Research Interests: Plant biochemistry; Cellular and molecular biology related to the regulation of plant growth and development.

Basic plant biology: The primary signal transduction systems in plants involve hormonal messengers that translate developmental, positional and environmental information into optimized growth and development. The levels of the hormone messengers in plant tissues are determined by four general processes: biosynthesis, conjugation reactions, catabolism and transport. Each of these processes must be under close regulation because the levels of the phytohormone are critical for the regulation of growth and developmental processes. It is a fundamental goal of this laboratory to understand in precise detail how the levels of auxin (indole-3-acetic acid, IAA), the first discovered plant hormone, are regulated in specific cells and tissues within plants.

Why study auxin and what might it do for horticulture?  Auxins are most well known for their two uses:  1) They form the active ingredient in rooting hormone mixtures, and 2) they are used for the selective control of broadleaf weeds in lawns and pastures. However, auxins control a wide variety of plant processes from early embryo growth to the regulation of plant senescence. In fact, they control the size of every plant cell, are part of the system that defines plant size and shape and control the growth of fruit as well as the formation of wood and vascular tissues.

The fact that auxins are involved in so many aspects of plant growth and development often make it difficult to focus on just which processes would benefit by knowing more about auxins. Work from our laboratory suggests several areas where benefits can be realized over the next several years. These include: 1) the development of improved strategies for the genetic and/or chemical manipulation of rooting in cuttings from woody plants; 2) the development of improved methods for the micropropagation and artificial seed production from difficult to propagate plant species; 3) the control of fruit size, the rate of fruit ripening and the production of seedless fruits; 4) improved performance of plants following exposure to environmental or biological stress conditions; 5) the development of dwarfing methods using non-traditional approaches; 6) the development of improved methods for regeneration of horticultural species from cell cultures for plant improvement.

The laboratory is widely recognized for research aimed at understanding auxin biosynthesis and metabolism. Previous work from our group have shown 1) that indole-3-butryic acid is a native auxin in plants; 2) that multiple pathways are present in plants, including one that is independent of the amino acid tryptophan, and the use of these pathways is under environmental and developmental regulation, 3) that auxins exist in plant both as the free form as well as conjugated to various other compounds including proteins, and 4) that auxins control the rate of ripening in some fruit tissues. We continue to expand on these findings and develop new ways to use our knowledge of auxin biology to improve and develop new plant materials.

Our laboratory uses a wide variety of research approaches to understand auxin biology: from development of new genomic, proteinomic and metabolomic methods, molecular biology, protein and enzyme isolation, analytical biochemistry/chemistry to growth chamber, greenhouse and field evaluations of plant materials. We also maintain extensive collaborations with academic, industry and commercial grower colleagues.      

References:

• Wright, A.D., Sampson, M.B., Neuffer, M.G., Michalczuk, L., Slovin, J.P. and Cohen, J.D. Indole-3-acetic acid biosynthesis in the mutant maize orange pericarp, a tryptophan auxotroph. Science 254:998-1000 (1991)
• Sztein A.E., Cohen J.D. and Cooke T.J.  Evolutionary patterns in the auxin metabolism of green plants.  Int. J. Plant Sci. 161:849-859 (2000)
• Zhao Y., Christensen S.K., Fankhauser C., Cashman J.R., Cohen J.D., Weigel D. and Chory J.  A role for flavin monooxygenase-like enzymes in auxin biosynthesis.  Science 291:306-309 (2001)
• Ribnicky, D.M., Cohen, J.D., Hu, W.-S. and Cooke, T.J. An extraordinary auxin surge following fertilization in carrot: Its significance for plant totipotency. Planta 214: 505-509 (2002)
• Cooke TJ, Poli DB, Sztein AE, Cohen JD Evolutionary patterns in auxin action. Plant Mol Biol  49:319-38 (2002)
• Ljung K, Hull AK, Kowalczyk M, Marchant A, Celenza J, Cohen JD, Sandberg G. Biosynthesis, conjugation, catabolism and homeostasis of indole-3-acetic acid in Arabidopsis thaliana.  Plant Mol Biol. 50:309-32 (2002)
• Chou J.-C, Mulbry WW, Cohen JD N-Carbobenzyloxy-D-aspartic acid as a competitive inhibitor of indole-3-acetyl-L-aspartic acid hydrolase of Enterobacter agglomerans.  Plant Growth Regulation 37:241-248 (2002)
• Sztein AE, Ilic N, Cohen JD, Cooke TJ  Indole-3-acetic acid biosynthesis in isolated axes from germinating bean seeds: The effect of wounding on the biosynthetic pathway.  Plant Growth Regulation 36:201-207 (2002)
• Epstein E, Cohen JD, Slovin JP The biosynthetic pathway for indole-3-acetic acid changes during tomato fruit development.  Plant Growth Regulation 38:15-20 (2002)
• Cohen JD, Slovin JP and Hendrickson AM Two genetically discrete pathways convert tryptophan to auxin: more redundancy in auxin biosynthesis.  Trends in Plant Science 8:197-199 (2003)
• Keller CP,Stahlberg R, Barkawi LS, and Cohen JD Long-term inhibition by auxin of leaf blade expansion in bean (Phaseolus vulgaris) and Arabidopsis thaliana. Plant Physiol 134: 1217-1226 (2004)
• Cooke TJ, Poli DB, Cohen JD Did auxin play a crucial role in the evolution of novel body plans during the Late Silurian-Early Devonian radiation of land plants?  In: The Evolution of Plant Physiology:  From Whole Plants to Ecosystems.  AR Hemsley and I Poole, eds. Linnean Society of London and Elsevier Academic Press, Amsterdam pp. 85-107 (2004)
• Normanly J, Slovin JP, Cohen JD  Auxin biosynthesis and metabolism.  In: Plant Hormones: Biosynthess, Signal Transduction, Action! (3^rd edition).  P.J. Davies, ed.  Kluwer Academic Publ., Dordrecht, pp. 36-62 (2004)
• Kunkel BN, Agnew J, Collins J, Cohen JD, Chen Z Molecular genetic analysis of AvrRpt2 activity in promoting virulence of Pseudomonas syringae. In: Genomic and Genetic Analysis of Plant Parasitism and Defense, S Tsuyumu, T Shiraishi, T Wolpert, JE Leach (Eds), APS Press, pp 92-102 (2005)
• Ilic N, Cohen JD Synthesis of [¹³C]-isotopomers of indole and tryptophan for use in the analysis of indole-3-acetic acid biosynthesis.  J Labelled Compd Radiopharm 47: 635–646 (2004)
• Chou JC, Welch WH, Cohen JD. His-404 and His-405 are essential for enzyme catalytic activities of a bacterial indole-3-acetyl-L-aspartic acid hydrolase. Plant Cell Physiol. 45:1335-1341 (2004)
• Ilic N, Habus I, Barkawi LS, Park S, Stefanic Z, Kojic-Prodic B, Cohen JD, Magnus V Aminoethyl-substituted indole-3-acetic acids for the preparation of tagged and carrier-linked auxin.  Bioorganic and Medicinal Chemistry 13:3229-3240 (2005)

• Iyer M, Slovin JP, Epstein E, Cohen JD Transgenic tomato plants with a modified ability to synthesize indole-3-acetyl-$-1-O-D-glucose.  J Plant Growth Regul 24:142-152 (2005)

  Ludwig-Müller J, Walz A, Slovin JP, Epstein E, Cohen JD, Dong W, Town CD  Overexpression of maize IAGLU in Arabidopsis thaliana alters plant growth and sensitivity to IAA but not IBA and 2,4-D. J Plant Growth Regul 24:127-141 (2005)

• Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development 132:4107-4118 (2005)
• Engelen-Eigles G, Holden G, Cohen JD, Gardner G The effect of temperature, photoperiod, and light quality on gluconasturtiin concentration in watercress (Nasturtium officinale R. Br). J Agric Food Chem 54:328-334 (2006)

•  Seidel C, Walz A, Park S, Cohen JD, Ludwig-Mueller J Indole-3-acetic acid protein conjugates: novel players in auxin homeostasis. Plant Biol 8:340-345 (2006)

• Park S, Cohen JD, Slovin JP Strawberry fruit protein with a novel indole-acyl modification.  Planta 224:1015-1022 (2006)

• Cohen JD, Gray WM Auxin metabolism and signaling. In: Hedden P, Thomas, S (eds), Plant Hormone Signaling (Annual Plant Reviews, Vol. 24).  Blackwell Publishing, Oxford, pp. 37-66 (2006)

• Stoll DR, Cohen JD and Carr PW Fast, comprehensive online two-dimensional high performance liquid chromatography through the use of high temperature ultra-fast gradient elution reversed-phase liquid chromatography. J Chromatogr A 1122:123-137. (2006)

• Porter SEG, Stoll DR, Rutan SC, Carr PW, Cohen JD  Analysis of four-way two-dimentional liguid chromatography-diode array data: Application to metabolomics. Anal Chem 78:5559-5569 (2006)

• Barkawi LS, Tam Y-Y, Tillman JA, Pederson B, Calio J, Al-Amier H, Emerick M, Normanly J,Cohen JD A high-throughput method for the quantitative analysis of indole-3-acetic acid and other auxins from plant tissue. Analytical Biochemistry doi:10.1016/j.ab.2007.08.009