Dr. Steven Rothstein

Dr. Steven Rothstein
Adjunct Professor; Professor Emeritus
Department of Molecular and Cellular Biology
Phone number: 
58524 / 54841
SSC 4469
SSC 4407-8
  • BA - Swarthmore College
  • PhD- University of Wisconsin

My research interest is to use molecular genetic, biochemical and genomic information to understand problems of fundamental importance in plant biology which also have an impact on the improvement of important crop plants. One of the most important issues in crop agriculture is the economic and environmental cost of using large quantities of nitrogen fertilizer. Our current principle interest is in understanding the regulation of nitrogen metabolism with the long-term goal of generating the basic knowledge necessary to be able to improve the nitrogen use efficiency of crop plants. We are utilizing the genetic and genomic resources developed by the Arabidopsis scientific community to study this problem. In particular, we are interested in identifying regulatory genes important for these processes and manipulating their expression so that we can learn how to alter this trait in a positive fashion. The genes to be tested are being identified using a combination of bioinformatics analysis of sequence information, transcript profiling, biochemical analysis and by studying a large number of defined mutations in the genes of interest.


  1. D Yan, V Easwaran, V Chau, M Okamoto, M Ierullo, M Kimura, A Endo, R Yano, A Pasha, Y Gong, Y-M Bi, N Provard, D Guttman, A Krapp, SJ Rothstein and E Nambara. NIN-like protein 8 is a master regulator of nitrate-promoted seed germination in Arabidopsis. Nature Communications doi: 10.1038/ncomm13179, 2016.
  2. K Mahmood, Z Xu, A El-Kereamy, JA Casaretto and SJ Rothstein. The Arabidopsis Transcription Factor ANAC032 Represses Anthocyanin biosynthesis in Response to High Sucrose and Oxidative and Abiotic Stresses. Frontiers in Plant Science doi: 10.3389/fpls.2016.01548, 2016.
  3. K Mahmood, A El-Dereamy, S-H Kim, E Nambara and SJ Rothstein. ANAC032 Positively Regulates Age-Dependent and Stress-Induced Senescence in Arabidopsis thaliana. Plant and Cell Physiology 57 2029-2046, 2016.
  4. K Ranathunge, L Schreiber, Y-M Bi and SJ Rothstein. Ammonium-induces architectural and anatomic changes with altered suberin and lignin levels significantly change water and solute permeabilities of rice (Oryza sativa L.) roots. Planta 243 231-249, 2016.
  5. L Gaufichon, SJ Rothstein and A Suzuki. Asparagine metabolic pathways in Arabidopsis. Plant and Cell Physiology 19 5785-5798, 2016.
  6. JA Casaretto, A El-Kereamy, B Zeng, SM Stiegelmeyer, X Chen, Y-M Bi, and SJ Rothstein. Expression of OsMYB55 in maize activates stress-responsive genes and enhances heat and drought tolerance. BMC Genomics 17 doi: 10.1185/s12864-016-2659-5, 2015.
  7. A El-Kereamy, Y-M Bi, K. Mahmood, K. Ranathunge, MW Yaish and SJ Rothstein. Overexpression of the CC-type glutoredoxin, OsGRX6 affects hormone and nitrogen status in rice plants. Frontiers in Plant Science doi: 10.3389/fps.2015.00934, 2015. 
  8. G Lu, V Coneva, JA Cassaretto, S Ying, K Mahmood, F Liu, E Nambara, Y-M Bi, and SJ Rothstein. OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution. Plant Journal 83, 913-925, 2015.
  9. M Han, M Okamoto, PH Beatty, PH, SJ Rothstein and AG Good. The genetics of nitrogen use efficiency in crop plants. Annual Review of Genetics 49, DOI: 10.1146/annurev-genet-112414-055037, 2015.
  10. GN Nguyen, SJ Rothstein, G Spangenberg, G and S Kant. Role of microRNAs in plant response to nitrogen and phosphorous limiting conditions. Frontiers in Plant Science 6, doi 10.3389/fpls.2015.00629, 2015.
  11. V Yadav, I Molina, K Ranathunge, IQ Castillo, SJRothstein and JW Reed. ABCG transporters are required for suberin and pollen wall extracellular barriers in Arabidopsis. Plant Cell 26, 3569-3588, 2014.
  12. M Misyura, DR Guevara, S Subedi, D Hudson, PD McNicholas, J Colasantiand SJ Rothstein Nitrogen limitation and high density responses in rice suggest a role for ethylene under high density stress. BMC Genomics 15 doi:1186/1471-2164-15-681, 2014.
  13. SJ Rothstein; Y-M Bi, V Coneva, M Han and AG Good, The challenges of commercializing second-generation transgenic crop traits necessitate the development of international public sector research infrastructure. 
Journal of Experimental Botany 65, 5673-5682, 2014.
  14. K Ranathunge, A El-Kereamy, S Gidda, Y-M Bi and SJ Rothstein. OsAMT1;1trangenic rice plants with enhanced NH4+ permeability show superior growth and higher yield under optimal and suboptimal NH4+ conditions. Journal of Experimental Botany 65, 965-979, 2014.
  15. Y-M Bi, A Meyer, GS Downs, X Shi, A El-Keramy, L Lukens and SJ Rothstein. High throughput sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation. BMC Genomics 15, doi:10.1186/1471-2164-15-77, 2014.
  16. DR Guevara, A El-Kereamy, MW Yaish, Y-M Bi and SJ Rothstein. Functional characterization of the rice UDP-glucose 4 epimerase 1, OsUGE1: A potential role in cell wall carbohydrate partitioning during limiting nitrogen conditions. PloS ONE 9 e96158, 2014.
  17. JL Ericson, J Ziegler, DR Guevara, S Abel, RB Klosgen, J Mathur, SJ Rothstein, and MH SchattatAgrobacterium-derived cytokinin influences plastid morphology and starch accumulation in Nicotiana benthamiana during transient assays. BMC Plant Biology 14, 127.109, 2014.
  18. C Liseron-Monfils, Y-M Bi, GS Downs, W Wu, T Signorelli, G Lu, X Chen, J Colasanti, SJ Rothstein and M Raizada. Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs. Plant Signaling and Behavior 8, e26056, 2013.
  19. D Hudson, DR Guevara, AJ Hand, Z Xu, L Hao, X Chen, T Zhu, Y-M Bi, and SJ Rothstein. Rice cytokinin GATA transcription factor1 regulates chloroplast development and plant architecture. Plant Physiology 162, 132-144, 2013.
  20. Downs, GS, Bi, Y-M., Colasanti, J., Wu, W., Chen, X., Zhu, T., Rothstein, SJ, and Lukens, L. A developmental transcriptional network for Zea mays defines coexpression modules Plant Physiology, pp112.213231 2013.
  21. Humbert, S, Subedi, S, Cohn, J, Zeng, B., Bi, Y-M., Chen, X., McNicholas, PD, and Rothstein, SJ Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses BMC Genomics 14: doi:10.1186/1471-2164-14-3, 2013.
  22. Misyura, M., Colasanti, J and Rothstein, SJ Physiological and genetic analysis of Arabidopsis anthocyanin mutants under chronic adverse environmental J Experimental Botany 64: 229-240. doi:10, 1093/jxb/ers328106, 2013. 
  23. Tian, G, Lu, Q., Kohalmi, SE, Rothstien, SJ and Cui, Y. Evidence that the Arabidopsis Ubiquitin C-terminal Hydorlases 1 and 2 assemble with the 26S proteasome and the TREX-2 complex. Plant Signaling and Behavior 7: 1415-1419, 2012.
  24. Xurong Tang, Shaomin Bian, Mingjuan Tang, Qing Lu, Shengben Li, Xigang Liu,
Gang Tian, Vi Nguyen, Edward W. T. Tsang, Aiming Wang, Steven J. Rothstein, Xuemei Chen, Yuhai Cui. MicroRNA–Mediated Repression of the Seed Maturation Program during Vegetative Development in Arabidopsis. pLOS Genetics 8(11): e1003091. Doi10.1371, 2012.
  25. Kant, S., Senaweera, S., Rodin, J, Materne, M., Burch, D, Rothstein, SJ, Spangernberg, G. Improving yield potential in corps under elevated CO2: integrating photosynthetic and nitrogen utilization efficiencies. Frontiers in Plant Sciences; 3: 162; doi: 10.3389/fpls, 2012.
  26. Coneva, V., Guevara, D., Rothstein, SJ, Colasanti, J. Transcript and metabolite signature of maize source leaves suggests a link between transitory starch to sucrose balance and the autonomous floral transition. J. Exp Bot; doi10.1093/jxb/ers/ers158, 2012.
  27. Humbert, S, Zhong, S., Deng, Y., Howell, SH, and Rothstein, SJ. Alteration of the bZIP60/IRE1 Pathway affects Plant Response to ER Stress in Arabidopsis thaliana. PLOS1 7(6) e39023, 2012.
  28. Xu, Z, Zhong, S, Li, X, Rothstein, SJ, Zhong, S., Bi, Y, and Xie, C. (2011) Genome-Wide Identification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots PLOS1, e28009, 2011.
  29. Hudson, D, Guevara, D, Yaish, MW, Hannam, C. Long, N. Clarke, JD, Bi, YM, and Rothstein, SJ. GNC and CGA1 Modulate Chlorophyll biosynthesis and glutamate Synthase (Glu1/Fd- GOGAT Expression in Arabidopsis. PLOS1, e26765, 2012. 
  30. Xu, X., Zhong, S., Li,X., Rothstein, SJ, Zhang, S., Bi, Y, Xie, C. Genome-Wide Idntification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots. PLOS1 6(11) e28009, 2011.
  31. Brauer, E., Bi, YM, Bozzo, GG, Rothstein, SJ and Shelp, B. Reappraisal of nitrogen use efficiency in rice overexpressing gluamine synthetase1 Physiologia Plantarum 141, 361-372, 2011. 
  32. Xurong Tang, Myung-Ho Lim, Julie Pelletier, Mingjuan Tang, Vi Nguyen, Wilfred A. Keller, Edward W. T. Tsang, Aiming Wang, Steven J. Rothstein, John J. Harada, and Yuhai Cui Synergistic repression of the embryonic programme by SET DOMAIN GROUP 8 and EMBRYONIC FLOWER 2 in Arabidopsis seedlings J Exp Bot. 63(3): 1391–1404, 2012.
  33. Yaish, M.W., Colasanti, J., and Rothstein, S.J. The role of epigenetic processes in controlling flowering time inplants exposed to stress. J. Experimental Botany, 2011.
  34. El-Kereamy, A., Guevara, D., Bi, Y. M., Chen, X., Rothstein,S.J. Exploring the molecular and metabolic factors contributing to the adaptation of maize seedlings to nitrate limitation. Frontiers in Plant Science: Volume 2, Article 49, doi: 10.3389/fpls, 2011.
  35. Kant, S, Bi, Y-M., and Rothstein, S.J. Understanding Plant Response to nitrogen limitation for the improvement of crop nitrogen use efficiency J of Exp Bot, 62, 1499-1508, 2011. 
  36. Gidda, S.K., Shockey, J.M., Falcone, M., Kim, P.K., Rothstein, S.J., Andrews, D.W., Dyer, J.M., and Mullen, R.T. Hydrophobic-Domain-Dependent Protein-Protein Interactions Mediate the Localization of GPAT Enzymes to ER Subdomains Traffic: 12, 452-472, 2011.
  37. Surya Kant, Mingsheng Peng, Steven J Rothstein, Genetic control of nitrate dependent phosphate homeostasis in Arabidopsis pLOS Genetics Volume 7; Issue 3, Article number e1002021, 2011. 
  38. Yan Deng, Sabrina Humbert, Jian-Xiang Liu, Renu Srivastava, Steven J. Rothstein and Stephen H. Howell Heat induces the splicing of AtbZIP60 mRNA by IRE1b in the unfolded protein response in Arabidopsis seedlings. Proc Natl Acad Sci USA 108,7247-7252, 2011.
  39. Mahmood Yaish, Ashraf El-Kereamy, Tong Zhu, Perrin Beatty, Allen Good, Yong Mei Bi and Steven J Rothstein. The APETALA-2-Like Transcription Factor OsAP2-39 Controls Key Interactions between Abscisic acid and Gibberellin in Rice. pLOS Genetics. Volume: 6 Issue: 9 Article Number: e1001098, 2010. 
  40. Qing Lu, Xurong Tang, Gang Tian, Fang Wang, Kede Liu, Vi Nguyen, Susanne E. Kohalmi, Wilfred A. Keller, Edward W.T. Tsang, John J. Harada, Steven J. Rothstein, and Yuhai Cui The Arabidopsis Homolog of the Yeast TREX-2 mRNA Export Complex: Components, Anchoring Nucleoporin, and Links with the 26S Proteasome. Plant Journal, 61, 259-270, 2010.
  41. Surya Kant, Yong-Mei Bi, Tong Zhu and Steven J. Rothstein. SAUR39, a small auxin-up RNA gene, acts as a negative regulator of auxin synthesis and transport in rice. Plant Physiology, 151, 691-670, 2009.
  42. Yong-Mei Bi, Surya Kant, Joseph Clarke, Lixin Hao, Rong Zhao, Satinder Gidda, Robert Mullen, Tong Zhu and Steven Rothstein. Increased Nitrogen Use Efficiency in Rice Plants Over-Expressing a Nitrogen-Responsive Early Nodulin Gene Identified Using Expression Profiling. Plant Cell and Environment, 32, 1749-1760, 2009. 
  43. Fabien Potel, Marie-Hélène Valadier, Sylvie Ferrario-Méry, Olivier Grandjean, Halima Morin, Laure Gaufichon, Stéphanie Boutet, Jérémy Lothier, Steven Rothstein, Naoya Hirose, and Akira Suzuki. Assimilation of excess ammonium into amino acids and nitrogen translocation in Arabidopsis thaliana. Roles of glutamate synthases and carbamoylphosphate synthetase in leaves FEBS Letters, 276, 4061-4076, 2009.
  44. Satinder K. Gidda , Jay M. Shockey , Steven J. Rothstein , John M. Dyer, Robert T. Mullen. Arabidopsis thaliana GPAT8 and GPAT9 are localized to the ER and possess distinct ER retrieval signals: Functional divergence of the dilysine ER retrieval motif in plant cells. Plant Physiology and Biochemistry, 47, 867-879, 2009.
  45. Mahmoud Yaish, Mingsheng Peng, and Steven Rothstein. MBD9 Modulates Plant Development through the Dual Pathways of DNA Methylation and Histone Acetylation. Plant Journal, 59, 123-135. 2009.
  46. R. Andrew Schofield, Yong-Mei Bi, Surya Kant, Steven J. Rothstein Over expression of STP13, a hexose transporter improves plant growth and nitrogen use in Arabidopsis thaliana seedlings. Plant Cell and Environment 32: 271-285, 2009. 
  47. Peng, M., Hudson, D., Schofield, A., Tsao, R., Yang, R., Gu, H., Bi, Y.-M., and Rothstein, S.J. Adaptation of Arabidopsis to nitrogen limitation involves induction of anthocyanin synthesis which is controlled by the NLA gene. Journal of Experimental Botany. 59: 2933 – 2944, 2008.
  48. Echarte, L., S. Rothstein, and M. Tollenaar The response of leaf photosynthesis and dry matter accumulation to nitrogen supply in an older and a newer maize hybrid. Crop Science, 48(2): p. 656-665, 2008.
  49. Lingard MJ, SK Gidda, S Bingham, SJ Rothstein, RT Mullen, and RN Trelease. Arabidopsis PEX11 isoforms c, d and e, FIS1b, and DRP3A cooperatively participate in cell-cycle-associated replication of peroxisomes. Plant Cell 20: 1567-1585, 2008. 
  50. Kant S, Bi YM, Weretilnyk E, Barak S & Rothstein SJ The Arabidopsis Halophytic Relative, Thellungiella halophila, Tolerates Nitrogen limiting Conditions by Maintaining Growth, Nitrogen Uptake and Assimilation. Plant Physiol. 147:1168-80, 2008. 
  51. Rothstein, SJ. Returning to our roots: The importance of making plant biology research relevant to meet future agricultural challenges. Plant Cell. 19: 2695-2699, 2007.
  52. Peng, M., Hannam, C., Gu, H., Bi, Y.-M., Rothstein, S.J. Mutation in NLA which encodes a RING-type ubiquitin ligase, disrupts Arabidopsis adaptability to nitrogen limitation. Plant J. 50: 320-337, 2007.
  53. Bi, Y.-M., Wang, R.-L., Zhu, T., Rothstein, S.J. .Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis. BMC Genomics. 8: article number 281, 2007.
  54. Peng, M., Bi, Y-M, Zhy, T. and Rothstein, SJ Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase NLA. Plant Molecular Biology. 65: 775-797, 2007.
  55. Shockey JM, Gidda SK, Chapital DC, Dhanoa, DK, Bland, JM, Rothstein, SJ, Mullen, RT and Dyer, JM. Tung tree DGA1 and DGAT2 have nonredundant funcions in triacylglyerol biosynthesis and are localized to different subdomains of the endoplasmic reticulum Plant Cell 18: 2294-2313, 2006.
  56. Peng, M, Bi, Y-M., Cui, Y. and Rothstein, S.J AtMBD9: A Protein Having a Methyl-CpG-Binding Domain Regulates Flowering Time and Shoot Branching in Arabidopsis -. Plant Journal, 46: 282-296, 2006.
  57. Bi, Y-M, Zhang, Y., Signorelli, T., Zhao, R., Zhu, T. and Rothstein, S. Genetic Analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll sensitivity and glucose sensitivity. Plant J 44: 680-692, 2005.


  • Xu, Zhenhua (Dr.)

Research Associate

  • Casaretto, Jose (Dr.)


  • Zeng, Bin

Research Manager

  • Yong-Mei Bi (Dr.)