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6. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

Author

Olson, Ake, Aerts, Andrea, Asiegbu, Fred, Belbahri, Lassaad, Bouzid, Ourdia, Broberg, Anders, Canback, Bjorn, Coutinho, Pedro M., Cullen, Dan, Dalman, Kerstin, Deflorio, Giuliana, Diepen, Linda T. A. van, Dunand, Christophe, Duplessis, Sebastien, Durling, Mikael, Gonthier, Paolo, Grimwood, Jane, Fossdal, Carl Gunnar, Hansson, David, Henrissat, Bernard, Hietala, Ari, Himmelstrand, Kajsa, Hoffmeister, Dirk, Hogberg, Nils, James, Timothy Y., Karlsson, Magnus, Kohler, Annegret, Lucas, Susan, Lunden, Karl, Morin, Emmanuelle, Murat, Claude, Park, Jongsun, Raffaello, Tommaso, Rouze, Pierre, Salamov, Asaf, Schmutz, Jeremy, Solheim, Halvor, Stahlberg, Jerry, Velez, Heriberto, Vries, Ronald P. de, Wiebenga, Ad, Woodward, Steve, Yakovlev, Igor, Garbelotto, Matteo, Martin, Francis, Grigoriev, Igor V., and Stenlid, Jan

Subjects
genome, Heterobasidion, parasitism, pathology, saprotrophy, trade-off, wood decay
Abstract

Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato.We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified.A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production.Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

Published
2012

10. Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding : insights from crystal structures and MD simulation

Author

Haataja, Topi, Gado, Japheth E., Nutt, Anu, Anderson, Nolan T., Nilsson, Mikael, Momeni, Majid Haddad, Isaksson, Roland, Valjamae, Priit, Johansson, Gunnar, Payne, Christina M., Stahlberg, Jerry, Haataja, Topi, Gado, Japheth E., Nutt, Anu, Anderson, Nolan T., Nilsson, Mikael, Momeni, Majid Haddad, Isaksson, Roland, Valjamae, Priit, Johansson, Gunnar, Payne, Christina M., and Stahlberg, Jerry

Abstract

Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) (EC3.2.1.176) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p-nitrophenyl-beta-d-cellobioside (pNPC), p-nitrophenyl-beta-d-lactoside (pNPL) and methylumbelliferyl-beta-d-cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o-nitrophenyl-beta-d-cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium. Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non-productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non-productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates (k(cat)) than TrCel7A, but higher Michaelis-Menten (K-M) constants as well. Furthermore, oNPC turned out to be useful as an active-site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.

Published
2023
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22. Classification and Nomenclature of Metacaspases and Paracaspases: No More Confusion with Caspases

Author

Minina, Elena A., Staal, Jens, Alvarez, Vanina E., Berges, John A., Berman-Frank, Ilana, Beyaert, Rudi, Bidle, Kay D., Bornancin, Frédéric, Casanova, Magali, Cazzulo, Juan J., Choi, Chang Jae, Coll, Nuria S., Dixit, Vishva M., Dolinar, Marko, Fasel, Nicolas, Funk, Christiane, Gallois, Patrick, Gevaert, Kris, Gutierrez-Beltran, Emilio, Hailfinger, Stephan, Klemenčič, Marina, Koonin, Eugene V., Krappmann, Daniel, Linusson, Anna, Machado, Maurício F.M., Madeo, Frank, Megeney, Lynn A., Moschou, Panagiotis N., Mottram, Jeremy C., Nyström, Thomas, Osiewacz, Heinz D., Overall, Christopher M., Pandey, Kailash C., Ruland, Jürgen, Salvesen, Guy S., Shi, Yigong, Smertenko, Andrei, Stael, Simon, Ståhlberg, Jerry, Suárez, María Fernanda, Thome, Margot, Tuominen, Hannele, Van Breusegem, Frank, van der Hoorn, Renier A.L., Vardi, Assaf, Zhivotovsky, Boris, Lam, Eric, and Bozhkov, Peter V.

Published
2020
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23. Antibacterial pyrrolidinyl and piperidinyl substituted 2,4-diacetylphloroglucinols from Pseudomonas protegens UP46

Author

Levenfors, Jolanta J., Nord, Christina, Bjerketorp, Joakim, Stahlberg, Jerry, Larsson, Rolf, Guss, Bengt, Öberg, Bo, Broberg, Anders, Levenfors, Jolanta J., Nord, Christina, Bjerketorp, Joakim, Stahlberg, Jerry, Larsson, Rolf, Guss, Bengt, Öberg, Bo, and Broberg, Anders

Abstract

In the search for new antibiotic compounds, fractionation of Pseudomonas protegens UP46 culture extracts afforded several known Pseudomonas compounds, including 2,4-diacetylphloroglucinol (DAPG), as well as two new antibacterial alkaloids, 6-(pyrrolidin-2-yl)DAPG (1) and 6-(piperidin-2-yl)DAPG (2). The structures of 1 and 2 were determined by nuclear magnetic resonance spectroscopy and mass spectrometry. Compounds 1 and 2 were found to have antibacterial activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus cereus, with minimal inhibitory concentration (MIC) 2 and 4 mu g ml(-1), respectively, for 1, and 2 mu g ml(-1) for both pathogens for 2. The MICs for 1 and 2, against all tested Gram-negative bacteria, were >32 mu g ml(-1). The half maximal inhibitory concentrations against HepG2 cells for compounds 1 and 2 were 11 and 18 mu g ml(-1), respectively, which suggested 1 and 2 be too toxic for further evaluation as possible new antibacterial drugs. Stable isotope labelling experiments showed the pyrrolidinyl group of 1 to originate from ornithine and the piperidinyl group of 2 to originate from lysine. The P. protegens acetyl transferase (PpATase) is involved in the biosynthesis of monoacetylphloroglucinol and DAPG. No optical rotation was detected for 1 or 2, and a possible reason for this was investigated by studying if the PpATase may catalyse a stereo-non-specific introduction of the pyrrolidinyl/piperidinyl group in 1 and 2, but unless the PpATase can be subjected to major conformational changes, the enzyme cannot be involved in this reaction. The PpATase is, however, likely to catalyse the formation of 2,4,6-triacetylphloroglucinol from DAPG.

Published
2020
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25. Synthesis of 5-fluoro N-acetylglucosamine glycosides and pyrophosphates via epoxide fluoridolysis: Versatile reagents for the study of glycoconjugate biochemistry

Author

Hartman, Matthew C.T., Coward, James K., Ayed, AyedaKay, Kay, Lewis E., and Teeri, Tuula T.; Becker, Dieter; Stahlberg, Jerry

Subjects
Glycosides -- Research, Glycols -- Research, Enzymes -- Research, Chemistry
Abstract

Numerous carbohydrate-processing enzymes facilitate catalysis via stabilization of positive charges near the C1, C4, C5 or C6 positions, but reactions catalyzed by these enzymes are diverse. An easy method that allows easy access to different varieties of 5-fluoro group glycosides as well as glycosyl phosphates is developed with the aim to solve the difficulties faced in introducing the 5-fluoro substituent after radical halogenation.

Published
2002

26. Four-dimensional NMR spectroscopy of a 723-residue protein: Chemical shift assignments and secondary structure of malate synthase G

Author

Tugarinov, Vitali, Muhandiram, Ranjith, Ayed, AyedaKay, Lewis E., and Teeri, Tuula T.; Becker, Dieter; Stahlberg, Jerry

Subjects
Proteins -- Properties, Polymers -- Chemical properties, Polymers -- Research, Nuclear magnetic resonance -- Research, Escherichia coli -- Research, Escherichia coli -- Atomic properties, Chemistry
Abstract

A four-dimensional (4-D) nuclear magnetic resonance (NMR) study of Escherichia coli-malate synthase G (MSG), a 723-residue monomeric enzyme (81.4 kDa), is described. Virtually complete backbone (super 1)HN, (super 15)N, (super 13)C, and (super 13)C(super beta) chemical shift assignments of this largely alpha-helical protein are reported, which helps in characterizing the dynamical properties of the enzyme that are likely important for function.

Published
2002

27. The active site of cellobiohydrolase Cel6A from trichoderma ressei: The roles of aspartic acids D221 and D175

Author

Koivula, Anu; Piens, Kathleen; Sinnott, Michael L.; Jones, T. Alwyn, Ruohonen, Laura; Claeyssens, Marc; Jin-yu Zou, Wohlfahrt, Gerd; Weber, Martin; Kleywegt, Gerard J., Reinikainen, Tapani; Vasella, Andrea; Szardenings, Michael, and Teeri, Tuula T.; Becker, Dieter; Stahlberg, Jerry

Subjects
Glycosides -- Research, Glycosides -- Atomic properties, Catalysts -- Research, Catalysts -- Chemical properties, Aspartate -- Research, Aspartate -- Chemical properties, Polymers -- Research, Chemistry
Abstract

Structural studies of the tunnel-shaped active site of Cel6A, which is an inverting glycosidase, contains two aspartic acids, D221 and D175 and are at hydrogen-bonding distance from each other. The site-directed mutagenesis, X-ray crystallography, and enzyme kinetic studies are conducted to confirm the role of residue D221 as the catalytic acid, and it is suggested that the single-displacement mechanism of Cel6A may not directly involve a catalytic base.

Published
2002

32. Structure-based analysis and optimization of a highly enantioselective catalyst for the Strecker reaction

Author

Vachal, Petr, Jacobsen, Eric N., Wohlfahrt, Gerd; Weber, Martin; Kleywegt, Reinikainen, Tapani; Vasella, Andrea; Sz, and Teeri, Tuula T.; Becker, Dieter; Stahlberg, Jerry

Subjects
Metal catalysts -- Research, Catalysts -- Research, Catalysts -- Analysis, Chemistry
Abstract

The Strecker reaction, the hydrocynation of imines is one of the most widely studied reactions especially since the structurally novel metal-free catalyst system that displays high enantioselectivity is seen in this reaction. The structural and mechanistic studies that shed light on this issue and lay the foundation for rational catalyst optimization is reported.

Published
2002

33. Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes

Author

Abbott, Wade, Alber, Orly, bayer, Ed, Berrin, Jean-Guy, Boraston, Alisdair, Brumer, Harry, Brzezinski, Ryszard, Clarke, Anthony, Cobucci-Ponzano, Beatrice, Cockburn, Darrell, Coutinho, Pedro, Czjzek, Mirjam, Dassa, Bareket, Davies, Gideon John, Eijsink, Vincent, Eklöf, Jens, Felice, Alfons, Ficko-Blean, Elisabeth, Fincher, Geoff, Fontaine, Thierry, Fujimoto, Zui, Fujita, Kiyotaka, Fushinobu, Shinya, Gilbert, Harry, Gloster, Tracey, Goddard-Borger, Ethan, Greig, Ian, Hehemann, Jan-Hendrik, Hemsworth, Glyn, Henrissat, Bernard, Hidaka, Masafumi, Hurtado-Guerrero, Ramon, Igarashi, Kiyohiko, Ishida, Takuya, Janeček, Štefan, Jongkees, Seino, Juge, Nathalie, Kaneko, Satoshi, Katayama, Takane, Kitaoka, Motomitsu, Konno, Naotake, Kracher, Daniel, Kulminskaya, Anna, Lammerts van Bueren, Alicia, Larsen, Stine, Lee, Junho, Linder, Markus, Lo Leggio, Leila, Ludwig, Roland, Luis, Ana, Maksimainen, Mirko, Mark, Brian, McLean, Richard, Michel, Gurvan, Montanier, Cedric, Moracci, Marco, Mori, Haruhide, Nakai, Hiroyuki, Nerinckx, Wim, Ohnuma, Takayuki, Pickersgill, Richard, Piens, Kathleen, Pons, Tirso, Rebuffet, Etienne, Reilly, Peter, Remaud-Simeon, Magali, Rempel, Brian, Robinson, Kyle, Rose, David, Rouvinen, Juha, Saburi, Wataru, Sakamoto, Yuichi, Sandgren, Mats, Shaikh, Fathima, Shoham, Yuval, St. John, Franz, Stahlberg, Jerry, Suits, Michael, Sulzenbacher, Gerlind, Sumida, Tomomi, Suzuki, Ryuichiro, Svensson, Birte, Taira, Toki, Taylor, Ed, Tonozuka, Takashi, Urbanowicz, Breeanna, Vaaje-Kolstad, Gustav, Van den Ende, Wim, Varrot, Annabelle, Verluys, Maxime, Vincent, Florence, Vocadlo, David, Wakarchuk, Warren, Wennekes, Tom, Williams, Rohan, Williams, Spencer, Wilkens, Casper, Wilson, David, Withers, Stephen, Yaoi, Katsuro, Yip, Vivian, Zhang, Ran, Abbott, Wade, Alber, Orly, bayer, Ed, Berrin, Jean-Guy, Boraston, Alisdair, Brumer, Harry, Brzezinski, Ryszard, Clarke, Anthony, Cobucci-Ponzano, Beatrice, Cockburn, Darrell, Coutinho, Pedro, Czjzek, Mirjam, Dassa, Bareket, Davies, Gideon John, Eijsink, Vincent, Eklöf, Jens, Felice, Alfons, Ficko-Blean, Elisabeth, Fincher, Geoff, Fontaine, Thierry, Fujimoto, Zui, Fujita, Kiyotaka, Fushinobu, Shinya, Gilbert, Harry, Gloster, Tracey, Goddard-Borger, Ethan, Greig, Ian, Hehemann, Jan-Hendrik, Hemsworth, Glyn, Henrissat, Bernard, Hidaka, Masafumi, Hurtado-Guerrero, Ramon, Igarashi, Kiyohiko, Ishida, Takuya, Janeček, Štefan, Jongkees, Seino, Juge, Nathalie, Kaneko, Satoshi, Katayama, Takane, Kitaoka, Motomitsu, Konno, Naotake, Kracher, Daniel, Kulminskaya, Anna, Lammerts van Bueren, Alicia, Larsen, Stine, Lee, Junho, Linder, Markus, Lo Leggio, Leila, Ludwig, Roland, Luis, Ana, Maksimainen, Mirko, Mark, Brian, McLean, Richard, Michel, Gurvan, Montanier, Cedric, Moracci, Marco, Mori, Haruhide, Nakai, Hiroyuki, Nerinckx, Wim, Ohnuma, Takayuki, Pickersgill, Richard, Piens, Kathleen, Pons, Tirso, Rebuffet, Etienne, Reilly, Peter, Remaud-Simeon, Magali, Rempel, Brian, Robinson, Kyle, Rose, David, Rouvinen, Juha, Saburi, Wataru, Sakamoto, Yuichi, Sandgren, Mats, Shaikh, Fathima, Shoham, Yuval, St. John, Franz, Stahlberg, Jerry, Suits, Michael, Sulzenbacher, Gerlind, Sumida, Tomomi, Suzuki, Ryuichiro, Svensson, Birte, Taira, Toki, Taylor, Ed, Tonozuka, Takashi, Urbanowicz, Breeanna, Vaaje-Kolstad, Gustav, Van den Ende, Wim, Varrot, Annabelle, Verluys, Maxime, Vincent, Florence, Vocadlo, David, Wakarchuk, Warren, Wennekes, Tom, Williams, Rohan, Williams, Spencer, Wilkens, Casper, Wilson, David, Withers, Stephen, Yaoi, Katsuro, Yip, Vivian, and Zhang, Ran

Abstract

CAZypedia was initiated in 2007 to create a comprehensive, living encyclopedia of the carbohydrate-active enzymes (CAZymes) and associated carbohydrate-binding modules involved in the synthesis, modification and degradation of complex carbohydrates. CAZypedia is closely connected with the actively curated CAZy database, which provides a sequence-based foundation for the biochemical, mechanistic and structural characterization of these diverse proteins. Now celebrating its 10th anniversary online, CAZypedia is a successful example of dynamic, community-driven and expert-based biocuration.

Published
2018

38. Synthesis of cyclic [beta]-glucan using laminarinase 16A glycosynthase mutant from the basidiomycete phanerochaete Chrysosporium

Author

Vasur, Jonas, Kawai, Rie, Jonsson, K. Hanna M., Widmalm, Goran, Engstrom, Ake, Frank, Martin, Andersson, Evalena, Hansson, Henrik, Forsberg, Zarah, Igarashi, Kiyohiko, Samejima, Masahiro, Sandgren, Mats, and Stahlberg, Jerry

Subjects
Fluorides -- Chemical properties, Gene mutations -- Analysis, Oligosaccharides -- Structure, Oligosaccharides -- Chemical properties, Basidiomycota -- Physiological aspects, Basidiomycota -- Genetic aspects, Chemistry
Abstract

The first synthesis of cyclic [beta]-1,3-heptaglucan from the reaction between 1,3(4)-[beta]-D-glucanase nucleophile mutant E115S of phanerochaete Chrysosporium Laminarinase 16A (Lam16A) and [alpha]-laminariheptaosyl fluoride ([alpha]L7F) is described. The study provides insight into the glcosynthase mechanism that joins the reducing and nonreducing ends of a single oligosaccharide.

Published
2010

41. Adaptation of Dekkera bruxellensis to lignocellulose-based substrate

Author

Tiukova, Ievgeniia A., Pita, Will de Barros, Sundell, David, Momeni, Majid Haddad, Horn, Svein Jarle, Stahlberg, Jerry, de Morais, Marcos Antonio, Jr., Passoth, Volkmar, Tiukova, Ievgeniia A., Pita, Will de Barros, Sundell, David, Momeni, Majid Haddad, Horn, Svein Jarle, Stahlberg, Jerry, de Morais, Marcos Antonio, Jr., and Passoth, Volkmar

Abstract

Adaptation of Dekkera bruxellensis to lignocellulose hydrolysate was investigated. Cells of D. bruxellensis were grown for 72 and 192H in batch and continuous culture, respectively (adapted cells). Cultivations in semisynthetic medium were run as controls (nonadapted cells). To test the adaptation, cells from these cultures were reinoculated in the lignocellulose medium, and growth and ethanol production characteristics were monitored. Cells adapted to lignocellulose hydrolysate had a shorter lag phase, grew faster, and produced a higher ethanol concentration as compared with nonadapted cells. A stability test showed that after cultivation in rich medium, cells partially lost the adapted phenotype but still showed faster growth and higher ethanol production as compared with nonadapted cells. Because alcohol dehydrogenase genes have been described to be involved in the adaptation to furfural in Saccharomyces cerevisiae, an analogous mechanism of adaptation to lignocelluloses hydrolysate of D. bruxellensis was hypothesized. However, gene expression analysis showed that genes homologous to S. cerevisiae ADH1 were not involved in the adaptation to lignocelluloses hydrolysate in D. bruxellensis.

Published
2014
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42. Bulletin of Applied Glycoscience

Author

Wu, Miao, additional, Westereng, Bjorge, additional, Horn, Svein J., additional, Vaaje-Kolstad, Gustav, additional, Sandgren, Mats, additional, Stahlberg, Jerry, additional, and Eijsink, Vincent, additional

Published
2012
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