Biomass Depolymerization programs

Lignocellulose Synthesis and Depolymerization

Mechanisms used by plants to modify the properties of cell walls during various aspects of growth and development may also provide insights into possible ways of reducing cell wall recalcitrance to enzymatic hydrolysis during bioconversion of plant biomass to fuels. Several studies suggest that there is a link between the cell expansion that occurs during plant growth and cell wall digestibility. This program identifies and studies plant proteins that contribute to cell wall loosing during cell expansion and to determine their impact on cell wall digestibility.

program Highlights

2014 Highlights

One theme of our research concerns an investigation of the molecular mechanisms that control synthesis and secretion of polysaccharide hydrolases by the fungus Neurospora crassa. In collaboration with several other EBI research groups, we are investigating the mechanisms by which several mutations impair the ability of the fungus to secrete large amounts of hydrolytic enzymes. Another theme of research in our group involves an investigation of the biochemical, transcriptional and signal transduction mechanisms that regulate the polysaccharide and lignin composition of biomass. We are investigating the mechanisms that control the quantity and quality of cellulose deposition, the function of polysaccharide acetylation, the polymerization of lignin, and the mechanisms by which plants respond to infection by pathogenic fungi that are capable of rapid depolymerization of cell walls.

2013 Highlights

One theme of our research concerns an investigation of the molecular mechanisms that control synthesis and secretion of polysaccharide hydrolases by the fungus Neurospora crassa. In collaboration with several other EBI research groups, we are investigating the mechanisms by which several mutations impair the ability of the fungus to secrete large amounts of hydrolytic enzymes. We have also investigated the response of the fungus to growth on pectin using transcriptional profiling followed by direct tests of the roles of implicated enzymes using the comprehensive collection of insertion mutants of Neurospora. This resulted in the identification of several new transporters for pectin components that may be useful in engineering other organisms to utilize pectin or hemicellulose sugars. Another theme of research in our group involves an investigation of the biochemical, transcriptional and signal transduction mechanisms that regulate the polysaccharide and lignin composition of biomass. We are investigating the mechanisms that control the quantity and quality of cellulose deposition, the function of polysaccharide acetylation, the polymerization of lignin, and the mechanisms by which plants respond to infection by pathogenic fungi that are capable of rapid depolymerization of cell walls.

2012 Highlights

Plant biomass is primarily composed of three types of polysaccharides: cellulose, hemicellulose and pectin, and lignin. A major theme of research in our group involves an investigation of the biochemical, transcriptional and signal transduction mechanisms that regulate the polysaccharide and lignin composition of biomass. We are investigating the mechanisms that control the quantity and quality of cellulose deposition, the function of polysaccharide acetylation, the polymerization of lignin, and the mechanisms by which plants respond to infection by pathogenic fungi.

 

A notable finding in 2012 was the identification of a mutation in the cellulose synthase subunit CESA1 that renders cellulose less crystalline and more amenable to enzymatic depolymerization (Harris et al., 2012). The molecular mechanism of the effect is unknown at present, but the result raises the possibility of developing biofuel feedstocks and forage species that are more susceptible to enzymatic depolymerization. We also developed a new tool for visualizing the process of polysaccharide deposition during cell wall synthesis and deposition (Anderson et al., 2012). In brief, we discovered that plants would incorporate exogenously provided fucose-alkyne into the pectic polysaccharide, rhamnogalacturonan I (RGI). The incorporated fucose-alkyne could then be tagged with fluorophores by using “click chemistry.” This allowed visualization of RGI by confocal microscopy as it was synthesized in the Golgi, transported to the plasma membrane and incorporated into the cell wall.

 

A second theme in the group concerns an investigation of the molecular mechanisms that control synthesis and secretion of polysaccharide hydrolases by the fungus Neurospora crassa. In collaboration with several other EBI research groups, we are investigating the mechanisms by which several mutations impair the ability of the fungus to secrete large amounts of hydrolytic enzymes. We have also investigated the response of the fungus to growth on pectin using transcriptional profiling followed by direct tests of the roles of implicated enzymes using the comprehensive collection of insertion mutants of Neurospora. This resulted in the identification of several new transporters for pectin components that may be useful in engineering other organisms to utilize pectin.

2011 Highlights

The Somerville lab has developed imaging tools for observing enzymes that produce cellulose in living cells and have used these tools to characterize the process. They also identified a mutant of cellulose synthase that causes the cellulose to be less crystalline and more readily depolymerized by cellulase enzymes. Further study will determine whether plants can grow with that change in their cellulose. The Somerville lab also has used innovative chemical methods (“click chemistry”) to track the cellular transport of cell wall polysaccharides in living systems, which provides a new way to understand how polysaccharides that comprise cell walls are secreted and assembled into the final structures.

2010 Highlights

Somerville’s group has used a genetic approach to implicate several dozen genes in control of cell expansion, and are also characterizing some of the xylanases and cellulases used by plants for cell wall modification.  Using a new fluorescent stain for cellulose that permits visualization of cellulose microfibrils in live cells, researchers discovered that the structure of cellulose microfibrils is strongly altered in a mutant deficient in xyloglucan. This observation substantiated a theory that hemicelluloses modulate cellulose microfibril aggregation.

2009 Highlights

It is thought that during the growth phase of the cell cycle, polysaccharides are modified to allow slippage. Mutants of Arabidopsis with altered expansion have been identified and candidate genes have been identified for several of the mutations. Further work will be required to verify the participation and mode of action of the corresponding proteins.

 

Publications

Published in 2014

Identification and Characterization of a Galacturonic Acid Transporter from Neurospora crassa and its Application for Saccharomyces cerevisiae Fermentation Processes, J. P. Benz, R. J. Protzko, J. M. S. Andrich, J. E. Dueber, C. R. Somerville, Biotechnology of Biofuels, V. 7, pp. 20, February 6, 2014.

 

Activation Tag Screening Reveals the Function of Polygalacturonase Involved in Expansion 1 in Cell Elongation and Flower Development in Arabidopsis thaliana, C. Xiao, C. R. Somerville, C. T. Anderson, Plant Cell, V. 26, pp. 1018-1035, 2014.

 

Data-Based Standards Should Guide Biofuel Production, H. L. Youngs, C. R. Somerville, Science, V. 344, pp. 1096-1097, 2014. 

 

Interaction of the Arabidopsis Rab GTPase SMG1 with its Effector PMR4 Results in Callose-Dependent Penetration Resistance to Powdery Mildew, D. Ellinger, A. Glöckner, J. Koch, M. Naumann, C. Manisseri, C. R. Somerville, C. A. Voigt, Plant Cell, V. 26, pp. 3185-3200, doi:10.1105/tpc.114.12779, July 23, 2014.

 

How Big is the Bioenergy Piece of the Pie? Who Cares – It’s Pie!, H. L. Youngs, C. R. Somerville, Biotechnology and Bioengineering, V. 111, pp. 1717-1718, July 24, 2014. 

 

Making the Most Abundant Biomolecule on the Planet: A Blueprint for Cellulose Biosynthesis, Deposition, and Regulation in Plants, I. Wallace, C. R. Somerville, book chapter, Plant Cell Wall Patterning and Cell Shape, H. Fukuda, Ed., Wiley, 432 pp., 2014. 

 

The Arabidopsis COBRA Protein Facilitates Cellulose Crystallization at the Plasma Membrane, N. Sorek , H. Sorek, A. Kijac, H. Szemenyei, S. Bauer, K. Hématy, D.E. Wemmer, C.R. Somerville. Journal of Biological Chemistry, doi: 10.1074/jbc.M114.607192, Oct 20, 2014.

Published in 2013

The Endocytosis of Cellulose Synthase in Arabidopsis Is Dependent on U2, a Clathrin-Mediated Endocytosis Adaptin, Logan Bashline, Shundai Li, Charles T. Anderson, Lei Lei, Ying Gu, Plant Physiology, doi: 10.1104/pp.113.221234.

 

Elevated Early Callose Deposition Results in Complete Penetration Resistance to Powdery Mildew in Arabidopsis, D. Ellinger, M. Naumann, C. Falter, C. Zaikozics, T. Jamrow, C. Manisseri, S. C. Somerville, C. A. Voigt (2013), Plant Physiology 161: pp. 1433-1444, doi:10.1104/pp.112.211011.

 

Differences in Early Callose Deposition During Adapted and Non-Adapted Powdery Mildew Infection of Resistant Arabidopsis Lines, M. Naumann, S. C. Somerville, C. A. Voigt (2013), Plant Signaling and Behavior 8(6), doi: pii: e24408 [Epub ahead of print].

 

A Comparative Systems Analysis of Polysaccharide-Elicited Responses in Neurospora crassa Reveals Carbon Source-Specific Cellular Adaptations, J. P. Benz, B. H. Chau, D. Zheng, S. Bauer, N. L. Glass, C. R. Somerville, Molecular Microbiology, 91(2), pp. 275-299, doi: 10.1111/mmi.12459, November 15, 2013.

 

Identification and Characterization of a Galacturonic Acid Transporter from Neurospora crassa and Its Application for Saccharomyces cerevisiae Fermentation Processes, J. P. Benz, R. J. Protzko, J. M. S. Aldrich, S. Bauer, S. Dueber, C. R. Someville, Biotechnology for Biofuels, 7, pp. 20.

 

California's Energy Future: The Potential for Biofuels, Heather Youngs and Chris Somerville, California Council on Science and Technology, May 31, 2013.

Published in 2012

Complexes with Mixed Primary and Secondary Cellulose Synthases are Functional in Arabidopsis thaliana Plants, Andrew Carroll, Nasim Mansoori, Shundai Li, Lei Lei, Samantha Vernhettes, Richard Visser, Chris Somerville, Yong Gu, Luisa Trindade, Plant Physiology, 160, 726-737, http://dx. doi.org/10.1104/pp.112.199208, August 26, 2012.

 

Deciphering the Parts List for the Mechanical Plant,  Chris Somerville, Daedalus, 141 (3), 89-977,doi/pdf/10.1162/DAED_a_00164, Summer 2012, 2012.

 

Development of Feedstocks for Cellulosic Biofuels, Heather Youngs and Chris Somerville, F1000 Biology Reports, 4(10), doi: 10.3410/B4-10, May 2, 2012.

 

Metabolic Click Labeling With a Fucose Analog Reveals Pectin Delivery, Architecture, And Dynamics in Arabidopsis Cell Walls, Charlie Anderson, Ian Wallace, and Chris Somerville, Proceedings of the National Academy of Sciences 109, 1329-1334.

 

Cellulose Microfibril Crystallinity Is Reduced By Mutating C-Terminal Transmembrane Region Residues CESA1 and CESA3, Darby Harris, Kendall Corbin, Tuo Wang, Ryan Gutierrez, Anna Bertolo, Carloalberto Petti, Detlef Smilgies, Jose Estevez, Dario Bonetta, Breeanna Urbanowicz, David Ehrhardt, Chris Somerville, Jocelyn Rose, Mel Hong, and Seth DeBolt, Proceedings of the National Academy of Sciences 109, 4098-4103.

 

Growing Better Biofuel Crops, Heather Youngs and Chris Somerville, The Scientist 26, 46-52.

 

CHITINASE-LIKE1/POM-POM1 and its Homolog CTL2 Are Glucan-Interacting Proteins Important for Cellulose Biosynthesis in Arabidopsis, Clara Sanchez-Rodriguez, Stefan Bauer, Kian Hematy, Friederike Saxe, Ana Belen Ibanez, Vera Vodermaier, Cornelia Konlechner, Arun Sampathkumar, Markus Ruggeberg, Ernst Aichinger, Lutz Neumetzler, Ingo Burgert, Chris Somerville, Marie-Theres Hauser, Staffan Persson, The Plant Cell, doi: http://dx.doi.org/10.1105/tpc.111.094672, February 2012.


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