Suppl. Fig. S1 Fig. S1 (A, C, E, G, I, K) Double-logarithmic plot of gene expression signals of two biological replicates (B, D, F, H, J, L) Distribution plot of signal ratios between the two biological replicates A C E G K B D F H J L I

Suppl. Fig. S1(continued) M N O Fig. S1M: comparison of the average changes of expression in C-starved seedlings versus the full nutrition Fig. S1N: comparison of the average changes of expression 30 min after adding 15 mM sucrose or 15 mM mannitol Fig. S1O: comparison of the average changes of expression 3 h after adding 15 mM sucrose or 15 mM mannitol

Fig. S2. Global changes of gene expression after resupplying 15 mM sucrose to C-starved seedlings, compared to the differences between C-replete and C-starved seedlings. y=1.343x-0.002 R2=0.683 For each individual gene called present on the ATH1 array in at least one of the four treatments, the ratio of the signal for the probe set in C-replete seedlings, in C-starved seedlings and 3 h after readdition of 15 mM sucrose to C-starved seedlings was calculated, averaged across two independently grown and analysed biological replicates, the values in C-replete seedlings and after sucrose resupply normalized on the levels in C-starved seedlings, converted to a log2 scale, and plotted against each other. Blue indicates genes that are induced and red indicates genes that are repressed, both in C-replete compared to C-starved seedlings and after sucrose resupply, with dark, medium and light shading to distinguish between genes where the change was >4-fold in both cases, >2-fold in both cases, and >2-fold in only one of the conditions. Genes that showed opposite and >2-fold changes in the two conditions are colored grey.

Suppl. Fig. S3. Sucrose-responsive TFs. Comparison with Contento et al Suppl. Fig. S3. Sucrose-responsive TFs. Comparison with Contento et al., (2004) and Price et al., (2004) MYB NAC SBP WRKY C2C2 (Zn) GATA C2H2 CCAAT binding bZIP HD2 HMG1/2 HSF MADS box AP2/EREBP IAA bHLH C2C2(Zn) CO-like The changes in transcript abundance are shown for 50 TFs identified in our experimental conditions (real time RT-PCR data, see Supplemental Table III: raw data for the real time RT-PCR analysis of TFs levels). From the left, the first (black) column in each set of six per gene represents the change in full nutrition versus C-starved conditions in our experiments. The second (bright green) and third (dark green) columns represent the changes after 30 min and 3 h 15 mM sucrose addition to C-starved seedlings. The fourth (light green) and fifth (green) columns show the fold difference in expression between the full nutrition and C-starvation for 24 and 48 h (Contento et al., 2004). The sixth column (yellow) shows the fold difference in expression due to the addition of 167 mM glucose to C-starved seedlings (Price et al., 2004). These data are not included for all TRs, because only shortlisted genes from tables were available.

Suppl. Fig. S4 (A) Full Nutrition versus C-starvation NIP1.1 TIP4.1 GPT2 MATE efflux Carrier, At1g66760 STP1 Hexose transporter At1g77210 ZIP9 Set of lipid transport proteins (B) 3h after sucrose readdition versus C starvation NIPs PIPs, TIPs GPT2 UDPGal transporters at the ERs TPT AKT2 NRT2.1, NRT1.1 CPAs, ZIPs AMT1.1, AMT1.3 Phosphate transporters At2g46430 At2g46440 Sugar-responsive genes involved in transport. The figure shows the MapMan overviews for the comparison full nutrition versus C-starved seedlings (A) and 3 hours of 15 mM sucrose readdition versus C-starved seedlings (B). A 2 -fold change is required to produce a visible coloration and the scale saturates at 8-fold

Suppl. Fig. S5 DNA synthesis Histones DNA repair Histone 1 (A) Full Nutrition versus C starvation (B) 30 min after sucrose readition versus C starvation (C) 3h after sucrose readdition versus C starvation Sugar-responsive genes involved in DNA synthesiss. The figure shows the MapMan overviews for the comparison full nutrition versus C-starved seedlings (A) and 30 min (B) and 3 hours (C) after adding 15 mM sucrose readdition, versus C-starved seedlings. A 2-fold change is required to produce a visible coloration and the scale saturates at an 8-fold change

Suppl. Fig. S6. Changes of expression for diagnostic genes for the cell cycle. A) Transcript levels in C-replete seedlings relative to the level in C-deficient seedlings., (B) Transcript levels in C-deficient seedlings 30min after sucrose addition relative to the level in C-deficient seedlings, (C) Transcript levels in C-deficient seedlings 3h after sucrose addition. Genes that are diagnostic for different phases of the cell cycle were downloaded from Menges et al. (2003). A list of these genes is available in the supplemental material (supplemental Table IX). Their response in the various treatments was calculated relative to the signal in C-starved seedlings, and displayed using a false color as in Fig. 5. A B C

Suppl. Fig.. S7. Comparison of the global response of gene expression to addition of sucrose to carbon-starved seedlings, and changes of sugars in 5-week old rosettes in response to endogenous changes of sugars. A-B, Changes in response to illumination for 4 h at 350 compared to 50 ppm [CO2]. C-D, Changes between the start and end of the light period in wild-type plants. E-F, Changes between the start and end of the light period in the starchless pgm mutant. G-H, Changes after a 6 h extension of the night, compared to the end of the night in wild-type plants. I-J, Loading of the transcripts in the first component of a principle component analysis of a data set including all wild-type and pgm diurnal cycle samples. The responses in these treatments are plotted against the response 30 min (A, C, E, G) and 3 h (B, D, F, H) after adding sucrose to carbon-starved seedlings, The data for all rosette treatments of are from Bläsing et al. (2005). A direct comparison on a gene-by-gene basis is available as supplemental Table II. A B C D H G F E

A B C D Added Sugar Endo-genous Suppl. Fig. S8. Response to 15 mM sucrose and 100 mM glucose in our experiments with the response to 167 mM glucose in Price et al. (2004). y=0.560x-0.053 R2=0.640 y=0.746x-0.079 R2=0.495 y=1.143x-0.106 R2=0.690 B C A Comparison of 100mM glucose added in our experimental system, compared to 167 mM glucose in the study of Price et al. (2005). Comparison of 15mM sucrose versus the addition of 167 mM glucose in the study of Price et al. (2004). Comparison of 15mM sucrose versus 100mM glucose in our experimental system. Comparison of the responses of HSP genes and stress-related genes identified as sugar-induced in Price et al. (2004)) with our treatments in which sugar were added or in which endogenous sugar levels were added (Bläsing et al., 2005). In panels A-C, dark blue and dark red represent strong induction (>2-fold) and repression (<2-fold) respectively, in both treatments. Blue represents genes that are strongly induced (>2-fold) in one case, and slightly (0.5<log2≤1) in the other; orange represents genes that are strongly repressed (<2-fold) in one case and slightly (-1≤log2<-0.5)in the other; grey represents one gene induced (> 2-fold) and the other repressed (< 2-fold); cyan blue represents induced (> 2-fold) in one state but in the other (-0.5<log2<0.5); pink represents repressed (< 2-fold) in one state but in the other. Panels A and B show only the 6099 genes identified by Price et al. (2004) as either glucose, glucose&nitrogen or nitrogen-responsive (cut off 2-fold). Panel C was uses all the data set from the 22K ATH1 array. In panel D, the data sets shown are the response to addition of 15 mM sucrose or 100 mM glucose data in our experiments, the addition of 167 mM glucose to seedlings in Price et al. (2004), the response to ambient compared to compensation point [CO2] (Bläsing et al., 2005), and the response of sugar-induced and –repressed genes during diurnal cycles in wild-type Col-0 and the starchless pgm mutant (Bläsing et al., 2005). The raw data for this figure is given in supplemental Table XIV. Green and red-shaded bars indicate induced and repressed genes (dark and pale = >3- and >2-fold change, respectively). . 167mM Glc 3h 100mM Glc 3h 100mM Suc 3h 100mM Suc 30´ 100mM Suc FN Alter [CO2] Diurnal (WT) Diurnal (pgm) Added Sugar Endo-genous D

Response in our experiments after 3h Suppl. Fig. S9. Response to 15 mM sucrose and 100 mM glucose in our experiments with the response to 167 mM glucose in Li et al. (2006). Response to 167 mM glucose after 2 h in Li et al. (2006) Response in our experiments after 3h B A