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Moy A, Nkongolo K. Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine ( Pinus banksiana) Based on Transcriptomic Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1042. [PMID: 38611570 PMCID: PMC11013723 DOI: 10.3390/plants13071042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.
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Affiliation(s)
| | - Kabwe Nkongolo
- Biomolecular Sciences Program, Department of Biology, School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
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2
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Tryfona T, Pankratova Y, Petrik D, Rebaque Moran D, Wightman R, Yu X, Echevarría-Poza A, Deralia PK, Vilaplana F, Anderson CT, Hong M, Dupree P. Altering the substitution and cross-linking of glucuronoarabinoxylans affects cell wall architecture in Brachypodium distachyon. THE NEW PHYTOLOGIST 2024; 242:524-543. [PMID: 38413240 DOI: 10.1111/nph.19624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
The Poaceae family of plants provides cereal crops that are critical for human and animal nutrition, and also, they are an important source of biomass. Interacting plant cell wall components give rise to recalcitrance to digestion; thus, understanding the wall molecular architecture is important to improve biomass properties. Xylan is the main hemicellulose in grass cell walls. Recently, we reported structural variation in grass xylans, suggesting functional specialisation and distinct interactions with cellulose and lignin. Here, we investigated the functions of these xylans by perturbing the biosynthesis of specific xylan types. We generated CRISPR/Cas9 knockout mutants in Brachypodium distachyon XAX1 and GUX2 genes involved in xylan substitution. Using carbohydrate gel electrophoresis, we identified biochemical changes in different xylan types. Saccharification, cryo-SEM, subcritical water extraction and ssNMR were used to study wall architecture. BdXAX1A and BdGUX2 enzymes modify different types of grass xylan. Brachypodium mutant walls are likely more porous, suggesting the xylan substitutions directed by both BdXAX1A and GUX2 enzymes influence xylan-xylan and/or xylan-lignin interactions. Since xylan substitutions influence wall architecture and digestibility, our findings open new avenues to improve cereals for food and to use grass biomass for feed and the production of bioenergy and biomaterials.
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Affiliation(s)
- Theodora Tryfona
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Yanina Pankratova
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, NW14-3212, USA
| | - Deborah Petrik
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Diego Rebaque Moran
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, SE-106, Sweden
- Centro de Biotecnologia y Genomica de Plants (UPM-INIA/CSIC), Universidad Politecnica de Madrid, Pozuelo de Alarcon (Madrid), 28223, Spain
| | | | - Xiaolan Yu
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Alberto Echevarría-Poza
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Parveen Kumar Deralia
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, SE-106, Sweden
- Wallenberg Wood Science Centre, KTH Royal Institute of Technology, Stockholm, SE-11, Sweden
| | - Charles T Anderson
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, NW14-3212, USA
| | - Paul Dupree
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
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3
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Gallinari RH, Lyczakowski JJ, Llerena JPP, Mayer JLS, Rabelo SC, Menossi Teixeira M, Dupree P, Araujo P. Silencing ScGUX2 reduces xylan glucuronidation and improves biomass saccharification in sugarcane. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:587-601. [PMID: 38146142 PMCID: PMC10893953 DOI: 10.1111/pbi.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 12/27/2023]
Abstract
There is an increasing need for renewable energy sources to replace part of our fossil fuel-based economy and reduce greenhouse gas emission. Sugarcane bagasse is a prominent feedstock to produce cellulosic bioethanol, but strategies are still needed to improve the cost-effective exploitation of this potential energy source. In model plants, it has been shown that GUX genes are involved in cell wall hemicellulose decoration, adding glucuronic acid substitutions on the xylan backbone. Mutation of GUX genes increases enzyme access to cell wall polysaccharides, reducing biomass recalcitrance in Arabidopsis thaliana. Here, we characterized the sugarcane GUX genes and silenced GUX2 in commercial hybrid sugarcane. The transgenic lines had no penalty in development under greenhouse conditions. The sugarcane GUX1 and GUX2 enzymes generated different patterns of xylan glucuronidation, suggesting they may differently influence the molecular interaction of xylan with cellulose and lignin. Studies using biomass without chemical or steam pretreatment showed that the cell wall polysaccharides, particularly xylan, were less recalcitrant in sugarcane with GUX2 silenced than in WT plants. Our findings suggest that manipulation of GUX in sugarcane can reduce the costs of second-generation ethanol production and enhance the contribution of biofuels to lowering the emission of greenhouse gases.
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Affiliation(s)
- Rafael Henrique Gallinari
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Jan J. Lyczakowski
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityKrakowPoland
| | - Juan Pablo Portilla Llerena
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
- Department of Plant Biology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
| | | | - Sarita Cândida Rabelo
- Department of Bioprocess and Biotechnology, School of AgricultureSão Paulo State University—UNESPBotucatuBrazil
| | - Marcelo Menossi Teixeira
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
| | - Paul Dupree
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Pedro Araujo
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
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4
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Li W, Lin YCJ, Chen YL, Zhou C, Li S, De Ridder N, Oliveira DM, Zhang L, Zhang B, Wang JP, Xu C, Fu X, Luo K, Wu AM, Demura T, Lu MZ, Zhou Y, Li L, Umezawa T, Boerjan W, Chiang VL. Woody plant cell walls: Fundamentals and utilization. MOLECULAR PLANT 2024; 17:112-140. [PMID: 38102833 DOI: 10.1016/j.molp.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Cell walls in plants, particularly forest trees, are the major carbon sink of the terrestrial ecosystem. Chemical and biosynthetic features of plant cell walls were revealed early on, focusing mostly on herbaceous model species. Recent developments in genomics, transcriptomics, epigenomics, transgenesis, and associated analytical techniques are enabling novel insights into formation of woody cell walls. Here, we review multilevel regulation of cell wall biosynthesis in forest tree species. We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees. We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | | | - Ying-Lan Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Nette De Ridder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Taku Demura
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laigeng Li
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Toshiaki Umezawa
- Laboratory of Metabolic Science of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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5
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Liszka A, Wightman R, Latowski D, Bourdon M, Krogh KBRM, Pietrzykowski M, Lyczakowski JJ. Structural differences of cell walls in earlywood and latewood of Pinus sylvestris and their contribution to biomass recalcitrance. FRONTIERS IN PLANT SCIENCE 2023; 14:1283093. [PMID: 38148867 PMCID: PMC10749964 DOI: 10.3389/fpls.2023.1283093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/13/2023] [Indexed: 12/28/2023]
Abstract
Scots pine (Pinus sylvestris L.) is an evergreen coniferous tree with wide distribution and good growth performance in a range of habitats. Therefore, wood from P. sylvestris is produced in many managed forests and is frequently used in industry. Despite the importance of pine wood, we still do not fully understand its molecular structure what limits improvements in its processing. One of the basic features leading to variation in wood properties is the presence of earlywood and latewood which form annual growth rings. Here, we characterise biochemical traits that differentiate cell walls of earlywood and latewood in Scots pine. We discover that latewood is less recalcitrant to enzymatic digestion, with galactoglucomannan showing particularly pronounced difference in accessibility. Interestingly, characterisation of lignin reveals a higher proportion of coniferaldehydes in pine latewood and suggests the presence of a different linkage landscape in this wood type. With complementary analysis of wood polysaccharides this enabled us to propose the first detailed molecular model of earlywood and latewood and to conclude that the variation in lignin structure is likely the main determinant of differences in recalcitrance observed between the two wood types in pine. Our discoveries lay the foundation for improvements in industrial processes that use pine wood since we show clear pathways for increasing the efficiency of enzymatic processing of this renewable material. Our work will help guide future breeding of pine trees with desired timber properties and can help link molecular structure of softwood cell walls to function of the different types of xylem in conifers.
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Affiliation(s)
- Aleksandra Liszka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Dariusz Latowski
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | | | - Marcin Pietrzykowski
- Department of Ecological Engineering and Forest Hydrology, Faculty of Forestry, University of Agriculture in Krakow, Krakow, Poland
| | - Jan J. Lyczakowski
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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6
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Bourdon M, Lyczakowski JJ, Cresswell R, Amsbury S, Vilaplana F, Le Guen MJ, Follain N, Wightman R, Su C, Alatorre-Cobos F, Ritter M, Liszka A, Terrett OM, Yadav SR, Vatén A, Nieminen K, Eswaran G, Alonso-Serra J, Müller KH, Iuga D, Miskolczi PC, Kalmbach L, Otero S, Mähönen AP, Bhalerao R, Bulone V, Mansfield SD, Hill S, Burgert I, Beaugrand J, Benitez-Alfonso Y, Dupree R, Dupree P, Helariutta Y. Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils. NATURE PLANTS 2023; 9:1530-1546. [PMID: 37666966 PMCID: PMC10505557 DOI: 10.1038/s41477-023-01459-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/14/2023] [Indexed: 09/06/2023]
Abstract
Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin-cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.
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Affiliation(s)
- Matthieu Bourdon
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
| | - Jan J Lyczakowski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Sam Amsbury
- Centre for Plant Science, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
- Wallenberg Wood Science Centre (WWSC), KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Nadège Follain
- Normandie Université, UNIROUEN Normandie, INSA Rouen, CNRS, PBS, Rouen, France
| | - Raymond Wightman
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Chang Su
- Wood Development Group, University of Helsinki, Helsinki, Finland
| | - Fulgencio Alatorre-Cobos
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Conacyt-Unidad de Bioquimica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Maximilian Ritter
- Wood Materials Science, Institute for Building Materials, ETH Zürich, Zürich, Switzerland
- Empa Wood Tec, Cellulose and Wood Materials Laboratory, Dübendorf, Switzerland
| | - Aleksandra Liszka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Shri Ram Yadav
- Wood Development Group, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Anne Vatén
- Wood Development Group, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Stomatal Development and Plasticity group, University of Helsinki, Helsinki, Finland
| | - Kaisa Nieminen
- Wood Development Group, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Production systems / Tree Breeding Department, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Gugan Eswaran
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Juan Alonso-Serra
- Wood Development Group, University of Helsinki, Helsinki, Finland
- UMR 5667 Reproduction et Développement Des Plantes, ENS de Lyon, France
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, Department of Physiology, Development and Neuroscience, Cambridge, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry, UK
| | - Pal Csaba Miskolczi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Lothar Kalmbach
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Molecular Plant Physiology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Sofia Otero
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Science and Technology Office of the Congress of Deputies, Madrid, Spain
| | - Ari Pekka Mähönen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Rishikesh Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stefan Hill
- Scion, Te Papa Tipu Innovation Park, Rotorua, New Zealand
| | - Ingo Burgert
- Wood Materials Science, Institute for Building Materials, ETH Zürich, Zürich, Switzerland
- Empa Wood Tec, Cellulose and Wood Materials Laboratory, Dübendorf, Switzerland
| | - Johnny Beaugrand
- Biopolymères Interactions Assemblages (BIA), INRA, Nantes, France
| | - Yoselin Benitez-Alfonso
- The Centre for Plant Science, The Bragg Centre, The Astbury Centre, University of Leeds, Leeds, UK
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Wood Development Group, University of Helsinki, Helsinki, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
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7
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Cunha AEP, Simões RS. Dissolving Kraft Pulp Production and Xylooligosaccharide Coproduction: Effect of Pre-Hydrolysis Conditions. ACS OMEGA 2023; 8:13626-13638. [PMID: 37091417 PMCID: PMC10116639 DOI: 10.1021/acsomega.2c07594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Due to cotton's declining sustainability, more lignocellulosic materials are being used to produce dissolving pulp for textile applications. Pre-hydrolysis kraft is one of the main processes used to produce this material. Pre-hydrolysis under conventional conditions removes most of the hemicelluloses, but the majority end up as xylose and furfural, traditionally burned in a recovery boiler. The xylooligosaccharides (XOS), derived from hemicelluloses are a specialty product and can be recovered but requires adapted operative conditions. Thus, the objective was to recover XOS and evaluate the effect of pre-hydrolysis conditions on the final pulp characteristics. A flow-through reactor (FTR) was used to study the pre-hydrolysis, which allowed for modification of the retention time of the xylan in the free liquor after extraction from wood. The results have shown that by changing the fluid retention time in the pre-hydrolysis, the proportion of XOS/xylose/furfural recovered can be strongly changed. The hemicellulose content of the dissolving pulp decreased from 6.8% to about 2.6% using the FTR pretreatment.
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8
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Oliveira DM. Glucuronic acid: not just another brick in the cell wall. THE NEW PHYTOLOGIST 2023; 238:8-10. [PMID: 36862529 DOI: 10.1111/nph.18804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
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9
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Derba-Maceluch M, Mitra M, Hedenström M, Liu X, Gandla ML, Barbut FR, Abreu IN, Donev EN, Urbancsok J, Moritz T, Jönsson LJ, Tsang A, Powlowski J, Master ER, Mellerowicz EJ. Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls. THE NEW PHYTOLOGIST 2023; 238:297-312. [PMID: 36600379 DOI: 10.1111/nph.18712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin-carbohydrate complex assembly.
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Affiliation(s)
- Marta Derba-Maceluch
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Madhusree Mitra
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | | | - Xiaokun Liu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | | | - Félix R Barbut
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Ilka N Abreu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Evgeniy N Donev
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - János Urbancsok
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, H4B 1R6, Canada
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, H4B 1R6, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
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10
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Wang S, Robertz S, Seven M, Kraemer F, Kuhn BM, Liu L, Lunde C, Pauly M, Ramírez V. A large-scale forward genetic screen for maize mutants with altered lignocellulosic properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1099009. [PMID: 36959947 PMCID: PMC10028098 DOI: 10.3389/fpls.2023.1099009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The development of efficient pipelines for the bioconversion of grass lignocellulosic feedstocks is challenging due to the limited understanding of the molecular mechanisms controlling the synthesis, deposition, and degradation of the varying polymers unique to grass cell walls. Here, we describe a large-scale forward genetic approach resulting in the identification of a collection of chemically mutagenized maize mutants with diverse alterations in their cell wall attributes such as crystalline cellulose content or hemicellulose composition. Saccharification yield, i.e. the amount of lignocellulosic glucose (Glc) released by means of enzymatic hydrolysis, is increased in two of the mutants and decreased in the remaining six. These mutants, termed candy-leaf (cal), show no obvious plant growth or developmental defects despite associated differences in their lignocellulosic composition. The identified cal mutants are a valuable tool not only to understand recalcitrance of grass lignocellulosics to enzymatic deconstruction but also to decipher grass-specific aspects of cell wall biology once the genetic basis, i.e. the location of the mutation, has been identified.
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Affiliation(s)
- Shaogan Wang
- Institute for Plant Cell Biology and Biotechnology-Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefan Robertz
- Institute for Plant Cell Biology and Biotechnology-Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Merve Seven
- Institute for Plant Cell Biology and Biotechnology-Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Florian Kraemer
- Department of Plant and Microbial Biology, Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Benjamin M. Kuhn
- Department of Plant and Microbial Biology, Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Lifeng Liu
- Department of Plant and Microbial Biology, Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA, United States
| | - China Lunde
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, United States
| | - Markus Pauly
- Institute for Plant Cell Biology and Biotechnology-Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Plant and Microbial Biology, Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Vicente Ramírez
- Institute for Plant Cell Biology and Biotechnology-Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Plant and Microbial Biology, Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA, United States
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11
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Glucuronoyl esterases - enzymes to decouple lignin and carbohydrates and enable better utilization of renewable plant biomass. Essays Biochem 2023; 67:493-503. [PMID: 36651189 PMCID: PMC10154605 DOI: 10.1042/ebc20220155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/09/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Glucuronoyl esterases (GEs) are microbial enzymes able to cleave covalent linkages between lignin and carbohydrates in the plant cell wall. GEs are serine hydrolases found in carbohydrate esterase family 15 (CE15), which belongs to the large α/β hydrolase superfamily. GEs have been shown to reduce plant cell wall recalcitrance by hydrolysing the ester bonds found between glucuronic acid moieties on xylan polysaccharides and lignin. In recent years, the exploration of CE15 has broadened significantly and focused more on bacterial enzymes, which are more diverse in terms of sequence and structure to their fungal counterparts. Similar to fungal GEs, the bacterial enzymes are able to improve overall biomass deconstruction but also appear to have less strict substrate preferences for the uronic acid moiety. The structures of bacterial GEs reveal that they often have large inserts close to the active site, with implications for more extensive substrate interactions than the fungal GEs which have more open active sites. In this review, we highlight the recent work on GEs which has predominantly regarded bacterial enzymes, and discuss similarities and differences between bacterial and fungal enzymes in terms of the biochemical properties, diversity in sequence and modularity, and structural variations that have been discovered thus far in CE15.
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12
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Yu L, Yoshimi Y, Cresswell R, Wightman R, Lyczakowski JJ, Wilson LFL, Ishida K, Stott K, Yu X, Charalambous S, Wurman-Rodrich J, Terrett OM, Brown SP, Dupree R, Temple H, Krogh KBRM, Dupree P. Eudicot primary cell wall glucomannan is related in synthesis, structure, and function to xyloglucan. THE PLANT CELL 2022; 34:4600-4622. [PMID: 35929080 PMCID: PMC9614514 DOI: 10.1093/plcell/koac238] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Hemicellulose polysaccharides influence assembly and properties of the plant primary cell wall (PCW), perhaps by interacting with cellulose to affect the deposition and bundling of cellulose fibrils. However, the functional differences between plant cell wall hemicelluloses such as glucomannan, xylan, and xyloglucan (XyG) remain unclear. As the most abundant hemicellulose, XyG is considered important in eudicot PCWs, but plants devoid of XyG show relatively mild phenotypes. We report here that a patterned β-galactoglucomannan (β-GGM) is widespread in eudicot PCWs and shows remarkable similarities to XyG. The sugar linkages forming the backbone and side chains of β-GGM are analogous to those that make up XyG, and moreover, these linkages are formed by glycosyltransferases from the same CAZy families. Solid-state nuclear magnetic resonance indicated that β-GGM shows low mobility in the cell wall, consistent with interaction with cellulose. Although Arabidopsis β-GGM synthesis mutants show no obvious growth defects, genetic crosses between β-GGM and XyG mutants produce exacerbated phenotypes compared with XyG mutants. These findings demonstrate a related role of these two similar but distinct classes of hemicelluloses in PCWs. This work opens avenues to study the roles of β-GGM and XyG in PCWs.
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Affiliation(s)
- Li Yu
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Yoshihisa Yoshimi
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | | | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | | | | | - Konan Ishida
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Stephan Charalambous
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | | | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Henry Temple
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
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13
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Beck S, Choi P, Mushrif SH. Origins of covalent linkages within the lignin-carbohydrate network of biomass. Phys Chem Chem Phys 2022; 24:20480-20490. [PMID: 35993292 DOI: 10.1039/d2cp01683d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Covalent linkages between lignin and the surrounding carbohydrate network, often referred to as lignin-carbohydrate complexes (LCCs), have been proposed to affect the organization of the biomass microstructure and directly correlate with the recalcitrant nature of biomass. However, the existence and frequency of these LCC linkages remain controversial and largely unknown, primarily due to the harsh experimental techniques available to characterize them. During the predominant lignin polymerization pathway a reactive intermediate is formed. Though this intermediate can covalently bind to the surrounding cellulose/hemicellulose matrix, it has been traditionally assumed to react exclusively with water, leading to purely physical interactions between lignin and cellulose/hemicellulose in the cell wall. This work, for the first time, provides direct evidence of the molecular mechanism of the formation of benzyl ether and benzyl ester LCC linkages via the speculated lignin polymerization pathway. The formation of these LCC linkages showed thermodynamic favorability, while remaining kinetically facile, compared to the previously assumed mechanism of the lignin intermediate reacting with water. The present work suggests that the surrounding carbohydrate matrix could play a role in the organization of lignin deposition and these covalent linkages could be a key factor in biomass recalcitrance.
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Affiliation(s)
- Seth Beck
- Department of Chemical and Materials Engineering, University of Alberta, 9211-116 St NW, Edmonton, AB, T6G 1H9, Canada.
| | - Phillip Choi
- Department of Chemical and Materials Engineering, University of Alberta, 9211-116 St NW, Edmonton, AB, T6G 1H9, Canada.
| | - Samir H Mushrif
- Department of Chemical and Materials Engineering, University of Alberta, 9211-116 St NW, Edmonton, AB, T6G 1H9, Canada.
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14
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Wilkens C, Vuillemin M, Pilgaard B, Polikarpov I, Morth JP. A GH115 α-glucuronidase structure reveals dimerization-mediated substrate binding and a proton wire potentially important for catalysis. Acta Crystallogr D Struct Biol 2022; 78:658-668. [PMID: 35503213 PMCID: PMC9063842 DOI: 10.1107/s2059798322003527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
The crystal structure of a GH115 α-glucuronidase obtained in complex with xylohexaose and Ca2+ reveals that the two molecules constituting the homodimer cooperatively bind the substrate and that a divalent ion is involved in formation of the Michaelis–Menten complex and is likely to contribute to the formation of a protein wire that is essential for catalysis. Xylan is a major constituent of plant cell walls and is a potential source of biomaterials, and the derived oligosaccharides have been shown to have prebiotic effects. Xylans can be highly substituted with different sugar moieties, which pose steric hindrance to the xylanases that catalyse the hydrolysis of the xylan backbone. One such substituent is α-d-glucuronic acid, which is linked to the O2′ position of the β-1,4 d-xylopyranoses composing the main chain of xylans. The xylan-specific α-glucuronidases from glycoside hydrolase family 115 (GH115) specifically catalyse the removal of α-d-glucuronic acid (GlcA) or methylated GlcA (MeGlcA). Here, the molecular basis by which the bacterial GH115 member wtsAgu115A interacts with the main chain of xylan and the indirect involvement of divalent ions in the formation of the Michaelis–Menten complex are described. A crystal structure at 2.65 Å resolution of wtsAgu115A originating from a metagenome from an anaerobic digester fed with wastewater treatment sludge was determined in complex with xylohexaose, and Asp303 was identified as the likely general acid. The residue acting as the general base could not be identified. However, a proton wire connecting the active site to the metal site was observed and hence a previous hypothesis suggesting a Grotthuss-like mechanism cannot be rejected. Only a single molecule was found in the asymmetric unit. However, wtsAgu115A forms a dimer with a symmetry-related molecule in the crystal lattice. The xylohexaose moieties of the xylohexaose are recognized by residues from both protomers, thus creating a xylohexaose recognition site at the dimer interface. The dimer was confirmed by analytical size-exclusion chromatography in solution. Kinetic analysis with aldouronic acids resulted in a Hill coefficient of greater than 2, suggesting cooperativity between the two binding sites. Three Ca2+ ions were identified in the wtsAgu115A structures. One Ca2+ ion is of particular interest as it is coordinated by the residues of the loops that also interact with the substrate. Activity studies showed that the presence of Mg2+ or Mn2+ resulted in a higher activity towards aldouronic acids, while the less restrictive coordination geometry of Ca2+ resulted in a decrease in activity.
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15
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Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion. Nat Commun 2022; 13:1449. [PMID: 35304453 PMCID: PMC8933493 DOI: 10.1038/s41467-022-28938-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Glucuronoyl esterases (GEs) are α/β serine hydrolases and a relatively new addition in the toolbox to reduce the recalcitrance of lignocellulose, the biggest obstacle in cost-effective utilization of this important renewable resource. While biochemical and structural characterization of GEs have progressed greatly recently, there have yet been no mechanistic studies shedding light onto the rate-limiting steps relevant for biomass conversion. The bacterial GE OtCE15A possesses a classical yet distinctive catalytic machinery, with easily identifiable catalytic Ser/His completed by two acidic residues (Glu and Asp) rather than one as in the classical triad, and an Arg side chain participating in the oxyanion hole. By QM/MM calculations, we identified deacylation as the decisive step in catalysis, and quantified the role of Asp, Glu and Arg, showing the latter to be particularly important. The results agree well with experimental and structural data. We further calculated the free-energy barrier of post-catalysis dissociation from a complex natural substrate, suggesting that in industrial settings non-catalytic processes may constitute the rate-limiting step, and pointing to future directions for enzyme engineering in biomass utilization. Zong and coworkers combine computational and experimental methods to decipher in detail the mechanism of action of glucuronoyl esterases, enzymes with significant biotechnological potential for decoupling lignin from polysaccharides in biomass.
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16
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Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw. THE PLANT GENOME 2022; 15:e20174. [PMID: 34806838 DOI: 10.1002/tpg2.20174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
| | | | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56-58, Stockholm, 100 44, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Dep. of Plant Biology, Swedish Univ. of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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17
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Yoshida K, Sakamoto S, Mitsuda N. In Planta Cell Wall Engineering: From Mutants to Artificial Cell Walls. PLANT & CELL PHYSIOLOGY 2021; 62:1813-1827. [PMID: 34718770 DOI: 10.1093/pcp/pcab157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/03/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
To mitigate the effects of global warming and to preserve the limited fossil fuel resources, an increased exploitation of plant-based materials and fuels is required, which would be one of the most important innovations related to sustainable development. Cell walls account for the majority of plant dry biomass and so is the target of such innovations. In this review, we discuss recent advances in in planta cell wall engineering through genetic manipulations, with a focus on wild-type-based and mutant-based approaches. The long history of using a wild-type-based approach has resulted in the development of many strategies for manipulating lignin, hemicellulose and pectin to decrease cell wall recalcitrance. In addition to enzyme-encoding genes, many transcription factor genes important for changing relevant cell wall characteristics have been identified. Although mutant-based cell wall engineering is relatively new, it has become feasible due to the rapid development of genome-editing technologies and systems biology-related research; we will soon enter an age of designed artificial wood production via complex genetic manipulations of many industrially important trees and crops.
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Affiliation(s)
- Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa, 245-0051 Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
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18
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Pacheco D, Cotas J, Rocha CP, Araújo GS, Figueirinha A, Gonçalves AM, Bahcevandziev K, Pereira L. Seaweeds’ carbohydrate polymers as plant growth promoters. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2021. [DOI: 10.1016/j.carpta.2021.100097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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19
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Zerva A, Pentari C, Ferousi C, Nikolaivits E, Karnaouri A, Topakas E. Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2021; 342:126058. [PMID: 34597805 DOI: 10.1016/j.biortech.2021.126058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The field of enzymatic degradation of lignocellulose is actively growing and the recent updates of the last few years indicate that there is still much to learn. The growing number of protein sequences with unknown function in microbial genomes indicates that there is still much to learn on the mechanisms of lignocellulose degradation. In this review, a summary of the progress in the field is presented, including recent discoveries on the nature of the structural polysaccharides, new technologies for the discovery and functional annotation of gene sequences including omics technologies, and the novel lignocellulose-acting enzymes described. Novel enzymatic activities and enzyme families as well as accessory enzymes and their synergistic relationships regarding biomass breakdown are described. Moreover, it is shown that all the valuable knowledge of the enzymatic decomposition of plant biomass polymers can be employed towards the decomposition and upgrading of synthetic polymers, such as plastics.
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Affiliation(s)
- Anastasia Zerva
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Pentari
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Ferousi
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Anthi Karnaouri
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece; Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
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20
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Zhu J, Wang H, Guo F, Salmén L, Yu Y. Cell wall polymer distribution in bamboo visualized with in situ imaging FTIR. Carbohydr Polym 2021; 274:118653. [PMID: 34702472 DOI: 10.1016/j.carbpol.2021.118653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
To better understand the high recalcitrance of bamboo during bioconversion, the fine spatial distribution of polymers in bamboo was studied with Imaging FTIR microscopy under both transmission and ATR modes, combined with PCA data processing. The results demonstrated that lignin, xylan and hydroxycinnamic acid (HCA) were more concentrated in the fibers near the xylem conduit, while cellulose was evenly distributed across the whole fiber sheath. PCA processing produced a clear separation between bamboo fibers and parenchyma cells, indicating that the parenchyma cells contains more pectin and HCA than fibers. It also demonstrated that cellulose, xylan and S-lignin were concentrated most heavily in bamboo fiber secondary cell walls, while G-lignin, pectin and HCA were found more in the compound middle lamella. The revealed information regarding polymer distribution is of great significance for better understanding of the inherent design mechanism of plant cell wall and its efficient utilization.
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Affiliation(s)
- Jiawei Zhu
- Institute of New Bamboo and Rattan Based Materials, International Center for Bamboo and Rattan, Beijing 100102, PR China; SFA and Beijing Co-built Key Laboratory of Bamboo and Rattan Science & Technology, State Forestry Administration, Beijing 100102, PR China
| | - Hankun Wang
- Institute of New Bamboo and Rattan Based Materials, International Center for Bamboo and Rattan, Beijing 100102, PR China; SFA and Beijing Co-built Key Laboratory of Bamboo and Rattan Science & Technology, State Forestry Administration, Beijing 100102, PR China
| | - Fei Guo
- College of Material Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | | | - Yan Yu
- College of Material Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
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21
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Lyczakowski JJ, Yu L, Terrett OM, Fleischmann C, Temple H, Thorlby G, Sorieul M, Dupree P. Two conifer GUX clades are responsible for distinct glucuronic acid patterns on xylan. THE NEW PHYTOLOGIST 2021; 231:1720-1733. [PMID: 34086997 DOI: 10.1111/nph.17531] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Wood of coniferous trees (softwood), is a globally significant carbon sink and an important source of biomass. Despite that, little is known about the genetic basis of softwood cell wall biosynthesis. Branching of xylan, one of the main hemicelluloses in softwood secondary cell walls, with glucuronic acid (GlcA) is critical for biomass recalcitrance. Here, we investigate the decoration patterns of xylan by conifer GlucUronic acid substitution of Xylan (GUX) enzymes. Through molecular phylogenetics we identify two distinct conifer GUX clades. Using transcriptional profiling we show that the genes are preferentially expressed in secondary cell wall forming tissues. With in vitro and in planta assays we demonstrate that conifer GUX enzymes from both clades are active glucuronyltransferases. Conifer GUX enzymes from each clade have different specific activities. While members of clade one add evenly spaced GlcA branches, the members of clade two are also capable of glucuronidating two consecutive xyloses. Importantly, these types of xylan patterning are present in softwood. As xylan patterning might modulate xylan-cellulose and xylan-lignin interactions, our results further the understanding of softwood cell wall biosynthesis and provide breeding or genetic engineering targets that can be used to modify softwood properties.
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Affiliation(s)
- Jan J Lyczakowski
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Li Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | | | - Henry Temple
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | | | | | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
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22
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de Vries L, Guevara-Rozo S, Cho M, Liu LY, Renneckar S, Mansfield SD. Tailoring renewable materials via plant biotechnology. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:167. [PMID: 34353358 PMCID: PMC8344217 DOI: 10.1186/s13068-021-02010-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/06/2021] [Indexed: 05/03/2023]
Abstract
Plants inherently display a rich diversity in cell wall chemistry, as they synthesize an array of polysaccharides along with lignin, a polyphenolic that can vary dramatically in subunit composition and interunit linkage complexity. These same cell wall chemical constituents play essential roles in our society, having been isolated by a variety of evolving industrial processes and employed in the production of an array of commodity products to which humans are reliant. However, these polymers are inherently synthesized and intricately packaged into complex structures that facilitate plant survival and adaptation to local biogeoclimatic regions and stresses, not for ease of deconstruction and commercial product development. Herein, we describe evolving techniques and strategies for altering the metabolic pathways related to plant cell wall biosynthesis, and highlight the resulting impact on chemistry, architecture, and polymer interactions. Furthermore, this review illustrates how these unique targeted cell wall modifications could significantly extend the number, diversity, and value of products generated in existing and emerging biorefineries. These modifications can further target the ability for processing of engineered wood into advanced high performance materials. In doing so, we attempt to illuminate the complex connection on how polymer chemistry and structure can be tailored to advance renewable material applications, using all the chemical constituents of plant-derived biopolymers, including pectins, hemicelluloses, cellulose, and lignins.
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Affiliation(s)
- Lisanne de Vries
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, the Wisconsin Energy Institute, University of Wisconsin - Madison, Madison, WI , 53726, USA
| | - Sydne Guevara-Rozo
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - MiJung Cho
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Li-Yang Liu
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Scott Renneckar
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, the Wisconsin Energy Institute, University of Wisconsin - Madison, Madison, WI , 53726, USA.
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23
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Krska D, Mazurkewich S, Brown HA, Theibich Y, Poulsen JCN, Morris AL, Koropatkin NM, Lo Leggio L, Larsbrink J. Structural and Functional Analysis of a Multimodular Hyperthermostable Xylanase-Glucuronoyl Esterase from Caldicellulosiruptor kristjansonii. Biochemistry 2021; 60:2206-2220. [PMID: 34180241 PMCID: PMC8280721 DOI: 10.1021/acs.biochem.1c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The hyperthermophilic bacterium Caldicellulosiruptor kristjansonii encodes an unusual enzyme, CkXyn10C-GE15A, which
incorporates two catalytic domains, a xylanase and a glucuronoyl esterase,
and five carbohydrate-binding modules (CBMs) from families 9 and 22.
The xylanase and glucuronoyl esterase catalytic domains were recently
biochemically characterized, as was the ability of the individual
CBMs to bind insoluble polysaccharides. Here, we further probed the
abilities of the different CBMs from CkXyn10C-GE15A
to bind to soluble poly- and oligosaccharides using affinity gel electrophoresis,
isothermal titration calorimetry, and differential scanning fluorimetry.
The results revealed additional binding properties of the proteins
compared to the former studies on insoluble polysaccharides. Collectively,
the results show that all five CBMs have their own distinct binding
preferences and appear to complement each other and the catalytic
domains in targeting complex cell wall polysaccharides. Additionally,
through renewed efforts, we have achieved partial structural characterization
of this complex multidomain protein. We have determined the structures
of the third CBM9 domain (CBM9.3) and the glucuronoyl esterase (GE15A)
by X-ray crystallography. CBM9.3 is the second CBM9 structure determined
to date and was shown to bind oligosaccharide ligands at the same
site but in a different binding mode compared to that of the previously
determined CBM9 structure from Thermotoga maritima. GE15A represents a unique intermediate between reported fungal
and bacterial glucuronoyl esterase structures as it lacks two inserted
loop regions typical of bacterial enzymes and a third loop has an
atypical structure. We also report small-angle X-ray scattering measurements
of the N-terminal CBM22.1–CBM22.2–Xyn10C construct,
indicating a compact arrangement at room temperature.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Yusuf Theibich
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | | | - Adeline L Morris
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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24
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Preparation and Swelling Behaviors of High-Strength Hemicellulose-g-Polydopamine Composite Hydrogels. MATERIALS 2021; 14:ma14010186. [PMID: 33401706 PMCID: PMC7795248 DOI: 10.3390/ma14010186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 11/26/2022]
Abstract
Hemicellulose-based composite hydrogels were successfully prepared by adding polydopamine (PDA) microspheres as reinforcing agents. The effects of PDA microsphere size, dosage, and nitrogen content in hydrogel on the mechanical and rheological properties was studied. The compressive strength of hydrogel was increased from 0.11 to 0.30 MPa. The storage modulus G’ was increased from 7.9 to 22.0 KPa. The gaps in the hemicellulose network are filled with PDA microspheres. There is also chemical cross-linking between them. These gaps increased the density of the hydrogel network structure. It also has good water retention and pH sensitivity. The maximum cumulative release rate of methylene blue was 62.82%. The results showed that the release behavior of hydrogel was pH-responsive, which was beneficial to realizing targeted and controlling drug release.
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25
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Morán-Velázquez DC, Monribot-Villanueva JL, Bourdon M, Tang JZ, López-Rosas I, Maceda-López LF, Villalpando-Aguilar JL, Rodríguez-López L, Gauthier A, Trejo L, Azadi P, Vilaplana F, Guerrero-Analco JA, Alatorre-Cobos F. Unravelling Chemical Composition of Agave Spines: News from Agave fourcroydes Lem. PLANTS 2020; 9:plants9121642. [PMID: 33255527 PMCID: PMC7759909 DOI: 10.3390/plants9121642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/14/2020] [Accepted: 11/15/2020] [Indexed: 02/07/2023]
Abstract
Spines are key plant modifications developed to deal against herbivores; however, its physical structure and chemical composition have been little explored in plant species. Here, we took advantage of high-throughput chromatography to characterize chemical composition of Agave fourcroydes Lem. spines, a species traditionally used for fiber extraction. Analyses of structural carbohydrate showed that spines have lower cellulose content than leaf fibers (52 and 72%, respectively) but contain more than 2-fold the hemicellulose and 1.5-fold pectin. Xylose and galacturonic acid were enriched in spines compared to fibers. The total lignin content in spines was 1.5-fold higher than those found in fibers, with elevated levels of syringyl (S) and guaiacyl (G) subunits but similar S/G ratios within tissues. Metabolomic profiling based on accurate mass spectrometry revealed the presence of phenolic compounds including quercetin, kaempferol, (+)-catechin, and (-)-epicatechin in A. fourcroydes spines, which were also detected in situ in spines tissues and could be implicated in the color of these plants' structures. Abundance of (+)-catechins could also explain proanthocyanidins found in spines. Agave spines may become a plant model to obtain more insights about cellulose and lignin interactions and condensed tannin deposition, which is valuable knowledge for the bioenergy industry and development of naturally dyed fibers, respectively.
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Affiliation(s)
- Dalia C. Morán-Velázquez
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (D.C.M.-V.); (L.F.M.-L.); (L.R.-L.)
| | - Juan L. Monribot-Villanueva
- Red de Estudios Moleculares Avanzados (REMAV), Instituto de Ecología A. C. Carretera Antigua a Coatepec 351, Xalapa 91070, Mexico;
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK;
| | - John Z. Tang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Itzel López-Rosas
- CONACYT-Research Fellow Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
| | - Luis F. Maceda-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (D.C.M.-V.); (L.F.M.-L.); (L.R.-L.)
| | | | - Lorena Rodríguez-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (D.C.M.-V.); (L.F.M.-L.); (L.R.-L.)
| | - Adrien Gauthier
- UniLaSalle—AGHYLE Research Unit UP 2018.C101, 3 Rue du Tronquet—CS 40118-76134, 76134 Mont-Saint-Aignan, France;
| | - Laura Trejo
- CONACYT-Research Fellow Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, UNAM, Santa Cruz, Tlaxcala 90640, Mexico;
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden;
| | - José A. Guerrero-Analco
- Red de Estudios Moleculares Avanzados (REMAV), Instituto de Ecología A. C. Carretera Antigua a Coatepec 351, Xalapa 91070, Mexico;
- Correspondence: (J.A.G.-A.); (F.A.-C.)
| | - Fulgencio Alatorre-Cobos
- CONACYT-Research Fellow Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
- Correspondence: (J.A.G.-A.); (F.A.-C.)
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26
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Parween S, Anonuevo JJ, Butardo VM, Misra G, Anacleto R, Llorente C, Kosik O, Romero MV, Bandonill EH, Mendioro MS, Lovegrove A, Fernie AR, Brotman Y, Sreenivasulu N. Balancing the double-edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1763-1777. [PMID: 31945237 PMCID: PMC7336377 DOI: 10.1111/pbi.13339] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/15/2019] [Accepted: 01/05/2020] [Indexed: 05/07/2023]
Abstract
Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS contributes to a lower glycemic index. A genome-wide association study coupled with targeted gene association studies was conducted utilizing a diverse panel of 281 resequenced Indica rice lines comprising of ~2.2 million single nucleotide polymorphisms. Low-to-intermediate RS phenotypic variations were identified in the rice diversity panel, resulting in novel associations of RS to several genes associated with amylopectin biosynthesis and degradation. Selected rice lines encoding superior alleles of SSIIa with medium RS and inferior alleles with low RS groups were subjected to detailed transcriptomic, metabolomic, non-starch dietary fibre (DF), starch structural and textural attributes. The gene regulatory networks highlighted the importance of a protein phosphatase alongside multiple genes of starch metabolism. Metabolomics analyses resulted in the identification of several metabolite hubs (carboxylic acid, sugars and polyamines) in the medium RS group. Among DF, mannose and galactose from the water-insoluble fraction were found to be highly associated with low and medium RS lines, respectively. Starch structural analyses revealed that a moderate increase in RS is also linked to an elevation of amylose 1 and amylose 2 fractions. Although rice lines with medium RS content negatively affected textural and viscosity properties in comparison to low RS, the textural property of medium RS lines was in the same acceptable range as IR64, a rice mega variety popular in Asia.
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Affiliation(s)
- Sabiha Parween
- International Rice Research InstituteMetro ManilaPhilippines
| | | | - Vito M. Butardo
- International Rice Research InstituteMetro ManilaPhilippines
- Present address:
Department of Chemistry and BiotechnologyFaculty of Science, Engineering and TechnologySwinburne University of TechnologyHawthornVictoriaAustralia
| | - Gopal Misra
- International Rice Research InstituteMetro ManilaPhilippines
| | - Roslen Anacleto
- International Rice Research InstituteMetro ManilaPhilippines
| | - Cindy Llorente
- International Rice Research InstituteMetro ManilaPhilippines
| | - Ondrej Kosik
- Department of Plant SciencesRothamsted ResearchHarpendenHertsUK
| | - Marissa V. Romero
- Philippine Rice Research InstituteMaligayaScience City of MuñozPhilippines
| | | | - Merlyn S. Mendioro
- Institute of Biological SciencesCollege of Arts and ScienceUniversity of PhilippinesLos BanosPhilippines
| | | | | | - Yariv Brotman
- Department of Life SciencesBen‐Gurion University of the NegevBeershebaIsrael
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27
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Gallinari RH, Coletta RD, Araújo P, Menossi M, Nery MF. Bringing to light the molecular evolution of GUX genes in plants. Genet Mol Biol 2020; 43:e20180208. [PMID: 32232316 PMCID: PMC7198009 DOI: 10.1590/1678-4685-gmb-2018-0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/06/2019] [Indexed: 11/30/2022] Open
Abstract
Hemicellulose and cellulose are essential polysaccharides for plant development and major components of cell wall. They are also an important energy source for the production of ethanol from plant biomass, but their conversion to fermentable sugars is hindered by the complex structure of cell walls. The glucuronic acid substitution of xylan (GUX) enzymes attach glucuronic acid to xylan, a major component of hemicellulose, decreasing the efficiency of enzymes used for ethanol production. Since loss-of-function gux mutants of Arabidopsis thaliana enhance enzyme accessibility and cell wall digestion without adverse phenotypes, GUX genes are potential targets for genetically improving energy crops. However, comprehensive identification of GUX in important species and their evolutionary history are largely lacking. Here, we identified putative GUX proteins using hidden Markov model searches with the GT8 domain and a GUX-specific motif, and inferred the phylogenetic relationship of 18 species with Maximum likelihood and Bayesian approaches. Each species presented a variable number of GUX, and their evolution can be explained by a mixture of divergent, concerted and birth-and-death evolutionary models. This is the first broad insight into the evolution of GUX gene family in plants and will potentially guide genetic and functional studies in species used for biofuel production.
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Affiliation(s)
- Rafael Henrique Gallinari
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Rafael Della Coletta
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Pedro Araújo
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Marcelo Menossi
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Mariana Freitas Nery
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
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28
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Cragg SM, Friess DA, Gillis LG, Trevathan-Tackett SM, Terrett OM, Watts JEM, Distel DL, Dupree P. Vascular Plants Are Globally Significant Contributors to Marine Carbon Fluxes and Sinks. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:469-497. [PMID: 31505131 DOI: 10.1146/annurev-marine-010318-095333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
More than two-thirds of global biomass consists of vascular plants. A portion of the detritus they generate is carried into the oceans from land and highly productive blue carbon ecosystems-salt marshes, mangrove forests, and seagrass meadows. This large detrital input receives scant attention in current models of the global carbon cycle, though for blue carbon ecosystems, increasingly well-constrained estimates of biomass, productivity, and carbon fluxes, reviewed in this article, are now available. We show that the fate of this detritus differs markedly from that of strictly marine origin, because the former contains lignocellulose-an energy-rich polymer complex of cellulose, hemicelluloses, and lignin that is resistant to enzymatic breakdown. This complex can be depolymerized for nutritional purposes by specialized marine prokaryotes, fungi, protists, and invertebrates using enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases to release sugar monomers. The lignin component, however, is less readily depolymerized, and detritus therefore becomes lignin enriched, particularly in anoxic sediments, and forms a major carbon sink in blue carbon ecosystems. Eventual lignin breakdown releases a wide variety of small molecules that may contribute significantly to the oceanic pool of recalcitrant dissolved organic carbon. Marine carbon fluxes and sinks dependent on lignocellulosic detritus are important ecosystem services that are vulnerable to human interventions. These services must be considered when protecting blue carbon ecosystems and planning initiatives aimed at mitigating anthropogenic carbon emissions.
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Affiliation(s)
- Simon M Cragg
- Institute of Marine Sciences, University of Portsmouth, Portsmouth PO4 9LY, United Kingdom;
| | - Daniel A Friess
- Department of Geography, National University of Singapore, Singapore 117570;
| | - Lucy G Gillis
- Leibniz-Zentrum für Marine Tropenforschung (ZMT), 28359 Bremen, Germany;
| | - Stacey M Trevathan-Tackett
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, Victoria 3125, Australia;
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom;
| | - Daniel L Distel
- Ocean Genome Legacy Center of New England Biolabs, Marine Science Center, Northeastern University, Nahant, Massachusetts 01908, USA;
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
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29
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Krska D, Larsbrink J. Investigation of a thermostable multi-domain xylanase-glucuronoyl esterase enzyme from Caldicellulosiruptor kristjanssonii incorporating multiple carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:68. [PMID: 32308737 PMCID: PMC7151638 DOI: 10.1186/s13068-020-01709-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/02/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Efficient degradation of lignocellulosic biomass has become a major bottleneck in industrial processes which attempt to use biomass as a carbon source for the production of biofuels and materials. To make the most effective use of the source material, both the hemicellulosic as well as cellulosic parts of the biomass should be targeted, and as such both hemicellulases and cellulases are important enzymes in biorefinery processes. Using thermostable versions of these enzymes can also prove beneficial in biomass degradation, as they can be expected to act faster than mesophilic enzymes and the process can also be improved by lower viscosities at higher temperatures, as well as prevent the introduction of microbial contamination. RESULTS This study presents the investigation of the thermostable, dual-function xylanase-glucuronoyl esterase enzyme CkXyn10C-GE15A from the hyperthermophilic bacterium Caldicellulosiruptor kristjanssonii. Biochemical characterization of the enzyme was performed, including assays for establishing the melting points for the different protein domains, activity assays for the two catalytic domains, as well as binding assays for the multiple carbohydrate-binding domains present in CkXyn10C-GE15A. Although the enzyme domains are naturally linked together, when added separately to biomass, the expected boosting of the xylanase action was not seen. This lack of intramolecular synergy might suggest, together with previous data, that increased xylose release is not the main beneficial trait given by glucuronoyl esterases. CONCLUSIONS Due to its thermostability, CkXyn10C-GE15A is a promising candidate for industrial processes, with both catalytic domains exhibiting melting temperatures over 70 °C. Of particular interest is the glucuronoyl esterase domain, as it represents the first studied thermostable enzyme displaying this activity.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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30
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Conacher CG, García-Aparicio MP, Coetzee G, van Zyl WH, Gӧrgens JF. Scalable methanol-free production of recombinant glucuronoyl esterase in Pichia pastoris. BMC Res Notes 2019; 12:596. [PMID: 31533815 PMCID: PMC6751620 DOI: 10.1186/s13104-019-4638-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/11/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Glucuronoyl esterase (GE) is an emerging enzyme that improves fractionation of lignin-carbohydrate complexes. However, the commercial availability of GE is limited, which hinders the research of GE-based bioprocesses for its industrial application in lignocellulose biorefineries. This study evaluated a workable, cost-effective, and commercially scalable production strategy to improve the ease of GE-based research. This strategy consisted of a constitutive and methanol-free enzyme production step coupled with a two-step filtration process. The aim was to determine if this strategy can yield copious amounts of GE, by secretion into the extracellular medium with an acceptable purity that could allow its direct application. This approach was further validated for cellobiose dehydrogenase, another emerging lignocellulose degrading enzyme which is scarcely available at high cost. RESULTS The secreted recombinant enzymes were functionally produced in excess of levels previously reported for constitutive production (1489-2780 mg L-1), and were secreted at moderate to high percentages of the total extracellular protein (51-94%). The constant glycerol feed, implemented during fed-batch fermentation, lead to a decline in growth rate and plateaued productivity. Tangential flow ultrafiltration was used to concentrate cell-free enzyme extracts 5-6-fold, reaching enzyme activity levels (1020-202 U L-1) that could allow their direct application.
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Affiliation(s)
- C G Conacher
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - M P García-Aparicio
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa. .,Departments of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
| | - G Coetzee
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - W H van Zyl
- Departments of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - J F Gӧrgens
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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31
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Liu X, Jiang Z, Liu Y, You X, Yang S, Yan Q. Biochemical characterization of a novel exo-oligoxylanase from Paenibacillus barengoltzii suitable for monosaccharification from corncobs. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:190. [PMID: 31384297 PMCID: PMC6661730 DOI: 10.1186/s13068-019-1532-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Xylan is the major component of hemicelluloses, which are the second most abundant polysaccharides in nature, accounting for approximately one-third of all renewable organic carbon resources on earth. Efficient degradation of xylan is the prerequisite for biofuel production. Enzymatic degradation has been demonstrated to be more attractive due to low energy consumption and environmental friendliness, when compared with chemical degradation. Exo-xylanases, as a rate-limiting factor, play an important role in the xylose production. It is of great value to identify novel exo-xylanases for efficient bioconversion of xylan in biorefinery industry. RESULTS A novel glycoside hydrolase (GH) family 8 reducing-end xylose-releasing exo-oligoxylanase (Rex)-encoding gene (PbRex8) was cloned from Paenibacillus barengoltzii and heterogeneously expressed in Escherichia coli. The deduced amino acid sequence of PbRex8 shared the highest identity of 74% with a Rex from Bacillus halodurans. The recombinant enzyme (PbRex8) was purified and biochemically characterized. The optimal pH and temperature of PbRex8 were 5.5 and 55 °C, respectively. PbRex8 showed prominent activity on xylooligosaccharides (XOSs), and trace activity on xylan. It also exhibited β-1,3-1,4-glucanase and xylobiase activities. The enzyme efficiently converted corncob xylan to xylose coupled with a GH family 10 endo-xylanase, with a xylose yield of 83%. The crystal structure of PbRex8 was resolved at 1.88 Å. Structural comparison suggests that Arg67 can hydrogen-bond to xylose moieties in the -1 subsite, and Asn122 and Arg253 are close to xylose moieties in the -3 subsite, the hypotheses of which were further verified by mutation analysis. In addition, Trp205, Trp132, Tyr372, Tyr277 and Tyr369 in the grove of PbRex8 were found to involve in glucooligosaccharides interactions. This is the first report on a GH family 8 Rex from P. barengoltzii. CONCLUSIONS A novel reducing-end xylose-releasing exo-oligoxylanase suitable for xylose production from corncobs was identified, biochemically characterized and structurally elucidated. The properties of PbRex8 may make it an excellent candidate in biorefinery industries.
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Affiliation(s)
- Xueqiang Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, Beijing, 100083 China
| | - Zhengqiang Jiang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Yu Liu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Xin You
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Shaoqing Yang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Qiaojuan Yan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, Beijing, 100083 China
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An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials. Sci Rep 2019; 9:4903. [PMID: 30894609 PMCID: PMC6426972 DOI: 10.1038/s41598-019-41300-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/26/2019] [Indexed: 11/08/2022] Open
Abstract
β-glucosidases play a critical role among the enzymes in enzymatic cocktails designed for plant biomass deconstruction. By catalysing the breakdown of β-1, 4-glycosidic linkages, β-glucosidases produce free fermentable glucose and alleviate the inhibition of other cellulases by cellobiose during saccharification. Despite this benefit, most characterised fungal β-glucosidases show weak activity at high glucose concentrations, limiting enzymatic hydrolysis of plant biomass in industrial settings. In this study, structural analyses combined with site-directed mutagenesis efficiently improved the functional properties of a GH1 β-glucosidase highly expressed by Trichoderma harzianum (ThBgl) under biomass degradation conditions. The tailored enzyme displayed high glucose tolerance levels, confirming that glucose tolerance can be achieved by the substitution of two amino acids that act as gatekeepers, changing active-site accessibility and preventing product inhibition. Furthermore, the enhanced efficiency of the engineered enzyme in terms of the amount of glucose released and ethanol yield was confirmed by saccharification and simultaneous saccharification and fermentation experiments using a wide range of plant biomass feedstocks. Our results not only experimentally confirm the structural basis of glucose tolerance in GH1 β-glucosidases but also demonstrate a strategy to improve technologies for bioethanol production based on enzymatic hydrolysis.
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Zhong R, Cui D, Ye ZH. Secondary cell wall biosynthesis. THE NEW PHYTOLOGIST 2019; 221:1703-1723. [PMID: 30312479 DOI: 10.1111/nph.15537] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/28/2018] [Indexed: 05/19/2023]
Abstract
Contents Summary 1703 I. Introduction 1703 II. Cellulose biosynthesis 1705 III. Xylan biosynthesis 1709 IV. Glucomannan biosynthesis 1713 V. Lignin biosynthesis 1714 VI. Concluding remarks 1717 Acknowledgements 1717 References 1717 SUMMARY: Secondary walls are synthesized in specialized cells, such as tracheary elements and fibers, and their remarkable strength and rigidity provide strong mechanical support to the cells and the plant body. The main components of secondary walls are cellulose, xylan, glucomannan and lignin. Biochemical, molecular and genetic studies have led to the discovery of most of the genes involved in the biosynthesis of secondary wall components. Cellulose is synthesized by cellulose synthase complexes in the plasma membrane and the recent success of in vitro synthesis of cellulose microfibrils by a single recombinant cellulose synthase isoform reconstituted into proteoliposomes opens new doors to further investigate the structure and functions of cellulose synthase complexes. Most genes involved in the glycosyl backbone synthesis, glycosyl substitutions and acetylation of xylan and glucomannan have been genetically characterized and the biochemical properties of some of their encoded enzymes have been investigated. The genes and their encoded enzymes participating in monolignol biosynthesis and modification have been extensively studied both genetically and biochemically. A full understanding of how secondary wall components are synthesized will ultimately enable us to produce plants with custom-designed secondary wall composition tailored to diverse applications.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Dongtao Cui
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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Wierzbicki MP, Maloney V, Mizrachi E, Myburg AA. Xylan in the Middle: Understanding Xylan Biosynthesis and Its Metabolic Dependencies Toward Improving Wood Fiber for Industrial Processing. FRONTIERS IN PLANT SCIENCE 2019; 10:176. [PMID: 30858858 PMCID: PMC6397879 DOI: 10.3389/fpls.2019.00176] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/04/2019] [Indexed: 05/14/2023]
Abstract
Lignocellulosic biomass, encompassing cellulose, lignin and hemicellulose in plant secondary cell walls (SCWs), is the most abundant source of renewable materials on earth. Currently, fast-growing woody dicots such as Eucalyptus and Populus trees are major lignocellulosic (wood fiber) feedstocks for bioproducts such as pulp, paper, cellulose, textiles, bioplastics and other biomaterials. Processing wood for these products entails separating the biomass into its three main components as efficiently as possible without compromising yield. Glucuronoxylan (xylan), the main hemicellulose present in the SCWs of hardwood trees carries chemical modifications that are associated with SCW composition and ultrastructure, and affect the recalcitrance of woody biomass to industrial processing. In this review we highlight the importance of xylan properties for industrial wood fiber processing and how gaining a greater understanding of xylan biosynthesis, specifically xylan modification, could yield novel biotechnology approaches to reduce recalcitrance or introduce novel processing traits. Altering xylan modification patterns has recently become a focus of plant SCW studies due to early findings that altered modification patterns can yield beneficial biomass processing traits. Additionally, it has been noted that plants with altered xylan composition display metabolic differences linked to changes in precursor usage. We explore the possibility of using systems biology and systems genetics approaches to gain insight into the coordination of SCW formation with other interdependent biological processes. Acetyl-CoA, s-adenosylmethionine and nucleotide sugars are precursors needed for xylan modification, however, the pathways which produce metabolic pools during different stages of fiber cell wall formation still have to be identified and their co-regulation during SCW formation elucidated. The crucial dependence on precursor metabolism provides an opportunity to alter xylan modification patterns through metabolic engineering of one or more of these interdependent pathways. The complexity of xylan biosynthesis and modification is currently a stumbling point, but it may provide new avenues for woody biomass engineering that are not possible for other biopolymers.
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Affiliation(s)
| | | | | | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Figueiredo R, Araújo P, Llerena JPP, Mazzafera P. Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective. Food Energy Secur 2019. [DOI: 10.1002/fes3.163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Raquel Figueiredo
- Department of Plant Biology Institute of Biology State University of Campinas Campinas Brazil
| | - Pedro Araújo
- Department of Genetics, Evolution and Bioagents Institute of Biology State University of Campinas Campinas Brazil
| | - Juan Pablo P. Llerena
- Department of Plant Biology Institute of Biology State University of Campinas Campinas Brazil
| | - Paulo Mazzafera
- Department of Plant Biology Institute of Biology State University of Campinas Campinas Brazil
- Department of Crop Science College of Agriculture Luiz de Queiroz University of São Paulo Piracicaba Brazil
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36
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Jan J. Lyczakowski. THE NEW PHYTOLOGIST 2019; 221:1195-1196. [PMID: 30644582 DOI: 10.1111/nph.15483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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37
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Lyczakowski JJ, Bourdon M, Terrett OM, Helariutta Y, Wightman R, Dupree P. Structural Imaging of Native Cryo-Preserved Secondary Cell Walls Reveals the Presence of Macrofibrils and Their Formation Requires Normal Cellulose, Lignin and Xylan Biosynthesis. FRONTIERS IN PLANT SCIENCE 2019; 10:1398. [PMID: 31708959 PMCID: PMC6819431 DOI: 10.3389/fpls.2019.01398] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/10/2019] [Indexed: 05/18/2023]
Abstract
The woody secondary cell walls of plants are the largest repository of renewable carbon biopolymers on the planet. These walls are made principally from cellulose and hemicelluloses and are impregnated with lignin. Despite their importance as the main load bearing structure for plant growth, as well as their industrial importance as both a material and energy source, the precise arrangement of these constituents within the cell wall is not yet fully understood. We have adapted low temperature scanning electron microscopy (cryo-SEM) for imaging the nanoscale architecture of angiosperm and gymnosperm cell walls in their native hydrated state. Our work confirms that cell wall macrofibrils, cylindrical structures with a diameter exceeding 10 nm, are a common feature of the native hardwood and softwood samples. We have observed these same structures in Arabidopsis thaliana secondary cell walls, enabling macrofibrils to be compared between mutant lines that are perturbed in cellulose, hemicellulose, and lignin formation. Our analysis indicates that the macrofibrils in Arabidopsis cell walls are dependent upon the proper biosynthesis, or composed, of cellulose, xylan, and lignin. This study establishes that cryo-SEM is a useful additional approach for investigating the native nanoscale architecture and composition of hardwood and softwood secondary cell walls and demonstrates the applicability of Arabidopsis genetic resources to relate fibril structure with wall composition and biosynthesis.
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Affiliation(s)
- Jan J. Lyczakowski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Natural Material Innovation Centre, University of Cambridge, Cambridge, United Kingdom
| | - Matthieu Bourdon
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Oliver M. Terrett
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Institute of Biotechnology/Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Raymond Wightman
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Raymond Wightman, ; Paul Dupree,
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Natural Material Innovation Centre, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Raymond Wightman, ; Paul Dupree,
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38
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Xin D, Chen X, Wen P, Zhang J. Insight into the role of α-arabinofuranosidase in biomass hydrolysis: cellulose digestibility and inhibition by xylooligomers. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:64. [PMID: 30949240 PMCID: PMC6429694 DOI: 10.1186/s13068-019-1412-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/15/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND α-l-Arabinofuranosidase (ARA), a debranching enzyme that can remove arabinose substituents from arabinoxylan and arabinoxylooligomers (AXOS), promotes the hydrolysis of the arabinoxylan fraction of biomass; however, the impact of ARA on the overall digestibility of cellulose is controversial. In this study, we investigated the effects of the addition of ARA on cellulase hydrolytic action. RESULTS We found that approximately 15% of the xylan was converted into AXOS during the hydrolysis of aqueous ammonia-pretreated corn stover and that this AXOS fraction was approximately 12% substituted with arabinose. The addition of ARA removes a portion of the arabinose decoration, but the resulting less-substituted AXOS inhibited cellulase action much more effectively; showing an increase of 45.7%. Kinetic experiments revealed that AXOS with a lower degree of arabinose substitution showed stronger affinity for the active site of cellobiohydrolase, which could be the mechanism of increased inhibition. CONCLUSIONS Our findings strongly suggest that the ratio of ARA and other xylanases should be carefully selected to avoid the strong inhibition caused by the less-substituted AXOS during the hydrolysis of arabinoxylan-containing biomass. This study advances our understanding of the inhibitory mechanism of xylooligomers and provides critical new insights into the relationship of ARA addition and cellulose digestibility.
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Affiliation(s)
- Donglin Xin
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Xiang Chen
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Peiyao Wen
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Junhua Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
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Mahon EL, Mansfield SD. Tailor-made trees: engineering lignin for ease of processing and tomorrow's bioeconomy. Curr Opin Biotechnol 2018; 56:147-155. [PMID: 30529238 DOI: 10.1016/j.copbio.2018.10.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/19/2018] [Accepted: 10/31/2018] [Indexed: 10/27/2022]
Abstract
Lignocellulosic biomass represents an abundant source of cellulosic fibres and fermentable sugars. However, lignin, a polyphenolic constituent of secondary-thickened plant cell walls significantly contributes to biomass recalcitrance during industrial processing. Efforts to reduce plant total lignin content through genetic engineering have improved processing efficiency, but often incur an agronomic penalty. Alternatively, modifications that alter the composition of lignin and/or its interaction with other cell wall polymers display improved processing efficiency without compromising biomass yield. We propose that future efforts to improve woody feedstocks should focus on altering lignin composition and cell wall ultrastructure. Here, we describe potential future modifications to lignin and/or other cell wall characteristics that may serve as strategic targets in the production of trees that are tailor-made for specific pretreatments and end-product applications.
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Affiliation(s)
- Elizabeth L Mahon
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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40
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Terrett OM, Dupree P. Covalent interactions between lignin and hemicelluloses in plant secondary cell walls. Curr Opin Biotechnol 2018; 56:97-104. [PMID: 30423528 DOI: 10.1016/j.copbio.2018.10.010] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 01/21/2023]
Abstract
The plant secondary cell wall is a complex structure composed of polysaccharides and lignin, and is a key evolutionary innovation of vascular land plants. Although cell wall composition is well understood, the cross-linking of the different polymers is only now yielding to investigation. Cross-linking between hemicelluloses and lignin occurs via two different mechanisms: incorporation into lignin by radical coupling of ferulate substitutions on xylan in commelinid monocots, and incorporation of hemicellulosic glycosyl residues by re-aromatisation of lignification intermediates. Recent genetic evidence indicates that hemicellulose:lignin cross-linking has a substantial impact on plant cell wall recalcitrance. Engineering plant biomass with modified frequencies of cross-links will have significant impacts on biomass utilisation.
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Affiliation(s)
- Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK.
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Yu L, Lyczakowski JJ, Pereira CS, Kotake T, Yu X, Li A, Mogelsvang S, Skaf MS, Dupree P. The Patterned Structure of Galactoglucomannan Suggests It May Bind to Cellulose in Seed Mucilage. PLANT PHYSIOLOGY 2018; 178:1011-1026. [PMID: 30185440 PMCID: PMC6236596 DOI: 10.1104/pp.18.00709] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/21/2018] [Indexed: 05/04/2023]
Abstract
The interaction between mannan polysaccharides and cellulose microfibrils contributes to cell wall properties in some vascular plants, but the molecular arrangement of mannan in the cell wall and the nature of the molecular bonding between mannan and cellulose remain unknown. Previous studies have shown that mannan is important in maintaining Arabidopsis (Arabidopsis thaliana) seed mucilage architecture, and that Cellulose Synthase-Like A2 (CSLA2) synthesizes a glucomannan backbone, which Mannan α-Galactosyl Transferase1 (MAGT1/GlycosylTransferase-Like6/Mucilage Related10) might decorate with single α-Gal branches. Here, we investigated the ratio and sequence of Man and Glc and the arrangement of Gal residues in Arabidopsis mucilage mannan using enzyme sequential digestion, carbohydrate gel electrophoresis, and mass spectrometry. We found that seed mucilage galactoglucomannan has a backbone consisting of the repeating disaccharide [4)-β-Glc-(1,4)-β-Man-(1,], and most of the Man residues in the backbone are substituted by single α-1,6-Gal. CSLA2 is responsible for the synthesis of this patterned glucomannan backbone and MAGT1 catalyses the addition of α-Gal. In vitro activity assays revealed that MAGT1 transferred α-Gal from UDP-Gal only to Man residues within the CSLA2 patterned glucomannan backbone acceptor. These results indicate that CSLAs and galactosyltransferases are able to make precisely defined galactoglucomannan structures. Molecular dynamics simulations suggested this patterned galactoglucomannan is able to bind stably to some hydrophilic faces and to hydrophobic faces of cellulose microfibrils. A specialization of the biosynthetic machinery to make galactoglucomannan with a patterned structure may therefore regulate the mode of binding of this hemicellulose to cellulose fibrils.
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Affiliation(s)
- Li Yu
- Department of Biochemistry and The Leverhulme Trust Centre for Natural Material Innovation, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Jan J Lyczakowski
- Department of Biochemistry and The Leverhulme Trust Centre for Natural Material Innovation, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Caroline S Pereira
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas SP 13084-862, Brazil
| | - Toshihisa Kotake
- Department of Biochemistry and The Leverhulme Trust Centre for Natural Material Innovation, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8642, Japan
| | - Xiaolan Yu
- Department of Biochemistry and The Leverhulme Trust Centre for Natural Material Innovation, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - An Li
- Department of Biochemistry and The Leverhulme Trust Centre for Natural Material Innovation, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Soren Mogelsvang
- Department of Biochemistry and The Leverhulme Trust Centre for Natural Material Innovation, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas SP 13084-862, Brazil
| | - Paul Dupree
- Department of Biochemistry and The Leverhulme Trust Centre for Natural Material Innovation, University of Cambridge, Cambridge CB2 1QW, United Kingdom
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Monrad RN, Eklöf J, Krogh KBRM, Biely P. Glucuronoyl esterases: diversity, properties and biotechnological potential. A review. Crit Rev Biotechnol 2018; 38:1121-1136. [PMID: 29739247 DOI: 10.1080/07388551.2018.1468316] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Glucuronoyl esterases (GEs) belonging to the carbohydrate esterase family 15 (CE15) are involved in microbial degradation of lignocellulosic plant materials. GEs are capable of degrading complex polymers of lignin and hemicellulose cleaving ester bonds between glucuronic acid residues in xylan and lignin alcohols. GEs promote separation of lignin, hemicellulose and cellulose which is crucial for efficient utilization of biomass as an energy source and feedstock for further processing into products or chemicals. Genes encoding GEs are found in both fungi and bacteria, but, so far, bacterial GEs are essentially unexplored, and despite being discovered >10 years ago, only a limited number of GEs have been characterized. The first laboratory scale example of improved xylose and glucuronic acid release by the synergistic action of GE with cellulolytic enzymes was only reported recently (improved C5 sugar and glucuronic acid yields) and, until now, not much is known about their biotechnology potential. In this review, we discuss the diversity, structure and properties of microbial GEs and consider the status of their action on natural substrates and in biological systems in relation to their future industrial use.
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Affiliation(s)
| | | | | | - Peter Biely
- b Institute of Chemistry, Slovak Academy of Sciences , Bratislava , Slovak Republic
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