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Table 1 The biomass composition and general growth parameters of the M. buryatense 5G(B1) cells

From: Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)

Compound % SD mmol/g DCW biomass Organism source References
Amino acids 54.8 3.1   M. buryatense 5GB1  
 Alanine    0.446   This study
 Arginine    0.202   This study
 Asparagine    0.119   This study
 Aspartate    0.348   This study
 Cysteine    0.03   This study
 Glutamate    0.396   This study
 Glutamine    0.15   This study
 Histidine    0.088   This study
 Glycine    0.443   This study
 Isoleucine    0.256   This study
 Leucine    0.26   This study
 Lysine    0.25   This study
 Methionine    0.12   This study
 Phenylalanine    0.196   This study
 Proline    0.195   This study
 Serine    0.23   This study
 Threonine    0.26   This study
 Tryptophan    0.072   This study
 Tyrosine    0.14   This study
 Valine    0.341   This study
Ectoine 0.38 0.1 0.027 M. buryatense 5G [23, 24]
Lipids
 FAME 10.9 0.56   M. buryatense 5GB1 This study
  C14 (myristate)    0.016   This study
  C15 (pentadecylic acid)    0.002   This study
  C16 (palmitate)    0.307   This study
  C18 (stearate)    0.001   This study
 Phospholipids     M. buryatense 5G Recalculated from [23]
  Phosphatidylserine*    0.014   [23]
  Phosphatidylethanolamine*    0.122   [23]
  Dipalmitoyl phosphatidate*    0.007   [23]
  Phosphatidylglycerol*    0.031   [23]
 Sterols 0.08 0.08 M. buryatense 5GB1 This study
  squalene    0.04   
  lanosterol    0.04   
Intracellular metabolites 1.5    
Ribulose-5-phosphate/ribose-5-phosphate   0.001 M. alcaliphilum 20Z [42]
Fructose-1, 6-bisphosphate    0.001 M. alcaliphilum 20Z [42]
Fructose-6-phosphate    0.003 M. alcaliphilum 20Z [42]
Glucose-6-phosphate    0.002 M. alcaliphilum 20Z [42]
Glyceraldehyde-3-phosphate/dihydroxyacetone   0.003 M. alcaliphilum 20Z [42]
6-Phosphogluconic acid    0.00015 M. alcaliphilum 20Z [42]
2-Dehydro-3-deoxy-phosphogluconate    0.000003 M. alcaliphilum 20Z [42]
Phosphoglycerate    0.006 M. alcaliphilum 20Z [42]
Phosphoenolpyruvate    0.005 M. alcaliphilum 20Z [42]
Pyruvate    0.015 M. alcaliphilum 20Z [42]
Acetyl-CoA    0.0001 M. alcaliphilum 20Z [42]
Succinate    0.002 M. alcaliphilum 20Z [42]
Malate    0.004 M. alcaliphilum 20Z [42]
Fumarate    0.001 M. alcaliphilum 20Z [42]
Citrate    0.001 M. alcaliphilum 20Z [42]
Glycerate    0.001 M. alcaliphilum 20Z [42]
 ATP    0.005 Methylomonas methanica [43, 44]
 ADP    0.002 M. extorquens AM1 [16]
 AMP    0.001 M. extorquens AM1 [16]
 NAD    0.002 M. extorquens AM1 [16]
 NADH    0.002 M. extorquens AM1 [16]
 NADP    0.001 M. extorquens AM1 [16]
 NADPH    0.001 M. extorquens AM1 [16]
 polyP (PPi)    0.029 Methylomonas methanica [43, 44]
Cofactors
 Cytochrome c    0.00036 M. alcaliphilum 20Z [37]
 B12    0.00000006 M. alcaliphilum 20Z [41]
 Ubiquinol-8    0.00022 Assumption [16]
 Protoheme    0.00022 Assumption [16]
 coenzyme-A    0.00022 Assumption [16]
 FMN    0.00022 Assumption [16]
 FMNH2    0.00022 Assumption [16]
 FAD    0.00022 Assumption [16]
 SAM    0.00022 Assumption [16]
 Glutathione    0.00022 Assumption [16]
Carbohydrates 3.78 1.56    
 Mannose    0.002 M. alcaliphilum 20Z [24]
 Ramnose    0.0002 M. alcaliphilum 20Z [24]
 Glycogen    0.117 M. buryatense 5GB1 [26]
 Sucrose    0.01 M. alcaliphilum 20Z [45]
 Ribose    0.036 M. alcaliphilum 20Z [24]
 Maltose    0.008 M. alcaliphilum 20Z [24]
 Arabinose    0.022 M. alcaliphilum 20Z [24]
 Galactose    0.005 M. alcaliphilum 20Z [24]
Cell wall 9.127     
 Peptidoglycan   0.053 Escherichia coli [46]
 LPS (lipid IVA and KDO)   0.002 M. buryatense 5GB1 This study
RNA 9.7 3.6   M. buryatense 5GB1 This study
 ATP    0.050   
 UTP    0.050   
 CTP    0.047   
 GTP    0.047   
DNA 4.0 0.28   M. buryatense 5GB1 This study
 dATP    0.0021   
 dTTP    0.0021   
 dCTP    0.0020   
 dGTP    0.0020   
Ash (without P and S data) 5.2 1.03 M. buryatense 5GB1 [27]
 Copper    0.01   
 Magnesium    0.07   
 Iron    0.0059   
 Cobalt    0.001   
 Calcium    0.01   
Biomass (measured) 99.5 10.2    
3-PG 0.5   0.003   
Total 100.0     
Excreted products
 Formate 2.8 0.17 0.6 M. buryatense 5GB1 [27]
 Acetate 0.7 0.02 0.114 M. buryatense 5GB1 [27]
 Lactate 0.4 0.13 0.044 M. buryatense 5GB1 [27]
 EPS 10 4.5   M. buryatense 5GB1 This study
  Glucose    0.0420 M. buryatense 5GB1 This study
  Fucose    0.0075 M. buryatense 5GB1 This study
  Xylose    0.0023 M. buryatense 5GB1 This study
  Inositol    0.0021 M. buryatense 5GB1 This study
  Galactose    0.0588 M. buryatense 5GB1 This study
  Mannose    0.0669 M. buryatense 5GB1 This study
  Ribose    0.0342 M. buryatense 5GB1 This study
  Rhamnose    0.0432 M. buryatense 5GB1 This study
  Glucosamine    0.0415 M. buryatense 5GB1 This study
  Galactosamine    0.0394 M. buryatense 5GB1 This study
  Cysteine    0.0185 M. buryatense 5GB1 This study
  Threonine    0.0375 M. buryatense 5GB1 This study
  Serine    0.0214 M. buryatense 5GB1 This study
  Glutamate    0.0319 M. buryatense 5GB1 This study
  Glycine    0.0830 M. buryatense 5GB1 This study
  Valine    0.0228 M. buryatense 5GB1 This study
  Methionine    0.0066 M. buryatense 5GB1 This study
  Isoleucine    0.0146 M. buryatense 5GB1 This study
  Leucine    0.0169 M. buryatense 5GB1 This study
  Phenylalanine    0.0139 M. buryatense 5GB1 This study
Growth parameters
 Methane uptake (mmol g CDW−1 h−1)    18.46 ± 1.36 M. buryatense 5GB1 [27]
 Oxygen uptake (mmol g CDW−1 h−1)    23.55 ± 1.13 M. buryatense 5GB1 [27]
 O2/CH4 uptake Ratio    1.25 ± 0.05 M. buryatense 5GB1 [27]
 Specific growth rate (h−1)    0.232 ± 0.006 M. buryatense 5GB1 [27]