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Supplemental Materials:
Padilla-Chacon et al.
Running title: Heterologous expression of Hxt2 in Arabidopsis thaliana
Supplemental Methods
Data treatment and conversion to a Mapman compatible format
The data column with the expression ratio value (WT versus transgenic) was used as primary
data. The two sampling time points (6h and 12h after addition 3% glucose) were statistically
treated as biological replicates and mean values and standard errors were calculated
accordingly. Using the AGI locus number in one column, we generated an additional ID column
with the corresponding identifier number from Affymetrix microarrays. This was done with a
javascript macro and using the excel lookup functions. Since the microarray chip from Arizona
university contains various amounts of duplicated spots, and since different AGI codes can be
converted to the same Affymetrix at_ID_code, we had to filter the data table in order to contain
only unique at-ID_codes. For that purpose, for the duplicated IDs we estimated average
transcript levels using the apply function of the statistical program (R). Subsequently, a filter
was used to mark as non significant all those genes for which the standard error was larger
than the mean expression value of the genes. Values were also marked as non-significant
when the difference between the two contrasting samples (WT versus transgenic) was smaller
than the sum of the two standard errors.
Visualization of Microarray results with Mapman
The visualization tool MapMan (Thimm et al., 2004; http://gabi.rzpd.de/projects/MapMan/) was
used to analyze the microarray data. The mapping files structure the Arabidopsis genes into
main BINS and sub BINS for display on the schematic maps of metabolism and cellular
processes. The overview figures (Figs S2-4) were prepared using mapping file version
Ath_AFFY_ATH1_TAIR8.
The mean ratio values between wild type and transgenic line L2 were converted to log2 scale,
and imported into MapMan, which converts the data values to a false color scale. Transcripts
called not present are shown as gray, transcripts that change by less than a given threshold are
white, transcripts that increase are blue, and transcripts that decrease are red. In the scale
used for the present figures, a 2-fold change was required to produce a visible coloration, and
the scale saturated at an 8-fold change (= 3 on a log2 scale).
Supplemental Results
The metabolic overview figures (see MapMan figures below) suggest a coordinated
reprogramming of gene expression when comparing WT and L2 seedlings exposed to high
glucose. There were significant changes for many genes directly involved in metabolism,
transport and assimilation. For example, a MATE family transporter protein (Fig S1) and the
sucrose transporter SUT4 gene were induced (Fig S4). Raffinose and minor sugar metabolism
metabolism was also affected (Fig S1 and S2). The transcript levels of some key glycolytic
enzymes were also induced including pyruvate kinase and glyceralheyde-3P deshydrogenase.
The fact that not only glucose and fructose phosphorylating activities increased (see Fig 6), but
also some other genes in glycolysis is additional evidence that glycolytic flux was indeed
increased in the transgenic lines gown at high glucose.
Sucrose synthase was weakly induced and cytosolic invertase was repressed (Fig S3). A
1
invertase inhibitor was also induced (Fig S1). This change presumably reflects a coordinated
switch. The starch synthesis the small subunit of ADP-glucose pyrophosphorylase was
repressed. There were relatively few changes in the expression of genes involved in cell wall
polysaccharide synthesis. Interestingly, a subset of genes for cell wall-modifying enzymes was
also induced, including some members of the expansin family. Few genes involved in fatty acid
metabolism were altered, for example, diacylglicerol kinase was repressed. In the nitrogen
metabolism the gene of glutamate deshydrogenase was strongly induced. Our results suggest
that there is a reprogramming of metabolism by heterologous expression of the transporter
Hxt2, something that would not to be expected if Hxt2 would function only as a sugar
transporter per se. Therefore, we postulate that Hxt2 alters sugar signaling and perception, and
that this effect is not only reflected as a phenotype of less glucose sensitivity (see Fig 4), but
also observed at the level of gene expression.
Some of the changes in the Mapman figures are not apparent from raw inspection of lists of
affected genes because many of the changes are relatively small. Some minor changes
become only visible when genes are systematically collected in BIN groups or functional
categories.
Supplemental Discussion on Yeast Sugar Transporters and Signalling
Yeast have developed a system to sense extracellular concentrations of sugars that ensures a
coordination between the supply of carbohydrates from the environment and the enzymatic
machinery of the cells (Lalonde et al., 1999; Lalonde et al., 2004). External glucose is sensed
by SNF3 and RGT2. Despite their high homology with glucose permeases, these
transmembrane proteins do not mediate significant glucose transport (Ozcan et al., 1996).
However, both have a large intracellular domain, and from functional analyses, it appears that
the sensing function requires two interacting domains: the membrane-spanning domain
necessary for glucose recognition and the C-terminal extensions necessary for intracellular
reporting. Both are required for the transmission of the glucose signal (Ozcan et al., 1998).
SNF3 is required for repression of the high-affinity transporters Hxt2, Hxt6 and Hxt7 at high
glucose concentrations (Liang and Gaber, 1996; Vagnoli et al., 1998). The C-terminal domains
of SNF3 and RGT2 mediate the signaling function of proteins. The C-terminal extension of
SNF3 contains two nearly identical repeats of 25 amino acids. Deletions of these extensions
leads to a loss of sensor function (Ozcan et al., 1998; Vagnoli et al., 1998).
2
Supplemental Figures
Metabolism
Log2FC p-value
-2.15
0.003
-2.12
0.008
-2.04
0.002
-1.91
0.005
-1.75
0.005
-1.70
0.003
-1.68
0.003
-1.64
0.004
-1.50
0.007
-1.49
0.006
-1.49
0.004
-1.42
0.005
-1.42
0.005
-1.40
0.010
-1.37
0.006
-1.36
0.005
-1.36
0.005
-1.34
0.006
-1.31
0.006
-1.29
0.009
-1.27
0.007
-1.24
0.006
-1.17
0.009
-1.17
0.009
-1.16
0.010
-1.14
0.009
-1.14
0.009
1.13
0.009
1.19
0.008
1.23
0.007
At3g55680
At5g20250
At5g55370
At5g07440
At1g02880
At3g26445
At5g02230
At2g29300
At1g71120
At5g57590
At5g19690
At4g39800
At5g27410
At1g31490
At1g54630
At1g21840
At4g28395
At1g55810
At1g77420
At4g31790
At4g11640
At4g36530
At5g37170
At5g07000
At5g04490
At2g22250
At4g21860
At1g17745
At4g26860
At5g01210
Membrane
Log2FC p-value
Transcription
Log2FC p-value
Unknown
Log2FC p-value
invertase/pectin methylesterase inhibitor family protein
profile PF04043:
Plant
invertase/pectin
inhibitor
-1.92 TIGR00797:
0.001
At1g27000
bZIP
family Pfam
transcription
factor
-2.13 contains
0.009 Pfam
At1g66760
MATE
efflux
family protein methylesterase
contains TIGRfam
profile:
MATE efflux family
protein,
profile PF01554:
Uncharacterized membrane
protein family
-1.98
0.003
At1g69760
raffinose synthase family protein / seed imbibition-1.84
protein,0.004
putative At1g79450
(din10) similar toLEM3
seed (ligand-effect
imbibition protein
GB:AAA32975
from [Hordeum
vulgare];
contains
nonconsensus
ATContains
donor
splice
site at
intron domain.
1; contains
Pfam
profile
PF05691:
Raffinose
0.004
At1g21760
F-box
familyGI:4585976;
protein
PF|00646
F-box
ESTs
gb|Z37267,
gb|R90412,
gb|Z37268 and gb|T88189 come from
-1.87
0.003
At1g10150
modulator
3) family GI:167100
protein /-1.90
CDC50
family protein
similar
to GI:4966357;
GI:11994416;
GI:9757735
from
[Arabidopsis
thaliana]
long-chain-alcohol O-fatty-acyltransferase family-1.80
protein /0.005
wax synthase
family protein
contains similarity
to transporter
wax synthase
similarity
to
wax synthase
wax
- Simmondsia
PID:g5020219
similar to wax
synthase
from Simmondsiariboside-insensitive
c
-1.77
0.002
At5g36670
PHD fingerchinensis,
family
protein
-1.84 [gi:5020219]
0.002
At3g12300
At1g70330
equilibrative
nucleoside
family
protein
contains
similarity
tosynthase
SWISS-PROT:Q14542
equilibrative
nucleoside transporter
2 (Equilibrative
nitrobenzylmercaptopurine
nucleoside tra
glutamate dehydrogenase 2 (GDH2) identical to -1.68
glutamate
dehydrogenase
2 (GDHauxin
2) [Arabidopsis
thaliana]
SWISS-PROT:Q38946
-1.59 0.003
At5g39810
family protein contains similarity
to to
hypothetical
of [Arabidopsis
thaliana] thaliana] gi|4322486|gb|AAD16
-1.83 proteins
0.002
At5g07490
0.006
At5g57090
transport protein
(EIR1)
identical to auxin transport
protein EIR1
[ArabidopsisMADS-box
thaliana] gi|3377507|gb|AAC39513;
identical
root gravitropism
control
protein [Arabidopsis
thiamin pyrophosphokinase, putative similar to thiamin
[Mus musculus]
gi|6468206|dbj|BAA87040
At5g65210
bZIP family GI:4585976;
transcription GI:11994416;
factor (TGA1) GI:9757735
identical to transcription
factor thaliana]
(TGA1)
GI:16550 from [Arabidopsis thaliana]
-1.76
0.002
At5g17210
-1.67 pyrophosphokinase
0.003
At1g79450
LEM3 (ligand-effect
modulator 3) family protein /-1.57
CDC50 0.004
family protein
similar to GI:4966357;
from
[Arabidopsis
glycosyl transferase family 17 protein contains Pfam
PF04724:
Glycosyltransferase
family 17 oligopeptide transport (POT) family
-1.49 protein
0.003contains
At5g64950
mitochondrial
transcription
termination factor-related / -1.70
mTERF-related
Pfam profile PF02536: mTERF
0.003 contains
At4g19645
-1.57profile
0.003
At5g62730
proton-dependent
Pfam profile:
PF00854 POT
family
haloacid dehalogenase-like hydrolase family protein
contains
accession IPR005834:
Haloacid
dehalogenase-like
-1.47 NSF
0.007
At1g32430
F-box VTI1a
family protein
domain Pfam:PF00646
-1.69
0.006
At4g23670
-1.52
0.003InterPro
At5g39510
vesicle transport
v-SNARE
11 (VTI11) /hydrolase
vesicle soluble
attachment
protein receptor
(VTI1A)contains
identicalF-box
to SP|Q9SEL6
Vesicle transport
v-SNARE
11 (AtVTI11) (Vesicle transport v-SNARE protein V
tropinone reductase, putative / tropine dehydrogenase,
to tropinonesulfate
reductase
SP:P50165
fromto[Datura
0.004 thaliana]
At5g10960
CCR4-NOT transcription complex, subu
-1.64to SWISS-PROT:Q9UFF9
0.003
At5g07570
-1.43 putative
0.006 similar
At1g77990
transporter
identical
sulfatestramonium]
transporter-1.43
[Arabidopsis
GI:1498120CCR4-NOT transcription complex protein, putative similar
GDSL-motif lipase/hydrolase family protein similar
to family
II lipases
EXL3 GI:15054386
[Arabidopsisfamily
thaliana];
contains
Pfam
profile PF00657:
GDSL-like
Lipase/Acylhydrolase
0.009
At4g31720
transcription transporter,
initiation factor
IID II(TFIID) 23-30kDa subunit
familyAt1g32400
protein contains Pfam profile: PF03540 transcriptio
-1.63(TAF2H)
0.003
-1.34
0.008
At5g02180
amino from
acid transporter
protein
belongs
to -1.41
INTERPRO:IPR002422
amino
acid/polyamine
family
aminotransferase class III family protein low similarity
acidankyrin
aminotransferase
BioA
[Mesorhizobium
loti] GI:12044306;
contains
Pfam profile PF00202:
class
III family protein contains
-1.36 Pfam:PF00023
0.008
At5g15790
zinc fingeraminotransferase,
(C3HC4-type RING
finger)
profile:At1g04030
PF00097 zinc finger, C3HC4 type (RING finger)
-1.60 Pfam
0.003
-1.31 to 7,8-diaminopelargonic
0.005
At4g03500
repeat family
protein
contains ankyrin
repeats,
oligosaccharyl transferase STT3 subunit family protein
Oligosaccharyl
transferase STT3 subunit {Saccharomyces
contains
Pfam profile
PF02516:
Oligosaccharyl
transferase
STT3Pfam
subunit
-1.28cerevisiae};
0.007
At3g18960
transcriptional
factor
B3 family
protein
contains
profile
B3At1g24370
DNA
binding
domain
-1.56 PF02362:
0.003
-1.31 similar
0.006to SP|P39007
At1g30540
ATPase, BadF/BadG/BcrA/BcrD-type
family contains
Pfam
PF01869:
BadF/BadG/BcrA/BcrD
ATPase
family;
similar
to Transcriptional
regulators
of
NagC/XylR
(ROK)
family,
sugar kinase (GI:15023013) [Clo
inositol-3-phosphate synthase isozyme 1 / myo-inositol-1-phosphate
synthase 1 / MI-1-P
synthase
1 / IPS
1 identical
Inositol-3-phosphate
synthase isozyme
(EC 5.5.1.4)
(Myo-inositol-1phosphate
synthase
1) (MI-1-P
1) (IPS 1) {Arabi
-1.15
0.008nodule
At5g07610
F-box
family
protein
similar to unknown
protein (emb|CAB85517.1)
-1.54
0.003synthase
At1g36050
-1.31 0.006
At5g50790
nodulin
MtN3 family
protein
similartotoSP|P42801
MtN3 GI:1619602
(root
development)
from 1[Medicago
truncatula]
aminotransferase class IV family protein contains-1.31
Pfam profile:
aminotransferase
class
IV
-1.15
zinc-binding
family protein
similar to zinc-binding protein
[Pisum0.003
sativum] At3g12940
GI:16117799; contains Pfam profile PF04640 : Prot
-1.54
0.008 PF01063
At4g35080
high-affinity
nickel-transport
family protein contains
Pfam0.009
domain, At1g32700
PF03824: High-affinity
nickel-transport
protein
transferase family protein contains similarity to anthranilate
N-hydroxycinnamoyl
GI:3288180,
from cancer
(Dianthus
caryophyllus);
Pfam
profile
PF02458
transferase
family
1.22 resistance
0.007
At4g28890
zinc finger
RING finger)
family protein contains
profile:At5g50900
PF00097 zinc finger, C3HC4 type (RING finger)
-1.51 Pfam
0.008
-1.26 0.007
At1g71960benzoyltransferase
ABC transporter family
protein GI:2239091
similar to breast
proteincontains
GB:AAC97367
from(C3HC4-type
[Homo
sapiens]
acyl carrier protein 3, chloroplast (ACP-3) nearly -1.18
identical0.008
to SP|P25702
Acyl carrierS1
protein
3, chloroplast protein-related
precursor (ACP)
{Arabidopsis
thaliana}
1.22similarity
0.007to S1
At4g25470
DRE-binding
protein (DREB1C)
/ CRT/DRE-binding factor
to DREB1C GI:3738228 from [Arabidopsis thali
-1.512 (CBF2)
0.006identical
At3g61710
At1g11765
self-incompatibility
contains
weak
self-incompatibility
protein [Papaver
rhoeas] gi|452430|emb|CAA52380
expressed protein weak similarity to SP|Q07402 -1.16
Urease accessory
protein ureF [strain
TB-90] {Bacillus sp.}(AGP21)
0.010
At1g55330
arabinogalactan-protein
1.31
0.007
At3g08020
PHD finger protein-related contains low similarity to PHD-finger
domain proteins
-1.50
0.008
At5g15990
lipid transfer protein, putative identical to anther-specific
[gi:2746339]; contains
Pfam protease
family0.006
domain
1.34
At4g34370
IBR domain-containing
protein
similar
to SP|Q94981
Ariadne-1
protein
(Ari-1)
{Drosophila melanogaster}; contains Pfam prof
-1.50
At1g53560
-1.16 gene
0.010ATA7
At4g18190
purine permease
family inhibitor/seed
protein similarstorage/LTP
to purine permease
[Arabidopsis
thaliana] GI:7620007;
contains Pfam
profile
PF03151:
Domain of
unknown0.005
function,
DUF250
uracil phosphoribosyltransferase, putative / UMP-1.15
pyrophosphorylase,
putative / UPRTase,
putative similar MLO
to SP|O65583
Uracil/ MLO-like
phosphoribosyltransferase
(EC 2.4.2.9)
(UMP
pyrophosphorylase)
(UPRTase)
{Arabidopsis
thaliana};
contains
Pfam
profile
PF00485:
PhSWISS-PROT:P93766, NC
1.92 protein
0.0014 (MLO4)
At3g04250
family
protein-related
contains
TIGRFAM
TIGR01640:
F-box
protein
interaction
domain
-1.41
0.004
At5g46560
0.009
At1g11000
seven transmembrane
family protein
identical
to F-box
membrane
protein
Mlo4 [Arabidopsis
thaliana]
gi|14091578|gb|AAK53797;
similar
to MLO
protein
hydrolase, alpha/beta fold family protein similar to
monoglyceride
from [Homo
sapiens] GI:14594904,
musculus]
GI:2632162;
profile PF00561:
hydrolase,
alpha/beta
fold family
1.93 contains
0.001 Pfam
agamous-like
box
protein
AGL1 / shatterproof
1-1.40
(AGL1) (Keratinocyte
(SHP1)
to SP|P29381
Agamous-like
MADS box prot
0.005 identical
At4g01915
-1.13
0.010 lipase
At4g18905
transducin
family protein /[Mus
WD-40
repeat family
protein
contains
5 At3g58780
(4 significant)
WD-40
repeats; MADS
similar
to periodic
tryptophan
protein 1 homolog
protein
IEF SSP 9502)
(PWP1)(SP:Q13610)
(P
diphthine synthase, putative (DPH5) similar to Diphthine
(Diphtamide biosynthesis
methyltransferase)
(DPH5)
[Saccharomyces
cerevisiae];
similar to CGI-30
DPH5, Saccharo
-1.38 to methyltransferase
0.005
At1g76185
1.19 synthase
0.008
At1g74240
mitochondrial
substrate carrier
family(SP:P32469)
protein contains
Pfam profile: PF00153
mitochondrial
carrierprotein
protein(GI:4680699) [Homo sapiens]; similar
At5g36690
At2g35520
At5g25470
sulfotransferase family protein similar to steroid sulfotransferase 3 [Brassica napus] GI:3420008, steroid sulfotransferase 1 [Brassica napus] GI:3420004; contains Pfam profile PF00685: Sulfotransferase domain
-1.30
0.005
At1g14530
phosphatidate cytidylyltransferase family protein contains Pfam profile: PF01148 phosphatidate cytidylyltransferase
-1.30
0.005
At5g55240
aminotransferase class I and II family protein similar to aspartate aminotransferase from Bacillus stearothermophilus SP|Q59228, Thermus aquaticus SP|O33822; contains Pfam profile PF00155 aminotransferase, classes
I and II 0.006
-1.29
At2g47760
methionine sulfoxide reductase domain-containing protein / SeIR domain-containing protein low similarity to pilin-like transcription factor [Homo sapiens] GI:5059062, SP|P14930 Peptide methionine sulfoxide reductase msrA/msrB
(EC 1.8.4.6)
{Neisseria gonor
-1.28
0.008
At1g79970
D-3-phosphoglycerate dehydrogenase / 3-PGDH
identical
to
SP|O04130
-1.28
0.006
At3g25930
Log2FC p-value
Log2FC p-value
alanine racemase family protein contains Pfam domain, PF01168: Alanine racemase, N-terminal domain
-1.24
0.007
At1g80550
-1.65 0.004
At5g18600 glutaredoxin family protein contains glutaredoxin-1.28
domain,0.007
INTERPRO:IPR002109
At3g61110 40S ribosomal protein S27 (ARS27A) identical to cDNA-1.22
ribosomal protein S27 (ARS27A) GI:4193381
transferase family protein contains Pfam profile PF02458 transferase family
0.007
At3g58080
-1.55 0.005
At5g51630 disease resistance protein (TIR-NBS-LRR class),-1.21
putative0.008
domain At1g01100
signature TIR-NBS-LRR
exists,
suggestive
a disease
resistance
60S acidic
ribosomal
proteinofP1
(RPP1A)
similar to protein.
60S ACIDIC RIBOSOMAL PROTEIN P1 GB:O23095 from [Arabidopsis t
-1.20
0.007
At5g53905
-1.43 0.004
At1g50950 thioredoxin-related contains weak hit to Pfam PF00085:
Thioredoxin;
contains
2
predicted
transmembrane
domains
-1.18 0.008
At3g09100 mRNA capping enzyme family protein similar to mRNA-1.19
capping enzyme [Xenopus laevis] GI:7239232; contains Pfam profiles
0.008
At2g01100
-1.38 0.004
At4g21380 S-locus protein kinase, putative (ARK3) identical-1.17
to PIR|T05180|T05180
S-receptor29
kinase
ARK3 precursor - [Arabidopsis
thaliana]/ RNA-binding protein cp29, putative similar to 29 kDa ribonucleoprotein chlor
0.008
At1g60000
kDa ribonucleoprotein,
chloroplast, putative
-1.18
0.008
At3g12590
-1.36 0.006
At2g23080 casein kinase II alpha chain, putative identical to-1.17
probable0.010
casein kinase
II, alpha chain
[Arabidopsis
thaliana]
SWISS-PROT:O64817;
similar
to casein
kinase
II, alpha
chainfactor,
1 [Arabidopsis
thaliana]
SWISS-PR
At5g42820
U2 snRNP
auxiliary
factor small
subunit, putative strong
similarity
to U2
snRNP
auxiliary
small subunit
[Oryza
sativa] G
-1.14
0.009
At1g67570
-1.34 0.009
At1g16920 Ras-related GTP-binding protein, putative similar 1.14
to GTP0.009
binding protein
GI:218228DNA-directed
from [Vicia faba];
to cDNA
small GTP-binding
proteinto(Rab11)
GI:451859
At2g24120
RNA identical
polymerase,
chloroplast
(RPOPT) identical
SP|O24600
DNA-directed RNA polymerase, chloroplast pre
-1.14
0.009
At1g80860
-1.33 0.006
At1g22280 protein phosphatase 2C, putative / PP2C, putative1.14
similar0.010
to protein
phosphatase type
2C GI:4336436 family
from [Lotus
japonicus]
At2g47220
3' exoribonuclease
domain
1 protein-related similar to polynucleotide phosphorylase [Pisum sativum] GI:2286200, poly
-1.14
0.009
At4g09260
-1.30 0.006
At5g63140 calcineurin-like phosphoesterase family protein contains
Pfam profile:
PF00149 calcineurin-like
phosphoesterase
1.24 0.006
At5g04210
RNA recognition
motif (RRM)-containing protein contains InterPro entry IPR000504: RNA-binding region RNP-1 (RNA recogn
-1.12
0.010
At5g16800
-1.30 0.007
At5g64620 invertase/pectin methylesterase inhibitor family protein
similarity
to SP|P83326 mitochondrial
Pectinesterasetranscription
inhibitor (Pectin
methylesterase
inhibitor)
(PMEI) {Actinidia
chinensis};
contains
Pfam profile
PF04043: Plant
1.56 low
0.005
At2g44020
termination
factor-related
/ mTERF-related
contains
Pfam profile
PF02536:
mTERF
-1.11
0.010
At3g08030
meprin and TRAF homology domain-containing protein / MATH domain-containing protein weak similarity to ubiquitin-specific protease 12 [Arabidopsis thaliana] GI:11993471; contains weak hit to Pfam PF00917: MATH domain
-1.25 0.008
At1g74520 ABA-responsive protein (HVA22a) identical to AtHVA22a [Arabidopsis thaliana] GI:4884932
1.13
0.009
At3g03280
aspartyl protease family protein contains Pfam profile PF00026: Eukaryotic aspartyl protease; similar to CND41, chloroplast nucleoid DNA binding protein (GI:2541876) {Nicotiana tabacum}
-1.22 0.009
At1g07960 thioredoxin family protein low similarity to protein disulfide isomerase 4 [Giardia intestinalis] GI:13489047; contains Pfam profile PF00085: Thioredoxin
1.22
0.007
At2g34220
ubiquitin-protein ligase, putative similar to SP|P39940 Ubiquitin--protein ligase RSP5 (EC 6.3.2.-) {Saccharomyces cerevisiae}; contains Pfam profiles PF00240: Ubiquitin family, PF00632: HECT-domain (ubiquitin-transferase)
-1.20 0.007
At5g64813 GTP-binding protein-related contains weak similarity to Ras-related protein Rab-27A (Rab-27) (GTP-binding protein Ram) (Swiss-Prot:P51159) [Homo sapiens]
1.26
0.010
At3g02950
Der1-like family protein / degradation in the ER-like family protein contains Pfam profile: PF04511 Der1-like family
-1.13 0.009
At4g25780 pathogenesis-related protein, putative similar to gene PR-1 protein - Medicago truncatula, SP|Q40374; contains Pfam profile PF00188: SCP-like extracellular protein
1.28
0.006
At3g07660
protease inhibitor/seed storage/lipid transfer protein (LTP) family protein similar to lipid transfer protein - Hordeum vulgare, EMBL:AF109195; contains Pfam protease inhibitor/seed storage/LTP family domain PF00234
1.14 0.010
At5g26751 shaggy-related protein kinase alpha / ASK-alpha (ASK1) identical to shaggy-related protein kinase alpha SP:P43288 GI:460832 from [Arabidopsis thaliana]
1.29
0.006
At2g39705
Ulp1 protease family protein contains Pfam profile PF02902: Ulp1 protease family, C-terminal catalytic domain; similar to EST gb|N96456
1.17 0.008
At2g14440 leucine-rich repeat protein kinase, putative similar to light repressible receptor protein kinase [Arabidopsis thaliana] gi|1321686|emb|CAA66376; contains leucine rich repeat (LRR) domains, Pfam:PF00560; co
1.29
0.009
At5g37470
protease inhibitor/seed storage/lipid transfer protein (LTP) family protein contains Pfam protease inhibitor/seed storage/LTP family domain PF00234
1.42 0.005
At2g37290 RabGAP/TBC domain-containing protein low similarity to Rab6 GTPase activating protein, GAPCenA [Homo sapiens] GI:12188746; contains Pfam profile PF00566: TBC domain
1.35
0.006
At3g10770
1.47 0.008
At1g62820 calmodulin, putative similar to calmodulin SP:P04465 from [Trypanosoma brucei gambiense]; contains INTERPRO:IPR002048 calcium-binding EF-hand domain
1.49
0.007
At5g47870
1.53 0.005
At3g23860 GTP-binding protein-related low similarity to SP|Q99ME9 Nucleolar GTP-binding protein 1 (Chronic renal failure gene protein) {Mus musculus}
1.58
0.003
At3g14730
1.64 0.004
At1g22920 COP9 signalosome subunit 5B / CSN subunit 5B (CSN5B) / c-JUN coactivator protein AJH1, putative (AJH1) COP9 complex subunit CSN5-1; identical to Arabidopsis homologs of a c-Jun coactivator AJH1 G
1.61
0.002
At1g30320
1.65
0.004
At4g21865
1.68
0.009
At2g25800
1.80
0.002
At1g19500
serine racemase, putative similar to serine racemase
musculus]
GI:6448865; extracellular
contains Pfam
profile
PF00291: Pyridoxal-phosphate
dependent
-1.36
0.007
1.37 [Mus
0.005
At5g19110
dermal
glycoprotein-related
/ EDGP-related
similar toenzyme
extracellular dermal glycoprotein EDGP precursor [Daucus carota] GI:285741
hydrolase, alpha/beta fold family protein low similarity to hydrolase [Sphingomonas sp.] GI:3426124; contains Pfam profile PF00561: hydrolase, alpha/beta fold family
-1.35
0.005
O-methyltransferase family 2 protein similar to caffeic acid 3-O-methyltransferase [Populus tremuloides][SP|Q00763]
-1.31
0.006
Signaling
RNA related
Proteases
Log2FC p-value
-1.52
0.004
-1.39
0.007
-1.32
0.006
-1.30
0.008
-1.18
0.008
1.40
0.009
1.42
0.004
At3g58430
At1g08210
At4g12570
At4g04860
At5g09370
At1g10570
At4g08530
Figure S1. Transcript levels measured by microarray (log2 fold change between WT and transgenic).
Plants were cultivated in 1% sucrose for 12 days and then transferred to a media without sugars for 48 h
in dark before being induced with 3% glucose for 6 and 12 h. Total RNA was extracted and hybridized
to the 22k (ATv3.4.2.Z) Arabidopsis microarray (Arizona University). Statistical analysis was performed
with both R and excel using stringent selection criteria (p<0.01, log2 fold change >1, and net intensity
>30). Significantly regulated genes were grouped into functional categories by manual curation of the
currently available TAIR annotations. Within each functional category, genes are listed by the
magnitude of the log2 fold change (log2FC). Blue color indicates up-regulation, whereas red color
down-regulation.
3
light
reactions
raffinose metabolism
cell wall
modification
lipids
metabolism
glycolisis
N-metabolism
Figure S2. MapMan overview of metabolism
Expression of genes involved in metabolism after addition of 3% glucose for 6 and 12h. The experiment
was carried out as described in "Materials and Methods." The results are the mean of two biological
replicates. The results are displayed using the MapMan software (Thimm et al., 2004). The results are
shown as fold changes between wild type to transgenic seedlings after 6 and 12 h of having being
transferred to 3% glucose. All results are shown on a log2 scale coded to red or blue color.
4
glucose-6P
isomerase
aldolase
glycealdihyde-3P-deshydrogenase
piruvate kinase
Figure S3 MapMan overview of glycolysis. See also legend of Fig S1
sucrose
synthase
small subunit of AGPase
neutral
Invertase
sucrose transporter SUT4
ß-amylase
glucan
phosphorilase
Figure S4 MapMan overview of sucrose synthesis and degradation, and starch metabolism. See also
legend of Fig S1.
5