Supplementary data
Table S1: The strain pde2∆ cyr1∆ msn2/4∆ exhibits a normal transcriptional cAMP response
ORF
Gene
cAMPa
Biological process (MIPS)
Reference
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
ribosome biogenesis
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Griffioen et al., 1994; Klein and Struhl, 1994
Induced by cAMP
YGL147C
YGL031C
YLR340W
YLL045C
YHR010W
YGR148C
YIL018W
YOR234C
YBL027W
YHL033C
YIL133C
YKL006W
YKL180W
YOL127W
YJL189W
YGR085C
YBR084C-A
RPL9A
RPL24A
RPP0
RPL8B
RPL27A
RPL24B
RPL2B
RPL33B
RPL19B
RPL8A
RPL16A
RPL14A
RPL17A
RPL25
RPL39
RPL11B
RPL19A
4,11
2,63
2,79
3,66
3,19
3,15
2,45
3,49
2,20
2,55
2,00
2,60
2,70
3,52
2,07
2,14
2,15
Repressed by cAMP
YGR088W
YFL014W
YLL026W
YCR021C
YBR072W
YAL062W
YOL126C
YGR019W
YBL075C
YHR008C
CTT1
HSP12
HSP104
HSP30
HSP26
GDH3
MDH2
UGA1
SSA3
SOD2
-9,11
-7,74
-10,18
-7,12
-6,13
-6,64
-6,35
-6,30
-3,46
-6,52
stress response
stress response
stress response
stress response
stress response
amino acid degradation
glyoxylate cycle
amino acid biosynthesis
stress response
detoxification
Marchler et al., 1993; Winderickx et al., 1996
Varela et al., 1995; Donalis and Stahl, 2001
Boy-Marcotte et al., 1998; Donalis and Stahl, 2001
Puig and Perez-Ortin, 2000; Donalis and Stahl, 2001
Amoros and Estruch, 2001; Donalis and Stahl, 2001
Boy-Marcotte et al., 1998
Tadi et al., 1998
Tadi et al., 1998
Winderickx et al., 1996; Boy-Marcotte et al., 1998
Flattery-O'Brien et al., 1997; Boy-Marcotte et al.,
HSP42
HSP78
TSL1
GPD1
UGA2
APE2
ALD3
-7,12
-3,64
-3,64
-6,21
-4,72
-6,90
-2,52
-2,60
-3,50
-3,04
protein folding
stress response
energy reserve metabolism
carbohydrate metabolism
amino acid degradation
amino acid metabolism
fermentation
amino acid biosynthesis
proteolytic degradation
carbohydrate metabolism
Moskvina et al., 1998; Donalis and Stahl, 2001
Moskvina et al., 1998; Donalis and Stahl, 2001
Winderickx et al., 1996
Boy-Marcotte et al., 1998
Tadi et al., 1998
Tadi et al., 1998
Boy-Marcotte et al., 1998
Tadi et al., 1998
Tadi et al., 1998
Winderickx et al., 1996; Boy-Marcotte et al., 1998
1998
YDR171W
YDR258C
YML100W
YDL022W
YBR006W
YKL157W
YMR169C
YHR033W
YBR286W
YBR126C
APE3
TPS1
a
Strains were grown exponentially on YPgalactose in the absence or presence of 3mM cAMP. Only genes of which
the average fold change difference in expression exceeded 2 were deemed significantly. Positive values refer to
induction of gene expression by addition of cAMP, negative values refer to repression of gene expression by addition
of cAMP.
Roosen et al.
1
Roosen et al.
2
Figure S1: Cyclic AMP-dependency for growth. A) Growth of mutant strains in the absence
and presence of 3 mM cAMP on glucose or glycerol/ethanol containing medium on minimal
synthetic complete medium. B) Alleviation of the growth defect of the pde2 cyr1 msn2
msn4 sch9 mutant strain. Growth can only be restored by reintroduction of SCH9, not by
overexpression of TPK1 or BCY1.
Figure S2: Northern Blot analysis of randomly selected genes confirmed the genome-wide
expression profiles. Strains (1) pde2 cyr1 msn2 msn4, (2) pde2 cyr1 msn2 msn4
sch9, (3) pde2 cyr1 msn2 msn4 YIpSCH9 and (4) W303-1A in the absence (a) or in the
presence (b) of 3mM cAMP. Quantitative expression values are shown relative to actine (ACT1)
as a control.
Roosen et al.
3