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Chapter 12 Assimilation of Mineral Nutrients Nutrient assimilation Incorporation of mineral nutrients into organic substances such as amino acids, nucleic acids, enzyme cofactors, lipids, and pigments The Nitrogen Cycle Thiobacillus Denitrificans (Denitrification) Lightning Bacteria or cyanobacteria 75% 15% N2 + H2 Fertilizer Nitrosomonas Nitrococcus 10% Thiobacillus denitrificans Nitrobacter (Nitrification) Plants Microorganisms Food chain Flag leaf NH4+ toxicity can dissipate pH gradient ammonium ammonia Nitrate assimilation at roots NO3- Nitrate-proton cotransporter Root cell NO3- (Nitrate) NADH (or NADPH) NAD+ (or NADP+) GS/GOGAT Nitrate reductase NO2(Nitrite, toxic) Glutamine Plastids NO2- Glutamate NH4+ NADPH nitrite (Ammonium) reductase Nitrate reductase Homodimers, two identical subunits Polypeptide sequences are similar in eukaryotes (except the hinge regions) Each subunit with 100kD Each subunit contains 3 prosthetic groups: FAD, heme, and molybdenum complexed to pterin (an organic molecule). Nitrate reductase is the main molybdenumcontaining protein in vegetative tissues. The nitrate reductase dimer NAD+, H+ NO2+ NO2+ (+3) (+5) NAD+, H+ Three binding domains Addition of nitrate stimulates nitrate reductase mRNA accumulation and enzyme activity in roots and shoots of barley Other factors regulate nitrate reductase Nitrate reductase-Pi (inactive form) Phosphatase Nitrate reductase (active form) Light [carbohydrate] Nitrate reductase Nitrate reductase -Pi (active form) Serine/Threonine (inactive form) protein kinase Dark [Mg+2] Regulation of nitrate reductase activity through phosphorylation and dephosphorylation provides more rapid control than can be achieved through synthesis or degradation of the enzyme (minutes versus hours). In many plants, when the roots receive small amounts of nitrate, nitrate is reduced primarily in the roots. As the supply of nitrate increases, a greater proportion of the absorbed nitrate is translocated to the shoot and assimilated there. Generally, plants native to temperate region assimilate NO3- at roots. Plants native to tropical or subtropical region assimilate NO3- at shoots. Nitrite reductase converts nitrite to ammonium in roots NO3- Root cell NO3NADH or NADPH NAD+ or NADP+ Nitrate reductase Plastids NO2- NO2- NADPH-nitrite reductase NH4+ Nitrite reductase converts nitrite to ammonium in leaves NO3- Mesophyll cell NO3NADH Nitrate reductase Chloroplasts NAD+ NO2- NO2- Ferredoxinnitrite reductase NH4+ Nitrite reductase Nitrite (NO2-) is a highly reactive, potentially toxic ion. Plant cells immediately transport the nitrite into chloroplasts or plastids. The enzyme nitrite reductase reduces nitrite to ammonium. Leaf chloroplasts and root plastids contain different forms of nitrite reductase. Nitrite reductase is synthesized in cytoplasm with an Nterminal transit peptide. Both nitrite reductases consist of a single 63kD polypeptide. Each polypeptide contains two prosthetic groups, an ironsulfur group and a specialized heme. NO3-, high sucrose conc, and light induce the transcription of nitrite reductase mRNA. Asparagine and glutamine repress the induction. A. Chloroplasts 2 eNADP+, H+ Ferredoxin - a protein of 12 ~ 24 kD - containing a FeS group - e- carried by the iron NADPH Pentose phosphate pathway B. Root plastids Relative amounts of nitrate and other nitrogen compounds in the xylem exudate of various plant species R-CO-NH2 Ammonium assimilation NH3 is almost certainly protonated to form NH4+. NH4+ is toxic to plants. Inhibit dinitrogenase Interfere energy metabolism by dissociating ATP formation from ETC in both mitochondria and chloroplasts. To avoid these problems, NH4+ generated from nitrate assimilation or photorespiration is rapidly converted into amino acids. Conversion of ammonium to amino acids requires two enzymes, glutamine synthetase (GS) and glutamate synthase (GOGAT). Ammonium can be assimilated by one of several processes GS GOGAT Glutamine synthetase (GS) Glutamine synthetase Glutamate + NH4+ -----------------> Glutamine GS Two classes of glutamine synthetase (GS) in cytosol The cytosolic form GS express in germinating seeds or in the vascular bundles of roots and shoots, and produce glutamine for intracellular nitrogen transport in root plastids and in shoot chloroplasts GS in root plastids : generating amide nitrogen (glutamine & asparagine) for local consumption. The GS in shoot chloroplast reassimilates photorespiratory NH4+. Ammonium assimilation via GS/GOGAT Germinating seeds/vascular bundles of roots and shoots 2-oxoglutarate 2 Glutamate GOGAT Glutamine GS Plastids NO2- Nitrite reductase NH4+ NH4+ Glutamate Ammonium assimilation in roots NO3- Root cell NO3NADH or NADPH NAD+ or NADP+ Nitrate reductase Plastids NO2- NO2- NH4+ NADPH nitrite (Ammonium) reductase Glutamate GS/NADHGOGAT Ammonium assimilation in leaves NO3- Mesophyll cell NO3NADH Nitrate reductase Chloroplasts NAD+ NO2- NO2- Ferredoxin-nitrite reductase Glutamate NH4+ GS/Fd-GOGAT Light and carbohydrate levels alter the expression of the plastid forms of the enzyme, but they have little effect on the cytosolic forms. Glutamate synthase (glutamine:2-oxoglutarate aminotransferase, GOGAT) Plants contain two types of GOGAT. NADH-GOGAT Ferredoxin-GOGAT (Fd-GOGAT) NADH-GOGAT NADH-GOGAT is located in plastids of roots or vascular bundles of leaves. In roots, NADH-GOGAT is involved in the assimilation of NH4+ absorbed from the rhizosphere. Fd-GOGAT Fd-GOGAT is found in chloroplasts and serves in photorespiratory nitrogen metabolism. Ammonium can be assimilated via an alternative pathway Alternative pathway for assimilating ammonium Two types of Glutamate dehydrogenase (GDH) : NADH-GDH is found in mitochondria. NADPH-GDH is found in chloroplasts. Although both forms are relatively abundant, they cannot substitute for the GS-GOGAT pathway for assimilation of ammonium, and their primary function is in deaminating glutamate during the reallocation of nitrogen. Transamination reactions transfer nitrogen Once assimilated into glutamine and glutamate, nitrogen is incorporated into other amino acids via transamination reactions. Aminotransferase catalyze the transamination reaction. Aminotransferase are found in the cytoplasm, chloroplasts, mitochondria, glyoxysomes, and peroxisomes. An example of aminotransferase Ammonium Assimilation via GS/GOGAT Root plastids/shoot chloroplast NO2- NH4+ Nitrite reductase Glutamate GS Glutamate 2 Glutamate GOGAT Glutamine 2-oxoglutarate Oxaloacetate Aspartate aminotransferase 2-oxoglutarate + Aspartate Transamination reactions Asparagine synthetase (AS) Glutamine Asparagine Glutamate Asparagine and glutamine link carbon and nitrogen metabolism Asparagine serves not only as a protein precursor, but as a key compound for nitrogen transport and storage because of its stability and high nitrogen-tocarbon ratio (1:2). The major pathway for asparagine synthesis involves the transfer of the amide nitrogen from glutamine to asparagine. Asparagine synthetase (AS) catalyzes the asparagine synthesis reaction. AS is found in the cytosol of leaves and roots, and in nitrogen-fixing nodules. amide Biosynthetic pathways for the carbon skeletons of the 20 amino acids in plants Amino acid biosynthesis The nitrogen-containing amino groups derives from transamination reactions with glutamine or glutamate. The carbon skeleton for amino acids derive from 3-phosphoglycerate, phosphoenolpyruvate, or pyruvate generated during glycolysis, or from aketoglutarate or oxaloacetate generated in the citric acid cycle. Human and most animals cannot synthesize certain amino acids. Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine and arginine => essential amino acids Obtain these essential amino acids from their diet. In contrast, plants synthesize all the 20 amino acids. High levels of light and carbohydrates stimulate GS and GOGAT, inhibit AS, and thus favor nitrogen assimilation into glutamine and glutamate, compounds that are rich in carbon and participate in the synthesis of new plant materials. In contrast, energy-limiting conditions inhibit GS and GOGAT, stimulate AS, and thus favor nitrogen assimilation into asparagine, a compound that is rich in nitrogen and sufficient stable for longdistance transport or long-term storage. N:C ratio Allantoin (尿囊素 ) Allantoic acid Asparagine Citrulline Glutamine Glutamate = 1:1 = 1:1 = 1:2 = 1:2 = 1:2.5 = 1:5 The more nitrogen ratio the molecule contains, the higher efficiency the molecule transports nitrogen. (Synthesized in peroxisome) (ER) (amide : glutamine & asparagine ) p.310 Fig.12-21 Biological nitrogen fixation Biological nitrogen fixation Biological nitrogen fixation accounts for most of the fixation of atmospheric N2 into ammonium. N2 + 8H+ + 16ATP ---------------> 2NH3 + H2 + 16ADP + 16Pi nitrogenase Two major types of nitrogen fixation : Prokaryotes that are free-living in the soil, lake, and ocean. Symbiotic bacteria (Nonsymbiotic N2 fixation) N2 fixation Symbiotic N2 fixation Rhizobia – Legume Unicellular G(-) Rhizobial symbiosis Actinomycetes – Nonleguminous plants Frankia spp, Alnus (alder), Myrica (bayberry), Casuarina (Australian pine) Filamentous bacteria – G(+) Live freely in soil, but fix nitrogen in symbiotic association with host. Actinorhizal symbiosis Nonsymbiotic N2 fixation N2 fixation Symbiotic N2 fixation Nonsymbiotic N2 fixation Cyanobacteria (Blue-green algae) : Nostoc, Anabaena, Calothrix, etc. Other bacteria Aerobic : Azotobacter, Beijerinckia, Derxia, etc. Facultative : Bacillus, Klebsiella, etc. Anaerobic : Nonphotosynthetic - Clostridium, Methanococcus Photosynthetic – Rhodospirillum, Chromatium Cyanobacterium Anabaena Heterocysts Thick-walled cells Differentiate when filamentous cyanobacteria are deprived of NH4+. Heterocysts lack photosystem II, so they do not generate oxygen. Exist among aerobic cyanobacteria that fix nitrogen. Root nodules on soybean 黃豆, 大豆 紫花苜蓿 扁豆 豌豆 蠶豆 苜蓿 菜豆 Symbiosis The symbiosis between legumes and rhizobia is not obligatory. Legume seedlings can be unassociated with rhizobia throughout their life cycle. Rhizobia also occur as free-living organisms in the soil. Under nitrogen-limited conditions, the symbionts seek out one another through an elaborate exchange of signals. Nodule formation Recognition and Colonization Chemotaxis (response to flavonoids and betaine) pea roots – Rhizobium leguminosarum Flavonoids (host) -> activate expression of nod genes -> Nod factor (lipo-chito-oligosaccharide) Lectin – Nod factor -------------------------> initiate nodule formation e.g. pea lectin gene -> white clover -> nodulated by R. leguminosarum bv. viciae (pea) Rhicadhesin : a calcium-binding protein (of all rhizobia) Invasion of root hairs Nodulation Flavonoids Nod factor Lectin Root hair Constitutive expression nod D Nod factor nod box nodA nodB nodC Rhizobia The common nod genes – nodA, nodB, and nodC – are found in all rhizobial strains and are required for synthesizing the basic structure. Root Flavonoids Nod factor Lectin Root hair Constitutive expression nod D Nod factor nod box nodA nodB nodC Rhizobia The common nod genes – nodA, nodB, and nodC – are found in all rhizobial strains and are required for synthesizing the basic structure. Root Nod Factors NodA is an N-acyltransferase that catalyzes the addition of a fatty acyl chain. NodB is a chitin-oligosaccharide deacetylase that removes the acetyl group from the terminal nonreducing sugar. NodC is a chitin-oligosaccharide synthase that links N-acetyl-D-glucosamine monomers. General structure for Nod factors NodP NodQ NodH etc NodC NodB NodA 18C NodE 16C NodF 20C (varied unsaturation NodL = 1-4 (n=2~3) b-1,4-linked N-acetyl-D-glucosamine backbone Flavonoids Nod factor Nod factor nod D Lectin nod box nodF nodE nodL nod box nodP nodQ nodH Rhizobiz Root The host-specific nod genes – nodP, nodQ, and nodH, or nodF, nodE, and nodL differ among rhizobial species and determine the host range. NodE and NodF determine the length and degree of saturation of the fatty acyl chain. NodL adds specific substitutions at the reducing or nonreducing sugar moieties of the chitin backbone. The host-specific nod genes – nodP, nodQ, and nodH, or nodF, nodE, and nodL - differ among rhizobial species and determine the host range. General structure for Nod factors NodP NodQ NodH etc NodC NodB NodA 18C NodE 16C NodF 20C (varied unsaturation NodL = 1-4 (n=2~3) b-1,4-linked N-acetyl-D-glucosamine backbone Determination of host specificity The binding of flavonoids to the NodD gene product is one of the major determinants of rhizobial host specificity because each plant species produces its own specific set of flavonoid molecules and each rhizobial species recognizes only a limited number of flavonoid structures. Some strains, such as R. leguminosarum bv. trifolii, have a very narrow host range, responding to only a few kinds of flavonoids, while others, such as Rhizobium sp. strain NGR234, have broad host range and respond to a much larger number of different flavonoids. Recognition Flavonoids Nod factor Lectin Root hair Constitutive expression nod D Nod factor nod box nodA nodB nodC Rhizobia Root A particular legume host responds to a specific Nod factor. The legume receptors for Nod factor appear to involve special lectins (sugar binding proteins) produced in the root hairs. Nod factors activate these lectins, increasing their hydrolysis of phosphoanhydride bonds of nucleoside di- and triphosphates. This lectin activation directs particular rhizobia to appropriate hosts and facilitates attachment of the rhizobia to the cell walls of a root hair. A major goal of agricultural biotechnology research is the development, by genetic manipulation, of Rhizobium strains that can increase plant productivity more than naturally occurring strains can. However, to date, no simple genetic means has been devised to use nod genes to enable inoculated strains of Rhizobium to outcompete indigenous strains. The indigenous strains might be more efficient at nodulation and, as a consequence, might prevent an inoculated strain from becoming established. Nevertheless, host specificity can be altered by the transfer of a nodD gene from a broad-specificity rhizobial strain to one with a narrow specificity. Bacteroid Stages in the initiation and development of a soybean root nodule. (A) Events involved in the initiation of the nodule: (1) the root excretes substances; (2) these substances attract rhizobia and stimulate them to produce celldivision factors; (3) cells in the root cortex divide to form the primary nodule meristem. (B) Stages of infection and nodule formation: (4) bacteria attach to the root hair; (5) cells in the pericycle near the xylem poles are stimulated to divide; (6) the infection thread forms and extends inward as the primary nodule meristem and the pericylce continue to divide; (7) the two masses of dividing cells fuse into a single clump while the infection thread continues to grow; (8) the nodule elongates and differentiates, including the vascular connection to the root stele. Bacteroids are released into the cells in the center. Nitrogen fixation by the nitrogenase enzyme complex Nitrogen fixation by the nitrogenase enzyme complex N2 + 8H+ + 16ATP ---------------> 2NH3 + H2 + 16ADP + 16Pi Nitrogenase Nitrogenase (Dinitrogenase) Only prokaryotes have this enzyme. ~20% of the total protein in the cell contains two components – Fe protein and MoFe protein Fe protein contains 2 identical subunits (dimer) – nif H Each subunit has MW of 30 ~ 72 kD. Each subunit contains an Fe-S cluster (4Fe and 4S2-). MoFe protein 2 pairs of identical subunits (tetramer, nif D & nif K) A total of MW 180 ~ 235kD Each subunit has 2 Mo-Fe-S clusters. Both Fe proteins and MoFe proteins are sensitive to O2. The nitrogenase reaction in bacteroids TCA cycle Fe+2 Fe+3 NADH Fe+3 NAD+, H + Ferredoxin - 12 ~ 24 kD - a FeS group - e- carried by the iron - nif F Fe+2 Fe+3 nif H Fe+2 nif D, nif K Fe+2 Fe+3 Fe+2 Fe+3 Fe+2 Fe+3 Proposed structure of the iron-molybdenum cofactor bound to a molecule of dinitrogen (N2) MoFe cofactor of MoFe protein MoFe proteins can reduce numerous substrates Under natural conditions it reacts only with N2 and H+. Dinitrogenase is sensitive to O2 How to reconcile the conflicting demands of O2 for respiratory (producing ATP for nitrogen fixation) and the sensitivity of dinitrogenase to O2 ? Live anaerobically Bacteroids Nitrogen-fixation vesicles (multilayered envelope consisting of hopanoids-steroid lipids) Leghemoglobin O2-binding proteins located in the cytoplasm of the bacteroid-infected cells (nodule cells) at high concentration (~ 30% of total proteins or 700mM). Control the release of O2 in the region of bacteroids. Leghemoglobin An oxygen-binding heme protein that help transport only enough oxygen to the respiring symbiotic bacterial cells. Leghemoglobin has a high affinity for oxygen, about ten times higher than the b chain of human hemoglobin. Present in the cytoplasm of infected nodule cells at high concentration (~ 30% of total proteins or 700mM in soybean nodules) Leghemoglobin contains two parts : globin portion and heme portion. The host plant produces the globin portion in response to infection by bacteria; the bacterial symbiont produces the heme portion. O2 leghemoglobin-O2 Peribacteroid membrane H2O In soybean, 12 g of carbon are required to fix 1 g of N2 => Nitrogen fixation is energy demanding. Genetic engineering of the nitrogenase gene cluster The first nif genes identified by complementation were isolated from klebsiella pneumoniae. The entire set of the nif genes are arranged in a single cluster that occupies approximately 24 Kb. The cluster contains of 7 operons that encode 20 proteins. Alfalfa plants that were inoculated by the Rhizobium meliloti contain an extra copy of the nifA gene (a positive activator) grew larger and produced more biomass than plants treated with the nontransformed strain. Genetic modification of plants with the entire nif genes cluster would not be effective because the normal level of oxygen in the host cell would inactivate nitrogenase. pLAFR1 Isolation of nif genes by genetic complementation The nif gene cluster (Fe protein) Ferredoxin (MoFe protein) N2 + 8H+ + 8e- +16ATP ---------------> 2NH3 + H2 + 16ADP + 16Pi Nitrogenase Accompany of H2 envolving during N2 fixation is energy consuming. N2 fixer contains O2-dependent “uptake hydrogenase” which recovers some of the energy lost to H2 production by coupling H2 oxidation to ATP production. Recycling of the hydrogen gas produced by nitrogen fixation H+ H2 e- Some strains of B. japonicum could use hydrogen as an energy source for growth under low-oxygen concentration condition. O2 leghemoglobin-O2 H2O Amides and ureides are the major transported forms of nitrogen. Amide (醯胺, R-CO-NH2) : glutamine, asparagine Ureides (醯脲): allantoic acid (尿囊酸), allantoin (尿囊 素), and citrulline (瓜氨酸), (Synthesized in peroxisome) (ER) The major ureide compounds used to transport nitrogen NH4+ is reassimilated via GS/GOGAT systems Release NH4+ Other tissue allantoinase peroxisome Urate oxidase Legume Tropical legume Soybean, cowpeas, Southern peas, kidney beans, peanut, and mung beans Use ureides for nitrogen transport => ureide exporters Temperate legume Peas, lupins (羽扇豆), alfalfa, clovers, broad bean, and lentil (扁豆) Use glutamine or asparagine (amide) for nitrogen translocation => amide exporters N:C ratio Allantoin (尿囊素 ) Allantoic acid Asparagine Citrulline Glutamine Glutamate = 1:1 = 1:1 = 1:2 = 1:2 = 1:2.5 = 1:5 The more nitrogen ratio the molecule contains, the higher efficiency the molecule transports nitrogen. Importance of sulfur in cells Confer disulfide bridge in proteins Participate in Fe-S clusters for electron transport Several enzymes need sulfur. Some secondary metabolites contain sulfur. Sulfur assimilation Most of the sulfur in higher plants derives from sulfate (SO4-2) absorbed from the soil solution via an H+-SO4-2 symporter. The first step in the synthesis of sulfur-containing organic compounds is the reduction of sulfate (+6) to cysteine (-4). The enzymes involved in cysteine synthesis have been found in the cytosol, plastids and mitochondria. Sulfate assimilation occurs mainly in leaves. Sulfur assimilated in leaves is exported as glutathione via the phloem to sites of protein synthesis. Glutathione : r-glutamylcysteinylglycine Reduced Oxidized Phosphate assimilation Plant roots absorb phosphate (H2PO4-) via H+H2PO4- symporter from the soil. The main entry point of phosphate into assimilatory pathway is ATP. The phosphate is subsequently incorporated into a variety of organic compounds, including sugar phosphates, phospholipids, and nucleotides. Cation assimilation Plants assimilate macronutrient cations (P, Mg, and Ca) and micronutrient cations (Cu, Fe, Mn, Co, Na, and Zn). Cations taken up by plant cells form complexes with organic compounds. Cations form coordination bonds and electrostatic bonds with carbon compounds. Examples of coordination complexes A major constituent of pectins Examples of electrostatic complexes Uptake of iron from soil Most of the iron in the plant is found in the heme molecule of cytochromes within the chloroplasts and mitochondria. In addition, iron also exists in iron-sulfur proteins (ferredoxin). The ferrochelatase reaction A precursor of heme group in cytochrome Uptake of iron from soil Supplied FeSO4 or Fe(NO3)2, iron is present primarily as ferric iron (Fe+3) in oxides such as Fe(OH)3 and can precipitate out of solution. At neutral pH, ferric iron is highly insoluble, and the Ksp is 2X10-39. If phosphate salts are present, insoluble iron phosphate Fe2(PO4)3 will form. How to increase iron solubility in soil and its availability for plants? Soil acidification increases the solubility of ferric iron. Reduction of ferric iron (Fe+3) to the more soluble ferrous form (Fe+2) at the root surface and release the iron from the chelator. (continued) Problem in maintaining availability of iron Root cells may reduce the Fe+3 to Fe+2. After uptake into the root, iron is kept soluble by chelation with organic chelator citric acid. Chelator agents such as citric acid, caffeic acid, tartaric acid, EDTA, and DTPA are used to solve the problems. The chelator DTPA and chelated to iron DTPA DTPA-Fe p.78 Fig. 5.2 Two strategies for plants to uptake Fe Strategy I Nongrain dicot (leafy vegetable) Pea, tomato, soybean Strategy II Monocot grain Barley, maize, oat Strategy I : nongrain dicot (leafy vegetable) ATP rhizosphere Soil colloid Fe+3 H+ Proton pump Cytoplasm H+ ADP + Pi Fe+3 Fe+3 NADH Fe+3 Ferric reductase Chelator Fe+2 NAD+ Ferritin Fe+2 Iron transporter Plasma membrane Fe+2 Fe+2 In soil or nutrient solution Fe+2[SO4-2 or (NO3-)2] -> Fe(OH)3 or Fe2(PO4)3 (precipitate) Fe+3 + chelator (EDTA, citric acid, caffeic acid, and tartaric acid) -> chelator-Fe+3 -> root surface -> chelator-Fe +3 -> chelator + Fe+2 Fe+2 is absorbed by roots (Fe+2 + citric acids) -> xylem chelator diffuse back to soil or solution Chelators The chelator DTPA and chelated to iron DTPA DTPA-Fe p.78 Fig. 5.2 增加米中鐵的含量 從黃豆(Soybean)選殖ferritin Control Fk1 FK11 Seed 14 38 35 gene並轉殖入米中 Leaf Stem Root 119 170 956 (mg-Fe/g-DW) 104 162 962 98 175 966 Fe+3 Strategy I nongrain dicot (leafy vegetable) Phytosiderophores (PS) Strategy II Monocot grain (Graminae) Phytosiderophores (PS) PS are nitrogen containing compounds. PS are found in members of family, Graminae. PS are synthesized and released under iron stress. PS have high affinity for Fe+3 and can scavenge iron from rhizosphere. Iron-PS complexes (ferrisiderophore) is then reabsorbed into the roots. End