Markus Pauly
Markus Pauly
Biofuels, Carbon Sequestration
Professor, Fred Dickinson Chair of Wood Science and Technology
Energy Biosciences Building 212C
2151 Berkeley Way, Berkeley, California 94720-5230
Phone 510.642.1722
Lab Phone 510.643.1027
Fax 510.642.1490

PhD  Technical University Aachen, Germany
M.S.  Technical University Aachen, Germany, 1993

The most abundant renewable plant resource on this planet are the lignicellulosics present in the plant cell wall. They present a sophisticated, highly complex material consisting mainly of various polysaccharides and polyphenols. The Pauly lab uses a synthetic biology approach whereby all necessary components of the biosynthetic machinery of hemicellulosic and pectinaceous polysaccharides are identified. To achieve this goal we use various genetic approaches including forward, reverse, and chemical genetics with the model organism Arabidopsis, but also maize as a grass species.

Plant Cell Wall feedstocks


Plant Cell Walls as a renewable resource for Biofuels and other commodity Chemicals

With an estimated annual production of 180 billion tons per year plant cell walls (lignocellulosics) present an enormous renewable resource, of which only 2% are utilized by humans. The major bottleneck in utilizing this carbon neutral resource for the sustainable production of second generation biofuels is the recalcitrance of the wall material to degradation. With our various research projects we aim at characterizing the structural features of the wall that lead to this recalcitrance. In the long run such knowledge will aid us in overcoming them.

The structure of the Plant Cell Wall

Higher plant cells are encased in cell walls that define their shape and contribute to the strength and structural integrity not only of individual cells, but also of the entire plant. Despite its necessary rigidity, the cell wall is a highly dynamic entity that is metabolically active. It plays crucial roles in diverse cell activities such as growth, differentiation, cell-to-cell communication and transport, senescence, abscission, and plant-pathogen interactions. Microcrystalline cellulose is embedded in a hydrated matrix consisting of coextensive networks of complex heteropolysaccharides and sometimes glycoproteins and polyphenols, such as lignin.

Our research entails the establishment of an analytical platform for the analysis of wall polysaccharides, a forward genetic approach to identify novel wall structures and reverse genetic approaches to gain insights into wall biosynthesis.

Analytical Platform for the Microanalysis of Wall Polysaccharides

Our lab uses mainly classical carbohydrate chemistry based methods to describe the structure of particular wall polysaccharides. These methods encompass solubilization of various wall polymers using sequential extraction procedures that make use of wall degrading enzymes and chemicals. The resulting fractions are then analysed using techniques such as monosaccharide composition and glycosidic linkage analysis see videos (Lignin analysis:; Carbohydrate analysis We also determine the presence of ester substituents (such as O-acetyl-substituents). Since such an analysis is rather labor-intensive and time consuming, an oligosaccharide mass profiling method (OLIMP) using specific polysaccharide hydrolases in combination with mass spectrometry has been developed (Video: The sensitivity of OLIMP allows for the rapid assessment of even minute amount of tissue-materials. A profile can be obtained from preparations of as little as 500 Arabidopsis cells prepared by a laser-dissection catapulting instrument.

Forward Genetic Approach: Identification of Structural Wall Mutants

We identify wall mutants by screening of populations of chemically mutagenised seeds for novel structural wall mutants.

An Arabidopsis mutants population was screened using OLIMP. It has lead to the identification of 36 distinct mutants with altered xyloglucan structures including the abundance of ester-substituents. Map-based cloning of the mutated genes gave valuable insights into biosynthesis, metabolism and function of structural variations of xyloglucan. For example, it became evident that the microheterogeneity of wall polysaccharides is dependent not on its biosynthetic machinery but on apoplastic "trimming" of the sidechains by glycosidases.      

A maize mutant population was screened for altered sugar content. Indeed, one of the mutants, termed "candy-leaf 1" or Cal-1, exhibited a 250% increase in glucan content. Cal-1 is currently tested in the field for enhanced yields of biofuel production. 

Massive parallel sequencing: Cell Wall Biosynthesis

Although information about the structural components of cell walls has increased considerably in recent years, very little is known about the biosynthesis of individual wall components on a molecular level. We employed Ilumina sequencing of plant species that synthesize only a single polysaccharide. This approach lead to the identification of genes in whole biosynthetic pathways. A reverse genetic approach is then employed with the correspondent Arabidopsis genes/mutants to ascertain the function of the gene and its role in polysaccharide biosynthesis. Currently, numerous novel genes involved in the synthesis of nucleotide sugars, the substrates for polysaccharide synthesis, have been identified through bioinformatic means by comparison to gene-sequences of well-characterized bacterial enzymes. In addition, we have identified genes that are responisble for polysaccharide O-acetylation. This substitution is an impediment to enzymatic degradation in a biorefinery and once released presents an inhibitor to many fermenting organisms.

The overall goal of these projects is to be able to assemble and reconstruct whole plant polysaccharide pathways in yeast that would produce the particular hemicellulose. 

Recent Publications

(last 5 years, out of 108 total)

Liberatore KL, Xu C, MacAlister CA, Jiang K, Brooks C, Ogawa-Ohnishi M, Xiong G, Pauly M, Matsubayashi Y, Lippman ZB, 2015, A cascade of arabinosyltransferases controls stem cell homeostasis in tomato, Nature Genetics 47: 784-792

Loque D, Scheller HV, Pauly M, 2015, Engineering of plant cell walls for enhanced biofuel production, Current opinion in Plant Biology, 25: 151-161

De Souza A, Pauly M, 2015, Comparative genomics of pectinacetylesterases: insights on function and biology, in press in Plant Signal and Behavior

Yang F, Afzal W, Cheng K, Liu N, Pauly M, Bell AT, Liu Z, Prausnitz JM, 2015, Nitric-acid hydrolysis of miscanthus giganteus to fermentable sugars, Biotechnology and Bioprocess Engineering, 20 (2): 304-314

Liu L, Paulitz J, Pauly M, 2015, The presence of fucogalactoxyloglucan and its synthesis in rice indicates conserved functional importance in plants, Plant Physiology 168: 549-560

Draeger C, Fabrice TN, Mouille G, Kuhn B, Moller I, Abdou MT, Frey B, Pauly M, Bacic T, Ringli C, 2015, Arabidopsis LEUCINE-RICH REPEAT EXTENSIN (LRX) proteins modify cell wall composition and influence plant growth, BMC Plant Biology 15: 155-166

Xiong G, Dama M, Pauly M, 2015, Glucuronic acid moieties on xylan are functionally equivalent to O-acetyl-substituents, Molecular Plant 8: 1119-1121

Ebert B, Rautengarten C, Guo X, Xiong G, Herter T, Chan LJG, Adams PD, Petzold CJ, Pauly M, Willats WGT, Heazlewood JL, Scheller HV, 2014, Identification and characterization of a Golgi localized UDP-xylose transporter family from Arabidopsis, Plant Cell, 27 (4):1218-1227

Schultink A, Naylor D, Dama M, Pauly M, 2015, The role of the plant specific AXY9 gene in plant cell wall polysaccharide O-acetylation, Plant Physiology, 167 (4):1271-1283

Mansoori N, Schultink A, Schubert J, Pauly M, 2015, Expression of heterologous xyloglucan xylosyltransferases in Arabidopsis to investigate their role in determining xyloglucan xylosylation substitution patterns, Planta, 241:1145-1158

Ben-Toy D, Abraham Y, Stav S, Thompson K, Loraine A, Elbaum R, Souza A, Pauly M, Kieber JJ, Harpaz-Saad S, 2015, COBRA-LIKE 2, a member of the GPI-anchored COBRA-LIKE family, plays a role in cellulose deposition in Arabidopsis seed coat mucilage, Plant Physiology, 167 (3), 711-724

Taylor-Teeples M, Lin L, Trabucco GM, de Lucas M, Turco G, Doherty C, Toal TW, Gaudinier A, Young NF, Xiong G, Corwin J, Tsoukalas N, Pauly M, Kliebenstein DJ, Tagkopoulos I, Breton G, Ahnert S, Kay SA, Brady SM, Hazen SP, 2015, Environmental, developmental and genotype-dependent regulation of xylem cell specification and secondary cell wall biosynthesis in Arabidopsis thaliana, Nature, 517, 571-575

de Souza A, Hull PA, Gille S, Pauly M, 2014, Identification and characterization of the distinct plant pectin esterases PAE8 and PAE9 and its mutants, Planta, 240 (5) 1123-1138

Rautengarten C, Ebert B, Moreno I, Temple H, Herter T, Link B, Doñas D, Moreno A, Saéz-Aguayo S, Blanco MF, Mortimer J, Schultink A, Reiter WD, Dupree P, Pauly M, Heazlewood JL, Scheller HV, Orellana A, 2014, Identification of six Golgi localized bi-functional UDP-Rhamnose / UDP-Galactose transporters in Arabidopsis, PNAS, 111 (31) 11563-11568

Liu Z, Padmanabhan S, Cheng K, Xie H, Gokhale A, Na H, Pauly M, Bell AT, Prausnitz JM, 2014, Two-step delignification of Miscanthus to enhance enzymatic hydrolysis: Aqueous ammonia followed by sodium hydroxide and oxidants, Energy and Fuels, 28, 542-548

Knoch E, Dilokpimol A, Tryfona T, Poulsen CP, Xiong G, Harholt J, Peterson BL, Ulvskov P, Hadi MZ, Kotake T, Tsumuraya Y, Pauly M, Dupree P, Geshi N, 2013, A b-glucuronosyl-transferase from Arabidopsis thaliana involved in the biosynthesis of type II arabinogalactan has a role in cell elongation during seedling growth, Plant Journal, 76 (6), 1016-1029

Manabe Y, Verhertbruggen Y, Gille S, Harbolt J, Chong SL, Pawar P, Mellerowicz E, Tenkanen M, Cheng K, Pauly M, Scheller HV, 2013, RWA proteins play vital and distinct roles in cell wall O-acetylation in Arabidopsis thaliana, Plant Physiology, 163, 1107-1117

Schultink A, Cheng K, Yung-Bom K, Cosgrove D, Pauly M, 2013, The identification of two arabinosyltransferases from tomato reveals functional redundancy of xyloglucan side-chain substituents, Plant Physiology, 163, 86-94

Pauly M, Gille S, Liu L, Mansoori N, de Souza A, Schultink A, Xiong G, 2013, Hemicellulose biosynthesis, Planta, 238 (4), 627-642

Koenig D, Jimenez-Gomez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C,Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN, 2013,Comparative transcriptomics in wild and domesticated tomato, PNAS, 110 (28) E2655-E2662

Xiong G, Cheng K, Pauly M, 2013, Reduction in xylan O-acetylation results in increased recalcitrance to saccharification as indicated by the Arabidopsis mutant tbl29, in press in Molecular Plant

Gille S, Sharma V, Baidoo EEK, Keasling JD, Scheller HV, Pauly M, 2013, Arabinosylation of an AGP-like polymer impacts root growth as exemplified by the Arabidopsis glycosyltransferase mutant ray1, in press in Molecular Plant

Cheng K, Sorek H, Zimmermann H, Wemmer DE, Pauly M, 2013, Solution-state 2D NMR spectroscopy of plant cell walls enabled by a DMSO-d6[Emim]OAc solvent, Analytical Chemistry, 85 (6) 3213-3221

Liu Z, Padmanabhan S, Cheng K, Xie H, Schwyter P, Pauly M, Bell AT, Prausnitz JM, 2012, Aqueous-ammonia delignification of miscanthus and enzymatic hydrolysis to sugars, Bioresource Technology, 135 23-29

Handford M, Furlán CR, Marchant L, Segura M, Gómez D, Alvarez-Buylla E, Xiong G, Pauly M, Orellana A, 2012, Arabidopsis plants lacking AtUTr7, a Golgi-localized UDP-glucose/UDP-galactose transporter, exhibit alterations in lateral roots, Molecular Plant, 5 (6) 1263-1280

Park SH, Mei C, Pauly M, Ong RG, Dale BE, Sabzikar R, Fotoh H, Nguyen T, Sticklen M, 2012, Down regulation of maize cinnamoyl-CoA reductase via RNAi technology creates brown midrib and improves AFEX-pretreated conversion into fermentable sugars for biofuels, Crop Science 52 (6) 2687-2701

Chiniquy D, Sharma V, Schultink A, Baidoo EE, Rautengarten C, Cheng K, Carroll A, Ulvskov P, Harholt J, Keasling JD, Pauly M, Scheller HV, Ronald PC, 2012, XAXT1, a grass specific xylan:xylosyltransferase in the glycosyltransferase family 61, Proceedings of the National Academy of the USA 109 (42) 17117-17122

Jensen JK, Schultink A, Keegstra K, Wilkerson CG, Pauly M, 2012, RNA-Seq. of developing nasturtium seeds (Tropaeolum majus): Identification and characterization of an additional glactosyltransferase involved in xyloglucan biosynthesis, Molecular Plant, 5 (5) 984-992

Gille S, Pauly M, 2012, Mechanism of plant cell wall O-acetylation, Frontiers in Plant Physiology 3:12, doi: 10.3389/fpls.2012.00012

Gille S, Souza A, Xiong G, Benz M, Schultink A, Ida-Reca B, Pauly M, 2011, O-acetylation of xyloglucan requires AXY4/AXY4L, proteins with a TBL and DUF231 domain, Plant Cell 23 (11) 4041-4053

Chuck G, Tobias C, Kraemer F, Sun L, Li C, Arora R, Singh S, Dibble D, Vogel J, Simmons B, Pauly M, Hake S, 2011, Overexpression of the maize conrgrass1 microRNA gene prevents flowering, improves digestability and increases starch content of biofuel crop plants, Proceedings of the National Academy of the USA 108 (42) 17550-17555

Gunl M, Neumetzler L, Kraemer F, Souza A, Schultink A, Pena M, York WS, Pauly M, 2011, AXY8 encodes an a-fucosidase, underpinning the importance of apoplastic metabolism on the fine structure of plant cell wall polysaccharides, Plant Cell 23 (11), 4025-4040

Troncoso-Ponce MA, Kilaru A, Cao X, Durrett T, Fan J, Jensen J, Pauly M, Wilkerson C, Ohlrogge J, 2011, Comparative deep transcriptional profiling of four developing oilseeds, Plant Journal 68, 1014-1027

Gille S, Kun C, Skinner ME, Liepman AH, Wilkerson C, Pauly M, 2011, Deep Sequencing of Voodoo Lily (Amorphophallus konjac): An approach to identify relevant genes involved in the synthesis of the hemicellulose glucomannan, Planta, 234, 515-526

Manabe Y, Nafisi M, Verhertbruggen Y, Orfila C, Gille S, Rautengarten C, Cherk C, Marcus SE, Somerville S, Pauly M, Knox JP, Sakuragi Y, Scheller HVS, 2011, Loss-of-function mutation of reduced wall acetylation 2 in Arabidopsis leads to reduced cell wall acetylation and increased resistance to Botrytis cinerea, Plant Physiology, 155 (3), 1068-1078
Gunl M, Pauly M, 2011, AXY3 encodes a a-xylosidase that impacts the abundance and accessibility of the hemicellulose xyloglucan in Arabidopsis plant cell walls, Planta, 233 (4), 707-719
Gunl M, Kraemer FJ, Pauly M, 2011, Oligosaccharide mass profiling (OLIMP) of cell wall polysaccharides by MALDI-TOF/MS, Methods in Molecular Biology Vol 715: The Plant Cell Wall, 43-54, Editor Popper Z, Humana Press
Perrson S, Sorensen I, Moller I, Willats W, Pauly M, 2011, Dissection of the Plant Cell Wall by High Throughput Methods, Annual Plant Reviews Vol 41: Plant Polysaccharides: Biosynthesis and Bioengineering, 43-64, Editor Ulvskov P, Wiley-Blackwell
Suen G, Scott  JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomas AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR, 2010, An insect herbivore microbiome with high plant biomass degrading capacity, PLoS Genetics, 6 (9), 433-443 
Pauly M, 2010, A blue-print of the protoplast’s dwelling, Plant Physiology, Classic collection, 154, 1
Kaida R, Serada S, Norioko N, Norioka S, Neumetzler L, Pauly M, Sampedro J, Zarra I, Hayashi T, Kaneko TS, 2010, Potential role for purple acid phosphatase in the dephosphorylation of wall proteins in tobacco cells, Plant Physiology, 153 (2), 603-610
Lopes FJF, Pauly M, Lau EY, Diola V, Passos JL, Loureiro ME, Brommonshenkel SH, 2010, The EgMUR3 xyloglucan galactosyltransferase from Eucalyptus grandis complements the mur3 cell wall phenotype in Arabidopsis thaliana, Tree Genetics and Genomes, 6, 745-756
Gunl M, Gille S, Pauly M, 2010, OLIigo Mass Profiling (OLIMP) of extracellular polysaccharides, in production in Journal of visualized Experiments Journal of visualized Experiments,, doi: 10.3791/2046
Pauly M, Keegstra K, 2010, Plant cell walls as precursors for biofuels, Current Opinion in Plant Biology, 13 (3), 305-312
Santoro N, Cantu SL, Tornqvist CEI, Falbel TG, Bolivar JL, Patterson SE, Pauly M, Walton JD, 2010, A high throughput platform for screening milligram quantities of plant biomass for lignocellulosic digestability, BioEnergy Research, 3 (1), 93-102    
Foster CE, Martin T, Pauly M, 2010, Comprehensive compositional analysis of Plant Cell Walls (lignocellulosic biomass); Part II: carbohydrates, Journal of visualized Experiments, 37,, doi: 10.3791/1837
Foster CE, Martin T, Pauly M, 2010, Comprehensive compositional analysis of Plant Cell Walls (lignocellulosic biomass); Part I: lignin, Journal of visualized Experiments, 37;, doi: 10.3791/1745
Gille S, Haensel U, Ziemann M, Pauly M, 2009, Identification of plant cell wall mutants by means of a forward chemical genetic approach using hydrolases, Proc. Nat. Academy Sciences U.S.A. 106 (34), 14699-14704

Pauly M, Keegstra K, 2008, Cell wall carbohydrates and their modification as raw materials for biofuels, Plant Journal 54, 559-568


Recent Teaching

Bio1A - Biology - Molecules of Life/ the cell

MCB 102 - Principles of Biochemistry - Metabolism

199 - Supervised Independent Study

299 - Supervised Independent Study

PMB 122 - Bioenergy