Useful facts and figures, including ade6 alleles, restriction sites, and codon usage.

 

Cell Size & 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

Size of Genome

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

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

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+

allele nt
(if A of ATG is 1) aa comments References
M26 G135T G46 to stop dark pink on low ade. UGA codon, can suppress with sup3/9/12. Hyper-rec. Adjacent codon to M375 Szankasi et al 1988
51 C1266T H423Y Schär et al 1993
52 T955C L319S Pale pink on low ade. Will complement with M210 (D. Pankratz). Schär et al 1993
149 C1180T S394L Schär and Kohli 1993
M210 C1466T 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
M216 G46A G16D pale pink on low ade. Will complement with M210 and 149 Szankasi et al 1988
M375 G132T G45 to stop dark pink on low ade. UGA codon; suppressed by sup3/9/12 Adjacent codon to M26. Szankasi et al 1988
M387 G1270C R424P G to C marker effect Schär et al 1993
406 G2A M1I Schär and Kohli 1993
421 G1176A G393S Schär and Kohli 1993
424 C1261T S421L Schär and Kohli 1993
424 T1222-T Frameshift Schär and Kohli 1993
469
=L469 C1468T R490 to stop dark pink on low ade. UGA codon; Can suppress with sup3/9/12. Destroys Xho site Szankasi et al 1988
485 C1244G Y415 to stop G to C marker effect. UAG codon (not suppressible) Schär and Kohli 1993
555 C124T ? Ludin, MS thesis
687 T341 +T Frameshift (114) Schär and Kohli 1993
704 T645A C215 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.
706 C48T R51 to stop v. dark pink on low ade. UGA codon. Can suppress with sup3/9/12. Grimm et al, 1994
A1943 G1068A G357R Schär and Kohli 1993
T1994 C1119T Q374 to stop UAG codon Schär and Kohli 1993
A2097 T1222A L408 to stop UAA codon Schär and Kohli 1993
A2196 T1321A L441 to stop UAG codon Schär and Kohli 1993
A2244 T1369A M487K Schär and Kohli 1993
T2291 G1416T G473 to stop UGA codon Schär and Kohli 1993
N/N internal deletion v. dark pink on low ade. Minigene. ?

Other Mutant Alleles

allele nt
(if A of ATG is 1) aa comments References
his7-366 C868T H290Y Haochen Yu, pombelist

 

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.

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 1000 Fraction (153 genes) Fraction (High expr)
Gly GGG 281.00 3.62 0.07 0.00
Gly GGA 1204.00 15.52 0.29 0.00
Gly GGT 1942.00 25.04 0.47 0.86
Gly GGC 713.00 9.19 0.17 0.14
Glu GAG 1622.00 20.91 0.33 0.70
Glu GAA 3366.00 43.40 0.67 0.30
Asp GAT 2979.00 38.41 0.70 0.49
Asp GAC 1267.00 16.34 0.30 0.51
Val GTG 607.00 7.83 0.12 0.00
Val GTA 913.00 11.77 0.19 0.01
Val GTT 2385.00 30.75 0.49 0.47
Val GTC 979.00 12.62 0.20 0.51
Ala GCG 365.00 4.71 0.08 0.00
Ala GCA 1141.00 14.71 0.24 0.04
Ala GCT 2288.00 29.50 0.48 0.55
Ala GCC 1018.00 13.13 0.21 0.41
Arg AGG 356.00 4.59 0.09 0.00
Arg AGA 810.00 10.44 0.20 0.00
Ser AGT 1012.00 13.05 0.15 0.03
Ser AGC 701.00 9.04 0.10 0.03
Lys AAG 1993.00 25.70 0.40 0.90
Lys AAA 2979.00 38.41 0.60 0.10
Asn AAT 2561.00 33.02 0.64 0.20
Asn AAC 1416.00 18.26 0.36 0.80
Met ATG 1692.00 21.82 1.00 1.00
Ile ATA 847.00 10.92 0.18 0.00
Ile ATT 2845.00 36.68 0.60 0.55
Ile ATC 1079.00 13.91 0.23 0.45
Thr ACG 461.00 5.94 0.11 0.02
Thr ACA 1036.00 13.36 0.25 0.00
Thr ACT 1808.00 23.31 0.43 0.42
Thr ACC 909.00 11.72 0.22 0.56

 

Amino Acid Triplet codon Total number per 1000 Fraction (153 genes) Fraction (High expr)
Trp TGG 695.00 8.96 1.00 1.00
End TGA 29.00 0.37 0.15 0.00
Cys TGT 710.00 9.15 0.61 0.18
Cys TGC 447.00 5.76 0.39 0.82
End TAG 47.00 0.61 0.24 0.00
End TAA 120.00 1.55 0.61 1.00
Tyr TAT 1667.00 21.49 0.64 0.25
Tyr TAC 957.00 12.34 0.36 0.75
Leu TTG 1865.00 24.05 0.25 0.32
Leu TTA 1942.00 25.04 0.26 0.10
Phe TTT 2285.00 29.46 0.70 0.38
Phe TTC 966.00 12.46 0.30 0.63
Ser TCG 561.00 7.23 0.08 0.03
Ser TCA 1309.00 16.88 0.19 0.00
Ser TCT 2350.00 30.30 0.34 0.35
Ser TCC 947.00 12.21 0.14 0.55
Arg CGG 247.00 3.18 0.06 0.00
Arg CGA 596.00 7.68 0.15 0.00
Arg CGT 1505.00 19.41 0.37 0.88
Arg CGC 502.00 6.47 0.13 0.12
Gln CAG 838.00 10.81 0.28 0.14
Gln CAA 2184.00 28.16 0.72 0.86
His CAT 1257.00 16.21 0.71 0.41
His CAC 517.00 6.67 0.29 0.59
Leu CTG 491.00 6.33 0.07 0.03
Leu CTA 599.00 7.72 0.08 0.00
Leu CTT 2051.00 26.45 0.27 0.40
Leu CTC 555.00 7.16 0.07 0.15
Pro CCG 331.00 4.27 0.09 0.00
Pro CCA 967.00 12.47 0.26 0.03
Pro CCT 1734.00 22.36 0.46 0.56
Pro CCC 710.00 9.15 0.19 0.42