Regulatory Genomics of Plant Growth
The cell wall is a distinguishing feature of plants. It is a complex composite of polysaccharides, proteins, and lignin, with lignin and cellulose representing two of the most abundant bio-organic compounds on the planet. It is essential to plants that structurally important polysaccharides are resistant to facile deconstruction by herbivores and microbes. Cell wall properties leading to increased crop health and productivity may in fact have a negative consequence on their quality as livestock feed or as a biofuel feedstock. My research focuses on understanding the regulatory mechanism underlying plant cell wall biosynthesis and the nature of natural genetic variation leading to differences in cell wall phenotypes.
There has been an explosion of interest and optimism in the prospect of exploiting plant cell wall sugars to produce biofuel. Amenability to such a process is dependent upon overall cell wall composition and the manner in which those components interact. One mechanism regulating cell wall biosynthesis is the activity of transcription factors that control higher order events of growth and differentiation and the likely direct regulation of processive and non-processive glycosyltransferases as well as the phenylpropanoid metabolic grid. We seek systems level insight into regulatory networks affecting monocot and dicot growth and development and cell wall biosynthesis that will ultimately lead to a better understanding of bioenergy-related properties.
Our approach relies on the well developed resources of the model plant species Arabidopsis thaliana which include a fully sequenced genome, a whole genome tiling array, large collections of full-length cDNAs, loss-of-function and gain-of-function mutants, and extensive recombinant and association mapping populations. We also study Brachypodium distachyon, a new model system for herbaceous plants that are candidates for biofuel crops such as switchgrass and Miscanthus. In the case of Arabidopsis and soon Brachypodium, we are aware of the upstream regulatory sequences and have captured full length genes as an experimental reagent. We now seek to find direct interactions between proteins and promoter sequences in order to assemble a model that describes the system. Accordingly, we perturb the system model to determine function and provide insight into exactly how crop plants can be deterministically improved. The exploration of natural genetic variation can provide insight into how this might be done. Understanding the type of variation that is exploited by plant breeders, DNA sequence variation leading to changes in gene expression or amino acid sequence, for example, will provide more educated decisions on future crop improvement approaches.
Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T.W., Gaudinier, A., Young, N.F., Trabucco, G.M., Veling, M.T., Lamothe, R., Handakumbura, P.P., Xiong, G., Corwin, J., Tsoukalas, N., Pauly, M., Kliebenstein, D.J., Tagkopoulos, I, Breton, G., Pruneda-Paz, J.L., Ahnert, S.E., Kay, S.A., Hazen, S.P., Brady, S.M. 2015. An Arabidopsis gene regulatory network for xylem specification and secondary wall biosynthesis. Nature, 517: 571-575. Featured in Nature News & Views.
Li, L., Zhang, Q., Pedmale, U.V., Nito, K., Fu, W., Lin, L., Hazen, S.P., Chory, J. 2014. PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade. Molecular Plant, 7: 1582-1585.
Matos, D.A., Cole, B.J., Whitney, I.P., MacKinnon, KJ-M, Kay, S.A., Hazen, S.P. 2104. Daily changes in temperature, not the circadian clock, regulate growth rate in Brachypodium distachyon. PLoS ONE, 9: e100072.
da Costa, R., Lee, S.J., Allison, G.G., Hazen, S.P., Winters, A., Bosch, M. 2014. Genotype, development and tissue derived variation of cell wall properties in the lignocellulosic energy crop Miscanthus. Annals of Botany, 114: 1265-1277.
Bosch, M., Hazen, S.P. 2013. Lignocellulosic feedstocks: research progress and challenges in optimizing biomass quality and yield. Frontiers in Plant Science, 4: 474.
Matos, D.A., Whitney, I.P., Harrington, M.J., Hazen, S.P. 2013. Cell walls and the developmental anatomy of the Brachypodium distachyon stem internode. PLoS ONE, 8 (11): e80640.
Handakambura, P.P., Matos, D.A., Osmont, K.S., Harrington, M.J., Heo, K., Kafle, K., Kim, S.H., Baskin, T.I., Hazen, S.P. 2013. Perturbation of Brachypodium distachyon CELLULOSE SYNTHASE A4 or 7 results in abnormal cell walls. BMC Plant Biology, 13: 131.
Trabucco, G.M., Matos, D.A., Lee, S.J., Saathoff, A.J., Priest, H.D., Mockler, T.C., Sarath, G., Hazen, S.P. (2013) Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon. BMC Biotechnology, 13: 61.
Handakumbura, P.P., Hazen, S.P. 2012. Transcriptional regulation of grass secondary cell wall biosynthesis: playing catch-up with Arabidopsis thaliana. Frontiers in Plant Science. 3: 74.
Lee, S.J., Warnick, T.A., Leschine, S.B., Hazen, S.P. 2012. A high-throughput biological conversion assay for determining lignocellulosic quality. In J Normanly, ed, Methods in Molecular Biology: High Throughput Phenotyping in Plants. Springer.
Lee, S.J., Warnick, T.A., Pattathil, S., Alvelo-Maurosa, J.G., Serapiglia, M.J., McCormick, H., Brown, V., Young, N.F., Schnell, D.J., Smart, L.B., Hahn, M.G., Pedersen, J.F., Leschine, S.B., Hazen, S.P. 2012. Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality. Biotechnology for Biofuels, 5: 5.
Brkljacic, J., Grotewold, E., Scholl, R., Mockler, T., Garvin, D.F., Vain, P., Brutnell, T., Sibout, R., Bevan, M., Budak, H., Caicedo, A.L., Gao, C., Gu, Y., Hazen, S.P., Holt, III B.F., Hong, S.-Y., Jordan, M., Manzaneda, A.J., Mitchell-Olds, T., Mochida, K., Mur, L.A.J., Park, C.-M., Sedbrook, J., Watt, M., Zheng, S.J., Vogel, J.P. 2011. Brachypodium as a model for the grasses: Today and the future. Plant Physiology, 157: 3-13.
The International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463: 763-768.
Hazen, S.P., Naef, F., Quisel, T., Gendron, J.M., Chen, H., Ecker, J.R., Borevitz, J.O., Kay, S.A. 2009. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biology, 10: R17.
Michael, T.P., Breton, G., Hazen, S.P., Priest, H.D., Mockler, T.C., Kay, S.A., Chory, J.A. 2008. Morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biology, 6(9): e225.
Garvin, D.F., Gu, Y., Hasterok, R., Hazen, S.P., Jenkins, G., Mockler, T.P., Mur, L., Vogel, JP. 2008. Development of genetic and genomic resources for Brachypodium distachyon, a new model system for grass crop research. Plant Genome, 48: S-69-S-84.
Michael, T.P., Mockler, T.C., Breton, G., McEntee, C., Byer, A., Trout, J.D., Hazen, S.P., Priest, H.D., Sullivan, C.M., Shen, R., Givan, S.A., Yanovsky, M., Hong, F., Kay, S.A., Chory, J.A. 2008. Network discovery pipeline elucidates conserved time of day specific cis-regulatory modules. PLoS Genetics, 4(2): e14.
Borevitz, J.O., Hazen, S.P., Michael, T.P., Morris, G.P., Baxter, I., Hu, T.T., Chen, H., Werner, J, Salt D, Kay SA, Chory J, Weigel, D., Nordborg, M., Jones, J.D.G., Ecker, J.R. 2007. Genome wide patterns of single feature polymorphism diversity in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA, 29: 12057-12062.
Singer, T.S., Fan, Y., Chang, H-S., Zhu, T., Hazen, S.P., Briggs, S.P. 2006. A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome array hybridization, PLoS Genetics, 2: e144.
Rensink, W.A., Hazen, S.P. 2006. Statistical issues in microarray data analysis. In J Salinas, JJ Sanchez-Serrano, eds, Methods in Molecular Biology, vol. 323: Arabidopsis Protocols, Second Edition Humana Press Inc., Totowa, NJ. pp 359-366.
Hazen, S.P., Schultz, T.F., Pruneda-Paz, J.L., Borevitz, J.O., Ecker JR, Kay SA (2005) LUX ARRHYTHMO encodes a Myb transcription factor essential for circadian rhythms. Proceedings of the National Academy of Sciences, USA, 120: 10387-10392.
Hazen, S.P., Borevitz, J.O., Harmon, F.G., Pruneda-Paz, J.L., Schultz, T.F., Yanovsky, M.J., Liljegren, S.J., Ecker, J.R., Kay, S.A. 2005. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. Plant Physiology, 138: 990-997.
Baxter, I.R., Young, J.C., Armstrong, G., Foster, N., Bogenschutz, N., Cordova, T., Peer, W.A., Hazen, S.P., Murphy, A.S., Harper, J.F. 2005. A plasma membrane H+-ATPase is required for the formation of proanthocyanidins in the seed coat endothelium of Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA, 102: 2649-2654.
Hazen, S.P., Pathan, M.S., Sanchez, A.C., Baxter, I., Dunn, M., Estes, B., Chang, H-S., Zhu, T., Kreps, J.A., Nguyen, H.T. 2005. Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Functional and Integrative Genomics, 5: 104-116.
Hazen, S.P., Kay, S.A. 2003. Gene arrays aren’t just for measuring gene expression. Trends in Plant Science, 8: 413-416.
Hazen, S.P., Wu, Y., Kreps, J.A. 2003. Gene expression profiling of plant response to abiotic stress. Functional and Integrative Genomics, 3: 105-111.
Hazen, S.P., Hawley, R.M., Davis, G.L., Henrissat, B., Walton, J.D. 2003. Quantitative trait loci and comparative genomics of cereal cell wall composition. Plant Physiology, 132: 263-271.
Hazen, S.P., Scott-Craig, J.S., Walton, J.D. 2002. Cellulose synthase-like (CSL) genes of rice. Plant Physiology, 128: 336-340.
Hazen, S.P., Leroy, P., Ward, R.W. 2002. AFLP in Triticum aestivum L.: patterns of genetic diversity and genome distribution. Euphytica, 125: 89-102.
Hazen, S.P., Zhu, L., Kim, H.S., Tang, G., Ward, R.W. 2002. Genetic similarity of winter wheat in Shaanxi province, China and other common wheat germplasm pools. Genetic Resources and Crop Evolution, 49: 439-448.
Hazen, S.P., Ng, P.K.W., Ward, R.W. 1997. Variation in grain functional quality for soft winter wheat. Crop Science, 37: 1086-1093.
Hazen, S.P., Ward, R.W. 1997. Variation in soft winter wheat characteristics measured by the single kernel characterization system. Crop Science, 37: 1079-1086.