Metabolism

B. subtilis is a chemoheterotrophic organism. It uses glucose and ammonium/glutamine as preferred sources of carbon and nitrogen, respectively. The bacteria can grow on a minimal medium. It produces all cofactors.

A suite of models of B. subtilis metabolism can by found in SubtiPathways.

Metabolic categories

2. Metabolism

• 2.1. Electron transport and ATP synthesis
  • 2.1.1. Regulators of electron transport
  • 2.1.2. Respiration
    • 2.1.2.1. Terminal oxidases
    • 2.1.2.2. Anaerobic respiration
    • 2.1.2.3. Respiration/ other
  • 2.1.3. Electron transport/ other
  • 2.1.4. ATP synthesis
• 2.2. Carbon metabolism
  • 2.2.1. Carbon core metabolism
    • 2.2.1.1. Glycolysis
    • 2.2.1.2. Gluconeogenesis
    • 2.2.1.3. Pentose phosphate pathway
    • 2.2.1.4. TCA cycle
    • 2.2.1.5. Overflow metabolism
  • 2.2.2. Utilization of specific carbon sources
    • 2.2.2.1. Utilization of organic acids
    • 2.2.2.2. Utilization of acetoin
    • 2.2.2.3. Utilization of glycerol/ glycerol 3-phosphate
    • 2.2.2.4. Utilization of ribose
    • 2.2.2.5. Utilization of xylan/ xylose
    • 2.2.2.6. Utilization of arabinan/ arabinose/ arabitol
    • 2.2.2.7. Utilization of fructose
    • 2.2.2.8. Utilization of galactose
    • 2.2.2.9. Utilization of mannose
    • 2.2.2.10. Utilization of mannitol
    • 2.2.2.11. Utilization of glucitol
    • 2.2.2.12. Utilization of rhamnose
    • 2.2.2.13. Utilization of gluconate
    • 2.2.2.14. Utilization of glucarate/ galactarate
    • 2.2.2.15. Utilization of hexuronate
    • 2.2.2.16. Utilization of inositol
    • 2.2.2.17. Utilization of amino sugars
    • 2.2.2.18. Utilization of beta-glucosides
    • 2.2.2.19. Utilization of sucrose
    • 2.2.2.20. Utilization of trehalose
    • 2.2.2.21. Utilization of melibiose
    • 2.2.2.22. Utilization of maltose
    • 2.2.2.23. Utilization of starch/ maltodextrin
    • 2.2.2.24. Utilization of glucomannan
    • 2.2.2.25. Utilization of pectin
    • 2.2.2.26. Utilization of other polymeric carbohydrates
• 2.3. Amino acid/ nitrogen metabolism
  • 2.3.1. Biosynthesis/ acquisition of amino acids
    • 2.3.1.1. Biosynthesis/ acquisition of glutamate/ glutamine/ ammonium assimilation
    • 2.3.1.2. Biosynthesis/ acquisition of proline
    • 2.3.1.3. Biosynthesis/ acquisition of arginine
    • 2.3.1.4. Biosynthesis/ acquisition of aspartate/ asparagine
    • 2.3.1.5. Biosynthesis/ acquisition of lysine/ threonine
    • 2.3.1.6. Biosynthesis/ acquisition of serine/ glycine/ alanine
    • 2.3.1.7. Biosynthesis/ acquisition of cysteine
    • 2.3.1.8. Biosynthesis/ acquisition of methionine/ S-adenosylmethionine
    • 2.3.1.9. Biosynthesis/ acquisition of branched-chain amino acids
    • 2.3.1.10. Biosynthesis/ acquisition of aromatic amino acids
    • 2.3.1.11. Biosynthesis/ acquisition of histidine
  • 2.3.2. Utilization of amino acids
    • 2.3.2.1. Utilization of glutamine/ glutamate
    • 2.3.2.2. Utilization of proline
    • 2.3.2.3. Utilization of arginine/ ornithine
    • 2.3.2.4. Utilization of histidine
    • 2.3.2.5. Utilization of asparagine/ aspartate
    • 2.3.2.6. Utilization of alanine/ serine
    • 2.3.2.7. Utilization of threonine/ glycine
    • 2.3.2.8. Utilization of branched-chain amino acids
    • 2.3.2.9. Utilization of gamma-amino butyric acid
  • 2.3.3. Utilization of nitrogen sources other than amino acids
    • 2.3.3.1. Utilization of nitrate/ nitrite
    • 2.3.3.2. Utilization of urea
    • 2.3.3.3. Utilization of amino sugars
    • 2.3.3.4. Utilization of peptides
    • 2.3.3.5. Utilization of proteins
  • 2.3.4. Putative amino acid transporter
• 2.4. Lipid metabolism
  • 2.4.1. Utilization of lipids
    • 2.4.1.1. Utilization of phospholipids
    • 2.4.1.2. Utilization of fatty acids
    • 2.4.1.3. Utilization of lipids/ other
  • 2.4.2. Biosynthesis of lipids
    • 2.4.2.1. Biosynthesis of fatty acids
    • 2.4.2.2. Biosynthesis of phospholipids
    • 2.4.2.3. Biosynthesis of isoprenoids
  • 2.4.3. Lipid metabolism/ other
• 2.5. Nucleotide metabolism
  • 2.5.1. Utilization of nucleotides
  • 2.5.2. Biosynthesis/ acquisition of nucleotides
    • 2.5.2.1. Biosynthesis/ acquisition of purine nucleotides
    • 2.5.2.2. Purine salvage and interconversion
    • 2.5.2.3. Biosynthesis/ acquisition of pyrimidine nucleotides
    • 2.5.2.4. Biosynthesis/ acquisition of nucleotides/ other
  • 2.5.3. Metabolism of signalling nucleotides
  • 2.5.4. Nucleotide metabolism/ other
• 2.6. Additional metabolic pathways
  • 2.6.1. Biosynthesis of cell wall components
    • 2.6.1.1. Biosynthesis of peptidoglycan
    • 2.6.1.2. Biosynthesis of lipoteichoic acid
    • 2.6.1.3. Biosynthesis of teichoic acid
    • 2.6.1.4. Biosynthesis of teichuronic acid
  • 2.6.2. Biosynthesis of cofactors
    • 2.6.2.1. Biosynthesis/ acquisition of biotin
    • 2.6.2.2. Biosynthesis/ acquisition of riboflavin/ FAD
    • 2.6.2.3. Biosynthesis/ acquisition of thiamine
    • 2.6.2.4. Biosynthesis of coenzyme A
    • 2.6.2.5. Biosynthesis of folate
    • 2.6.2.6. Biosynthesis of heme/ siroheme
    • 2.6.2.7. Biosynthesis of lipoic acid
    • 2.6.2.8. Biosynthesis of menaquinone
    • 2.6.2.9. Biosynthesis of molybdopterin
    • 2.6.2.10. Biosynthesis of NAD(P)
    • 2.6.2.11. Biosynthesis of pyridoxal phosphate
  • 2.6.3. Phosphate metabolism
  • 2.6.4. Sulfur metabolism
  • 2.6.5. Iron metabolism
    • 2.6.5.1. Acquisition of iron
    • 2.6.5.2. Biosynthesis of iron-sulfur clusters
  • 2.6.6. Miscellaneous metabolic pathways
    • 2.6.6.1. Biosynthesis of antibacterial compounds
    • 2.6.6.2. Biosynthesis of bacillithiol
    • 2.6.6.3. Biosynthesis of dipicolinate
    • 2.6.6.4. Biosynthesis of glycine betaine
    • 2.6.6.5. Biosynthesis of glycogen
    • 2.6.6.6. Metabolism of polyamines

Models of metabolism

Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations.
Genome Biol: 2009, 10(6);R69
[PubMed:19555510] [WorldCat.org] [DOI] (I p)

Anne Goelzer, Fadia Bekkal Brikci, Isabelle Martin-Verstraete, Philippe Noirot, Philippe Bessières, Stéphane Aymerich, Vincent Fromion
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis.
BMC Syst Biol: 2008, 2;20
[PubMed:18302748] [WorldCat.org] [DOI] (I e)

You-Kwan Oh, Bernhard O Palsson, Sung M Park, Christophe H Schilling, Radhakrishnan Mahadevan
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.
J Biol Chem: 2007, 282(39);28791-28799
[PubMed:17573341] [WorldCat.org] [DOI] (P p)

Metabolic flux analyses

Roelco J Kleijn, Joerg M Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich, Uwe Sauer
Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis.
J Biol Chem: 2010, 285(3);1587-96
[PubMed:19917605] [WorldCat.org] [DOI] (I p)

Minimal genome projects

Yusuke Azuma, Motonori Ota
An evaluation of minimal cellular functions to sustain a bacterial cell.
BMC Syst Biol: 2009, 3;111
[PubMed:19943949] [WorldCat.org] [DOI] (I e)