John Cushman 2003JOHN C. CUSHMAN

Professor 
Department of Biochemistry & Molecular Biology
University of Nevada, Reno/MS 200
1664 North Virginia Street
Reno, Nevada 89557

Office: (775) 784-1918  Lab: (775) 784-6258
Email: jcushman@unr.edu 
Location: Fleischmann Agriculture Building, Office 311
Personal Web Site:

Education

B.S. 1982 Ursinus College
M.S. 1984 Rutgers University - New Brunswick
Ph.D. 1986 Rutgers University - New Brunswick

Course Information

Major Academic Interests: Research interests focus on understanding the mechanisms by which plants perceive and respond to environmental insults such as high salinity, water deficit (drought), and freezing.  More detailed descriptions of each research project can be found by clicking on highlighted text.  Major research projects include:

  • 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 (d13C) 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.
      
  • Developing Paradigms for Functional Genomics of Protein Kinases and Phosphoproteins Using the calcium-dependent protein kinase (CDPK) Superfamily. The goal of this program is to identify CDPK substrates using substrate traps and interaction screens such as the yeast two-hybrid system, to determine the subcellular locations of membrane-associated or compartmentalized CDPKs, to use mass spectrometry to initiate identification of all CDPK phosphorylation sites in the plant phosphorylome, and to develop lectures and on-line resources targeted for colleges without science research programs. 
      
  • Integrative Functional Genomic Resource Development in Vitis vinifera: Abiotic Stress and Wine Quality. Our research goals are to understand how abiotic stresses (e.g. water-deficit, salinity, cold) influence wine quality by developing genomics resources in Vitis vinifera and using integrative functional genomics tools to identify key determinants of wine flavor, color, and aroma.
  • 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.
  • Resurrection Plants: Novel Genetic Resources and Alternative Dehydration Stress Tolerant Crops.The long-term goals of this integrated research-extension project are to identify and isolate novel genes and unique gene regulatory networks that are responsible for water-deficit and desiccation tolerance in plants, to assess their functional roles in stress tolerance, and to create a novel outreach/extension program that addresses the development of alternative, drought tolerant forage crops through genetic engineering and breeding strategies.

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. Our research is funded by the National Science Foundation (Plant Genome and 2010 Programs) and the Nevada Agricultural Experiment Station.

Recent Publications (last 3 years):

Dodd AN, Griffiths H, Taybi T, Cushman JC, Borland AM (2003) Integrating diel starch metabolism with the circadian and environmental regulation of Crassulacean acid metabolism in Mesembryanthemum crystallinum. Planta 216: 789-797

Cushman JC (2003) Functional Genomics of Plant Abiotic Stress Tolerance. In: Genomics of Plants and Fungi. Ed. R.A. Prade and H.J. Bohnert. Marcel Dekker, Inc. New York, NY. 18: 315-357.

Soulages JL,Kim K, Arrese EL, Walters C, Cushman JC (2003) Conformation of a Group 2 Late Embryogenesis Abundant (LEA) Protein from Soybean: Evidence of Poly (L-Proline)-type II (PII) Structure. Plant Physiol. 131:963-975.

Abebe T, Guenzi AC, Martin B, Cushman JC (2003) Tolerance of mannitol-accumulating transgenic wheat to water stress and salinity.  Plant Physiol. 131: 1748-1755.

Ermolova NV, Cushman MA, Taybi T, Condon SA, Cushman JC, Chollet R (2003) Expression, purification, and initial characterization of a recombinant form of plant PEP-carboxylase kinase from CAM-induced Mesembryanthemum crystallinum with enhanced solubility in Escherichia coli. Protein Express Purific. 29:123-131.

Gehrig HH, Aranda J, Cushman MA, Virgo A, Cushman JC, Hammel BE, Winter K. (2003) Cladogram of Panamanian Clusia based on nuclear DNA: Implications for the origins of Crassulacean Acid Metabolism. Plant Biol. 5:59-70.

Mao C, Cushman JC, May G, Weller JW (2003) ESTAP-an automated system for the analysis of EST data. Bioinformatics. 19:1720-1722.

Agarie S, Cushman JC. (2003) Genetic and biochemical studies on salt tolerance in the facultative CAM halophyte, Mesembryanthemum crystallinum. Proc. Japan/Taiwan Symposium on Molecular Biology of Functional Regulation in Plant and Microbe. Saga University, Saga, Japan. pp. 92-103.

Cushman JC (2004) C3 photosynthesis to Crassulacean acid metabolism shift in Mesembryanthemum crystallinum: A stress tolerance mechanism. Encyclo. Plant Crop Sci. DOI: 10.1081?E-EPCS, pp. 242-244.

Chehab EW, Patharkar OR, Hegeman AD, Taybi T, Cushman JC. (2004) Autophosphorylation and subcellular dynamics of a salt- and water deficit stress-induced calcium-dependent protein kinase from Mesembryanthemum crystallinum. Plant Physiol. 135:1430-1446.

Kore-eda S, Cushman MA, Akselrod I, Bufford D, Fredrickson M, Clark E, Cushman JC (2004) Transcript profiling of salinity stress responses by large-scale expressed sequence tag analysis in Mesembryanthemum crystallinum. Gene. 341:83-92.

Boxall SF, Foster JM, Bohnert HJ, Cushman JC, Nimmo HG, Hartwell J. (2005) Conservation and divergence of the central circadian clock in the stress-inducible CAM plant Mesembryanthemum crystallinum: clock operation in a CAM halophyte reveals clock compensation against abiotic stress. Plant Physiol. 137: 969-982.

Cushman JC (2005) Crassulacean acid metabolism: recent advances and future opportunities.  Functional Plant Biology.32: 375-380.

Kore-eda S, Noake C, Ohishi M, Ohnishi J, Cushman JC (2005) Transcriptional regulation of organellar metabolite transporters during induction of crassulacean acid metabolism in Mesembryanthemum crystallinum. Functional Plant Biology. 32:451-466.

Gehrig, HH, Wood J, Cushman MA, Virgo A, Cushman JC, Winter K. (2005) Large gene family of phosphoenolpyruvate carboxylase in the Crassulacean acid metabolism plant Kalanchoe pinnata (Crassulaceae). Functional Plant Biology. 32: 467-472.

Goes da Silva F, Iandolino A, Lim H, Baek JM, Leslie A, Xu J, Cook DR, and Al-Kayal F, Bohlman MC, Cushman MA, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, Rowe J, Tattersall EA, Cramer GR, Cushman JC (2005). Characterizing the grape transcriptome: analysis of ESTs from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol. 139: 574-597.

TattersallEAR, ErgulA, AlKayalF, DeLuc L, Cushman JC, Grant R. Cramer (2005) Comparison of methods for isolating high-quality RNA from leaves of grapevine. Amer. J. Vitic. Enol. 56:400-406.

Cramer GR, Cushman JC, Schooley DA, Quilici D, Vincent D, Bohlman MC, Ergul A, Tattersall EAT, Tillett R, Evans J, Delacruz R, Schlauch K, Mendes P. (2005). Progress in bioinformatics – the challenge of integrating transcriptomic, proteomic and metabolomic information. Acta Hort 689: 417-425

Borland AM, Elliott S, Pater B, Taybi T, Cushman JC, Barnes B (2006) Is Crassulacean acid metabolism a consequence or cause of oxidative stress? J. Exp. Bot. 57:319-328.

Rodriguez Milla MA, Townsend J, Chang I-F, Cushman JC (2006) The Arabidopsis AtDi-19 gene family encodes a novel type of Cys2/His2 zinc-finger protein implicated in ABA-independent dehydration, high-salinity stress and light signaling pathways. Plant Molecular Biology.In press.

Rodriguez Milla MA, Uno Y, Townsend J, Maher E, Cushman JC (2006) Arabidopsis AtCPK11, a calcium-dependent protein kinase, phosphorylates AtDi19, a nuclear zinc finger protein. FEBS Lett.  580: 904-911.

Dyachenko OV, Zakharchenko NS, Shevchuk TV, Bohnert HJ, Cushman JC, Buryanov YI. (2006) Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress. Biochemistry (Moscow) 71: 461-465.

Iturriaga, G, Cushman MAF, Cushman JC (2006) An ESTs catalogue from the resurrection plant Selaginella lepidophylla reveals stress related genes. Plant Science. In press.