John C. Cushman
Department of Biochemistry and Molecular Biology
University of Nevada/Mail Stop 330
1664 North Virginia Street
Reno, Nevada 89557
Functional Genomics of Crassulacean Acid Metabolism (CAM). CAM is water-conserving photosynthetic pathway that helps plants survive in seasonally arid climates or those with intermittent water supply (e.g. epiphytic habitats). Our research objectives are to understand how the expression of CAM is controlled by environmental stress (salinity, water deficit) and the circadian clock. Our approach is to conduct integrated transcriptome, proteome, and metabolome analyses.
Mechanisms of the Evolutionary Origins of Crassulacean Acid Metabolism in Tropical Orchids. Crassulacean acid metabolism (CAM) has evolved multiple times in 33 families and 328 genera comprising more than 6% of all vascular plant species making it the second most common mode of photosynthesis among vascular plants. Our goal is to understand the molecular mechanisms responsible for the evolution of this important photosynthetic adaptation. Our approach is to survey foliar carbon isotopic composition (delta13C) to map the occurrence of CAM in closely related species within the Oncidiinae, a subtribe within Orchidaceae, and then identify molecular genetic changes specific to plants that exhibit CAM
The Virtual Berry Project: Functional Genomics of Grape Berry Development. Berries from wine and table grape (Vitis vinifera) are the most widely cultivated and economically important fruit crop worldwide. In contrast to well-studied climacteric fruit models, such as tomato,relatively little is known about the molecular genetic mechanisms that govern grape berry development and ripening. Our research goal is to develop a model system in which to apply functional genomics approaches to the study of the developing berry.
Integrating the Unknowneome with abiotic stress response networks in Arabidopsis. The long-term goal of this research is to assign a function to every unknown gene in Arabidopsis thaliana. Our research focus is on genes and networks that function in abiotic stress, such as chilling, water deficit, salt, flooding, high light and oxidative environments. Our approaches are to test the function of unknown genes using gain/loss of function assays in planta and to establish a protein-protein "interactome" database to reveal potential network connections between genes of known and unknown function.
Gene Discovery in Resurrection Species.The long-term goal of this integrated research-education-extension project is to use resurrection plants as models to develop and enhance course offerings in Plant Breeding and Biotechnology and related topics, to develop an integrated research and extension project using Sporobolus as a forage grass, and to gain a basic understanding of the unique gene and gene regulatory networks that are necessary and sufficient for vegetative tissues to withstand dehydration and then rapidly recover upon rehydration that will serve as a case study for advanced teaching modules for crop improvement strategies.
Biofuels from Salt Basin Algae: A Renewable Energy Crop for Carbon Sequestration. The long-term goal of the proposed research is to optimize and implement the use of halophytic microalgae as a biofuel crop. Halophytic green algae are ideally suited as a non-seasonal, renewable energy resource for the arid western U.S. because they are 30 times more productive than terrestrial feedstocks (e.g., soy, canola), can be grown on marginal lands with brackish or saline water unsuitable for traditional agriculture, and provide unlimited potential for sequestration of CO2 from biomass, coal, and gas-fired power plants.
Our research is funded by the National Science Foundation (Integrative Organismal Biology and 2010 Programs), United States Department of Agriculture (NRI-CRGP), Department of Transportation (SunGrant Initiative), and the Nevada Agricultural Experiment Station.
Students and postdoctoral research associates with broad interests in plant molecular genetics, genetic engineering of plants, and plant biochemistry are welcomed to pursue training opportunities in this laboratory.
Major research projects include:
Research interests focus on understanding the mechanisms by which plants perceive and respond to environmental stresses such as high salinity and drought. Detailed descriptions of specific research projects that emphasize different aspects of this general theme can be found by clicking on highlighted text.
Courses & Teaching Responsibilities
BCH 705 - Molecular Genetics
BCH 706 - Functional Genomics
BCH 718 - Plant Molecular Biology and Biotechnology
Biochemistry Graduate Program Director
Awards, Honors, & Professional Recognition
2003 Outstanding CABNR Researcher Award
Associate Editor: Plant Cell & Environment
Editorial Board Member: Journal of Experimental Botany, Journal of Plant Physiology, Tree Physiology
Current Graduate Students
Other Lab Members
Dr. Gouthu Satyanarayana (Postdoctoral Research Associate)
Rebecca Albion (Research Associate II)
Book or Chapter(s) in Books
Cushman JC, Oliver MJ 2010, "Understanding vegetative desiccation tolerance using integrated functional genomics approaches within a comparative evolutionary framework." In: Ecological Studies: Desiccation Tolerance in Plants. Eds: Ulrich Luttge, Erwin Beck, and Dorothea Bartels. Springer, Heidelberg. Chapter 16, pp. xxx-xxx.
Schlauch KA, Grimplet J, Cushman JC, Cramer GR. 2009, "Transcriptomics: methods for microarray data analysis and visualization using the Affymetrix GeneChip® Vitis vinifera genome array." In: Methods in Grapevine Research. Eds: Serge Delrot.
Tillett RL, Cushman JC. 2009, "Vitis Functional Genomics: Open Systems for Transcriptome Analysis." In: Encyclopedia of Plant Genomics. Eds: José M. Martinez-Zapater and Anne-Francoise Adam Blondon. Science Publishers.
Deluc LG, Decendit A, Papastomoulis Y, Mérillon J-M, Cushman JC, Cramer GR. 2011, "Water deficit increases stilbene metabolism in Cabernet Sauvignon berries." . J. Agric. Food Chem. In press.
Sunagawa H, Agarie S, Cushman JC. 2010, "Crassulacean acid metabolism alleviates reactive oxygen species in the facultative CAM plant, the common ice plant, Mesembryanthemum crystallinum." Plant Production Science. 13: 256-260.
Oliver MJ, Cushman JC, Koster KL 2010, "Dehydration Tolerance in Plants." Methods in Molecular Biology: Plant Stress Tolerance. 639: 3-24.
Silvera K, Neubig KM, Whitten WM, Williams NH, Winter K, Cushman JC. 2010, "Evolution along the Crassulacan acid metabolism continuum." Functional Plant Biology (Cover article) 37: 995-1010
Alkayal MF, Albion RL, Tillett RL, Mark S. Lemos, Hernandez-Gomez L, Cushman JC. 2010, "Expressed Sequence Tag (EST) profiling in salinity shocked Dunaliella salina reveals high expression of protein synthetic apparatus components." Plant Science. 179:437-449.
Silvera K, Santiago LS, Cushman JC, Winter K 2010, "Incidence of Crassulacean acid metabolism in the Orchidaceae derived from carbon isotope ratios: a checklist of the flora of Panama and Costa Rica." Botanical Journal of the Linnean Society. 163: 194-222.
Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JEW 2010, "The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA." BMC Plant Biology. 10:83.
Silvera K, Santiago LS, Cushman JC, Winter K. 2009, "Crassulacean acid metabolism and epiphytism linked to adaptive radiations in the Orchidaceae." Plant Physiol. 149:1838-1847.
Uno Y, Rodriguez Milla MA, Maher E, Cushman JC. 2009, "Identification of proteins that interact with catalytically active calcium-dependent protein kinases from Arabidopsis." Mol. Gen. Genet. 281:375-390.
Grimplet J, Ben Jouira H, Wheatley M, Deluc L, Cramer GR, Cushman JC. 2009, "Proteomic and selected metabololite analysis of grape berry tissues under well-watered and water-deficit stress conditions." Proteomics. 9:2503-2528.
Chang IF, Curran A, Woolsey R, Quilici D, Cushman JC, Mittler R, Harmon A, Harper J. 2009, "Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana." Proteomics 9:2967-2985.
Deluc LG, Quilici DR, Decendit A, Grimplet J, Wheatley MD, Schlauch KA, Mérillon J-M, Cushman JC, Cramer GR. 2009, "Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay." BMC Genomics. 10:212.
Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu J-K, Cushman JC, Gollery M, Girke T. 2008, "Annotating genes of known and unknown function by large-scale co-expression analysis." Plant Physiol. 147: 41-57.
Morsy MR, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC. 2008, "Charting Plant Interactomes: Possibilities and Challenges." Trends in Plant Science. 13: 183-191.
Song L, Ciftci-Yilmaz S, Harper J, Cushman JC, Mittler R. 2008, "Enhanced tolerance to oxidative stress in transgenic Arabidopsis thaliana plants expressing proteins of unknown function." Plant Physiol. 148: 280-292.
Cushman JC, Agarie S, Albion RL, Elliot SM, Taybi T, Borland AM 2008, "Isolation and characterization of mutants of ice plant, Mesembryanthemum crystallinum, deficient in Crassulacean acid metabolism." Plant Physiol. 147: 228-238.
Cushman JC, Tillett RL, Wood JA, Branco JA, Schlauch KA. 2008, "Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)." J. Exp. Botany. 59:1875-1894.
Faculty by research area
- Mastick, C
- Mastick C.
- Mastick G.
- Van der Linden
- von Bartheld
- von Bartheld