Nitrogen assimilation

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Nitrogen assimilation is the formation of organic nitrogen compounds like amino acids from inorganic nitrogen compounds present in the environment. Organisms like plants, fungi and certain bacteria that can fix nitrogen gas (N2) depend on the ability to assimilate nitrate or ammonia for their needs. Other organisms, like animals, depend entirely on organic nitrogen from their food.

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Nitrogen assimilation in plants

Plants absorb nitrogen from the soil in the form of nitrate (NO3−) and ammonium (NH4+). In aerobic soils where nitrification can occur, nitrate is usually the predominant form of available nitrogen that is absorbed. [1] [2] However this is not always the case as ammonia can predominate in grasslands [3] and in flooded, anaerobic soils like rice paddies. [4] Plant roots themselves can affect the abundance of various forms of nitrogen by changing the pH and secreting organic compounds or oxygen. [5] This influences microbial activities like the inter-conversion of various nitrogen species, the release of ammonia from organic matter in the soil and the fixation of nitrogen by non-nodule-forming bacteria.

Ammonium ions are absorbed by the plant via ammonia transporters. Nitrate is taken up by several nitrate transporters that use a proton gradient to power the transport. [6] [7] Nitrogen is transported from the root to the shoot via the xylem in the form of nitrate, dissolved ammonia and amino acids. Usually [8] (but not always [9] ) most of the nitrate reduction is carried out in the shoots while the roots reduce only a small fraction of the absorbed nitrate to ammonia. Ammonia (both absorbed and synthesized) is incorporated into amino acids via the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway. [10] While nearly all [11] the ammonia in the root is usually incorporated into amino acids at the root itself, plants may transport significant amounts of ammonium ions in the xylem to be fixed in the shoots. [12] This may help avoid the transport of organic compounds down to the roots just to carry the nitrogen back as amino acids.

Nitrate reduction is carried out in two steps. Nitrate is first reduced to nitrite (NO2−) in the cytosol by nitrate reductase using NADH or NADPH. [7] Nitrite is then reduced to ammonia in the chloroplasts (plastids in roots) by a ferredoxin dependent nitrite reductase. In photosynthesizing tissues, it uses an isoform of ferredoxin (Fd1) that is reduced by PSI while in the root it uses a form of ferredoxin (Fd3) that has a less negative midpoint potential and can be reduced easily by NADPH. [13] In non photosynthesizing tissues, NADPH is generated by glycolysis and the pentose phosphate pathway.

In the chloroplasts, [14] glutamine synthetase incorporates this ammonia as the amide group of glutamine using glutamate as a substrate. Glutamate synthase (Fd-GOGAT and NADH-GOGAT) transfer the amide group onto a 2-oxoglutarate molecule producing two glutamates. Further transaminations are carried out make other amino acids (most commonly asparagine) from glutamine. While the enzyme glutamate dehydrogenase (GDH) does not play a direct role in the assimilation, it protects the mitochondrial functions during periods of high nitrogen metabolism and takes part in nitrogen remobilization. [15]

pH and Ionic balance during nitrogen assimilation

Different plants use different pathways to different levels. Tomatoes take in a lot of K and accumulate salts in their vacuoles, castor reduces nitrate in the roots to a large extent and excretes the resulting alkali. Soy bean plants moves a large amount of malate to the roots where they convert it to alkali while the potassium is recirculated. Nitrate ion balance-variants.png
Different plants use different pathways to different levels. Tomatoes take in a lot of K and accumulate salts in their vacuoles, castor reduces nitrate in the roots to a large extent and excretes the resulting alkali. Soy bean plants moves a large amount of malate to the roots where they convert it to alkali while the potassium is recirculated.

Every nitrate ion reduced to ammonia produces one OH− ion. To maintain a pH balance, the plant must either excrete it into the surrounding medium or neutralize it with organic acids. This results in the medium around the plants roots becoming alkaline when they take up nitrate.

To maintain ionic balance, every NO3− taken into the root must be accompanied by either the uptake of a cation or the excretion of an anion. Plants like tomatoes take up metal ions like K+, Na+, Ca2+ and Mg2+ to exactly match every nitrate taken up and store these as the salts of organic acids like malate and oxalate. [16] Other plants like the soybean balance most of their NO3− intake with the excretion of OH− or HCO3−. [17]

Plants that reduce nitrates in the shoots and excrete alkali from their roots need to transport the alkali in an inert form from the shoots to the roots. To achieve this they synthesize malic acid in the leaves from neutral precursors like carbohydrates. The potassium ions brought to the leaves along with the nitrate in the xylem are then sent along with the malate to the roots via the phloem. In the roots, the malate is consumed. When malate is converted back to malic acid prior to use, an OH− is released and excreted. (RCOO− + H2O -> RCOOH +OH−) The potassium ions are then recirculated up the xylem with fresh nitrate. Thus the plants avoid having to absorb and store excess salts and also transport the OH−. [18]

Plants like castor reduce a lot of nitrate in the root itself, and excrete the resulting base. Some of the base produced in the shoots is transported to the roots as salts of organic acids while a small amount of the carboxylates are just stored in the shoot itself. [19]

Nitrogen use efficiency

Nitrogen use efficiency (NUE) is the proportion of nitrogen present that a plant absorbs and uses. Improving nitrogen use efficiency and thus fertilizer efficiency is important to make agriculture more sustainable, [20] by reducing pollution (fertilizer runoff) and production cost and increasing yield. Worldwide, crops generally have less than 50% NUE. [21] Better fertilizers, improved crop management, [21] selective breeding, [22] and genetic engineering [20] [23] can increase NUE.

Nitrogen use efficiency can be measured at various levels: the crop plant, the soil, by fertilizer input, by ecosystem productivity, etc. [24] At the level of photosynthesis in leaves, it is termed photosynthetic nitrogen use efficiency (PNUE). [25] [26]

Related Research Articles

Urea, also called carbamide, is an organic compound with chemical formula CO(NH2)2. This amide has two amino groups joined by a carbonyl functional group. It is thus the simplest amide of carbamic acid.

The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions that produces urea (NH2)2CO from ammonia (NH3). Animals that use this cycle, mainly amphibians and mammals, are called ureotelic.

<span class="mw-page-title-main">Fertilizer</span> Substance added to soils to supply plant nutrients for a better growth

A fertilizer or fertiliser is any material of natural or synthetic origin that is applied to soil or to plant tissues to supply plant nutrients. Fertilizers may be distinct from liming materials or other non-nutrient soil amendments. Many sources of fertilizer exist, both natural and industrially produced. For most modern agricultural practices, fertilization focuses on three main macro nutrients: nitrogen (N), phosphorus (P), and potassium (K) with occasional addition of supplements like rock flour for micronutrients. Farmers apply these fertilizers in a variety of ways: through dry or pelletized or liquid application processes, using large agricultural equipment or hand-tool methods.

<span class="mw-page-title-main">Nitrogen cycle</span> Biogeochemical cycle by which nitrogen is converted into various chemical forms

The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmospheric nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.

<span class="mw-page-title-main">Glutamine</span> Chemical compound

Glutamine is an α-amino acid that is used in the biosynthesis of proteins. Its side chain is similar to that of glutamic acid, except the carboxylic acid group is replaced by an amide. It is classified as a charge-neutral, polar amino acid. It is non-essential and conditionally essential in humans, meaning the body can usually synthesize sufficient amounts of it, but in some instances of stress, the body's demand for glutamine increases, and glutamine must be obtained from the diet. It is encoded by the codons CAA and CAG. It is named after glutamic acid, which in turn is named after its discovery in cereal proteins, gluten.

<span class="mw-page-title-main">Ammonium</span> Chemical compound

Ammonium is a modified form of ammonia that has an extra hydrogen atom. It is a positively charged (cationic) molecular ion with the chemical formula NH+4 or [NH4]+. It is formed by the addition of a proton to ammonia. Ammonium is also a general name for positively charged (protonated) substituted amines and quaternary ammonium cations, where one or more hydrogen atoms are replaced by organic or other groups. Not only is ammonium a source of nitrogen and a key metabolite for many living organisms, but it is an integral part of the global nitrogen cycle. As such, human impact in recent years could have an effect on the biological communities that depend on it.

<span class="mw-page-title-main">Iron deficiency (plant disorder)</span>

Iron (Fe) deficiency is a plant disorder also known as "lime-induced chlorosis". It can be confused with manganese deficiency. If soil iron concentration is high, in spite of this it can become unavailable for absorption if soil pH is higher than 6.5. Excess of elements such as manganese in the soil can interfere with plant iron uptake triggering iron deficiency.

<span class="mw-page-title-main">Plant nutrition</span> Study of the chemical elements and compounds necessary for normal plant life

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Nutrient sensing is a cell's ability to recognize and respond to fuel substrates such as glucose. Each type of fuel used by the cell requires an alternate pathway of utilization and accessory molecules such as enzymes and cofactors. In order to conserve resources a cell will only produce molecules that it needs at the time. The level and type of fuel that is available to a cell will determine the type of enzymes it needs to express from its genome for utilization. Receptors on the cell membrane's surface designed to be activated in the presence of specific fuel molecules communicate to the cell nucleus via a means of cascading interactions. Nutrient receptors are receptors that are primarily designed to perform the function of nutrient sensing, whereas other receptors are extensively multifunctional and perform many functions besides nutrient sensing. In this way the cell is aware of the available nutrients and is able to produce only the molecules specific to that nutrient type.

<span class="mw-page-title-main">Glutamate dehydrogenase</span> Hexameric enzyme

Glutamate dehydrogenase is an enzyme observed in both prokaryotes and eukaryotic mitochondria. The aforementioned reaction also yields ammonia, which in eukaryotes is canonically processed as a substrate in the urea cycle. Typically, the α-ketoglutarate to glutamate reaction does not occur in mammals, as glutamate dehydrogenase equilibrium favours the production of ammonia and α-ketoglutarate. Glutamate dehydrogenase also has a very low affinity for ammonia, and therefore toxic levels of ammonia would have to be present in the body for the reverse reaction to proceed. However, in brain, the NAD+/NADH ratio in brain mitochondria encourages oxidative deamination. In bacteria, the ammonia is assimilated to amino acids via glutamate and aminotransferases. In plants, the enzyme can work in either direction depending on environment and stress. Transgenic plants expressing microbial GLDHs are improved in tolerance to herbicide, water deficit, and pathogen infections. They are more nutritionally valuable.

<span class="mw-page-title-main">Glutamine synthetase</span> Class of enzymes

Glutamine synthetase (GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:

<span class="mw-page-title-main">Nitrate reductase</span> Class of enzymes

Nitrate reductases are molybdoenzymes that reduce nitrate to nitrite. This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.

Natronomonas is a genus of the Halobacteriaceae.

In enzymology, a glutamate synthase (NADH) (EC 1.4.1.14) is an enzyme that catalyzes the chemical reaction

Glutaminolysis (glutamine + -lysis) is a series of biochemical reactions by which the amino acid glutamine is lysed to glutamate, aspartate, CO2, pyruvate, lactate, alanine and citrate.

<span class="mw-page-title-main">Purine nucleotide cycle</span> Protein metabolic pathway

The Purine Nucleotide Cycle is a metabolic pathway in protein metabolism requiring the amino acids aspartate and glutamate. The cycle is used to regulate the levels of adenine nucleotides, in which ammonia and fumarate are generated. AMP converts into IMP and the byproduct ammonia. IMP converts to S-AMP (adenylosuccinate), which then converts to AMP and the byproduct fumarate. The fumarate goes on to produce ATP (energy) via oxidative phosphorylation as it enters the Krebs cycle and then the electron transport chain. Lowenstein first described this pathway and outlined its importance in processes including amino acid catabolism and regulation of flux through glycolysis and the Krebs cycle.

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<span class="mw-page-title-main">Yeast assimilable nitrogen</span> Form of nitrogen available to wine yeast to use during fermentation

Yeast assimilable nitrogen or YAN is the combination of free amino nitrogen (FAN), ammonia (NH3) and ammonium (NH4+) that is available for a yeast, e.g. the wine yeast Saccharomyces cerevisiae, to use during fermentation. Outside of the fermentable sugars glucose and fructose, nitrogen is the most important nutrient needed to carry out a successful fermentation that doesn't end prior to the intended point of dryness or sees the development of off-odors and related wine faults. To this extent winemakers will often supplement the available YAN resources with nitrogen additives such as diammonium phosphate (DAP).

Glutamate synthase is an enzyme and frequently abbreviated as GOGAT. This enzyme manufactures glutamate from glutamine and α-ketoglutarate, and thus along with glutamine synthetase plays a central role in the regulation of nitrogen assimilation in photosynthetic eukaryotes and prokaryotes. This is of great importance as primary productivity in many marine environments is regulated by the availability of inorganic nitrogen.

Seventeen elements or nutrients are essential for plant growth and reproduction. They are carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), magnesium (Mg), iron (Fe), boron (B), manganese (Mn), copper (Cu), zinc (Zn), molybdenum (Mo), nickel (Ni) and chlorine (Cl). Nutrients required for plants to complete their life cycle are considered essential nutrients. Nutrients that enhance the growth of plants but are not necessary to complete the plant's life cycle are considered non-essential, although some of them, such as silicon (Si), have been shown to improve nutrent availability, hence the use of stinging nettle and horsetail macerations in Biodynamic agriculture. With the exception of carbon, hydrogen and oxygen, which are supplied by carbon dioxide and water, and nitrogen, provided through nitrogen fixation, the nutrients derive originally from the mineral component of the soil. The Law of the Minimum expresses that when the available form of a nutrient is not in enough proportion in the soil solution, then other nutrients cannot be taken up at an optimum rate by a plant. A particular nutrient ratio of the soil solution is thus mandatory for optimizing plant growth, a value which might differ from nutrient ratios calculated from plant composition.

References

  1. ↑ Xu, G.; Fan, X.; Miller, A. J. (2012). "Plant Nitrogen Assimilation and Use Efficiency". Annual Review of Plant Biology. 63: 153–182. doi:10.1146/annurev-arplant-042811-105532. PMID   22224450. S2CID   20690850.
  2. ↑ Nadelhoffer, KnuteJ.; JohnD. Aber; JerryM. Melillo (1984-10-01). "Seasonal patterns of ammonium and nitrate uptake in ten temperate forest ecosystems". Plant and Soil. 80 (3): 321–335. doi:10.1007/BF02140039. ISSN   0032-079X. S2CID   40749543.
  3. ↑ Jackson, L. E.; Schimel, J. P.; Firestone, M. K. (1989). "Short-term partitioning of ammonium and nitrate between plants and microbes in an annual grassland". Soil Biology and Biochemistry. 21 (3): 409–415. doi:10.1016/0038-0717(89)90152-1.
  4. ↑ Ishii, S.; Ikeda, S.; Minamisawa, K.; Senoo, K. (2011). "Nitrogen cycling in rice paddy environments: Past achievements and future challenges". Microbes and Environments. 26 (4): 282–292. doi: 10.1264/jsme2.me11293 . PMID   22008507.
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  9. ↑ Stewart, G. R.; Popp, M.; Holzapfel, I.; Stewart, J. A.; Dickie-Eskew, A. N. N. (1986). "Localization of Nitrate Reduction in Ferns and Its Relationship to Environment and Physiological Characteristics". New Phytologist. 104 (3): 373–384. doi: 10.1111/j.1469-8137.1986.tb02905.x .
  10. ↑ Masclaux-Daubresse, C.; Reisdorf-Cren, M.; Pageau, K.; Lelandais, M.; Grandjean, O.; Kronenberger, J.; Valadier, M. H.; Feraud, M.; Jouglet, T.; Suzuki, A. (2006). "Glutamine Synthetase-Glutamate Synthase Pathway and Glutamate Dehydrogenase Play Distinct Roles in the Sink-Source Nitrogen Cycle in Tobacco". Plant Physiology. 140 (2): 444–456. doi:10.1104/pp.105.071910. PMC   1361315 . PMID   16407450.
  11. ↑ Kiyomiya, S.; Nakanishi, H.; Uchida, H.; Tsuji, A.; Nishiyama, S.; Futatsubashi, M.; Tsukada, H.; Ishioka, N. S.; Watanabe, S.; Ito, T.; Mizuniwa, C.; Osa, A.; Matsuhashi, S.; Hashimoto, S.; Sekine, T.; Mori, S. (2001). "Real time visualization of 13N-translocation in rice under different environmental conditions using positron emitting Ttacer imaging system". Plant Physiology. 125 (4): 1743–1753. doi:10.1104/pp.125.4.1743. PMC   88831 . PMID   11299355.
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  16. ↑ Kirkby, Ernest A.; Alistair H. Knight (1977-09-01). "Influence of the Level of Nitrate Nutrition on Ion Uptake and Assimilation, Organic Acid Accumulation, and Cation-Anion Balance in Whole Tomato Plants". Plant Physiology. 60 (3): 349–353. doi:10.1104/pp.60.3.349. ISSN   0032-0889. PMC   542614 . PMID   16660091.
  17. ↑ Touraine, Bruno; Nicole Grignon; Claude Grignon (1988-11-01). "Charge Balance in NO3−-Fed Soybean Estimation of K+ and Carboxylate Recirculation". Plant Physiology. 88 (3): 605–612. doi:10.1104/pp.88.3.605. ISSN   0032-0889. PMC   1055632 . PMID   16666356.
  18. ↑ Touraine, Bruno; Bertrand Muller; Claude Grignon (1992-07-01). "Effect of Phloem-Translocated Malate on NO3− Uptake by Roots of Intact Soybean Plants". Plant Physiology. 99 (3): 1118–1123. doi:10.1104/pp.99.3.1118. ISSN   0032-0889. PMC   1080591 . PMID   16668978.
  19. ↑ Allen, Susan; J. A. Raven (1987-04-01). "Intracellular pH Regulation in Ricinus communis Grown with Ammonium or Nitrate as N Source: The Role of Long Distance Transport". Journal of Experimental Botany. 38 (4): 580–596. doi:10.1093/jxb/38.4.580. ISSN   0022-0957.
  20. 1 2 "Nitrogen Use Efficiency". Seed Biotechnology Center. UC Davis. Archived from the original on 2021-05-16. Retrieved 2019-11-23.
  21. 1 2 Fageria, N.K.; Baligar, V.C. (2005). "Enhancing Nitrogen Use Efficiency in Crop Plants". Advances in Agronomy. 88: 97–185. doi:10.1016/S0065-2113(05)88004-6. ISBN   9780120007868.
  22. ↑ Sharma, Narendra; Sinha, Vimlendu Bhushan; Prem Kumar, N. Arun; Subrahmanyam, Desiraju; Neeraja, C. N.; Kuchi, Surekha; Jha, Ashwani; Parsad, Rajender; Sitaramam, Vetury; Raghuram, Nandula (20 January 2021). "Nitrogen Use Efficiency Phenotype and Associated Genes: Roles of Germination, Flowering, Root/Shoot Length and Biomass". Frontiers in Plant Science. 11: 587464. doi: 10.3389/fpls.2020.587464 . PMC   7855041 . PMID   33552094.
  23. ↑ Melino, Vanessa J; Tester, Mark A; Okamoto, Mamoru (February 2022). "Strategies for engineering improved nitrogen use efficiency in crop plants via redistribution and recycling of organic nitrogen". Current Opinion in Biotechnology. 73: 263–269. doi:10.1016/j.copbio.2021.09.003. hdl: 10754/672009 . PMID   34560475. S2CID   237626832.
  24. ↑ Congreves, Kate A.; Otchere, Olivia; Ferland, Daphnée; Farzadfar, Soudeh; Williams, Shanay; Arcand, Melissa M. (4 June 2021). "Nitrogen Use Efficiency Definitions of Today and Tomorrow". Frontiers in Plant Science. 12: 637108. doi: 10.3389/fpls.2021.637108 . PMC   8220819 . PMID   34177975.
  25. ↑ McKinley, Duncan C.; Blair, John M. (2008). "Woody Plant Encroachment by Juniperus virginiana in a Mesic Native Grassland Promotes Rapid Carbon and Nitrogen Accrual". Ecosystems. 11 (3): 454–468. doi:10.1007/s10021-008-9133-4. S2CID   23911766.
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