Function and Biotechnological potential of seed Transcription Factors

Transcription factors (TFs) are regulatory proteins that have a key role in evolution and have also a great biotechnological potential. They are crucial in regulating gene expression in a combinatorial way and they have been important in domestication and plant breeding; some examples are Teosinte Branched 1 that affects plant architecture (branching), the Green Revolution Genes (GRAS) responsible of the semi-dwarf cultivars of presently grown cereals, the DOF1 gene that improve nitrogen assimilation and growth under low nitrogen conditions, etc (Doebly et al, 1997; Peng et al., 1999; Yanagisawa et al., 2004). Three TFs: BLZ2, BPBF and GAMYB, that have been characterized in our group (see enclosed references), are important for seed protein content and weight per 100 seeds, two aspects affecting yield in barley.

The two main lines of research are:

• Transcriptional networks in the Triticeae seeds: comparison between Hordeum vulgare and Brachypodium distachyon (MICINN; BFU2009-11809)

  The aim of this line is to discover the TFs involved in two phases of seed development (maturation when storage products are accumulated in endosperm and germination when they are hydrolyzed), as well as, the TFs own regulation. This research is carried out in two plant species Hordeum vulgare L. (barley), an important european crop and Brachypodium distachyon, a model plant for the Triticeae that has been recently sequenced and is easily transformable through the Ti plasmid procedure.

• Transcriptional networks and their evolution in the Brassicaceae (MICINN-EUI2008-03716; Trilateral Germany-France-Spain Action: George Coupland (Coordinator); Javier Paz-Ares; Pilar Carbonero; Vincent Colot; Detlef Weigel; Alexander Ke; Hadi Quesneville)

  The aim of this project is to identify key promoter motifs associated with germination gene expression patterns, to directly determine the number of binding sites for selected TFs across the genomes of sequenced Arabidopsis thaliana and Arabidopsis lyrata species, and of Arabis alpina that will be sequenced in this project, and how conserved the number and positions of these sites are between these species.

Relevant results

TFs interacting with cis-motifs from seed specific genes expressed during endosperm development and seed germination in barley

Our group has characterized transcription factors of the bZIP (BLZ1-BLZ4; Opaque-2 subfamily),DOF (BPBF, SAD, HvDOF19, HvDOF17) and MYB (GAMYB of the R2R3MYB subfamily; HvMCB1 and Hv MYBS3 of the R1MYB-SHAQYF subfamily) classes binding to conserved cis-motives present in the promoters of Seed Storage Protein (SSP) genes that are expressed in the developing endosperm. During barley post-germination, aleurone cells (located in the endosperm external layer) switch from dormant to a very high metabolic activity where GAs, synthesised in and transported from the embryo, activate the hydrolases that will degrade protein and starch reserves accumulated during seed maturation. Barley cv Himalaya aleurone layers are very easy to isolate and have become a model system to study GA and ABA responses. Several cis-motives in the hydrolase gene promoters are coincident with those found in the SSP gene promotors and the TFs recognizing them are also expressed in aleurone.Some of them are repressors in one phase and activators in the other while other TFs are either activators or repressors in both phases of seed development (maturation and germination). Here again, the combinatorial interaction of TFs, their relative abundance and their affinities for the cis-motives are important and also their own regulation.

Similarities between transcriptional regulation in seeds of Arabidopsis thaliana and Hordeum vulgare

Among the analogies on transcriptional regulation on different seed types, we have studied the similarities on functionality of the bZIPs of the OPAQUE2 family (BLZ1/BLZ2 and AtbZIP10/AtbZIP25) and the B3 family (AtFUS3/HvFUS3; ABI3/VIP1). The evolution of the DOF family of TFs from the green cellular algae to vascular plants has also been studied.

Recent Publications

Iglesias-Fernandez, R.; Barrero-Sicilia, C.; Carrillo-Barral, N.; Onate-Sanchez, L.; Carbonero, P. 2013. "Arabidopsis thaliana bZIP44: a transcription factor affecting seed germination and expression of the mannanase encoding gene AtMAN7". Plant J.

Hernando-Amado S., Gonzalez-Calle V., Carbonero P., Barrero-Sicilia C. 2012. "The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expresión profiling" BMC Plant Biology 12: 202

Rodríguez-Gacio, M.C.; Iglesias-Fernández, R.; Carbonero, P.; Matilla, A.J. 2012. "Softening-up mannan-rich cell walls". Journal of Experimental Botany 63: 3976-3988.

Rueda-Romero, P.; Barrero-Sicilia, C.; Gómez-Cadenas, A.; Carbonero, P.; Oñate-Sánchez, L. 2012. "Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14". Journal of Experimental Botany 63:1937–1949.

Barrero-Sicilia, C.; Hernando-Amado, S.; González-Melendi, P.; Carbonero, P. 2011. "Structure, expression profile and subcellular localisation of four different sucrose synthase genes from barley". Planta 234:391-403.

Castrillo, G.; Turck, F.; Leveugle, M.; Lecharny, A.; Carbonero, P.; Coupland, G.; Paz-Ares, J.; Oñate-Sánchez, L. 2011. "Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors". PLoS One 6:e21524.

Iglesias-Fernández, R.; Rodríguez-Gacio, M.C.; Barrero-Sicilia, C.; Carbonero, P.; Matilla, A. 2011. "Three endo-beta-mannanase genes expressed in the micropylar endosperm and in the radicle influence germination of Arabidopsis thaliana seeds". Planta 233:25-36.

Iglesias-Fernandez, R.; Rodríguez-Gacio, M.C.; Barrero-Sicilia, C.; Carbonero, P.; Matilla, A.J. 2011. "Molecular analysis of endo-beta-mannanase genes upon seed imbibition suggest a cross-talk between radicle and micropylar endosperm during germination of Arabidopsis thaliana". Plant Signaling & Behavior 6:80-82.

Moreno-Risueno, M.A.; Gonzalez, N.; Diaz, I.; Parcy, F.; Carbonero, P.; Vicente-Carbajosa, J. 2008. "FUSCA3 from barley unveils a common transcriptional regulation of seed-specific genes between cereals and Arabidopsis". Plant Journal. 53(6):882-894

Moreno-Risueno, M.A.; Diaz, I.; Carrillo, L.; Fuentes, R.; Carbonero, P. 2007. "The HvDOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone". Plant Journal. 51(3):352-365

Moreno-Risueno, M.A.; Martinez, M.; Vicente-Carbajosa, J.; Carbonero, P. 2007. "The family of DOF transcription factors: from green unicellular algae to vascular plants". Molecular genetics and genomics. 277(4):379-390