.…”

Section: Anabolism and Catabolism In Individuals And Ecosystemsmentioning

confidence: 99%

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The compositional and evolutionary logic of metabolism

2012

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Metabolism is built on a foundation of organic chemistry, and employs structures and interactions at many scales. Despite these sources of complexity, metabolism also displays striking and robust regularities in the forms of modularity and hierarchy, which may be described compactly in terms of relatively few principles of composition. These regularities render metabolic architecture comprehensible as a system, and also suggests the order in which layers of that system came into existence. In addition metabolism also serves as a foundational layer in other hierarchies, up to at least the levels of cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, motivates us to interpret metabolism as a source of causation or constraint on many forms of organization in the biosphere. Many of the forms of modularity and hierarchy exhibited by metabolism are readily interpreted as stages in the emergence of catalytic control by living systems over organic chemistry, sometimes recapitulating or incorporating geochemical mechanisms. We identify as modules, either subsets of chemicals and reactions, or subsets of functions, that are re-used in many contexts with a conserved internal structure. At the small molecule substrate level, module boundaries are often associated with the most complex reaction mechanisms, catalyzed by highly conserved enzymes. Cofactors form a biosynthetically and functionally distinctive control layer over the small-molecule substrate. The most complex members among the cofactors are often associated with the reactions at module boundaries in the substrate networks, while simpler cofactors participate in widely generalized reactions. The highly tuned chemical structures of cofactors (sometimes exploiting distinctive properties of the elements of the periodic table) thereby act as 'keys' that incorporate classes of organic reactions within biochemistry. Module boundaries provide the interfaces where change is concentrated, when we catalogue extant diversity of metabolic phenotypes. The same modules that organize the compositional diversity of metabolism are argued, with many explicit examples, to have governed long-term evolution. Early evolution of core metabolism, and especially of carbon-fixation, appears to have required very few innovations, and to have used few rules of composition of conserved modules, to produce adaptations to simple chemical or energetic differences of environment without diverse solutions and without historical contingency. We demonstrate these features of metabolism at each of several levels of hierarchy, beginning with the small-molecule metabolic substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Content from this work may be used under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 licence.

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Section: Hierarchy In Metabolism and The Role Of Individuals And Ecomentioning

confidence: 99%

Section: Anabolism and Catabolism In Individuals And Ecosystemsmentioning

confidence: 99%

The compositional and evolutionary logic of metabolism

2012

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“…According to [11], phosphoenolpyruvate and oxaloacetate are nodal molecules of all anabolic networks (in addition to acetate, pyruvate, and 2-oxoglutarate). From the diagrams in Figures 3 and 4, it is clear that facies with phosphoenolpyruvate -oxaloacetate paragenesis are an area of bifurcation (network node) that determines the development of the primordial 3-HP (fumarate) and RC cycles (succinate), system of gluconeogenesis (3-phosphoglycerate ↔ fructose 1,6-bisphosphate → fructose 6-phosphate) and the RPP cycle (3-phosphoglycerate → ribulose-1,5-bisphosphate → 3-phosphoglycerate).…”

Section: The Chemical Potentials Of Methane Molecular Hydrogen and mentioning

confidence: 99%

“…It has also been suggested that the last common ancestor (LCA) of all extant cell lineages was a chemolithoautotrophic thermophilic anaerobe [10][11][12][13][14] capable of synthesizing organic 'building blocks' from the inorganic carbon. Thus, these microorganisms can serve as a model for studying primordial metabolism.…”

Section: Introductionmentioning

confidence: 99%

The Emergence of Bioenergetics: The Formation of a Gluconeogenesis System and Reductive Pentose Phosphate Pathway of CO2 Fixation in Ancient Hydrothermal Systems

Marakushev¹,

Belonogova²

2016

Bioenergetics

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The origin of phosphorus metabolism is one of the central problems in the context of the emergence of life on Earth. It has been shown that the C-H-O system can be transformed into a four-component C-H-O-P system with the formation of a gluconeogenesis path in a possible Archean hydrothermal condition under the influence of a phosphorus chemical potential. This system became the energy supply basis for protometabolism, and facilitated the formation of a new CO 2 fixation cycle (the reductive pentose phosphate pathway).The modular design of central metabolism in the C-H-O-P system is derived from the parageneses (associations) of certain substances, and the emerging modules in turn associate with each other in certain physical and chemical hydrothermal conditions. The assembly of malate, oxaloacetate, pyruvate, and phosphoenolpyruvate is a reversible "turnstile -like" mechanism with a switching of reaction direction that determines the trend of specific metabolic systems development.

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“…For reductive autotrophs, all synthetic pathways begin in the five pillars of anabolism [3]: acetate, pyruvate, phosphoenol pyruvate, aspartate, and 2-oxogluta-rate. We assume that the reductive tricarboxylic acid cycles in which the preceding are components is the core of all autotrophic anabolism.…”

mentioning

confidence: 99%