Regulation and Modeling of Lignin Biosynthesis

Dr. Cranos Williams, Senior Collaborator; EnBiSys Researchers: Megan L. Matthews, Zohaib K. Qazi, Dr. Jina Song

Collaborating PIs: Dr. Vincent Chiang, Dept. of Forestry and Environmental Resources, Dr. Ronald Sederoff, Dept. of Forestry and Environmental Resources; Dr. Joel Ducoste, Dept. of Civil, Construction, and Environmental Engineering; Dr. Fikret Isik, Dept. of Forestry and Environmental Resources

Lignin is a phenylpropanoid polymer that is entangled with the cellulose in the secondary cell walls of all vascular plants. The accumulation of lignin plays several important roles in vascular plants and trees. It creates a hydrophobic surface for water transport, acts as a barrier to pests and pathogens, and provides mechanical strength for cell walls. The ability of woody plants to establish forest ecosystems depends on lignin. However, lignin quantity and structures are also main barriers to the utilization of plant biomass for fuel, food, and fiber. This project seeks to build models that quantitatively capture the organization and regulation of the monolignol biosynthesis pathway and to reveal new regulatory and control mechanisms that could be used to identify the appropriate genetic modifications that would yield desired lignin and wood properties.

This project uses Populus trichocarpa (black cottonwood) and an integrative systems approach including advanced quantitative methods of genomics, proteomics, biochemistry, structural chemistry, and mathematical modeling to provide the most comprehensive analysis of the regulation of lignin biosynthesis in wood formation. The goal of the integrative analysis approach is to identify how modifications at the genetic level propagate  through multiple levels of  the monolignol biosynthesis pathway to produce favorable lignin traits and wood properties (i.e. decoding the genotype to phenotype response). This involves: (1) quantitatively measuring, evaluating and modeling relationships between lignin specific transcripts and proteins; (2) using ordinary differential equations to mathematically describe the effect of protein abundances on metabolic flux and metabolite concentrations in the monolignol biosynthesis pathway; and (3) measuring, evaluating and quantitatively modeling relationships between the monolignol biosynthesis pathway and key lignin and wood properties. The long-term goal of this project is a predictive model of the lignin biosynthesis pathway for greater understanding of the plant response to environmental stress and for more precise strategies to improve plant productivity and the production of energy, materials, and food. 

This is a highly collaborative project involving researchers from multiple universities and many different departments and disciplines. 

Work supported by the National Science Foundation: DBI-0922391

Contributions to Date:  Researchers in the EnBiSys Lab used systems modeling approaches to infer the presence of novel enzyme complexes that control the flux associated with critical branches in the monolignol biosynthesis pathway.  This complex was experimentally verified by our collaborators and subsequently modeled using system identification approaches.  This flux model was later integrated into a larger Predictive Kinetic Metabolic Flux ordinary differential equation model of the entire monolignol biosynthesis pathway.  The EnBiSys Lab is currently using computational intelligence and machine learning approaches to build an integrative  model model of the monoligninol biosynthesis pathway in P. trichocarpa. We and our collaborators are continuously evolving this model as we discover new insights about the underlying mechanisms governing the synthesis of lignin using a combination of new experiments, computational learning algorithms, and the current behavior of our systems model.

The most up to date version of our model is described in:

  • J.P. Wang, M.L. Matthews, C.M. Williams,, “Integrative analysis of lignin biosynthesis to improve wood properties,” In preparation.

Other publications produced from this project:

  • H.-C. Chen, J. Song, J. P. Wang, Y.-C. Lin, J. Ducoste, C. M. Shuford, J. Liu, Q. Li, R. Shi, A. Nepomuceno, F. Isik, D. C. Muddiman, C. Williams, R. R. Sederoff, and V. L. Chiang, “Systems biology of lignin biosynthesis in populus trichocarpa: Heteromeric 4-coumaric acid:coenzyme a ligase protein complex formation, regulation, and numerical modeling,” The Plant Cell Online, 2014. (Impact Factor=10.125) Link
  • J. P. Wang, P. P. Naik, H.-C. Chen, R. Shi, C.-Y. Lin, J. Liu, C. M. Shuford, Q. Li, Y.-H. Sun, S. Tunlaya-Anukit, C. M. Williams, D. C. Muddiman, J. J. Ducoste, R. R. Sederoff, and V. L. Chiang, “Complete proteomic-based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic flux and lignin in populus trichocarpa,” The Plant Cell Online, 2014. (Impact Factor=10.125) Link
  • H. Chen, J. Song, C. Williams, C. Shuford, J. Liu, J. Wang, Q. Li, R. Shi, E. Gokce, J. Ducoste, D. Muddiman, R. Sederoff, and V. Chiang, “Monolignol Pathway 4-Coumaric Acid: CoA Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of CoA Ligation Fluxes,” Plant Physiology, vol. 161, pp. 1501-1516, 2013. (Impact Factor=7.054)
  • J. Wang, C. Shuford, Q. Li, J. Song, Y. Lin, Y. Sun, H. Chen, C. Williams, D. Muddiman, R. Sederoff, and V. Chiang. “Functional redundancy of the two 5-hydroxylases in mono- lignol biosynthesis of Populus trichocarpa: LC–MS/MS based protein quantification and metabolic flux analysis”. Planta, pages 1–14, 2012. 10.1007/s00425-012-1663-5. (Impact Factor=3.098) Link