Many photosynthetic life forms (plants, algae, phototrophic and chemoautotrophic bacteria, and archaea) require a way to utilize carbon into their metabolic pathways. This usually occurs in pathways that fix carbon from carbon dioxide (CO2). In the 3-hydroxypropionate bicycle, photosynthetic organisms like Chloroflexus aurantiacus, fix CO2 and bicarbonate (HCO3- ) as part of their metabolic processes. [1]
The 3-hydroxypropionate bicycle, also known as the 3-hydroxypropionate pathway, is a process that allows some bacteria to generate 3-hydroxypropionate using carbon dioxide. [2] It is divided into two parts or reactions. The overall reaction of the 3-hydroxypropionate pathway is 3 HCO3− + 5 ATP + 6 NADPH + 1 quinone → 1 pyruvate + 6 NADP + 1 quinoneH2 + 3 ADP + 3 phosphate + 2 AMP + 2 pyrophosphate. [3]
In this pathway CO2 is fixed (i.e. incorporated) by the action of two enzymes, acetyl-CoA carboxylase and propionyl-CoA carboxylase. These enzymes generate malonyl-CoA and (S)-methylmalonyl-CoA, respectively.
Malonyl-CoA, in a series of reactions, is further split into acetyl-CoA and glyoxylate. Glyoxylate is incorporated into beta-methylmalyl-coA which is then split, again through a series of reactions, to release pyruvate as well as acetate, which is used to replenish the cycle. [3]
This pathway has been demonstrated in Chloroflexus , a nonsulfur photosynthetic bacterium; however, other studies suggest that 3-hydroxypropionate bicycle is used by several chemotrophic archaea. [1] [4] T In E. coli 3-hydroxypropionate bicycle has been studied and found to be insensitive to oxygen. This means that within the pathways there is nothing that oxygen can affect because in either part of the pathway or the oxygen is used to drive the reaction forward. [5]
The citric acid cycle—also known as the Krebs cycle, Szent–Györgyi–Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of biochemical reactions to release the energy stored in nutrients through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins. The chemical energy released is available under the form of ATP. The Krebs cycle is used by organisms that respire (as opposed to organisms that ferment) to generate energy, either by anaerobic respiration or aerobic respiration. 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 components of metabolism. Even though it is branded as a "cycle", it is not necessary for metabolites to follow only one specific route; at least three alternative segments of the citric acid cycle have been recognized.
Acetyl-CoA is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid cycle to be oxidized for energy production.
The green sulfur bacteria are a phylum, Chlorobiota, of obligately anaerobic photoautotrophic bacteria that metabolize sulfur.
Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on Earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.
Chloroflexus aurantiacus is a photosynthetic bacterium isolated from hot springs, belonging to the green non-sulfur bacteria. This organism is thermophilic and can grow at temperatures from 35 to 70 °C. Chloroflexus aurantiacus can survive in the dark if oxygen is available. When grown in the dark, Chloroflexus aurantiacus has a dark orange color. When grown in sunlight it is dark green. The individual bacteria tend to form filamentous colonies enclosed in sheaths, which are known as trichomes.
C3 carbon fixation is the most common of three metabolic pathways for carbon fixation in photosynthesis, the other two being C4 and CAM. This process converts carbon dioxide and ribulose bisphosphate (RuBP, a 5-carbon sugar) into two molecules of 3-phosphoglycerate through the following reaction:
Biological carbon fixation, or сarbon assimilation, is the process by which living organisms convert inorganic carbon to organic compounds. These organic compounds are then used to store energy and as structures for other biomolecules. Carbon is primarily fixed through photosynthesis, but some organisms use chemosynthesis in the absence of sunlight. Chemosynthesis is carbon fixation driven by chemical energy rather than from sunlight.
Oxaloacetic acid (also known as oxalacetic acid or OAA) 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.
An acetogen is a microorganism that generates acetate (CH3COO−) as an end product of anaerobic respiration or fermentation. However, this term is usually employed in a narrower sense only to those bacteria and archaea that perform anaerobic respiration and carbon fixation simultaneously through the reductive acetyl coenzyme A (acetyl-CoA) pathway (also known as the Wood-Ljungdahl pathway). These genuine acetogens are also known as "homoacetogens" and they can produce acetyl-CoA (and from that, in most cases, acetate as the end product) from two molecules of carbon dioxide (CO2) and four molecules of molecular hydrogen (H2). This process is known as acetogenesis, and is different from acetate fermentation, although both occur in the absence of molecular oxygen (O2) and produce acetate. Although previously thought that only bacteria are acetogens, some archaea can be considered to be acetogens.
In biochemistry, mixed acid fermentation is the metabolic process by which a six-carbon sugar is converted into a complex and variable mixture of acids. It is an anaerobic (non-oxygen-requiring) 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.
Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.
Phosphoenolpyruvate carboxylase (also known as PEP carboxylase, PEPCase, or PEPC; EC 4.1.1.31, PDB ID: 3ZGE) is an enzyme in the family of carboxy-lyases found in plants and some bacteria that catalyzes the addition of bicarbonate (HCO3−) to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate and inorganic phosphate:
In biochemistry, fatty acid synthesis is the creation of fatty acids from acetyl-CoA and NADPH through the action of enzymes called fatty acid synthases. This process takes place in the cytoplasm of the cell. Most of the acetyl-CoA which is converted into fatty acids is derived from carbohydrates via the glycolytic pathway. The glycolytic pathway also provides the glycerol with which three fatty acids can combine to form triglycerides, the final product of the lipogenic process. When only two fatty acids combine with glycerol and the third alcohol group is phosphorylated with a group such as phosphatidylcholine, a phospholipid is formed. Phospholipids form the bulk of the lipid bilayers that make up cell membranes and surrounds the organelles within the cells. In addition to cytosolic fatty acid synthesis, there is also mitochondrial fatty acid synthesis (mtFASII), in which malonyl-CoA is formed from malonic acid with the help of malonyl-CoA synthetase (ACSF3), which then becomes the final product octanoyl-ACP (C8) via further intermediate steps.
The Wood–Ljungdahl pathway is a set of biochemical reactions used by some bacteria. It is also known as the reductive acetyl-coenzyme A (acetyl-CoA) pathway. This pathway enables these organisms to use hydrogen as an electron donor, and carbon dioxide as an electron acceptor and as a building block for biosynthesis.
In enzymology, a biotin carboxylase (EC 6.3.4.14) is an enzyme that catalyzes the chemical reaction
3-hydroxypropionate dehydrogenase (NADP+) (EC 1.1.1.298) is an enzyme with systematic name 3-hydroxypropionate:NADP+ oxidoreductase. This enzyme catalyses the following chemical reaction
Malonyl CoA reductase (malonate semialdehyde-forming) (EC 1.2.1.75, NADP-dependent malonyl CoA reductase, malonyl CoA reductase (NADP)) is an enzyme with systematic name malonate semialdehyde:NADP+ oxidoreductase (malonate semialdehyde-forming). This enzyme catalyse the following chemical reaction
Acrylyl-CoA reductase (NADPH) (EC 1.3.1.84) is an enzyme with systematic name propanoyl-CoA:NADP+ oxidoreductase. This enzyme catalyses the following chemical reaction
Methanococcus maripaludis is a species of methanogenic archaea found in marine environments, predominantly salt marshes. M. maripaludis is a non-pathogenic, gram-negative, weakly motile, non-spore-forming, and strictly anaerobic mesophile. It is classified as a chemolithoautotroph. This archaeon has a pleomorphic coccoid-rod shape of 1.2 by 1.6 μm, in average size, and has many unique metabolic processes that aid in survival. M. maripaludis also has a sequenced genome consisting of around 1.7 Mbp with over 1,700 identified protein-coding genes. In ideal conditions, M. maripaludis grows quickly and can double every two hours.
Photosynthesis converts carbon dioxide to carbohydrates via several metabolic pathways that provide energy to an organism and preferentially react with certain stable isotopes of carbon. The selective enrichment of one stable isotope over another creates distinct isotopic fractionations that can be measured and correlated among oxygenic phototrophs. The degree of carbon isotope fractionation is influenced by several factors, including the metabolism, anatomy, growth rate, and environmental conditions of the organism. Understanding these variations in carbon fractionation across species is useful for biogeochemical studies, including the reconstruction of paleoecology, plant evolution, and the characterization of food chains.