Metabolism

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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
  • 2.2. 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
  • 2.5. Nucleotide metabolism
  • 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)


Reviews

Yasutaro Fujita
Carbon catabolite control of the metabolic network in Bacillus subtilis.
Biosci Biotechnol Biochem: 2009, 73(2);245-59
[PubMed:19202299] [WorldCat.org] [DOI] (I p)

Abraham L Sonenshein
Control of key metabolic intersections in Bacillus subtilis.
Nat Rev Microbiol: 2007, 5(12);917-27
[PubMed:17982469] [WorldCat.org] [DOI] (I p)

Yasutaro Fujita, Hiroshi Matsuoka, Kazutake Hirooka
Regulation of fatty acid metabolism in bacteria.
Mol Microbiol: 2007, 66(4);829-39
[PubMed:17919287] [WorldCat.org] [DOI] (P p)

J Stülke, W Hillen
Regulation of carbon catabolism in Bacillus species.
Annu Rev Microbiol: 2000, 54;849-80
[PubMed:11018147] [WorldCat.org] [DOI] (P p)


Relevant papers on other organisms

Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley M Deacon, John Wooley, Scott A Lesley, Ian A Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik
Three-dimensional structural view of the central metabolic network of Thermotoga maritima.
Science: 2009, 325(5947);1544-9
[PubMed:19762644] [WorldCat.org] [DOI] (I p)

Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen, Joshua D Rabinowitz
Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.
Mol Syst Biol: 2009, 5;302
[PubMed:19690571] [WorldCat.org] [DOI] (I p)

Bryson D Bennett, Elizabeth H Kimball, Melissa Gao, Robin Osterhout, Stephen J Van Dien, Joshua D Rabinowitz
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.
Nat Chem Biol: 2009, 5(8);593-9
[PubMed:19561621] [WorldCat.org] [DOI] (I p)

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