Rice Systems Biology
A thorough understanding of the complex signal transduction
processes in monocots requires appropriate tools, as many aspects of
their development and physiology are different from those of dicots.
Rice, because of its diploid genetics, small genome size, extensive
genetic map, available genome sequence, and relative ease of
transformation, is considered a model monocot. Therefore the structural
and functional analysis of rice has broad practical implications for
the other economically important cereals. Rice is one of the few higher
eukaryotic genomes that have been fully sequenced. The convergence of
genomic sequence, informatics, and protein-protein interaction
technologies has created the opportunity to dramatically enhance our
understanding of cell signaling in the cereals, using rice as a model
system. Development and application of these technologies will augment
traditional approaches to create higher yielding varieties of cereal
We are extending this work through collaboration with Edward Marcotte (U. Texas, Austin) and Inusk Lee (Yonsei University) to develop a probabilistic functional network (RiceNet) for rice and to test its predictive capacity. Probabilistic functional gene networks provide frameworks for integrating heterogeneous functional genomics and proteomics data into objective models of cellular systems. We expect this work to facilitate generation of testable hypotheses regarding specific rice gene functions and associations with abiotic (and biotic) stress responses. The project integrates the computational and proteomics expertise of Marcotte’s and Lee's laboratories with the biological and rice functional genomics expertise available in my laboratory.
RiceNet - Probalistic Functional Gene Network of Oryza Sativa
Rice Array Database - NSF Rice and Xanthomonas whole genome Oligonucleotide Array Project
Rice Interactomics -Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30-60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein-protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance.
Ding et al., Plant Physiology, 2008 (pdf)
Differentially expressed interactome components based on specific biotic stress-response (XA21/NH1/NRR) and abiotic stress-response (SUB1A) 45K NSF arrays 1 day after application of stress. The interactome components that show differential expression in a given stress array are shown as filled nodes. Array experiments are described in Figure 2E. Red-filled nodes represent proteins for which transcripts accumulate in Xoo- resistant responses, including an Xa21-dependent (Xa21-TP309 vs TP309) up-regulated gene (Xa21), Nh1-dependent (Nh1 overexpression vs. LG) up-regulated genes (Pbz1, Sub1C, and Xb3), Nrr -dependent (Nrr overexpression vs. LG) down-regulated genes (Gip13, Nh1, OsWrky62, and Xb11), Nh1-dependent up- and Nrr-dependent down-regulated genes (OsWrky76 and Nrrh1), and Nh1-dependent up- and Xa21-dependent up-regulated gene (Nrrh2). The blue-filled-node represents the protein for which transcript amounts diminish in Xoo-resistant responses, a Xa21-dependent down-regulated gene (Os01g14810). Yellow-filled nodes represent proteins for which transcripts accumulate in Sub1A-containing rice (Sub1A vs. M202) upon submergence (OsMpk5, OsWrky71, Sab9, and Xb15). Green-filled nodes represent proteins for which transcript levels diminish in Sub1A-containing rice upon submergence (Sab16, Sab21, and Scb2). In addition, two interactome components showed differential expression patterns in both biotic and abiotic stress-response arrays. Sab8 (dark blue-filled node) showed Xa21- and Sub1a-dependent decreased gene expression; whereas, Grnl1 (purple-filled node) showed Xa21- and Sub1a-dependent increased gene expression. Nodes depicted as rounded rectangles and diamonds represent kinases and transcription factors, respectively.