john cushman

John Cushman

Professor, Biochemistry and Molecular Biology


Research interests

  • Opuntia ficus-indica: A Highly Water-Use Efficient And Productive Biomass Feedstock For Semi-Arid Lands: The goal of this research to expand the use of cactus pear (Opuntia ficus-indica) as highly water-use efficient, highly productive, and climate-resilient biomass feedstock for semi-arid regions of the U.S. The major research goals are to: 1) develop molecular identifiers from complete chloroplast genome sequence information for resolving the genetic structure of the germplasm collection of O. ficus-indica to remove genetically identical accessions and resolved species designations; 2) evaluate available public germplasm collection of O. ficus-indica for biomass productivity under standard irrigation and fertilization conditions in the field; 3) evaluate elite germplasm for optimal water and fertilization inputs, refine productivity models, and perform life-cycle assessment (LCA) and life-cycle costing (LCC) analyses; 4) develop effective strategies to overcome barriers to production including overcoming Opuntia stunting disease (OSD) and supporting effective insect management programs for insect pests.  An innovative extension program will inform interested stakeholders about the benefits of cactus pear production systems in arid and semi-arid regions and to disseminate research results through public outreach and education.     
  • Genetic improvement and field testing of Tef: A forage, fodder, and highly nutritious, gluten-free grain crop for dryland agriculture: Tef (Eragrostis tef (Zucc.) Trotter, Poaceae) is a warm season, C4-photosynthesis grass that is gaining popularity in the U.S. as a high-quality forage, fodder, and highly nutritious, gluten-free grain. Tef productivity is limited by susceptibility to lodging due to its characteristic tall and weak stems, low seed production per unit area (or productivity), and small seed size. The long-term goals of the proposed integrated research and extension project are to accelerate E. tef domestication to suit U.S. agriculture needs through improving existing genomic resources, evaluating the agronomic performance of highly productive and drought tolerance accessions, and improving lodging resistance and overall grain yield.
  • Optimized crassulacean acid metabolism (CAM) engineering for improving water-use efficiency in plants: Crassulacean acid metabolism and tissue succulence are metabolic and anatomical adaptations that improve water-use efficiency and drought (and salinity) stress tolerance in plants. These traits are among the most widespread and successful adaptations in the plant kingdom for mitigating drought stress, and thus, represent highly useful traits for the design of climate-resilient crops. The goal of this project is to test optimized synthetic versions of crassulacean acid metabolism alone and in combination with engineered tissue succulence. The proposed synthetic gene circuits developed by this project can be applied widely to other food, feed, fiber, and biofuel crops to improve their productivity, reduce photorespiration, improve water-use efficiency, and drought/salinity stress tolerance under the hotter and drier environments of the future.

Our research is funded by the National Science Foundation (NSF), the United States Department of Agriculture (USDA) National Institutes of Food, and Agriculture, and the Nevada Agricultural Experiment Station (NAES).

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


  • BCH/JOUR 496/696 - Scientific Communication Masterclass
  • BCH 703 - Grant Writing for Molecular Biosciences
  • BCH 705 - Molecular Genetics
  • BCH 706 - Functional Genomics
  • BCH 718 - Plant Molecular Biology and Biotechnology
  • BCH 794 - Plant Biochemistry Colloquium

Honors and awards

  • 2022 AAAS Fellow
  • 2017 Regents' Researcher Award
  • 2013 Outstanding UNR Researcher Award
  • 2011-2013 Foundation Professor
  • 2003 Outstanding CABNR Researcher Award


Guest editor, Annals of Botany; Handling Editor, Journal of Plant Physiology; Associate Editor, Journal of the Professional Association for Cactus Development; 


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


Publications are listed below.

Book Chapter(s)

The role of drought-induced proteins regulating drought tolerance in cereals.


Tuberosa, R. (ed.). In: Developing drought-resistant cereals, Burleigh Dodds Science Publishing, Cambridge, UK. DOI: 10.19103/AS.2022.0109.04

Mengistu M, Cushman JC

Climate change responses and adaptations in crassulacean acid metabolism (CAM) plants.


In: Photosynthesis, Respiration, and Climate Change. Eds. Danielle Way, Katie M. Becklin. Advances in Photosynthesis and Respiration. Springer, New York, NY USA. In press.

Pereira, P.N., Niechayev, N.A., Blair, B.B., and Cushman, J.C.


Comprehensive expression profiling analysis to investigate salt and drought responding genes in wild barley (Hordeum spontaneum L.).


Plant Stress 11: 100315. DOI: 10.1016/j.stress.2023.100315.

Bakir M, Uncuoglu AA, Ozmen CY, Baydu FY, Kazan K, Kibar U, Schlauch KA, Cushman JC, Ergul A

Crassulacean acid metabolism (CAM) at the crossroads: Special issue in the Annals of Botany to honor 50 years of CAM research by Klaus Winter


Annals of Botany. DOI: 10.1093/aob/mcad160

Sage RF, Edwards EJ, Heyduk K, Cushman JC

Developmental dynamics of crassulacean acid metabolism (CAM) in Opuntia ficus-indica


Annals of Botany. DOI: 10.1093/aob/mcad070

Niechayev NA, Meyer JA, Cushman JC

Epidermal bladder cells as a herbivore defense mechanism


Current Biology. 33: 4662-4673. DOI: 10.1016/j.cub.2023.09.063

Moog MW, Yang X, Bendtsen AK, Dong L, Crocoll C, Imamura T, Mori M, Cushman JC, Kant M, Palmgren M

Evolutionary blocks to anthocyanin accumulation and the loss of an anthocyanin carrier protein in betalain-pigmented Caryophylalles


New Phytologist. 241: 471-489. DOI: 10.1111/nph.19341

Pucker B, Walker-Hale N, Yim WC, Cushman JC, Crum A, Yang Y, Brockington S

The starch-deficient plastidic PHOSPHOGLUCOMUTASE mutant of the constitutive crassulacean acid metabolisms (CAM) species Kalanchoe fedtschenkoi impacts diel regulation and timing of stomatal CO2 responsiveness


Annals of Botany. DOI: 10.1093/aob/mcad017

Hurtado-Castano N, Atkins E, Barnes J, Boxall SF, Dever LV, Knerova J, Hartwell J, Cushman JC, Borland AM

Tissue succulence in plants: Carrying water for climate change


Journal of Plant Physiology. 289: 154081. DOI: 10.1016/j.jplph.2023.154081

Peréz-Lopéz AV, Lim SD, Cushman JC.

Multi-scale catalytic fast pyrolysis of Grindelia reveals opportunities for generating low oxygen content bio-oils from drought tolerant biomass


Energy & Fuels. 36 (1): 425–434. DOI: 10.1021/acs.energyfuels.1c02403

Cross P, Iisa K, To A, Nimlos M, Carpenter D, Mayer JA, Cushman JC, Neupane B, Miller G, Adhikari S, Mukarakate C

NaCl-promoted respiration and cell division in halophytism of a halophyte, the common ice plant Mesembryanthemum crystallinum L


J. Fac. Agr. Kyushu Univ. 67 (2): 153-164.

Sato R, Tran DQ, Yoshida K, Dang J, Konishi A, Ohnishi S, Cushman JC, Agarie S

Plant responses and adaptations to climate change


The Plant Journal. 109 (2): 319–322. DOI: 10.1111/tpj.15641 (Cover Article)

Cushman JC, Denby K, Mittler R.

Realizing the potential of Camelina sativa as a bioenergy crop for a changing global climate


MDPI Plants. 11 (6): 772. DOI: 10.3390/plants11060772 (Cover Article)

Neupane D, Lohaus RH, Solomon JKQ, Cushman JC

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome


The Plant Cell, Volume 34, Issue 11, November 2022, Pages 4143–4172

Won Cheol Yim, Mia L Swain, Dongna Ma, Hong An, Kevin A Bird, David D Curdie, Samuel Wang, Hyun Don Ham, Agusto Luzuriaga-Neira, Jay S Kirkwood, Manhoi Hur, Juan K Q Solomon, Jeffrey F Harper, Dylan K Kosma, David Alvarez-Ponce, John C Cushman, Patrick P Edger, Annaliese S Mason, J Chris Pires, Haibao Tang, Xingtan Zhang

Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical...

Characterization of a microbial consortium for improved biological degradation of Opuntia ficus-indica biomass for biofuel production.


Heliyon. 7 (8): e07854. DOI: 10.1016/j.heliyon.2021.e07854

Blair BB, Yim WC, Cushman JC.

Five-year field trial of the biomass productivity and irrigation response of cactus pear (Opuntia spp.) as a bioenergy feedstock for arid lands.


Global Change Biology: Bioenergy. 13(4): 719-741. DOI: 10.1111/gcbb.12805.

Neupane D, Mayer JA, Niechayev NA, Bishop CD, Cushman JC

Grain mineral nutrient profiling and iron bioavailability of an ancient crop teff (Eragrostis tef)


International Journal of Food Sciences and Nutrition. 15 (10): 1314–1324. DOI: 10.21475/ajcs.21.15.10.p3264

Ligaba-Osena A, Mengistu MA, Craft E, Bodis M, Giri S, Beyene G, Cushman JC, Glahn R, Pineros M.

Membrane profiling by free flow Electrophoresis and SWATH-MS to characterize subcellular compartment proteomes in Mesembryanthemum crystallinum.


International Journal of Molecular Sciences. 22:5020. DOI: 10.3390/ijms22095020.

Guo Q, Liu L, Yim WC, Cushman JC, Barkla BJ.

An Agrobacterium-mediated transformation via organogenesis regeneration of a facultative CAM plant, the common ice plant Mesembryanthemum crystallinum L.


Plant Production Science 23: 343–349. DOI: 10.1080.1343943x.2020.1730700.

Agarie, S., Umemoto, M., Sunagawa, H., Anai, T., Cushman, J.C.

Biosystems design to accelerate the C3-to-CAM progression.


Biodesign Research. Article ID 3686791. DOI: 10.34133/2020/3686791.

Yuan, G., Hassan, M.M., Liu, D., Lim, S.D., Yim, W.C., Cushman, J.C., Markel, K., Shih, P.M., Lu, H., Weston, D.J., Chen, J-G., Tschaplinski, T.J., Tuskan, G.A., Yang, X.

Five-year field trial of eight Camelina sativa varieties for biomass to be used for biofuel under irrigated conditions in a semi-arid climate.


MDPI Agronomy. 10: 562. DOI: 10.3390/agronomy10040562.

Lohaus, R.H., Neupan, D., Mengistu, M.A., Solomon, J.K.Q., and Cushman, J.C.

Genomic adaptations of the green alga Dunaliella salina to life under high salinity.


Algal Research. 50: 101990. DOI: 10.1016/j.algal.2020.101990.

Polle, J.E.W., Calhoun, S., McKie-Krisberg, Z., Prochnik, S., Neofotis, P., Yim, W.C., Hathwaik, L.T., Jenkins, J., Molina, H., Bunkenborg, J., Grigoriev, I. Barry, K., Schmutz, J., Jin, E., Cushman, J.C., and Magnusson, J.R.

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism.


GigaScience. 9: 1-17. DOI: 10.1093/gigascience.gia018.

Zhang, J., Hu, R., Sreedasyam, A. Garcia, T.M., Lipzen, A., Wang, M., Yerramsetty, P., Liu, D., Ng, V., Schmutz, J., Cushman, J.C., Borland, A.M., Pasha, A., Provart, N.J., Chen, J-G., Muchero, W., Tuskan, G.A., and Yang, X.

Plant tissue succulence engineering improves water-use efficiency, water-deficit stress attenuation, and salinity tolerance in Arabidopsis.


The Plant Journal. 103: 1049–1072. DOI: 10.1111/tpj.14783.

Lim, S.D., Meyer, J.A., Yim, W.C., and Cushman, J.C.

Systems biology and synthetic biology in relation to drought tolerance and avoidance in plants.


Frontiers in Plant Science. 11: 394. DOI: 10.3389/fpls.2020.00394.

Yang, X., Cushman, J.C., Borland, A.M., and Liu, Q.

A method for simultaneous isolation of chloroplasts and mitochondria from ice plant.


Plant Cell Biotechnology and Molecular Biology. 20: 47–54. DOI: 10.1016/j.pep.2018.11.010.

Hong, H.T.K., Phuong, T.T.B., Wheatley, M.D., and Cushman, J.C.

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

Characterization of seed oil and fatty acid methyl esters (FAMEs) from wild-type and an ethyl methanesulfonate (EMS) mutant of Camelina sativa with reduced seed-coat mucilage.


Journal of American Oil Chemists’ Society. 97: 157–174. DOI: 10.1002/aocs.12322.

Lohaus, R.H., Zager, J.J., Kosma, D.K., and Cushman, J.C.

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. 9: 91–102. 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: 6489–6493. DOI: 10.1093/jxb/erz465. Cover article.

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. 205:625–634. DOI: 10.1111/jac.12353. Cover article

Mayer JA, Cushman JC

The bracteatus pineapple genome and domestication of clonally propagated crops.


Nature Genetics. 51: 1549–1558 DOI: 10.1038/s41588-019-0506-8.

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

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.

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.

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


Frontiers in Plant ScienceFront Plant Sci. doi: 10.3389/fpls.2016.01143

Chiang C, Yim WC, Sun Y, 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.