Markus Pauly

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

Energy Biosciences Institute, 130 Calvin Hall, MC 5230
Berkeley, California 94720
mpauly69@berkeley.edu
office: 510-642-1722   lab: 510-642-1722   fax:  510-642-1490

     Recent publications     

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. The wall can be described as a liquid crystal.


Microcrystalline cellulose is embedded in a hydrated matrix consisting of coextensive networks of complex heteropolysaccharides and sometimes glycoproteins. Cell walls also constitute renewable resources and are often present in by-products of industrial production, such as pulps. Genetic engineering of crop plant cell walls can identify biopolymers with novel functional properties, as well as simplify their extraction, thus increasing the value of these "waste-products." Cell walls will become more important in the future, as they are an abundant resource that can contribute to our biofuel needs.

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

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. 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. 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.

We identify wall mutants by screening of populations of chemically mutagenised Arabidopsis seeds for novel structural wall mutants using OLIMP. This approach takes advantage of the speed of OLIMP. It has lead to the identification of 60 distinct mutants with altered xyloglucan structures including the abundance of ester-substituents. Map-based cloning of the mutated genes should give valuable insights into biosynthesis, metabolism and function of structural variations of xyloglucan.

We also study cell walls via chemical genetics. Arabidopsis seeds can be germinated and grown in liquid culture with the addition of agents such as specific polysaccharide hydrolases. Due to the presence of the enzyme, the seedlings exhibit distinct phenotypes (e.g., alterations in stomata development, growth and hypersensitive response phenotypes) that can be reversed when the agent, i.e. the enzyme, is removed.

Enzyme containing medium was employed to screen mutagenized or T-DNA tagged Arabidopsis seed populations for the identification of mutants that exhibit a more severe phenotype ("hypersensitive mutants"), or that resemble the wild type phenotype grown without the enzyme ("resistant mutants"). Several mutants, identified by their altered visible phenotype when subjected to the hydrolase, exhibit an altered wall structure. Further characterization of the mutant phenotype as well as understanding the genetic basis for the phenotype should result not only in additional mutants with novel wall structures but also mutants impaired or altered in oligosaccharin signalling pathways

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 employ a reverse genetic approach after identifying candidate genes involved in this process. 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.

The analysis of Arabidopsis insertional knock-out alleles of these candidate genes has already revealed, in some cases, a function for the gene (e.g., a UDP-rhamnose synthase), a plant with an altered polysaccharide composition (e.g., drastic reduction of rhamnogalacturonan I), and its effect on plant growth and morphology (e.g., detrimental seed development and morphology).

(last 5 years, out of 60 total)

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, in press in Proc. Nat. Academy Sciences U.S.A.

Obel N, Erben V, Schwarz T, Kuehnel S, Fodor A, Pauly M, 2009, Microanalysis of plant cell wall polysaccharides, in press in Molecular Plant

Perrson S, Willats W, Pauly M, 2009, Dissection of the Plant Cell Wall by High Throughput Methods, Plant Cell Walls, Udskov editor, in press

Pauly M, Keegstra K, 2008, Tear down this wall, Current Opinion in Plant Biology 11 (3), 233-235

Cavalier DM, Lerouxel O, Neumetzler L, Yamauchi K, Reinecke A, Freshour G, Zabotina O, Hahn MG, Burgert I, Pauly M, Raikhel N, Keegstra K, 2008, Disruption of two Arabidopsis thaliana xylosyltransferase genes results in plants deficient in xyloglucan, a major primary cell wall component, Plant Cell 20:1519-1537

Jensen J, Sorensen S, Harholt J, Geshi N, Sakuragi Y, Moller I, Zandleven J, Bernal AJ, Jensen NB, Sorensen C, Pauly M, Beldman G, Willats WGT, Scheller HV, 2008, Identification of a xylogalactuonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis, Plant Cell 20: 1289-1302

Wen F, Rhodesia MC, Nguyen T, Zeng, W, Keegstra K, Immerzeel P, Pauly M, Hawes MC, 2008, Inducible expression of Pisum sativum xyloglucan fucosyltransferase in the pea root cap meristem, and effects of antisense mRNA expression on root cap cell wall structural integrity, Plant Cell Reports 27:1125-1135

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

Leboeuf E, Immerzeel P, Gibon, Y, Steup M, Pauly M, 2008, High throughput functional assessment of polysaccharide-active enzymes using MALDI-TOF mass spectrometry as exemplified on plant cell wall polysaccharides, Analytical biochemistry, 373 (1):9-17

Bernal AJ, Jensen JK, Harholt J, Sorensen S, Moller I, Blaukopf C, Johansen B, de Lotto R, Pauly M, Scheller HV, Willats WGT, 2007, Disruption of AtCSLD5 results in reduced growth, reduced xylan and homogalacturonan synthase activity and altered xylan occurrence in Arabidopsis, Plant Journal, 52, 791-802

Rösti J, Barton CJ, Albrecht S, Dupree P, Pauly M, Findlay K, Roberts K, Seifert GJ, 2007, UDP-glucose 4 epimerase isoforms UGE2 and UGE4 cooperate in providing UDP-galactose for cell wall biosynthesis and growth of Arabidopsis thaliana, Plant Cell 19:1565-1579

Egelund J, Obel N, Ulvskov P, Geshi N, Pauly M, Bacic A, Peterson BL, 2007, Molecular characterization of two Arabidopsis thaliana glycosyltransferase mutants, rra1 and rra2, which have a reduced residual arabinose content in a polymer tightly associated with the cellulosic wall residue, Plant Molecular Biology 64(4): 439-451

Krupkova E, Immerzeel P, Pauly M, Schmülling T, 2007, The tumorous shoot development2 gene of Arabidopsis encoding a putative methyltransferase is required for cell adhesion and co-ordinated plant development, Plant Journal 50: 735-750

Kannangara R, Branigan C, Liu Y, Penfield T, Rao V, Mouille G, Höfte H, Pauly M, Riechmann JL, Broun P, 2007, Transcription factor WIN1/SHN1 regulates cutin biosynthesis in Arabidopsis thaliana, Plant Cell 19: 1278-1294

Lionetti V, Railola A, Camardella L, Giovane A, Obel N, Pauly M, Favaron F, Cervone F, Bellincampi D, 2007, Overexpression of pectin methylesterase inhibitors in Arabidopsis restricts fungal infection by Botrytis cinerea, Plant Physiology 143:1871-1880

Obel N, Neumetzler L, Pauly M, 2007, Hemicelluloses and cell expansion, in The expanding cell, Springer publishing, Verbelen C, Vissenberg K eds. p 57-88

Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor MI, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M, Sweetlove LJ, Fernie AR, 2006, Plant Physiology 142 (4):1380-1396

Bosca S, Barton CJ, Taylor NG, Ryden P, Neumetzler L, Pauly M, Roberts K, Seifert GJ, 2006, Interactions between MUR10/CesA7-dependent secondary cellulose biosynthesis and primary cell wall structure. Plant Physiology 142:1353-1363.

Immerzeel P, Pauly M, 2006, Profiling methods for the analysis of cell wall polysaccharides, New Zealand Journal of Forestry research, 36 (1):145-156

Mouille G, Witucka-Wall H, Bryant MP, Loudet O, Rihouey C, Lerouxel O, Lerouge P, Hoefte H, Pauly M, 2006, QTL analysis of primary cell wall composition in Arabidopsis thaliana, Plant Physiology, 141 (7):1035-1044

Diet A, Link B, Seifert GJ, Schellenberg B, Wagner U, Pauly M, Reiter WD, Ringli C, 2006, The Arabidopsis root hair cell wall formation mutant lrx1 is suppressed by mutations in the RHM1 gene encoding a UDP-L-rhamnose synthase, Plant Cell, 18, 1630-1641

Harholt J, Jensen JK, Sorensen SO, Orfila C, Pauly M, Scheller HV, 2006, Arabinan deficient 1 is a putative arabinosyltransferase involved in biosynthesis of pectin arabinan in Arabidopsis, Plant Physiology, 140 (1): 49-58

Abdulrazzak N, Pollet B, Ehlting J, Larsen K, Asnaghi C, Ronseau S, Proux C, Erhardt M, Seltzer V, Renau JP, Ullmann P, Pauly M, Lapierre C, Werck-Reichhart D, 2006, A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of non redundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansin and plant growth, Plant Physiology, 140 (1), 30-48

Obel N, Erben V, Pauly M, 2006, Functional wall glycomics through oligosaccharide mass profiling, in The Science and Lore of the Plant Cell Wall: Biosynthesis, Structure and Function, Hayashi, T., ed., Brownwater press, 258-266

Fettke J, Poeste S, Eckermann N, Thissen A, Pauly M, Geigenberger P, Steup M, 2005, Analysis of cytosolic heteroglycans from leaves of transgenic potato (Solanum tuberosum L) plants that under- or overexpress the pho2 phosphorylase isozyme, Plant and Cell Physiology, 46 (12), 1987-2004

Gibeaut DM, Pauly M, Bacic A, Fincher GB, 2005, Changes in the cell wall polysaccharides in developing barley coleoptiles, Planta, 221 (5):720-738

Kanter U, Usadel B, Guerinaeu F, Li Y, Pauly M, Tenhaken R, 2005, The inositol oxygenase gene family of Arabidopsis is involved in the biosynthesis of nucleotide sugar precursors for cell wall matrix polysaccharides, Planta, 221 (2), 243-254

Usadel B, Kuschinsky AM, Steinhauser D, Pauly M, 2005, Transcriptional co-response analysis as a tool to identify new components of the wall biosynthetic machinery, Plant Biosystems, 139(1), 69-73

Vissenberg K, Fry SC, Pauly M, Höfte H, Verbelen H, 2005, XTH acts at the microfibril-matrix interphase during cell elongation, Journal of Experimental Botany, 56 (412): 673-683