Glyoxylate and dicarboxylate metabolism

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Glyoxylate and dicarboxylate metabolism describes a variety of reactions involving glyoxylate or dicarboxylates. Glyoxylate is the conjugate base of glyoxylic acid, and within a buffered environment of known pH such as the cell cytoplasm these terms can be used almost interchangeably, as the gain or loss of a hydrogen ion is all that distinguishes them, and this can occur in the aqueous environment at any time. Likewise dicarboxylates are the conjugate bases of dicarboxylic acids, a general class of organic compounds containing two carboxylic acid groups, such as oxalic acid or succinic acid.

Glyoxylic acid chemical compound

Glyoxylic acid or oxoacetic acid is an organic compound. Together with acetic acid, glycolic acid, and oxalic acid, glyoxylic acid is one of the C2 carboxylic acids. It is a colourless solid that occurs naturally and is useful industrially.

pH measure of the acidity or basicity of an aqueous solution

In chemistry, pH is a scale used to specify how acidic or basic a water-based solution is. Acidic solutions have a lower pH, while basic solutions have a higher pH. At room temperature (25 °C), pure water is neither acidic nor basic and has a pH of 7.

Cytoplasm all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures

In cell biology, the cytoplasm is all of the material within a cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The main components of the cytoplasm are cytosol – a gel-like substance, the organelles – the cell's internal sub-structures, and various cytoplasmic inclusions. The cytoplasm is about 80% water and usually colorless.

A compact graphical description of major biochemical reactions involved can be found at KEGG [1] This provides information on the relevant enzymes and details the relationship with several other metabolic processes: glycine, serine, and threonine metabolism which provides hydroxypyruvate and glyoxylate, purine metabolism which provides glyoxylate, pyruvate metabolism which provides (S)-malate and formate, carbon fixation which consumes 3-phospho-D-glycerate and provides D-ribulose 1,5-P2, ascorbate and aldarate metabolism which shares tartronate-semialdehyde, nitrogen metabolism which shares formate, pyruvate metabolism and the citrate cycle which share oxaloacetate, and vitamin B6 metabolism which consumes glycolaldehyde.

KEGG biological database

KEGG is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.

Enzyme biological molecule

Enzymes are macromolecular biological catalysts. Enzymes accelerate chemical reactions. The molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and a new field of pseudoenzyme analysis has recently grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.

Purine metabolism refers to the metabolic pathways to synthesize and break down purines that are present in many organisms.

The glyoxylate cycle describes an important subset of these reactions involved in biosynthesis of carbohydrates from fatty acids or two-carbon precursors which enter the system as acetyl-coenzyme A. Its crucial enzymes are isocitrate lyase and malate synthase. However, alternate pathways have been proposed in organisms lacking isocitrate lyase. [2]

Glyoxylate cycle A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.

The glyoxylate cycle, a variation of the tricarboxylic acid cycle, is an anabolic pathway occurring in plants, bacteria, protists, and fungi. The glyoxylate cycle centers on the conversion of acetyl-CoA to succinate for the synthesis of carbohydrates. In microorganisms, the glyoxylate cycle allows cells to utilize simple carbon compounds as a carbon source when complex sources such as glucose are not available. The cycle is generally assumed to be absent in animals, with the exception of nematodes at the early stages of embryogenesis. In recent years, however, the detection of malate synthase (MS) and isocitrate lyase (ICL), key enzymes involved in the glyoxylate cycle, in some animal tissue has raised questions regarding the evolutionary relationship of enzymes in bacteria and animals and suggests that animals encode alternative enzymes of the cycle that differ in function from known MS and ICL in non-metazoan species.

Isocitrate lyase

Isocitrate lyase, or ICL, is an enzyme in the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate. Together with malate synthase, it bypasses the two decarboxylation steps of the tricarboxylic acid cycle and is used by bacteria, fungi, and plants.

In enzymology, a malate synthase (EC 2.3.3.9) is an enzyme that catalyzes the chemical reaction

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Citric acid cycle A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate.

The citric acid cycle (CAC) – also known as theTCA cycle or theKrebs cycle – is a series of chemical reactions used by all aerobic organisms to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins, into adenosine triphosphate (ATP) and carbon dioxide. In addition, the cycle provides precursors of certain amino acids, as well as the reducing agent NADH, that are used in numerous other reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically. Even though it is branded as a 'cycle', it is not necessary for metabolites to follow only one specific route; at least three segments of the citric acid cycle have been recognized.

Cellular respiration Cellular enzymatic release of energy from compounds

Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy in the process, as weak so-called "high-energy" bonds are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. Cellular respiration is considered an exothermic redox reaction which releases heat. The overall reaction occurs in a series of biochemical steps, most of which are redox reactions themselves. Although cellular respiration is technically a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow release of energy from the series of reactions.

Gluconeogenesis The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.

Gluconeogenesis (GNG) is a metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates. From breakdown of proteins, these substrates include glucogenic amino acids ; from breakdown of lipids, they include glycerol, odd-chain fatty acids ; and from other steps in metabolism they include pyruvate and lactate.

Oxaloacetic acid chemical compound

Oxaloacetic acid (also known as oxalacetic acid) is a crystalline organic compound with the chemical formula HO2CC(O)CH2CO2H. Oxaloacetic acid, in the form of its conjugate base oxaloacetate, is a metabolic intermediate in many processes that occur in animals. It takes part in gluconeogenesis, the urea cycle, the glyoxylate cycle, amino acid synthesis, fatty acid synthesis and the citric acid cycle.

Glyoxysomes are specialized peroxisomes found in plants (particularly in the fat storage tissues of germinating seeds) and also in filamentous fungi. Seeds that contain fats and oils include corn, soybean, sunflower, peanut and pumpkin. As in all peroxisomes, in glyoxysomes the fatty acids are oxidized to acetyl-CoA by peroxisomal β-oxidation enzymes. When the fatty acids are oxidized hydrogen peroxide (H2O2) is produced as oxygen (O2) is consumed. Thus the seeds need oxygen to germinate. Besides peroxisomal functions, glyoxysomes possess additionally the key enzymes of glyoxylate cycle (isocitrate lyase and malate synthase) which accomplish the glyoxylate cycle bypass.

Fumarase protein-coding gene in the species Homo sapiens

Fumarase is an enzyme that catalyzes the reversible hydration/dehydration of fumarate to malate. Fumarase comes in two forms: mitochondrial and cytosolic. The mitochondrial isoenzyme is involved in the Krebs Cycle, and the cytosolic isoenzyme is involved in the metabolism of amino acids and fumarate. Subcellular localization is established by the presence of a signal sequence on the amino terminus in the mitochondrial form, while subcellular localization in the cytosolic form is established by the absence of the signal sequence found in the mitochondrial variety.

Mixed acid fermentation

Mixed acid fermentation is the biological process by which a six-carbon sugar e.g. glucose is converted into a complex and variable mixture of acids. It is an anaerobic fermentation reaction that is common in bacteria. It is characteristic for members of the Enterobacteriaceae, a large family of Gram-negative bacteria that includes E. coli.

In enzymology, a 4-hydroxy-2-oxoglutarate aldolase is an enzyme that catalyzes the chemical reaction

In enzymology, a 4-hydroxy-4-methyl-2-oxoglutarate aldolase is an enzyme that catalyzes the chemical reaction

In enzymology, a malyl-CoA lyase is an enzyme that catalyzes the chemical reaction

Methylisocitrate lyase

In enzymology, a methylisocitrate lyase is an enzyme that catalyzes the chemical reaction

Oxalate decarboxylase

In enzymology, an oxalate decarboxylase (EC 4.1.1.2) is an enzyme that catalyzes the chemical reaction

In enzymology, an oxalomalate lyase is an enzyme that catalyzes the chemical reaction

In enzymology, formate C-acetyltransferase is an enzyme. Pyruvate formate lyase is found in Escherichia coli and other organisms. It helps regulate anaerobic glucose metabolism. Using radical non-redox chemistry, it catalyzes the reversible conversion of pyruvate and coenzyme-A into formate and acetyl-CoA. The reaction occurs as follows:

Isocitrate lyase family is a family of evolutionarily related proteins.

Microbial production of Succinic acid can be performed with wild bacteria like Actinobacillus succinogenes, Mannheimia succiniciproducens and Anaerobiospirillum succiniciproducens or genetically modified Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisia. Understanding of the central carbon metabolism of these organisms is crucial in determining the maximum obtainable yield of succinic acid on the carbon source employed as substrate.

References

  1. ↑ "Glyoxylate and dicarboxylate metabolism". at KEGG.
  2. ↑ "Subsystem: Glyoxylate bypass". National Microbial Pathogen Data Resource. Archived from the original on 2011-10-05.
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