Note_Biomass – Biomass

Name
WID Note_Biomass
Name Biomass
 
Comments
Comments The biomass composition of M. genitalium was compiled from several sources: The Feist et al E. coli FBA model [PUB_0558] Reviews of the biomass composition of E. coli [PUB_0393, PUB_0395, PUB_0645] The CyberCell database of small and large molecule copy numbers, and in particular metal ions [PUB_0394] Literature on the metal ion content of cells [PUB_0678, PUB_0679, PUB_0680] The Bennett et al metabolome-scale comprehensive measurement of small molecule concentrations in three conditions: glucose, glycerol, acetate [PUB_0392] Measurement of the copper content of cells [PUB_0403] Lipoglycan content of Mycoplasmas [PUB_0658] Membrane composition of E. coli -- PE (74%), PG (19%), CL (3%); lipid/protein weight ratio 0.4 [PUB_0645]. Additional sources: [PUB_0675, PUB_0676, PUB_0677, PUB_0778, PUB_0779].
References
  1. Andrews AJ, Fierke C. Eds Hartmann RK, Bindereif A, Schön A, Westhof E. Handbook of RNA Biochemistry. (2005). WholeCell: PUB_0678, ISBN: 9783527619504, URL: http://www3.interscience.wiley.com/cgi-bin/summary/117904175/SUMMARY

  2. Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 5, 593-9 (2009). WholeCell: PUB_0392, PubMed: 19561621

  3. Cronan JE. Bacterial membrane lipids: where do we stand?. Annu Rev Microbiol 57, 203-24 (2003). WholeCell: PUB_0675, PubMed: 14527277

  4. Feig AL, Uhlenbeck OC. Eds Gesteland RF, Cech TR, Atkins JF. . Cold Spring Harbor Laboratory Press (1999). WholeCell: PUB_0679, ISBN: 9780879697396, URL: http://cshmonographs.org/index.php/monographs/article/viewArticle/5115

  5. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3, 121 (2007). WholeCell: PUB_0558, PubMed: 17593909

  6. ... 10 more

  7. Gennis RB. Biomembranes: molecular structure and function. Springer (1988). WholeCell: PUB_0645, ISBN: 9780387967608

  8. Kurz JC, Fierke CA. The affinity of magnesium binding sites in the Bacillus subtilis RNase P x pre-tRNA complex is enhanced by the protein subunit. Biochemistry 41, 9545-58 (2002). WholeCell: PUB_0680, PubMed: 12135377

  9. McElhaney RN, Tourtellotte ME. Mycoplasma membrane lipids: variations in fatty acid composition. Science 164, 433-4 (1969). WholeCell: PUB_0779, PubMed: 5777213

  10. Mendel RR, Smith AG, Marquet A, Warren MJ. Metal and cofactor insertion. Nat Prod Rep 24, 963-71 (2007). WholeCell: PUB_0403, PubMed: 17898892

  11. Neidhardt FC, Ingraham JL, Schaechter M. Physiology of the Bacterial Cell: A Molecular Approach. Sinauer Associates Inc (1990). WholeCell: PUB_0393, ISBN: 9780878936083

  12. Pirt SJ. . (1975). WholeCell: PUB_0395, None

  13. Rottem S, Razin S. Membrane lipids of Mycoplasma hominis. J Bacteriol 113, 565-71 (1973). WholeCell: PUB_0778, PubMed: 4347923

  14. Smith PF. Lipoglycans from mycoplasmas. Crit Rev Microbiol 11, 157-86 (1984). WholeCell: PUB_0658, PubMed: 6375975

  15. Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res 32, D293-5 (2004). WholeCell: PUB_0394, PubMed: 14681416, URL: http://redpoll.pharmacy.ualberta.ca/CCDB/

  16. Zhang YM, Rock CO. Membrane lipid homeostasis in bacteria. Nat Rev Microbiol 6, 222-33 (2008). WholeCell: PUB_0677, PubMed: 18264115

 
Metadata
Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:57