NITROGEN AND PROTEIN METABOLISM

• Nitrogen


  An essential element of biological molecules, such as amino acids, nucleotides, proteins, and DNA
• Nitrogen metabolism in prokaryotes


  Coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds
• Ammonia


  The only compound that is absolutely required in nitrogen anabolism in bacteria
• Sources of nitrogen in the gastric environment

  • Amino acids
  • Urea
• Protein Digestion


  1. Proteinase and peptidase

  2. Hydrolysis of protein that escapes host enzymatic digestion in the small intestine

  3. Free amino acids and peptides taken up by bacteria

  
• The fate of dietary protein in the gut is determined by a network of metabolic processes including both host and microbial digestion and utilization

  
• Oxidative Deamination


  1. Removing the amine group from the amino acid, freeing the carbon skeleton

  2. Products are ammonia and keto-acids

  
• Reductive Deamination


  1. Conversion of a carbonyl group into an amine group

  2. Conversion of an aldehyde or a ketone into an amine via an intermediate imine

  
• Decarboxylation


  1. A chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2)

  2. Refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain
• Ammonia generated through amino acid catabolism can be used as a nitrogen source for de novo protein synthesis or may be excreted
• Keto acids proceed through decarboxylation reactions and can be used to generate short-chain fatty acids (SCFAs) including butyrate, acetate, propionate, lactate, succinate, and formate

  
• Sulfur is also liberated from amino acids during these processes
• Transamination Reactions


  1. Transfer of an amino group from one molecule to another

  2. Exemplified by the reaction between glutamic acid and oxaloacetic acid to produce α-ketoglutaric acid and aspartic acid

  3. Aminotransferase enzyme is involved

  
• Nitrification


  1. Biological conversion of ammonia or ammonium to nitrite or nitrate

  2. Bacteria that convert ammonia to nitrites

  3. Bacteria that convert nitrites (toxic to plants) to nitrates

  
• Denitrification


  Microbial process of reducing nitrate and nitrite to gaseous forms of nitrogen, principally nitrous oxide (N2O) and nitrogen (N2)

  
• Protein Catabolism


  Breakdown of proteins into absorbable monomers for further degradation or reassembly
• Bacteria use energy-dependent AAA+ proteases to power degradation of misfolded and native regulatory proteins
• Given that proteolysis is an irreversible event, specificity and selectivity in degrading substrates is key
• Purine and Pyrimidine Biosynthesis

  1. Using 5-phosphoribosyl-1-pyrophosphate (PRPP), the de novo pathway enzymes build purine and pyrimidine nucleotides from "scratch" using simple molecules such as CO2, amino acids and tetrahydrofolate

  2. This route of nucleotide synthesis has a high requirement for energy as compared that of the salvage pathway

  3. The de novo pyrimidine biosynthesis pathway is essential for the proliferation of many pathogens

  4. One of the pathway enzymes, dihydroorotase (DHO), catalyzes the reversible interconversion of N-carbamoyl-L-aspartate to 4,5-dihydroorotate
• The substantial difference between bacterial and mammalian DHOs makes it a promising drug target for disrupting bacterial growth and thus an important candidate to evaluate as a response to antimicrobial resistance on a molecular level