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Jose Pruneda-Paz


Most organisms live in environmental conditions that oscillate with a 24 hour period and evolved an endogenous mechanism, known as the circadian clock, which coordinates the temporal organization of biological processes to optimal times of the day or night. Biological clocks allows an organism to anticipate the onset of periodic environmental changes providing an adaptive advantage that results in increased fitness and survival.

In plants, the pervasiveness of the clock control extends to nearly every aspect of growth and development through an extensive transcriptional regulatory network that impose circadian oscillations to more than one third of the whole transcriptome.

My laboratory is focused in studying the molecular mechanisms by which the circadian clock controls critical biological processes (i.e. outputs). In particular, we use plant-pathogen interactions as an experimental platform and aim to understand the transcriptional networks that control the circadian regulation of plant defense responses. Host-pathogen interactions are regulated by sophisticated mechanisms shaped by millions of years of coevolution. In fact, immune responses are regulated by the circadian clock not only in plants but also in other organisms such as flies and mice, suggesting that this is an evolutionary advantageous mechanism. Since the clock function and plant-pathogen responses are largely dependent on the regulation of gene expression, an extensive transcriptional network is anticipated at the interface of clock and defense signaling pathways. Using forward and reverse genetics, as well as systems approaches, we are primarily focused on identifying critical components of these transcriptional regulatory networks.

Plant pests account for great losses in crop yield around the world, thus our findings may ultimately transform our understanding of plant microbial infections and how to treat them. Moreover, plant research made major impact in understanding critical mechanisms of great biological and biomedical relevance including RNA-silencing, DNA-methylation, proteasomal-control of protein stability and programmed cell death among others. Therefore, our research could potentially uncover highly conserved regulatory networks orchestrating immune defenses in other organisms as well.

Select Publications

  • Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA (2015) “Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis”. Proc Natl Acad Sci USA, 112(34):E4802-10. PMID: 26261339
  • Zheng XY, Zhou M, Yoo H, Pruneda-Paz JL, Spivey NW, Kay SA, Dong X (2015) “Spatial and temporal regulation of biosynthesis of the plant immune signal salicylic acid”. Proc Natl Acad Sci USA, 112(30):9166-73. PMID: 26139525.
  • Taylor-Teeples M, Lin L, de Lucas M, Turco G, Toal TW, Gaudinier A,Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP, Xiong G, Wang C, Corwin J, Tsoukalas N, Pauly M, Kliebenstein DJ, Dehesh K, Tagkopoulos I, Breton G, Pruneda-Paz JL, Ahnert SE, Kay SA, Brady SM, Hazen SP (2015) “An Arabidopsis Gene Regulatory Network for Xylem Specification and Secondary Wall Biosynthesis”. Nature, 517(7536):571-5. PMID: 25533953.
  • Zhou Y, Liu X, Engstrom EM, Nimchuk ZL, Pruneda-Paz JL, Tarr PT, Yan A, Kay SA, Meyerowitz EM (2015) “Control of plant stem cell function by conserved interacting transcriptional regulators”. Nature, 517(7534):377-80. PMID: 25363783.
  • Kolmos E, Chow BY, Pruneda-Paz JL, Kay SA (2014) “HsfB2b-mediated repression of PRR7 directs abiotic stress responses of the circadian clock”. Proc Natl Acad Sci USA, 111(45):16172-7. PMID: 25352668.
  • Guan P, Wang R, Nacry P, Breton G, Kay SA, Pruneda-Paz JL, Davani A, Crawford NM (2014) “Nitrate foraging by Arabidopsis roots is mediated by the transcription factor TCP20 through the systemic signaling pathway”. Proc Natl Acad Sci USA, 111(42):15267-72. PMID: 25288754.
  • Nagel D, Pruneda-Paz JL, Kay SA (2014) “FLOWERING BHLH 1 Affects Warm Temperature Responses in the Arabidopsis Circadian Clock”. Proc Natl Acad Sci USA 111(40):14595-600. PMID: 25246594.
  • Pruneda-Paz JL*1, Breton G*, Nagel DH, Kang SE, Bonaldi K, Doherty C, Ravelo S, Galli M, Ecker JR, Kay SA1 (2014) “A Genome Scale Resource for the Functional Characterization of Arabidopsis Transcription factors”. Cell Reports 8: 1-11. PMID: 25043187. (*co-first authors, 1co-corresponding authors).
  • Chow BY, Sanchez SE, Breton G, Pruneda-Paz JL, Krogan NT, Kay SA (2014) “Transcriptional Regulation of LUX by CBF1 Mediates Cold Input to the Circadian Clock in Arabidopsis”. Curr Biol. 4(13):1518-24. PMID: 24954045.
  • Niwa M, Daimon Y, Kurotani KI, Higo A, Pruneda-Paz JL, Breton G, Mitsuda N, Kay SA, Ohme-Takagi M, Endo M, Araki T (2013) “BRANCHED1 Interacts with FLOWERING LOCUS T to Repress the Floral Transition of the Axillary Meristems in Arabidopsis”. Plant Cell 25(4):1228-42. PMID:23613197.
  • Li L, Ljung K, Breton G, Schmitz R, Pruneda-Paz J, Cowing-Vitron C, Cole BJ, Ivans LJ, Pedmale UV Jung HS, Ecker JR, Kay SA, Chory J (2012) “Linking photoreceptor excitation to changes in plant architecture”. Genes Dev. 26(8):785-90. PMID:22508725.
  • Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, Kang SE, Kay SA (2012) “Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor”. Proc Natl Acad Sci U S A, 109(8):3167-72. PMID:22315425.
  • Gaudinier A, Zhang L, Reece-Hoyes JS, Taylor-Teeples M, Pu L, Liu Z, Breton G, Pruneda-Paz JL, Kim D, Kay SA, Walhout AJ, Ware D, Brady SM (2011) “Enhanced Y1H assays for Arabidopsis”. Nat. Methods 8(12):1053-5. PMID:22037706.
  • Pruneda-Paz JL and Kay SA. (2010) An expanding universe of circadian networks in higher plants. Trends Plant Sci. 15(5):259-265.
  • Baudry A, Ito S, Song YH, Strait AA, Kiba T, Lu S, Henriques R, Pruneda-Paz JL, Chua NH, Tobin EM, Kay SA, Imaizumi T. (2010) “FKF1 and LKP2 act in concert with ZTL to control Arabidopsis clock progression”. Plant Cell 22(3): 606-22. PMID:20354196.
  • Pruneda-Paz JL, Breton G, Para A, Kay SA. (2009) A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323(5920):1481-1485.
  • Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. (2005) LUX ARRHYTHMO encodes a novel Myb transcription factor essential for circadian rhythms. Proc. Natl. Acad. Sci. U S A 102:10387-10392.
  • Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA. (2005) Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. Plant Physiol. 138(2):990-907.
  • Pruneda-Paz JL, Linares M, Cabrera JE, Genti-Raimondi S. (2004) TeiR, a LuxR-type transcription factor required for testosterone degradation in Comamonas testosteroni. J. Bacteriol. 186(5):1430-1437.


Dr. Pruneda-Paz received his Ph.D. in Biochemistry from the National University of Cordoba (Argentina), and carried out his postdoctoral research at The Scripps Research Institute and the University of California, San Diego.

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