Soil organic matter contain protein which is a source of nitrogen for soil microorganisms, plants and animals. Proteins are peptide molecule containing two or more amino acid and are essential for all living organisms especially as a structural component. Besides proteins the other sources that contribute nitrogen in soil are chitin from fungus or insect necromass, chlorophyll and nucleic acid. During decomposition the microbial biomass absorb and release (mineralization) nutrient from organic matter. Plant cell wall contain relatively small amount of protein whereas, certain algal cell wall are exclusively made up of protein.  The cell wall of unicellular alga Chlamydomonas reinhardtii   is entirely made from hydroxyproline-rich glycoprotein (HRGPs) (Adair and Appel 1989).  The best known structural protein are extensin or HRGPs. Specific extensin is synthesized in only one or few cell types in a plant. Soybean extensin are found in sclerenchyma and in hourglass cells in the seed coat (Cassab and Varner 1987). Hydroxyproline/ proline rich protein (H/PRP) are found in both monocot and dicot plants. Glycine rich proteins (GRPs) are localized mainly in the vascular tissue of the plant (Ringli et al., 2001).

Enzyme proteases are produced by plants, animals and microorganisms. Microbial proteases hydrolyze the breakdown of proteinaceous substances which enter the ecosystem. Breakdown of protein or peptide into amino acid is known as proteolysis. The proteolytic enzyme cleaves the peptide bond in protein.  Upon protein degradation the amino acid are used and recycled.  Lathrop and Brown (1911) found that almost 98% of the nitrogen in soil is of organic nature. The ammonia and nitrate nitrogen constitute the remainder.

The initial step of protein degradation are carried out by extracellular proteolytic enzymes excreted by microorganisms such as fungi, bacteria, actinomycetes and plants. The microorganisms produce intercellular and extracellular proteases (Rao et al., 1998 and Gupta et al., 2002). The excreted  extracellular enzyme break down the protein in plant tissue into smaller polypeptide and amino acid, which are then transported into the cell where they are broken down further and used as source of energy and as intermediates for biosynthesis.

PROTEASES OF PLANT ORIGIN – Papain, bromelain, keratinases and ficin.

  • Papain a plant protease (Schechler and Berger 1967) is extracted from Carica papaya
  • Bromelain is from stem and juice of pineapple.
  • Keratinases – Some plant produce proteases which can degrade hair (Rao et al., 1998)
  • Ficin derived from figs latex

PROTEASES OF ANIMAL ORIGIN – Trypsin, chymotrypsin, pepsin and rennin’s (Boyer 1971 and Hoffman 1974).

  • Trypsin is intestinal digestive enzyme responsible for hydrolysis of food protein
  • Chymotrypsin acts as digestive enzyme and is present in animal pancreatic juices
  • Pepsin is an acidic protease and found in the stomach of all vertebrates
  • Rennin is a pepsin like protease occurring in the stomach of ruminants animals

Proteases are classified on the basis of type of reaction catalyzed, chemical nature of catalytic site and structure. On the basis of their site of action proteases are subdivided into:

  1. Endopeptidases:  Endopeptidase act on the inner region of the peptide chain.

    2.  Exopeptidases: Exopeptidase act near the terminal amino and carboxylic position in chain. The proteases that act on free amino terminal is called aminopeptidase whereas, the carboxypeptidase acts on carboxyl terminal of polypeptide chain.

Root derived proteases break down protein in the rhizosphere. Godlewski and Adamczyk (2007) reported that plant root secrete proteases. One of the mechanisms by which root access protein (Paungfoo-Lonhienne et al., 2008) is that root exudes proteolytic enzyme that digest protein at root surface and in the apoplast of root cortex. The other mechanisms is that root cells take up the intact protein most likely via endocytosis. Arabidopsis genome encode for 828 proteases (Rawlings et al., 2006).  Woody plants rely on ecto- or ericoid mycorrhizal fungal symbiont to break down soil protein.  Rineau et al., (2016) reported fungi growing in older forest (contains more organic matter) have high protein degradation ability.

 Protein hydrolysis leads to disruption of complex molecule to simple molecule. The amino acid and amines are further decomposed and converted into ammonia. Claus (1989) reported that the physical, chemical properties of soil such as temperature, moisture, aeration, pH and nutrient supply control the rate of microbial ammonification.  Ammonia is extremely soluble in water hence it is normally trapped in moisture in soil after it is excreted by soil microorganisms. To be used as nutrient by plant nitrogen must be available in the soil as the nitrate ion (NO3).

Microorganisms compete with plants for available nitrate. Soil microorganisms chemically reduce nitrates by assimilative or dissimilative nitrate reduction.

  • Assimilative nitrate reduction: The microorganisms reduce nitrate first to nitrite and then to ammonia (NH3). The ammonia is immediately assimilated by the cell for making amino acid and other nitrogen containing organic building blocks.


  • Dissimilative nitrate reduction: Some microorganism reduce nitrate to nitrite while others reduce nitrite to nitrous oxide and dinitrogen (N2). This is denitrification and the final product (N2) of denitrification escapes in the atmosphere.

Oxygen affects both nitrifying and denitrifying microorganisms when both oxygen and ammonia are present in the soil.  The nitrifying bacteria oxidizes ammonia and releases nitrate in to the soil. The presence oxygen will allow facultative anaerobe capable of denitrification to respire using oxygen instead of nitrate as a terminal electron acceptor. Thus nitrate is formed and not depleted from the soil in presence of oxygen.


Adair, W. S. and Appel, H. 1989 Identification of a Highly Conserved Hydroxyproline-rich Glycoprotein in the Cell Walls of Chlamydomonas reinhardtii and Two Other Volvocales.  Planta 179 (3):  381–386

Boyer, P. D. 1971 The enzymes. 3rd ed. New York, N.Y: Academic Press, Inc.

Claus, G. W.  1989 Ammonification – Microbial Deamination of Nitrogenous Organic Compounds in Understanding Microbes A Laboratory Text Book for Microbiology W H Freeman and Co. New York pp: 499-506

Cassab, G. I. and Varner, J. E. 1987 Immunocytolocalization of Extensin in Developing Soybean Seed Coats by Immunogold-Silver Staining and by Tissue Printing on Nitrocellulose Paper.  The Journ. of Cell Biol. 105 (6): 2581-2588

Godlewski, M. and Adamczyk, B. 2007 The Ability of Plants to Secrete Proteases by Roots.  Plant Physiol.  and Biochem. 45 (9):  657–664

Gupta, R., Beg, Q. K. and Lorenz, P. 2002 Bacterial Alkaline Proteases: Molecular Approaches and Industrial Applications.  Appl. Microbiol. Biotechnol. 59 (1):15–32

doi: 10.1007/s00253-002-0975-y

Hoffman, T. 1974 Food related enzymes. Adv. Chem. Ser. 136: 146–185

Lathrop, E. C. and Brown, B. E. 1911 Studies in Organic Soil Nitrogen.  J. Ind. Eng. Chem. 3: 657 – 660

Paungfoo-Lonhienne, C., Lonhienne, T. G. A., Rentsch, D., Robinson, N., Christie, M., Webb, R. I., Gamage, H. K., Carroll, B. J., Schenk, P.  M. and Schmidt, S.  2008   Plants Can Use Protein as a Nitrogen Source without Assistance from Other Organisms.  Proc. Natl. Acad. Sci. 105 (11): 4524 – 4529

doi: 10.1073/pnas.0712078105

Rao, M. B., Tanksale, A. M., Ghatge, M. S. and Deshpande, V. V. 1998   Molecular and Biotechnological Aspects of Microbial Proteases.  Microbiol.  Mol.  Biol.  Rev. 62(3): 597–635

Rawlings, N. D., Morton, F. R. and Barrett, A. J.  2006  MEROPS: The Peptidase Database. Nucleic Acids Res. 34 (Database Issue): D270–D272

Rineau, F.,  Stas, J.,  Nguyen, N. H., Kuyper, T. W., Carleer, R.,  Vangronsveld, J.,  Colpaert, J. V. and Kennedy,  P. G. 2016 Ectomycorrhizal Fungal Protein Degradation Ability Predicted by Soil Organic Nitrogen Availability.  Appl. Environ. Microbiol. 82 (5):  1391-1400

doi: 10.1128/AEM.03191-15

Ringli, C., Keller, B. and Ryser, U.  2001 Glycine-rich Proteins as Structural Components of Plant Cell Walls.  Cellular and Molecular Life Sciences 58: 1430–1441

Schechler, I. and Berger, A. 1967 On the Size of the Active Site in Proteases I Papain. Biochem. Biophys. Res. Commun. 27 (2):157–162



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