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 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: http://www.jove.com/details.php?id=1745; Carbohydrate analysis http://www.jove.com/details.php?id=1837). 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:http://www.jove.com/details.php?id=2046). 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.
(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
Pauly M, Keegstra K, 2008, Cell wall carbohydrates and their modification as raw materials for biofuels, Plant Journal 54, 559-568
Bio1A - Biology - Molecules of Life/ the cell
MCB 102 - Principles of Biochemistry - Metabolism
199 - Supervised Independent Study
299 - Supervised Independent Study
PMB 122 - Bioenergy