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Transcriptional
regulation,
Post-
INTRODUCTION
There is a clear relationship between the nutritional state of the cell and
its ability to resist stress conditions. When nutrients are available, a high
activity of the Ras/adenylate cyclase/protein kinase A (PKA) pathway
determines growth stimulation and cell division, as well as repression of
stress, respiration, the protein kinase C (PKC) pathway and autophagy related
genes [1]. Depletion of any essential nutrient stops the cell cycle,
activates the stress response, and cells enter the stationary phase; when all
the essential nutrients are available again, cells exit this phase [2]. These
changes are regulated, at least partially, by PKA pathway and cyclindependent kinases Pho80/85p, which control the entry into the stationary
phase, activating the transcription of genes characteristic of this phase via
several transcription factors, such as Msn2/4p [3].
S. cerevisiae gene SPI1 is a good example of a stress-response gene. It encodes
a
serine/threonine-rich
protein
anchored
to
the
cell
wall
by
glycophosphatidylinositol (GPI) [4]. It has been shown that it is important
in resistance to herbicides, wall lytic enzymes, food preservatives and weak
lipophilic acids [5, 6]; besides, its overexpression causes pseudohyphal
growth [7]. Its expression is induced in several adverse conditions,
particularly under oxidative, heat, ethanol,acetaldehyde and hyperosmotic
stresses, lack of nitrogen and amino acids, and acidic or basic pH [8, 9],
being particularly high during diauxic change, the stationary phase and
of
of
by
in
Fig. 3. Study of SPI1 expression during the growth and its role in the response to
nutrient starvation. A
SPI1 expression in BY4742 was analysed by Northern blot. We
present the quantification and the standard deviation of the data obtained with three
different cultures. B
Loss of viability in starvation medium (S medium) in wild
type strain (represented by squares and continuous line) and spi1 (diamonds and
discontinuous line). Counts were made by plate count in YPD plates and are presented
as N/No [(cfu/ml)/ initial (cfu/ml)] to cancel the effects due to different initial
cfu/mL number. C
Comparison of
-galactosidase activity of SPI1p/lacZ fusion
(squares) and Northern blot of SPI1 mRNA (diamonds, discontinuous line) during growth
in the strain BY4742. D
Same as C but for YPH499 strain. The data were multiplied
by the factor needed to be represented in the same scale. For Northern blot analyses
shown in this figure, data were obtained by normalization to rRNA. Statistically
significant differences are marked with asterisks ( p-value < 0.05, p-value <
0.005).
Fig. 4. Effect of several mutants in the expression of SPI1 during exponential [C]
and postdiauxic phase [PD]. A
Study by Northern blot in deletion strains in the
MSN2/MSN4 and YAK1 genes, in W303-1a strain grown in YPD. B
Study by Northern
blot of the effect of POP2 gene deletion in BY4742 strain in YPD. C
Study of the
effect of deletions in WSC2 and PHO84 in BY4741 strain in SC-URA using SPI1p/lacZ
fusion. D
Study of the effect of deletions in SOK2 and PHD1 in MLY40 strain in
SC-URA using SPI1p/lacZ fusion. E
Effect of mutations in PKC pathway genes in SPI1
expression. Northern blot after 0, 6 and 9 hours at 37C in W303-1a and the
The transcriptional factor Sok2p and its antagonist Phd1p, also related to
the PKA pathway, regulate the expression of SPI1 in these conditions (Fig.
4D). In the mutant sok2, induced (post-diauxic) and basal (exponential
phase) expression is lower, as we previously described [11], whereas in the
mutant phd1 the mRNA levels are higher than in the wild type strain, under
both control and post-diauxic conditions (Fig. 4D).
The PKC pathway has a role in the regulation of SPI1 transcription at the postdiauxic phase
Since Spi1p is a cell wall protein, we also studied the involvement of the
PKC pathway in the expression of SPI1. In the thermosensitive mutant pkc1ts,
SPI1 expression decreases in post-diauxic phase cultures changed from 30 to
37C in rich medium (Fig. 4E), although the differences are not
statistically significant.
Also wsc2 shows significantly lower induction of SPI1 in post-diauxic
conditions (Fig. 4C), pointing to activation via the canonical transduction
pathway of PKC, which starts in this sensor protein. However, in mpk1 the
induction was not affected in the post-diauxic phase (Suppl. Fig. 4),
supporting the results of other authors who proposed that there is a bypass
on the pathway at this level [22]. We also studied the expression in yeast
transformed with multicopy plasmid containing MPK1 and PKC1. The
overexpression of both genes increases the SPI1 expression in a statistically
significant manner, both under control and post-diauxic conditions (Fig. 4D).
DISCUSSION
The results obtained from the phylogenetic analysis suggest that Sed1p
duplication and subsequent differentiation of one copy could be the origin of
Spi1p. Homologues of Sed1p and Spi1p are present in yeasts only in the
subphylum Saccharomycotina/class Saccharomycetes/order Saccharomycetales,
whereas in filamentous fungi they are present in the subphylum Pezizomycotina,
classes Leotiomycetes (B. fuckeliana and S. sclerotiorum) and Sordariomycetes
(G. zeae, N. crassa and M. grisea), but they are not found in Eurotiomycetes
class (including other sequenced model organisms belonging to Aspergillus
genus) or throughout the subphylum Taphrinomycotina (which includes other
sequenced model organisms such as Schizosaccharomyces pombe and Pneumocystis
carini). Based on the phylogenetic relationship of Ascomycota proposed by
Scannell et al. [23], these results suggest that Sed1p and orthologous genes
appear in the evolution of the subphylum Pezizomycotina when Eurotiomycetes
diverge from Sordariomycetes and Leotiomycetes, and are maintained later on
(Leotiomycetes, Sordariomycetes and Saccharomycetales) or duplicate (Saccharomyces
sensu stricto), explaining the lack of these genes in Eurotiomycetes and
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Ende, H. and Klis, F M. Low external pH induces HOG1-dependent changes in
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5. Simoes, T., Teixeira, M.C., Fernandes, A.R. and Sa-Correia, I. Adaptation
of Saccharomyces cerevisiae to the herbicide 2,4-dichlorophenoxyacetic acid,
mediated by Msn2p- and Msn4p-regulated genes: important role of SPI1.
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6. Simoes, T., Mira, N.P., Fernandes, A.R. and Sa-Correia, I. The SPI1 gene,
encoding a glycosylphosphatidylinositol-anchored cell wall protein, plays
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11. Cardona, F., Aranda, A. and del Olmo, M. Ubiquitin ligase Rsp5p is
involved in the gene expression changes during nutrient limitation in
Saccharomyces cerevisiae. Yeast 26 (2009) 1-15.
12. Cardona, F., Carrasco, P., Perez-Ortin, J. E., del Olmo, M. and Aranda,
A.A novel approach for the improvement of stress resistance in wine yeasts.
Int. J. Food Microbiol. 114 (2007) 83-91.
13. Cardona, F., Orozco, H., Friant, S., Aranda, A. and del Olmo, M.L. The
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31. Pan, X. and Heitman, J. Sok2 regulates yeast pseudohyphal differentiation
SUPPLEMENTARY METHODS
these
analyses
(http://expasy.org/tools/)
we
and
used
the
Conserved
resources
available
Domains
(CDD)
at
ExPASy
of
NCBI
Structural predictions
For structural modelling we used the resources available at ExPASy. We
obtained similar results with several tools for secondary structure (only results obtained
from PSIPRED are showed). For homology modelling, no adequate structural templates
found.
Threading structural modelling with acceptable results was made using
LOMETS meta-server (http://zhanglab.ccmb.med.umich.edu/LOMETS/). The
structures generated were evaluated using the tools available in SWISS-MODEL. The
models and the quality assessment data were deposited in Protein Model Database
(http://mi.caspur.it/PMDB/) to make them publicly available (PMDB IDs: Spi1p
PM0077324; Sed1p PM0077325).
Supp. Fig. 1a. Unedited alignment of amino acid sequences used for the phylogenetic study. The alignment was made
using ClustalX 2.0. The conserved motif repeated twice in A. gossypii protein and in Sed1p is squared.
Supp. Fig. 1b. Unedited alignment of amino acid sequences using Probcons. The conserved motif is squared. Note
that the results are similar to those obtained used with Clustal 2.0, at least for the sequence used for the phylogenetic
analysis (Fig. 1).
(a)
40
35
30
25
SPI1
20
lacZ
15
10
5
0
0
10
20
30
40
50
60
70
t (h)
(b)
30
25
OD600
20
BY4742_SD
YPH499_SD
15
BY4742_YPD
YPH499_YPD
10
5
0
0
20
40
60
80
100
120
t (h)
Supp. Fig. 2. (a) Comparison of RNAm expression by northern blot of SPI1 and lacZ controlled by SPI1 promoter in
the strain YPH499. (b) Comparison of the growth (measured as 600 nm optical density) of BY4742 and YPH499
strains in rich (YPD) and minimal media (SD). Strains and media are indicated in the legend.
30,00
20,00
15,00
10,00
5,00
W303-1a
MCY829
hog1
sko1
pho4
pho85
sst2
WT
mig1
msn5
msn1
WT
yap1
puf5
mpk1
crz1
cnb1
0,00
WT
SPI1 mRNA
25,00
BY4742
Supp. Fig. 3. Mutant strains tested without effect in SPI1 induction in post-diauxic conditions. SPI1 expression
analysed by northern blot is showed after 8h growing in YPD from DO600= 0.3.
MLSNAKLLLSLAMASTALGLVSNSSSSVIVVPSSDATIAGNDTATPAPEPSSAAPIFYNSTATAT
QYEVVSEFTTYCPEPTTFVTNGATFTVTAPTTLTITNCPCTIEKPTSETSVSSTHDVETNSNAAN
ARAIPGALGLAGAVMMLL
b
Spi1p
Sed1p
WW4
USP7
AP
FHA
FHA
FHA
Supp. Fig. 4. (a) Amino acid sequence of Spi1p and domains found by SMART. Domains are squared by the
following colours: Red, signal peptide; pink, low complexity areas; blue, intrinsic disorder; RPT (blue), internal
repeats. (b) Distribution of domains found by SMART in Sed1p and Spi1p. The same colour code than in (a) is used.
(c) Alignment of the amino acid sequence of Spi1p and its homolog Sed1p. It is shown in pink the serine-threonine
rich domain, characteristic of these proteins and potential substrate of serine-threonine kinases. For Sed1p it is shown
in blue the repeated domain, present only once in Spi1p (RPT in B). It is also shown squared the motifs recognized as
domains (indicated by the name) or substrate of post-translational modifications. Black continued: N-miristoilation;
red dashed: phosphorylation; green dashed: N-glycosylation; FHA: phosphothreonine union; WW4: phosphorylationdependent interaction domain; USP7: binding domain; AP: interaction with AP (Adaptor Protein; typical of the
endocytic route, very common in membrane or cell wall proteins, especially those involved in transport).
Supp. Fig. 5. Secondary structure prediction of Spi1p. c-helices are shown as green cylinders (H above the amino
acid sequence) and d-sheets as yellow arrows (E above the amino acid sequence). The probability is shown as blue
bars over the prediction. The results show that in Spi1p there are 9 putative regions adopting a d-sheet structure, four
of them dubious due to their small size and/or their low probability. The first one corresponds to the signal
peptide, the fourth includes one conserved region (VVSeFTTYCP; Figure 1b), fifth and sixth are also within one
conserved domain (TTFVT-TFTVT; Figure 1b). The seventh is the most conserved (TTLTITNCP), and probably is
important in the function of the protein. Probably these motifs, due to its evolutionary conservation, are part of the
secondary structure and play a central role in the function of protein. An g-helix is also predicted at the C-terminus of
the protein, although with low probability.
y=90
x=90
Supp. Fig. 6. Tertiary structure prediction obtained for Spi1p by threading using LOMETs meta-server. The structure
shows the -sheet barrels forming Ig-like domains. -sheets and coiled coil regions are dark-coloured, whereas gloops are light-coloured. Three views of the protein are showed, referring the turn of the axis to the first view. The
results show that the protein folds in a domain similar to the eight-stranded anti-parallel d-sheets barrel (Ig-like
domain), typical of porins, adhesins and other cell wall or outer-membrane proteins that bind hydrophobic ligands.
The search of structural homologues using 3D-BLAST tool shows that there are similar d-sheets barrels in solved
structures, as 2nnc (sulphur carrier protein from sulphur bacterium; identity = 40.7%), 1st8 (fructan 1-exohydrolase
from plants; identity = 34.3%) and 3por (calcium porin from non-sulphur photosynthetic bacterium, identity =
31.6%). These results point to a channel and/or enzymatic function of this protein in the yeast cell wall.
x=90
y=90
Supp. Fig. 7. Tertiary structure prediction obtained for Sed1p by threading using LOMETs meta-server [3]. The
structure shows a three-lobular structure formed by Ig-like domains. Helixes are shown in yellow and coiled-coil
regions in green. Three views of the protein are showed. The turn of the axis shown is referred to the first panel. The
results shows that it is also composed by three lobes of d-sheets barrels as those that form Spi1p, showing that also
these proteins has related three-dimensional structure. 3D-BLAST points to bacterial adhesins and surface antigens as
structures close to Sed1p. It is also remarkably that the alignment of Spi1p and Sed1p (Supplementary figure 2c)
shows that cysteines forming disulfide bonds that maintain the Ig-like domain (see models deposited at PMDB) are
often conserved in both proteins.
Suppl. Tab. 1
(a) S. cerevisiae strains used in this work
Strain
W303-1a
W303-1a msn2Fmsn4F
W303-1a cnb1F
W303-1a crz1F
W303-1a mpk1F
W303-1a pkc1ts
Genotype
MATa, ade 2-1, ura 3-1, leu 2-3, his 3-1, trp1-1
W303-1a msn2F3::HIS3, msn4-1::TRP1
W303-1a , cnb1::LEU2
W303-1a , crz1::G418
W303-1a mpk1::TRP1
W303-1a pkc1ts-X
W303-1a puf5F
W303-1a uth4::KanMX4
W303-1a yak1F
W303-1a yak1::KanMX4
W303-1a yap1F
MCY829
MCY msn1F
MCY msn5F
MCY mig1F
BY4741
BY4741 pho84F
BY4741 wsc2F
BY4742
BY4742 hog1F
BY4742 pho85F
BY4742 pop2F
BY4742 pho4F
BY4742 sko1F
BY4742 sst2F
MLY40
MLY40 phd1F
MLY40 sok2F
W303-1a yap1::KanMX4
MATa his3-F200 lys2-801 ura3-52
MCY829 msn1-F1::URA3
MCY829 msn5-F2::HIS3
MCY829 leu2::HIS3 mig1-F2::LEU2
MAT a, his3-1, leu2-0, met15-0, ura3-0
BY4741 pho84::KanMX4
BY4741 wsc2::KanMX4
MATc, his3-1, leu2-0, lys2-0, ura3-0
BY4742 hog1::KanMX4
BY4742 pho85::KanMX4
BY4742 pop2::KanMX4
BY4742 pho4::KanMX4
BY4742 sko1::KanMX4
BY4742 sst2::KanMX4
MATc, ura 3-52
MLY40 phd1::G418
MLY40 sok2::hygB
Reference
[1]
[2]
[3]
[4]
[5]
[6]
P. Carrasco,
doctoral thesis
P. Carrasco,
doctoral thesis
F. Rndez-Gil
[7]
[7]
[8]
[9]
Euroscarf
Euroscarf
Euroscarf
Euroscarf
Euroscarf
Euroscarf
Euroscarf
Euroscarf
Euroscarf
Euroscarf
[10]
[10]
[10]
Plasmid
YEp352
YEp352-PKC1
YEp352-MPK1
YEp357
YEp357SPI1p/lacZ
Description
Reference
Multicopy shuttle vector. URA3 marker.
[11]
Multicopy shuttle vector. URA3 marker. PKC1 in PstI/BglII
[12]
Multicopy shuttle vector. URA3 marker. MPK1 in SphI/Ncori.
[12]
Multicopy shuttle vector. URA3 marker. lacZ.
[13]
Multicopy shuttle vector. URA3 marker. lacZ expression controlled by
[14]
SPI1 promoter.
Suppl. Tab. 2.
(a) Analysis of transcription factors (TF), using YEASTRACT tool (http://www.yeastract.com/), which regulate SPI1
expression documented by direct or indirect evidences. Abbreviations: northern blot (NB); expression microarrays
(ARR); chromatin inmunoprecipitation (ChIP); ChIP-on-CHIP (ChIP-CH), mutant (mt), wild-type (WT).
TF
Reference
Adr1p
[15]
Aft1p
[16]
Cat8p
[15]
Cin5p
[17]
Direct: ChIP
[15]
[18]
Cst6p
[15]
Gat4p
Gcr2p
[15]
[19]
Gis1p
[15]
Gzf3p
Haa1p
[15]
[20]
Hap4p
[21]
Hot1p
[22]
Direct: ChIP
[15]
[23]
[24]
[25]
Ino2p
[26]
Ino4p
Mbp1p
[26]
[15]
Mcm1p
[27]
Indirect: NB (WT/TFmt)
Met31p
[15]
Met4p
[28]
Mga1p
[15]
Mig1p
[15]
[15]
[29]
[30]
Indirect: NB (WT/TFmt)
[31]
Indirect: NB (WT/TFmt)
[32]
Indirect: NB (WT/TFmt)
Pdr3p
[33]
Put3p
[15]
Crz1p
Hsf1p
Msn2p/Msn4p
Evidence
Indirect: NB (WT/TFmt)
TF
Reference
Rds2p
[34]
Direct: ChIP-CH
Rfx1p
[15]
Rgm1p
[15]
Rme1p
[15]
[15]
[35]
Rpn4p
[36]
Sfl1p
[37]
[38]
Direct: ChIP-CH
[15]
[22]
Direct: ChIP
[39]
Direct: ChIP
[40]
Direct: ChIP-CH
[41]
[15]
[42]
Ste12p
[41]
Direct: ChIP-CH
Stp2p
[15]
Tec1p
[41]
Direct: ChIP-CH
[15]
[28]
Rox1p
Skn7p
Sko1p
Sok2p
Yap1p
Analysis
of
transcription
Evidence
factors
found
with
Funcassociate
2.0
(b) Transcriptional factors (TF), using YEASTRACT, which presents consensus binding motif in the sequence of the
SPI1 promoter. The position in the sequence respect the transcription start (ATG) is indicated, as well as its
orientation (forward in black and reverse in red). TF which have been demonstrated as SPI1 regulators, by direct or
indirect evidences (see a) are underlined.
TF
TF
Ash1p
Nrg1p
Azf1p
-197
Pho4p
-889
Cbf1p
-888
Pip2p
-366
Crz1p
-358
Rph1p
Fkh1/2p
Rtg1/3p
-575
Gcr1p
Sko1p
-708
Gis1p
Gln3p
-303
Hac1p
-134
Ste12p
-993
Hsf1p
-187, -177
Tec1p
-207
Mcm1p
Xbp1p
Mot3p
-306, -978
Yap1p
-9, -834
Msn2/4p
Yap3
-9
Yrr1p
-561
Stb5p
Supplementary References
1.
2.
Estruch, F. and Carlson, M.: Two homologous zinc finger genes identified
by multicopy suppression in a SNF1 protein kinase mutant of
Saccharomyces cerevisiae. Mol Cell Biol. 13 (1993) 3872-3881.
3.
4.
5.
6.
7.
8.
Alepuz, P.M., Matheos, D., Cunningham, K.W. and Estruch, F.: The
Saccharomyces cerevisiae RanGTP-binding protein msn5p is involved in
different signal transduction pathways. Genetics 153 (1999) 1219-1231.
9.
10.
121.
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