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CEPCEB Members
Our primary goal is to define mechanisms of signal transduction and gene regulation that are critical to the response of plants to adverse changes in the environment. Much of our research has focused on sensing and response to cellular oxygen deprivation (hypoxia/anoxia) that is a major consequence of flooding, submergence or high metabolic activity (i.e., in meristems). Much of our research focuses on the regulation of gene expression by selective mRNA translation. We use molecular-genetic, biochemical, chemical genomics and systems-biological approaches to study these processes. The longterm goal is to increase crop tolerance of flooding/submergence and to contribute to the general understanding of low-oxygen sensing and translational regulation in eukaryotic cells.
The comparison of the response to submergence stress of two lines that differ only in `~180 kB at the Sub1 locus confirmed that submergence tolerance is a consequence of conservation of carbohydrates and a strategy of “coping” with the stress (Fukao et al., 2006). By contrast, submergence intolerant rice accelerates leaf elongation under submergence and exhausts its carbohydrate reserves. The rapid-growth strategy is similar to the flooding “escape” response of deepwater rice, which accelerates growth in order to maintain leaves above the surface of the water. Rice genotypes with Sub1A-1 are restricted in leaf elongation and carbohydrate consumption. The dampening of ethylene production and GA responsiveness in Sub1 rice allows plants to maintain the capacity for re-growth upon de-submergence.
Our IRRI collaborators are using traditional breeding and molecular-marker assisted selection to move Sub1 into lines that are popular in flood prone regions of India and Asia . Evaluation of the Swarna+Sub1 line has demonstrated that this submergence tolerance can be achieved without loss of favorable growth traits as well as grain and yield characteristics.
Our current research on Sub1 focuses on global-level identification of genes and metabolic processes that are differentially regulated by the Sub1 haplotype and Sub1A-1 and the identification of the regulation of the SUB1 ERF proteins. We are also focused on developing rice lines that are both submergence and salt tolerant. We aim to define genetic mechanisms of response to multiple stresses that are of concern to farmers in both developed and underdeveloped countries. Funding: USDA-NRICGP and USAID/IRRI Linkage Project. Publications and Press Releases on Rice Submergence (Bibliography page)
A challenge in the study of multi-cellular organisms is the dissection of events that occur in specific tissue and cell-types of individual organs. It is well established that gene regulation can be measured by the high-throughput evaluation of steady-state mRNA abundance. The abundance of individual transcripts is regulated in specific cell types, during development and in response to environmental cues. Our work has shown that gene expression is also highly regulated at the level of mRNA translation. Individual mRNAs compete for the factors required for the initiation of translation (Kawaguchi et al., 2004; Kawaguchi and Bailey-Serres, 2005; Branco-Price et al., 2005). Because of this, only a small percentage of the mRNAs encoding a specific protein may be present in polysome complexes and undergoing translation. Abiotic stresses such as hypoxia (HS) and dehydration stress cause a global reduction in protein synthesis. However, a sub-set of cellular mRNAs escapes this repression and continue to recruit ribosomes and maintain translation.
We have developed technology that allows for rapid purification of endogenous polysome complexes from crude cell extracts of Arabidopsis (Zanetti et al., 2005). The expression of an FLAG-tagged ribosomal protein L18 produced in a transgenic plant allows the immunoprecipitation of polysome complexes. The mRNAs in these complexes can be evaluated by hybridization to DNA microarrays. By use of promoters that are expressed in specific cell types of the root and aerial tissue of Arabidopsis, we are using this methodology to study dynamic changes in the abundance of translated mRNAs in seedlings responding from oxygen deprivation. Publications and Websites Related to Translation and Polysomal mRNA Analyses (Bibliography page) Arabidopsis Proteins of Unknown Function A large proportion of the genes that are upregulated in response to hypoxia and other abiotic stresses are proteins with no biological function. We have embarked on an ambitious Arabidopsis 2010 Collaborative Research Project to characterize stress-induced proteins of unknown function (http://bioinfo.ucr.edu/projects/internal/Unknowns/external/index.html ). The goal of the “Unknown-eome” project is to facilitate the assignment of function to stress-induced gene in Arabidopsis thaliana. To date, the function of the proteins encoded by more than 20% of plant genes is completely unknown, with the function of up to 43% of these proteins poorly characterized. By use of gene expression analysis, phenotype screens, yeast-two hybrid and proteomic studies we will establish interaction networks for genes that are upregulated respond to environmental stress, such as hypoxia, chilling, drought, salt, high light, and oxidative environments. The goals of the Bailey-Serres lab focus on hypoxia-induced genes that have been recognized in a number of independent studies and have orthologs in other plants. A number of our target genes have hypoxia-induced orthologs in diverse eukaryotes.
Publications and Websites Related to Proteins of Unknown Function (Bibliography page) Sensing, Signaling and Responding to Oxygen Deprivation The response of root tips to oxygen deprivation includes the regulation of gene expression at transcriptional and post-transcriptional levels. A greater understanding of the signal transduction mechanisms that control these changes in gene expression will enhance the breeding and genetic engineering of crops with desired traits. Our research has indicated that regulation of the activity of a Rop-GTPase and a Rop-GAP are critical to the response to oxygen deprivation. RopGAP4 is a member of a multigene family that regulates activity of Rop, a RHO-like monomeric GTPase. Comparison of the response of the ropgap4 mutant and a dominant negative-Rop mutant revealed that an increase in cytosolic free Ca2+ and Rop activation is required to induce Adh1 expression. Our model predicts that Rop activation stimulates a Ca2+-dependent and DPI-sensitive NADPH oxidase resulting in a hydrogen-peroxide signal that is necessary for Adh1 expression. The regulation of RopGAP4 expression via the same pathway as Adh1 is necessary for stress tolerance. These findings reveal that a rheostat regulates the signal transduction pathway that activates Adh1 gene expression in Arabidopsis. Current research is focused on refinement of the understanding of the role of reactive oxygen species, Rop activity and MAPK signaling in response to oxygen deprivation in Arabidopsis. Publications Related to the Oxygen Stress Response in Arabidopsis (Bibliography page)
Plant Ribosomes - Proteins, Protein Phosphorylation and Heterogeneity We have used biochemical, genomic and proteomic approaches to characterize the proteins of plant ribosomes. These studies have evaluated the abundance and phosphorylation of the P-proteins of the large ribosomal subunit and the regulated phosphorylation of ribosomal protein S6 of the small subunit. We have identified up to 80 distinct classes of cytosolic ribosomal proteins in Arabidopsis. Seventy-four of these proteins were confirmed to be components of the ribosome by mass spectrometry. Our phylogenetic analyses reveal that three ribosomal protein gene families (P3, L7, and S15a) contain members that are evolutionarily divergent from the mammalian and fungal orthologs. The proteomic analysis of Arabidopsis ribosomes confirmed that RACK1, a ~36 kDa protein with similarity to the beta-subunit of heterotrimeric G-proteins, is associated with plant ribosomes. Future studies will consider the functional significance of plant-specific ribosomal proteins and heterogeneity in ribosomal protein composition and modifications. Publications Related to Plant Ribosomes (Bibliography page)
Current Laboratory Personnel and Projects
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Most rice cultivars thrive in a flooded paddy. Tolerance of a flooded root system is engendered by morphological adaptations such as stem to root aerenchyma (air passages) and a thicken root cuticle. However, rice is generally intolerant of complete submergence. Each year, season floods result in unanticipated submergence of rice fields, resulting in agricultural losses of over $1 billion (U.S.). These crop losses are primarily experienced by the poorest farmers in Asia and Africa . A semi-dominant quantitative trait locus called 
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