Biosynthetic Pathways of Secondary Metabolites PDF

Biosynthetic pathways of Secondary metabolites INTRODUCTION Metabolism -Metabolism constituents all the chemical transformations occurring in the cells of living organisms and these transformations are essential for life of an organism. Metabolites -End product of metabolic processes and intermedia...

Biosynthetic pathways of Secondary metabolites INTRODUCTION Metabolism -Metabolism constituents all the chemical transformations occurring in the cells of living organisms and these transformations are essential for life of an organism. Metabolites -End product of metabolic processes and intermediates formed during metabolic processes. Primary metabolites : A primary metabolite is a kind of metabolite that is directly involved in normal growth, development, and reproduction. It usually performs a physiological function in the organism (i.e. an intrinsic function). It is also referred to as a central metabolite, which has an even more restricted meaning (present in any autonomously growing cell or organism). Primary metabolites are typically formed during the growth phase as a result of energy metabolism, and are deemed essential for proper growth. Examples of primary metabolites include alcohols such as ethanol, lactic acid, and certain amino acids. Within the field of industrial microbiology, alcohol is one of the most common primary metabolites used for large-scale production. Additionally, primary metabolites such as amino acids including L-glutamate and L- lysine, which are commonly used as supplement which are isolated via the mass production of a specific bacterial species, Corynebacteria glutamicum. Another example of a primary metabolite commonly used in industrial microbiology includes citric acid. Citric acid, produced by Aspergillus niger, is one of the most widely used ingredients in food production. It is commonly used in pharmaceutical and cosmetic industries as well. Secondary metabolite Secondary metabolites are typically organic compounds produced through the modification of primary metabolite synthases. Secondary metabolites do not play a main role in growth, development, and reproduction like primary metabolites do, and are typically formed during the end or near the stationary phase of growth. Many of the identified secondary metabolites have a role in ecological function, including defense mechanism, by serving as antibiotics and by producing pigments. Examples of secondary metabolites with importance in industrial microbiology include atropine and antibiotics such as erythromycin and bacitracin. Atropine, derived from various plants, is a secondary metabolite with important use in the clinic. Atropine is a competitive antagonist for acetylcholine receptors, specifically those of the muscarinic type, which can be used in the treatment of bradycardia. Antibiotics such as erythromycin and bacitracin are also considered to be secondary metabolites. Erythromycin, derived from Saccharopolyspora erythraea, is a commonly used antibiotic with a wide antimicrobial spectrum. It is mass produced and commonly administered orally. Lastly, another example of an antibiotic which is classified as a secondary metabolite is bacitracin. Bacitracin, derived from organisms classified under Bacillus subtilis, is an antibiotic commonly used a topical drug. Photosynthesis Photosynthesis: is the process by which light energy is captured, converted and stored in a simple sugar molecule. This process occurs in chloroplasts and other parts of green organisms. It is a backbone process, in the sense that all life on earth depends on it’s functioning. The following equation sums up the process: 6CO2 (carbon dioxide) + 12 H2O (water) + light energy -> C6H12O6 (glucose) + 6O2 (oxygen) +6H2O (water) Photosynthesis Steps:  During the process of photosynthesis, carbon dioxide enters through the stomata, water is absorbed by the root hairs from the soil and is carried to the leaves through the xylem vessels. Chlorophyll absorbs the light energy from the sun to split water molecules into hydrogen and oxygen.  The hydrogen from water molecules and carbon dioxide absorbed from the air are used in the production of glucose. Furthermore, oxygen is liberated out into the atmosphere through the leaves as a waste product.  Glucose is a source of food for plants that provide energy for growth and development, while the rest is stored in the roots, leaves and fruits, for their later use.  Pigments are other fundamental cellular components of photosynthesis. They are the molecules that impart color and they absorb light at some specific wave length and reflect back the unabsorbed light. All green plants mainly contain chlorophyll a, chlorophyll b and carotenoids which are present in the thylakoids of chloroplasts. It is primarily used to capture light energy. Chlorophyll-a is the main pigment. The process of photosynthesis occurs in two stages:  Light-dependent reaction or light reaction  Light independent reaction or dark reaction Light Reaction of Photosynthesis (or) Light-dependent Reaction  Photosynthesis begins with the light reaction which is carried out only during the day in the presence of sunlight. In plants, the light- dependent reaction takes place in the thylakoid membranes of chloroplasts.  The Grana, membrane-bound sacs like structures present inside the thylakoid functions by gathering light and is called photosystems.  These photosystems have large complexes of pigment and proteins molecules present within the plant cells, which play the primary role during the process of light reactions of photosynthesis.  There are two types of photosystems: photosystem I and photosystem II.  Under the light-dependent reactions, the light energy is converted to ATP and NADPH, which are used in the second phase of photosynthesis.  During the light reactions, ATP and NADPH are generated by two electron-transport chains, water is used and oxygen is produced. The chemical equation in the light reaction of photosynthesis can be reduced to: 2H2O + 2NADP+ + 3ADP + 3Pi → O2 + 2NADPH + 3ATP Dark Reaction of Photosynthesis (or) Light-independent Reaction  Dark reaction is also called carbon-fixing reaction.  It is a light-independent process in which sugar molecules are formed from the water and carbon dioxide molecules.  The dark reaction occurs in the stroma of the chloroplast where they utilize the NADPH and ATP products of the light reaction.  Plants capture the carbon dioxide from the atmosphere through stomata and proceed to the Calvin photosynthesis cycle.  In the Calvin cycle, the ATP and NADPH formed during light reaction drive the reaction and convert 6 molecules of carbon dioxide into one sugar molecule or glucose. The chemical equation for the dark reaction can be reduced to: 3CO2 + 6 NADPH + 5H2O + 9ATP → G3P + 2H+ + 6 NADP+ + 9 ADP + 8 Pi * G3P – glyceraldehyde-3-phosphate Reactions of the Calvin cycle The Calvin cycle reactions can be divided into three main stages: carbon fixation, reduction, and regeneration of the starting molecule. Carbon fixation. A CO2 molecule combines with a five-carbon acceptor molecule, ribulose-1,5-bisphosphate (RuBP). This step makes a six-carbon compound that splits into two molecules of a three-carbon compound, 3-phosphoglyceric acid (3-PGA). This reaction is catalyzed by the enzyme RuBP carboxylase/oxygenase, or rubisco. Reduction. In the second stage, ATP and NADPH are used to convert the 3-PGA molecules into molecules of a three-carbon sugar, glyceraldehyde-3-phosphate (G3P). This stage gets its name because NADPH donates electrons to, or reduces, a three-carbon intermediate to make G3P. Regeneration. Some G3P molecules go to make glucose, while others must be recycled to regenerate the RuBP acceptor. Regeneration requires ATP and involves a complex network of reactions. Glycolysis Glycolysis: is the metabolic pathway that converts glucose into pyruvate. Occurs in the cytosol and is oxygen-independent. The free energy released during the biochemical reactions in glycolysis is used to generate a net gain of two molecules of ATP. Citric Acid Cycle (Kreb’s cycle) The overall reaction of glucose in terms of ADP and ATP is C6H12O6 + 6CO2 + 38 ADP + 38P (inorganic) → 6H2O + 6CO2 + 38 ATP The Krebs cycle or TCA cycle (tricarboxylic acid cycle) or Citric acid cycle is a series of enzyme catalyzed reactions occurring in the mitochondrial matrix, where acetyl-CoA is oxidized to form carbon dioxide and coenzymes are reduced, which generate ATP in the electron transport chain. It is an eight-step process. Krebs cycle or TCA cycle takes place in the matrix of mitochondria under aerobic condition.  Biosynthetic pathways of Secondary metabolites Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined together to form macromolecules. This process often consists of metabolic pathways. The building blocks are tiny chemical molecules produced from primary metabolites mostly from photosynthesis, glycolysis, and or Krebs cycle. They are very important in biosynthesis and production of secondary metabolites. These are considered to be intermediates, few important ones are acetyl CoA, shikimic acid , mevalonic acid malonic acid. The building blocks can be segregated based on the number of Carbon units C1 derived from S methyl of L-methionine C2 derived from acetyl –CoA C5 derived from isoprene units C6-C3 units (phenyl propyl units) are derived from phenylalanine or tyrosine through shikimic acid pathway. The Basic Metabolic Pathways Leading To Production of Secondary MetabolitesThrough Photosynthesis Biosynthesis pathway of natural products: 1. Shikimic-acid (shikimate) pathway The shikimic acid pathway (shikimate pathway) is the basic process for biosynthesis of phenolic compounds, alkaloid, and others. It takes place in chloroplast plant cells and have the phenylpropanoid precursors. These aromatic compounds are types of secondary metabolites that abundant in plant, and the expression of them are triggered by environmental stresses, such as pathogens and herbivores attack, inappropriate pH and temperature, UV radiation, saline stress, and heavy metal stress. Shikimic acid pathway is a seven-step metabolic pathway used by bacteria, archaea, fungi, algae, some protozoans, and plants for the biosynthesis of folates and aromatic amino acids (phenylalanine, tyrosine, and tryptophan).The pathway starts with two substrates, phosphoenol pyruvate and erythrose-4-phosphate, and ends with chorismate, a substrate for the three aromatic amino acids. Figure 1: overview of shikimate pathway with the enzymatic process  Figure2.The synthesize process of three aromatic amino acids as protein building blocks produces through shikimate(chorismate) biosynthetic pathway Shikimate biosynthetic pathway is also known as the chorismate pathway. Figure 1 shows the overview of shikimate pathway with the enzymatic process, Phosphoenolpyruvate and erythrose-4-phosphate react to form 3-deoxy-D- arabino- heptulosonate 7-phosphate, in a reaction catalyzed by the enzyme DAHP synthase. The next enzyme involved is shikimate kinase, an enzyme that catalyzes the ATP dependent phosphorylation of shikimate to form shikimate 3-phosphate. Shikimate-3-phosphate is then coupled with phosphoenol pyruvate to give 5- enolpyruvylshikimate-3-phosphate via the enzyme 5-enolpyruvylshikimate-3- phosphate (EPSP) synthase. Then 5-enolpyruvylshikimate-3-phosphate is transformed into chorismate by a chorismate synthase. and the next phase is aromatic amino acid synthesis that produced by shikimate pathway in Figure 2: Tryptophan (L-Trp), Tyrosine (L-Tyr), and Phenylalanine (L- Phe), as molecular building blocks for protein , alkaloids , phenols and other biosynthesis. The shikimate pathway is being a metabolic pathway that connecting central and specialized metabolism in the plant cell and carbon degradation during the synthesis of secondary metabolite compounds. 2. Malonic-acid (Malonate/Acetate) pathway Acetate pathway operates functionally with the involvement of acyl carrier protein (ACP) to yield fatty acylthioesters of ACP. These acyl thioesters forms the important intermediates in fatty acid synthesis. These C2 acetyl CoA units at the later stage produces even number of fatty acids from n-tetranoic (butyric) to n-ecosanoic (arachidic acid). In fatty acid synthesis, acetyl‐CoA is the direct precursor only of the methyl end of the growing fatty acid chain. All the other carbons come from the acetyl group of acetyl‐ CoA but only after it is modified to provide the actual substrate for fatty acid synthase. Malonyl‐CoA contains a 3‐carbondicarboxylic acid, malonate, bound to Coenzyme A. Malonate is formed from acetyl‐CoA by the addition of CO2 using the biotin cofactor of the enzyme acetyl‐CoA carboxylase. Figure 3. The acetate –malonate pathway for biosynthesis of fatty acids 3. Mevalonic-acid (Mevalonate) pathway The mevalonic acid (MVA) pathway or mevalonate pathway also known as the isoprenoid pathway that involves the synthesis of 3-hydroxy-3- methylglutaryl-CoA reductase (HMGCR). Moreover, the MVA pathway is the core of metabolic pathway for multiple cellular metabolisms in eukaryotic, archaea, and some bacteria organisms, including cholesterol biosynthesis and protein. Cholesterol is produced as the molecules that used to build the membrane cell structure, steroid hormones, myelin sheets in neuron system, precursors of vitamin D, formation and release of synaptic vesicles. Mevalonic acid further produced isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP). These two main intermediates IPP and DMAPP set the ‘active isoprene’ unit as a basic building block of isoprenoid compounds. Both of these units yield geranyl pyrophosphate (C10-monoterpenes) which further association with IPP produces farnesyl pyrophosphate (C15-sesquiterpenes). Farnesyl pyrophosphate with one more unit of IPP develops into geranyl-geranyl pyrophosphate (C20-diterpenes). The farnesyl pyrophosphate multiplies with its own unit to produce squalene, and its subsequent cyclization gives rise to cholesterols and other groups like triterpenoids. Figure4.Mevalonate(MVA)pathway.