The Plant Molecular Biology faculty in MCDB address fundamental biological questions important to plant growth and development at molecular, cellular and organismal levels. Plants not only provide us with food, fiber and biofuels but have also provided the experimental systems for major advances in science such as the discovery of hereditary laws (Gregor Mendel's work in garden peas), the discovery of transposable elements (Barbara McClintock's work in maize), and the discovery of RNA interference (co-suppression in petunia). Faculty research interests include cell fate determination, cellular development, signal transduction, gene regulation by light and environmental cues, RNA splicing, plant pathogen interactions, circadian biology and hybrid vigor in several experimental systems such as algae, Arabidopsis, cotton, and fern.
Jerry Brand, Professor and Director, UTEX The Culture Collection of Algae
Research: Research in the Brand laboratory focuses on the biology of microalgae, especially cyanobacteria. Current projects on cyanobacterial-based microbial biofilms mats address the relationship of primary carbon and nitrogen fixation by cyanobacteria to other organisms within the microbial community. Another current project examines the natural potential of cyanobacteria to produce certain isoprenoid compounds and the potential to alter that potential genetically. Other laboratory projects associated with the Culture Collection of Algae (UTEX) are the development of improved methods for cryopreserving microalgae and “bar-coding” strains of microalgae by determining nucleotide sequences of select genes.
Lineage-specific fragmentation and nuclear relocation of the mitochondrial cox2 gene in chlorophycean green algae (Chlorophyta). 2012. Elizabeth Rodriguez-Salinas, ER, Hector Riveros-RosasH, Li, Z., Fucˇikova, K, Jerry J. Brand, JJ, Louise A. Lewis, LA and Diego Gonzalez-Halphen, D. Molecular Phylogenetics and Evolution 64, 166-176.
Perkerson, R. B. III, Johansen, J. J., Kovacik, L., Brand, J, Kaslovsky, J, and Casamatta, D. 2011. A unique pseudoanabaenalean (Cyanobacteria) genus Nodulosinea Gen Nov. based on morphological and molecular data. J. Phycol. 1397-1412.
Li, Z., Yu, J., Kim, K. and Brand, J. 2010. Nitrogen fixation by a marine non-heterocystous cyanobacterium requires a heterotrophic bacterial consort. Environmental Microbiology 12, 1185-1193.
Yu, J., Li, Z. and Brand, J. 2009. Characterization of green algae isolated from infected human skin. Phycological Research 57, 251 - 258.
Paik, M., Kim, H., Lee, J., Brand, J. and Kim, K. 2009. Separation of triacylglycerols and free fatty acids in microalgae lipids by solid-phase extraction with sodium carbonate for separate fatty acid profiling analysis as tert-butyldimethylsilyl esters by gas chromatography. Journal of Chromatography A1216, 5917-5923.
Z. Jeffrey Chen, D. J. Sibley Centennial Professor in Plant Molecular Genetics
Research:The goal of our research is to provide mechanistic insights into polyploidy and hybrid vigor in Arabidopsis, cotton, and corn. We investigate how epigenetic modifications in hybrids and allopolyploids (doubled interspecific hybrids) alter allelic expression of circadian clock genes and their downstream pathways in chlorophyll biosynthesis and starch metabolism, leading to growth vigor. We test the roles of siRNAs and miRNAs in genome stability, hybrid incompatibility, and morphological development in Arabidopsis polyploids, corn hybrids, and cotton fibers.
Shi, X., Ng, D. W-K., Zhang, C., Comai, L. Ye, W., and Chen, Z. J. (2012) Cis- and trans-regulatroy divergence between progenitor species determines gene expression novelty in Arabidopsis allopolyploids. Nature Communications 3:950.
Lu, J., Zhang, C., Baulcombe, D. C., and Chen, Z. J. (2012) Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc. Natl. Acad. Sci. USA 109:5529-5534.
Guan X., Lee, J.J., Pang, M., Shi, X., Stelly, D.M., and Chen, Z.J. (2011) Activation of Arabidopsis seed hair development by cotton fiber-related genes. PLoS ONE 6(7): e21301.
Ni, Z., Kim, E., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z. J. (2009) Altered circadian rhythms regulate growth vigor in hybrids and allopolyploids. Nature 457:327-331.
Chen, Z. J., Scheffler, B. E., Dennis, E., Triplett, B. A., Zhang, T., Chen, X., Stelly, D. M., Rabinowicz, P. D., Town, C. D., Arioli, T., Brubaker, C., Cantrell, R. G., Lacape, J. M., Ulloa, M., Chee, P., Gingle, A. R., Haigler, C. H., Percy, R., Saha, S., Wilkins, T., Wright, R. J., Van Deynze, A., Zhu, Y., Yu, S., Guo, W., Abdurakhmonov, I., Katageri, I., Ananda-Kumar, P., Rahman, M., Yusuf Zafar, Y., Yu, J. Z., Kohel, R. J., Wendel, J. F., and Paterson, A. H. (2007) Toward sequencing cotton (Gossypium
) genomes. Plant Physiol.
David Herrin, Professor
Research: The common thread in our research has been the chloroplast genome of green algae and land plants, especially the remarkable introns that inhabit it. Most organellar introns are ribozymes that catalyze their own splicing, but do as RNPs. Many of the introns are mobile DNAs that are not restricted by the uniparental inheritance of the genome, since they will “home” into any available, cognate sites; thus spreading themselves in the Cp DNA population. The mobility-related processes are being studied for their genetic and evolutionary value, and because they are providing new tools and techniques for Cp genome manipulation.
2012 Liu, L., J. Lee and D.L. Herrin, Mapping of the CSS (Chloroplast Splicing Suppressor) Gene(s) to a Recombinationally-Deficient Region of Chromosome III in Chlamydomonas reinhardtii. Genome, in press.
2012 Luo, L. and D.L. Herrin, A Novel Rhodanese is Required to Maintain Chloroplast Translation in Chlamydomonas. Plant Mol. Biol. 79:495-508.
2010 Kwon, T., E. Huq and D.L. Herrin, Microhomology-Mediated and Nonhomologous Repair of a Double-Strand Break in the Chloroplast Genome of Arabidopsis. Proc. Natl. Acad. Sci USA 107:13954-9.
2010 Odom, O.W. and D.L. Herrin, An Unprecedented Group II Intron from Chlamydomonas subcaudata
(Chlorophyceae) that has Two Large Open Reading Frames – Potentially Encoding a Reverse Transcriptase-Maturase-Endonuclease and a Novel Protein. J. Phycol
Enamul Huq, Associate Professor
Research:Research in the Huq lab is focused on understanding how plants sense, interpret and respond to environmental light conditions that regulate almost every aspect of the plant life cycle from seed germination to flowering time. Specifically, we focus on the red/far-red photoreceptors (phytochromes) and their interacting factors (Phytochrome Interacting Factors, PIFs) to understand early signaling events that regulate a large number of gene expression and ultimately leads to photomorphogenesis. Future challenges include identification of kinases and E3 ligases involved in ubiquitin-mediated degradation of PIFs that is central to early phytochrome signaling events.
Shen, H., Zhu, L., Bu, Q. and Huq, E. (2012) MAX2 affects multiple hormones to promote photomorphogenesis. Mol Plant 5 (3): 750-762.
Bu, Q., Zhu, L., Dennis, M., Yu, L., Lu, S.X., Person, M.D., Tobin, E.M., Browning, K. and Huq, E. (2011) Phosphorylation by CK2 enhances the rapid light-induced degradation of PHYTOCHROME INTERACTING FACTOR 1 in Arabidopsis. J. Biol. Chem. 286: 12066-12074.
Toledo-Ortíz, G., Huq, E. and Rodríguez-Concepción, M. (2010) Direct regulation of phytoene synthase gene expression and carotenoid biosynthesis by Phytochrome-Interacting Factors. Proc. Natl. Acad. Sci. USA 107: 11626-11631.
Shen, H., Ling, Z., Castillon, A., Majee, M., Downie, B. and Huq, E. (2008) Light-induced phosphorylation and degradation of the negative regulator PIF1 depends upon its direct physical interactions with photoactivated phytochromes. Plant Cell 20:1586-1602.
John La Claire, Professor
Research: We are using molecular and chemical approaches toward unraveling the synthesis of ichthyotoxins by the harmful alga, Prymnesium parvum, as well as the effects of physicochemical factors upon the structure and toxicity of these polyketide compounds.
Manning, S.R. and J. W. La Claire II. 2010. Multiplex PCR methods for the species-specific detection and quantification of Prymnesium parvum (Haptophyta). Journal of Applied Phycology 22:587-579.
Manning, S.R. and J. W. La Claire II. 2010. Prymnesins: toxic metabolites of the golden alga, Prymnesium parvum Carter (Haptophyta). Marine Drugs 8:678-704 (Open Access)
La Claire, J.W., II. 2006. Analysis of expressed sequence tags from the harmful alga, Prymnesium parvum (Prymnesiophyceae, Haptophyta). Marine Biotechnology 8:534-546.
Alan Lloyd, Professor
Research: Research in the Lloyd lab focuses on developmental and pigment pathways that occur in the plant epidermis. We investigate how plants regulate pattern formation and cell fate determination using Arabidopsis trichomes and the seed coat as a model. And we are interested in how plants regulate and produce red, purple, and yellow pigments. Recently we have been studying how beets make the red betalains. These pigments are particularly interesting, because of their evolutionary isolation in only a single order of plants, the Caryophyllales.
Web site: http://www.biosci.utexas.edu/MCDB/profiles.aspx?id=1669
Symonds VV, Hatlestad G, Lloyd AM (2011) Natural allelic variation defines a role for ATMYC1: trichome cell fate determination. PLoS Genetics Vol. 7, No. 6. (9 June 2011), e1002069. doi:10.1371/journal.pgen.1002069
Gonzalez A, Huo Y, Mendenhall J, Lloyd AM (2009) TTG1 complex mybs, Myb5 and TT2, control outer seed coat development. Developmental Biology 325:412-421.
Zhao M, Morohashi K, Hatlestad G, Grotewold E, Lloyd AM (2008) The TTG1-bHLH-MYB complex controls trichome cell fate and patterning through direct targeting of regulatory loci. Development 135:1991-1999.
Gonzalez A, Zhao M, Leavitt J, Lloyd AM (2008) Regulation of the anthocyanin pigment pathway by myb and bHLH transcription factor complexes. Plant Journal 53: 814-827.
Mona Mehdy, Associate Professor
Research: Our long-standing interest has been to understand molecular mechanisms of mRNA destabilization in plants during the defense response to pathogens. More recently, we have undertaken the functional analysis of an Arabidopsis defense-down-regulated arabinogalactan protein AGP31 during normal growth and development. In addition, we have initiated work on a fresh water microalgal species to assess herbivore resistance mechanisms, inspired by the potential of microalgae as a biofuel source.
Liu, C. and Mehdy, M.C. (2007) A non-classical arabinogalactan-protein gene highly expressed in the vascular bundle, AGP31, is transcriptionally repressed by methyl jasmonic acid in Arabidopsis. Plant Physiology 145: 863-874.
Stan Roux, Professor
Research: We are studying how extracellular nucleotides and apyrase (NTPDase) enzymes help to mediate changes in plant growth and development, including especially those initiated by the stimuli of light and gravity. We are using molecular approaches to characterize the signaling steps that link the stimuli of extracellular nucleotides to modifications in how plants grow and develop.
Clark G, Fraley D, Steinebrunner I, Cervantes A, Onyirimba J, Liu A, Torres T, Tang W, Kim J, Roux SJ.  Extracellular nucleotides and apyrases regulate stomatal aperture in Arabidopsis. Plant Physiol. 156 (4): 1740-1753.
Clark, G., Torres, J., Finlayson, S., Guan, X., Handley, C., Lee, J., Kays, J.E., Chen, Z.J., Roux, S.J.  Apyrase (NTPDase) and extracellular nucleotides regulate cotton fiber elongation in cultured ovules. Plant Physiology 152: 1073-1083.
Salmi M, ul Haque A, Bushart TJ, Stout SC, Roux SJ, Porterfield DM. 2011. Changes in gravity rapidly alter the magnitude and direction of a cellular calcium current. Planta 233 (5): 911-920.
Sibum Sung, Assistant Professor
Research: Research in the Sung Lab is focused on the regulation of flowering time by environmental cues, such as photoperiod and temperature. In particular, we are interested in understanding molecular mechanisms underlying the epigenetic regulation of floral genes by environmental changes in a model plant, Arabidopsis.
Heo, J. B. and S. Sung,2011, Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331: 76-9.
Kim D. H. and S. Sung, 2010, The Plant Homeo Domain finger protein, VIN3-LIKE 2, is necessary for photoperiod-mediated epigenetic regulation of the floral repressor, MAF5, Proc. Natl. Acad. Sci., 107(39): 17029-17034.
Kim D. H., B.R. Zografos, and S. Sung, 2010, Vernalization-mediated VIN3 induction overcomes the LIKE-HETEROCHROMATIN PROTEIN 1/Polycomb Repression Complex 2 -mediated epigenetic repression. Plant Physiol., 154: 949-957
Kim, D.-H., M. Doyle, S. Sung, and R. M. Amasino, 2009, VERNALIZATION: WINTER AND THE TIMING OF FLOWERING IN PLANTS. Annual Rev. Cell Dev. Biol., 25:277-299.