MyMpn
The Mycoplasma pneumoniae database
e.g Mpn001 or dnaN or polymerase
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COMPARATIVE OMICS
Transcriptome
Methylome
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Genome comparison of M. pneumoniae and M. genitalium
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Mycoplasma Pneumoniae Statistics
Biophysic property/energy cost
M. pneumoniae
E. coli
B.subtilis
L.lactis
cell volume (cytoplasm) in L
6.7 x 10
-17
6.7 x 10
-16
(CCBD)
number of genes
733
4,467 (NCBI)
4,225 (NCBI)
2,425 (NCBI)
number of ORFs
689
4,132 (NCBI)
4,105 (NCBI)
2,321 (NCBI)
protein weight in fg
10*
165 (CCBD)
total number of proteins
~130,000**
3,600,000 (CCBD)
number of ribosomes
~300
6,800 - 72,000 (Bionumbers)
total number of mRNA molecules
~230[Weiner 2003]
4,000 (CCBD)
total number of rRNA molecules (~3/ribosome)
900
18,000 (CCBD)
total number of tRNAs (estimated from
E.coli
)
3,300
200,000 (CCBD)
total number of DNA bases
1,632,788
9,279,350 (NCBI)
8,429,260 (NCBI)
4,731,178 (NCBI)
average length of mRNA molecules in nts
1,000
estimated oxygen solubility in mM
0.2[Duetz 2000]
average translation rate in aas/s.ribosome
15
40 (CCBD);15-21(Bionumbers)
estimated protein half-life in h (based on
E. coli
)
20
20
estimated mRNA half-life in min
6.7
(a)
6.8 (Selinger
et al
, 2003)
5
$
(Hambraeus 2003)
5.8 (Rendon 2005)
1 glucose yields ATPs
2-4
(b)
36-38 (CCBD)
36-38
2-3 (Solem 2007)
energy cost to elongate RNA by 1nt in ATPs
2.4-5.4
#
2.4 (Nielsen, 1997)
energy cost to elongate DNA by 1base in ATPs
6.4
##
3.4
energy cost for making all proteins in ATPs
1.87 x 10
9
(c)
-2.39 x10
9
(d)
energy cost for making mRNA in ATPs
1.24 x 10
7
(c)
-2.86 x 10
7
(d)
energy cost for making rRNA in ATPs
8.94 x 10
6
energy cost for making tRNA in ATPs
1.43 x 10
6
energy cost for making DNA in ATPs
1,04 x 10
7
7.23 x 10
7
(CCBD)
glucose uptake rate in molecules/s
18,900-44,700
(e)
3.3 x 10
5
(Edwards
et al
, 2000)
1.5-3 x 10
7
(Natarajan
et al
, 2000)
energy cost for doubling biomass in ATPs/s
73,140
(c,f,g)
95,570
(d,f,g)
glucose needed in molecules/s
18,290-36,570
(e,c,f,g)
23,890-47,780
(e,d,f,g)
glucose molecules to make 1 cell
4.74-9.48 x 10
8
(e,c,f,g)
6.19-12.4 x 10
8
(e,d,f,g)
1.40 x 10
9
(Bionumbers)
Metabolites
M. pneumoniae
E. coli
B.subtilis
L.lactis
average Fructose-1,6-bisphosphate in mM
0.34 (SD=7.2%)
2.95 (Lowry
et al
1971)
50 (Papagianni 2007)
average Glycerol-3-phosphate in mM
0.19 (SD=16.2%)
0.195 (bionumbers)
36.6 (starvation; Neves 2002)
average Phosphoenolpyruvate in mM
0.11 (SD=0.9%)
2.73 (Lowry
et al
1971)
0.091-0.3 (Bionumbers)
<0.02 (Fry 2000)
11 (Papagianni 2007)
average Glucose-6-phosphate in mM
0.09 (SD=7.1%)
0.04956 (Lowry
et al
1971)
0.801 (Bionumbers)
<0.1 (Fry 2000)
20 (Papagianni 2007)
average Fructose-6-phosphate in mM
0.08 (SD=1.0%)
23 (Papagianni 2007)
average Ribose-5-phosphate in mM
0.03 (SD=8.2%)
average Dihydroxy-acetone-phosphate in mM
0.10 (SD=50%)
0.203 (bionumbers)
average ATP concentration in mM
4.1[Krebes 1995]
2.6 (bionumbers), 1.3-7.0 (CCBD)
6 (Papagianni 2007)
(a)
Estimated from 32P labeling of RNA and from recovery of RNA levels after heat shock
(b)
acetic fermentation generates 4 ATPs, while lactic fermentation generates 2
(c)
assuming no degradation
(d)
assuming degradation of proteins and mRNA
(e)
depending on the growth phase
(f)
assuming that the energy cost for protein, RNA and DNA synthesis is 90% of the total energy cost
(g)
assuming 8 h cell division time
(*)
Cell Biomass was estimated by measuring protein and DNA concentration along the growth and taking into consideration the size of M. pneumoniae chromosome.
(**)
The total number of protein molecules was estimated from the cell protein biomass (10 fg), by considering an average molecular weight for an amino acid of ~135 dalton, and an average protein length of 345 amino acids.
(#)
RNA synthesis from monophosphate nucleotides requires 2.4 ATPs/nt, while de novo synthesis 3 more ATP.
(##)
DNA synthesis from monophosphate deoxynucleotides requires 3.4 ATPs/b, while de novo synthesis 3 more ATP. Nt: nucleotide, aa: amino acid. SD is the standard deviation of the experimental measurements expressed as percentage of the average value.
Comparison between
Mycoplasma pneumoniae
and some other bacteria
Species
Taxonomy
Genome size (Mb)
ORFs
%G+C
rRNA operons
>ribosomes per cell
Doubling time (hours)
Dimensions (microns)
Cell volume (microns³)
Life style
Culture density (cells/ml)
Escherichia coli
Proteobacteria / Gamma proteobacteria
4.6
4489
50.8
7
7000-50000
0.33
0.8 * 1-3
1.0048
Mutualist / pathogen
10^8
Salmonella typhimurium
Proteobacteria / Gamma proteobacteria
4.85
4423
52
7
?
1.3
1 * 2-3
1.9625
Free living/ pathogen
10^9
Haemophilus influenzae
Proteobacteria / Gamma proteobacteria
1.91
1792
38
6
50000
0.5
0.43
0.04160866
Pathogen
10^10
Pseudomonas aeruginosa
Proteobacteria / Gamma proteobacteria
6.6
5925
66
4
?
1.5
0.5-1.0 * 1-5
1.10390625
Pathogen
10^8
Yersinia pestis
Proteobacteria / Gamma proteobacteria
4.65
4198
47.64
6
?
2
0.7 * 2
0.7693
Pathogen
10^8
Burkholderia pseudomallei
Proteobacteria / Beta Proteobacteria
7.24
6347
68
4
?
1.5-2.3
0.4-0.8 * 2-5
0.9891
Free living/ pathogen
10^8
Caulobacter crescentus
Proteobacteria / Alphaproteobacteria
4.01
3737
67
2
?
1.15
0.7 * 2-3
0.576975
Free living
10^8
Pelagibacter ubique
Proteobacteria / Alphaproteobacteria
1.3
1354
29
1
?
1.6
0.2 * 0.4
0.01256
Free living
10^6
Rickettsia prowazekii
Proteobacteria / Alphaproteobacteria
1.11
834
29
1
1500
10
0.3-0.5 * 0.8-2
0.17584
Pathogen
10^7
Mycobacterium tuberculosis
Actinobacteria / Actinobacteria
4.4
3924
65
1
4000
24
0.4 * 1-2
0.1884
Pathogen
10^8?
Mycobacterium leprae
Actinobacteria / Actinobacteria
3.26
1605 (2720)
57.8
1
5000
336
0.4 * 1-2
0.1884
Pathogen
14*10^7?
Borrelia recurrentis
Spirochaetes / Spriochaetes
1.24
990
27.5
3
20000?
12
0.8 * 1.8
0.90432
Pathogen
?
Staphylococcus aureus
Firmicutes / Cocci
2.8
2900
32.8
5
83000
0.5
1
0.52333333
Pathogen
10^9
Bacillus subtilis
Firmicutes / Bacilli
4.2
4100
43
10
6000
0.4
0.7-0.8 * 2-3
1.10390625
Free living
10^8
Lactococcus lactis
Firmicutes / Bacilli
2.36
2300
35
6
?
0.4-0.8
0.5-1
0.22078125
Free living
10^8
Clostridium botulinum
Firmicutes / Clostridia
3.86
3548
28
8
?
5
0.5-0.8 * 3-8
0.6908
Pathogen
10^8
Mycoplasma penetrans
Firmicutes / Mollicutes
1.36
1038
25
1
?
?
0.3 * 1.4
0.09891
Pathogen
10^8?
Mycoplasma gallisepticum
Firmicutes / Mollicutes
0.99
726
31.45
1
?
2-3
0.5 * 0.7
0.137375
Pathogen
3 * 10^8
Mycoplasma pneumoniae
Firmicutes / Mollicutes
0.81
686
40
1
300
8
0.4 * 0.6
0.07536
Pathogen
10^9
Mycoplasma genitalium
Firmicutes / Mollicutes
0.58
479
31.7
1
?
12
0.3 * 0.5
0.035325
Pathogen
>10^7
Thermus aquaticus
Euryarchaeota / Thermococci
2.08
2306
51
1
?
1
0.5-0.8 * 5-10
2.393622
Free living
10^9
Thermococcus kodakaraensis
Euryarchaeota / Thermococci
2.08
2358
52
1
?
0.9
1-2
1.76625
Free living
10^8
References:
Bionumbers
CCBD
Edwards JS and Palsson BO (2000). The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97:5528-5533.
Krebes, K. A., Dirksen, L. B. and Krause, D. C. (1995). Phosphorylation of Mycoplasma pneumoniae cytadherence-accessory proteins in cell extracts. J Bacteriol 177, 4571-4.
Lowry OH, Carter J, Ward JB, Glaser L (1971). The effect of carbon and nitrogen sources on the level of metabolic intermediates in Escherichia coli. J Biol Chem 246:6511-6521.
Natarajan A and Srienc F (2000). Glucose uptake rates of single E. coli cells grown in glucose-limited chemostat cultures. J Microbiol Methods 42:87-96.
Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C (2003). Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res 13:216-223.