Note_Biomass – Biomass

WID Note_Biomass
Name Biomass
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].
  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:

  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:

  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:

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

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