Nitrogen metabolism: Introduction and Overview

Nitrogen metabolism


  • Nitrogen metabolism is controlled by process such as nitrate or ammonium transport through cell membranes in roots.
  • Plants are autotrophic in nature and they can synthesize all of the organic material from inorganic material which is obtained from the surrounding environment. The incorporation of inorganic nutrients into organic or biomolecules is called Nutrient assimilation.
  • Nutrient assimilation is endothermic process, means energy absorbing process.
  • Plant roots actively absorb mineral, nutrient from the soil, plant root absorb mineral in oxidized and reduced form that transport only reduced form of the biomolecule which is highly stable and less reactive in nature.

Nitrogen metabolism

Catabolism of soil organic material

  • Ammonification: Oxidation of organic molecule and formation of ammonia is called ammonification, microorganisms involved in this process are ramocis, B.mycoids .
  • Nitrification: Oxidation of ammonia and formation of nitrite and nitrate called nitrification, microorganisms involved in the conversion of ammonia into nitrite are Nitrosomonas and Nitrosococcus, whereas Nitrobacter and Nitrocystis involved in the conversion of nitrite into nitrate.
  • Denitrification: Oxidation of nitrate and formation of molecular nitrogen is called denitrification, microorganisms such as dentrificans, Pseudomonas take part in this process.
  • Denitrification process decrease the soil fertility because by this process ammonia, nitrite, and nitrate which is easily absorb by plant roots is converted into molecular nitrogen (which is not use by plant directly).

Nitrate Assimilation

  • Plant root actively absorb nitrate from the soil by using Nitrate/proton Co-transporter (by secondary active transport).
  • In cytosol nitrate is converted into nitrite by using enzyme nitrate reductase.
  • It is homodimer in nature and both subunits are interconnected with each other hinge region.
  • Each subunit consist 3 factors:
    • FAD
    • Heme
  • Both subunits are independent to each other.
  • FAD domain accept electron from NADH or NADPH and transfer to MoCo via heme. MoCo transfer the electron to nitrate and forms nitrite.
  • Nitrate reductase is regulated at transcriptional and Post-translational level.
  • At post-translational level, it is regulated by covalent modification (phosphorylation and dephosphorylation).
  • Negative regulator of nitrate reductase: magnesium ion, AMP, NADP+, Darkness, ammonia, nitrite, Asn/Gln.

Nitrite reductase

  • Nitrite is highly toxic in nature that’s why it is rapidly transported from cytosol to chloroplast.
  • Nitrite reductase located in chloroplast and it is encoded by nuclear genome.
  • Nitrite reductase translated in cytosol using 80s ribosome and after complete translation. It is transported in stroma of the chloroplast (post-translational translocation) by using Tic- Toc pathway.
  • It is made by single polypeptide and contain two cofactor: FeS and
  • It accept electron from reduced ferredoxin.

Ammonium assimilation

  • Plant avoid ammonium toxicity by rapidly converting ammonia into amino acids.
  • It is completed by two different enzymes.
    • Glutamine synthase
    • Glutamate synthase/GOGAT (glutamate-2-oxo-glutarate amino transferase.)
  • GOGAT is two types:
    • NADH dependent.
    • Ferredoxin dependent- found in green part of the plant and mainly assimilate “photo respiratory ammonia, while NADH dependent GOGAT found in non green parts and helps in assimilation of soil derived ammonium ion.

Biological nitrogen fixation

  • Both bacteria and plants are free living organisms but under nitrogen deficiency condition, they come in contact with each other and form symbiotic relationship in temporary manner called protocoperation.
  • Under nitrogen deficiency condition, plant roots secretes Isoflavenoids and betain, which acts as a chemoattractant.
  • Receptors of the chemoattractant located on bacterial plasma membrane, after binding of chemoattractant to its receptor, bacteria move towards the plant root chemotaxis process.
  • NOD-A gene encodes N-acetyl transferase that catalyse addition of fatty acyl chain.
  • NOD-B gene encodes chitin-oligosaccharide deacetylase that remove acetyl group from terminal non- reducing sugar.
  • NOD-C gene encodes chitin -oligosaccharide synthase that link N-acetyl-D-glucosamine monomer.
  • NOD factor- it is encoded by NOD-D
  • NOD factors are lipochitin oligosaccharide signal molecule which having chitin-beta-1-4 linked N-acetyl-D-glucosamine backbone.
  • NOD-D is not part of Nod-box.
  • NOD-D gene regulatory NOD gene which is constitutively expressed and regulate the expression of other NOD gene.
  • NOD factor binds at the NOD-operon and increase the expression of other NOD gene.


  • Nitrogen fixing bacteria having special enzyme called nitrogenase.
  • Nitrogenase is encoded by nif-gene nitrogen is made by two sub units smaller subunit and largest subunit and both subunits directly depend on each other.
  • In presence of Oxygen both subunits are inactivated because oxygen are strong electrophile.
Smaller subunit
  • It consists two identical subunit and each subunit contain FeS cluster.
  • It accept electron from reduced ferredoxin and transfer to larger subunit.
  • It also hydrolyse 16 ATP and inactivated by oxygen.

Larger subunit

  • It is made by four subunit and it contains Mo-Fe-S.
  • It accept electron from smaller subunit and transfer to molecular nitrogen and form ammonium ion.
  • It is also sensitive to oxygen.

Reference and Sources


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