john cushman

John Cushman

Professor & Graduate Student Director


  • 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 using a model facultative CAM species called the common or crystalline ice plant (Mesembryanthemum crystallinum).


  • Evolutionary Origins of Crassulacean acid metabolism in Neotropical 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.


  • 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.


  • Improved Abiotic Stress Tolerance in Camelina: The long-term goal of this research program is to improve the drought tolerance and other production traits of Camelina so that is might serve as a biofuel crop within the northern Nevada and the Great Basin. The goals are to test different varieties of Camelina to determine which might be suitable for regional growing conditions, develop improved traits such as heat, drought, and salinity tolerance, herbicide resistance, and shatter resistance of pods, using various genetic approaches, create a transcriptome database for all tissues under abiotic stress conditions, and provide educational outreach to inform stakeholders about the utility of Camelina as a regional biodiesel feedstock.


  • Development of Opuntia (Prickly Pear Cactus) as a Low-water-input Oleogenic Biofuel and Biomass Feedstock: The long-term goals of this research program are to enhance existing transcriptome resources for Opuntia ficus-indica, generate oleogenic cactus that accumulates lipids within vegetative and fruit tissues, evaluate such cactus for increased accumulation of lipids and other feedstock characteristics, and provide educational outreach to inform stakeholders using an educational display on biofuels production.


  • Engineering CAM Photosynthetic Machinery into Bioenergy Crops for Biofuels Production in Marginal Environments: The long-term goal of this research program is to enhance water use efficiency (WUE) and adaptability to hotter/drier climates of C3 species by introducing Crassulacean acid metabolism (CAM) thereby developing new capabilities for biomass production on marginal or abandoned agricultural lands while minimizing water and nitrogen inputs. The specific goals are to define the genetic basis of a set of CAM modules in eudicot and monocot species using network modeling data derived from 'omics data sets, characterize the regulation of carboxylation, decarboxylation, and stomatal control modules using comparative genomic, network/molecular dynamics modeling, and loss-of-function testing, deploy advanced genetic engineering technologies to enable stacking of large numbers of transgenes to improve transgene persistence, and to transfer fully functional CAM modules, and analyze the effects of different CAM modules on stomatal control, CO2 assimilation and transpiration rates, water use efficiency, and biomass yields in Arabidopsis and Poplar.

Our research is funded by the Department of Energy (DOE) and the Nevada Agricultural Experiment Station (NAES).

Students and postdoctoral research associates with broad interests in plant molecular genetics and plant biochemistry related to abiotic stress tolerance and bioenergy production systems are welcomed to pursue training opportunities in this laboratory.


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


Book Chapter(s)

CAM Plants


Encyclopedia of Applied Plant Sciences, Vol 1, Waltham, MA: Academic Press, 2017, pp. 60–77.

Cushman, JC

Strain Selection Strategies for Improvement of Algal Biofuel Feedstocks.


In: Biofuels and Bioenergy. Eds: John Bryant, Clive Butler, and John Love. Wiley-Blackwell, UK. pp. 173-189.

Hathwaik L, Cushman JC

Transcriptomics analysis methods: microarray data processing, analysis and visualization using the Affymetrix GeneChip® Vitis vinifera genome array


Methods and Results in Grapevine Research. Delrot S, Medrano H, Or E, Bavaresco L, Grando S (Eds.). Springer, Chap 22, pp. 317-334.

Schlauch KA, Grimplet J, Cushman JC, Cramer GR.

Understanding vegetative desiccation tolerance using integrated functional genomics approaches within a comparative evolutionary framework.


Ecological Studies: Desiccation Tolerance in Plants. Eds: Ulrich Luttge, Erwin Beck, and Dorothea Bartels. Springer, Heidelberg. 215: 307-338.

Cushman JC, Oliver MJ.

Vitis functional genomics: Open systems for transcriptome analysis.


Genetics, Genomics and Breeding of Grapes. Eds: José M. Martinez-Zapater and Anne-Francoise Adam Blondon. Science Publishers, Enfield, New Hampshire. Chapter 10, pp. 235-269.

Tillett RL, Cushman JC

Transcriptomics: methods for microarray data analysis and visualization using the Affymetrix GeneChip® Vitis vinifera genome array.


In: Methods in Grapevine Research. Eds: Serge Delrot.

Schlauch KA, Grimplet J, Cushman JC, Cramer GR.


Biology and chemistry of an Umbravirus-like 2989 bp single-stranded RNA as a possible causal agent for Opuntia stunting disease (engrosamiente de cladidios) – A review


Journal of the Professional Association for Cactus Development. 21: 1–31.

Felker P, Bunch R, Russo G, Preston K, Tine JA, Suter B, Mo X, Cushman JC, Yim WC

Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales


New Phytologist 01 August 2019

Sheehan H, Feng T, Walker-Hale N, Lopez-Nieves S, Pucker B, Guo R, Yim WC, Badgami R, Timoneda A, Zhao L, Tiley H, Copetti D, Sanderson MJ, Cushman JC, Moore MJ, Smith SA, Brockington SF

The evolution of l-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that l-DOPA 4,5-dioxygenase...

Exploring the relationship between crassulacean acid metabolism (CAM) and mineral nutrition with a special focus on nitrogen


International Journal of Molecular Sciences. 20: 4363. DOI: 10.3390/ijms20184363.

Pereira PN, Cushman JC.

Ion accumulation and expression of ion homeostasis-related genes associated with halophytism, NaCl-promoted growth in a halophyte, Mesembryanthemum crystallinum L.


Protein Production Science. DOI: 10.1080/1343943X.2019.1647788.

Tran DQ, Konishi A, Cushman JC, Morokuma M, Toyota M, Agarie S.

Laying the foundation for crassulacean acid metabolism (CAM) biodesign: Characterization of individual C4 metabolism genes from the common ice plant in Arabidopsis


Frontiers in Plant Science. 10: 101

Lim SD, Lee S, Choi W-G, Yim WC, and Cushman

New perspectives on Crassulacean acid metabolism


Journal of Experimental Botany. 70: in press.

Hultine K, Cushman JC, Williams DG.

Nutritional and mineral content of prickly pear cactus: A highly water-use efficient forage, fodder, and food species


Journal of Agronomy and Crop Science 00:1-10

Mayer JA, Cushman JC

The bracteatus pineapple genome and domestication of clonally propagated crops.


Nature Genetics. 51: 1549–1558

Chen L-Y, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Along M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, Lin Z, Zhang J, Juang L, Wang H, Hwa T-Y, Kao S-M, Choi JY, Sharma A, Song J, Wang H, Yim WC, Cushman JC, Paull RE, Matsumoto T, Qin Y, Wu Q, Wang J, Yu Q, Wu J, Zhang S, Boches P, Tung C-W, Wang M-L, d’Eckenbrugge GC, Sanewski GM, Purrugganan MD, Schatz MC, Bennetzen JL, Lexer C, Ming R.

Understanding trait diversity associated with crassulacean acid metabolism (CAM)


Current Opinion in Plant Biology 49: 74-85

Niechayev NA, Pereira PN, Cushman JC

Biology and chemistry of an umbravirus-like 2989 bp single-stranded RNA as a causal agent for Opuntia stunting disease (engrossamiento de cladodios) – A review


Journal of the Professional Association for Cactus Development. 20: in press.

Felker P, Bunch R, Russo G, Preston K, Tine JA, Suter B, Mo X, Cushman JC, and Yim WC

Fast pyrolysis of Opuntia ficus-indica and Grindelia squarrosa.


Sustainable Chemistry & Engineering. 32: 3510–3518.

Cross P, Mukarakate C, Nimlos M, Carpenter D, Donohoe B, Mayer JA, Cushman JC, Neupane B, Miller G, Adhikari S.

Simultaneous chloroplast, mitochondria isolation and mitochondrial protein preparation for two-dimensional electrophoresis analysis of ice plant leaves under well-watered and water-deficit stressed treatments


Protein Expression and Purification. 155: 86–94

Hong HTK, Phuong TTB, Thuy NTT, Wheatley MD, and Cushman JC

An rbcL mRNA binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria.


Journal of Experimental Botany DOI:10.1093/jxb/erx264

Yerramsetty PK, Agar EM, Yim WC, Cushman JC, Berry JO

Divide and Conquer (DC) BLAST: Fast and easy BLAST execution within HPC environments.


PeerJ. 5: e3486.

Yim WC, Cushman JC

Draft nuclear genome sequence of the halophilic and beta-carotene-accumulating green alga Dunaliella salina strain CCAP19/18.


Genome Announcements. 5:e01105-17.

Polle JE, Barry K, Cushman J, Schmutz J, Tran D, Hathwaik LT, Yim WC, Jenkins J, McKie-Krisberg Z, Prochnik S, Lindquist E.

Leaf carbohydrates influence transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in the facultative CAM plant, Mesembryanthemum crystallinum.


Journal of Plant Physiology. 218: 144-154.

Taybi T, Cushman JC, Borland AM.

MYB and HD-ZIP IV homologs related to trichome formation are involved in epidermal bladder cell development in the halophyte Mesembryanthemum crystallinum L.


Plant Production Science 20 (1): 72-82.

Roeurn S, Hoshino N, Soejima K, Inoue Y, Cushman JC, Agarie S.

Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics.


BMC Plant Biology. 17: 67.

Yobi A, Tillett RL, Yim WC, Espinoza C, Wone BWM, Schlauch KA, Cushman JC, Oliver MJ.

Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple.


The Plant Journal. 92: 19-30

Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger PP, Yim WC, Priest HD, Meyers BC, Mockler T, Smith JA, Cushman JC, Ming R.

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.


Nature Communications. 18:1899.

Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Yim WC, Ha J, Heyduk K, Goodstein DM, Guo H-B, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell JA, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LD, Palla KJ, Albion R, Garcia T, Mayer JA, Lim SD, Wai CM, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen J-G, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JC, Smith JAC, Cushman JC, Schmutz J, Tuskan G

Identification of ice plant (Mesembryanthemum crystallinum L.) microRNAs using RNA-Seq and analysis of their potential functional roles in high salinity responses in seedlings.


Frontiers in Plant Biology. 7: 1143.

Chiang C-P, Yim WC, Sun Y-H, Ohnishi M, Mimura T, Cushman JC, Yen HE.

Orchestration of carbohydrate processing for crassulacean acid metabolism.


Current Opinion in Plant Biology. 31: 118–124.

Borland AM, Guo H-B, Yang X, Cushman JC.

Suppression subtractive hybridization library construction and identification of epidermal bladder cell-related genes in the common ice plant, Mesembryanthemum crystallinum L.


Plant Product. Sci. 19: 552-561.

Roeurn S, Hoshino N, Soejima K, Inoue Y, Cushman JC, Agarie S

Transcript, protein and metabolite temporal dynamics in the CAM plant Agave


Nature Plants 2: 16178

Abraham PE, Yin H, Borland AM, Weighill D, Lim SD, De Paoli HC, Engle N, Jones PC, Agh R, Weston DJ, Wullschleger SD, schaplinski T, Jacobson D, Cushman JC, Hettich RL, Tuskan GA, Yang, Y

A roadmap for research on crassulacean acid metabolism to enhance sustainable food and bioenergy production in a hotter, drier world.


New Phytologist. 207: 491–504.

Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA, Owen NA, Griffiths H, Smith JAC, De Paoli HC, Weston DJ, Cottingham R, Hartwell J, Davis SC, Silvera K, Ming R, Schlauch KA, Abraham P, Stewart JR, Guo H-B, Albion RA, Ha J, Lim SD, Wone BWM, Yim WC, Garcia T, Mayer JA, Petereit J, Nair SS, Casey E, Hettich RL, Ceusters J, Ranjan P, Palla KJ, Yin H, Reyes-García C, Andrade JL, Freschi L, Beltran JD, Dever LV, Boxall SF, Waller J, Davies J, Bupphada P, Kadu N, Winter K, Sage

Biomass characterization of Agave and Opuntia as potential biofuel feedstocks.


Biomass and Bioenergy. 76: 43-53. DOI: 10.1016/j.biombioe.2015.03.004

Yang L, Carl S, Lu M, Mayer JA, Cushman JC, Tian E, Lin H.

Development and use of bioenergy feedstocks for semi-arid and arid lands.


Journal of Experimental Botany. 66: 4177-4193.

Cushman JC, Davis SC, Yang X, Borland AM

Evaluation of diverse microalgal species as potential biofuel feedstocks grown using municipal wastewater.


Frontiers in Energy Research. 3 (20): 1-8.

Hiibel SR, Lemos MS, Kelly BP, Cushman JC.

The pineapple genome and the evolution of CAM photosynthesis.


Nature Genetics. 47: 1435–1442.

Ming R, Van Buren R, Wai CM, Tang H, Schatz MC, Bowers, JE, Lyons E, Wang M-L, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck F, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Yuan Q, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA

Transgressive, reiterative selection of Dunaliella salina with enhanced lipid and starch production using continuous buoyant density gradient centrifugation.


Algal Research. 9:194-203.

Hathwaik LT, Redelman D, Samburova V, Zielinska B, Shintani DK, Harper JF, Cushman JC.

Climate-resilient agroforestry: Physiological responses to climate change and engineering of crassulacean acid metabolism (CAM) as a mitigation strategy.


Plant, Cell and Environment. 38: 1833-1849.

Borland AM, Wullschleger SD, Wilson DJ, Tuskan GA, Hartwell J, Yang X, Cushman JC.

Engineering Crassulacean acid metabolism to improve water-use efficiency.


Trends Plant Sci. 19: 327-338. Video abstract for this article is available at:

Borland AM, Hartwell J, Weston D, Schlauch KA, Tschaplinski TJ, Tuskan GA, Yang X, Cushman JC.

Interview with John C. Cushman.


Trends Plant Sci. 19: 274-275.

Cushman JC.

Multiple isoforms of phophoenolpyruvate carboxylase in the Orchidacea (subtribe Oncidiinae): implications for the evolution of crassulacean acid metabolism.


J. Exp. Bot. 65:3623-3636. doi: 10.1093/jxb/eru234

Silvera K, Winter K, Rodgriguez BL, Albion, RL, Cushman JC.

Synthetic biology as it relates to CAM photosynthesis: Challenges and opportunities.


J. Exp. Bot. 65:3381-3393.

DePaoli HC, Borland AM, Tuskan GA, Cushman JC, Yang X.

Biomass production, nutritional, and mineral content of desiccation-sensitive and desiccation-tolerant species of Sporobolus under multiple irrigation regimes.


J. Agron. Crop Science. 199: 309-320.

Yobi A, Schlauch KA, Perryman B, Oliver MJ, Cushman JC.

Metabolic rates associated with membrane fatty acids in mice selected for increased maximal metabolic rate.


Comp. Biochem. Physiol. A Mol. Integr. Physiol. 165: 70-78. Doi: 10.1016/j.cbpa.2013.02.010.

Wone BW, Donovan ER, Cushman JC, Hayes JP.

Metabolomic profiling in Selaginella lepidophylla provides new insights in the mechanistic basis of desiccation tolerance.


Molec. Plant. 6: 369-385. DOI: 10.1093/mp/sss155.

Yobi A, Wone BWM, Guo L, Alexander DC, Ryals JA, Oliver M, Cushman JC.

A CAM- and starch-deficient mutant of the facultative CAM species Mesembryanthemum crystallinum reconciles sink demands by repartitioning carbon during acclimation to salinity


Journal of Experimental Botany. 63: 1985-1996.

Haider MS, Barnes JD, Cushman JC, and Borland AM

Analysis of triacylglycerols and free fatty acids in algae using ultra-high-pressure liquid chromatography mass spectrometry.


J. Am. Oil Chem. Soc. 90: 53-64. DOI 10.1007/s11746-012-2138-3.

Samburova V, Lemos MS, Hiibel SR, Hoekman SK, Cushman JC, Zielinska B.

Generic recircumscriptions of Oncidiinae (Orchidaceae: Cymbidieae) based on maximum likelihood analysis of combined DNA datasets.


Botanical Journal of the Linnean Society. 168: 117-146.

Neubig KM, Whitten WM, Williams NH, Blanco MA, Endara L, Burleigh G, Silvera K, Cushman JC, Chase MW

The Vitis vinifera C-repeat binding protein 4 (VvCBF4) transcriptional factor enhances freezing tolerance in wine grape.


Plant Biotechnology Journal. 10:105-124

Tillett RL, Wheatley MD, Tattersall EAR, Schlauch KA, Cramer, GR, Cushman JC

Untargeted global metabolomic profiling reveals novel biochemical differences critical for desiccation tolerance within a sister group comparison of Selaginella species.


The Plant J. 72: 983-999.

Yobi A, Wone BWM, Guo L, Alexander DC, Ryals JA, Oliver M, Cushman JC.

A sister group metabolomic contrast using untargeted global metabolomic analysis delineates the biochemical regulation underlying desiccation tolerance in Sporobolus stapfianus.


The Plant Cell. 23: 1231-1248.

Oliver MJ, Guo L, Alexander DC, Ryals JA, Wone BWM, Cushman JC.

Calcium-dependent protein kinases from Arabidopsis show substrate specificity differences in an analysis of 102 substrates.


Frontiers in Plant Biology. 2: 1-15.

Curran A, Chang I-F, Chang C-L, Garg S, Rodriguez Milla M, Barron YD, Li Y, Romanowsky SD, Cushman JC, Gribskov M, Peck SC, Harmon AC, Harper JF.

mRNA expression profiling of abiotic stress responses in leaf and berry tissue of wine grape (Vitis vinifera) using expressed sequence tags.


BMC Plant Biology. 11:86.

Tillett RL, Albion RL, Schlauch KA, Cramer GR, and Cushman JC.

The microbial opsin family of optogenetic tools.


Cell. 147:1446-1457.

Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman JC, Polle J, Magnuson J, Hegemann P, Deisseroth K.

The unicellular green alga Dunaliella salina Teod. as a model for abiotic stress tolerance: Genetic advances and future prospects.


Algae. 26:3-20.

Ramos AA, Polle J, Tran D, Cushman JC, Jin ES, Varela JC.

Water deficit increases stilbene metabolism in Cabernet Sauvignon berries.


J. Agric. Food Chem. 59: 289-297.

Deluc LG, Decendit A, Papastomoulis Y, Mérillon J-M, Cushman JC, Cramer GR.

Crassulacean acid metabolism alleviates reactive oxygen species in the facultative CAM plant, the common ice plant, Mesembryanthemum crystallinum.


Plant Production Science. 13: 256-260.

Sunagawa H, Agarie S, Cushman JC.

Dehydration Tolerance in Plants.


Methods in Molecular Biology: Plant Stress Tolerance. 639: 3-24.

Oliver MJ, Cushman JC, Koster KL

Evolution along the Crassulacan acid metabolism continuum.


Functional Plant Biology (Cover article) 37: 995-1010

Silvera K, Neubig KM, Whitten WM, Williams NH, Winter K, Cushman JC.

Expressed Sequence Tag (EST) profiling in salinity shocked Dunaliella salina reveals high expression of protein synthetic apparatus components.


Plant Science. 179:437-449.

Alkayal MF, Albion RL, Tillett RL, Mark S. Lemos, Hernandez-Gomez L, Cushman JC.

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.

Silvera K, Santiago LS, Cushman JC, Winter K

The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA.


BMC Plant Biology. 10:83.

Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JEW

Crassulacean acid metabolism and epiphytism linked to adaptive radiations in the Orchidaceae.


Plant Physiol. 149:1838-1847.

Silvera K, Santiago LS, Cushman JC, Winter K.

Identification of proteins that interact with catalytically active calcium-dependent protein kinases from Arabidopsis.


Mol. Gen. Genet. 281:375-390.

Uno Y, Rodriguez Milla MA, Maher E, Cushman JC.

Proteomic and selected metabololite analysis of grape berry tissues under well-watered and water-deficit stress conditions.


Proteomics. 9:2503-2528.

Grimplet J, Ben Jouira H, Wheatley M, Deluc L, Cramer GR, Cushman JC.

Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana.


Proteomics 9:2967-2985.

Chang IF, Curran A, Woolsey R, Quilici D, Cushman JC, Mittler R, Harmon A, Harper J.

Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay.


BMC Genomics. 10:212.

Deluc LG, Quilici DR, Decendit A, Grimplet J, Wheatley MD, Schlauch KA, Mérillon J-M, Cushman JC, Cramer GR.

Lay or Popular Publications

Water in arid climates – economic opportunities for agriculture.


Reno Gazette-Journal (Business). March 19, 2012.

Cushman JC.