PombeNet
Goin' fission....

Almanac of fission yeast

Useful facts and figures, including ade6 alleles, restriction sites, and codon usage.
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Cell size and growth
Doubling time Depends on media: typically 2 to 5 hours
haploid cell 12-15 µm at division, 3 - 4 µm width - constant
diploid cell 20 - 25 µm length at division, 4 - 5 µm width - constant
1 - 2 x 109 cells (haploid) 0.5 g wet weight


Average Values for Haploid
2C DNA content 33.8 fg per cell
RNA content 3 pg per cell (1 - 2% of which is polyA+)
protein content 210 pg per cell
Size of genome
Total genetic size 2100 centiMorgan
Total physical size 13.8 Megabase (Mb)
Number of chromosomes 3
Chromosome I 5.7 Mb
Chromosome II 4.6 Mb
Chromosome III 3.5 Mb
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Just where are all those ade6 alleles anyway?

There are numerous ade6 alleles used for various reasons in various strains, which gets confusing for everyone. Here is a guide to some of them. We would like to be inclusive, so please send us references and info for any other alleles you know about! Enormous thanks to Juerg Kohli, who corrected what we had and provided much more. Also, thanks to John Armstrong, Ramsey MacFarlane, Greg Freyer, Jun Gao, Dan Pankratz and Katja Ludin for providing additional information.
Alleles of ade6+
allelent
(if A of ATG is 1)
aacommentsReferences
M26G135TG46 to stopdark pink on low ade. UGA codon, can suppress with sup3/9/12. Hyper-rec. Adjacent codon to M375 Szankasi et al 1988
51C1266TH423Y   Schär et al 1993
52T955CL319S Pale pink on low ade. Will complement with M210 (D. Pankratz). Schär et al 1993
149C1180TS394L  Schär and Kohli 1993
M210C1466T P489L dark pink on low ade. Will complement with M216. Although most agree on this mutation, Greg Freyer reports his as a G1470A lesion, making a G491S mutation. In all cases, it destroys the Xho site. Macfarlane and Wahls labs
M216G46AG16Dpale pink on low ade. Will complement with M210 and 149 Szankasi et al 1988
M375G132TG45 to stopdark pink on low ade. UGA codon; suppressed by sup3/9/12 Adjacent codon to M26. Szankasi et al 1988
M387G1270CR424P G to C marker effect Schär et al 1993
406G2AM1I  Schär and Kohli 1993
421G1176A        G393S   Schär and Kohli 1993
424C1261TS421L   Schär and Kohli 1993
424T1222-TFrameshift  Schär and Kohli 1993
469
=L469
C1468TR490 to stop dark pink on low ade. UGA codon; Can suppress with sup3/9/12. Destroys Xho site Szankasi et al 1988
485C1244GY415 to stop G to C marker effect. UAG codon (not suppressible) Schär and Kohli 1993
555C124T ?  Ludin, MS thesis
687T341 +TFrameshift (114)  Schär and Kohli 1993
704T645AC215 to stop v. dark pink on low ade. Can suppress with sup3. (Note conflict: reported by Schär and Kohli 1993 as C845A?; C282 to stop. It is possible there are two different UGA nonsense alleles both suppressible by sup3-5, and both are called 704) Park JM, Intine RV, Maraia RJ. Gene Expr. 2007;14(2):71-81.
706C48TR51 to stopv. dark pink on low ade. UGA codon. Can suppress with sup3/9/12. Grimm et al, 1994
A1943G1068AG357R   Schär and Kohli 1993
T1994C1119TQ374 to stop UAG codon Schär and Kohli 1993
A2097T1222AL408 to stop UAA codon Schär and Kohli 1993
A2196T1321AL441 to stop UAG codon Schär and Kohli 1993
A2244T1369AM487K   Schär and Kohli 1993
T2291G1416TG473 to stop UGA codon Schär and Kohli 1993
N/Ninternal deletion  v. dark pink on low ade. Minigene.?

Other mutant alleles

allelent
(if A of ATG is 1)
aacommentsReferences
his7-366 C868TH290YHaochen Yu, pombelist
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Restriction site usage

This table was generated by A. John Callegari at Sloan Kettering (callegaa AT mskcc.org). Send questions or comments to John.
Enzyme
Restriction site usage in S. pombe genome
Sites in Pombe Genome Random DNA Expect Average fragment size
PvuII 2,142 3,076 5,882
PmlI 684 3,076 18,421
AluI 47,242 49,218 266
RsaI 29,655 49,218 424
BsaBI 3,103 3,076 4060
BsrBI 1,328 3,076 9487
DraI 15,932 3,076 790
EcoRV 4,965 3,076 2537
HpaI 1,801 3,076 6,996
NaeI 365 3,076 34,520
StuI 911 3,076 13,830
AscI 9 192 1,400,000
NotI 13 192 969,230
BamHI 1,460 3,076 8,630
BglII 2,042 3,076 6,170
EcoRI 4,180 3,076 3,014
HindIII 6,457 3,076 1,951
MluI 823 3,076 15,309
PvuI 1,012 3,076 12,450
KpnI 1,165 3,076 10,815


Stats are based on the three chromosomes downloaded from genbank in August, 2006. There are 12.6 megabases in this sequence, suggesting that about 8.7% of the genome is missing (mostly likely repetitive DNA).Therefore, these stats must be viewed as approximations.
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Codon Usage Table

Created with the GCG CODONFREQUENCY program , using 153 fission yeast genes. Three highly expressed genes, fyi1+/spi1+, adh+, and tpi1+, were also compared. Reference: Forsburg, Yeast 10:1045, 1994
Amino
Acid
Triplet
codon
Total
number
per 1000Fraction
(153 genes)
Fraction
(High expr)
Gly GGG281.003.620.070.00
Gly GGA1204.0015.520.290.00
GlyGGT1942.0025.040.470.86
GlyGGC713.009.190.170.14
GluGAG1622.0020.910.330.70
GluGAA3366.0043.400.670.30
AspGAT2979.0038.410.700.49
AspGAC1267.0016.340.300.51
ValGTG607.007.830.120.00
ValGTA913.0011.770.190.01
ValGTT2385.0030.750.490.47
ValGTC979.0012.620.200.51
AlaGCG365.004.710.080.00
AlaGCA1141.0014.710.240.04
AlaGCT2288.0029.500.480.55
AlaGCC1018.0013.130.210.41
ArgAGG356.004.590.090.00
ArgAGA810.0010.440.200.00
SerAGT1012.0013.050.150.03
SerAGC701.009.040.100.03
LysAAG1993.0025.700.400.90
LysAAA2979.0038.410.600.10
AsnAAT2561.0033.020.640.20
AsnAAC1416.0018.260.360.80
MetATG1692.0021.821.001.00
IleATA847.0010.920.180.00
IleATT2845.0036.680.600.55
IleATC1079.0013.910.230.45
ThrACG461.005.940.110.02
ThrACA1036.0013.360.250.00
ThrACT1808.0023.310.430.42
ThrACC909.0011.720.220.56
Amino
Acid
Triplet
codon
Total
number
per 1000Fraction
(153 genes)
Fraction
(High expr)
TrpTGG695.008.961.001.00
EndTGA29.00 0.370.150.00
CysTGT710.009.150.610.18
CysTGC447.005.760.390.82
End TAG47.00 0.610.240.00
EndTAA120.001.550.611.00
TyrTAT1667.0021.490.640.25
TyrTAC957.0012.340.360.75
LeuTTG1865.0024.050.250.32
LeuTTA1942.0025.040.260.10
PheTTT2285.0029.460.700.38
PheTTC966.0012.460.300.63
SerTCG561.007.230.080.03
SerTCA1309.0016.880.190.00
SerTCT2350.0030.300.340.35
SerTCC947.0012.210.140.55
ArgCGG247.003.180.060.00
ArgCGA596.007.680.150.00
ArgCGT1505.0019.410.370.88
ArgCGC502.006.470.130.12
GlnCAG838.0010.810.280.14
GlnCAA2184.0028.160.720.86
HisCAT1257.0016.210.710.41
HisCAC517.006.670.290.59
LeuCTG491.006.330.070.03
LeuCTA599.007.720.080.00
LeuCTT2051.0026.450.270.40
LeuCTC555.007.160.070.15
ProCCG331.004.270.090.00
ProCCA967.0012.470.260.03
ProCCT1734.0022.360.460.56
ProCCC710.009.150.190.42