51
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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52
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Garcia-Santamarina S, Probst C, Festa RA, Ding C, Smith AD, Conklin SE, Brander S, Kinch LN, Grishin NV, Franz KJ, Riggs-Gelasco P, Lo Leggio L, Johansen KS, Thiele DJ. A lytic polysaccharide monooxygenase-like protein functions in fungal copper import and meningitis. Nat Chem Biol 2020; 16:337-344. [PMID: 31932719 PMCID: PMC7036007 DOI: 10.1038/s41589-019-0437-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022]
Abstract
Infection by the fungal pathogen Cryptococcus neoformans causes lethal meningitis, primarily in immune-compromised individuals. Colonization of the brain by C. neoformans is dependent on copper (Cu) acquisition from the host, which drives critical virulence mechanisms. While C. neoformans Cu+ import and virulence are dependent on the Ctr1 and Ctr4 proteins, little is known concerning extracellular Cu ligands that participate in this process. We identified a C. neoformans gene, BIM1, that is strongly induced during Cu limitation and which encodes a protein related to lytic polysaccharide monooxygenases (LPMOs). Surprisingly, bim1 mutants are Cu deficient, and Bim1 function in Cu accumulation depends on Cu2+ coordination and cell-surface association via a glycophosphatidyl inositol anchor. Bim1 participates in Cu uptake in concert with Ctr1 and expression of this pathway drives brain colonization in mouse infection models. These studies demonstrate a role for LPMO-like proteins as a critical factor for Cu acquisition in fungal meningitis.
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Affiliation(s)
- Sarela Garcia-Santamarina
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Genome Biology Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Corinna Probst
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Richard A Festa
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Irvine Scientific, Santa Ana, CA, USA
| | - Chen Ding
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Aaron D Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Steven E Conklin
- Department of Chemistry, Duke University, Durham, NC, USA
- Division of Clinical Chemistry, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Søren Brander
- Department of Geoscience and Natural Resource, University of Copenhagen, Copenhagen, Denmark
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Katja Salomon Johansen
- Department of Geoscience and Natural Resource, University of Copenhagen, Copenhagen, Denmark
| | - Dennis J Thiele
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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53
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Zhang W, Yu C, Wang X, Hai L, Hu J. RETRACTED: Increased abundance of nitrogen fixing bacteria by higher C/N ratio reduces the total losses of N and C in cattle manure and corn stover mix composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 103:416-425. [PMID: 31952023 DOI: 10.1016/j.wasman.2020.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief. The article duplicates significant parts of a paper that had already appeared in Bioresource Technology, Volume 297, February 2020, 122410, https://doi.org/10.1016/j.biortech.2019.122410. One of the conditions of submission of a paper for publication is that authors declare explicitly that the paper has not been previously published and is not under consideration for publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a misuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.
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Affiliation(s)
- Wenming Zhang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China; Department of Agriculture and Biosystem Engineering, Iowa State University, Ames 50010, United States.
| | - Chenxu Yu
- Department of Agriculture and Biosystem Engineering, Iowa State University, Ames 50010, United States
| | - Xujie Wang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Long Hai
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Juan Hu
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology Chinese Academy of Sciences, Changchun 130102, PR China
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54
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Zhou X, Qi X, Huang H, Zhu H. Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity. Int J Mol Sci 2019; 20:ijms20184594. [PMID: 31533304 PMCID: PMC6771041 DOI: 10.3390/ijms20184594] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are key enzymes in both the natural carbon cycle and the biorefinery industry. Understanding the molecular basis of LPMOs acting on polysaccharide substrates is helpful for improving industrial cellulase cocktails. Here we analyzed the sequences, structures, and substrate binding modes of LPMOs to uncover the factors that influence substrate specificity and regioselectivity. Our results showed that the different compositions of a motif located on L2 affect the electrostatic potentials of substrate binding surfaces, which in turn affect substrate specificities of AA10 LPMOs. A conserved Asn at a distance of 7 Å from the active center Cu might, together with the conserved Ser immediately before the second catalytic His, determine the localization of LPMOs on substrate, and thus contribute to C4-oxidizing regioselectivity. The findings in this work provide an insight into the molecular basis of substrate specificity and regioselectivity of LPMOs.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Xiaohua Qi
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Hongxia Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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55
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Petrović DM, Várnai A, Dimarogona M, Mathiesen G, Sandgren M, Westereng B, Eijsink VGH. Comparison of three seemingly similar lytic polysaccharide monooxygenases from Neurospora crassa suggests different roles in plant biomass degradation. J Biol Chem 2019; 294:15068-15081. [PMID: 31431506 DOI: 10.1074/jbc.ra119.008196] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/02/2019] [Indexed: 11/06/2022] Open
Abstract
Many fungi produce multiple lytic polysaccharide monooxygenases (LPMOs) with seemingly similar functions, but the biological reason for this multiplicity remains unknown. To address this question, here we carried out comparative structural and functional characterizations of three cellulose-active C4-oxidizing family AA9 LPMOs from the fungus Neurospora crassa, NcLPMO9A (NCU02240), NcLPMO9C (NCU02916), and NcLPMO9D (NCU01050). We solved the three-dimensional structure of copper-bound NcLPMO9A at 1.6-Å resolution and found that NcLPMO9A and NcLPMO9C, containing a CBM1 carbohydrate-binding module, bind cellulose more strongly and were less susceptible to inactivation than NcLPMO9D, which lacks a CBM. All three LPMOs were active on tamarind xyloglucan and konjac glucomannan, generating similar products but clearly differing in activity levels. Importantly, in some cases, the addition of phosphoric acid-swollen cellulose (PASC) had a major effect on activity: NcLPMO9A was active on xyloglucan only in the presence of PASC, and PASC enhanced NcLPMO9D activity on glucomannan. Interestingly, the three enzymes also exhibited large differences in their interactions with enzymatic electron donors, which could reflect that they are optimized to act with different reducing partners. All three enzymes efficiently used H2O2 as a cosubstrate, yielding product profiles identical to those obtained in O2-driven reactions with PASC, xyloglucan, or glucomannan. Our results indicate that seemingly similar LPMOs act preferentially on different types of copolymeric substructures in the plant cell wall, possibly because these LPMOs are functionally adapted to distinct niches differing in the types of available reductants.
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Affiliation(s)
- Dejan M Petrović
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Maria Dimarogona
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.,Laboratory of Biotechnology and Structural Biology, Department of Chemical Engineering, University of Patras, 26504 Patras, Greece
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
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56
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Zhou H, Li T, Yu Z, Ju J, Zhang H, Tan H, Li K, Yin H. A lytic polysaccharide monooxygenase from Myceliophthora thermophila and its synergism with cellobiohydrolases in cellulose hydrolysis. Int J Biol Macromol 2019; 139:570-576. [PMID: 31381927 DOI: 10.1016/j.ijbiomac.2019.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/22/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have attracted vast attention because of their unique mechanism of oxidative degradation of carbohydrate polymers and the potential application in biorefineries. This study characterized a novel LPMO from Myceliophthora thermophila, denoted MtLPMO9L. The structure model of the enzyme indicated that it belongs to the C1-oxidizing LPMO, which has neither an extra helix in the L3 loop nor extra loop region in the L2 loop. This was confirmed subsequently by the enzymatic assays since MtLPMO9L only acts on cellulose and generates C1-oxidized cello-oligosaccharides. Moreover, synergetic experiments showed that MtLPMO9L significantly improves the efficiency of cellobiohydrolase (CBH) II. In contrast, the inhibitory rather than synergetic effect was observed when combining used MtLPMO9L and CBHI. Changing the incubation time and concentration ratio of MtLPMO9L and CBHI could attenuate the inhibitory effects. This discovery suggests a different synergy detail between MtLPMO9L and two CBHs, which implies that the composition of cellulase cocktails may need reconsideration.
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Affiliation(s)
- Haichuan Zhou
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Tang Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zuochen Yu
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jiu Ju
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huiyan Zhang
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haidong Tan
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kuikui Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Heng Yin
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian 116023, China.
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57
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Cell surface display of proteins on filamentous fungi. Appl Microbiol Biotechnol 2019; 103:6949-6972. [PMID: 31359105 DOI: 10.1007/s00253-019-10026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Protein display approaches have been useful to endow the cell surface of yeasts with new catalytic activities so that they can act as enhanced whole-cell biocatalysts. Despite their biotechnological potential, protein display technologies remain poorly developed for filamentous fungi. The lignocellulolytic character of some of them coupled to the cell surface biosynthesis of valuable molecules by a single or a cascade of several displayed enzymes is an appealing prospect. Cell surface protein display consists in the co-translational fusion of a functional protein (passenger) to an anchor one, usually a cell-wall-resident protein. The abundance, spacing, and local environment of the displayed enzymes-determined by the relationship of the anchor protein with the structure and dynamics of the engineered cell wall-are factors that influence the performance of display-based biocatalysts. The development of protein display strategies in filamentous fungi could be based on the field advances in yeasts; however, the unique composition, structure, and biology of filamentous fungi cell walls require the customization of the approach to those microorganisms. In this prospective review, the cellular bases, the design principles, and the available tools to foster the development of cell surface protein display technologies in filamentous fungi are discussed.
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58
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Lange L, Barrett K, Pilgaard B, Gleason F, Tsang A. Enzymes of early-diverging, zoosporic fungi. Appl Microbiol Biotechnol 2019; 103:6885-6902. [PMID: 31309267 PMCID: PMC6690862 DOI: 10.1007/s00253-019-09983-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/26/2022]
Abstract
The secretome, the complement of extracellular proteins, is a reflection of the interaction of an organism with its host or substrate, thus a determining factor for the organism’s fitness and competitiveness. Hence, the secretome impacts speciation and organismal evolution. The zoosporic Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, and Cryptomycota represent the earliest diverging lineages of the Fungal Kingdom. The review describes the enzyme compositions of these zoosporic fungi, underscoring the enzymes involved in biomass degradation. The review connects the lifestyle and substrate affinities of the zoosporic fungi to the secretome composition by examining both classical phenotypic investigations and molecular/genomic-based studies. The carbohydrate-active enzyme profiles of 19 genome-sequenced species are summarized. Emphasis is given to recent advances in understanding the functional role of rumen fungi, the basis for the devastating chytridiomycosis, and the structure of fungal cellulosome. The approach taken by the review enables comparison of the secretome enzyme composition of anaerobic versus aerobic early-diverging fungi and comparison of enzyme portfolio of specialized parasites, pathogens, and saprotrophs. Early-diverging fungi digest most major types of biopolymers: cellulose, hemicellulose, pectin, chitin, and keratin. It is thus to be expected that early-diverging fungi in its entirety represents a rich and diverse pool of secreted, metabolic enzymes. The review presents the methods used for enzyme discovery, the diversity of enzymes found, the status and outlook for recombinant production, and the potential for applications. Comparative studies on the composition of secretome enzymes of early-diverging fungi would contribute to unraveling the basal lineages of fungi.
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Affiliation(s)
- Lene Lange
- Bioeconomy, Research & Advisory, Karensgade 5, Valby, DK-2500, Copenhagen, Denmark.
| | - Kristian Barrett
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Bo Pilgaard
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Frank Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, H4B1R6, Canada
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59
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Vu VV, Hangasky JA, Detomasi TC, Henry SJW, Ngo ST, Span EA, Marletta MA. Substrate selectivity in starch polysaccharide monooxygenases. J Biol Chem 2019; 294:12157-12166. [PMID: 31235519 DOI: 10.1074/jbc.ra119.009509] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/21/2019] [Indexed: 11/06/2022] Open
Abstract
Degradation of polysaccharides is central to numerous biological and industrial processes. Starch-active polysaccharide monooxygenases (AA13 PMOs) oxidatively degrade starch and can potentially be used with industrial amylases to convert starch into a fermentable carbohydrate. The oxidative activities of the starch-active PMOs from the fungi Neurospora crassa and Myceliophthora thermophila, NcAA13 and MtAA13, respectively, on three different starch substrates are reported here. Using high-performance anion-exchange chromatography coupled with pulsed amperometry detection, we observed that both enzymes have significantly higher oxidative activity on amylose than on amylopectin and cornstarch. Analysis of the product distribution revealed that NcAA13 and MtAA13 more frequently oxidize glycosidic linkages separated by multiples of a helical turn consisting of six glucose units on the same amylose helix. Docking studies identified important residues that are involved in amylose binding and suggest that the shallow groove that spans the active-site surface of AA13 PMOs favors the binding of helical amylose substrates over nonhelical substrates. Truncations of NcAA13 that removed its native carbohydrate-binding module resulted in diminished binding to amylose, but truncated NcAA13 still favored amylose oxidation over other starch substrates. These findings establish that AA13 PMOs preferentially bind and oxidize the helical starch substrate amylose. Moreover, the product distributions of these two enzymes suggest a unique interaction with starch substrates.
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Affiliation(s)
- Van V Vu
- Nguyen Tat Thanh Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam.
| | - John A Hangasky
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Tyler C Detomasi
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Skylar J W Henry
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
| | - Elise A Span
- Biophysics Graduate Group, University of California, Berkeley, California 94720
| | - Michael A Marletta
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720; Department of Chemistry, University of California, Berkeley, California 94720; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720.
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60
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Yadav SK, Singh R, Singh PK, Vasudev PG. Insecticidal fern protein Tma12 is possibly a lytic polysaccharide monooxygenase. PLANTA 2019; 249:1987-1996. [PMID: 30903269 DOI: 10.1007/s00425-019-03135-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/09/2019] [Indexed: 05/25/2023]
Abstract
Amino acid sequence and crystal structure analyses of Tma12, an insecticidal protein isolated from the fern Tectaria macrodonta, identify it as a carbohydrate-binding protein belonging to the AA10 family of lytic polysaccharide monooxygenases, and provide the first evidence of AA10 proteins in plants. Tma12, isolated from the fern Tectaria macrodonta, is a next-generation insecticidal protein. Transgenic cotton expressing Tma12 exhibits resistance against whitefly and viral diseases. Beside its insecticidal property, the structure and function of Tma12 are unknown. This limits understanding of the insecticidal mechanism of the protein and targeted improvement in its efficacy. Here we report the amino acid sequence analysis and the crystal structure of Tma12, suggesting that it is possibly a lytic polysaccharide monooxygenase (LPMO) of the AA10 family. Amino acid sequence of Tma12 shows 45% identity with a cellulolytic LPMO of Streptomyces coelicolor. The crystal structure of Tma12, obtained at 2.2 Å resolution, possesses all the major structural characteristics of AA10 LPMOs. A H2O2-based enzymatic assay also supports this finding. It is the first report of the occurrence of LPMO-like protein in a plant. The two facts that Tma12 possesses insecticidal activity and shows structural similarity with LPMOs collectively advocate exploration of microbial LPMOs for insecticidal potential.
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Affiliation(s)
- Sunil K Yadav
- Genetics and Plant Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Rahul Singh
- Genetics and Plant Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Pradhyumna Kumar Singh
- Genetics and Plant Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
| | - Prema G Vasudev
- Metabolic and Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
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61
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Petrović DM, Bissaro B, Chylenski P, Skaugen M, Sørlie M, Jensen MS, Aachmann FL, Courtade G, Várnai A, Eijsink VGH. Methylation of the N-terminal histidine protects a lytic polysaccharide monooxygenase from auto-oxidative inactivation. Protein Sci 2019; 27:1636-1650. [PMID: 29971843 DOI: 10.1002/pro.3451] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/29/2022]
Abstract
The catalytically crucial N-terminal histidine (His1) of fungal lytic polysaccharide monooxygenases (LPMOs) is post-translationally modified to carry a methylation. The functional role of this methylation remains unknown. We have carried out an in-depth functional comparison of two variants of a family AA9 LPMO from Thermoascus aurantiacus (TaLPMO9A), one with, and one without the methylation on His1. Various activity assays showed that the two enzyme variants are identical in terms of substrate preferences, cleavage specificities and the ability to activate molecular oxygen. During the course of this work, new functional features of TaLPMO9A were discovered, in particular the ability to cleave xyloglucan, and these features were identical for both variants. Using a variety of techniques, we further found that methylation has minimal effects on the pKa of His1, the affinity for copper and the redox potential of bound copper. The two LPMOs did, however, show clear differences in their resistance against oxidative damage. Studies with added hydrogen peroxide confirmed recent claims that low concentrations of H2 O2 boost LPMO activity, whereas excess H2 O2 leads to LPMO inactivation. The methylated variant of TaLPMO9A, produced in Aspergillus oryzae, was more resistant to excess H2 O2 and showed better process performance when using conditions that promote generation of reactive-oxygen species. LPMOs need to protect themselves from reactive oxygen species generated in their active sites and this study shows that methylation of the fully conserved N-terminal histidine provides such protection.
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Affiliation(s)
- Dejan M Petrović
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Piotr Chylenski
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Morten Skaugen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Marianne S Jensen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NOBIPOL, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Gaston Courtade
- Department of Biotechnology and Food Science, NOBIPOL, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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62
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Corrêa TLR, Júnior AT, Wolf LD, Buckeridge MS, dos Santos LV, Murakami MT. An actinobacteria lytic polysaccharide monooxygenase acts on both cellulose and xylan to boost biomass saccharification. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:117. [PMID: 31168322 PMCID: PMC6509861 DOI: 10.1186/s13068-019-1449-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/22/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) opened a new horizon for biomass deconstruction. They use a redox mechanism not yet fully understood and the range of substrates initially envisaged to be the crystalline polysaccharides is steadily expanding to non-crystalline ones. RESULTS The enzyme KpLPMO10A from the actinomycete Kitasatospora papulosa was cloned and overexpressed in Escherichia coli cells in the functional form with native N-terminal. The enzyme can release oxidized species from chitin (C1-type oxidation) and cellulose (C1/C4-type oxidation) similarly to other AA10 members from clade II (subclade A). Interestingly, KpLPMO10A also cleaves isolated xylan (not complexed with cellulose, C4-type oxidation), a rare activity among LPMOs not described yet for the AA10 family. The synergistic effect of KpLPMO10A with Celluclast® and an endo-β-1,4-xylanase also supports this finding. The crystallographic elucidation of KpLPMO10A at 1.6 Å resolution along with extensive structural analyses did not indicate any evident difference with other characterized AA10 LPMOs at the catalytic interface, tempting us to suggest that these enzymes might also be active on xylan or that the ability to attack both crystalline and non-crystalline substrates involves yet obscure mechanisms of substrate recognition and binding. CONCLUSIONS This work expands the spectrum of substrates recognized by AA10 family, opening a new perspective for the understanding of the synergistic effect of these enzymes with canonical glycoside hydrolases to deconstruct ligno(hemi)cellulosic biomass.
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Affiliation(s)
- Thamy Lívia Ribeiro Corrêa
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Atílio Tomazini Júnior
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Lúcia Daniela Wolf
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | | | - Leandro Vieira dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
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Manjeet K, Madhuprakash J, Mormann M, Moerschbacher BM, Podile AR. A carbohydrate binding module-5 is essential for oxidative cleavage of chitin by a multi-modular lytic polysaccharide monooxygenase from Bacillus thuringiensis serovar kurstaki. Int J Biol Macromol 2019; 127:649-656. [DOI: 10.1016/j.ijbiomac.2019.01.183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/03/2019] [Accepted: 01/28/2019] [Indexed: 01/09/2023]
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Courtade G, Aachmann FL. Chitin-Active Lytic Polysaccharide Monooxygenases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:115-129. [PMID: 31102244 DOI: 10.1007/978-981-13-7318-3_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the cleavage of 1,4-glycosidic bonds various plant cell wall polysaccharides and chitin. In contrast to glycoside hydrolases, LPMOs are active on the crystalline regions of polysaccharides and thus synergize with hydrolytic enzymes. This synergism leads to an overall increase in the biomass-degradation activity of enzyme mixtures. Chitin-active LPMOs were discovered in 2010 and are currently classified in families AA10, AA11, and AA15 of the Carbohydrate-Active enZYmes database, which include LPMOs from bacteria, fungi, insects, and viruses. LPMOs have become important enzymes both industrially and scientifically and, in this chapter, we provide a brief introduction to chitin-active LPMOs including a summary of the 20+ chitin-active LPMOs that have been characterized so far. Then, we describe their structural features, catalytic mechanism, and appended carbohydrate modules. Finally, we show how chitin-active LPMOs can be used to perform chemo-enzymatic modification of chitin substrates.
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Affiliation(s)
- Gaston Courtade
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway.
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Fowler CA, Sabbadin F, Ciano L, Hemsworth GR, Elias L, Bruce N, McQueen-Mason S, Davies GJ, Walton PH. Discovery, activity and characterisation of an AA10 lytic polysaccharide oxygenase from the shipworm symbiont Teredinibacter turnerae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:232. [PMID: 31583018 PMCID: PMC6767633 DOI: 10.1186/s13068-019-1573-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/21/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND The quest for novel enzymes for cellulosic biomass-degradation has recently been focussed on lytic polysaccharide monooxygenases (LPMOs/PMOs), Cu-containing proteins that catalyse the oxidative degradation of otherwise recalcitrant polysaccharides using O2 or H2O2 as a co-substrate. RESULTS Although classical saprotrophic fungi and bacteria have been a rich source of lytic polysaccharide monooxygenases (LPMOs), we were interested to see if LPMOs from less evident bio-environments could be discovered and assessed for their cellulolytic activity in a biofuel context. In this regard, the marine shipworm Lyrodus pedicellatus represents an interesting source of new enzymes, since it must digest wood particles ingested during its natural tunnel boring behaviour and plays host to a symbiotic bacterium, Teredinibacter turnerae, the genome of which has revealed a multitude of enzymes dedicated to biomass deconstruction. Here, we show that T. turnerae encodes a cellulose-active AA10 LPMO. The 3D structure, at 1.4 Å resolution, along with its EPR spectrum is distinct from other AA10 polysaccharide monooxygenases insofar as it displays a "histidine-brace" catalytic apparatus with changes to the surrounding coordination sphere of the copper. Furthermore, TtAA10A possesses a second, surface accessible, Cu site 14 Å from the classical catalytic centre. Activity measurements show that the LPMO oxidises cellulose and thereby significantly augments the rate of degradation of cellulosic biomass by classical glycoside hydrolases. CONCLUSION Shipworms are wood-boring marine molluscs that can live on a diet of lignocellulose. Bacterial symbionts of shipworms provide many of the enzymes needed for wood digestion. The shipworm symbiont T. turnerae produces one of the few LPMOs yet described from the marine environment, notably adding to the capability of shipworms to digest recalcitrant polysaccharides.
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Affiliation(s)
| | - Federico Sabbadin
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Luisa Ciano
- Department of Chemistry, University of York, York, YO10 5DD UK
- Present Address: School of Chemistry and Photon Science Institute, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Glyn R. Hemsworth
- Department of Chemistry, University of York, York, YO10 5DD UK
- Present Address: Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT UK
| | - Luisa Elias
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Neil Bruce
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Simon McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | | | - Paul H. Walton
- Department of Chemistry, University of York, York, YO10 5DD UK
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Arora R, Bharval P, Sarswati S, Sen TZ, Yennamalli RM. Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region. J Mol Graph Model 2018; 88:1-10. [PMID: 30612037 DOI: 10.1016/j.jmgm.2018.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/03/2018] [Accepted: 12/18/2018] [Indexed: 12/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), which are found in fungi, bacteria, and viruses, are redox enzymes utilizing copper to break glycosidic bonds in recalcitrant crystalline form of polysaccharides, such as chitin and cellulose. They are classified by the Carbohydrate-Active enZYmes (CAZy) database under various families. LPMOs's structure with a flat substrate binding region has been shown to contribute to its function, however, the role that LPMOs structural dynamics play during polysaccharide degradation and its mechanism of binding towards substrate are relatively unknown. Here, we report an exhaustive implementation of coarse-grained simulations using Elastic Network Models on multiple LPMO structures to shed light on how their structural dynamics contribute to their chemical function. Using Gaussian network models and Anisotropic network models, we show that the substrate binding region is highly flexible with significant and sustained micro-scale level conformational changes. Significantly, the loops on the binding side of the substrate are most mobile, in concert with the dynamic modes influencing the motions during binding. We also observed dynamic differences between four families of LPMO, namely AA9, AA10, AA11, and AA13 that consist of more than one structure. Specifically, the patterns of motion in the loop regions among the AA9 structures are distinct from those in the AA10 structures.
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Affiliation(s)
- Radhika Arora
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Priya Bharval
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Sheena Sarswati
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Taner Z Sen
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA, 94710, USA; Iowa State University, Department of Genetics, Development, and Cell Biology, Ames, IA, 50011, USA
| | - Ragothaman M Yennamalli
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India.
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67
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Zhang H, Dong S, Lou T, Wang S. Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208. J Basic Microbiol 2018; 59:267-276. [PMID: 30589093 DOI: 10.1002/jobm.201800563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 11/10/2022]
Abstract
Marine Streptomyces sp. CC0208 isolated from the Bohai Bay showed high efficiency of cellulose degradation under optimized fermentation parameters. Also, as one of the bioinformatics-based approaches for the discovery of novel natural product and enzyme effectively, genome mining has been developed and applied widely. Herein, we reported the complete genome sequence of Streptomyces sp. CC0208.Whole-genome sequencing analysis revealed a genome size of 9,325,981 bp with a linear chromosome, GC content of 70.59% and 8487 protein-coding genes. Abundant genes have predicted functions in antibiotic metabolism and enzymes. A 20 enzymes closely associated with cellulose degradation were discovered. A total of 25 biosynthetic gene clusters (BGCs) of secondary metabolites were identified, including diverse classes of natural products. The availability of genome sequence of Streptomyces sp. CC0208 not only will assist in cracking the mechanism of cellulose degradation but also will provide the insights into the significant secondary metabolic potentials for the production of diverse compound classes based on rational strategies.
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Affiliation(s)
- Hongyu Zhang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shirui Dong
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Tingting Lou
- Tianjin Entry and Exit Inspection and Quarantine Bureau, Tianjin, China
| | - Suying Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
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68
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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69
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70
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Mutahir Z, Mekasha S, Loose JSM, Abbas F, Vaaje-Kolstad G, Eijsink VGH, Forsberg Z. Characterization and synergistic action of a tetra-modular lytic polysaccharide monooxygenase from Bacillus cereus. FEBS Lett 2018; 592:2562-2571. [PMID: 29993123 DOI: 10.1002/1873-3468.13189] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/29/2018] [Accepted: 07/04/2018] [Indexed: 12/19/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) contribute to enzymatic conversion of recalcitrant polysaccharides such as chitin and cellulose and may also play a role in bacterial infections. Some LPMOs are multimodular, the implications of which remain only partly understood. We have studied the properties of a tetra-modular LPMO from the food poisoning bacterium Bacillus cereus (named BcLPMO10A). We show that BcLPMO10A, comprising an LPMO domain, two fibronectin-type III (FnIII)-like domains, and a carbohydrate-binding module (CBM5), is a powerful chitin-active LPMO. While the role of the FnIII domains remains unclear, we show that enzyme functionality strongly depends on the CBM5, which, by promoting substrate binding, protects the enzyme from inactivation. BcLPMO10A enhances the activity of chitinases during the degradation of α-chitin.
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Affiliation(s)
- Zeeshan Mutahir
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Sophanit Mekasha
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jennifer S M Loose
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Faiza Abbas
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
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71
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Courtade G, Forsberg Z, Heggset EB, Eijsink VGH, Aachmann FL. The carbohydrate-binding module and linker of a modular lytic polysaccharide monooxygenase promote localized cellulose oxidation. J Biol Chem 2018; 293:13006-13015. [PMID: 29967065 DOI: 10.1074/jbc.ra118.004269] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/23/2018] [Indexed: 01/24/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the oxidative cleavage of polysaccharides such as cellulose and chitin, a feature that makes them key tools in industrial biomass conversion processes. The catalytic domains of a considerable fraction of LPMOs and other carbohydrate-active enzymes (CAZymes) are tethered to carbohydrate-binding modules (CBMs) by flexible linkers. These linkers preclude X-ray crystallographic studies, and the functional implications of these modular assemblies remain partly unknown. Here, we used NMR spectroscopy to characterize structural and dynamic features of full-length modular ScLPMO10C from Streptomyces coelicolor We observed that the linker is disordered and extended, creating distance between the CBM and the catalytic domain and allowing these domains to move independently of each other. Functional studies with cellulose nanofibrils revealed that most of the substrate-binding affinity of full-length ScLPMO10C resides in the CBM. Comparison of the catalytic performance of full-length ScLPMO10C and its isolated catalytic domain revealed that the CBM is beneficial for LPMO activity at lower substrate concentrations and promotes localized and repeated oxidation of the substrate. Taken together, these results provide a mechanistic basis for understanding the interplay between catalytic domains linked to CBMs in LPMOs and CAZymes in general.
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Affiliation(s)
- Gaston Courtade
- From NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Zarah Forsberg
- the Faculty of Chemistry, Biotechnology and Food Science, NMBU Norwegian University of Life Sciences, N-1432 Ås, Norway, and
| | | | - Vincent G H Eijsink
- the Faculty of Chemistry, Biotechnology and Food Science, NMBU Norwegian University of Life Sciences, N-1432 Ås, Norway, and
| | - Finn L Aachmann
- From NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway,
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Loose JSM, Arntzen MØ, Bissaro B, Ludwig R, Eijsink VGH, Vaaje-Kolstad G. Multipoint Precision Binding of Substrate Protects Lytic Polysaccharide Monooxygenases from Self-Destructive Off-Pathway Processes. Biochemistry 2018; 57:4114-4124. [DOI: 10.1021/acs.biochem.8b00484] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer S. M. Loose
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Magnus Ø. Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Roland Ludwig
- BOKU-University of Natural Resources and Life Sciences, Department of Food Science and Technology, Biocatalysis and Biosensing Laboratory, 1180 Vienna, Austria
| | - Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
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73
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Bissaro B, Isaksen I, Vaaje-Kolstad G, Eijsink VGH, Røhr ÅK. How a Lytic Polysaccharide Monooxygenase Binds Crystalline Chitin. Biochemistry 2018; 57:1893-1906. [PMID: 29498832 DOI: 10.1021/acs.biochem.8b00138] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are major players in biomass conversion, both in Nature and in the biorefining industry. How the monocopper LPMO active site is positioned relative to the crystalline substrate surface to catalyze powerful, but potentially self-destructive, oxidative chemistry is one of the major questions in the field. We have adopted a multidisciplinary approach, combining biochemical, spectroscopic, and molecular modeling methods to study chitin binding by the well-studied LPMO from Serratia marcescens SmAA10A (or CBP21). The orientation of the enzyme on a single-chain substrate was determined by analyzing enzyme cutting patterns. Building on this analysis, molecular dynamics (MD) simulations were performed to study interactions between the LPMO and three different surface topologies of crystalline chitin. The resulting atomistic models showed that most enzyme-substrate interactions involve the polysaccharide chain that is to be cleaved. The models also revealed a constrained active site geometry as well as a tunnel connecting the bulk solvent to the copper site, through which only small molecules such as H2O, O2, and H2O2 can diffuse. Furthermore, MD simulations, quantum mechanics/molecular mechanics calculations, and electron paramagnetic resonance spectroscopy demonstrate that rearrangement of Cu-coordinating water molecules is necessary when binding the substrate and also provide a rationale for the experimentally observed C1 oxidative regiospecificity of SmAA10A. This study provides a first, experimentally supported, atomistic view of the interactions between an LPMO and crystalline chitin. The confinement of the catalytic center is likely crucially important for controlling the oxidative chemistry performed by LPMOs and will help guide future mechanistic studies.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science , Norwegian University of Life Sciences , Chr. M. Falsensvei 1 , N-1432 Aas , Norway
| | - Ingvild Isaksen
- Faculty of Chemistry, Biotechnology, and Food Science , Norwegian University of Life Sciences , Chr. M. Falsensvei 1 , N-1432 Aas , Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology, and Food Science , Norwegian University of Life Sciences , Chr. M. Falsensvei 1 , N-1432 Aas , Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science , Norwegian University of Life Sciences , Chr. M. Falsensvei 1 , N-1432 Aas , Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology, and Food Science , Norwegian University of Life Sciences , Chr. M. Falsensvei 1 , N-1432 Aas , Norway
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Meier KK, Jones SM, Kaper T, Hansson H, Koetsier MJ, Karkehabadi S, Solomon EI, Sandgren M, Kelemen B. Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. Chem Rev 2018; 118:2593-2635. [PMID: 29155571 PMCID: PMC5982588 DOI: 10.1021/acs.chemrev.7b00421] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M. Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Martijn J. Koetsier
- DuPont Industrial Biosciences, Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Bradley Kelemen
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
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Krolicka M, Hinz SWA, Koetsier MJ, Joosten R, Eggink G, van den Broek LAM, Boeriu CG. Chitinase Chi1 from Myceliophthora thermophila C1, a Thermostable Enzyme for Chitin and Chitosan Depolymerization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:1658-1669. [PMID: 29359934 PMCID: PMC5847117 DOI: 10.1021/acs.jafc.7b04032] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A thermostable Chitinase Chi1 from Myceliophthora thermophila C1 was homologously produced and characterized. Chitinase Chi1 shows high thermostability at 40 °C (>140 h 90% activity), 50 °C (>168 h 90% activity), and 55 °C (half-life 48 h). Chitinase Chi1 has broad substrate specificity and converts chitin, chitosan, modified chitosan, and chitin oligosaccharides. The activity of Chitinase Chi1 is strongly affected by the degree of deacetylation (DDA), molecular weight (Mw), and side chain modification of chitosan. Chitinase Chi1 releases mainly (GlcNAc)2 from insoluble chitin and chito-oligosaccharides with a polymerization degree (DP) ranging from 2 to 12 from chitosan, in a processive way. Chitinase Chi1 shows higher activity toward chitin oligosaccharides (GlcNAc)4-6 than toward (GlcNAc)3 and is inactive for (GlcNAc)2. During hydrolysis, oligosaccharides bind at subsites -2 to +2 in the enzyme's active site. Chitinase Chi1 can be used for chitin valorisation and for production of chitin- and chito-oligosaccharides at industrial scale.
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Affiliation(s)
- Malgorzata Krolicka
- Department
of Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
| | | | | | - Rob Joosten
- DuPont
Industrial Biosciences, Wageningen, The Netherlands
| | - Gerrit Eggink
- Department
of Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
- Wageningen
Food & Biobased Research, Wageningen, The Netherlands
| | | | - Carmen G. Boeriu
- Wageningen
Food & Biobased Research, Wageningen, The Netherlands
- E-mail: . Phone: +31 317 480168
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76
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Monge EC, Tuveng TR, Vaaje-Kolstad G, Eijsink VGH, Gardner JG. Systems analysis of the glycoside hydrolase family 18 enzymes from Cellvibrio japonicus characterizes essential chitin degradation functions. J Biol Chem 2018; 293:3849-3859. [PMID: 29367339 DOI: 10.1074/jbc.ra117.000849] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/10/2018] [Indexed: 01/01/2023] Open
Abstract
Understanding the strategies used by bacteria to degrade polysaccharides constitutes an invaluable tool for biotechnological applications. Bacteria are major mediators of polysaccharide degradation in nature; however, the complex mechanisms used to detect, degrade, and consume these substrates are not well-understood, especially for recalcitrant polysaccharides such as chitin. It has been previously shown that the model bacterial saprophyte Cellvibrio japonicus is able to catabolize chitin, but little is known about the enzymatic machinery underlying this capability. Previous analyses of the C. japonicus genome and proteome indicated the presence of four glycoside hydrolase family 18 (GH18) enzymes, and studies of the proteome indicated that all are involved in chitin utilization. Using a combination of in vitro and in vivo approaches, we have studied the roles of these four chitinases in chitin bioconversion. Genetic analyses showed that only the chi18D gene product is essential for the degradation of chitin substrates. Biochemical characterization of the four enzymes showed functional differences and synergistic effects during chitin degradation, indicating non-redundant roles in the cell. Transcriptomic studies revealed complex regulation of the chitin degradation machinery of C. japonicus and confirmed the importance of CjChi18D and CjLPMO10A, a previously characterized chitin-active enzyme. With this systems biology approach, we deciphered the physiological relevance of the glycoside hydrolase family 18 enzymes for chitin degradation in C. japonicus, and the combination of in vitro and in vivo approaches provided a comprehensive understanding of the initial stages of chitin degradation by this bacterium.
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Affiliation(s)
- Estela C Monge
- From the Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250 and
| | - Tina R Tuveng
- the Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Gustav Vaaje-Kolstad
- the Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Vincent G H Eijsink
- the Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Jeffrey G Gardner
- From the Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250 and
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77
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Blake AD, Beri NR, Guttman HS, Cheng R, Gardner JG. The complex physiology of
Cellvibrio japonicus
xylan degradation relies on a single cytoplasmic β‐xylosidase for xylo‐oligosaccharide utilization. Mol Microbiol 2018; 107:610-622. [DOI: 10.1111/mmi.13903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew D. Blake
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Nina R. Beri
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Hadassa S. Guttman
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Raymond Cheng
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Jeffrey G. Gardner
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
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78
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Production and spectroscopic characterization of lytic polysaccharide monooxygenases. Methods Enzymol 2018; 613:63-90. [DOI: 10.1016/bs.mie.2018.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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79
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Fontaine SS, Novarro AJ, Kohl KD. Environmental temperature alters the digestive performance and gut microbiota of a terrestrial amphibian. J Exp Biol 2018; 221:jeb.187559. [DOI: 10.1242/jeb.187559] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/27/2018] [Indexed: 12/25/2022]
Abstract
Environmental temperature and gut microbial communities can both have profound impacts on the digestive performance of ectothermic vertebrates. Additionally, the diversity, composition, and function of gut microbial communities themselves are influenced by temperature. It is typically assumed that the temperature-dependent nature of ectotherm digestive performance is due to factors such as host physiological changes and adaptation to local climatic conditions. However, it is also possible that temperature-induced alterations to gut microbiota may influence the relationship between temperature and digestion. To explore the connections between these three factors, we compared digestive performance and gut microbial community diversity and composition in red-backed salamanders housed at three experimental temperatures—10°C, 15°C, and 20°C. We also investigated associations between specific bacterial taxa and temperature, or salamander digestive performance. We found that salamander digestive performance was greatest at 15°C, while gut microbial diversity was reduced at 20°C. Further, gut microbial community composition differed among the three temperature treatments. The relative abundances of 25 bacterial genera were dependent on temperature, with high temperatures being associated with reductions in relative abundance of disease-resistant bacteria and increases in pathogenic taxa. The relative abundances of four bacterial genera were correlated with salamander energy assimilation, two of which are known to digest chitin, a main component of the red-backed salamander diet. These findings suggest that gut microbiota may mediate the relationship between temperature and digestion in ectotherms. We discuss how global climate change may impact ectotherms by altering host-microbe interactions.
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Affiliation(s)
- Samantha S. Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260 USA
| | | | - Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260 USA
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80
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Forsberg Z, Bissaro B, Gullesen J, Dalhus B, Vaaje-Kolstad G, Eijsink VGH. Structural determinants of bacterial lytic polysaccharide monooxygenase functionality. J Biol Chem 2017; 293:1397-1412. [PMID: 29222333 DOI: 10.1074/jbc.m117.817130] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/22/2017] [Indexed: 12/18/2022] Open
Abstract
Bacterial lytic polysaccharide monooxygenases (LPMO10s) use redox chemistry to cleave glycosidic bonds in the two foremost recalcitrant polysaccharides found in nature, namely cellulose and chitin. Analysis of correlated mutations revealed that the substrate-binding and copper-containing surface of LPMO10s composes a network of co-evolved residues and interactions, whose roles in LPMO functionality are unclear. Here, we mutated a subset of these correlated residues in a newly characterized C1/C4-oxidizing LPMO10 from Micromonospora aurantiaca (MaLPMO10B) to the corresponding residues in strictly C1-oxidizing LPMO10s. We found that surface properties near the catalytic copper, i.e. side chains likely to be involved in substrate positioning, are major determinants of the C1:C4 ratio. Several MaLPMO10B mutants almost completely lost C4-oxidizing activity while maintaining C1-oxidizing activity. These mutants also lost chitin-oxidizing activity, which is typically observed for C1/C4-oxidizing, but not for C1-oxidizing, cellulose-active LPMO10s. Selective loss in C1-oxidizing activity was not observed. Additional mutational experiments disclosed that neither truncation of the MaLPMO10B family 2 carbohydrate-binding module nor mutations altering access to the solvent-exposed axial copper coordination site significantly change the C1:C4 ratio. Importantly, several of the mutations that altered interactions with the substrate exhibited reduced stability. This effect could be explained by productive substrate binding that protects LPMOs from oxidative self-inactivation. We discuss these stability issues in view of recent findings on LPMO catalysis, such as the involvement of H2O2 Our results show that residues on the substrate-binding surface of LPMOs have co-evolved to optimize several of the interconnected properties: substrate binding and specificity, oxidative regioselectivity, catalytic efficiency, and stability.
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Affiliation(s)
- Zarah Forsberg
- From the Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway,
| | - Bastien Bissaro
- From the Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France, and
| | - Jonathan Gullesen
- From the Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Bjørn Dalhus
- the Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, 0318 Oslo, Norway, and.,the Department of Microbiology, Clinic for Laboratory Medicine, Oslo University Hospital, Rikshospitalet, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Gustav Vaaje-Kolstad
- From the Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Vincent G H Eijsink
- From the Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
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81
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Nelson CE, Attia MA, Rogowski A, Morland C, Brumer H, Gardner JG. Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification. Environ Microbiol 2017; 19:5025-5039. [PMID: 29052930 DOI: 10.1111/1462-2920.13959] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/27/2017] [Accepted: 10/08/2017] [Indexed: 12/16/2022]
Abstract
Lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1→3)/β(1→4) mixed-linkage glucan (MLG) and β(1→3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active enZymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach, we have delineated the physiological roles of the four C. japonicus glycoside hydrolase family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activity profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1→3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1→3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.
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Affiliation(s)
- Cassandra E Nelson
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
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82
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Quantification of the catalytic performance of C1-cellulose-specific lytic polysaccharide monooxygenases. Appl Microbiol Biotechnol 2017; 102:1281-1295. [PMID: 29196788 PMCID: PMC5778151 DOI: 10.1007/s00253-017-8541-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/25/2017] [Accepted: 09/09/2017] [Indexed: 01/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have recently been shown to significantly enhance the degradation of recalcitrant polysaccharides and are of interest for the production of biochemicals and bioethanol from plant biomass. The copper-containing LPMOs utilize electrons, provided by reducing agents, to oxidatively cleave polysaccharides. Here, we report the development of a β-glucosidase-assisted method to quantify the release of C1-oxidized gluco-oligosaccharides from cellulose by two C1-oxidizing LPMOs from Myceliophthora thermophila C1. Based on this quantification method, we demonstrate that the catalytic performance of both MtLPMOs is strongly dependent on pH and temperature. The obtained results indicate that the catalytic performance of LPMOs depends on the interaction of multiple factors, which are affected by both pH and temperature.
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83
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Courtade G, Forsberg Z, Vaaje-Kolstad G, Eijsink VGH, Aachmann FL. Chemical shift assignments for the apo-form of the catalytic domain, the linker region, and the carbohydrate-binding domain of the cellulose-active lytic polysaccharide monooxygenase ScLPMO10C. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:257-264. [PMID: 28822070 DOI: 10.1007/s12104-017-9759-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
The apo-form of the 21.4 kDa catalytic domain and the 10.7 kDa carbohydrate binding domain of the AA10 family lytic polysaccharide monooxygenase ScLPMO10C from Streptomyces coelicolor have been isotopically labeled and recombinantly expressed in Escherichia coli. In this paper, we report the 1H, 13C, and 15N chemical shift assignments of each individual domain as well as an ensemble of the assignment for the full-length protein, including its approximately 30-amino acid long linker.
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Affiliation(s)
- Gaston Courtade
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Finn L Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway.
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84
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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.
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85
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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]
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86
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Berrin JG, Rosso MN, Abou Hachem M. Fungal secretomics to probe the biological functions of lytic polysaccharide monooxygenases. Carbohydr Res 2017; 448:155-160. [DOI: 10.1016/j.carres.2017.05.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/29/2022]
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87
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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]
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88
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Bacik JP, Mekasha S, Forsberg Z, Kovalevsky AY, Vaaje-Kolstad G, Eijsink VGH, Nix JC, Coates L, Cuneo MJ, Unkefer CJ, Chen JCH. Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation. Biochemistry 2017; 56:2529-2532. [DOI: 10.1021/acs.biochem.7b00019] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- John-Paul Bacik
- Protein
Crystallography Station, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sophanit Mekasha
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Zarah Forsberg
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Andrey Y. Kovalevsky
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Gustav Vaaje-Kolstad
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Vincent G. H. Eijsink
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Jay C. Nix
- Advanced
Light Source, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Leighton Coates
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Matthew J. Cuneo
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Clifford J. Unkefer
- Protein
Crystallography Station, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Julian C.-H. Chen
- Protein
Crystallography Station, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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89
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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]
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90
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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.
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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
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91
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Gardner JG. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus. World J Microbiol Biotechnol 2016; 32:121. [PMID: 27263016 DOI: 10.1007/s11274-016-2068-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023]
Abstract
Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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92
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Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG. Proteomic investigation of the secretome ofCellvibrio japonicusduring growth on chitin. Proteomics 2016; 16:1904-14. [DOI: 10.1002/pmic.201500419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 04/05/2016] [Accepted: 05/09/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tina Rise Tuveng
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Magnus Øverlie Arntzen
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Oskar Bengtsson
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Jeffrey G. Gardner
- Department of Biological Sciences; University of Maryland - Baltimore County; Baltimore MD USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Vincent G.H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
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93
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Gregory RC, Hemsworth GR, Turkenburg JP, Hart SJ, Walton PH, Davies GJ. Activity, stability and 3-D structure of the Cu(ii) form of a chitin-active lytic polysaccharide monooxygenase from Bacillus amyloliquefaciens. Dalton Trans 2016; 45:16904-16912. [DOI: 10.1039/c6dt02793h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The enzymatic deconstruction of recalcitrant polysaccharide biomass is central to the conversion of these substrates for societal benefit, such as in biofuels.
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