DOI: 10.1038/ncomms3235
1 Instituto
Gulbenkian de Ciencia, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal. Correspondence and requests for materials should be addressed to
M.G.F. (email: mgferreira@igc.gulbenkian.pt).
ARTICLE
ARTICLE
Band
A/B
C
D
E
F
Chr. Size
(Mb)
5.7
I
4.6
II
III
SPW23
R435
R418
A1263
A1153
A826
A571
NCYC132
Size
(Mb)
3.50/2.00
1.53
1.20
1.01
0.90
L972
ATCC2476
SPW23
R435
R418
A1263
A1153
A826
A571
NCYC132
L972
ATCC2476
G
0.63
H/I/J 0.60/0.53/0.50
K/L
0.47/0.38
M
0.24
N
0.18
0.14
O
3.5
L O
J
M
P
N
D
H
F
K
E
I
Chr. I
ATCC2476
L972
NCYC132
A826
A1153
A1263
A571
R418
R435
SPW23
A
G
QC
II
III
Europe
L972
Africa
NCYC132
America
A826
A1263
A1153
R435
L972
964%
NCYC132
12%
879%
A826
45%
148%
579%
A1263
56%
258%
5013%
7211%
A1153
34%
208%
598%
637%
826%
R435
00%
139%
4011%
5110%
768%
858%
SPW23
106%
4313%
7310%
7211%
629%
7410%
SPW23
896%
Figure 1 | Chromosomal analysis of natural isolates of S. pombe. (a) Whole-chromosome PFGE analysis of S. pombe chromosomes. L972 reference strain
contains three chromosomes: Chr. I 5.7 Mb, Chr. II 4.6 Mb and Chr. III 3.5 Mb. (b) PFGE of chromosomal DNA digested with NotI reveals different restriction
patterns for each strain. The differences are not due to NotI polymorphisms, as all 13 are present and recognized by NotI enzyme (Supplementary Fig. S1).
(c) Localization of NotI restriction sites in reference strain L972. (d) Schematic representation of the three chromosomes in the different strains. Only
the minimal CRs detected are represented (see Supplementary Figs S2 and S3). These were mapped using chromosome-specic probes present at different
positions, including the centromere-specic region imrL (imrL1, imrL2 and imrL3). Symbols in A1153, A1263 and A826 represent other not fully
characterized CRs. (e) Meiotic viability of natural isolates. Each cross represents the analysis of 1443 tetrads (containing the four meiotic products).
Intervals correspond to 2 s.e. for a binomial distribution.
S. octosporus
S. cryophilus
S. japonicus
0.0005 (0.0001)
0.0531 (0.0416)
0.0548 (0.0429)
0.0622 (0.0487)
cen2
(intergenic
region)
0.0068 (0.0037)
n.s.
n.s.
n.s.
cox1
(mitochondrial
gene)
0.0145 (0.0100)
0.0572 (0.0351)
0.0585 (0.0361)
0.0660 (0.0412)
p is the average number of nucleotide differences per site between two sequences. s.d. is shown
in parentheses.
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Inv1
Inv2
T3
T4
T5
T6
T7
T8
T9
T10
Inv1
Inv2
T3
T4
Offspring viability
100%
T5
Parental
500 kb
75%
50%
25%
0%
T6
T7
T8
T9
PP
T10
Inv2
T3
T4
T5
T6
T8
PR
RR
T9
Recombinant offsrping
100%
75%
arg7 +
50%
mat1 +
lys4 +
25%
Chr II
0%
lys4
arg7 arg7
lys4
lys4
PP
arg7
arg7
lys4
PR
Figure 2 | Genetically engineered CRs reduce meiotic tness. (a) Schematic representation of karyotypes for 10 different genetically engineered S. pombe
strains. All the strains are isogenic except for the rearrangement and its breakpoint. Chromosomes are drawn to scale. Inexions represent the
centromeres. To generate the CR strains, Cre recombinase was expressed in parental strains using a plasmid and selecting for two colonies, each
representing a totally independent recombination event. (b) Meiotic viability of homozygotic and heterozygotic crosses. CRs reduce meiotic viability in
heterozygotic crosses from 8 to 48% with the exception of T8 that exhibits no apparent reduction. Meiotic viability corresponds to the number of viable
haploid spores that have formed a colony divided by the total number of spores. Each cross represents the analysis of 1863 tetrads. Error bars represent
2 s.e. for a binomial distribution. Pparental strain; Rrearranged strain. (c) Frequency of recombination between loci at the breakpoints and
the mat1 locus. Inversions suppress recombination between any of the breakpoints and the mat1 locus by B30%. In contrast, translocations do not
signicantly reduce recombination frequency. Only rearrangements involving chromosome II were scored. Error bars correspond to 2 s.e. for a binomial
distribution.
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a
YES
YES 3% EtOH
15%
***
***
10%
***
5%
0%
5%
Mitosis No mating
***
***
***
***
***
***
GFP
20%
***
**
**
Versus
Mating
Control - GFP
Meiosis
Rearrangement
No mating
With mating
10%
***
15%
20%
Inv1
YES
Inv2
pH 3
T3
T4
HU
MBC
5g l1 7 mM
T5
T6
YES
Caff
malt 10 mM
T7
YES
raff
***
T8
T9
T10
EMM
YES
36C
glu 3% EtOH
Inv1
Inv2
T3
T4
T5
T6
T7
T8
T9
T10
Frequency of karyotype
YES
0
0
0
10
10
0
15
0
Time (generations)
Control - GFP
10
15
YES +
3% EtOH
0
1
15
10
15
Rearrangement
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Chr. I (kb)
5.6
5.6
5.6
5.4
5.6
5.3
4.6
7.0
5.6
6.1
6.1
Chr. II (kb)
4.5
4.5
4.5
4.7
5.4
4.8
5.5
4.5
6.0
4.0
4.5
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Kanr
Inv1
Parental
ura4 +
kan r
padh1
T5
Parental
padh1
+Cre
kan r
ura4 +
Parental
T6
Parental
Rearrangement
T7
Parental
0 mg l1
100 mg l1
200 mg l1
400 mg l1
T5
T5
SPCC
777.12c +
SPAC
2F7.02c +
mrpl16 +
rrp12 +
bit61 +
bit61 +
SPAC
2F7.02c +
SPCC
777.12c +
SPAC
227.17c +
Parental
NS
0.1
cta1
pcr1 +
10
rec
0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30
pcr1+
ntp1+
cta1+
hsp9 +
SPAB1539.07c +
hsp9 +
*
mRNA levels (a.u.)
hsp9
T7
0.001
dak2+
adh4 +
dak2 +
pcr1+
+
cta1 +
0.01
ntp1 +
SPAC13A11.06 +
zwf1+
cta1 +
T5
0.1
C
1
2c
AC
PA + bit6
SP
7.1
+ S
77
c
7c
2
C
1
0
.
C
7
7.
22
SP
2F
12
rrp
0.0001
6
pl1
mr
ntp1+
pcr1+
SPBC1539.07c +
SPBC1539.07c +
hsp9 +
NS
T7
dak2 +
adh4 +
SPAC13A11.06 +
zwf1+
NS
T5
ntp1+
NS
0.0001
T7
SPAC13A11.06 +
zwf1 +
NS
0.001
t7
dak2 +
adh4 +
NS
0.01
cu
Parental
T7
NS
P
SPAC
227.17c +
cut7 +
rec10 +
mrpl16 +
rec10 +
cut7 +
rrp12 +
SPAC
13A11.06 +
**
1
0.1
0.01
0.001
0.0001
0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30 0 15 30
+
+
dak2 + pcr1
ntp1+
cta1+
hsp9 + SPAC
13A11.06 +
Figure 5 | Mitotic tness of CRs varies in different environments. (a) Cre-loxP recombination scheme. Recombination between the promoter construct
(padh1-loxP-kanMX6) and the gene construct (loxP-ura4-kanMX6) results in the formation of the rearrangement and ura4 expression. Black and
grey boxes represent loxP sequences and circles indicate centromeres. (b) T5 and T7 have lower expression of the antibiotic resistance gene Kanr inserted
near the breakpoint. Serial dilutions were spotted on plates containing 0, 100, 200 and 400 mg l 1 of geneticin and allowed to grow for 4 days at 32 C.
(c) Schematic representation of genes near the breakpoints in the parental strain and their localization in T5 and T7. (d) CRs cause changes to expression
of genes near breakpoints. mRNA levels relative to controls near the breakpoint. Gene expression was assayed in cells that have grown in rich media (YES).
Error bars represent s.e. of three to six independent experiments. (*Po0.05 according to MannWhitney U-test). (e) Schematic representation of genes
involved in responses to general stress in S. pombe45 and to ethanol stress in S. cerevisiae44 in the parental strain and in T5 and T7. (f) Rearrangements
cause changes in gene expression. T5 has lower gene expression upon exposure to 3% EtOH, whereas T7 is higher even before ethanol exposure. Genes
are displayed by no particular order. Error bars represent s.e. of three to six independent experiments. Error bars represent s.e. (*Po0.05, **Po0.01
according to MannWhitney U-test). In applying the very conservative Bonferoni correction, there is not enough power to detect statistical signicance
in our gene expression studies.
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types. Strains were selected based on the simultaneous presence of padh1-loxPkanMX6 and loxP-ura4-kanMX6 fragment after PCR amplication. These strains
are referred to as parental strains. For generation of rearranged strains, parental
strains were transformed with pREP81-Cre or pREP81 plasmids and plated directly
in selective media EMMleu with 4 mM thiamine. Single colonies were inoculated
overnight in liquid media EMMleu and plated in EMMura 18/20 h after for
selection of the recombination event. Single colonies were then re-streaked into
EMMura and then to YES and genotyped. We selected two colonies, each
representing a totally independent recombination event. All the strains were frozen
immediately as soon as the genotype was conrmed. Cells were exposed to the
minimum possible time to the Cre recombinase, by promoting the loss of the
pREP81Cre plasmid straight after the recombination event. As parental strains are
ura4 and CRs are ura4 , we obtained equivalent strains ura4 (termed Parental
ura4 strains) to use in competition assays. To generate these strains, the same
parental cells that were used for pREP81-Cre transformation were crossed with
strain L972 or another prototrophic strain. GFP tagged cells were created by
insertion of 3nmt1-GFP-hphMX6 fragment60 near the breakpoint loci
(Supplementary Table S1).
Competitive tness assays. To measure the tness effects of CRs, we developed a
FACS-based competitive assay. Unlabelled CR strain and Parental ura4 strain
were independently competed against its reference GFP-labelled strain (ControlGFP, Supplementary Fig. S2). To do so, both CR and control strain were grown in
YES liquid medium for 24 h at 32 C with aeration and shaking. The following day
cultures were diluted and, once in mid-exponential phase, mixed at 1:1 ratios with
the uorescently labelled control strain with total initial cell density in the order of
2 105 cells per ml. The effective ratio of the mixture was measured using FACS.
Then, 600 ml of the mix was placed in a 96-deep-well plate and incubated in a minishaker (VWR) at 32 C with 850 r.p.m. agitation. Unless otherwise stated, cells were
grown at 32 C. Every 24 h cells were diluted 1:30 to fresh media. This was repeated
three times. After 4 days (B20 generations), nal ratios of unlabelled to GFPlabelled strain were measured. The number of GFP-positive (reference) and nonuorescent (experimental) cells was determined using a Cyan ADP Cell Analyzer
(Beckman Coulter, Inc.) counting 10,000 total cells for each sample. Selection
coefcients (DS) were calculated as:
1
ratio t0
frequency of unlabeled strain
DS ln
where ratio
2
ratio tf
t
frequency of labeled strain
with t0 the initial time (zero generations) and tf the nal time (20 generations). In
order to obtain the selection coefcient of the rearrangement, we extracted the
weight of the GFP, such that the nal selection coefcient is given by:
DS Rearrangement DS Unlabelled CR versus Control-GFP DS Unlabelled Control versus Control-GFP 3
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Growth assays. Strains were grown overnight in YES in a volume of 600 ml per
well in 96-deep-well plates. The following day, cells were diluted 1:30 to the
appropriate media and time points were recorded approximately every 2 h. Cell OD
was measured in a nal volume of 100 ml in 96-well at bottom at 600 nm in
Victor III apparatus (Perkin Elmer).
Viability assays. Drug sensitivity analysis was performed as described55. Briey,
exponentially growing cells in YES media were collected and counted. Five-fold
serial dilutions from a starting concentration of 1 107 cells per ml are prepared
and 5-ml spots of the serial dilutions are spotted into the specic media containing
agar plate.
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Author contributions
Acknowledgements
Additional information
This interdisciplinary work reects the scientic environment of the Instituto Gulbenkian de Ciencia (IGC). We thank M. Molnar and N. Kleckner (Harvard University) for
generously providing the Cre-loxP strains, the Portuguese Yeast Culture Collection and
CA Rosa (UF Minas Gerais) for the natural isolate strains, B. Arcangioli (I Pasteur) for
advices on disruption of switchable mating-type, J. Mata (University of Cambridge) for
technical assistance with RNA purication and gene expression analysis, P. Duarte and
S. Rosa (IGC) for technical assistance, M. Carneiro (IGC) for assistance with qRT-PCR,
R, Gardner and T. Lopes (IGC) for technical support with ow cytometry. We thank
Antonio Coutinho and Henrique Teotonio (IGC) for critically reading the manuscript.
This work was supported by the Portuguese Fundacao para a Ciencia e a Tecnologia
10
(FCT) PTDC/BIA-EVF/114460/2009. A.T.A. and L.P. were funded by FCT PhD and
Postdoctoral fellowships, respectively. MGF is a HHMI International Early Career
Scientist.
All authors designed the experiments, analysed data, discussed the results and wrote the
manuscript. A.T.A. performed most experiments and L.P. performed antagonistic
pleiotropy experiments. I.G. advised and gave support to all experiments. M.G.F.
supervised all the work performed.