Difference between revisions of "Metabolism"

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==Important original publications==
 
==Important original publications==
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<pubmed>19917605  21531833 22383848 21266987,21998563 24281055 24584250 </pubmed>
  
 
==Minimal genome projects==
 
==Minimal genome projects==

Revision as of 17:15, 4 March 2014

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.

The major categories

1. Cellular processes
2. Metabolism
3. Information processing
4. Lifestyles
5. Prophages and mobile genetic elements
6. Groups of genes

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

Sabine Pérès, Liza Felicori, Franck Molina
Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation.
PLoS One: 2013, 8(10);e76143
[PubMed:24204596] [WorldCat.org] [DOI] (I e)

Naama Tepper, Tomer Shlomi
An integrated computational approach for metabolic flux analysis coupled with inference of tandem-MS collisional fragments.
Bioinformatics: 2013, 29(23);3045-52
[PubMed:24123514] [WorldCat.org] [DOI] (I p)

Lope A Flórez, Katrin Gunka, Rafael Polanía, Stefan Tholen, Jörg Stülke
SPABBATS: A pathway-discovery method based on Boolean satisfiability that facilitates the characterization of suppressor mutants.
BMC Syst Biol: 2011, 5;5
[PubMed:21219666] [WorldCat.org] [DOI] (I e)

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)


Important original publications


Minimal genome projects


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

Additional publications: PubMed

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