Riassunti dei progetti del corso di dottorato di ricerca in biologia molecolare e cellulare
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Project leader: MARTIN KATER (martin.kater@unimi.it)Location: Department of Biosciences, University of Milan, ItalyRESEARCH PROJECT SUMMARYMining the Molecular Pathways Controlling Rice Reproductive Development Rice is one of the major food crops in the world. However, rice is also a model species for molecular genetics research in monocot species. The lab of Prof. Martin Kater is working for the last 15 years on rice reproductive development. The research is focuses on the molecular control of flower, ovule and seed development (see for instance Dreni et al., 2007, 2011, 2013; Yun et al., 2013; Li et al., 2011). The proposed PhD research project will be integrated in a research line that focuses on the molecular control of ovule and seed development. Recently, the Kater group identified OsMADS13 as a key regulator of ovule and seed development (Dreni et al., 2007). The PhD fellow will be involved in the identification of the regulatory pathways that are controlled by OsMADS13. This research has an unique starting point since a subset of candidate genes were already identified very recently by using a RNA-seq transcriptome analysis approach. For this analysis we used laser microdissected ovule primordia of wild-type and osmads13 mutant plants. Furthermore, we also profiled genome-wide expression of developing seeds in the osmads13 mutant and higher order mutants of genes (OsMADS3, OsMADS58 and OsMADS21) that act redundantly with OsMADS13 during seed development. The research program will focus on the identification of direct targets and their functional characterization. This research should finally provide deep insight into the molecular mechanisms that control the formation of seeds in monocot species. References: Dreni, L., Jacchia, S., Fornara, F., Fornari, M., Ouwerkerk, P., An, G., Colombo, L., Kater, M.M. (2007). The D-lineage MADS-box gene OsMADS13 Controls Ovule Identity in Rice. Plant J. 52, 690-699. Li, H., Liang, W., Hu, Y., Zhu, L., Yin, C., Xu, J, Dreni, L., Kater, M.M., and Zhang, D. (2011). Rice MADS6 Interacts with the Floral Homeotic Genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in Specifying Floral Organ Identities and Meristem Fate. Plant Cell 23, 2536-2552. Dreni, L., Pilatone, A., Yun, D., Erreni, S., Pajoro, A., Caporali, E., Zhang, D., and Kater, M.M. (2011). Functional Analysis of all AGAMOUS Subfamily Members in Rice Reveals their Roles in Reproductive Organ Identity Determination and Meristem Determinacy. Plant Cell 23, 2850-2863. Dreni, L, Osnato, M. and Kater M.M. (2013). The Ins and Outs of the Rice AGAMOUS Subfamily. Mol. Plant 6, 650-664. Yun, D., Liang, W., Dreni, L., Yin, C., Zhou, Z., Kater, M.M. and Zhang, D. (2013). OsMADS16 genetically interacts with OsMADS3 and OsMADS58 in specifying floral patterning in rice. Mol. Plant (in press) Project leader: FEDERICO LAZZARO (federico.lazzaro@unimi.it)Location: Department of Biosciences, University of Milan, ItalyRESEARCH PROJECT SUMMARYDetermine the biological significance of the rNMPs incorporated in genomic DNA Ribonuclease H (RNase H) are enzymes capable of removing the RNA moiety in RNA:DNA hybrid molecules. These enzymes are evolutionary conserved and in eukaryotic cells type 1 and 2 enzymes are present. Mutations in the RNase H2 enzyme, are found in a subset of patients suffering of a rare genetic disease, called Aicardi-Goutières Syndrome (AGS). AGS is a genetic encephalopathy whose clinical features mimic congenital viral infection. Initiation of autoimmunity is caused by interferon (IFN)-stimulatory nucleic acids derived from exogenous (e.g. viral infection) or endogenous sources (i.e. DNA replication, repair or retrotranscription) (Cerritelli & Crouch, 2009). It has been found that replicative DNA polymerases can incorporate rNTPs in place of dNTPs during DNA replication with an unexpected high frequency (~ 1/1000 nt) (McElhinny, Kumar, et al., 2010a; McElhinny, Watts, et al., 2010b). rNMPs embedded in chromosomal DNA represent an imprint, positioned in S-phase, that regulates DNA transactions (Dalgaard, 2012). RNase H enzymes are crucial for the removal of these rNMPs from genomic DNA and for the maintenance of chromosome integrity. Recently we have found that impairment of RNase H1 and RNase H2 in yeast causes rNMPs accumulation in the genome and chronic activation of the post-replication repair (PRR) system which is becoming essential for cell survival (Lazzaro et al., 2012). The high rate of rNTPs mis-incorporation observed under normal conditions (1/1000 dNTPs) suggests possible physiological functions for the presence of rNMPs in newly replicated DNA. In a collaborative study we recently demonstrated that the presence of rNMPs during leading strand DNA synthesis acts as a strand discrimination signal for the Mismatch DNA repair machinery(Ghodgaonkar et al., 2013). In this project we will focus our studies on: 1) mapping of specific regions where DNA replicative polymerases could incorporate rNMPs; 2) analysis of the structural effects of the presence of rNMPs within a DNA molecule using AFM studies in collaboration with Dr. Podestà (Dep. of Physics, Univ. Milano). (3) We will study the effects of rNMPs incorporation on chromatin structures and the biological consequences on DNA repair, transcription, silencing. Cerritelli, S. M., & Crouch, R. J. (2009). Ribonuclease H: the enzymes in eukaryotes. FEBS J, 276(6), 1494–1505. doi:10.1111/j.1742-4658.2009.06908.x Dalgaard, J. Z. (2012). ScienceDirect.com - Trends in Genetics - Causes and consequences of ribonucleotide incorporation into nuclear DNA. Trends Genet, 1–6. doi:10.1016/j.tig.2012.07.008 Ghodgaonkar, M. M., Lazzaro, F., Olivera-Pimentel, M., Artola-Borán, M., Cejka, P., Reijns, M. A., et al. (2013). Ribonucleotides Misincorporated into DNA Act as Strand-Discrimination Signals in Eukaryotic Mismatch Repair. Molecular Cell, 50(3), 323–332. doi:10.1016/j.molcel.2013.03.019 Lazzaro, F., Novarina, D., Amara, F., Watt, D. L., Stone, J. E., Costanzo, V., et al. (2012). RNase H and postreplication repair protect cells from ribonucleotides incorporated in DNA. Mol Cell, 45(1), 99–110. doi:10.1016/j.molcel.2011.12.019 McElhinny, S. A. N., Kumar, D., Clark, A. B., Watt, D. L., Watts, B. E., Lundstr o m, E.-B., et al. (2010a). Genome instability due to ribonucleotide incorporation into DNA. Nat Chem Biol, 6(10), 774–781. doi:10.1038/nchembio.424 McElhinny, S. A. N., Watts, B. E., Kumar, D., Watt, D. L., Lundstr o m, E.-B., Burgers, P. M. J., et al. (2010b). Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc Natl Acad Sci U S A, 107(11), 4949–4954. doi:10.1073/pnas.0914857107 Download 336.57 Kb. Share with your friends:
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