The energetics of the reductive citric acid cycle in the pyrite-pulled surface metabolism in the early stage of evolution

The chemoautotrophic theory concerning the origin of life postulates that a central role is played in the prebiotic chemical machinery by a reductive citric acid cycle operating without enzymes. The crucial point in this scenario is the formation of pyrite from hydrogen sulfide and ferrous sulfide, a reaction suggested to be linked to endergonic reactions, making them exergonic. This mechanism is believed to provide the driving force for the cycle to operate as a carbon dioxide fixation network. The present paper criticizes the thermodynamic calculations and their presentation in the original version of the archaic reductive citric acid cycle [W?chtersh?user, 1990. Evolution of the first metabolic cycles. Proc. Natl Acad. Sci. USA 87, 200-204.]. The most significant differences between the W?chtersh?user hypothesis and the present proposal: W?chtersh?user did not consider individual reactions in his calculations. A particularly questionable feature is the involvement of seven molecules of pyrite which does not emerge as a direct consequence of the chemical reactions presented in the archaic reductive citric acid cycle. The involvement of a considerable number of sulfur-containing organic intermediates as building blocks is also disputed. In the new scheme of the cycle proposed here, less free energy is liberated than hypothesized by W?chtersh?user, but it has the advantages that the free energy changes for the individual reactions can be calculated, the number of pyrite molecules involved in the cycle is reduced, and fewer sulfur-containing intermediates are required for the cycle to operate. In combination with a plausible route for the anaplerotic reactions [Kalapos, 1997a. Possible evolutionary role of methylglyoxalase pathway: anaplerotic route for reductive citric acid cycle of surface metabolists. J. Theor. Biol. 188, 201-206.], this new presentation of the cycle assigns a special meaning to hydrogen sulfide formation in the early stage of biochemical evolution.     

A fluorescent substrate for carbon–phosphorus lyase: Towards the pathway for organophosphonate metabolism in bacteria

Many species of bacteria can use naturally occurring organophosphonates as a source of metabolic phosphate by cleaving the carbon–phosphorus bond with a multi-enzyme pathway collectively called carbon–phosphorus lyase (CP-lyase). Very little is known about the fate of organophosphonates entering this pathway. In order to detect metabolic intermediates we have synthesized a fluorescently labelled organophosphonate and show that this is a viable substrate for the CP-lyase pathway in Escherichia coli and that the expected product of CP-bond cleavage is formed. The in vivo competence of one potential metabolic intermediate, 1-ethylphosphonate-α-d-ribofuranose, is also demonstrated.     

Reproductive energetics of the role reversing bushcricket,Kawanaphila nartee (Orthoptera: Tettigoniidae: Zaprochilinae)

Theory predicts that sexual differences in reproductive strategies arise because of differences in the magnitude of investment made by males and females in reproduction. In some bushcrickets, the typical sex role of competitive male and choosy female is reversed when populations are subject to nutrient stress. Here I present an energetic analysis of reproduction for the role reversing bushcricket, Kawanaphila nartee, that supports the contention that this sex role reversal is a consequence of reversal in the pattern of relative reproductive investment. When fed ad libitum, males spent 16% of their daily energy reserves on the spermatophore compared with 26% spent on calling to attract a mate. Females spent 29% of their daily energy reserves in producing and laying eggs. However, when allowed only limited access to food, female expenditure in eggs was reduced to 23% of daily reserves while male expenditure remained unchanged. After accounting for the incorporation of male nutrients into eggs, female energy expenditure in reproduction exceeded male expenditure when animals were fed ad libitum, but male expenditure exceeded female expenditure when diet was limited. This role reversal in relative energy expenditure that is associated with courtship role reversal supports classical and contemporary theories on the control of sexual selection.     

NADPH-dependent reductive metabolism of cis-5 unsaturated fatty acids. A revised pathway for the beta-oxidation of oleic acid

Cis-5 double bond in a fatty acid or when encountered through the beta-oxidation of an odd-numbered double-bond unsaturated fatty acid presents as a metabolic block to the further beta-oxidation. Cis-5-fatty acyl-CoA cannot be beta-oxidized to cis-3-enoyl-CoA as suggested by the conventional pathway. Instead, this metabolic block can only be removed through an NADPH-dependent reduction of 5-enoyl-CoA, possibly mediated by a 5-enoyl-CoA reductase. In the case of oleic acid two cycles of beta-oxidation yield cis-5-tetradecenoyl-CoA. This intermediate is then reduced to tetradecanoyl-CoA, which is metabolized further via normal beta-oxidation cycles. The conventional pathway through cis-3-dodecenoyl-CoA does not operate in rat liver.     

Protein energetics in maturation of the early secretory pathway

The early secretory pathway (ESP) consisting of the endoplasmic reticulum (ER), pre-Golgi intermediates and the Golgi stack links protein synthesis to folding and vesicle trafficking to generate the membrane architecture of the eukaryotic cell. The fundamental principles that contribute to organization of the ESP remain largely unknown. We raise the possibility that assembly of the ESP is largely built on a foundation that is influenced by the kinetic and thermodynamic properties of the protein fold. Folding energetics may provide an adjustable platform for adaptor-dependent interactions with the transport machinery, suggesting the possibility that protein cargo energetics plays a central role in directing both trafficking patterns and global compartmental organization of the ESP. In this view, cargo energetics likely coordinates the composition and maturation of ER and Golgi compartments with the physiological state of the cell in different tissue and environmental settings.     

The metabolism of benzoate by Moraxella species through anaerobic nitrate respiration. Evidence for a reductive pathway.

Moraxella sp. isolated from soil grows anaerobically on benzoate by nitrate respiration; nitrate or nitrite are obligatory electron acceptors, being reduced to molecular N2 during the catabolism of the substrate. This bacterium also grows aerobically on benzoate. 2. Aerobically, benzoate is metabolized by ortho cleavage of catechol followed by the beta-oxoadipate pathway. 3. Cells of Moraxella grown anaerobically on benzoate are devoid of ortho and meta cleavage enzymes; cyclohexanecarboxylate and 2-hydroxycyclohexanecarboxylate were detected in the anaerobic culture fluid. 4. [ring-U-14C]Benzoate, incubated anaerobically with cells in nitrate-phosphate buffer, gave rise to labelled 2-hydroxycyclohexanecarboxylate and adipate. When [carboxy-14C]benzoate was used, 2-hydroxycyclohexanecarboxylate was radioactive but the adipate was not labelled. A decarboxylation reaction intervenes at some stage between these two metabolites. 5. The anaerobic metabolism of benzoate by Moraxella sp. through nitrate respiration takes place by the reductive pathway (Dutton & Evans, 1969). Hydrogenation of the aromatic ring probably occurs via cyclohexa-2,5-dienecarboxylate and cyclohex-1-enecarboxylate to give cyclohexanecarboxylate. The biochemistry of this reductive process remains unclear. 6. CoA thiol esterification of cyclohexanecarboxylate followed by beta-oxidation via the unsaturated and hydroxy esters, would afford 2-oxocyclohexanecarboxylate. Subsequent events in the Moraxella culture differ from those occurring with Rhodopseudomonas palustris; decarboxylation precedes hydrolytic cleavage of the alicyclic ring to produce adipate in the former, whereas in the latter the keto ester undergoes direct hydrolytic fission to pimelate.     

In vitro reductive metabolism of N-nitrosodibenzylamine: Evidence for new reactive intermediates

N-Nitrosodibenzylamine was incubated with rabbit-whole-liver homogenates. Gas-chromatographic and mass spectrometric analysis of the incubation extracts showed the formation of bibenzyl. This biotransformation is the result of a 2-electron reduction of the substrate to 1-hydroxy-2,2-dibenzylhydrazine, an unstable compound which breaks down to bibenzyl and nitrogen. It is suggested that such reductive metabolism may be involved in the generation of toxic metabolites of nitrosamines.     

Amino acid metabolism and the energetics of growth

The nonessential amino acids are involved in a large number of functions that are not directly associated with protein synthesis. Recent studies using a combination of transorgan balance and stable isotopic tracers have demonstrated that a substantial portion of the extra‐splanchnic flux of glutamate, glutamine, glycine and cysteine derives from tissue synthesis. A key amino acid in this respect is glutamic acid. Little glutamic acid of dietary origin escapes metabolism in the small intestinal mucosa. Furthermore, because glutamic acid is the only amino acid that can be synthesized by mammals by reductive amination of a ketoacid, it is the ultimate nitrogen donor for the synthesis of other nonessential amino acids. Because the synthesis of glutamic acid and its product glutamine involve the expenditure of adenosine triphosphate (ATP), it seems possible that nonessential amino acid synthesis might have a significant bearing on the energetics of protein synthesis and, hence, of protein deposition. This paper discusses the topic of the energy cost of protein deposition, considers the metabolic physiology of amino acid oxidation and nonessential amino acid synthesis, and attempts to combine the information to speculate on the overall impact of amino acid metabolism on the energy exchanges of animals.     

The oxoglutarate reductive carboxylation pathway: a review.

Acetyl Coenzyme A is required for a variety of processes in the cytosol such as lipogenesis as well as a variety of acetylations. One mechanism whereby these acetyl groups are provided is a metabolic pathway by which oxoglutarate (or glutamate) is translocated from the mitochondria and is reductively carboxylated to isocitric acid in the cytosol. This is then converted to citrate which cleaved to acetyl CoA and oxaloacetate by ATP citrate lyase. This pathway has been termed the Oxoglutarate Reductive Carboxylation Pathway. The C₂ units produced are used for such acetyl CoA requiring processes as fatty acid and cholesterol biosynthesis; the C₄ units are used in some tissues for gluconeogenesis. In tissues other than those of the nervous system the contribution of carbon units by this pathway is profoundly influenced by the nutritional state of the animal. In starved animals, where fatty acid synthesis is curtailed, the conversion of labeled glutamate to C₄ and C₂ units for gluconeogenesis and fatty acids is severely depressed. In carbohydrate-fed animals, or with animals maintained under conditions which stimulate fatty acid synthesis, glutamate conversion by this pathway may reach 50–60% of the radiolabeled glutamate utilized. Other conditions which influence the function of this pathway are the developmental stage of the organism such as in the fetal vs adult ruminant or the developmental stage of the brain, the presence or absence of insulin, and the yearly cycle of hibernating animals.     

Microbial energetics should be considered in manipulating metabolism for biotechnological purposes

The conversion of substrates into products and biomass in a microbial culture is a chemical reaction, albeit a complicated one. The stoichiometry and kinetics of this reaction provide information which can be useful in demonstrating how the intrinsic properties of microorganisms or the conditions imposed on them influence productivity in bioreactors. Microbial energetics can be used to guide the selection of production strains both by culture screening and recombinant DNA techniques, to predict the maximum yield of a product from a particular organism, and to explain the influence of culture conditions on productivity.     

Hybrid electrosynthesis as non-genetic approach for regulating microbial metabolism towards waste valorization in circular framework

Biogenic waste (solid/liquid/gaseous) utilization in biological processes has disruptive potential of inclining towards carbon neutrality, while producing diverse products output. Anaerobic fermentation (methanogenesis and acidogenesis) routes are crucial bioprocesses for production of various renewable chemicals (carboxylate platform/organic acids, short/medium chain alcohols, aldehydes, biopolymers) and fuels (methane, hydrogen, hythane, biodiesel and electricity), while individual operations posing process limitations on their conversion efficiency. Advantageous benefit of using the individual bioprocess technicalities is of utmost importance in the context of sustainability to conceptualize and execute integrated waste biorefinery. The opinion article intends to document/familiarize the waste-fed biorefinery potential with application of hybrid advancements towards multiple product/energy/renewable chemical spectrum leading to carbon neutrality bioprocesses. Unique and notable challenges with diverse process integrations along with electrochemical/interspecies-redox metabolites-materials synergy/enzymatic interventions are specifically emphasized on application-oriented waste feedstock potential towards achieving sustainability.     

Uniform designation for genes of the Calvin-Benson-Bassham reductive pentose phosphate pathway of bacteria

Structural and regulatory genes encoding enzymes and proteins of the reductive pentose phosphate pathway have been isolated from a number of bacteria recently. In the phototroph Rhodobacter sphaeroides, and in two chemoautotrophic bacteria, Alcaligenes eutrophus and Xanthobacter flavus, these genes have been found in distinct operons. However, in these three organisms and in other bacteria where certain of these genes have been discovered, a uniform nomenclature to designate these genes has been lacking. This report represents an effort to provide uniformity to the designation of these genes from all bacteria.     

Designing metabolism: Alternative connectivities for the pentose phosphate pathway

We present a method for generating alternative biochemical pathways between specified compounds. We systematically generated diverse alternatives to the nonoxidative stage of the pentose phosphate pathway, by first finding pathways between 5-carbon and 6-carbon skeletons. Each solution of the equations for the stoichiometric coefficients of skeleton-changing reactions defines a set of networks. Within each set we selected networks with modules; a module is a coupled set of reactions that occurs more than one in a network. The networks can be classified into at least 53 families in at least seven superfamilies, according to the number, the input-output relations, and the internal structure of their modules. We then assigned classes of enzymes to mediate transformations of carbon skeletons and modifications of functional groups. The ensemble of candidate networks was too large to allow complete determination of the optimal network. However, among the networks we studied the real pathway is especially favorable in several respects. It has few steps, uses no reducing or oxidizing compounds, requires only one ATP in one direction of flux, and does not depend on recurrent inputs.     

Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture

Background  

Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organisms. Tryptophan limitation caused by production of interferon-γ by the host and subsequent induction of indoleamine dioxygenase is a key aspect of the host-parasite interaction. It appears that the chlamydiae have learned to recognize tryptophan depletion as a signal for developmental remodeling. The consequent non-cultivable state of persistence can be increasingly equated to chronic disease conditions.     

Physico-chemical properties of organic compounds and the energetics of metabolism

The existing reference system of thermodynamic potentials of substance formation does not outline some important properties inherent to energy transformation and utilization in the cell metabolism. To elicit these properties, a new reference system is suggested. On its basis, a generalized unit of chemical substance reductance, called redoxon, has been developed. The molecules of more reduced substances contain a higher number of redoxons. Energy value of one redoxon is nearly constant in organic compounds but strongly varying in inorganic ones. The stoichiometric and thermodynamic balances of biochemical reactions in the new reference system have been obtained. The suggested approach has been shown to be an adequate tool for the analysis of the mass-energy balance of metabolic processes including heterotrophic and autotrophic growth of intact cells and organisms.     

Towards understanding the biosynthetic pathway for ustilaginoidin mycotoxins in Ustilaginoidea virens

Ustilaginoidins, toxic to plants, animals and human, are one of major types of mycotoxins produced by Ustilaginoidea virens. In this study, a gene cluster containing the polyketide synthase gene UvPKS1 was analysed via gene replacement and biochemical studies to determine ustilaginoidin biosynthetic pathway in U. virens. UvPKS1 was first proven to be responsible for the first step of ustilaginoidin biosynthesis, since neither ustilaginoidin derivatives nor intermediates were produced when UvPKS1 was deleted. Replacement of ugsO greatly reduced ustilaginoidin production but increased the ratios of dehydrogenated/hydrogenated ustilagioidin derivatives. The enhanced growth rate of the ΔugsO mutant indicates that accumulation of certain ustilaginoidin derivatives may adversely affect mycelial growth in U. virens. Deletion of ugsT encoding a putative MFS transporter disrupted the ability to generate ustilaginoidins. The ustilaginoidin derivatives produced in the ΔugsJ mutant all lack C3-methyl, indicating that UgsJ is responsible for C3-methylation. Only monomeric intermediates, such as 3-methyl-dihydro-nor-rubrofusarin, but no ustilaginoidin derivatives were generated in the ΔugsL mutant, indicating that UgsL is responsible for the dimerization of nor-rubrofusarin derivatives to produce ustilaginoidins. However, ugsR2 deletion had no dramatic effect on ustilaginoidin biosynthesis. Together, biochemical analyses with bioinformatics and chemoinformatics uncover a multiple-step enzyme-catalysed pathway for ustilaginoidin biosynthesis in U. virens.     

Towards a molecular pathway for myoblast fusion in Drosophila

Intercellular fusion among myoblasts is required for the generation of multinucleated muscle fibers during skeletal muscle development. Recent studies in Drosophila have shed light on the molecular mechanisms that underlie this process, and a signaling pathway that relays fusion signals from the cell membrane to the cytoskeleton has emerged. In this article, we review these recent advances and discuss how Drosophila offers a powerful model system to study myoblast fusion in vivo.     

Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator

Formate can be directly produced from CO₂ and renewable electricity, making it a promising microbial feedstock for sustainable bioproduction. Cupriavidus necator is one of the few biotechnologically-relevant hosts that can grow on formate, but it uses the Calvin cycle, the high ATP cost of which limits biomass and product yields. Here, we redesign C. necator metabolism for formate assimilation via the synthetic, highly ATP-efficient reductive glycine pathway. First, we demonstrate that the upper pathway segment supports glycine biosynthesis from formate. Next, we explore the endogenous route for glycine assimilation and discover a wasteful oxidation-dependent pathway. By integrating glycine biosynthesis and assimilation we are able to replace C. necator's Calvin cycle with the synthetic pathway and achieve formatotrophic growth. We then engineer more efficient glycine metabolism and use short-term evolution to optimize pathway activity. The final growth yield we achieve (2.6 gCDW/mole-formate) nearly matches that of the WT strain using the Calvin Cycle (2.9 gCDW/mole-formate). We expect that further rational and evolutionary optimization will result in a superior formatotrophic C. necator strain, paving the way towards realizing the formate bio-economy.