Difference between revisions of "Metabolism"

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'''A suite of models of ''B. subtilis'' metabolism can by found in [[SubtiPathways|''Subti''Pathways]].'''
 
'''A suite of models of ''B. subtilis'' metabolism can by found in [[SubtiPathways|''Subti''Pathways]].'''
  
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== Metabolic categories ==
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==The major categories==
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2. Metabolism
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1. [[Cellular processes]]<br>
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2. [[Metabolism]]<br>
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3. [[Information processing]]<br>
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4. [[Lifestyles]]<br>
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5. [[Prophages and mobile genetic elements]]<br>
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6. [[Groups of genes]]<br>
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==2. Metabolism==
 
* 2.1. Electron transport and ATP synthesis
 
* 2.1. Electron transport and ATP synthesis
 
** 2.1.1. [[Regulators of electron transport]]
 
** 2.1.1. [[Regulators of electron transport]]

Revision as of 08:08, 16 November 2010

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

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


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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