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A Novel Endo-Polygalacturonase from Penicillium rolfsii with Prebiotics Production Potential: Cloning, Characterization and Application. Foods 2022; 11:foods11213469. [DOI: 10.3390/foods11213469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
In this study, a potential producer of prebiotics, a novel endo-polygalacturonase pePGA from Penicillium rolfsii BM-6, was successfully expressed in Komagataella phaffii, characterized and applied to produce pectic oligosaccharides. The optimum temperature and pH of pePGA were 60 °C and 6.0. The purified recombinant enzyme showed a good pH stability and was stable from pH 3.5 to 8.0. The Km, Vmax and kcat values of pePGA were 0.1569 g/L, 12,273 μmol/min/mg and 7478.4 s−1, respectively. More importantly, pePGA-POS, the pePGA hydrolysis products from commercial pectin, had good prebiotic and antibacterial activities in vitro. The pePGA-POS was able to significantly promote the growth of probiotics; meanwhile, the growth of Escherichia coli JM109, Staphylococcus aureus and Bacillus subtilis 168 was effectively inhibited by pePGA-POS. In addition, pePGA-POS also had the DPPH radical scavenging capacity. These properties of pePGA-POS make pePGA attractive for the production of prebiotics.
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Arnal G, Stogios PJ, Asohan J, Attia MA, Skarina T, Viborg AH, Henrissat B, Savchenko A, Brumer H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J Biol Chem 2019; 294:13233-13247. [PMID: 31324716 DOI: 10.1074/jbc.ra119.009861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Glycoside hydrolase family 74 (GH74) is a historically important family of endo-β-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" family, although more recent studies have generally indicated a high specificity toward the ubiquitous plant cell wall matrix glycan xyloglucan. Previous studies have indicated that GH74 xyloglucanases differ in backbone cleavage regiospecificities and can adopt three distinct hydrolytic modes of action: exo, endo-dissociative, and endo-processive. To improve functional predictions within GH74, here we coupled in-depth biochemical characterization of 17 recombinant proteins with structural biology-based investigations in the context of a comprehensive molecular phylogeny, including all previously characterized family members. Elucidation of four new GH74 tertiary structures, as well as one distantly related dual seven-bladed β-propeller protein from a marine bacterium, highlighted key structure-function relationships along protein evolutionary trajectories. We could define five phylogenetic groups, which delineated the mode of action and the regiospecificity of GH74 members. At the extremes, a major group of enzymes diverged to hydrolyze the backbone of xyloglucan nonspecifically with a dissociative mode of action and relaxed backbone regiospecificity. In contrast, a sister group of GH74 enzymes has evolved a large hydrophobic platform comprising 10 subsites, which facilitates processivity. Overall, the findings of our study refine our understanding of catalysis in GH74, providing a framework for future experimentation as well as for bioinformatics predictions of sequences emerging from (meta)genomic studies.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jathavan Asohan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, 13007 Marseille, France; INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 13007 Marseille, France
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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Jeng WY, Liu CI, Lu TJ, Lin HJ, Wang NC, Wang AHJ. Crystal Structures of the C-Terminally Truncated Endoglucanase Cel9Q from Clostridium thermocellum Complexed with Cellodextrins and Tris. Chembiochem 2019; 20:295-307. [PMID: 30609216 DOI: 10.1002/cbic.201800789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Indexed: 11/11/2022]
Abstract
Endoglucanase CtCel9Q is one of the enzyme components of the cellulosome, which is an active cellulase system in the thermophile Clostridium thermocellum. The precursor form of CtCel9Q comprises a signal peptide, a glycoside hydrolase family 9 catalytic domain, a type 3c carbohydrate-binding module (CBM), and a type I dockerin domain. Here, we report the crystal structures of C-terminally truncated CtCel9Q (CtCel9QΔc) complexed with Tris, Tris+cellobiose, cellobiose+cellotriose, cellotriose, and cellotetraose at resolutions of 1.50, 1.70, 2.05, 2.05 and 1.75 Å, respectively. CtCel9QΔc forms a V-shaped homodimer through residues Lys529-Glu542 on the type 3c CBM, which pairs two β-strands (β4 and β5 of the CBM). In addition, a disulfide bond was formed between the two Cys535 residues of the protein monomers in the asymmetric unit. The structures allow the identification of four minus (-) subsites and two plus (+) subsites; this is important for further understanding the structural basis of cellulose binding and hydrolysis. In the oligosaccharide-free and cellobiose-bound CtCel9QΔc structures, a Tris molecule was found to be bound to three catalytic residues of CtCel9Q and occupied subsite -1 of the CtCel9Q active-site cleft. Moreover, the enzyme activity assay in the presence of 100 mm Tris showed that the Tris almost completely suppressed CtCel9Q hydrolase activity.
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Affiliation(s)
- Wen-Yih Jeng
- University Center for Bioscience and Biotechnology, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.,Department of Biochemistry and Molecular Biology, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan
| | - Chia-I Liu
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, 250 Wuxing Street, Taipei, 110, Taiwan
| | - Te-Jung Lu
- Department of Medical Laboratory Science and Biotechnology, Chung Hwa University of Medical Technology, 89 Wenhua 1st Street, Tainan, 717, Taiwan
| | - Hong-Jie Lin
- University Center for Bioscience and Biotechnology, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan
| | - Nai-Chen Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Sec. 2, Taipei, 115, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Sec 2, Taipei, 115, Taiwan
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Guerriero G, Sergeant K, Legay S, Hausman JF, Cauchie HM, Ahmad I, Siddiqui KS. Novel Insights from Comparative In Silico Analysis of Green Microalgal Cellulases. Int J Mol Sci 2018; 19:E1782. [PMID: 29914107 PMCID: PMC6032398 DOI: 10.3390/ijms19061782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/08/2018] [Accepted: 06/08/2018] [Indexed: 11/24/2022] Open
Abstract
The assumption that cellulose degradation and assimilation can only be carried out by heterotrophic organisms was shattered in 2012 when it was discovered that the unicellular green alga, Chlamydomonas reinhardtii (Cr), can utilize cellulose for growth under CO₂-limiting conditions. Publications of genomes/transcriptomes of the colonial microalgae, Gonium pectorale (Gp) and Volvox carteri (Vc), between 2010⁻2016 prompted us to look for cellulase genes in these algae and to compare them to cellulases from bacteria, fungi, lower/higher plants, and invertebrate metazoans. Interestingly, algal catalytic domains (CDs), belonging to the family GH9, clustered separately and showed the highest (33⁻42%) and lowest (17⁻36%) sequence identity with respect to cellulases from invertebrate metazoans and bacteria, respectively, whereas the identity with cellulases from plants was only 27⁻33%. Based on comparative multiple alignments and homology models, the domain arrangement and active-site architecture of algal cellulases are described in detail. It was found that all algal cellulases are modular, consisting of putative novel cysteine-rich carbohydrate-binding modules (CBMs) and proline/serine-(PS) rich linkers. Two genes were found to encode a protein with a putative Ig-like domain and a cellulase with an unknown domain, respectively. A feature observed in one cellulase homolog from Gp and shared by a spinach cellulase is the existence of two CDs separated by linkers and with a C-terminal CBM. Dockerin and Fn-3-like domains, typically found in bacterial cellulases, are absent in algal enzymes. The targeted gene expression analysis shows that two Gp cellulases consisting, respectively, of a single and two CDs were upregulated upon filter paper addition to the medium.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Kjell Sergeant
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Sylvain Legay
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Henry-Michel Cauchie
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Irshad Ahmad
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
| | - Khawar Sohail Siddiqui
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
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DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase. Sci Rep 2017; 7:4756. [PMID: 28684739 PMCID: PMC5500549 DOI: 10.1038/s41598-017-02578-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
DNA polymerase (pol) processivity, i.e., the bases a polymerase extends before falling off the DNA, and activity are important for copying difficult DNA sequences, including simple repeats. Y-family pols would be appealing for copying difficult DNA and incorporating non-natural dNTPs, due to their low fidelity and loose active site, but are limited by poor processivity and activity. In this study, the binding between Dbh and DNA was investigated to better understand how to rationally design enhanced processivity in a Y-family pol. Guided by structural simulation, a fused pol Sdbh with non-specific dsDNA binding protein Sso7d in the N-terminus was designed. This modification increased in vitro processivity 4-fold as compared to the wild-type Dbh. Additionally, bioinformatics was used to identify amino acid mutations that would increase stabilization of Dbh bound to DNA. The variant SdbhM76I further improved the processivity of Dbh by 10 fold. The variant SdbhKSKIP241–245RVRKS showed higher activity than Dbh on the incorporation of dCTP (correct) and dATP (incorrect) opposite the G (normal) or 8-oxoG(damaged) template base. These results demonstrate the capability to rationally design increases in pol processivity and catalytic efficiency through computational DNA binding predictions and the addition of non-specific DNA binding domains.
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Tu T, Li Y, Su X, Meng K, Ma R, Wang Y, Yao B, Lin Z, Luo H. Probing the role of cation-π interaction in the thermotolerance and catalytic performance of endo-polygalacturonases. Sci Rep 2016; 6:38413. [PMID: 27929074 PMCID: PMC5143973 DOI: 10.1038/srep38413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023] Open
Abstract
Understanding the dynamics of the key pectinase, polygalacturonase, and improving its thermotolerance and catalytic efficiency are of importance for the cost-competitive bioconversion of pectic materials. By combining structure analysis and molecular dynamics (MD) simulations, eight mutagenesis sites having the potential to form cation-π interactions were identified in the widely used fungal endo-polygalacturonase PG63. In comparison to the wild-type, three single mutants H58Y, T71Y and T304Y showed improved thermostability (the apparent Tms increased by 0.6-3.9 °C) and catalytic efficiency (by up to 32-fold). Chromatogram analysis of the hydrolysis products indicated that a larger amount of shorter sugars were released from the polygalacturonic acid by these three mutants than by the wild-type. MD analysis of the enzyme-substrate complexes illustrated that the mutants with introduced cation-π interaction have modified conformations of catalytic crevice, which provide an enviable environment for the catalytic process. Moreover, the lower plasticity of T3 loop 2 at the edge of the subsite tunnel appears to recruit the reducing ends of oligogalacturonide into the active site tunnel and initiates new hydrolysis reactions. This study demonstrates the importance of cation-π interaction in protein conformation and provides a realistic strategy to enhance the thermotolerance and catalytic performance of endo-polygalacturonases.
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Affiliation(s)
- Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yeqing Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhemin Lin
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
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7
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Substitution of a non-active-site residue located on the T3 loop increased the catalytic efficiency of endo -polygalacturonases. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Pereira AB, Krieger N, Mitchell DA. Fingerprinting of oligosaccharide-hydrolyzing enzymes that catalyze branched reaction schemes. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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The GH26 β-mannanase RsMan26H from a symbiotic protist of the termite Reticulitermes speratus is an endo-processive mannobiohydrolase: heterologous expression and characterization. Biochem Biophys Res Commun 2014; 452:520-5. [PMID: 25173929 DOI: 10.1016/j.bbrc.2014.08.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 08/20/2014] [Indexed: 11/22/2022]
Abstract
Symbiotic protists in the gut of termites are prominent natural resources for enzymes involved in lignocellulose degradation. Here we report expression, purification, and biochemical characterization of a glycoside hydrolase family 26 mannanase RsMan26H from the symbiotic protist of the lower termite, Reticulitermes speratus. Biochemical analysis of RsMan26H demonstrates that this enzyme is an endo-processive mannobiohydrolase producing mannobiose from oligo- and polysaccharides, followed by a minor accumulation of oligosaccharides larger than mannobiose. To our knowledge, this is the first report describing the unique mannobiohydrolase enzyme from the eukaryotic origin.
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Mercadante D, Melton LD, Jameson GB, Williams MAK. Processive pectin methylesterases: the role of electrostatic potential, breathing motions and bond cleavage in the rectification of Brownian motions. PLoS One 2014; 9:e87581. [PMID: 24503943 PMCID: PMC3913658 DOI: 10.1371/journal.pone.0087581] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/23/2013] [Indexed: 12/26/2022] Open
Abstract
Pectin methylesterases (PMEs) hydrolyze the methylester groups that are found on the homogalacturonan (HG) chains of pectic polysaccharides in the plant cell wall. Plant and bacterial PMEs are especially interesting as the resulting de-methylesterified (carboxylated) sugar residues are found to be arranged contiguously, indicating a so-called processive nature of these enzymes. Here we report the results of continuum electrostatics calculations performed along the molecular dynamics trajectory of a PME-HG-decasaccharide complex. In particular it was observed that, when the methylester groups of the decasaccharide were arranged in order to mimic the just-formed carboxylate product of de-methylesterification, a net unidirectional sliding of the model decasaccharide was subsequently observed along the enzyme’s binding groove. The changes that occurred in the electrostatic binding energy and protein dynamics during this translocation provide insights into the mechanism by which the enzyme rectifies Brownian motions to achieve processivity. The free energy that drives these molecular motors is thus demonstrated to be incorporated endogenously in the methylesterified groups of the HG chains and is not supplied exogenously.
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Affiliation(s)
- Davide Mercadante
- The Riddet Institute, Palmerston North, New Zealand
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Laurence D. Melton
- The Riddet Institute, Palmerston North, New Zealand
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Geoffrey B. Jameson
- The Riddet Institute, Palmerston North, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University, Wellington, New Zealand
| | - Martin A. K. Williams
- The Riddet Institute, Palmerston North, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University, Wellington, New Zealand
- * E-mail:
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Khan M, Nakkeeran E, Umesh-Kumar S. Potential Application of Pectinase in Developing Functional Foods. Annu Rev Food Sci Technol 2013. [DOI: 10.1146/annurev-food-030212-182525] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The understanding that enzymatic degradation of fruit pectin can clarify juices and improve juice yields resulted in the search for microbial pectinases and application in vegetable- and fruit-processing industries. Identified enzymes were classified on the basis of their catalytic activity to pectin or its derivatives and in terms of industrial use. Discovery of gene sequences that coded the enzymes, protein engineering, and molecular biology tools resulted in defined microbial strains that over-produced the enzymes for cost-effective technologies. Recent perspectives on the use of pectin and its derivatives as dietary fibers suggest enzymatic synthesis of the right oligomers from pectin for use in human nutrition. While summarizing the activities of pectin-degrading enzymes, their industrial applications, and gene sources, this review projects another application for pectinases, which is the use of enzymatically derived pectin moieties in functional food preparation.
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Affiliation(s)
- Mahejibin Khan
- Department of Food Microbiology, Central Food Technological Research Institute (CSIR), Mysore 570020, India
| | - Ekambaram Nakkeeran
- School of Biosciences and Technology, Vellore Institute of Technology University, Vellore 632014, India
| | - Sukumaran Umesh-Kumar
- Department of Food Microbiology, Central Food Technological Research Institute (CSIR), Mysore 570020, India
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12
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Payne CM, Baban J, Horn SJ, Backe PH, Arvai AS, Dalhus B, Bjørås M, Eijsink VGH, Sørlie M, Beckham GT, Vaaje-Kolstad G. Hallmarks of processivity in glycoside hydrolases from crystallographic and computational studies of the Serratia marcescens chitinases. J Biol Chem 2012; 287:36322-30. [PMID: 22952223 DOI: 10.1074/jbc.m112.402149] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Degradation of recalcitrant polysaccharides in nature is typically accomplished by mixtures of processive and nonprocessive glycoside hydrolases (GHs), which exhibit synergistic activity wherein nonprocessive enzymes provide new sites for productive attachment of processive enzymes. GH processivity is typically attributed to active site geometry, but previous work has demonstrated that processivity can be tuned by point mutations or removal of single loops. To gain additional insights into the differences between processive and nonprocessive enzymes that give rise to their synergistic activities, this study reports the crystal structure of the catalytic domain of the GH family 18 nonprocessive endochitinase, ChiC, from Serratia marcescens. This completes the structural characterization of the co-evolved chitinolytic enzymes from this bacterium and enables structural analysis of their complementary functions. The ChiC catalytic module reveals a shallow substrate-binding cleft that lacks aromatic residues vital for processivity, a calcium-binding site not previously seen in GH18 chitinases, and, importantly, a displaced catalytic acid (Glu-141), suggesting flexibility in the catalytic center. Molecular dynamics simulations of two processive chitinases (ChiA and ChiB), the ChiC catalytic module, and an endochitinase from Lactococcus lactis show that the nonprocessive enzymes have more flexible catalytic machineries and that their bound ligands are more solvated and flexible. These three features, which relate to the more dynamic on-off ligand binding processes associated with nonprocessive action, correlate to experimentally measured differences in processivity of the S. marcescens chitinases. These newly defined hallmarks thus appear to be key dynamic metrics in determining processivity in GH enzymes complementing structural insights.
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Affiliation(s)
- Christina M Payne
- Biosciences Center, National Renewable Energy Laboratory, Golden Colorado 80401, USA
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13
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Andersen MR, Giese M, de Vries RP, Nielsen J. Mapping the polysaccharide degradation potential of Aspergillus niger. BMC Genomics 2012; 13:313. [PMID: 22799883 PMCID: PMC3542576 DOI: 10.1186/1471-2164-13-313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
Background The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation. Results Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from Aspergillus niger, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan. Conclusions The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in A. niger.
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Affiliation(s)
- Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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14
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Sakamoto T, Tanaka H, Nishimura Y, Ishimaru M, Kasai N. Characterization of an exo-β-1,3-D: -galactanase from Sphingomonas sp. 24T and its application to structural analysis of larch wood arabinogalactan. Appl Microbiol Biotechnol 2011; 90:1701-10. [PMID: 21452032 DOI: 10.1007/s00253-011-3219-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/21/2011] [Accepted: 02/24/2011] [Indexed: 11/26/2022]
Abstract
A type II arabinogalactan-degrading enzyme, termed Exo-1,3-Gal, was purified to homogeneity from the culture filtrate of Sphingomonas sp. 24T. It has an apparent molecular mass of 48 kDa by SDS-PAGE. Exo-1,3-Gal was stable from pH 3 to 10 and at temperatures up to 40 °C. The optimum pH and temperature for enzyme activity were pH 6 to 7 and 50 °C, respectively. Galactose was released from β-1,3-D: -galactan and β-1,3-D: -galactooligosaccharides by the action of Exo-1,3-Gal, indicating that the enzyme was an exo-β-1,3-D: -galactanase. Analysis of the reaction products of β-1,3-galactotriose by high-performance anion-exchange chromatography revealed that the enzyme hydrolyzed the substrate in a non-processive mode. Exo-1,3-Gal bypassed the branching points of β-1,3-galactan backbones in larch wood arabinogalactan (LWAG) to produce mainly galactose, β-1,6-galactobiose, and unidentified oligosaccharides 1 and 2 with the molar ratios of 7:19:62:12. Oligosaccharides 1 and 2 were enzymatically determined to be β-1,6-galactotriose and β-1,6-galactotriose substituted with a single arabinofuranose residue, respectively. The ratio of side chains enzymatically released from LWAG was in good agreement with the postulated structure of the polysaccharide previously determined by chemical methods.
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Affiliation(s)
- Tatsuji Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan.
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15
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Massa C, Guarnaccia C, Lamba D, Anselmi C. Insight into the structure of an endopolygalacturonase from the phytopathogen Burkholderia cepacia: a biochemical and computational study. Biochimie 2010; 92:1445-53. [PMID: 20637827 DOI: 10.1016/j.biochi.2010.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 07/07/2010] [Indexed: 11/30/2022]
Abstract
We have recently investigated and characterized the mode of action of BcPeh28A, an endopolygalacturonase (endoPG) from the phytopathogen Burkholderia cepacia. EndoPGs belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions of pectins. Here we report a 3-D structural model of BcPeh28A by combining mass spectrometry (MS) analysis, aimed at disulphide bridges mapping, and computational modelling tools. MS analyses have revealed the complete pattern of disulphide bridges in BcPeh28A, pointing out the presence of three disulphide bonds, defined as Cys3-25, Cys216-244 and Cys309-421. A 3-D model of BcPeh28A was generated by computational methods based on profile-profile sequence alignments and fold recognition algorithms. The final model exhibits a right-handed β-helix fold with eleven β-helical coils and includes the disulphide bonds as additional spatial restraints. Molecular dynamics simulations have been performed to test the conformational stability of the model. Finally, the structural analysis of the BcPeh28A model allows defining the architecture and the amino acid topology of the subsites involved in the catalysis and in the substrate binding specificity.
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Affiliation(s)
- Claudia Massa
- Structural Biology Laboratory, Sincrotrone Trieste S.C.p.A., AREA Science Park - Basovizza Strada Statale 14, km 163,5, I-34149 Trieste, Italy.
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16
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Ogura K, Yamasaki M, Yamada T, Mikami B, Hashimoto W, Murata K. Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action. J Biol Chem 2010; 284:35572-9. [PMID: 19846561 DOI: 10.1074/jbc.m109.068056] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Chlorella virus enzyme vAL-1 (38 kDa), a member of polysaccharide lyase family 14, degrades the Chlorella cell wall by cleaving the glycoside bond of the glucuronate residue (GlcA) through a beta-elimination reaction. The enzyme consists of an N-terminal cell wall-attaching domain (11 kDa) and a C-terminal catalytic module (27 kDa). Here, we show the enzyme characteristics of vAL-1, especially its pH-dependent modes of action, and determine the structure of the catalytic module. vAL-1 also exhibited alginate lyase activity at alkaline pH, and truncation of the N-terminal domain increased the lyase activity by 50-fold at pH 7.0. The truncated form vAL-1(S) released di- to hexasaccharides from alginate at pH 7.0, whereas disaccharides were preferentially generated at pH 10.0. This indicates that vAL-1(S) shows two pH-dependent modes of action: endo- and exotypes. The x-ray crystal structure of vAL-1(S) at 1.2 A resolution showed two antiparallel beta-sheets with a deep cleft showing a beta-jelly roll fold. The structure of GlcA-bound vAL-1(S) at pH 7.0 and 10.0 was determined: GlcA was found to be bound outside and inside the cleft at pH 7.0 and 10.0, respectively. This suggests that the electric charges at the active site greatly influence the binding mode of substrates and regulate endo/exo activity. Site-directed mutagenesis demonstrated that vAL-1(S) has a specific amino acid arrangement distinct from other alginate lyases crucial for catalysis. This is, to our knowledge, the first study in which the structure of a family 14 polysaccharide lyase with two different modes of action has been determined.
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Affiliation(s)
- Kohei Ogura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji 611-0011 , Japan
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17
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Wong DDWS, Chan VJ, McCormack AA, Batt SB. A novel xyloglucan-specific endo-β-1,4-glucanase: biochemical properties and inhibition studies. Appl Microbiol Biotechnol 2009; 86:1463-71. [DOI: 10.1007/s00253-009-2364-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/12/2009] [Accepted: 11/12/2009] [Indexed: 11/30/2022]
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18
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Processivity, synergism, and substrate specificity of Thermobifida fusca Cel6B. Appl Environ Microbiol 2009; 75:6655-61. [PMID: 19734341 DOI: 10.1128/aem.01260-09] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A relationship between processivity and synergism has not been reported for cellulases, although both characteristics are very important for hydrolysis of insoluble substrates. Mutation of two residues located in the active site tunnel of Thermobifida fusca exocellulase Cel6B increased processivity on filter paper. Surprisingly, mixtures of the Cel6B mutant enzymes and T. fusca endocellulase Cel5A did not show increased synergism or processivity, and the mutant enzyme which had the highest processivity gave the poorest synergism. This study suggests that improving exocellulase processivity might be not an effective strategy for producing improved cellulase mixtures for biomass conversion. The inverse relationship between the activities of many of the mutant enzymes with bacterial microcrystalline cellulose and their activities with carboxymethyl cellulose indicated that there are differences in the mechanisms of hydrolysis for these substrates, supporting the possibility of engineering Cel6B to target selected substrates.
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19
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Cartmell A, Topakas E, Ducros VMA, Suits MDL, Davies GJ, Gilbert HJ. The Cellvibrio japonicus mannanase CjMan26C displays a unique exo-mode of action that is conferred by subtle changes to the distal region of the active site. J Biol Chem 2008; 283:34403-13. [PMID: 18799462 PMCID: PMC2662245 DOI: 10.1074/jbc.m804053200] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 08/11/2008] [Indexed: 11/06/2022] Open
Abstract
The microbial degradation of the plant cell wall is a pivotal biological process that is of increasing industrial significance. One of the major plant structural polysaccharides is mannan, a beta-1,4-linked d-mannose polymer, which is hydrolyzed by endo- and exo-acting mannanases. The mechanisms by which the exo-acting enzymes target the chain ends of mannan and how galactose decorations influence activity are poorly understood. Here we report the crystal structure and biochemical properties of CjMan26C, a Cellvibrio japonicus GH26 mannanase. The exo-acting enzyme releases the disaccharide mannobiose from the nonreducing end of mannan and mannooligosaccharides, harnessing four mannose-binding subsites extending from -2 to +2. The structure of CjMan26C is very similar to that of the endo-acting C. japonicus mannanase CjMan26A. The exo-activity displayed by CjMan26C, however, reflects a subtle change in surface topography in which a four-residue extension of surface loop creates a steric block at the distal glycone -2 subsite. endo-Activity can be introduced into enzyme variants through truncation of an aspartate side chain, a component of a surface loop, or by removing both the aspartate and its flanking residues. The structure of catalytically competent CjMan26C, in complex with a decorated manno-oligosaccharide, reveals a predominantly unhydrolyzed substrate in an approximate (1)S(5) conformation. The complex structure helps to explain how the substrate "side chain" decorations greatly reduce the activity of the enzyme; the galactose side chain at the -1 subsite makes polar interactions with the aglycone mannose, possibly leading to suboptimal binding and impaired leaving group departure. This report reveals how subtle differences in the loops surrounding the active site of a glycoside hydrolase can lead to a change in the mode of action of the enzyme.
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Affiliation(s)
- Alan Cartmell
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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20
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Cloning and characterization of a novel exo-α-1,5-L-arabinanase gene and the enzyme. Appl Microbiol Biotechnol 2008; 79:941-9. [DOI: 10.1007/s00253-008-1504-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 04/04/2008] [Accepted: 04/14/2008] [Indexed: 10/22/2022]
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21
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Mizuno M, Koide A, Yamamura A, Akeboshi H, Yoshida H, Kamitori S, Sakano Y, Nishikawa A, Tonozuka T. Crystal Structure of Aspergillus niger Isopullulanase, a Member of Glycoside Hydrolase Family 49. J Mol Biol 2008; 376:210-20. [DOI: 10.1016/j.jmb.2007.11.098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 11/26/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
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22
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Massa C, Clausen MH, Stojan J, Lamba D, Campa C. Study of the mode of action of a polygalacturonase from the phytopathogen Burkholderia cepacia. Biochem J 2008; 407:207-17. [PMID: 17627609 PMCID: PMC2049012 DOI: 10.1042/bj20061833] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have recently isolated and heterologously expressed BcPeh28A, an endopolygalacturonase from the phytopathogenic Gram-negative bacterium Burkholderia cepacia. Endopolygalacturonases belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions of pectins. The mode of action of BcPeh28A on different substrates has been investigated and its enzymatic mechanism elucidated. The hydrolysis of polygalacturonate indicates that BcPeh28A is a non-processive enzyme that releases oligomers with chain lengths ranging from two to eight. By inspection of product progression curves, a kinetic model has been generated and extensively tested. It has been used to derive the kinetic parameters that describe the time course of the formation of six predominant products. Moreover, an investigation of the enzymatic activity on shorter substrates that differ in their overall length and methylation patterns sheds light on the architecture of the BcPeh28A active site. Specifically the tolerance of individual sites towards methylated saccharide units was rationalized on the basis of the hydrolysis of hexagalacturonides with different methylation patterns.
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Affiliation(s)
- Claudia Massa
- International School for Advanced Studies, Via Beirut 2/4, I-34014 Trieste, Italy.
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23
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Genta FA, Dumont AF, Marana SR, Terra WR, Ferreira C. The interplay of processivity, substrate inhibition and a secondary substrate binding site of an insect exo-β-1,3-glucanase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1079-91. [PMID: 17720633 DOI: 10.1016/j.bbapap.2007.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 06/23/2007] [Accepted: 07/16/2007] [Indexed: 10/23/2022]
Abstract
Abracris flavolineata midgut contains a processive exo-beta-glucanase (ALAM) with lytic activity against Saccharomyces cerevisiae, which was purified (yield, 18%; enrichment, 37 fold; specific activity, 1.89 U/mg). ALAM hydrolyses fungal cells or callose from the diet. ALAM (45 kDa; pI 5.5; pH optimum 6) major products with 0.6 mM laminarin as substrate are beta-glucose (61%) and laminaribiose (39%). Kinetic data obtained with laminaridextrins and methylumbelliferyl glucoside suggest that ALAM has an active site with at least six subsites. The best fitting of kinetic data to theoretical curves is obtained using a model where one laminarin molecule binds first to a high-affinity accessory site, causing active site exposure, followed by the transference of the substrate to the active site. The two-binding-site model is supported by results from chemical modifications of amino acid residues and by ALAM action in MUbetaGlu plus laminarin. Low laminarin concentrations increase the modification of His, Tyr and Asp or Glu residues and MUbetaGlu hydrolysis, whereas high concentrations abolish modification and inhibit MUbetaGlu hydrolysis. Our data indicate that processivity results from consecutive transferences of substrate between accessory and active site and that substrate inhibition arises when both sites are occupied by substrate molecules abolishing processivity.
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Affiliation(s)
- Fernando A Genta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, C.P. 26077, 05513-970, São Paulo, Brazil
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24
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Martens-Uzunova E, Zandleven J, Benen J, Awad H, Kools H, Beldman G, Voragen A, Van Den Berg J, Schaap P. A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation. Biochem J 2006; 400:43-52. [PMID: 16822232 PMCID: PMC1635439 DOI: 10.1042/bj20060703] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The fungus Aspergillus niger is an industrial producer of pectin-degrading enzymes. The recent solving of the genomic sequence of A. niger allowed an inventory of the entire genome of the fungus for potential carbohydrate-degrading enzymes. By applying bioinformatics tools, 12 new genes, putatively encoding family 28 glycoside hydrolases, were identified. Seven of the newly discovered genes form a new gene group, which we show to encode exoacting pectinolytic glycoside hydrolases. This group includes four exo-polygalacturonan hydrolases (PGAX, PGXA, PGXB and PGXC) and three putative exo-rhamnogalacturonan hydrolases (RGXA, RGXB and RGXC). Biochemical identification using polygalacturonic acid and xylogalacturonan as substrates demonstrated that indeed PGXB and PGXC act as exo-polygalacturonases, whereas PGXA acts as an exo-xylogalacturonan hydrolase. The expression levels of all 21 genes were assessed by microarray analysis. The results from the present study demonstrate that exo-acting glycoside hydrolases play a prominent role in pectin degradation.
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Affiliation(s)
- Elena S. Martens-Uzunova
- *Section Fungal Genomics, Laboratory of Microbiology, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Joris S. Zandleven
- †Laboratory of Food Chemistry, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Jaques A. E. Benen
- *Section Fungal Genomics, Laboratory of Microbiology, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Hanem Awad
- †Laboratory of Food Chemistry, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Harrie J. Kools
- *Section Fungal Genomics, Laboratory of Microbiology, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Gerrit Beldman
- †Laboratory of Food Chemistry, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Alphons G. J. Voragen
- †Laboratory of Food Chemistry, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Johan A. Van Den Berg
- *Section Fungal Genomics, Laboratory of Microbiology, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Peter J. Schaap
- *Section Fungal Genomics, Laboratory of Microbiology, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
- To whom correspondence should be addressed (email )
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25
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Hunt JJ, Cameron R, Williams MAK. On the simulation of enzymatic digest patterns: The fragmentation of oligomeric and polymeric galacturonides by endo-polygalacturonase II. Biochim Biophys Acta Gen Subj 2006; 1760:1696-703. [PMID: 17029794 DOI: 10.1016/j.bbagen.2006.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 08/08/2006] [Accepted: 08/19/2006] [Indexed: 11/24/2022]
Abstract
A simulation methodology for predicting the time-course of enzymatic digestions is described. The model is based solely on the enzyme's subsite architecture and concomitant binding energies. This allows subsite binding energies to be used to predict the evolution of the relative amounts of different products during the digestion of arbitrary mixtures of oligomeric or polymeric substrates. The methodology has been specifically demonstrated by studying the fragmentation of a population of oligogalacturonides of varying degrees of polymerization, when digested by endo-polygalacturonase II (endo-PG II) from Aspergillus niger.
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Affiliation(s)
- Jonathan J Hunt
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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26
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Grün CH, Dekker N, Nieuwland AA, Klis FM, Kamerling JP, Vliegenthart JFG, Hochstenbach F. Mechanism of action of theendo-(1 → 3)-α-glucanase MutAp from the mycoparasitic fungusTrichoderma harzianum. FEBS Lett 2006; 580:3780-6. [PMID: 16780840 DOI: 10.1016/j.febslet.2006.05.062] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 05/25/2006] [Accepted: 05/30/2006] [Indexed: 11/26/2022]
Abstract
(1-->3)-alpha-glucanases catalyze the hydrolysis of fungal cell wall (1-->3)-alpha-glucan, and function during cell division of yeasts containing this cell wall component or act in mycoparasitic processes. Here, we characterize the mechanism of action of the (1-->3)-alpha-glucanase MutAp from the mycoparasitic fungus Trichoderma harzianum. We observed that MutAp releases predominantly beta-glucose upon hydrolysis of crystalline (1-->3)-alpha-glucan, indicating inversion of the anomeric configuration. After having identified (1-->3)-alpha-glucan tetrasaccharide as the minimal substrate for MutAp, we showed that reduced (1-->3)-alpha-glucan pentasaccharide is cleaved into a trisaccharide and a reduced disaccharide, demonstrating that MutAp displays endo-hydrolytic activity. We propose a model for the catalytic mechanism of MutAp, whereby the enzyme breaks an intrachain glycosidic linkage of (1-->3)-alpha-glucan, and then continues its hydrolysis towards the non-reducing end by releasing beta-glucose residues in a processive manner.
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Affiliation(s)
- Christian H Grün
- Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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27
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Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ. Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc Natl Acad Sci U S A 2005; 102:2697-702. [PMID: 15708971 PMCID: PMC549454 DOI: 10.1073/pnas.0500051102] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Indexed: 11/18/2022] Open
Abstract
Enzymes acting on polymeric substrates are frequently classified as exo or endo, reflecting their preference for, or ignorance of, polymer chain ends. Most biotechnological applications, especially in the field of polysaccharide degradation, require either endo- or exo-acting hydrolases, or they harness the essential synergy between these two modes of action. Here, we have used genomic data in tandem with structure to modify, radically, the chain-end specificity of the Cellvibrio japonicus exo-arabinanase CjArb43A. The structure of Bacillus subtilis endo-arabinanase 43A (BsArb43A) in harness with chain-end recognition kinetics of CjArb43A directed a rational design approach that led to the conversion of the Cellvibrio enzyme from an exo to an endo mode of action. One of the exo-acting mutants, D35L/Q316A, displays similar activity to WT CjArb43A and the removal of the steric block mediated by the side chains of Gln-316 and Asp-53 at the -3 subsite confers its capacity to attack internal glycoside bonds. This study provides a template for the production of tailored industrial catalysts. The introduction of subtle changes informed by comparative 3D structural and genomic data can lead to fundamental changes in the mode of action of these enzymes.
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Affiliation(s)
- Mark R Proctor
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kindgom
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28
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Michel G, Helbert W, Kahn R, Dideberg O, Kloareg B. The Structural Bases of the Processive Degradation of ι-Carrageenan, a Main Cell Wall Polysaccharide of Red Algae. J Mol Biol 2003; 334:421-33. [PMID: 14623184 DOI: 10.1016/j.jmb.2003.09.056] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. iota-Carrageenases, which constitute family 82 of glycoside hydrolases, fold into a right-handed beta-helix. Here, the structure of Alteromonas fortis iota-carrageenase bound to iota-carrageenan fragments was solved at 2.0A resolution (PDB 1KTW). The enzyme holds a iota-carrageenan tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites -3, -4), thus providing the first direct determination of a 3D structure of iota-carrageenan. Electrostatic interactions between basic protein residues and the sulfate substituents of the polysaccharide chain dominate iota-carrageenan recognition. Glu245 and Asp247 are the proton donor and the base catalyst, respectively. C-terminal domain A, which was highly flexible in the native enzyme structure, adopts a alpha/beta-fold, also found in DNA/RNA-binding domains. In the substrate-enzyme complex, this polyanion-binding module shifts toward the beta-helix groove, forming a tunnel. Thus, from an open conformation which allows for the initial endo-attack of iota-carrageenan chains, the enzyme switches to a closed-tunnel form, consistent with its highly processive character, as seen from the electron-microscopy analysis of the degradation of iota-carrageenan fibers.
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Affiliation(s)
- Gurvan Michel
- Végétaux Marins et Biomolécules, UMR 7139 (CNRS/UPMC/Laboratories Goëmar), Station Biologique de Roscoff, Place Georges Teissier, BP 74, 29682 Roscoff Cedex, Brittany,
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29
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van Pouderoyen G, Snijder HJ, Benen JAE, Dijkstra BW. Structural insights into the processivity of endopolygalacturonase I fromAspergillus niger. FEBS Lett 2003; 554:462-6. [PMID: 14623112 DOI: 10.1016/s0014-5793(03)01221-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Endopolygalacturonase I is a processive enzyme, while the 60% sequence identical endopolygalacturonase II is not. The 1.70 A resolution crystal structure of endopolygalacturonase I reveals a narrowed substrate binding cleft. In addition, Arg96, a residue in this cleft previously shown to be critical for processivity, interacts with the substrate mimics glycerol and sulfate in several well-defined conformations in the six molecules in the asymmetric unit. From this we conclude that both Arg96 and the narrowed substrate binding cleft contribute to retaining the substrate while it moves through the active site after a cleavage event has occurred.
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Affiliation(s)
- Gertie van Pouderoyen
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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30
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Hirvonen M, Papageorgiou AC. Crystal structure of a family 45 endoglucanase from Melanocarpus albomyces: mechanistic implications based on the free and cellobiose-bound forms. J Mol Biol 2003; 329:403-10. [PMID: 12767825 DOI: 10.1016/s0022-2836(03)00467-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Cellulose, a polysaccharide of beta-1,4-linked D-glucosyl units, is the major component of plant cell walls and one of the most abundant biopolymers in nature. Cellulases (cellobiohydrolases and endoglucanases) are enzymes that catalyse the hydrolysis of cellulose to smaller oligosaccharides, a process of paramount importance in biotechnology. The thermophilic fungus Melanocarpus albomyces produces a 20 kDa endoglucanase known as 20K-cellulase that has been found particularly useful in the textile industry. The crystal structures of free 20K-cellulase and its complex with cellobiose have been determined at 2.0 A resolution. The enzyme, classified into the glycoside hydrolase family 45, exhibits the characteristic six-stranded beta-barrel found before in Humicola insolens endoglucanase V structure. However, the active site in the 20K-cellulase shows a closing of approximately 2.5-3.5A while a mobile loop identified previously in Humicola insolens endoglucanase V and implicated in the catalytic mechanism is well-defined in 20K-cellulase. In addition, the crystal structure of the cellobiose complex shows a shift in the cellobiose position at the substrate-binding cleft. It is therefore proposed that these alterations may reflect differences in the binding mechanism and catalytic action of the enzyme.
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Affiliation(s)
- Mika Hirvonen
- Turku Centre for Biotechnology, University of Turku, P.O. Box 123, Turku 20521, Finland
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Cotton P, Rascle C, Fevre M. Characterization of PG2, an early endoPG produced by Sclerotinia sclerotiorum, expressed in yeast. FEMS Microbiol Lett 2002; 213:239-44. [PMID: 12167544 DOI: 10.1111/j.1574-6968.2002.tb11312.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Sclerotinia sclerotiorum, a plant pathogenic ascomycete, contains a neutral endopolygalacturonase (endoPG) subfamily of genes that was previously isolated. We report here that pg2, a member of this subfamily, is early and strongly expressed during the first steps of pathogenesis of sunflower cotyledons. The corresponding protein, PG2, was produced in the heterologous Kluyveromyces lactis system and purified. Characterization of the recombinant enzyme revealed a narrow pH activity curve with an optimal pH of 4.5. Hydrolysis of polygalacturonic acid by PG2 resulted in the accumulation of oligomers ranging from 2- to 9-mer. This degradation profile indicates a random attack on the polymer and demonstrates an endo-mode of action. These results provide evidence that pg2 contributes to the infection process during the early phase of host colonization.
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Affiliation(s)
- Pascale Cotton
- Laboratoire de Biologie Cellulaire Fongique, UMR 5122 CNRS INSA UCB, Bat Lwoff, 10 rue Dubois, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France.
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