101
|
Improving extracellular production of Serratia marcescens lytic polysaccharide monooxygenase CBP21 and Aeromonas veronii B565 chitinase Chi92 in Escherichia coli and their synergism. AMB Express 2017; 7:170. [PMID: 28884316 PMCID: PMC5589716 DOI: 10.1186/s13568-017-0470-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) can oxidize recalcitrant polysaccharides and boost the conversion of the second most abundant polysaccharide chitin by chitinase. In this study, we aimed to achieve the efficient extracellular production of Serratia marcescens LPMO CBP21 and Aeromonas veronii B565 chitinase Chi92 by Escherichia coli. Twelve signal peptides reported with high secretion efficiency were screened to assess the extracellular production efficiency of CBP21 and Chi92, with glycine used as a medium supplement. The results showed that PelB was the most productive signal peptide for the extracellular production of CBP21 and Chi92 in E. coli. Furthermore, CBP21 facilitated the degradation of the three chitin substrates (colloidal chitin, β-chitin, and α-chitin) by Chi92. This study will be valuable for the industrial production and application of the two enzymes for chitin degradation.
Collapse
|
102
|
Veliz EA, Martínez-Hidalgo P, Hirsch AM. Chitinase-producing bacteria and their role in biocontrol. AIMS Microbiol 2017; 3:689-705. [PMID: 31294182 PMCID: PMC6604996 DOI: 10.3934/microbiol.2017.3.689] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/19/2017] [Indexed: 11/30/2022] Open
Abstract
Chitin is an important component of the exteriors of insects and fungi. Upon degradation of chitin by a number of organisms, severe damage and even death may occur in pathogens and pests whose external surfaces contain this polymer. Currently, chemical fungicides and insecticides are the major means of controlling these disease-causing agents. However, due to the potential harm that these chemicals cause to the environment and to human and animal health, new strategies are being developed to replace or reduce the use of fungal- and pest-killing compounds in agriculture. In this context, chitinolytic microorganisms are likely to play an important role as biocontrol agents and pathogen antagonists and may also function in the control of postharvest rot. In this review, we discuss the literature concerning chitin and the basic knowledge of chitin-degrading enzymes, and also describe the biocontrol effects of chitinolytic microorganisms and their potential use as more sustainable pesticides and fungicides in the field.
Collapse
Affiliation(s)
- Esteban A Veliz
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
| | | | - Ann M Hirsch
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
| |
Collapse
|
103
|
A novel expression system for lytic polysaccharide monooxygenases. Carbohydr Res 2017; 448:212-219. [DOI: 10.1016/j.carres.2017.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/13/2017] [Accepted: 02/13/2017] [Indexed: 01/12/2023]
|
104
|
Valenzuela SV, Ferreres G, Margalef G, Pastor FJ. Fast purification method of functional LPMOs from Streptomyces ambofaciens by affinity adsorption. Carbohydr Res 2017; 448:205-211. [DOI: 10.1016/j.carres.2017.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 01/03/2023]
|
105
|
Physiological and Molecular Understanding of Bacterial Polysaccharide Monooxygenases. Microbiol Mol Biol Rev 2017; 81:81/3/e00015-17. [PMID: 28659491 DOI: 10.1128/mmbr.00015-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria have long been known to secrete enzymes that degrade cellulose and chitin. The degradation of these two polymers predominantly involves two enzyme families that work synergistically with one another: glycoside hydrolases (GHs) and polysaccharide monooxygenases (PMOs). Although bacterial PMOs are a relatively recent addition to the known biopolymer degradation machinery, there is an extensive amount of literature implicating PMO in numerous physiological roles. This review focuses on these diverse and physiological aspects of bacterial PMOs, including facilitating endosymbiosis, conferring a nutritional advantage, and enhancing virulence in pathogenic organisms. We also discuss the correlation between the presence of PMOs and bacterial lifestyle and speculate on the advantages conferred by PMOs under these conditions. In addition, the molecular aspects of bacterial PMOs, as well as the mechanisms regulating PMO expression and the function of additional domains associated with PMOs, are described. We anticipate that increasing research efforts in this field will continue to expand our understanding of the molecular and physiological roles of bacterial PMOs.
Collapse
|
106
|
Kashyap P, Deswal R. A novel class I Chitinase from Hippophae rhamnoides: Indications for participating in ICE-CBF cold stress signaling pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:62-70. [PMID: 28483054 DOI: 10.1016/j.plantsci.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 05/23/2023]
Abstract
Plant chitinases are the members of PR (Pathogenesis related) proteins family and protect plants from biotic and abiotic stress. A novel chitinase HrCHI1 (Accession number JQ289153) of 954bp ORF encoding 317 amino acids protein was cloned, expressed and characterized from seabuckthorn, a cold/freeze tolerant shrub. The 3D structure (predicted with I-TASSER server) showed highest homology with Oryza sativa class I chitinase (PDB 2dkvA). Putative promoter region (obtained by genome walking) showed GCC box, E-boxes, the binding site for bHLH proteins and DRE elements, the CBF (C-repeat binding factor) binding site besides TATA and CAAT boxes. The gel shift assay with the nuclear extract indicated that the HrCHI1 might be participating in CBF/ERF dependent cold stress signaling pathway. The quantitative transcript profiling supported this observation as cold induced expression of HrCBF peaked earlier (at 1h) while HrCHI1 peaked latter (after 3h) indicating HrCHI1 expression might be induced by HrCBF. Further, HrCHI1 expression was methyl jasmonate (MeJa) dependent and salicylic acid (SA) independent. HrCHI1 was expressed in E. coli and purified using chitin affinity chromatography. It showed 512U/mg chitinase hydrolytic activity and resolved as a 34kDa spot with a slightly basic pI (8.5) on a 2-D gel. The E. coli cells containing recombinant chitinase showed higher rate of growth in cold in comparison with the cells containing the empty vector. In conclusion, we have isolated and characterized a cold responsive basic class I chitinase which is regulated by MeJa and seems to be functioning via CBF/ERF dependent cold stress signaling pathway.
Collapse
Affiliation(s)
- Prakriti Kashyap
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, India
| | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, India.
| |
Collapse
|
107
|
Structural diversity of lytic polysaccharide monooxygenases. Curr Opin Struct Biol 2017; 44:67-76. [DOI: 10.1016/j.sbi.2016.12.012] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/19/2016] [Accepted: 12/23/2016] [Indexed: 11/21/2022]
|
108
|
Danneels B, Tanghe M, Joosten HJ, Gundinger T, Spadiut O, Stals I, Desmet T. A quantitative indicator diagram for lytic polysaccharide monooxygenases reveals the role of aromatic surface residues in HjLPMO9A regioselectivity. PLoS One 2017; 12:e0178446. [PMID: 28562644 PMCID: PMC5451062 DOI: 10.1371/journal.pone.0178446] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 05/12/2017] [Indexed: 12/12/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have changed our understanding of lignocellulosic degradation dramatically over the last years. These metalloproteins catalyze oxidative cleavage of recalcitrant polysaccharides and can act on the C1 and/or C4 position of glycosidic bonds. Structural data have led to several hypotheses, but we are still a long way from reaching complete understanding of the factors that determine their divergent regioselectivity. Site-directed mutagenesis enables the investigation of structure-function relationship in enzymes and will be of major importance in unraveling this intriguing matter. In this context, it is crucial to have an enzyme assay or screening approach with a direct correlation with the desired functionality. LPMOs render this search extra challenging due to their insoluble substrates, complex pattern of reaction products and lack of synthetic standards of most oxidized products. Here, we describe a regioselectivity indicator diagram based on the time-course of only 2 HPAEC-PAD signals. The diagram was successfully used to confirm the hypothesis that aromatic surface residues influence the C1/C4 oxidation ratio in Hypocrea jecorina LPMO9A. Consequently, the diagram should become a valuable tool in the search towards better understanding and engineering of regioselectivity in LPMOs.
Collapse
Affiliation(s)
- Barbara Danneels
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Magali Tanghe
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Thomas Gundinger
- Research Division Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Ingeborg Stals
- Industrial Catalysis and Adsorption Technology (INCAT), Faculty of Engineering and Architecture, University of Ghent, Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- * E-mail:
| |
Collapse
|
109
|
Ezeilo UR, Zakaria II, Huyop F, Wahab RA. Enzymatic breakdown of lignocellulosic biomass: the role of glycosyl hydrolases and lytic polysaccharide monooxygenases. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1330124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
110
|
Jones TH, McClelland EE, McFeeters H, McFeeters RL. Novel Antifungal Activity for the Lectin Scytovirin: Inhibition of Cryptococcus neoformans and Cryptococcus gattii. Front Microbiol 2017; 8:755. [PMID: 28536555 PMCID: PMC5422485 DOI: 10.3389/fmicb.2017.00755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/12/2017] [Indexed: 11/13/2022] Open
Abstract
Pathogenic cryptococci are encapsulated yeast that can cause severe meningoencephalitis. Existing therapeutic options are dated and there is a growing need for new alternative antifungal agents for these fungi. Here we report novel inhibition of pathogenic cryptococci by the antimicrobial lectin Scytovirin. Inhibition was most potent against Cryptococcus neoformans var neoformans and C. gattii, with MFC values of 500 nM. Scytovirin binding was localized to the cell wall and shown to affect capsule size and release. No effect was observed on melanization or with cells grown in the presence the cell wall stressor Congo red. Synergy with existing antifungals was indicated, most strongly for amphotericin B. Overall, Scytovirin serves as a much needed new avenue for anticryptococcal development.
Collapse
Affiliation(s)
- Tyler H Jones
- Department of Chemistry, University of Alabama in Huntsville, HuntsvilleAL, USA
| | - Erin E McClelland
- Department of Biology, Middle Tennessee State University, MurfreesboroTN, USA
| | - Hana McFeeters
- Department of Chemistry, University of Alabama in Huntsville, HuntsvilleAL, USA
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in Huntsville, HuntsvilleAL, USA
| |
Collapse
|
111
|
Development of enzyme cocktails for complete saccharification of chitin using mono-component enzymes from Serratia marcescens. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.02.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
112
|
Genomic, proteomic and biochemical analysis of the chitinolytic machinery of Serratia marcescens BJL200. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:414-421. [DOI: 10.1016/j.bbapap.2017.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 11/23/2022]
|
113
|
Frandsen KEH, Poulsen JCN, Tovborg M, Johansen KS, Lo Leggio L. Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:64-76. [PMID: 28045386 DOI: 10.1107/s2059798316019641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/08/2016] [Indexed: 01/09/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 Å resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 Å. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.
Collapse
Affiliation(s)
- Kristian E H Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | | | | | - Katja S Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, Frederiksberg C, 1958 Copenhagen, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| |
Collapse
|
114
|
Kruer-Zerhusen N, Alahuhta M, Lunin VV, Himmel ME, Bomble YJ, Wilson DB. Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:243. [PMID: 29213309 PMCID: PMC5708082 DOI: 10.1186/s13068-017-0925-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/06/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Auxiliary activity (AA) enzymes are produced by numerous bacterial and fungal species to assist in the degradation of biomass. These enzymes are abundant but have yet to be fully characterized. Here, we report the X-ray structure of Thermobifida fusca AA10A (TfAA10A), investigate mutational characterization of key surface residues near its active site, and explore the importance of the various domains of Thermobifida fusca AA10B (TfAA10B). The structure of TfAA10A is similar to other bacterial LPMOs (lytic polysaccharide monooxygenases), including signs of photo-reduction and a distorted active site, with mixed features showing both type I and II copper coordination. The point mutation experiments of TfAA10A show that Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for the binding of substrate, but that the X1 module does not affect binding or activity. RESULTS In TfAA10A, Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for substrate binding, but that the X1 module does not affect binding or activity. The structure of TfAA10A is similar to other bacterial lytic polysaccharide monooxygenases with mixed features showing both type I and II copper coordination. CONCLUSIONS The role of LPMOs and the variability of abundance in genomes are not fully explored. LPMOs likely perform initial attacks into crystalline cellulose to allow larger processive cellulases to bind and attack, but the precise nature of their synergistic behavior remains to be definitively characterized.
Collapse
Affiliation(s)
| | | | | | | | | | - David B. Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY USA
| |
Collapse
|
115
|
Loose JSM, Forsberg Z, Kracher D, Scheiblbrandner S, Ludwig R, Eijsink VGH, Vaaje‐Kolstad G. Activation of bacterial lytic polysaccharide monooxygenases with cellobiose dehydrogenase. Protein Sci 2016; 25:2175-2186. [PMID: 27643617 PMCID: PMC5119556 DOI: 10.1002/pro.3043] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 11/10/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) represent a recent addition to the carbohydrate-active enzymes and are classified as auxiliary activity (AA) families 9, 10, 11, and 13. LPMOs are crucial for effective degradation of recalcitrant polysaccharides like cellulose or chitin. These enzymes are copper-dependent and utilize a redox mechanism to cleave glycosidic bonds that is dependent on molecular oxygen and an external electron donor. The electrons can be provided by various sources, such as chemical compounds (e.g., ascorbate) or by enzymes (e.g., cellobiose dehydrogenases, CDHs, from fungi). Here, we demonstrate that a fungal CDH from Myriococcum thermophilum (MtCDH), can act as an electron donor for bacterial family AA10 LPMOs. We show that employing an enzyme as electron donor is advantageous since this enables a kinetically controlled supply of electrons to the LPMO. The rate of chitin oxidation by CBP21 was equal to that of cosubstrate (lactose) oxidation by MtCDH, verifying the usage of two electrons in the LPMO catalytic mechanism. Furthermore, since lactose oxidation correlates directly with the rate of LPMO catalysis, a method for indirect determination of LPMO activity is implicated. Finally, the one electron reduction of the CBP21 active site copper by MtCDH was determined to be substantially faster than chitin oxidation by the LPMO. Overall, MtCDH seems to be a universal electron donor for both bacterial and fungal LPMOs, indicating that their electron transfer mechanisms are similar.
Collapse
Affiliation(s)
- Jennifer S. M. Loose
- Department of ChemistryBiotechnology and Food Science, Norwegian University of Life SciencesNO‐1430 ÅsNorway
| | - Zarah Forsberg
- Department of ChemistryBiotechnology and Food Science, Norwegian University of Life SciencesNO‐1430 ÅsNorway
| | - Daniel Kracher
- Department of Food Science and Technology, Food Biotechnology LaboratoryUniversity of Natural Resources and Life SciencesViennaAustria
| | - Stefan Scheiblbrandner
- Department of Food Science and Technology, Food Biotechnology LaboratoryUniversity of Natural Resources and Life SciencesViennaAustria
| | - Roland Ludwig
- Department of Food Science and Technology, Food Biotechnology LaboratoryUniversity of Natural Resources and Life SciencesViennaAustria
| | - Vincent G. H. Eijsink
- Department of ChemistryBiotechnology and Food Science, Norwegian University of Life SciencesNO‐1430 ÅsNorway
| | - Gustav Vaaje‐Kolstad
- Department of ChemistryBiotechnology and Food Science, Norwegian University of Life SciencesNO‐1430 ÅsNorway
| |
Collapse
|
116
|
Suginta W, Sirimontree P, Sritho N, Ohnuma T, Fukamizo T. The chitin-binding domain of a GH-18 chitinase from Vibrio harveyi is crucial for chitin-chitinase interactions. Int J Biol Macromol 2016; 93:1111-1117. [DOI: 10.1016/j.ijbiomac.2016.09.066] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 09/06/2016] [Accepted: 09/18/2016] [Indexed: 11/26/2022]
|
117
|
Yu MJ, Yoon SH, Kim YW. Overproduction and characterization of a lytic polysaccharide monooxygenase in Bacillus subtilis using an assay based on ascorbate consumption. Enzyme Microb Technol 2016; 93-94:150-156. [DOI: 10.1016/j.enzmictec.2016.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/24/2016] [Indexed: 12/17/2022]
|
118
|
Frandsen KEH, Lo Leggio L. Lytic polysaccharide monooxygenases: a crystallographer's view on a new class of biomass-degrading enzymes. IUCRJ 2016; 3:448-467. [PMID: 27840684 PMCID: PMC5094447 DOI: 10.1107/s2052252516014147] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/05/2016] [Indexed: 05/05/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are a new class of microbial copper enzymes involved in the degradation of recalcitrant polysaccharides. They have only been discovered and characterized in the last 5-10 years and have stimulated strong interest both in biotechnology and in bioinorganic chemistry. In biotechnology, the hope is that these enzymes will finally help to make enzymatic biomass conversion, especially of lignocellulosic plant waste, economically attractive. Here, the role of LPMOs is likely to be in attacking bonds that are not accessible to other enzymes. LPMOs have attracted enormous interest since their discovery. The emphasis in this review is on the past and present contribution of crystallographic studies as a guide to functional understanding, with a final look towards the future.
Collapse
Affiliation(s)
- Kristian E. H. Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| |
Collapse
|
119
|
Abstract
The recent discovery of copper-dependent lytic polysaccharide mono-oxygenases (LPMOs) has opened up a vast area of research covering several fields of application. The biotech company Novozymes A/S holds patents on the use of these enzymes for the conversion of steam-pre-treated plant residues such as straw to free sugars. These patents predate the correct classification of LPMOs and the striking synergistic effect of fungal LPMOs when combined with canonical cellulases was discovered when fractions of fungal secretomes were evaluated in industrially relevant enzyme performance assays. Today, LPMOs are a central component in the Cellic CTec enzyme products which are used in several large-scale plants for the industrial production of lignocellulosic ethanol. LPMOs are characterized by an N-terminal histidine residue which, together with an internal histidine and a tyrosine residue, co-ordinates a single copper atom in a so-called histidine brace. The mechanism by which oxygen binds to the reduced copper atom has been reported and the general mechanism of copper-oxygen-mediated activation of carbon is being investigated in the light of these discoveries. LPMOs are widespread in both the fungal and the bacterial kingdoms, although the range of action of these enzymes remains to be elucidated. However, based on the high abundance of LPMOs expressed by microbes involved in the decomposition of organic matter, the importance of LPMOs in the natural carbon-cycle is predicted to be significant. In addition, it has been suggested that LPMOs play a role in the pathology of infectious diseases such as cholera and to thus be relevant in the field of medicine.
Collapse
|
120
|
Abstract
Complex carbohydrates are ubiquitous in all kingdoms of life. As major components of the plant cell wall they constitute both a rich renewable carbon source for biotechnological transformation into fuels, chemicals and materials, and also form an important energy source as part of a healthy human diet. In both contexts, there has been significant, sustained interest in understanding how microbes transform these substrates. Classical perspectives of microbial polysaccharide degradation are currently being augmented by recent advances in the discovery of lytic polysaccharide monooxygenases (LPMOs) and polysaccharide utilization loci (PULs). Fundamental discoveries in carbohydrate enzymology are both advancing biological understanding, as well as informing applications in industrial biomass conversion and modulation of the human gut microbiota to mediate health benefits.
Collapse
|
121
|
Corrêa TLR, dos Santos LV, Pereira GAG. AA9 and AA10: from enigmatic to essential enzymes. Appl Microbiol Biotechnol 2016; 100:9-16. [PMID: 26476647 DOI: 10.1007/s00253-015-7040-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 12/15/2022]
Abstract
The lignocellulosic biomass, comprised mainly of cellulose, hemicellulose, and lignin, is a strong competitor for petroleum to obtain fuels and other products because of its renewable nature, low cost, and non-competitiveness with food production when obtained from agricultural waste. Due to its recalcitrance, lignocellulosic material requires an arsenal of enzymes for its deconstruction and the consequent release of fermentable sugars. In this context, enzymes currently classified as auxiliary activity 9 (AA9/formerly GH61) and 10 (AA10/formerly CBM 33) or lytic polysaccharide monooxygenases (LPMO) have emerged as cellulase boosting enzymes. AA9 and AA10 are the new paradigm for deconstruction of lignocellulosic biomass by enhancing the activity and decreasing the loading of classical enzymes to the reaction and, consequently, reducing costs of the hydrolysis step in the second-generation ethanol production chain. In view of that disclosed above, the goal of this work is to review experimental data that supports the relevance of AA9 and AA10 for the biomass deconstruction field.
Collapse
|
122
|
Brown AH, Walsh TR. Elucidating the influence of polymorph-dependent interfacial solvent structuring at chitin surfaces. Carbohydr Polym 2016; 151:916-925. [DOI: 10.1016/j.carbpol.2016.05.116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/28/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022]
|
123
|
Labroussaa F, Zeilinger AR, Almeida RPP. Blocking the Transmission of a Noncirculative Vector-Borne Plant Pathogenic Bacterium. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:535-544. [PMID: 27049684 DOI: 10.1094/mpmi-02-16-0032-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The successful control of insect-borne plant pathogens is often difficult to achieve due to the ecologically complex interactions among pathogens, vectors, and host plants. Disease management often relies on pesticides and other approaches that have limited long-term sustainability. To add a new tool to control vector-borne diseases, we attempted to block the transmission of a bacterial insect-transmitted pathogen, the bacterium Xylella fastidiosa, by disrupting bacteria-insect vector interactions. X. fastidiosa is known to attach to and colonize the cuticular surface of the mouthparts of vectors; a set of recombinant peptides was generated and the chemical affinities of these peptides to chitin and related carbohydrates was assayed in vitro. Two candidates, the X. fastidiosa hypothetical protein PD1764 and an N-terminal region of the hemagglutinin-like protein B (HxfB) showed affinity for these substrates. These proteins were provided to vectors via an artificial diet system in which insects acquire X. fastidiosa, followed by an inoculation access period on plants under greenhouse conditions. Both PD1764 and HxfAD1-3 significantly blocked transmission. Furthermore, bacterial populations within insects over a 10-day period demonstrated that these peptides inhibited cell adhesion to vectors but not bacterial multiplication, indicating that the mode of action of these peptides is restricted to limiting cell adhesion to insects, likely via competition for adhesion sites. These results open a new venue in the search for sustainable disease-control strategies that are pathogen specific and may have limited nontarget effects.
Collapse
Affiliation(s)
- Fabien Labroussaa
- Department of Environmental Science, Policy and Management, 130 Mulford Hall, University of California, Berkeley, CA 94720, U.S.A
| | - Adam R Zeilinger
- Department of Environmental Science, Policy and Management, 130 Mulford Hall, University of California, Berkeley, CA 94720, U.S.A
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, 130 Mulford Hall, University of California, Berkeley, CA 94720, U.S.A
| |
Collapse
|
124
|
Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase. Proc Natl Acad Sci U S A 2016; 113:5922-7. [PMID: 27152023 DOI: 10.1073/pnas.1602566113] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds using molecular oxygen and an external electron donor. We have used NMR and isothermal titration calorimetry (ITC) to study the interactions of a broad-specificity fungal LPMO, NcLPMO9C, with various substrates and with cellobiose dehydrogenase (CDH), a known natural supplier of electrons. The NMR studies revealed interactions with cellohexaose that center around the copper site. NMR studies with xyloglucans, i.e., branched β-glucans, showed an extended binding surface compared with cellohexaose, whereas ITC experiments showed slightly higher affinity and a different thermodynamic signature of binding. The ITC data also showed that although the copper ion alone hardly contributes to affinity, substrate binding is enhanced for metal-loaded enzymes that are supplied with cyanide, a mimic of O2 (-) Studies with CDH and its isolated heme b cytochrome domain unambiguously showed that the cytochrome domain of CDH interacts with the copper site of the LPMO and that substrate binding precludes interaction with CDH. Apart from providing insights into enzyme-substrate interactions in LPMOs, the present observations shed new light on possible mechanisms for electron supply during LPMO action.
Collapse
|
125
|
Dong Z, Zhang W, Zhang Y, Zhang X, Zhao P, Xia Q. Identification and Characterization of Novel Chitin-Binding Proteins from the Larval Cuticle of Silkworm, Bombyx mori. J Proteome Res 2016; 15:1435-45. [DOI: 10.1021/acs.jproteome.5b00943] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Zhaoming Dong
- State Key Laboratory
of Silkworm Genome Biology, ‡Chongqing Engineering and Technology
Research Center for Novel Silk Materials, and §College of Biotechnology, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400716, China
| | - Weiwei Zhang
- State Key Laboratory
of Silkworm Genome Biology, ‡Chongqing Engineering and Technology
Research Center for Novel Silk Materials, and §College of Biotechnology, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400716, China
| | - Yan Zhang
- State Key Laboratory
of Silkworm Genome Biology, ‡Chongqing Engineering and Technology
Research Center for Novel Silk Materials, and §College of Biotechnology, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400716, China
| | - Xiaolu Zhang
- State Key Laboratory
of Silkworm Genome Biology, ‡Chongqing Engineering and Technology
Research Center for Novel Silk Materials, and §College of Biotechnology, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400716, China
| | - Ping Zhao
- State Key Laboratory
of Silkworm Genome Biology, ‡Chongqing Engineering and Technology
Research Center for Novel Silk Materials, and §College of Biotechnology, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory
of Silkworm Genome Biology, ‡Chongqing Engineering and Technology
Research Center for Novel Silk Materials, and §College of Biotechnology, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400716, China
| |
Collapse
|
126
|
Walton PH, Davies GJ. On the catalytic mechanisms of lytic polysaccharide monooxygenases. Curr Opin Chem Biol 2016; 31:195-207. [PMID: 27094791 DOI: 10.1016/j.cbpa.2016.04.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/03/2016] [Accepted: 04/05/2016] [Indexed: 12/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are recently discovered copper-containing oxygenases. LPMOs oxidise recalcitrant polysaccharides such as chitin and cellulose, thereby making these substrates more tractable to canonical chitinase or cellulase action. As such, LPMOs are attracting much attention not only for their capacity to greatly increase the efficiency of production of cellulosic-based biofuels, but also for the new questions they pose about the mechanisms of biological oxidation of recalcitrant substrates. This review draws together the current thinking on the catalytic mechanisms of LPMOs and other copper catalysed oxygenations and provides a blueprint for further investigation into the mechanisms of action of these intriguing enzymes.
Collapse
Affiliation(s)
- Paul H Walton
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| |
Collapse
|
127
|
Chaplin AK, Wilson MT, Hough MA, Svistunenko DA, Hemsworth GR, Walton PH, Vijgenboom E, Worrall JAR. Heterogeneity in the Histidine-brace Copper Coordination Sphere in Auxiliary Activity Family 10 (AA10) Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:12838-12850. [PMID: 27129229 DOI: 10.1074/jbc.m116.722447] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 12/23/2022] Open
Abstract
Copper-dependent lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively deconstruct polysaccharides. The active site copper in LPMOs is coordinated by a histidine-brace. This utilizes the amino group and side chain of the N-terminal His residue with the side chain of a second His residue to create a T-shaped arrangement of nitrogen ligands. We report a structural, kinetic, and thermodynamic appraisal of copper binding to the histidine-brace in an auxiliary activity family 10 (AA10) LPMO from Streptomyces lividans (SliLPMO10E). Unexpectedly, we discovered the existence of two apo-SliLPMO10E species in solution that can each bind copper at a single site with distinct kinetic and thermodynamic (exothermic and endothermic) properties. The experimental EPR spectrum of copper-bound SliLPMO10E requires the simulation of two different line shapes, implying two different copper-bound species, indicative of three and two nitrogen ligands coordinating the copper. Amino group coordination was probed through the creation of an N-terminal extension variant (SliLPMO10E-Ext). The kinetics and thermodynamics of copper binding to SliLPMO10E-Ext are in accord with copper binding to one of the apo-forms in the wild-type protein, suggesting that amino group coordination is absent in the two-nitrogen coordinate form of SliLPMO10E. Copper binding to SliLPMO10B was also investigated, and again it revealed the presence of two apo-forms with kinetics and stoichiometry of copper binding identical to that of SliLPMO10E. Our findings highlight that heterogeneity exists in the active site copper coordination sphere of LPMOs that may have implications for the mechanism of loading copper in the cell.
Collapse
Affiliation(s)
- Amanda K Chaplin
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael T Wilson
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael A Hough
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Dimitri A Svistunenko
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Glyn R Hemsworth
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Paul H Walton
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Erik Vijgenboom
- the Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, P. O. Box 9505, 2300RA Leiden, The Netherlands
| | - Jonathan A R Worrall
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom,.
| |
Collapse
|
128
|
Forsberg Z, Nelson CE, Dalhus B, Mekasha S, Loose JSM, Crouch LI, Røhr ÅK, Gardner JG, Eijsink VGH, Vaaje-Kolstad G. Structural and Functional Analysis of a Lytic Polysaccharide Monooxygenase Important for Efficient Utilization of Chitin in Cellvibrio japonicus. J Biol Chem 2016; 291:7300-12. [PMID: 26858252 DOI: 10.1074/jbc.m115.700161] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Indexed: 01/11/2023] Open
Abstract
Cellvibrio japonicusis a Gram-negative soil bacterium that is primarily known for its ability to degrade plant cell wall polysaccharides through utilization of an extensive repertoire of carbohydrate-active enzymes. Several putative chitin-degrading enzymes are also found among these carbohydrate-active enzymes, such as chitinases, chitobiases, and lytic polysaccharide monooxygenases (LPMOs). In this study, we have characterized the chitin-active LPMO,CjLPMO10A, a tri-modular enzyme containing a catalytic family AA10 LPMO module, a family 5 chitin-binding module, and a C-terminal unclassified module of unknown function. Characterization of the latter module revealed tight and specific binding to chitin, thereby unraveling a new family of chitin-binding modules (classified as CBM73). X-ray crystallographic elucidation of theCjLPMO10A catalytic module revealed that the active site of the enzyme combines structural features previously only observed in either cellulose or chitin-active LPMO10s. Analysis of the copper-binding site by EPR showed a signal signature more similar to those observed for cellulose-cleaving LPMOs. The full-length LPMO shows no activity toward cellulose but is able to bind and cleave both α- and β-chitin. Removal of the chitin-binding modules reduced LPMO activity toward α-chitin compared with the full-length enzyme. Interestingly, the full-length enzyme and the individual catalytic LPMO module boosted the activity of an endochitinase equally well, also yielding similar amounts of oxidized products. Finally, gene deletion studies show thatCjLPMO10A is needed byC. japonicusto obtain efficient growth on both purified chitin and crab shell particles.
Collapse
Affiliation(s)
- Zarah Forsberg
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Cassandra E Nelson
- the Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, Maryland 21250
| | - Bjørn Dalhus
- the Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway, the Department of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, Rikshospitalet, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway, and
| | - Sophanit Mekasha
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Jennifer S M Loose
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Lucy I Crouch
- the Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Åsmund K Røhr
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Jeffrey G Gardner
- the Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, Maryland 21250
| | - Vincent G H Eijsink
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Gustav Vaaje-Kolstad
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway,
| |
Collapse
|
129
|
Crouch LI, Labourel A, Walton PH, Davies GJ, Gilbert HJ. The Contribution of Non-catalytic Carbohydrate Binding Modules to the Activity of Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:7439-49. [PMID: 26801613 PMCID: PMC4817175 DOI: 10.1074/jbc.m115.702365] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass is a sustainable industrial substrate. Copper-dependent lytic polysaccharide monooxygenases (LPMOs) contribute to the degradation of lignocellulose and increase the efficiency of biofuel production. LPMOs can contain non-catalytic carbohydrate binding modules (CBMs), but their role in the activity of these enzymes is poorly understood. Here we explored the importance of CBMs in LPMO function. The family 2a CBMs of two monooxygenases,CfLPMO10 andTbLPMO10 fromCellulomonas fimiandThermobispora bispora, respectively, were deleted and/or replaced with CBMs from other proteins. The data showed that the CBMs could potentiate and, surprisingly, inhibit LPMO activity, and that these effects were both enzyme-specific and substrate-specific. Removing the natural CBM or introducingCtCBM3a, from theClostridium thermocellumcellulosome scaffoldin CipA, almost abolished the catalytic activity of the LPMOs against the cellulosic substrates. The deleterious effect of CBM removal likely reflects the importance of prolonged presentation of the enzyme on the surface of the substrate for efficient catalytic activity, as only LPMOs appended to CBMs bound tightly to cellulose. The negative impact ofCtCBM3a is in sharp contrast with the capacity of this binding module to potentiate the activity of a range of glycoside hydrolases including cellulases. The deletion of the endogenous CBM fromCfLPMO10 or the introduction of a family 10 CBM fromCellvibrio japonicusLPMO10B intoTbLPMO10 influenced the quantity of non-oxidized products generated, demonstrating that CBMs can modulate the mode of action of LPMOs. This study demonstrates that engineered LPMO-CBM hybrids can display enhanced industrially relevant oxygenations.
Collapse
Affiliation(s)
- Lucy I Crouch
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Paul H Walton
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| |
Collapse
|
130
|
Mekasha S, Forsberg Z, Dalhus B, Bacik JP, Choudhary S, Schmidt-Dannert C, Vaaje-Kolstad G, Eijsink VGH. Structural and functional characterization of a small chitin-active lytic polysaccharide monooxygenase domain of a multi-modular chitinase fromJonesia denitrificans. FEBS Lett 2015; 590:34-42. [DOI: 10.1002/1873-3468.12025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Sophanit Mekasha
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Zarah Forsberg
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry; Institute for Clinical Medicine; University of Oslo; Norway
- Department of Microbiology; Clinic for Diagnostics and Intervention; Oslo University Hospital, Rikshospitalet; Norway
| | - John-Paul Bacik
- Bioscience Division; Protein Crystallography Station; Los Alamos National Laboratory; NM USA
| | - Swati Choudhary
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota; St. Paul MN USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota; St. Paul MN USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| |
Collapse
|
131
|
Lytic Polysaccharide Monooxygenases in Biomass Conversion. Trends Biotechnol 2015; 33:747-761. [DOI: 10.1016/j.tibtech.2015.09.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
|
132
|
The framework of polysaccharide monooxygenase structure and chemistry. Curr Opin Struct Biol 2015; 35:93-9. [PMID: 26615470 DOI: 10.1016/j.sbi.2015.10.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/15/2015] [Accepted: 10/21/2015] [Indexed: 01/20/2023]
Abstract
Polysaccharide monooxygenases, or PMOs (also known as lytic PMOs or LPMOs), are a group of enzymes discovered in recent years to catalyze the oxidative degradation of carbohydrate polymers. The PMO catalytic domain has a β-sandwich fold that bears a strong resemblance to both immunoglobulin (Ig) and fibronectin type III (FnIII) domains. PMOs are secreted by fungi and bacteria, and there is recent evidence for their roles in pathogenesis, in addition to biomass processing. This review addresses the biological origins and functions of emerging PMO families, as well as describes the aspects of PMO structure that support the chemistry of copper-catalyzed, oxidative polysaccharide degradation.
Collapse
|
133
|
Garcia-Seco D, Zhang Y, Gutierrez-Mañero FJ, Martin C, Ramos-Solano B. Application of Pseudomonas fluorescens to Blackberry under Field Conditions Improves Fruit Quality by Modifying Flavonoid Metabolism. PLoS One 2015; 10:e0142639. [PMID: 26559418 PMCID: PMC4641737 DOI: 10.1371/journal.pone.0142639] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/23/2015] [Indexed: 01/02/2023] Open
Abstract
Application of a plant growth promoting rhizobacterium (PGPR), Pseudomonas fluorescens N21.4, to roots of blackberries (Rubus sp.) is part of an optimised cultivation practice to improve yields and quality of fruit throughout the year in this important fruit crop. Blackberries are especially rich in flavonoids and therefore offer potential benefits for human health in prevention or amelioration of chronic diseases. However, the phenylpropanoid pathway and its regulation during ripening have not been studied in detail, in this species. PGPR may trigger flavonoid biosynthesis as part of an induced systemic response (ISR) given the important role of this pathway in plant defence, to cause increased levels of flavonoids in the fruit. We have identified structural genes encoding enzymes of the phenylpropanoid and flavonoid biosynthetic pathways catalysing the conversion of phenylalanine to the final products including flavonols, anthocyanins and catechins from blackberry, and regulatory genes likely involved in controlling the activity of pathway branches. We have also measured the major flavonols, anthocyanins and catechins at three stages during ripening. Our results demonstrate the coordinated expression of flavonoid biosynthetic genes with the accumulation of anthocyanins, catechins, and flavonols in developing fruits of blackberry. Elicitation of blackberry plants by treatment of roots with P.fluorescens N21.4, caused increased expression of some flavonoid biosynthetic genes and an accompanying increase in the concentration of selected flavonoids in fruits. Our data demonstrate the physiological mechanisms involved in the improvement of fruit quality by PGPR under field conditions, and highlight some of the genetic targets of elicitation by beneficial bacteria.
Collapse
Affiliation(s)
- Daniel Garcia-Seco
- Facultad de Farmacia, Universidad CEU San Pablo, Ctra. Boadilla del Monte km 5.3, Boadilla del Monte, Madrid, Spain
| | - Yang Zhang
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Cathie Martin
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Beatriz Ramos-Solano
- Facultad de Farmacia, Universidad CEU San Pablo, Ctra. Boadilla del Monte km 5.3, Boadilla del Monte, Madrid, Spain
| |
Collapse
|
134
|
Langner T, Göhre V. Fungal chitinases: function, regulation, and potential roles in plant/pathogen interactions. Curr Genet 2015; 62:243-54. [PMID: 26527115 DOI: 10.1007/s00294-015-0530-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/13/2022]
Abstract
In the past decades our knowledge about fungal cell wall architecture increased tremendously and led to the identification of many enzymes involved in polysaccharide synthesis and remodeling, which are also of biotechnological interest. Fungal cell walls play an important role in conferring mechanic stability during cell division and polar growth. Additionally, in phytopathogenic fungi the cell wall is the first structure that gets into intimate contact with the host plant. A major constituent of fungal cell walls is chitin, a homopolymer of N-acetylglucosamine units. To ensure plasticity, polymeric chitin needs continuous remodeling which is maintained by chitinolytic enzymes, including lytic polysaccharide monooxygenases N-acetylglucosaminidases, and chitinases. Depending on the species and lifestyle of fungi, there is great variation in the number of encoded chitinases and their function. Chitinases can have housekeeping function in plasticizing the cell wall or can act more specifically during cell separation, nutritional chitin acquisition, or competitive interaction with other fungi. Although chitinase research made huge progress in the last decades, our knowledge about their role in phytopathogenic fungi is still scarce. Recent findings in the dimorphic basidiomycete Ustilago maydis show that chitinases play different physiological functions throughout the life cycle and raise questions about their role during plant-fungus interactions. In this work we summarize these functions, mechanisms of chitinase regulation and their putative role during pathogen/host interactions.
Collapse
Affiliation(s)
- Thorsten Langner
- Institute for Microbiology, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Vera Göhre
- Institute for Microbiology, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
| |
Collapse
|
135
|
Expression and characterization of a lytic polysaccharide monooxygenase from Bacillus thuringiensis. Int J Biol Macromol 2015; 79:72-5. [PMID: 25936286 DOI: 10.1016/j.ijbiomac.2015.04.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 01/31/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are recently discovered oxidative enzymes that are capable of oxidative cleavage of recalcitrant polysaccharides such as chitin or cellulose. Despite the importance of LPMOs in biomass conversion and the large number of lpmo genes in microorganisms, only a few LPMOs have been well studied, and further characterization of these proteins is thus of interest. In this study, a chitin-active AA10 family LPMO from Bacillus thuringiensis subsp. kurstaki, BtLPMO10A, is described. This enzyme generates even-numbered oxidized oligosaccharides as the dominated products from crystalline chitin, however, interestingly, when colloidal chitin is used as the substrate, a ladder of oxidized oligosaccharides is observed. These results provide new insights into the action mode of LPMOs that may be affected by the substrates.
Collapse
|
136
|
Courtade G, Balzer S, Forsberg Z, Vaaje-Kolstad G, Eijsink VGH, Aachmann FL. (1)H, (13)C, (15)N resonance assignment of the chitin-active lytic polysaccharide monooxygenase BlLPMO10A from Bacillus licheniformis. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:207-10. [PMID: 25204609 DOI: 10.1007/s12104-014-9575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/02/2014] [Indexed: 05/02/2023]
Abstract
The chitin-active 19.2 kDa lytic polysaccharide monooxygenase BlLPMO10A from Bacillus licheniformis has been isotopically labeled and recombinantly expressed. In this paper, we report the (1)H, (13)C, (15)N resonance assignment of BlLPMO10A.
Collapse
Affiliation(s)
- Gaston Courtade
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway
| | | | | | | | | | | |
Collapse
|
137
|
Activation of enzymatic chitin degradation by a lytic polysaccharide monooxygenase. Carbohydr Res 2015; 407:166-9. [DOI: 10.1016/j.carres.2015.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 11/19/2022]
|
138
|
Beeson WT, Vu VV, Span EA, Phillips CM, Marletta MA. Cellulose degradation by polysaccharide monooxygenases. Annu Rev Biochem 2015; 84:923-46. [PMID: 25784051 DOI: 10.1146/annurev-biochem-060614-034439] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polysaccharide monooxygenases (PMOs), also known as lytic PMOs (LPMOs), enhance the depolymerization of recalcitrant polysaccharides by hydrolytic enzymes and are found in the majority of cellulolytic fungi and actinomycete bacteria. For more than a decade, PMOs were incorrectly annotated as family 61 glycoside hydrolases (GH61s) or family 33 carbohydrate-binding modules (CBM33s). PMOs have an unusual surface-exposed active site with a tightly bound Cu(II) ion that catalyzes the regioselective hydroxylation of crystalline cellulose, leading to glycosidic bond cleavage. The genomes of some cellulolytic fungi contain more than 20 genes encoding cellulose-active PMOs, suggesting a diversity of biological activities. PMOs show great promise in reducing the cost of conversion of lignocellulosic biomass to fermentable sugars; however, many questions remain about their reaction mechanism and biological function. This review addresses, in depth, the structural and mechanistic aspects of oxidative depolymerization of cellulose by PMOs and considers their biological function and phylogenetic diversity.
Collapse
Affiliation(s)
- William T Beeson
- Department of Chemistry, University of California, Berkeley, California 94720
| | | | | | | | | |
Collapse
|
139
|
Hamilton JJ, Marlow VL, Owen RA, Costa MDAA, Guo M, Buchanan G, Chandra G, Trost M, Coulthurst SJ, Palmer T, Stanley-Wall NR, Sargent F. A holin and an endopeptidase are essential for chitinolytic protein secretion in Serratia marcescens. ACTA ACUST UNITED AC 2015; 207:615-26. [PMID: 25488919 PMCID: PMC4259817 DOI: 10.1083/jcb.201404127] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pathogenic bacteria adapt to their environment and manipulate the biochemistry of hosts by secretion of effector molecules. Serratia marcescens is an opportunistic pathogen associated with healthcare-acquired infections and is a prolific secretor of proteins, including three chitinases (ChiA, ChiB, and ChiC) and a chitin binding protein (Cbp21). In this work, genetic, biochemical, and proteomic approaches identified genes that were required for secretion of all three chitinases and Cbp21. A genetic screen identified a holin-like protein (ChiW) and a putative l-alanyl-d-glutamate endopeptidase (ChiX), and subsequent biochemical analyses established that both were required for nonlytic secretion of the entire chitinolytic machinery, with chitinase secretion being blocked at a late stage in the mutants. In addition, live-cell imaging experiments demonstrated bimodal and coordinated expression of chiX and chiA and revealed that cells expressing chiA remained viable. It is proposed that ChiW and ChiX operate in tandem as components of a protein secretion system used by gram-negative bacteria.
Collapse
Affiliation(s)
- Jaeger J Hamilton
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Victoria L Marlow
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Richard A Owen
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Marília de Assis Alcoforado Costa
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Manman Guo
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Grant Buchanan
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7TJ, England, UK
| | - Matthias Trost
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Tracy Palmer
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Frank Sargent
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| |
Collapse
|
140
|
Nakagawa YS, Kudo M, Loose JSM, Ishikawa T, Totani K, Eijsink VGH, Vaaje-Kolstad G. A small lytic polysaccharide monooxygenase fromStreptomyces griseustargeting α- and β-chitin. FEBS J 2015; 282:1065-79. [DOI: 10.1111/febs.13203] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/10/2015] [Accepted: 01/15/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Yuko S. Nakagawa
- Department of Chemical Engineering; National Institute of Technology; Ichinoseki College; Japan
| | - Madoka Kudo
- Department of Chemical Engineering; National Institute of Technology; Ichinoseki College; Japan
| | - Jennifer S. M. Loose
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Takahiro Ishikawa
- Department of Chemical Engineering; National Institute of Technology; Ichinoseki College; Japan
| | - Kazuhide Totani
- Department of Chemical Engineering; National Institute of Technology; Ichinoseki College; Japan
| | - Vincent G. H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| |
Collapse
|
141
|
Paspaliari DK, Loose JSM, Larsen MH, Vaaje-Kolstad G. Listeria monocytogeneshas a functional chitinolytic system and an active lytic polysaccharide monooxygenase. FEBS J 2015; 282:921-36. [DOI: 10.1111/febs.13191] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 12/19/2014] [Accepted: 01/05/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Dafni K. Paspaliari
- Department of Veterinary Disease Biology; Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
| | - Jennifer S. M. Loose
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Marianne H. Larsen
- Department of Veterinary Disease Biology; Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
| | - Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| |
Collapse
|
142
|
Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| |
Collapse
|
143
|
Brown AH, Rodger PM, Evans JS, Walsh TR. Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in Nacre. Biomacromolecules 2014; 15:4467-79. [DOI: 10.1021/bm501263s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Aaron H. Brown
- Institute
for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | | | - John Spencer Evans
- Department
of Craniofacial Biology and Center for Skeletal Sciences, New York University, New York, New York 10010, United States
| | - Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| |
Collapse
|
144
|
Morgenstern I, Powlowski J, Tsang A. Fungal cellulose degradation by oxidative enzymes: from dysfunctional GH61 family to powerful lytic polysaccharide monooxygenase family. Brief Funct Genomics 2014; 13:471-81. [PMID: 25217478 PMCID: PMC4239789 DOI: 10.1093/bfgp/elu032] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our understanding of fungal cellulose degradation has shifted dramatically in the past few years with the characterization of a new class of secreted enzymes, the lytic polysaccharide monooxygenases (LPMO). After a period of intense research covering structural, biochemical, theoretical and evolutionary aspects, we have a picture of them as wedge-like copper-dependent metalloenzymes that on reduction generate a radical copper-oxyl species, which cleaves mainly crystalline cellulose. The main biological function lies in the synergism of fungal LPMOs with canonical hydrolytic cellulases in achieving efficient cellulose degradation. Their important role in cellulose degradation is highlighted by the wide distribution and often numerous occurrences in the genomes of almost all plant cell-wall degrading fungi. In this review, we provide an overview of the latest achievements in LPMO research and consider the open questions and challenges that undoubtedly will continue to stimulate interest in this new and exciting group of enzymes.
Collapse
|
145
|
Bai Y, Eijsink VGH, Kielak AM, van Veen JA, de Boer W. Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 2014; 18:38-49. [DOI: 10.1111/1462-2920.12545] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Yani Bai
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Aas Norway
| | - Anna M. Kielak
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Institute of Biology; Faculty of Science; Leiden University; Leiden The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Soil Quality Group; Wageningen University; P.O. Box 9101 Wageningen 6700 HB The Netherlands
| |
Collapse
|
146
|
Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases. Proc Natl Acad Sci U S A 2014; 111:8446-51. [PMID: 24912171 DOI: 10.1073/pnas.1402771111] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
For decades, the enzymatic conversion of cellulose was thought to rely on the synergistic action of hydrolytic enzymes, but recent work has shown that lytic polysaccharide monooxygenases (LPMOs) are important contributors to this process. We describe the structural and functional characterization of two functionally coupled cellulose-active LPMOs belonging to auxiliary activity family 10 (AA10) that commonly occur in cellulolytic bacteria. One of these LPMOs cleaves glycosidic bonds by oxidation of the C1 carbon, whereas the other can oxidize both C1 and C4. We thus demonstrate that C4 oxidation is not confined to fungal AA9-type LPMOs. X-ray crystallographic structures were obtained for the enzyme pair from Streptomyces coelicolor, solved at 1.3 Å (ScLPMO10B) and 1.5 Å (CelS2 or ScLPMO10C) resolution. Structural comparisons revealed differences in active site architecture that could relate to the ability to oxidize C4 (and that also seem to apply to AA9-type LPMOs). Despite variation in active site architecture, the two enzymes exhibited similar affinities for Cu(2+) (12-31 nM), redox potentials (242 and 251 mV), and electron paramagnetic resonance spectra, with only the latter clearly different from those of chitin-active AA10-type LPMOs. We conclude that substrate specificity depends not on copper site architecture, but rather on variation in substrate binding and orientation. During cellulose degradation, the members of this LPMO pair act in synergy, indicating different functional roles and providing a rationale for the abundance of these enzymes in biomass-degrading organisms.
Collapse
|
147
|
Gudmundsson M, Kim S, Wu M, Ishida T, Momeni MH, Vaaje-Kolstad G, Lundberg D, Royant A, Ståhlberg J, Eijsink VGH, Beckham GT, Sandgren M. Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction. J Biol Chem 2014; 289:18782-92. [PMID: 24828494 DOI: 10.1074/jbc.m114.563494] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of enzymes that employ a copper-mediated, oxidative mechanism to cleave glycosidic bonds. The LPMO catalytic mechanism likely requires that molecular oxygen first binds to Cu(I), but the oxidation state in many reported LPMO structures is ambiguous, and the changes in the LPMO active site required to accommodate both oxidation states of copper have not been fully elucidated. Here, a diffraction data collection strategy minimizing the deposited x-ray dose was used to solve the crystal structure of a chitin-specific LPMO from Enterococcus faecalis (EfaCBM33A) in the Cu(II)-bound form. Subsequently, the crystalline protein was photoreduced in the x-ray beam, which revealed structural changes associated with the conversion from the initial Cu(II)-oxidized form with two coordinated water molecules, which adopts a trigonal bipyramidal geometry, to a reduced Cu(I) form in a T-shaped geometry with no coordinated water molecules. A comprehensive survey of Cu(II) and Cu(I) structures in the Cambridge Structural Database unambiguously shows that the geometries observed in the least and most reduced structures reflect binding of Cu(II) and Cu(I), respectively. Quantum mechanical calculations of the oxidized and reduced active sites reveal little change in the electronic structure of the active site measured by the active site partial charges. Together with a previous theoretical investigation of a fungal LPMO, this suggests significant functional plasticity in LPMO active sites. Overall, this study provides molecular snapshots along the reduction process to activate the LPMO catalytic machinery and provides a general method for solving LPMO structures in both copper oxidation states.
Collapse
Affiliation(s)
- Mikael Gudmundsson
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Seonah Kim
- the National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Miao Wu
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Takuya Ishida
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden, the Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Majid Hadadd Momeni
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Gustav Vaaje-Kolstad
- the Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Daniel Lundberg
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Antoine Royant
- the Institut de Biologie Structurale, Université Grenoble Alpes-CNRS-CEA, 38042 Grenoble, France, and the European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Jerry Ståhlberg
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden, the Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Vincent G H Eijsink
- the Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Gregg T Beckham
- the National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401,
| | - Mats Sandgren
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden,
| |
Collapse
|
148
|
Qu M, Ma L, Chen P, Yang Q. Proteomic Analysis of Insect Molting Fluid with a Focus on Enzymes Involved in Chitin Degradation. J Proteome Res 2014; 13:2931-40. [DOI: 10.1021/pr5000957] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingbo Qu
- School
of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Li Ma
- Key
Laboratory of Insect Developmental and Evolutionary Biology, Institute
of Plant Physiology and Ecology, Shanghai Institutes for Biological
Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Chen
- School
of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- School
of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| |
Collapse
|
149
|
Forsberg Z, Røhr AK, Mekasha S, Andersson KK, Eijsink VGH, Vaaje-Kolstad G, Sørlie M. Comparative study of two chitin-active and two cellulose-active AA10-type lytic polysaccharide monooxygenases. Biochemistry 2014; 53:1647-56. [PMID: 24559135 DOI: 10.1021/bi5000433] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), found in family 9 (previously GH61), family 10 (previously CBM33), and the newly discovered family 11 of auxiliary activities (AA) in the carbohydrate-active enzyme classification system, are copper-dependent enzymes that oxidize sp(3)-carbons in recalcitrant polysaccharides such as chitin and cellulose in the presence of an external electron donor. In this study, we describe the activity of two AA10-type LPMOs whose activities have not been described before and we compare in total four different AA10-type LPMOs with the aim of finding possible correlations between their substrate specificities, sequences, and EPR signals. EPR spectra indicate that the electronic environment of the copper varies within the AA10 family even though amino acids directly interacting with the copper atom are identical in all four enzymes. This variation seems to be correlated to substrate specificity and is likely caused by sequence variation in areas that affect substrate binding geometry and/or by variation in a cluster of conserved aromatic residues likely involved in electron transfer. Interestingly, EPR signals for cellulose-active AA10 enzymes were similar to those previously observed for cellulose-active AA9 enzymes. Mutation of the conserved phenylalanine positioned in close proximity to the copper center in AA10-type LPMOs to Tyr (the corresponding residue in most AA9-type LPMOs) or Ala, led to complete or partial inactivation, respectively, while in both cases the ability to bind copper was maintained. Moreover, substrate binding affinity and degradation ability seemed hardly correlated, further emphasizing the crucial role of the active site configuration in determining LPMO functionality.
Collapse
Affiliation(s)
- Zarah Forsberg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| | | | | | | | | | | | | |
Collapse
|
150
|
Secreted major Venus flytrap chitinase enables digestion of Arthropod prey. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:374-83. [DOI: 10.1016/j.bbapap.2013.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022]
|