Glyoxylate cycle
Encyclopedia
Anabolism
Anabolism is the set of metabolic pathways that construct molecules from smaller units. These reactions require energy. One way of categorizing metabolic processes, whether at the cellular, organ or organism level is as 'anabolic' or as 'catabolic', which is the opposite...
metabolic pathway
Metabolic pathway
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
occurring in plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
s, bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, protist
Protist
Protists are a diverse group of eukaryotic microorganisms. Historically, protists were treated as the kingdom Protista, which includes mostly unicellular organisms that do not fit into the other kingdoms, but this group is contested in modern taxonomy...
s, fungi and several microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
s, such as E. coli and yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
. The glyoxylate cycle centers on the conversion of acetyl-CoA
Acetyl-CoA
Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. Its main function is to convey the carbon atoms within the acetyl group to the citric acid cycle to be oxidized for energy production. In chemical structure, acetyl-CoA is the thioester...
to succinate for the synthesis of carbohydrate
Carbohydrate
A carbohydrate is an organic compound with the empirical formula ; that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 . However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical...
s. In microorganisms, the glyoxylate cycle allows cells to utilize simple carbon compounds as a carbon source when complex sources such as glucose
Glucose
Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate...
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
Malate synthase
In enzymology, a malate synthase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are acetyl-CoA, H2O, and glyoxylate, whereas its two products are -malate and CoA....
(MS) and isocitrate lyase
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.The systematic...
(ICL), key enzymes involved in the gyloxylate cycle, in some animal tissue has raised questions regarding the evolutionary relationship of enzymes in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
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.
Similarities with TCA Cycle
The glyoxylate cycle utilizes three of the five enzymes associated with the tricarboxylic acid cycle and shares many of its intermediate steps. The two cycles vary when, in the gylcoxylate cycle, ICL converts isocitrate into glyoxylate and succinate instead of α-ketogluterate as seen in the TCA cycle. This bypasses the decarboxylation steps that take place in the TCA cycle, allowing simple carbon compounds to be used in the later synthesis of macromolecules, including glucose. The glyoxylate cycle then continues on, using glyoxylate and acetyl-CoAAcetyl-CoA
Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. Its main function is to convey the carbon atoms within the acetyl group to the citric acid cycle to be oxidized for energy production. In chemical structure, acetyl-CoA is the thioester...
to produce malate
Malate
Malate is the ionized form of malic acid. It is an important chemical compound in biochemistry. In the C4 carbon fixation process, malate is a source of CO2 in the Calvin cycle....
.
Role in Gluconeogenesis
Fatty acidFatty acid
In chemistry, especially biochemistry, a fatty acid is a carboxylic acid with a long unbranched aliphatic tail , which is either saturated or unsaturated. Most naturally occurring fatty acids have a chain of an even number of carbon atoms, from 4 to 28. Fatty acids are usually derived from...
s from lipid
Lipid
Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, triglycerides, phospholipids, and others...
s are commonly used as an energy source by vertebrates as fatty acids are degraded through beta oxidation
Beta oxidation
Beta oxidation is the process by which fatty acids, in the form of Acyl-CoA molecules, are broken down in mitochondria and/or in peroxisomes to generate Acetyl-CoA, the entry molecule for the Citric Acid cycle....
into acetate molecules. This acetate, bound to the active thiol
Thiol
In organic chemistry, a thiol is an organosulfur compound that contains a carbon-bonded sulfhydryl group...
group of coenzyme A
Coenzyme A
Coenzyme A is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle. All sequenced genomes encode enzymes that use coenzyme A as a substrate, and around 4% of cellular enzymes use it as a substrate...
, enters the citric acid cycle
Citric acid cycle
The citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or the Szent-Györgyi-Krebs cycle — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and...
(TCA cycle) where it is fully oxidized to carbon dioxide
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
. This pathway thus allows cells
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
to obtain energy
Energy
In physics, energy is an indirectly observed quantity. It is often understood as the ability a physical system has to do work on other physical systems...
from fat. To utilize acetate from fat for biosynthesis of carbohydrates, the glyoxylate cycle, whose initial reactions are identical to the TCA cycle, is used.
Cell-wall containing organisms, such as plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
s, fungi
Fungus
A fungus is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds , as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from plants, animals, and bacteria...
, and bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, require very large amounts of carbohydrate
Carbohydrate
A carbohydrate is an organic compound with the empirical formula ; that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 . However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical...
s during growth for the biosynthesis of complex structural polysaccharides, such as cellulose
Cellulose
Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....
, glucan
Glucan
A glucan molecule is a polysaccharide of D-glucose monomers linked by glycosidic bonds.Many beta-glucans are medically important.-Types:The following are glucans:-Alpha:...
s, and chitin
Chitin
Chitin n is a long-chain polymer of a N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world...
. In these organisms, in the absence of available carbohydrates (for example, in certain microbial environments or during seed germination in plants), the glyoxylate cycle permits the synthesis of glucose from lipids via acetate generated in fatty acid β-oxidation.
The glyoxylate cycle bypasses the steps in the citric acid cycle where carbon is lost in the form of CO2. The two initial steps of the glyoxylate cycle are identical to those in the citric acid cycle: acetate → citrate → isocitrate. In the next step, catalyzed by the first glyoxylate cycle enzyme, isocitrate lyase
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.The systematic...
, isocitrate undergoes cleavage into succinate and glyoxylate (the latter gives the cycle its name). Glyoxylate condenses with acetyl-CoA (a step catalyzed by malate synthase
Malate synthase
In enzymology, a malate synthase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are acetyl-CoA, H2O, and glyoxylate, whereas its two products are -malate and CoA....
), yielding malate
Malate
Malate is the ionized form of malic acid. It is an important chemical compound in biochemistry. In the C4 carbon fixation process, malate is a source of CO2 in the Calvin cycle....
. Both malate
Malate
Malate is the ionized form of malic acid. It is an important chemical compound in biochemistry. In the C4 carbon fixation process, malate is a source of CO2 in the Calvin cycle....
and oxaloacetate can be converted into phosphoenolpyruvate
Phosphoenolpyruvate
Phosphoenolpyruvic acid , or phosphoenolpyruvate as the anion, is an important chemical compound in biochemistry. It has the high-energy phosphate bond found in living organisms, and is involved in glycolysis and gluconeogenesis...
, which is the substrate of phosphoenolpyruvate carboxykinase
Phosphoenolpyruvate carboxykinase
Phosphoenolpyruvate carboxykinase is an enzyme in the lyase family used in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.It is found in two forms, cytosolic and mitochondrial....
, the first enzyme in gluconeogenesis
Gluconeogenesis
Gluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
. The net result of the glyoxylate cycle is therefore the production of glucose from fatty acids. Succinate generated in the first step can enter into the citric acid cycle to eventually form oxaloacetate.
Plants
In plants the glyoxylate cycle occurs in special peroxisomePeroxisome
Peroxisomes are organelles found in virtually all eukaryotic cells. They are involved in the catabolism of very long chain fatty acids, branched chain fatty acids, D-amino acids, polyamines, and biosynthesis of plasmalogens, etherphospholipids critical for the normal function of mammalian brains...
s which are called glyoxysome
Glyoxysome
Glyoxysomes are specialized peroxisomes found in plants and also in filamentous fungi....
s. This cycle allows seeds to use lipids as a source of energy to form the shoot during germination
Germination
Germination is the process in which a plant or fungus emerges from a seed or spore, respectively, and begins growth. The most common example of germination is the sprouting of a seedling from a seed of an angiosperm or gymnosperm. However the growth of a sporeling from a spore, for example the...
. The seed cannot produce biomass using photosynthesis because of lack of an organ to perform this function. The lipid stores of germinating seeds are used for the formation of the carbohydrates that fuel the growth and development of the organism.
The glyoxylate cycle can also provide plants with another aspect of metabolic diversity. This cycle allows plants to take in acetate
Acetate
An acetate is a derivative of acetic acid. This term includes salts and esters, as well as the anion found in solution. Most of the approximately 5 billion kilograms of acetic acid produced annually in industry are used in the production of acetates, which usually take the form of polymers. In...
both as a carbon source and as a source of energy. Acetate is converted to Acetyl CoA (similar to the TCA cycle). This Acetyl CoA can proceed through the glyoxylate cycle, and some succinate is released during the cycle. The four carbon succinate molecule can be transformed into a variety of carbohydrates through combinations of other metabolic processes; the plant can synthesize molecules using acetate as a source for carbon. The Acetyl CoA can also react with glyoxylate to produce some NADPH from NADP+, which is used to drive energy synthesis in the form of ATP later in the Electron Transport Chain
Electron transport chain
An electron transport chain couples electron transfer between an electron donor and an electron acceptor with the transfer of H+ ions across a membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate...
.
Pathogenic Fungi
The glyoxylate cycle may serve an entirely different purpose in some species of pathogenic fungi. The levels of the main enzymes of the glyoxylate cycle, ICL and MS, are greatly increased upon contact with a human host. Mutants of a particular species of fungi that lacked ICL were also significantly less virulent in studies with mice compared to the wild type. The exact link between these two observations is still being explored, but it can be concluded that the glyoxylate cycle is a significant factor in the pathogenesisPathogenesis
The pathogenesis of a disease is the mechanism by which the disease is caused. The term can also be used to describe the origin and development of the disease and whether it is acute, chronic or recurrent...
of these microbes
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
.
Vertebrates
Vertebrates were once thought to be unable to perform this cycle because there was no evidence of its two key enzymeEnzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s, isocitrate lyase and malate synthase. However, some research suggests that this pathway may exist in some, if not all, vertebrates.
Specifically, some studies show evidence of components of the glyoxylate cycle existing in significant amounts in the liver tissue of chickens. Data such as this supports the idea that the cycle could theoretically occur in even the most complex vertebrates. Other experiments have also provided evidence that the cycle is present among certain insect and marine invertebrate species, as well as strong evidence of the cycle's presence in nematode species. However, other experiments refute this claim Some publications conflict on the presence of the cycle in mammal
Mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
s: for example, one paper has stated that the glyoxalate cycle is active in hibernating bears, but this report was disputed in a later paper. On the other hand, no functional genes related to known forms of malate synthase or isocitrate lyase have been identified in placental mammal genomes, while malate synthase appears to be functional in some non-placental mammals and other vertebrates. Vitamin D may regulate this pathway in vertebrates.
Engineering Concepts
The prospect of engineering various metabolic pathways into mammals which do not possess them is a topic of great interest for bio-engineers today. The glyoxylate cycle is one of the pathways which engineers have attempted to manipulate into mammalian cells. This is primarily of interest for engineers in order to increase the production of wool in sheep, which is limited by the access to stores of glucose. By introducing the pathway into sheep, the large stores of acetate in cells could be used in order to synthesize glucoseGlucose
Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate...
through the cycle, allowing for increased production of wool. Mammals are incapable of executing the pathway due to the lack of two enzymes, isocitrate lyase
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.The systematic...
and malate synthase
Malate synthase
In enzymology, a malate synthase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are acetyl-CoA, H2O, and glyoxylate, whereas its two products are -malate and CoA....
, which are needed in order for the cycle to take place. It is believed by some that the genes to produce these enzymes, however, are pseudogenic in mammals, meaning that the gene is not necessarily absent, rather, it is merely "turned off".
In order to engineer the pathway into cells, the genes responsible for coding for the enzymes had to be isolated and sequenced, which was done using the bacteria E.Coli, from which the AceA gene, responsible for encoding for isocitrate lyase
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.The systematic...
, and the AceB gene, responsible for encoding for malate
Malate
Malate is the ionized form of malic acid. It is an important chemical compound in biochemistry. In the C4 carbon fixation process, malate is a source of CO2 in the Calvin cycle....
synthase were sequenced. Engineers have been able to successfully incorporate the AceA and AceB genes into mammalian cells in culture, and the cells were successful in translating and transcribing the genes into the appropriate enzymes, proving that the genes could successfully be incorporated into the cell’s DNA without damaging the functionality or health of the cell. However, being able to engineer the pathway into transgenic mice has proven to be difficult for engineers. While the DNA has been expressed in some tissues, including the liver and small intestine in test animals, the level of expression is not high, and not found to be statistically significant. In order to successfully engineer the pathway, engineers would have to fuse the gene with promoters which could be regulated in order to increase the level of expression, and have the expression in the right cells, such as epithelial cells.
Efforts to engineer the pathway into more complex animals, such as sheep, have not been effective. This illustrates that much more research needs to be done on the topic, and suggests it is possible that a high expression of the cycle in animals would not be tolerated by the chemistry of the cell. Incorporating the cycle into mammals will benefit from advances in nuclear transfer technology
Somatic cell nuclear transfer
In genetics and developmental biology, somatic-cell nuclear transfer is a laboratory technique for creating a clonal embryo, using an ovum with a donor nucleus . It can be used in embryonic stem cell research, or, potentially, in regenerative medicine where it is sometimes referred to as...
, which will enable engineers to examine and access the pathway for functional integration within the genome before its transfer to animals.
There are possible benefits, however, to the cycle's absence in mammalian cells. The cycle is present in microorganisms that cause disease but is absent in mammals, for example humans. There is a strong plausibility of the development of antibiotics that would attack the glyoxylate cycle, which would kill the disease-causing microorganisms that depend on the cycle for their survival, yet would not harm humans where the cycle, and thus the enzymes that the antibiotic would target, are absent.