Difference between revisions of "Metabolism"

From SubtiWiki
Jump to: navigation, search
(→‎Important original publications)
 
(17 intermediate revisions by 2 users not shown)
Line 2: Line 2:
  
 
'''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]].'''
 +
 +
==The major [[categories]]==
 +
 +
1. [[Cellular processes]]<br>
 +
2. [[Metabolism]]<br>
 +
3. [[Information processing]]<br>
 +
4. [[Lifestyles]]<br>
 +
5. [[Prophages and mobile genetic elements]]<br>
 +
6. [[Groups of genes]]<br>
 +
 +
==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==
 
==Models of metabolism==
−
<pubmed> 19555510 17573341 </pubmed>
+
<pubmed> 19555510 17573341 18302748 21219666 24204596 24123514 </pubmed>
 +
 
 +
==Important original publications==
 +
<pubmed>19917605  21531833 22383848 21266987,21998563 24281055 24584250 24727859 </pubmed>
  
−
==Metabolic flux analyses==
+
==Minimal genome projects==
−
<pubmed>19917605  </pubmed>
+
<pubmed>19943949 </pubmed>
  
 
==Reviews==
 
==Reviews==
Line 13: Line 148:
  
 
==Relevant papers on other organisms==
 
==Relevant papers on other organisms==
−
<pubmed> 19762644 19561621  19690571 </pubmed>
+
'''Additional publications:''' {{PubMed|19762644}}
 +
<pubmed> 19561621  19690571 22538926</pubmed>

Latest revision as of 07:05, 15 April 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

Hanna Meyer, Hendrikje Weidmann, Ulrike Mäder, Michael Hecker, Uwe Völker, Michael Lalk
A time resolved metabolomics study: the influence of different carbon sources during growth and starvation of Bacillus subtilis.
Mol Biosyst: 2014, 10(7);1812-23
[PubMed:24727859] [WorldCat.org] [DOI] (I p)

Victor Chubukov, Uwe Sauer
Environmental dependence of stationary-phase metabolism in Bacillus subtilis and Escherichia coli.
Appl Environ Microbiol: 2014, 80(9);2901-9
[PubMed:24584250] [WorldCat.org] [DOI] (I p)

Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich, Jörg Stelling, Uwe Sauer
Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis.
Mol Syst Biol: 2013, 9;709
[PubMed:24281055] [WorldCat.org] [DOI] (I e)

Joerg Martin Buescher, Wolfram Liebermeister, Matthieu Jules, Markus Uhr, Jan Muntel, Eric Botella, Bernd Hessling, Roelco Jacobus Kleijn, Ludovic Le Chat, François Lecointe, Ulrike Mäder, Pierre Nicolas, Sjouke Piersma, Frank Rügheimer, Dörte Becher, Philippe Bessieres, Elena Bidnenko, Emma L Denham, Etienne Dervyn, Kevin M Devine, Geoff Doherty, Samuel Drulhe, Liza Felicori, Mark J Fogg, Anne Goelzer, Annette Hansen, Colin R Harwood, Michael Hecker, Sebastian Hubner, Claus Hultschig, Hanne Jarmer, Edda Klipp, Aurélie Leduc, Peter Lewis, Frank Molina, Philippe Noirot, Sabine Peres, Nathalie Pigeonneau, Susanne Pohl, Simon Rasmussen, Bernd Rinn, Marc Schaffer, Julian Schnidder, Benno Schwikowski, Jan Maarten Van Dijl, Patrick Veiga, Sean Walsh, Anthony J Wilkinson, Jörg Stelling, Stéphane Aymerich, Uwe Sauer
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.
Science: 2012, 335(6072);1099-103
[PubMed:22383848] [WorldCat.org] [DOI] (I p)

Arren Bar-Even, Elad Noor, Avi Flamholz, Joerg M Buescher, Ron Milo
Hydrophobicity and charge shape cellular metabolite concentrations.
PLoS Comput Biol: 2011, 7(10);e1002166
[PubMed:21998563] [WorldCat.org] [DOI] (I p)

Heather Maughan, Wayne L Nicholson
Increased fitness and alteration of metabolic pathways during Bacillus subtilis evolution in the laboratory.
Appl Environ Microbiol: 2011, 77(12);4105-18
[PubMed:21531833] [WorldCat.org] [DOI] (I p)

Andreas Otto, Jörg Bernhardt, Hanna Meyer, Marc Schaffer, Florian-A Herbst, Juliane Siebourg, Ulrike Mäder, Michael Lalk, Michael Hecker, Dörte Becher
Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis.
Nat Commun: 2010, 1;137
[PubMed:21266987] [WorldCat.org] [DOI] (I p)

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

Additional publications: PubMed

Douglas W Raiford, Esley M Heizer, Robert V Miller, Travis E Doom, Michael L Raymer, Dan E Krane
Metabolic and translational efficiency in microbial organisms.
J Mol Evol: 2012, 74(3-4);206-16
[PubMed:22538926] [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)

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Metabolism&oldid=202996"