1
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Österberg M, Henn KA, Farooq M, Valle-Delgado JJ. Biobased Nanomaterials─The Role of Interfacial Interactions for Advanced Materials. Chem Rev 2023; 123:2200-2241. [PMID: 36720130 PMCID: PMC9999428 DOI: 10.1021/acs.chemrev.2c00492] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This review presents recent advances regarding biomass-based nanomaterials, focusing on their surface interactions. Plant biomass-based nanoparticles, like nanocellulose and lignin from industry side streams, hold great potential for the development of lightweight, functional, biodegradable, or recyclable material solutions for a sustainable circular bioeconomy. However, to obtain optimal properties of the nanoparticles and materials made thereof, it is crucial to control the interactions both during particle production and in applications. Herein we focus on the current understanding of these interactions. Solvent interactions during particle formation and production, as well as interactions with water, polymers, cells and other components in applications, are addressed. We concentrate on cellulose and lignin nanomaterials and their combination. We demonstrate how the surface chemistry of the nanomaterials affects these interactions and how excellent performance is only achieved when the interactions are controlled. We furthermore introduce suitable methods for probing interactions with nanomaterials, describe their advantages and challenges, and introduce some less commonly used methods and discuss their possible applications to gain a deeper understanding of the interfacial chemistry of biobased nanomaterials. Finally, some gaps in current understanding and interesting emerging research lines are identified.
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Affiliation(s)
- Monika Österberg
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Vuorimiehentie 1, 02150Espoo, Finland
| | - K Alexander Henn
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Vuorimiehentie 1, 02150Espoo, Finland
| | - Muhammad Farooq
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Vuorimiehentie 1, 02150Espoo, Finland
| | - Juan José Valle-Delgado
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Vuorimiehentie 1, 02150Espoo, Finland
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2
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Uchiyama T, Uchihashi T, Ishida T, Nakamura A, Vermaas JV, Crowley MF, Samejima M, Beckham GT, Igarashi K. Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface. SCIENCE ADVANCES 2022; 8:eade5155. [PMID: 36563138 PMCID: PMC9788756 DOI: 10.1126/sciadv.ade5155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/21/2022] [Indexed: 05/31/2023]
Abstract
Efficient depolymerization of crystalline cellulose requires cooperation between multiple cellulolytic enzymes. Through biochemical approaches, molecular dynamics (MD) simulation, and single-molecule observations using high-speed atomic force microscopy (HS-AFM), we quantify and track synergistic activity for cellobiohydrolases (CBHs) with a lytic polysaccharide monooxygenase (LPMO) from Phanerochaete chrysosporium. Increasing concentrations of LPMO (AA9D) increased the activity of a glycoside hydrolase family 6 CBH, Cel6A, whereas the activity of a family 7 CBH (Cel7D) was enhanced only at lower concentrations of AA9D. MD simulation suggests that the result of AA9D action to produce chain breaks in crystalline cellulose can oxidatively disturb the crystalline surface by disrupting hydrogen bonds. HS-AFM observations showed that AA9D increased the number of Cel7D molecules moving on the substrate surface and increased the processivity of Cel7D, thereby increasing the depolymerization performance, suggesting that AA9D not only generates chain ends but also amorphizes the crystalline surface, thereby increasing the activity of CBHs.
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Affiliation(s)
- Taku Uchiyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takayuki Uchihashi
- Department of Physics and Structural Biology Research Center, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Physics, Structural Biology Center, and Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8602, Japan
| | - Takuya Ishida
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
| | - Josh V. Vermaas
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael F. Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano 380-8533, Japan
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- VTT Technical Research Center of Finland Ltd., Tietotie 2, P.O. Box 1000, Espoo, FI-02044 VTT, Finland
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3
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Gacias-Amengual N, Wohlschlager L, Csarman F, Ludwig R. Fluorescent Imaging of Extracellular Fungal Enzymes Bound onto Plant Cell Walls. Int J Mol Sci 2022; 23:ijms23095216. [PMID: 35563607 PMCID: PMC9105846 DOI: 10.3390/ijms23095216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023] Open
Abstract
Lignocelluloytic enzymes are industrially applied as biocatalysts for the deconstruction of recalcitrant plant biomass. To study their biocatalytic and physiological function, the assessment of their binding behavior and spatial distribution on lignocellulosic material is a crucial prerequisite. In this study, selected hydrolases and oxidoreductases from the white rot fungus Phanerochaete chrysosporium were localized on model substrates as well as poplar wood by confocal laser scanning microscopy. Two different detection approaches were investigated: direct tagging of the enzymes and tagging specific antibodies generated against the enzymes. Site-directed mutagenesis was employed to introduce a single surface-exposed cysteine residue for the maleimide site-specific conjugation. Specific polyclonal antibodies were produced against the enzymes and were labeled using N-hydroxysuccinimide (NHS) ester as a cross-linker. Both methods allowed the visualization of cell wall-bound enzymes but showed slightly different fluorescent yields. Using native poplar thin sections, we identified the innermost secondary cell wall layer as the preferential attack point for cellulose-degrading enzymes. Alkali pretreatment resulted in a partial delignification and promoted substrate accessibility and enzyme binding. The methods presented in this study are suitable for the visualization of enzymes during catalytic biomass degradation and can be further exploited for interaction studies of lignocellulolytic enzymes in biorefineries.
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4
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Spiliopoulos P, Spirk S, Pääkkönen T, Viljanen M, Svedström K, Pitkänen L, Awais M, Kontturi E. Visualizing Degradation of Cellulose Nanofibers by Acid Hydrolysis. Biomacromolecules 2021; 22:1399-1405. [PMID: 33523637 PMCID: PMC8045026 DOI: 10.1021/acs.biomac.0c01625] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/16/2021] [Indexed: 12/23/2022]
Abstract
Cellulose hydrolysis is an extensively studied process due to its relevance in the fields of biofuels, chemicals production, and renewable nanomaterials. However, the direct visualization of the process accompanied with detailed scaling has not been reported because of the vast morphological alterations occurring in cellulosic fibers in typical heterogeneous (solid/liquid) hydrolytic systems. Here, we overcome this distraction by exposing hardwood cellulose nanofibers (CNFs) deposited on silica substrates to pressurized HCl gas in a solid/gas system and examine the changes in individual CNFs by atomic force microscopy (AFM). The results revealed that hydrolysis proceeds via an intermediate semi-fibrous stage before objects reminiscent of cellulose nanocrystals were formed. The length of the nanocrystal-like objects correlated well with molar mass, as analyzed by gel permeation chromatography, performed on CNF aerogels hydrolyzed under identical conditions. Meanwhile, X-ray diffraction showed a slight increase in crystallinity index as the hydrolysis proceeded. The results provide a modern visual complement to >100 years of research in cellulose degradation.
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Affiliation(s)
- Panagiotis Spiliopoulos
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O Box 16300, Aalto 00076, Finland
| | - Stefan Spirk
- Institute
of Bioproducts and Paper Technology, Graz
University of Technology, Graz 8010, Austria
| | - Timo Pääkkönen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O Box 16300, Aalto 00076, Finland
| | - Mira Viljanen
- Department
of Physics, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
| | - Kirsi Svedström
- Department
of Physics, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
| | - Leena Pitkänen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O Box 16300, Aalto 00076, Finland
| | - Muhammad Awais
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O Box 16300, Aalto 00076, Finland
| | - Eero Kontturi
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O Box 16300, Aalto 00076, Finland
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5
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Chundawat SPS, Nemmaru B, Hackl M, Brady SK, Hilton MA, Johnson MM, Chang S, Lang MJ, Huh H, Lee SH, Yarbrough JM, López CA, Gnanakaran S. Molecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose III. J Biol Chem 2021; 296:100431. [PMID: 33610545 PMCID: PMC8010709 DOI: 10.1016/j.jbc.2021.100431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 11/30/2022] Open
Abstract
Efficient enzymatic saccharification of cellulosic biomass into fermentable sugars can enable production of bioproducts like ethanol. Native crystalline cellulose, or cellulose I, is inefficiently processed via enzymatic hydrolysis but can be converted into the structurally distinct cellulose III allomorph that is processed via cellulase cocktails derived from Trichoderma reesei up to 20-fold faster. However, characterization of individual cellulases from T. reesei, like the processive exocellulase Cel7A, shows reduced binding and activity at low enzyme loadings toward cellulose III. To clarify this discrepancy, we monitored the single-molecule initial binding commitment and subsequent processive motility of Cel7A enzymes and associated carbohydrate-binding modules (CBMs) on cellulose using optical tweezers force spectroscopy. We confirmed a 48% lower initial binding commitment and 32% slower processive motility of Cel7A on cellulose III, which we hypothesized derives from reduced binding affinity of the Cel7A binding domain CBM1. Classical CBM–cellulose pull-down assays, depending on the adsorption model fitted, predicted between 1.2- and 7-fold reduction in CBM1 binding affinity for cellulose III. Force spectroscopy measurements of CBM1–cellulose interactions, along with molecular dynamics simulations, indicated that previous interpretations of classical binding assay results using multisite adsorption models may have complicated analysis, and instead suggest simpler single-site models should be used. These findings were corroborated by binding analysis of other type-A CBMs (CBM2a, CBM3a, CBM5, CBM10, and CBM64) on both cellulose allomorphs. Finally, we discuss how complementary analytical tools are critical to gain insight into the complex mechanisms of insoluble polysaccharides hydrolysis by cellulolytic enzymes and associated carbohydrate-binding proteins.
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Affiliation(s)
- Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
| | - Bhargava Nemmaru
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Markus Hackl
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sonia K Brady
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Mark A Hilton
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Madeline M Johnson
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Sungrok Chang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Hyun Huh
- Department of Physics and Astronomy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sang-Hyuk Lee
- Department of Physics and Astronomy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - John M Yarbrough
- Biosciences Center, National Renewable Energy Lab, Golden, Colorado, USA
| | - Cesar A López
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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6
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Negoro S, Kato DI, Ohki T, Yasuhira K, Kawashima Y, Nagai K, Takeo M, Shibata N, Kamiya K, Shigeta Y. Structural and functional characterization of nylon hydrolases. Methods Enzymol 2020; 648:357-389. [PMID: 33579412 DOI: 10.1016/bs.mie.2020.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Biodegradation of synthetic polymers is recognized as a useful way to reduce their environmental load and pollution, loss of natural resources, extensive energy consumption, and generation of greenhouse gases. The potential use of enzymes responsible for the degradation of the targeted polymers is an effective approach which enables the conversion of the used polymers to original monomers and/or other useful compounds. In addition, the enzymes are expected to be applicable in industrial processes such as improving the surface structures of the polymers. Especially, conversion of the solid polymers to soluble oligomers/monomers is a key step for the biodegradation of the polymers. Regarding the hydrolysis of polyamides, three enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (NylA), 6-aminohexanoate-dimer hydrolase (NylB), and 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC), are found in several bacterial strains. In this chapter, we describe our approach for the screening of microorganisms which degrade nylons and related compounds; preparation of substrates; assay of hydrolytic activity for soluble and insoluble substrates; and X-ray crystallographic and computational approaches for analysis of structure and catalytic mechanisms of the nylon-degrading enzymes.
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Affiliation(s)
- Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan.
| | - Dai-Ichiro Kato
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Taku Ohki
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Kengo Yasuhira
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Yasuyuki Kawashima
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Keisuke Nagai
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Naoki Shibata
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Katsumasa Kamiya
- Education Development Center, Kanagawa Institute of Technology, Atsugi, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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7
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Abstract
Some cellulases exhibit “processivity”: the ability to degrade crystalline cellulose through successive hydrolytic catalytic reactions without the release of the enzyme from the substrate surface. We previously observed the movement of fungal processive cellulases by high-speed atomic force microscopy, and here, we use the same technique to directly observe the processive movement of bacterial cellobiohydrolases settling a long-standing controversy. Although fungal and bacterial processive cellulases have completely different protein folds, they have evolved to acquire processivity through the same strategy of adding subsites to extend the substrate-binding site and forming a tunnel-like active site by increasing the number of loops covering the active site. This represents an example of protein-level convergent evolution to acquire the same functions from different ancestors. Cellulose is the most abundant biomass on Earth, and many microorganisms depend on it as a source of energy. It consists mainly of crystalline and amorphous regions, and natural degradation of the crystalline part is highly dependent on the degree of processivity of the degrading enzymes (i.e., the extent of continuous hydrolysis without detachment from the substrate cellulose). Here, we report high-speed atomic force microscopic (HS-AFM) observations of the movement of four types of cellulases derived from the cellulolytic bacteria Cellulomonas fimi on various insoluble cellulose substrates. The HS-AFM images clearly demonstrated that two of them (CfCel6B and CfCel48A) slide on crystalline cellulose. The direction of processive movement of CfCel6B is from the nonreducing to the reducing end of the substrate, which is opposite that of processive cellulase Cel7A of the fungus Trichoderma reesei (TrCel7A), whose movement was first observed by this technique, while CfCel48A moves in the same direction as TrCel7A. When CfCel6B and TrCel7A were mixed on the same substrate, “traffic accidents” were observed, in which the two cellulases blocked each other’s progress. The processivity of CfCel6B was similar to those of fungal family 7 cellulases but considerably higher than those of fungal family 6 cellulases. The results indicate that bacteria utilize family 6 cellulases as high-processivity enzymes for efficient degradation of crystalline cellulose, whereas family 7 enzymes have the same function in fungi. This is consistent with the idea of convergent evolution of processive cellulases in fungi and bacteria to achieve similar functionality using different protein foldings.
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8
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Igarashi K, Kaneko S, Kitaoka M, Samejima M. Effect of C-6 Methylol Groups on Substrate Recognition of Glucose/Xylose Mixed Oligosaccharides by Cellobiose Dehydrogenase from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2020; 67:51-57. [PMID: 34354528 PMCID: PMC8293687 DOI: 10.5458/jag.jag.jag-2020_0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/28/2020] [Indexed: 12/02/2022] Open
Abstract
Cellobiose dehydrogenase (CDH) is a flavocytochrome catalyzing oxidation of the reducing end of cellobiose and cellooligosaccharides, and has a key role in the degradation of cellulosic biomass by filamentous fungi. Here, we use a lineup of glucose/xylose-mixed β-1,4-linked disaccharides and trisaccharides, enzymatically synthesized by means of the reverse reaction of cellobiose phosphorylase and cellodextrin phosphorylase, to investigate the substrate recognition of CDH. We found that CDH utilizes β-D-xylopyranosyl-(1→4)-D-glucopyranose (Xyl-Glc) as an electron donor with similar Km and kcat values to cellobiose. β-D-Glucopyranosyl-(1→4)-D-xylopyranose (Glc-Xyl) shows a higher Km value, while xylobiose does not serve as a substrate. Trisaccharides show similar behavior; i.e., trisaccharides with cellobiose and Xyl-Glc units at the reducing end show similar kinetics, while the enzyme was less active towards those with Glc-Xyl, and inactive towards those with xylobiose. We also use docking simulation to evaluate substrate recognition of the disaccharides, and we discuss possible molecular mechanisms of substrate recognition by CDH.
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Affiliation(s)
- Kiyohiko Igarashi
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,2 VTT Technical Research Centre of Finland Ltd
| | - Satoshi Kaneko
- 3 Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus
| | - Motomitsu Kitaoka
- 4 Faculty of Agriculture, Niigata University.,5 Food Research Institute, National Agriculture and Food Research Organization
| | - Masahiro Samejima
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,6 Faculty of Engineering, Shinshu University
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9
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Blanco Parte FG, Santoso SP, Chou CC, Verma V, Wang HT, Ismadji S, Cheng KC. Current progress on the production, modification, and applications of bacterial cellulose. Crit Rev Biotechnol 2020; 40:397-414. [PMID: 31937141 DOI: 10.1080/07388551.2020.1713721] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Adoption of biomass for the development of biobased products has become a routine agenda in evolutionary metabolic engineering. Cellulose produced by bacteria is a "rising star" for this sustainable development. Unlike plant cellulose, bacterial cellulose (BC) shows several unique properties like a high degree of crystallinity, high purity, high water retention, high mechanical strength, and enhanced biocompatibility. Favored with those extraordinary properties, BC could serve as ideal biomass for the development of various industrial products. However, a low yield and the requirement for large growth media have been a persistent challenge in mass production of BC. A significant number of techniques has been developed in achieving efficient BC production. This includes the modification of bioreactors, fermentation parameters, and growth media. In this article, we summarize progress in metabolic engineering in order to solve BC growth limitation. This article emphasizes current engineered BC production by using various bioreactors, as well as highlighting the structure of BC fermented by different types of engineered-bioreactors. The comprehensive overview of the future applications of BC, aims to provide readers with insight into new economic opportunities of BC and their modifiable properties for various industrial applications. Modifications in chemical composition, structure, and genetic regulation, which preceded the advancement of BC applications, were also emphasized.
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Affiliation(s)
- Francisco German Blanco Parte
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Shella Permatasari Santoso
- Department of Chemical Engineering, Widya Mandala Surabaya Catholic University, Surabaya, Indonesia.,Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Chih-Chan Chou
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Vivek Verma
- Department of Materials Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, India.,Centre for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Hsueh-Ting Wang
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Suryadi Ismadji
- Department of Chemical Engineering, Widya Mandala Surabaya Catholic University, Surabaya, Indonesia.,Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Kuan-Chen Cheng
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan.,Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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10
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Souza HJB, Botrel DA, Barros Fernandes RV, Borges SV, Campelo Felix PH, Viana LC, Lago AMT. Hygroscopic, structural, and thermal properties of essential oil microparticles of sweet orange added with cellulose nanofibrils. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | - Lívia Cássia Viana
- Department of Forestry Engineering Gurupi University Campus, Federal University of Tocantins Gurupi Brazil
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11
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Nakazawa T, Tsuzuki M, Irie T, Sakamoto M, Honda Y. Marker recycling via 5-fluoroorotic acid and 5-fluorocytosine counter-selection in the white-rot agaricomycete Pleurotus ostreatus. Fungal Biol 2016; 120:1146-55. [PMID: 27567720 DOI: 10.1016/j.funbio.2016.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 01/06/2023]
Abstract
Of all of the natural polymers, lignin, an aromatic heteropolymer in plant secondary cell walls, is the most resistant to biological degradation. White-rot fungi are the only known organisms that can depolymerize or modify wood lignin. Investigating the mechanisms underlying lignin biodegradation by white-rot fungi would contribute to the ecofriendly utilization of woody biomass as renewable resources in the future. Efficient gene disruption, which is generally very challenging in the white-rot fungi, was established in Pleurotus ostreatus (the oyster mushroom). Some of the genes encoding manganese peroxidases, enzymes that are considered to be involved in lignin biodegradation, were disrupted separately, and the phenotype of each single-gene disruptant was analysed. However, it remains difficult to generate multi-gene disruptants in this fungus. Here we developed a new genetic transformation marker in P. ostreatus and demonstrated two marker recycling methods that use counter-selection to generate a multigene disruptant. This study will enable future genetic studies of white-rot fungi, and it will increase our understanding of the complicated mechanisms, which involve various enzymes, including lignin-degrading enzymes, underlying lignin biodegradation by these fungi.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Masami Tsuzuki
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toshikazu Irie
- Environmental Science Graduate School, The University of Shiga Prefecture, Hikone, Shiga, 522-8533, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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12
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Amore A, Ciesielski PN, Lin CY, Salvachúa D, Sànchez i Nogué V. Development of Lignocellulosic Biorefinery Technologies: Recent Advances and Current Challenges. Aust J Chem 2016. [DOI: 10.1071/ch16022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent developments of the biorefinery concept are described within this review, which focuses on the efforts required to make the lignocellulosic biorefinery a sustainable and economically viable reality. Despite the major research and development endeavours directed towards this goal over the past several decades, the integrated production of biofuel and other bio-based products still needs to be optimized from both technical and economical perspectives. This review will highlight recent progress towards the optimization of the major biorefinery processes, including biomass pretreatment and fractionation, saccharification of sugars, and conversion of sugars and lignin into fuels and chemical precursors. In addition, advances in genetic modification of biomass structure and composition for the purpose of enhancing the efficacy of conversion processes, which is emerging as a powerful tool for tailoring biomass fated for the biorefinery, will be overviewed. The continual improvement of these processes and their integration in the format of a modern biorefinery is paving the way for a sustainable bio-economy which will displace large portions of petroleum-derived fuels and chemicals with renewable substitutes.
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13
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Lyubchenko YL, Shlyakhtenko LS. Chromatin imaging with time-lapse atomic force microscopy. Methods Mol Biol 2015; 1288:27-42. [PMID: 25827873 DOI: 10.1007/978-1-4939-2474-5_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Time-lapse atomic force microscopy (AFM) is widely used for direct visualization of the nanoscale dynamics of various biological systems. The advent of high-speed AFM instrumentation made it possible to image the dynamics of proteins and protein-DNA complexes within millisecond time range. This chapter describes protocols for studies of structure and dynamics of nucleosomes with time-lapse AFM including the high-speed AFM instrument. The necessary specifics for the preparation of chromatin samples for imaging with AFM including the protocols for the surface preparation are provided.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025, Nebraska Medical Center, Omaha, NE, 68198-6025, USA,
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Greene ER, Himmel ME, Beckham GT, Tan Z. Glycosylation of Cellulases: Engineering Better Enzymes for Biofuels. Adv Carbohydr Chem Biochem 2015; 72:63-112. [PMID: 26613815 DOI: 10.1016/bs.accb.2015.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulose in plant cell walls is the largest reservoir of renewable carbon on Earth. The saccharification of cellulose from plant biomass into soluble sugars can be achieved using fungal and bacterial cellulolytic enzymes, cellulases, and further converted into fuels and chemicals. Most fungal cellulases are both N- and O-glycosylated in their native form, yet the consequences of glycosylation on activity and structure are not fully understood. Studying protein glycosylation is challenging as glycans are extremely heterogeneous, stereochemically complex, and glycosylation is not under direct genetic control. Despite these limitations, many studies have begun to unveil the role of cellulase glycosylation, especially in the industrially relevant cellobiohydrolase from Trichoderma reesei, Cel7A. Glycosylation confers many beneficial properties to cellulases including enhanced activity, thermal and proteolytic stability, and structural stabilization. However, glycosylation must be controlled carefully as such positive effects can be dampened or reversed. Encouragingly, methods for the manipulation of glycan structures have been recently reported that employ genetic tuning of glycan-active enzymes expressed from homogeneous and heterologous fungal hosts. Taken together, these studies have enabled new strategies for the exploitation of protein glycosylation for the production of enhanced cellulases for biofuel production.
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Enzymatic hydrolysis of nylons: quantification of the reaction rate of nylon hydrolase for thin-layered nylons. Appl Microbiol Biotechnol 2014; 98:8751-61. [DOI: 10.1007/s00253-014-5885-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/06/2014] [Accepted: 06/08/2014] [Indexed: 10/25/2022]
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Igarashi K, Uchihashi T, Uchiyama T, Sugimoto H, Wada M, Suzuki K, Sakuda S, Ando T, Watanabe T, Samejima M. Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin. Nat Commun 2014; 5:3975. [DOI: 10.1038/ncomms4975] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/25/2014] [Indexed: 11/09/2022] Open
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Nakamura A, Watanabe H, Ishida T, Uchihashi T, Wada M, Ando T, Igarashi K, Samejima M. Trade-off between processivity and hydrolytic velocity of cellobiohydrolases at the surface of crystalline cellulose. J Am Chem Soc 2014; 136:4584-92. [PMID: 24571226 DOI: 10.1021/ja4119994] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analysis of heterogeneous catalysis at an interface is difficult because of the variety of reaction sites and the difficulty of observing the reaction. Enzymatic hydrolysis of cellulose by cellulases is a typical heterogeneous reaction at a solid/liquid interface, and a key parameter of such reactions on polymeric substrates is the processivity, i.e., the number of catalytic cycles that can occur without detachment of the enzyme from the substrate. In this study, we evaluated the reactions of three closely related glycoside hydrolase family 7 cellobiohydrolases from filamentous fungi at the molecular level by means of high-speed atomic force microscopy to investigate the structure-function relationship of the cellobiohydrolases on crystalline cellulose. We found that high moving velocity of enzyme molecules on the surface is associated with a high dissociation rate constant from the substrate, which means weak interaction between enzyme and substrate. Moreover, higher values of processivity were associated with more loop regions covering the subsite cleft, which may imply higher binding affinity. Loop regions covering the subsites result in stronger interaction, which decreases the velocity but increases the processivity. These results indicate that there is a trade-off between processivity and hydrolytic velocity among processive cellulases.
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Affiliation(s)
- Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Nakamura A, Tsukada T, Auer S, Furuta T, Wada M, Koivula A, Igarashi K, Samejima M. The tryptophan residue at the active site tunnel entrance of Trichoderma reesei cellobiohydrolase Cel7A is important for initiation of degradation of crystalline cellulose. J Biol Chem 2013; 288:13503-10. [PMID: 23532843 DOI: 10.1074/jbc.m113.452623] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Mutation of Trp-40 in the Cel7A cellobiohydrolase from Trichoderma reesei (TrCel7A) causes a loss of crystalline cellulose-degrading ability. RESULTS Mutant W40A showed reduced specific activity for crystalline cellulose and diffused the cellulose chain from the entrance of the active site tunnel. CONCLUSION Trp-40 is essential for chain end loading to initiate processive hydrolysis of TrCel7A. SIGNIFICANCE The mechanisms of crystalline polysaccharide degradation are clarified. The glycoside hydrolase family 7 cellobiohydrolase Cel7A from Trichoderma reesei is one of the best studied cellulases with the ability to degrade highly crystalline cellulose. The catalytic domain and the cellulose-binding domain (CBD) are both necessary for full activity on crystalline substrates. Our previous high-speed atomic force microscopy studies showed that mutation of Trp-40 at the entrance of the catalytic tunnel drastically decreases the ability to degrade crystalline cellulose. Here, we examined the activities of the WT enzyme and mutant W40A (with and without the CBD) for various substrates. Evaluation and comparison of the specific activities of the enzymes (WT, W40A, and the corresponding catalytic subunits (WTcat and W40Acat)) adsorbed on crystalline cellulose indicated that Trp-40 is involved in recruiting individual substrate chains into the active site tunnel to initiate processive hydrolysis. This was supported by molecular dynamics simulation study, i.e. the reducing end glucose unit was effectively loaded into the active site of WTcat, but not into that of W40Acat, when the simulation was started from subsite -7. However, when similar simulations were carried out starting from subsite -5, both enzymes held the substrate for 50 ns, indicating that the major difference between WTcat and W40Acat is the length of the free chain end of the substrate required to allow initiation of processive movements; this also reflects the difference between crystalline and amorphous celluloses. The CBD is important for enhancing the enzyme population on crystalline substrate, but it also decreases the specific activity of the adsorbed enzyme, possibly by attaching the enzyme to non-optimal places on the cellulose surface and/or hindering processive hydrolysis.
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Affiliation(s)
- Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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Mizuno M, Kachi S, Togawa E, Hayashi N, Nozaki K, Itoh T, Amano Y. Structure of Regenerated Celluloses Treated with Ionic Liquids and Comparison of their Enzymatic Digestibility by Purified Cellulase Components. Aust J Chem 2012. [DOI: 10.1071/ch12342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this study, regenerated celluloses were prepared from microcrystalline cellulose (MCC) by treatment with three ionic liquids (ILs) having 1-ethyl-3-methylimidazolium (Emim) as the cation, and the IL N-(2-methoxyethyl)-N,N-diethyl-N-methylammonium alanine ([N221ME][Ala]), where the amino acid moiety is the anion. The crystal form of cellulose was transformed from cellulose I to cellulose II by dissolution with an IL and regeneration with anti-solvent. However, the crystallinity of the regenerated cellulose was different; the disordered chain region was increased in the order of [N221ME][Ala] < [Emim][OAc] < [Emim][DEP] < [Emim][Cl]. The monocomponent cellulase, especially endoglucanase, showed high hydrolyzing activity for regenerated cellulose compared with untreated cellulose. Furthermore, the degree of increase of hydrolyzing activity was almost coincident with the order of crystallinity. For the effective hydrolysis of cellulose treated with an IL, it is necessary to prepare the cellulase mixture containing an adequate ratio of each cellulase component according to crystal allomorph and the crystallinity of regenerated cellulose.
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