Figure S1. Distribution of blast hits in Zea mays chromosomes
Blast searches were done in B73 genome(release 4a.53) using different protein sequences as queries. See methods for details of the used databases and bioinformatic tools. Panel A) Pfam domain signature for the glucosyl hydrolase family 1 (PF00232) was used. Panel B and C) the full ZmBGLU1 and ZmBGLU2 protein sequences, respectively. Dark red arrows indicate high protein similarity (100-70%) whereas orange (70-50%) and yellow arrows indicate weaker similarity (<50%) at the protein level with respect to the query. The gene Zmbglu1 is closely located to Zmbglu2 on chromosome 10 (both enclosed in a box in the respective panel).
Figure S2.Similarity matrix determined by Blast analysis between different Zmbglu isoforms (GRMZM genes) and probes (MZ oligos) in the Arizona maize array. Black color indicates highest bitscore (maximal 139 bits for the 70 oligo), whereas white is not significant (P>0.001). On average, glu genes were represented by ~3.5 oligoprobes, with some isoforms like Glu1 having as much as 10 different probes and others like Glu23 having only one and Glu10 having none.
Figure S3.β-glucosidase specific primers. A) Zmbglu1 specific primer, B) Zmbglu 2 specific primer, C) 1% agarose electrophoresis, PCR amplification using gene specific primers and template (plasmid with Zmbglu1 or Zmbglu2 cDNA), line 1) bglu2 template and bglu2 primer, line 2) bglu2 template and bglu1 primer, line 3 bglu1 template and bglu1 primers, line 4) bglu1 template and bglu2 primers, and line 5 molecular weight marker, 1 kb pluss (Invitrogen).
Figure S4. β-glucosidase activity in maize seedling exposed to salt stress during 0-24 hours.
Figure S5. Heatmap visualization of the presence of cis elements and regulatory sequences in the promoter regions of all BGLU genes in maize. The top and left dendograms indicate clustering of samples or genes according to the promoter element. The corresponding names of the cis element are given at the bottom and the names of the genes on the right. The number of times that a given cis element is present in the promotor is indicated in gray scale: white indicates the absence of that element in the promoter. Black indicates that the element is present many times (e.g. 10 times).
Figure S6. Protein alignment of maize BGLUs.
The percentage identity is highlighted in different tones. Higher percentages are in dark violet and lower percentages are in light violet. Not conserved amino acids have no color. Sequence gaps without identity were deleted (gap sites are illustrated with blue triangles on the top of the alignment). The red bars at the bottom show the motif where there are amino acids implicated in catalysis. Red arrows on the bottom of alignment indicate amino acids described in the main text. The red square shows the KL motif described in the article, which might be involved in BGAF binding.
Table S1. Regulatory sequences and cis elements in the bglu promoters
Group 1 / Grup 2 / Group 3 / Group 4 / Group 5 / Group 6cis element name and function / Sequence / Beta glucosidase (glu): cis elements repetition number
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12 / 13 / 14 / 15 / 16 / 17 / 18 / 19 / 20 / 21 / 22 / 23 / 24
Promoter TATA Box
TATA Box1: Found in the 5'upstream region of rice alpha-amylase; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation (Grace et al. 2004) / CTATAAATAC / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / -
TATA Box2: Found in the 5'upstream region of pea legA gene; sporamin A of sweet potato; TATA box found in beta-phaseolin promoter; sequence and spacing ofTATA box elements are critical for accurate initiation (Grace et al., 2004) / TATAAAT / 2 / 2 / 1 / 2 / 1 / 3 / - / 2 / - / - / - / 2 / 2 / - / - / - / - / - / 1 / - / 1 / - / - / -
TATA Box3: found in the 5'upstream region of sweet potato sporamin A gene / TATTAAT / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / 2 / - / - / - / - / - / - / - / -
TATA Box4: found in the 5'upstream region of sweet potato sporamin A gene; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation (Grece et al., 2004) / TATATAA / 1 / - / - / - / - / 2 / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / -
TATA Box5: found in the 5'upstream region of pea (Pisum sativum) glutamine synthetase gene (Tjaden et al., 1995) / TTATTT / 1 / 2 / - / 3 / 1 / 1 / - / - / 2 / 1 / 1 / 4 / 1 / - / - / 2 / - / - / 1 / - / - / - / 3 / 1
TATA Box OSPAL: Binding site for OsTBP2, found in the promoter of rice pal gene
encoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNA
binding and bending activities of OsTBP2 and synergistically enhanced OsTBP2-mediated transcription from the pal promoter. / TATTTAA / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / 1 / - / - / - / - / - / - / - / 1 / -
TATAPVTRNALEU: TATA-like motif; A TATA-like sequence found in Phaseolus vulgaris tRNALeu gene promoter; Frequently observed upstream of plant tRNA genes; Found in maize glycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter; Binding site of TATA binding protein (TBP) (Yukawa et al., 2000) / TTTATATA / 1 / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
Biotic stress regulated
ARFAT: auxin response factor / TGTCTC / 1 / 1 / - / - / - / - / - / - / - / 1 / - / - / - / 3 / 1 / - / - / 1 / 2 / 1 / 1 / - / - / 1
ASF1MOTIFCAMV: involved in transcriptional activation of several genes by auxin and/or salicylic acid / TGACG / - / - / - / - / - / - / 1 / - / 1 / 1 / - / 1 / 4 / 1 / 2 / 1 / - / 1 / - / 2 / - / 1 / 1 / 1
BIHD1OS: a rice BELL homeodomain transcription factor in disease resistance responses / TGTCA / - / - / 2 / - / 2 / 2 / 2 / 1 / - / 2 / 2 / 4 / 2 / 2 / 3 / 1 / - / - / - / - / - / - / 4 / 1
BOXLCOREDCPAL: acts as a transcriptional activator of the carrot phenylalanine ammonia-lyase gene (DcPAL1) in response to elicitor treatment, UV-B irradiation / ACCWWCC / - / 1 / - / - / - / 1 / 2 / - / - / - / - / 1 / - / - / - / - / - / 1 / - / - / - / - / - / 2
MYB1LEPR: defence-related gene expression / GTTAGTT / - / - / - / - / - / - / - / - / - / 1 / 1 / - / - / - / - / - / - / - / - / - / - / 1 / - / -
CATATGGMSAUR: Sequence found in NDE element in soybean , Involved in auxin responsiveness / CATATG / - / - / 2 / 2 / - / - / - / - / - / 4 / - / 2 / - / - / 2 / 2 / - / - / - / - / - / - / - / -
WBOXNTERF3: May be involved in activation ofERF3 gene by wounding / TGACY / 1 / 1 / - / 1 / 1 / - / 1 / 1 / 1 / 1 / - / 1 / 2 / 2 / - / 1 / 2 / 1 / 1 / 1 / - / - / 2 / 1
GCCCORE: Appears to play important roles in regulating jasmonate-responsive and pathogen-responsive gene expression / GCCGCC / 1 / - / 1 / 1 / - / - / 1 / - / - / - / - / - / - / 1 / 2 / 1 / 1 / 3 / - / - / 3 / - / 1 / -
SEBFCONSSTPR10A: Binding site of the potato silencing element binding factor
(SEBF) gene found in promoter of pathogenesis-related gene / YTGTCWC / - / 1 / - / - / - / 1 / - / - / - / 2 / - / - / - / 4 / 2 / 1 / - / 1 / 2 / 1 / 1 / - / 2 / -
CAREOSREP1: cis-acting elements necessary and sufficient for gibberellin-upregulated proteinase expression in rice seeds / CAACTC / - / - / 1 / 1 / - / 1 / 1 / - / - / 1 / - / - / - / - / - / 1 / 1 / - / 1 / 1 / - / - / - / -
WBOXNTCHN48: elicitor-respsonsive transcription of defense genes in tobacco / CTGACY / 1 / - / - / 1 / - / - / - / 1 / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / 1
ELRECOREPCRP1: Elicitor Responsive Element / TTGACC / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / -
WRKY71OS: Binding site of rice WRKY71, a transcriptional repressor of the gibberellin signaling pathway, related with plant defence. / TGAC / 1 / 1 / 2 / 1 / 3 / 2 / 4 / 2 / 2 / 4 / 2 / 6 / 8 / 5 / 5 / 3 / 2 / 2 / 1 / 3 / - / 1 / 7 / 3
GT1GMSCAM4: "GT-1 motif" found in the promoter of soybean (Glycine max) CaM isoform, SCaM-4; Plays a role in pathogen- and salt-induced SCaM-4 gene expression / GAAAAA / - / - / 2 / - / 1 / 1 / 1 / - / 1 / 1 / 1 / - / 1 / - / - / 1 / - / 1 / - / - / 1 / 2 / 2 / -
PREATPRODH: Pro- or hypoosmolarity-responsive element / ACTCAT / - / - / 2 / 1 / - / - / - / - / - / - / 1 / - / 2 / - / - / 1 / - / 1 / - / - / - / - / - / -
Signal Molecules
CCAAT Box: Common sequence found in the 5'-non-coding regions of eukaryotic genes; found in the promoter of heat shock protein genes; Located immediately upstream from the most distal HSE of the promoter; act cooperatively with HSEs to increase the hs promoter activity (Rieping et al., 1992) / CCAAT / 1 / 1 / 2 / - / - / 1 / 1 / 2 / 1 / - / 1 / 2 / 1 / 1 / - / - / - / - / 2 / 1 / - / - / - / 2
T/GBOXATPIN2: jasmonate
signaling / AACGTG / 1 / - / 1 / 2 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
ARE1: antioxidant response element / RGTGACNNNGC / - / - / - / - / - / - / - / - / - / 1 / - / 1 / - / - / - / - / - / - / - / 1 / - / - / 1 / -
WBOXATNPR1: transcription factor
RT genes suggests their putative functions in response to environmental stresses / TTGAC / - / - / - / - / 1 / - / 2 / 1 / - / 1 / - / 2 / - / - / 1 / - / - / - / 1 / 1 / - / 1 / - / -
PRECONSCRHSP70A: plastid response element, Involved in induction of
DE HSP70A / SCGAYNRNNNNNNNNNNNNNNNHD / 2 / 1 / - / - / - / - / - / 1 / - / - / - / - / 1 / - / 1 / 1 / - / 1 / 1 / - / 1 / 1 / - / -
ACGTTBOX: ACGT cis-acting DNA sequence elements have been identified in a multitude of plant genes regulated by diverse environmental, physiological, and environmental cues. / AACGTT / - / - / - / - / - / - / - / - / 2 / - / - / - / - / - / - / - / 2 / - / - / - / - / - / - / -
Ethylene and ammonium regulated
AGCBOXNPGLB: "AGC box" repeated twice in a 61 bp enhancer element in tobacco, Ethylene-Induced / AGCCGCC / - / - / - / 1 / - / - / 1 / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / -
AMMORESIIUDCRNIA1: Involved in ammonium-response / GGWAGGGT / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / -
ERELEE4: ethylene responsive element / AWTTCAAA / - / - / - / 1 / 1 / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / -
ABA regulated
ABRECE1HVA22: possible binding
site for nuclear bZIP protein; ABA responsive complex consists of a G-box, namely ABRE3 (GCCACGTACA), and CE1 / TGCCACCGG / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / -
ACGTABREMOTIFA2OSEM: Experimentally determined sequence requirement of ACGT-core ofmotif A in ABRE of the rice gene, OSEM; See S000281; DRE and ABREare interdependent in the ABA-responsive expression of the rd29Ain Arabidopsis / ACGTGKC / - / - / 2 / - / - / - / - / - / - / - / - / - / 1 / - / - / 2 / - / - / - / - / - / - / 1 / -
ABADESI1: Responsive to ABA and desiccation / RTACGTGGCR / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
ABREATCONSENSUS: ABA-responsive elements / YACGTGGC / - / - / 2 / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / -
ABREATRD22: ABA responsive element / RYACGTGGYR / - / - / 2 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / -
DPBFCOREDCDC3: bZIP transcription factors, expression is normally
embryo-specific, and also can be induced by ABA / ACACNNG / - / 2 / 2 / 2 / 4 / 2 / - / - / 1 / 2 / 1 / 3 / 1 / 2 / 2 / 1 / - / 1 / - / - / - / - / 2 / 1
ABREOSRAB21:ABA responsive element / ACGTSSSC / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / 1 / - / - / - / - / - / -
DPBFCOREDCDC3: bZIP transcription factors, expression is normally
embryo-specific, and also can be induced by ABA / ACACNNG / - / 2 / 2 / 2 / 4 / 2 / - / - / 1 / 2 / 1 / 3 / 1 / 2 / 2 / 1 / - / 1 / - / - / - / - / 2 / 1
DRE2COREZMRAB17: "DRE2" core found in maize rab17 gene promoter;
rab17 is expressed during late embryogenesis, and is induced by ABA / ACCGAC / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 2 / - / 1 / - / - / 1 / - / - / - / -
DRE1COREZMRAB17: It is expressed during late embryogenesis,
and is induced by ABA / ACCGAGA / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
RYREPEATBNNAPA: Required for seed specific expression, dist B ABRE mediated transactivation by
DE ABI3 adn ABI3-dependent response to ABA / CATGCA / 2 / - / - / - / 3 / 2 / - / - / - / 1 / - / - / - / - / - / - / - / 1 / 2 / - / - / - / - / -
MYCATRD22: Dehydration and ABA-induction resposive gene in Arabidopsis / 1 / - / 1 / 1 / 2 / - / - / - / 1 / 1 / - / 1 / 1 / - / - / - / - / - / - / - / - / - / - / -
Dehydration regulated
ACGTATERD1: required for etiolation-induced expression of erd1 (early responsive to dehydration) in Arabidopsis / ACGT / 6 / 4 / 8 / 6 / 2 / - / 4 / - / 6 / - / - / - / 6 / 8 / - / 6 / 2 / 2 / - / - / - / 2 / 4 / -
MYCATERD1: necessary for expression of erd1 (early responsive to dehydration) in dehydrated Arabidopsis / CATGTG / 1 / - / 1 / 1 / 2 / - / - / - / 1 / 1 / - / 1 / - / - / - / - / - / - / - / - / - / - / - / -
MYB1AT: recognition site found in the promoters of the dehydration-responsive gene rd22 in Arabidopsis / WAACCA / - / - / 1 / 2 / - / 3 / - / 1 / - / - / - / - / - / - / 1 / - / 3 / 1 / - / 1 / - / 2 / 1 / 1
MYBATRD22: Binding site for MYB (ATMYB2) in dehydration-responsive gene / CTAACCA / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / 1
MYB2CONSENSUSAT MYB recognition site found in the promoters of the
dehydration-responsive gene rd22 / YAACKG / - / - / 1 / - / 2 / 1 / 1 / - / 1 / 1 / - / 1 / - / - / - / 1 / - / - / - / - / 1 / 1 / 1 / -
MYBCORE: involved in regulation of genes that are responsive to water stress in Arabidopsis / CNGTTR / 1 / 1 / 2 / - / 3 / 1 / 3 / 1 / 2 / 5 / - / 3 / - / - / - / 2 / 2 / - / 1 / 1 / 1 / 3 / 4 / -
MYCCONSENSUSAT: recognition site found in the promoters of the
dehydration-responsive gene rd22 and many other genes in Arabidopsis / CANNTG / 12 / 4 / 16 / 10 / 6 / 6 / - / 2 / 4 / 10 / 2 / 8 / 2 / 14 / 2 / 4 / 2 / - / 2 / 6 / 2 / 4 / - / 8
ABRELATERD1: required for etiolation-induced expression of erd1 (early responsive to dehydration) in Arabidopsis / ACGTG / 2 / 2 / 4 / 4 / - / - / 1 / 2 / - / - / - / - / 3 / 3 / - / 3 / - / 1 / - / - / - / - / 2 / -
CBFHV: Binding site of barley CBFs, CBFs are also known as
dehydration-responsive element binding proteins / RYCGAC / - / - / - / - / - / - / - / - / - / - / - / 2 / 3 / 2 / 3 / 2 / - / 1 / 2 / - / 1 / - / - / -
DRECRTCOREAT: dehydration-responsive element/C-repeat / RCCGAC / - / - / - / - / - / - / - / - / - / - / - / - / 2 / 1 / 3 / - / - / 1 / - / - / 1 / - / - / -
Cis element, oxygen or CO2 regulated
CURECORECR: GTAC is the core of a CuRE (copper-response element),also involved in oxygen-response of these genes / GTAC / 4 / 4 / 6 / 2 / 4 / - / 4 / 2 / - / 2 / - / 2 / 6 / 4 / 4 / 4 / 2 / 2 / - / - / 4 / 4 / 2 / 3
EECCRCAH1: Cis-acting elements and DNA-binding proteins involved in CO2-responsive transcriptional activation of Cah1 encoding a periplasmic carbonic anhydrase / GANTTNC / 1 / 1 / - / - / 1 / - / 1 / - / 1 / - / - / 1 / 1 / - / 1 / 1 / 2 / - / - / 2 / 1 / - / - / -
Temperature regulated
LTRE1HVBLT49: low-temperature-responsive element / CCGAAA / - / - / - / - / - / - / - / - / 1 / - / 2 / 1 / - / - / - / 1 / - / - / - / - / - / - / 2 / -
CRTDREHVCBF2: AP2 transcriptional activator HvCBF2 involved in regulation of low-temperature responsive genes / GTCGAC / - / - / - / - / - / - / - / - / - / - / - / 2 / - / - / - / - / - / - / 2 / - / - / - / - / -
LTRECOREATCOR15: Core of low temperature responsive element (LTRE) of cor15a gene in Arabidopsis / CCGAC / - / - / - / - / - / 3 / - / 2 / - / - / - / - / 2 / 1 / 3 / 1 / - / 3 / - / - / 1 / - / 1 / -
Light regulated
TBOXATGAPB: Mutations in the "Tbox" resulted in reductions oflight-activated gene transcription / ACTTTG / - / - / - / - / 1 / - / - / 1 / - / 1 / 1 / - / - / - / - / - / - / - / 2 / - / - / - / - / -
GT1CONSENSUS: Consensus GT-1 binding site in many light-regulated genes / GRWAAW / 2 / 2 / 3 / - / 2 / 1 / 5 / 5 / 2 / 1 / 5 / 1 / 4 / 2 / 3 / 1 / 1 / 3 / 3 / - / 1 / 2 / 7 / -
IBOXCORE: Conserved sequence upstream of light-regulated genes / GATAA / 3 / 1 / 2 / - / - / 1 / - / 1 / - / - / 2 / 2 / 2 / 1 / 2 / - / 2 / 1 / 1 / 2 / - / - / 3 / -
BOXCPSAS1: Box C in pea (P.s.) asparagine synthetase (AS1) gene; Found at
-45; AS1 is negatively regulated by light / CTCCCAC / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / -
BOXIIPCCHS: Essential for light regulation / ACGTGGC / - / - / 2 / - / - / - / 1 / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / -
INRNTPSADB: Light-responsive transcription of
psaDb depends on Inr, but not TATA box / YTCANTYY / - / - / 1 / 1 / - / - / 1 / 1 / 1 / 1 / 1 / - / 1 / - / 3 / - / 1 / 1 / - / - / 1 / 1 / - / -
GT1CORE: Binding site requirements for pea nuclear protein factor GT-1 correlate with sequences required for light-dependent transcriptional activation / GGTTAA / - / - / - / 2 / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / 1 / - / -
SORLIP1AT: Light-Induced Promotersin Arabidopsis / GCCAC / - / 2 / 2 / 1 / 1 / 1 / 1 / 2 / 1 / 1 / - / - / - / 2 / 6 / 1 / - / 3 / - / 1 / 5 / - / 1 / -
SORLIP2AT: Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis / GGGCC / - / - / 2 / - / 1 / - / - / 2 / - / - / 1 / 1 / - / 1 / 1 / - / - / 1 / 1 / 4 / - / - / - / -
EBOXBNNAPA: E-box of napA storage-protein gene of Brassica napus, recognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive / CANNTG / 12 / 4 / 16 / 10 / 6 / 6 / - / 2 / 4 / 10 / 2 / 8 / 2 / 14 / 2 / 4 / 2 / - / 2 / 6 / 2 / 4 / - / 8
IBOX: Conserved sequence upstream of light-regulated
Genes / GATAAG / 1 / - / - / - / - / 1 / - / - / - / - / - / 1 / - / - / 1 / - / 1 / - / - / - / - / - / 2 / -
SITEIIATCYTC: found in the promoter regions of cytochrome
genes (Cytc-1, Cytc-2) in Arabidopsis / TGGGCY / 1 / - / 2 / 1 / - / - / - / 1 / - / - / 2 / 1 / - / 1 / - / - / - / 1 / 2 / 3 / - / - / - / -
-10PEHVPSBD: found in the barley (H.v.) chloroplast
psbD gene promoter; Involved in the expression of the plastidgene psbD which encodes a photosystem II reaction centerchlorophyll-binding protein that is activated by blue, white or
UV-A light / TATTCT / - / - / - / - / 1 / - / - / - / - / 1 / 1 / - / 1 / - / - / - / - / - / - / 1 / - / - / - / 1
GATA Box: Required for high level, light regulated, and tissue specific expression; Conserved in the promoter of all LHCII type I Cab genes (Gilmartin et al., 1990). / GATA / 9 / 7 / 7 / 3 / 2 / 3 / 4 / 5 / 3 / 3 / 4 / 5 / 4 / 6 / 2 / 2 / 7 / 6 / 1 / 3 / 1 / 3 / 9 / 3
CIACADIANLELHC: Region necessary for circadian expression of tomato (L.e.) Lhc gene / CAANNNNATC / - / - / 1 / - / - / - / - / - / - / - / - / - / - / 1 / - / - / 1 / - / 1 / - / - / - / - / -
CDA1ATCAB2: binding site in DtRE (dark response element) f of chlorophyll a/b-binding protein2 (CAB2)gene, circadian clock-assosiated / CAAAACGC / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / -
EVENINGAT: Cis element Required forcircadian control of gene expression / AAAATATCT / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / -
Fermentative pathway regulated
ANAERO3CONSENSUS: One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway / TCATCAC / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / 1
ANAERO1CONSENSUS: One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway / AAACAAA / - / - / - / - / - / 1 / - / 1 / 1 / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / -
ACGTABOX: responsible forsugar repression / TACGTA / 2 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
ANAERO4CONSENSUS: One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway / GTTTHGCAA / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / -
ANAERO2CONSENSUS: involved in the fermentative pathway / AGCAGC / 1 / - / 1 / 1 / - / 1 / - / 1 / - / - / - / - / - / 3 / - / - / 3 / - / 2 / 3 / - / - / - / -
CMSRE1IBSPOA: Carbohydrate Metabolite Signal Responsive Element, involved in the
sucrose-inducible expression / TGGACGG / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / -
PYRIMIDINEBOXOSRAMY1A: Gibberellin-respons cis-element of GARE and pyrimidine box are
partially involved in sugar repression / CCTTTT / - / - / - / - / - / 2 / - / - / - / - / 1 / - / 1 / - / 1 / 1 / - / - / - / - / 2 / 2 / - / -
WBOXHVISO1: participates in sugarRT signaling in barley by binding to the sugar-responsive elements / TGACT / - / 1 / - / 1 / - / - / - / - / - / 1 / - / 1 / 1 / 1 / - / - / 2 / - / 1 / - / - / - / 1 / 1
ANAERO5CONSENSUS: One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway / TTCCCTGTT / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
MYBGAHV: Central element of gibberellin response complex, involving in sugar repression / TAACAAA / - / - / - / - / - / - / 1 / - / - / - / - / 1 / - / - / - / - / 1 / - / 1 / - / - / - / - / -
Related with growth and basal metabolism
CACTFTPPCA1: cis-Regulatory elements for mesophyll-specific gene expression / YACT / 8 / 11 / 11 / 9 / 10 / 6 / 3 / 8 / 4 / 6 / 11 / 6 / 7 / 12 / 9 / 5 / 4 / 4 / 5 / 5 / 9 / 3 / 7 / 11
CARGCW8GAT: currently the only reported member of the plant MADS domain family of transcriptional regulators that preferentially accumulates during embryo development / CWWWWWWWWG / 2 / 2 / 2 / - / 2 / 2 / - / 2 / - / - / - / 4 / 2 / - / - / - / 2 / - / - / - / 2 / - / - / -
CAAT Box: responsible for promoter activity, seed specificity, and temporal regulation of legA gene (storage proteins ) / CAAT / 5 / 4 / 4 / 2 / 3 / 5 / 2 / 5 / 1 / 1 / 4 / 10 / 5 / 1 / 2 / 2 / 5 / 2 / 7 / 1 / 1 / - / 6 / 6
ARR1AT: transcriptional activators / NGATT / 2 / 4 / 4 / 1 / 3 / 4 / 3 / 2 / 3 / - / 3 / 5 / 5 / 1 / 2 / 4 / 5 / 5 / 5 / - / 4 / - / 4 / 4
DOFCOREZM: Core site required for binding of Dof proteins in maize Dof1 and Dof2 transcription factors are associated with
expression of multiple genes involved in carbon metabolism inmaize / AAAG / 5 / 2 / 3 / 4 / 6 / 4 / 6 / 5 / 6 / 7 / 9 / 3 / 8 / 3 / 5 / 6 / 3 / 2 / 8 / 2 / 6 / 8 / 2 / 1
ABRERATCAL: "Repeated sequence motifs" identified
in the upstream regions of 162 Ca(2+)-responsive upregulated genes / MACGYGB / - / - / 3 / 1 / 1 / 3 / 2 / - / 1 / 1 / - / - / - / 3 / 2 / 1 / - / - / - / 2 / - / 1 / 1 / -
ROOTMOTIFTAPOX1: Motif found both inpromoters of rolD / ATATT / 2 / 1 / 3 / 3 / - / 4 / 4 / 2 / 3 / 2 / 3 / 4 / 7 / - / - / - / 1 / - / 1 / - / - / 2 / 4 / 4
POLASIG1: PolyA signal / AATAAA / - / 1 / - / 2 / 1 / - / 1 / - / - / 1 / 3 / 3 / 2 / - / - / 2 / - / - / - / - / - / - / 3 / 1
POLASIG3: Plant polyA signal / AATAAT / 2 / 1 / - / 1 / 1 / 2 / - / - / 1 / - / 1 / 1 / - / - / - / - / 1 / - / - / - / 1 / - / 6 / 2
RAV1AAT: The expression level of RAV1 were relatively high in rosette leaves and roots / CAACA / - / 5 / 2 / - / 1 / - / 2 / 2 / 2 / 5 / 1 / 1 / - / - / 1 / 2 / 2 / 1 / 4 / - / - / 2 / 3 / 1
SEF4MOTIFGM7S: consensus sequence found in 5'upstream region (-199) of beta-conglycinin / RTTTTTR / - / - / 1 / 1 / - / - / - / 2 / 1 / - / - / - / 2 / 1 / - / 1 / - / 1 / 1 / - / 1 / - / - / 1
TAAAGSTKST1: Target site for trans-acting StDof1 protein controlling
guard cell-specific gene expression / TAAAG / 2 / - / 1 / - / 1 / 1 / 1 / 2 / - / 2 / - / 3 / 2 / - / 1 / 1 / 2 / - / 4 / - / 1 / 1 / - / -
MYBST1: transcriptional activator / GGATA / - / 1 / 1 / 2 / - / - / 2 / 4 / - / - / 2 / 1 / 2 / 2 / - / 1 / 2 / 1 / - / 2 / 1 / 2 / 1 / 1
NODCON2GM: nodulin consensus sequences / CTCTT / 1 / - / 3 / - / 1 / 2 / 1 / 1 / 2 / 1 / 3 / - / 3 / 1 / 1 / 2 / 1 / - / 3 / 3 / - / - / - / 3
OSE2ROOTNODULE: One of the consensus sequence motifs of organ-specific elements (OSE) characteristic of the promoters activated in infected cells of root nodules / CTCTT / 1 / - / 3 / - / 1 / 2 / 1 / 1 / 2 / 1 / 3 / - / 3 / 1 / 1 / 2 / 1 / - / 3 / 3 / - / - / - / 3
GTGANTG10: "GTGA motif" found in the promoter of the tobacco late pollen gene g10 / GTGA / 5 / 8 / 4 / 4 / 7 / 4 / 4 / 1 / 7 / 4 / 3 / 3 / 6 / 8 / 4 / 3 / 4 / 4 / 1 / 7 / 4 / 1 / 9 / 8
POLLEN1LELAT52: One of two co-dependent regulatory elements responsible for pollen specific activation of tomato lat52 gene / AGAAA / 2 / - / 3 / - / 3 / 2 / 1 / 1 / 4 / 2 / - / 1 / 4 / 1 / - / 1 / 2 / 1 / 2 / - / 3 / 2 / 4 / 1
RHERPATEXPA7: Root Hair-specific cis-Elements / KCACGW / 1 / 2 / 1 / 3 / 1 / - / - / - / 2 / 2 / - / - / 1 / 2 / - / 2 / 1 / 3 / - / - / - / 1 / 1 / 1
CGACGOSAMY3: function as a coupling element for the G box element / CGACG / 1 / 3 / 1 / - / - / - / 1 / 1 / - / - / 1 / - / 1 / 1 / 2 / 4 / 1 / 3 / - / 2 / - / 1 / 1 / -
CGCGBOXAT: Multiple CGCG elements are found in promoters of many genes, involved in multiple signaling pathways in plants / VCGCGB / 2 / 2 / - / - / - / - / 2 / 2 / 2 / 2 / - / - / 10 / 6 / 12 / 2 / - / 10 / - / 10 / 22 / 14 / 4 / 4
SURECOREATSULTR11: Core of sulfur-responsive element / GAGAC / 1 / 1 / - / 2 / 1 / 1 / - / 1 / 1 / 1 / - / 1 / 2 / 6 / 2 / - / - / 2 / 3 / 1 / 2 / 1 / - / 3
MYBPZM: Maize P gene specifies red pigmentation of kernel pericarp,cob, and other floral organs / CCWACC / - / 1 / - / - / - / 1 / 1 / 1 / 1 / 1 / 1 / 2 / - / - / 1 / - / - / 1 / - / 1 / - / 1 / 2 / 2
CACGTGMOTIF: Binding site of Arabidopsis GBF4; C.roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct
interaction with the G-box / CACGTG / - / - / 2 / 2 / - / - / - / - / 2 / - / - / - / - / 2 / - / 2 / - / - / - / - / - / - / - / -
GAREAT: Gibberellin inducible and response during Arabidopsis seed
germination / TAACAAR / - / - / - / - / - / - / 1 / - / - / 1 / - / 1 / - / - / - / - / 1 / - / 1 / - / - / - / - / -
E2FCONSENSUS: E2F-DP-binding motifs
transcription factors that induce the transcription of genes required for cell cycle progression and DNA replication / WTTSSCSS / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / 5 / - / - / -
HEXAMERATH4: cis-elements regulating the expression of anArabidopsis histone H4 gene / CCGTCG / 1 / 1 / 1 / - / - / - / 1 / - / - / - / - / - / - / - / 1 / 1 / - / 1 / - / 1 / - / - / - / -
LEAFYATAG: Target sequence of LEAFY in the intron of AGAMOUS gene in Arabidopsis / CCAATGT / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
L1BOXATPDF1: Involved in L1 layer-specific expression / TAAATGYA / 1 / - / - / - / 1 / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
HEXMOTIFTAH3H4: histone DNA binding protein, important roles in regulation of replication / ACGTCA / - / - / - / - / - / - / 1 / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / -
QELEMENTZMZM13: ZM13 gene promoter, Involved in expression enhancing activity, ZM13 is a pollen-specific maize gene / AGGTCA / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / -
BOXIINTPATPB: plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes / ATAGAA / - / - / - / - / - / 1 / - / - / 1 / 1 / - / 3 / - / 1 / - / 1 / 1 / - / - / - / 1 / - / 1 / -
AMYBOX1 common to most actively transcribed genes in plants. Two consensus sequences, TAACAAGA and TATCCAT, were found in the 5' flanking regions of alpha-amylase genes of rice, barley and wheat / TAACARA / - / - / - / - / - / - / 1 / - / - / 1 / - / 2 / - / - / - / - / 1 / - / 1 / - / - / - / 1 / -
AMYBOX2: like AMYBOX1 / TATCCAT / - / - / - / - / - / - / 1 / - / - / - / 1 / - / - / - / - / - / 1 / - / - / - / - / - / - / -
SITEIOSPCNA: May contribute in part to transcriptional activation / CCAGGTGG / - / 1 / - / - / 1 / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
GCN4OSGLUB1: "GCN4 motif" found in GluB-1 gene in rice, required for
endosperm-specific expression / TGAGTCA / - / 1 / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / -
INTRONLOWER: 3' intron-exon splice junctions / TGCAGG / - / - / - / 2 / - / - / - / - / - / 3 / - / - / - / 1 / 1 / - / - / - / - / 1 / - / - / - / -
GARE2OSREP1: Gibberellin-responsive element / TAACGTA / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
-300CORE: Binds with BPBF (Barley PBF); PBF is a DNA-binding protein of the DOF class of transcription factors, endosperm-specific expression / TGTAAAG / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / -
ACGTCBOX: RITA-1 binding site, is highlyRT expressed during seed development / GACGTC / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 2 / - / - / - / - / - / 2 / - / -
ACGTOSGLUB1: "ACGT motif" found in GluB-1 gene in rice, required forendosperm-specific expression / GTACGTG / 1 / - / 1 / - / - / - / 1 / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / -
CPBCSPOR: The sequence critical for Cytokinin-enhanced Protein Binding in vitro / TATTAG / - / - / - / 1 / - / - / - / - / 1 / - / - / - / 1 / - / - / - / - / - / - / - / 1 / - / - / 1
MYBPLANT: Plant MYB binding site; Consensus sequence related to box P in promoters of phenylpropanoid biosynthetic genes / MACCWAMC / - / 1 / - / 1 / - / 2 / - / - / - / - / - / - / - / - / 2 / - / 1 / - / - / - / - / 1 / - / -
BS1EGCCR: cis-elements required for vascular expression of the cinnamoyl CoA reductase gene and for protein-DNA complex formation / AGCGGG / - / - / 1 / - / 1 / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / 2 / - / - / -
CTRMCAMV35S: Inveryed GAGA, Can enhance gene expression / TCTCTCTCT / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 3 / - / -
CANBNNAPA: embryo- and endosperm-specific transcription of napin (storage protein) gene / CNAACAC / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / 1 / - / -
AACACOREOSGLUB1: motifs found in rice glutelin genes, involved in controlling the endosperm-specific expression / AACAAAC / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / - / - / - / - / - / - / -
SP8BFIBSP8BIB: found in the 5' upstream region of three differnt genes coding for sporamin and beta-amylase / TACTATT / - / - / - / - / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1
-300ELEMENT: Present upstream of the promoter from the B-hordein gene of barley and the alpha-gliadin, gamma-gliadin, and low molecular weight glutenin genes of wheat. Differential gene expression in the developing barley endosperm / TGHAAARK / 1 / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / - / 1 / 1 / - / -
Table S2.Specific primers from bglu1 to bglu26. The sequence is given from 5´to 3´. Specificity was mostly achieved by placing nucleotide mismatches at the 3´end of the primers. The melting temperature was calculated with Primer3. The expected PCR product size are indicated when using either cDNA or genomic DNA as template. The higher size of the genomic product is due to the presence of an intron.
Primer Name / Sequence (5´-3´) / Tm (°C) / Product Size (pb)Bglu1F / GCCTTAGGAGCCACCTAGTAG / 60.79 / 308
671
Bglu1R / CAGTATCCTTTCCGGATGA / 60.03
Bglu2F / TCATCAACTTGTTGCTAGAGAAT / 59.41 / 105
202
Bglu2R / GTCTTATCTAAGAATCCGCCG / 61.46
Bglu3F / GGCCCATCTGCTAGGAC / 60.79 / 301
516
Bglu3R / GTGATCCGCTATCCAATCT / 59.03
Bglu4F / AAGGATAAGCAGTCAGCTGC / 61.12 / 382
522
Bglu4R / TGATAGGAATTGGCTCCAG / 60.18
Bglu5F / GAGAATGGAATCGGGGATA / 61.2 / 315
435
Bglu5R / CGTCTTGTCTTTCTTCTTGGA / 60.96
Bglu6F / AATGCGCTAACCCAACC / 61.08 / 169
291
Bglu6R / TTGTCATATGGCACACGG / 61.66
Bglu7F / ACGTTGACAATGGCGAC / 60.76 / 283
360
Bglu7R / TAGGCGCTGCCAGC / 61.07
Bglu8F / CGGCGGTTTTTTAGATAAGAGT / 62.1 / 192
657
Bglu8R / GATCCCGTTGGAGTGATTATC / 62.03
Bglu9F / TACCAGGTCGAAGGCG / 61.01 / 184
3155
Bglu9R / ATGAGAATCTGTAGGAGCTGAGA / 60.94
Bglu10F / GGTGACTATCCGGCCAG / 61.64 / 219
7686
Bglu10R / GGGGACACCATTTCGAATA / 62.1
Bglu11F / ACGTCTTCCTCGTCGTGT / 60.95 / 210
396
Bglu11R / GCATCCTACCTGCATGAGTAA / 61.61
Bglu12F / TTTGGAACAAAAAAATGTACAGTG / 61.48 / 275
515
Bglu12R / CCAACAACTCCTTTTTGCA / 61.25
Bglu13F / CGTCACCTGCACCCA / 61.71 / 310
383
Bglu13R / GTCTCGGGCCGTCAG / 61.75
Bglu14F / GCCGGACAGCCTGATCCAT / 62.41 / 225
342
Bglu14R / GTACCTTGTCCTTGCCGT / 60.13
Bglu15F / AGAGGAGAAGGAGAAGGCTG / 61.62 / 262
630
Bglu15R / AGCGTCGAACCCCATATT / 61.87
Bglu16F / CTGGGACATGGAACCTG / 60.04 / 194
386
Bglu16R / GTTTTCAGCAAGGATCATTGTA / 60.51
Bglu17F / CGGGGGAAGGACCTAAC / 61.89 / 264
502
Bglu17R / AAACCGGTAGGCATCAAAA / 61.81
Bglu18F / TCCAGCTACATGAAGGGG / 61.24 / 366
644
Bglu18R / GATGTAGCTCCTGTAGAACCG / 60.3
Bglu19F / GTTCCATGGGGGCTCT / 61.09 / 310
396
Bglu19R / CCTTGGGGTACCGGA / 60.45
Bglu20F / CGAAATTAGAGGATGATCTGC / 60.2 / 212
325
Bglu20R / GGGTATCCGTGTCAAATTG / 60.2
Bglu21F / CCCTTCGACAAGAACGG / 61.88 / 178
793
Bglu21R / TTCTGGAGGGAGGTGAAAG / 61.79
Bglu22F / CAAGGTGGGGATGGTTATACTA / 61.34 / 174
292
Bglu22R / GTACCCATATAGCCACTCGAAA / 61.6
Bglu23F / GAACGCCTTCGTCTCG / 60.71 / 183
394
Bglu23R / GCATCACTCCACTGCG / 60.09
Bglu24F / ATGTGATATTGACCCCTACACA / 60.53 / 216
477
Bglu24R / ACTGTAGTGCTGATATTGGGTATTT / 60.54
Bglu25F / CAAATAGCCAATATTAGCACTACAAC / 60.63 / 270
350
Bglu25R / TTCATAGCCTTTGATAAACTTGCTAT / 61.84
Bglu26F / GCGCTCTCTCTAGCTACTCATC / 61.35 / 227
316
Bglu26R / GGAGTAGCCGGCCGT / 62.57