Abstract
Legume seeds represent a major source of proteins for human and livestock diets. The model legume Medicago truncatula is characterized by a process of seed development very similar to that of other legumes, involving the interplay of sets of transcription factors (TFs). Here, we report the first expression profiling of over 700 M. truncatula genes encoding putative TFs throughout seven stages of seed development, obtained using real-time quantitative RT-PCR. A total of 169 TFs were selected which were expressed at late embryogenesis, seed filling or desiccation. The site of expression within the seed was examined for 41 highly expressed transcription factors out of the 169. To identify possible target genes for these TFs, the data were combined with a microarray-derived transcriptome dataset. This study identified 17 TFs preferentially expressed in individual seed tissues and 135 corresponding co-expressed genes, including possible targets. Certain of the TFs co-expressed with storage protein mRNAs correspond to those already known to regulate seed storage protein synthesis in Arabidopsis, whereas the timing of expression of others may be more specifically related to the delayed expression of the legumin-class storage proteins observed in legumes.
Similar content being viewed by others
References
Aida M, Ishida T, Tasaka M (1999) Shoot apical meristem and cotyledon formation during Arabidopsis embryogenesis: interaction among the CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS genes. Development 126:1563–1570
Ané JM, Zhu H, Frugoli J (2008) Recent advances in Medicago truncatula genomics. Int J Plant Genomics Article ID 256597, doi:10.1155/2008/256597
Bensmihen S, Giraudat J, Parcy F (2005) Characterization of three homologous basic leucine zipper transcription factors (bZIP) of the ABI5 family during Arabidopsis thaliana embryo maturation. J Exp Bot 56:597–603
Boulter D, Evans MI, Ellis RJ, Shirsat A, Gatehouse JA, Croy RRD (1987) Differential gene expression in the development of Pisum sativum. Plant Physiol Biochem 25:283–289
Bouton S, Viau L, Lelievre E, Limami A (2005) A gene encoding a protein with a proline-rich domain (MtPPRD1), revealed by suppressive subtractive hybridization (SSH), is specifically expressed in the Medicago truncatula embryo axis during germination. J Exp Bot 56:825–832
Brocard-Gifford IM, Lynch TJ, Finkelstein RR (2003) Regulatory networks in seeds integrating developmental, abscisic acid, sugar, and light signaling. Plant Physiol 131:78–92
Cernac A, Benning C (2004) WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. Plant J 40:575–85
Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11:113–116
Chen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T, Mauch F, Luan S, Zou G, Whitman SA (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell 14:559–574
Chern MS, Bobb AJ, Bustos MM (1996a) The regulator of MAT2 (ROM2) protein binds to early maturation promoters and represses PvALF-activated transcription. Plant Cell 8:305–321
Chern MS, Eiben HG, Bustos MM (1996b) The developmentally regulated bZIP factor ROM1 modulates transcription from lectin and storage protein genes in bean embryos. Plant J 10:135–148
Cook RD (1999) Medicago truncatula—A model in the making! Curr Opin Plant Biol 2:301–304
Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root and shoot specific genes. Plant J 38:366–379
De Folter S, Busscher J, Colombo L, Losa A, Angenent G (2004) Transcript profiling of transcription factor genes during silique development in Arabidopsis. Plant Mol Biol 56:351–366
Diaz I, Vicente-Carbajosa J, Abraham Z, Martínez M, Isabel-La Moneda I, Carbonero P (2002) The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development. Plant J 29:453–464
Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics 6:202–211
Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 99:10611–10616
Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY super family of plant transcription factors. Trends Plant Sci 5:199–206
Finkelstein RR, Wang ML, Lynch TJ, Rao S, Goodman HM (1998) The Arabidopsis abscisic acid response locus ABI4 encodes an APETALA 2 domain protein. Plant Cell 10:1043–1054
Flanagan CA, Ma H (1994) Spatially and temporally regulated expression of the MADS-box gene AGL2 in wild-type and mutant Arabidopsis flowers. Plant Mol Biol 26:581–595
Gallardo K, Le Signor C, Vandekerckhove J, Thompson RD, Burstin J (2003) Proteomics of Medicago truncatula seed development establishes the time frame of diverse metabolic processes related to reserve accumulation. Plant Physiol 133:664–682
Gallardo K, Firnhaber C, Zuber H, Héricher D, Belghazi M, Henry C, Küster H, Thompson R (2007) A combined proteome and transcriptome analysis of developing Medicago truncatula seeds: Evidence for metabolic specialization of maternal and filial tissues. Mol Cell Proteomics 6(12):2165–2179
Garcia D, Fitz Gerald JN, Berger F (2005) Maternal control of integument cell elongation and zygotic control of endosperm growth are coordinated to determine seed size in Arabidopsis. Plant Cell 17:52–60
Gatehouse JA, Evans IM, Croy RRD, Boulter D (1986) Differential expression of genes during legume seed development. Philosophical Transactions of the Royal Society of London. Biol Sci 314:367–384
Graham MA, Silverstein KA, Cannon SB, VandenBosch KA (2004) Computational identification and characterization of novel genes from legumes. Plant Physiol 135:1179–1197
Hardtke CS, Berleth T (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J 17:1405–1411
Kagaya Y, Toyoshima R, Okuda R, Usui H, Yamamoto A, Hattori T (2005) LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3. Plant Cell Physiol 46:399–406
Kroj T, Savino G, Valon C, Giraudat J, Parcy F (2003) Regulation of storage protein gene expression in Arabidopsis. Development 130:6065–6073
Kwong RW, Bui AQ, Lee H, Kwong LW, Fischer RL, Goldberg RB, Harada JJ (2003) LEAFY COTYLEDON1-LIKE defines a class of regulators essential for embryo development. Plant Cell 15:5–18
Lara P, Oñate-Sánchez L, Abraham Z, Ferrándiz C, Díaz I, Carbonero P, Vicente-Carbajosa J (2003) Synergistic activation of seed storage protein gene expression in Arabidopsis by ABI3 and two bZIPs related to OPAQUE2. J Biol Chem 278:21003–21011
Li G, Chandrasekharan MB, Wolffe AP, Hall TC (2001) Chromatin structure and phaseolin gene regulation. Plant Mol Biol 46:121–129
Long JA, moan EI, Medford JI, Barton MK (1996) A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature 404:66–69
Lotan T, Ohto M, Yee KM, West MA, Lo R, Kwong RW, Yamagishi K, Fischer RL, Goldberg RB, Harada JJ (1998) Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 93:1195–1205
Lu P, Porat R, Nadeau JA, O’Neill SD (1996) Identification of a meristem L1 layer-specific gene in Arabidopsis that is expressed during embryonic pattern formation and defines a new class of homeobox genes. Plant Cell 8:2155–2168
Mayer KF, Schoof H, Haecker A, Lenhard M, Jurgens G, Laux T (1998) Role of WUSCHEL in regulating stem cell fate in Arabidopsis shoot meristem. Cell 95:805–815
Meinke DW, Chen J, Beachy RN (1981) Expression of storage-protein genes during soybean seed development. Planta 153:130–139
Parcy F, Valon C, Raynal M, Gaubier-Comella P, Delseny M, Giraudat J (1995) Regulation of gene expression programs during Arabidopsis seed development: roles of the ABI3 locus and of endogenous abscisic acid. Plant Cell 6:1567–1582
Parcy F, Valon C, Kohara A, Miséra S, Giraudat J (1997) The ABSCISIC ACID-INSENSITIVE3, FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects of Arabidopsis seed development. Plant Cell 9:1265–1277
Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80:847–857
Rajjou L, Gallardo K, Debeaujon I, Vandekerckhove J, Job C, Job D (2003) The effect of ά-amanitin on the arabidopsis seed proteome highlights the distinct roles of stored and neosynthesized mRNAs during germination. Plant Physiology 134:1598–1613
Ramakers C, Ruijtera JM, Lekanne Deprez RH, Moormana AFM (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339:62–66
Reidt W, Wohlfarth T, Ellerström M, Czihal A, Tewes A, Ezcurra I, Rask L, Bäumlein H (2000) Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product. Plant J 21:401–408
Riechman JL (2002) Transcriptionnal regulation: a genomic overview (September, 30, 2002). In Sommerville CR and Meyerowitz EM (eds) Arabidopsis Book, American Society of Plant Biologists, Rockville, MD (http://www.aspb.org/publications/Arabidopsis/)
Riechman JL, Ratcliffe OJ (2000) A genomic perspective on plant transcription factors. Curr Opin Plant Biol 3:423–434
Rook F, Gerrits N, Kortstee A, van Kampen M, Borrias M, Weisbeek P, Smeekens S (1998) Sucrose-specific signalling represses translation of the Arabidopsis ATB2 bZIP transcription factor gene. Plant J 15:253–263
Ruuska SA, Girke T, Benning C, Ohlrogge JB (2002) Contrapuntal networks of gene expression during Arabidopsis seed filling. Plant Cell 14:1191–1206
Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blocker H, Perez-Alonso M, Obermaier B et al (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 408:820–822
Santos Mendoza M, Dubreucq B, Miquel M, Caboche M, Lepiniec L (2005) LEAFY COTYLEDON 2 activation is sufficient to trigger the accumulation of oil and seed specific mRNAs in Arabidopsis leaves. FEBS Lett 579:4666–4670
Schruff MC, Spielman M, Tiwari S, Adams S, Fenby N, Scott RJ (2006) The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development 133:251–61
Slabas AR, Fordham-Skelton AP, Fletcher D, Martinez-Rivas JM, Swinhoe R, Croy RR, Evans IM (1994) Characterisation of cDNA and genomic clones encoding homologues of the 65 kDa regulatory subunit of protein phosphatase 2A in Arabidopsis thaliana. Plant Mol Biol 26:1125–1138
Sozzani R, Maggio C, Varotto S, Canova S, Bergounioux C, Albani D, Cella R (2006) Interplay between Arabidopsis activating factors E2Fb and E2Fa in cell cycle progression and development. Plant Physiol 140(4):1355–1366
Sturn A, Quackenbush J, Trajanoski Z (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18:207–208
Suzuki A, Wu CY, Washida H, Takaiwa F (1998) Rice MYB protein OSMYB5 specifically binds to the AACA motif conserved among promoters of genes for storage protein glutelin. Plant Cell Physiol 39:555–559
Suzuki M, Wang HH, McCarty DR (2007) Repression of the LEAFY COTYLEDON1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes. Plant Physiol 143:902–11
Takatsuji H (1999) Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol Biol 39:1073–1078
Tsukagoshi H, Morikami A, Nakamura K (2007) Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings. Proc Natl Acad Sci USA 104:2543–2547
Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JM, Chueng F, Town CD (2007) Legume transcription factors: global regulators of plant development and response to the environment. Plant Physiol 144:538–549
Unger E, Parsons RL, Schmidt RJ, Bowen B, Roth BA (2002) Dominant negative mutants of Opaque2 suppress transactivation of a 22-kD zein promoter by Opaque2 in maize endosperm cells. Plant Cell 5:831–841
Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol 138:1195–1204
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3
Vicente-Carbojosa V, Carbonero P (2005) Seed maturation: developing an intrusive phase to accomplish a quiescent state. Int J Dev Biol 49:645–651
Walling L, Drews GN, Goldberg RB (1986) Transcriptional and post-transcriptional regulation of soybean seed protein mRNA levels. Proc Natl Acad Sci USA 83:2123–2127
Weber H, Borisjuk L, Heim U, Buchner P, Wobus U (1995) Seed coat-associated invertases of fava bean control both unloading and storage functions: cloning of cDNAs and cell type-specific expression. Plant Cell 7:1835–1846
Yamamoto MP, Onodera Y, Touno SM, Takaiwa F (2006) Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. Plant Physiol 141:1694–1707
Acknowledgements
We are grateful to all the members of laboratory, particularly Vincent Savois for his very valuable technical support with bioinformatics analyses; Judith Burstin and Michael Bourgeois for helpful discussions; Delphine Hericher and Françoise Moussy for useful assistance with plant growth. In addition, we would also like to acknowledge Dr. Hugues Barbier (Max Planck Institute for Plant Breeding Research MPIZ, Koeln, Germany) for advice and help with RNA extraction; Helge Küster and Christian Firnhaber (Bielefeld University, Germany) who have developed the Mt16kOLI1 microarrays for fruitful collaboration. Research was supported by the FP6 EU project Grain Legumes (FOOD-CT-2004-506223).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
11103_2008_9320_MOESM1_ESM.ppt
Experimental variation and assessment of reproducibility of 19,000 real-time RT-PCR reactions. Comparisons of log10 relative expression of all 19,000 real-time RT-PCR reactions obtained between the two biological replicates. The relative expression values from the first biological replicate (horizontal axis) were plotted against the relative expression values from the second biological replicate (vertical axis). The dotted line represents the cut off limit of the relative expression values taken for subsequent analyses, values with a lower relative expression being considered as missing data. Pearson’s correlation coefficient (R) was calculated and is indicated. (PPT 685 kb)
Rights and permissions
About this article
Cite this article
Verdier, J., Kakar, K., Gallardo, K. et al. Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling. Plant Mol Biol 67, 567–580 (2008). https://doi.org/10.1007/s11103-008-9320-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11103-008-9320-x