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Mrnjavac N, Degli Esposti M, Mizrahi I, Martin WF, Allen JF. Three enzymes governed the rise of O 2 on Earth. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149495. [PMID: 39004113 DOI: 10.1016/j.bbabio.2024.149495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
Current views of O2 accumulation in Earth history depict three phases: The onset of O2 production by ∼2.4 billion years ago; 2 billion years of stasis at ∼1 % of modern atmospheric levels; and a rising phase, starting about 500 million years ago, in which oxygen eventually reached modern values. Purely geochemical mechanisms have been proposed to account for this tripartite time course of Earth oxygenation. In particular the second phase, the long period of stasis between the advent of O2 and the late rise to modern levels, has posed a puzzle. Proposed solutions involve Earth processes (geochemical, ecosystem, day length). Here we suggest that Earth oxygenation was not determined by geochemical processes. Rather it resulted from emergent biological innovations associated with photosynthesis and the activity of only three enzymes: 1) The oxygen evolving complex of cyanobacteria that makes O2; 2) Nitrogenase, with its inhibition by O2 causing two billion years of oxygen level stasis; 3) Cellulose synthase of land plants, which caused mass deposition and burial of carbon, thus removing an oxygen sink and therefore increasing atmospheric O2. These three enzymes are endogenously produced by, and contained within, cells that have the capacity for exponential growth. The catalytic properties of these three enzymes paved the path of Earth's atmospheric oxygenation, requiring no help from Earth other than the provision of water, CO2, salts, colonizable habitats, and sunlight.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK.
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2
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Kholousi Adab F, Mehdi Yaghoobi M, Gharechahi J. Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme. Sci Rep 2024; 14:8560. [PMID: 38609443 PMCID: PMC11014956 DOI: 10.1038/s41598-024-59256-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.
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Affiliation(s)
- Faezeh Kholousi Adab
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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3
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Sulaeva I, Budischowsky D, Rahikainen J, Marjamaa K, Støpamo FG, Khaliliyan H, Melikhov I, Rosenau T, Kruus K, Várnai A, Eijsink VGH, Potthast A. A novel approach to analyze the impact of lytic polysaccharide monooxygenases (LPMOs) on cellulosic fibres. Carbohydr Polym 2024; 328:121696. [PMID: 38220335 DOI: 10.1016/j.carbpol.2023.121696] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/26/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Enzymatic treatment of cellulosic fibres is a green alternative to classical chemical modification. For many applications, mild procedures for cellulose alteration are sufficient, in which the fibre structure and, therefore, the mechanical performance of cellulosic fibres are preserved. Lytic polysaccharide monooxygenases (LPMOs) bear a great potential to become a green reagent for such targeted cellulose modifications. An obstacle for wide implementation of LPMOs in tailored cellulose chemistry is the lack of suitable techniques to precisely monitor the LPMO impact on the polymer. Soluble oxidized cello-oligomers can be quantified using chromatographic and mass-spectrometric techniques. A considerable portion of the oxidized sites, however, remain on the insoluble cellulose fibres, and their quantification is difficult. Here, we describe a method for the simultaneous quantification of oxidized sites on cellulose fibres and changes in their molar mass distribution after treatment with LPMOs. The method is based on quantitative, heterogeneous, carbonyl-selective labelling with a fluorescent label (CCOA) followed by cellulose dissolution and size-exclusion chromatography (SEC). Application of the method to reactions of seven different LPMOs with pure cellulose fibres revealed pronounced functional differences between the enzymes, showing that this CCOA/SEC/MALS method is a promising tool to better understand the catalytic action of LPMOs.
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Affiliation(s)
- Irina Sulaeva
- Core Facility "Analysis of Lignocellulosics" (ALICE), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - David Budischowsky
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Jenni Rahikainen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 Espoo, Finland
| | - Kaisa Marjamaa
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 Espoo, Finland
| | - Fredrik Gjerstad Støpamo
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Hajar Khaliliyan
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Ivan Melikhov
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Thomas Rosenau
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Kristiina Kruus
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 Espoo, Finland; School of Chemical Engineering, Aalto University, P.O. Box 16100, Espoo 00076 AALTO, Finland
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Antje Potthast
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria.
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4
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Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 2024; 383:eadj9223. [PMID: 38484069 PMCID: PMC7615765 DOI: 10.1126/science.adj9223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sarah Winkler
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Falk S. P. Nagies
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Eva Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - Avital Artan-Furman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Madhav P. Yadav
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Edward A. Bayer
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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5
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An P, Yang C, Li W, Zhao D, Xiang H. The Isolation and Characterization of a Novel Psychrotolerant Cellulolytic Bacterium, Microbacterium sp. QXD-8 T. Microorganisms 2024; 12:303. [PMID: 38399707 PMCID: PMC10892437 DOI: 10.3390/microorganisms12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 02/25/2024] Open
Abstract
Cellulolytic microorganisms play a crucial role in agricultural waste disposal. Strain QXD-8T was isolated from soil in northern China. Similarity analyses of the 16S rRNA gene, as well as the 120 conserved genes in the whole-genome sequence, indicate that it represents a novel species within the genus Microbacterium. The Microbacterium sp. QXD-8T was able to grow on the CAM plate with sodium carboxymethyl cellulose as a carbon source at 15 °C, forming a transparent hydrolysis circle after Congo red staining, even though the optimal temperature for the growth and cellulose degradation of strain QXD-8T was 28 °C. In the liquid medium, it effectively degraded cellulose and produced reducing sugars. Functional annotation revealed the presence of encoding genes for the GH5, GH6, and GH10 enzyme families with endoglucanase activity, as well as the GH1, GH3, GH39, and GH116 enzyme families with β-glucosidase activity. Additionally, two proteins in the GH6 family, one in the GH10, and two of nine proteins in the GH3 were predicted to contain a signal peptide and transmembrane region, suggesting their potential for extracellularly degrade cellulose. Based on the physiological features of the type strain QXD-8T, we propose the name Microbacterium psychrotolerans for this novel species. This study expands the diversity of psychrotolerant cellulolytic bacteria and provides a potential microbial resource for straw returning in high-latitude areas at low temperatures.
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Affiliation(s)
- Peng An
- College of Life Science, Sichuan Normal University, Chengdu 610101, China; (P.A.); (W.L.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Changjialian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- College of Life Science, Sichuan Normal University, Chengdu 610101, China; (P.A.); (W.L.)
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Shyaula M, Regmi S, Khadka D, Poudel RC, Dhakal A, Koirala D, Sijapati J, Singh A, Maharjan J. Characterization of Thermostable Cellulase from Bacillus licheniformis PANG L Isolated from the Himalayan Soil. Int J Microbiol 2023; 2023:3615757. [PMID: 37692921 PMCID: PMC10484656 DOI: 10.1155/2023/3615757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/13/2023] [Accepted: 08/12/2023] [Indexed: 09/12/2023] Open
Abstract
This study aimed to isolate, purify, and characterize a potential thermophilic cellulase-producing bacterium from the Himalayan soil. Eleven thermophilic bacteria were isolated, and the strain PANG L was found to be the most potent cellulolytic producer. Morphological, physiological, biochemical, and molecular characterization identified PANG L as Bacillus licheniformis. This is the first study on the isolation of thermostable cellulase-producing Bacillus licheniformis from the Himalayan soil. This bacterium was processed for the production of cellulase enzyme. The optimum conditions for cellulase production were achieved at 45°C after 48 h of incubation at pH 6.5 in media-containing carboxymethyl cellulose (CMC) and yeast extract as carbon and nitrogen sources, respectively, in a thermo-shaker at 100 rpm. The enzyme was partially purified by 80% ammonium sulphate precipitation followed by dialysis, resulting in a 1.52-fold purification. The optimal activity of partially purified cellulase was observed at a temperature of 60°C and pH 5. The cellulase enzyme was stable within the pH ranges of 3-5 and retained 67% of activity even at 55°C. Cellulase activity was found to be enhanced in the presence of metal ions such as Cd2+, Pb2+, and Ba2+. The enzyme showed the highest activity when CMC was used as a substrate, followed by cellobiose. The Km and Vmax values of the enzyme were 1.8 mg/ml and 10.92 μg/ml/min, respectively. The cellulase enzyme obtained from Bacillus licheniformis PANG L had suitable catalytic properties for use in industrial applications.
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Affiliation(s)
- Manita Shyaula
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Sunil Regmi
- Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Deegendra Khadka
- Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | | | - Agni Dhakal
- Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Devesh Koirala
- Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | | | - Anjana Singh
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Jyoti Maharjan
- Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
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7
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Ilić-Stojanović S, Nikolić L, Cakić S. A Review of Patents and Innovative Biopolymer-Based Hydrogels. Gels 2023; 9:556. [PMID: 37504436 PMCID: PMC10378757 DOI: 10.3390/gels9070556] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Biopolymers represent a great resource for the development and utilization of new functional materials due to their particular advantages such as biocompatibility, biodegradability and non-toxicity. "Intelligent gels" sensitive to different stimuli (temperature, pH, ionic strength) have different applications in many industries (e.g., pharmacy, biomedicine, food). This review summarizes the research efforts presented in the patent and non-patent literature. A discussion was conducted regarding biopolymer-based hydrogels such as natural proteins (i.e., fibrin, silk fibroin, collagen, keratin, gelatin) and polysaccharides (i.e., chitosan, hyaluronic acid, cellulose, carrageenan, alginate). In this analysis, the latest advances in the modification and characterization of advanced biopolymeric formulations and their state-of-the-art administration in drug delivery, wound healing, tissue engineering and regenerative medicine were addressed.
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Affiliation(s)
| | - Ljubiša Nikolić
- Faculty of Technology, University of Niš, Bulevar Oslobodjenja 124, 16000 Leskovac, Serbia
| | - Suzana Cakić
- Faculty of Technology, University of Niš, Bulevar Oslobodjenja 124, 16000 Leskovac, Serbia
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8
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Nefjodovs V, Andze L, Andzs M, Filipova I, Tupciauskas R, Vecbiskena L, Kapickis M. Wood as Possible Renewable Material for Bone Implants-Literature Review. J Funct Biomater 2023; 14:jfb14050266. [PMID: 37233376 DOI: 10.3390/jfb14050266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/25/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023] Open
Abstract
Bone fractures and bone defects affect millions of people every year. Metal implants for bone fracture fixation and autologous bone for defect reconstruction are used extensively in treatment of these pathologies. Simultaneously, alternative, sustainable, and biocompatible materials are being researched to improve existing practice. Wood as a biomaterial for bone repair has not been considered until the last 50 years. Even nowadays there is not much research on solid wood as a biomaterial in bone implants. A few species of wood have been investigated. Different techniques of wood preparation have been proposed. Simple pre-treatments such as boiling in water or preheating of ash, birch and juniper woods have been used initially. Later researchers have tried using carbonized wood and wood derived cellulose scaffold. Manufacturing implants from carbonized wood and cellulose requires more extensive wood processing-heat above 800 °C and chemicals to extract cellulose. Carbonized wood and cellulose scaffolds can be combined with other materials, such as silicon carbide, hydroxyapatite, and bioactive glass to improve biocompatibility and mechanical durability. Throughout the publications wood implants have provided good biocompatibility and osteoconductivity thanks to wood's porous structure.
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Affiliation(s)
- Vadims Nefjodovs
- Faculty of Residency, Riga Stradins University, Dzirciema iela 16, LV-1007 Riga, Latvia
- Microsurgery Centre of Latvia, Brivibas Gatve 410, LV-1024 Riga, Latvia
| | - Laura Andze
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
| | - Martins Andzs
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
| | - Inese Filipova
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
| | - Ramunas Tupciauskas
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
| | - Linda Vecbiskena
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
| | - Martins Kapickis
- Microsurgery Centre of Latvia, Brivibas Gatve 410, LV-1024 Riga, Latvia
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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10
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Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A 2022; 119:e2117467119. [PMID: 36215467 PMCID: PMC9586272 DOI: 10.1073/pnas.2117467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.
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11
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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12
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Zajki-Zechmeister K, Eibinger M, Nidetzky B. Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose. ACS Catal 2022; 12:10984-10994. [PMID: 36082050 PMCID: PMC9442579 DOI: 10.1021/acscatal.2c02377] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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13
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Tsudome M, Tachioka M, Miyazaki M, Uchimura K, Tsuda M, Takaki Y, Deguchi S. An ultrasensitive nanofiber-based assay for enzymatic hydrolysis and deep-sea microbial degradation of cellulose. iScience 2022; 25:104732. [PMID: 36039358 PMCID: PMC9418596 DOI: 10.1016/j.isci.2022.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/10/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mikiko Tsudome
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Mikako Tachioka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kohsuke Uchimura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Miwako Tsuda
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Corresponding author
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14
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Ye TJ, Huang KF, Ko TP, Wu SH. Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase. Acta Crystallogr D Struct Biol 2022; 78:633-646. [PMID: 35503211 PMCID: PMC9063844 DOI: 10.1107/s2059798322002601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
A unique endoglucanase with a carbohydrate-binding module inserted in the middle of the catalytic domain has been characterized structurally and functionally, providing insights into the mode of action responsible for its enhanced catalytic performance. Most known cellulase-associated carbohydrate-binding modules (CBMs) are attached to the N- or C-terminus of the enzyme or are expressed separately and assembled into multi-enzyme complexes (for example to form cellulosomes), rather than being an insertion into the catalytic domain. Here, by solving the crystal structure, it is shown that MtGlu5 from Meiothermus taiwanensis WR-220, a GH5-family endo-β-1,4-glucanase (EC 3.2.1.4), has a bipartite architecture consisting of a Cel5A-like catalytic domain with a (β/α)8 TIM-barrel fold and an inserted CBM29-like noncatalytic domain with a β-jelly-roll fold. Deletion of the CBM significantly reduced the catalytic efficiency of MtGlu5, as determined by isothermal titration calorimetry using inactive mutants of full-length and CBM-deleted MtGlu5 proteins. Conversely, insertion of the CBM from MtGlu5 into TmCel5A from Thermotoga maritima greatly enhanced the substrate affinity of TmCel5A. Bound sugars observed between two tryptophan side chains in the catalytic domains of active full-length and CBM-deleted MtGlu5 suggest an important stacking force. The synergistic action of the catalytic domain and CBM of MtGlu5 in binding to single-chain polysaccharides was visualized by substrate modeling, in which additional surface tryptophan residues were identified in a cross-domain groove. Subsequent site-specific mutagenesis results confirmed the pivotal role of several other tryptophan residues from both domains of MtGlu5 in substrate binding. These findings reveal a way to incorporate a CBM into the catalytic domain of an existing enzyme to make a robust cellulase.
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15
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Lombardi V, Trande M, Back M, Patwardhan SV, Benedetti A. Facile Cellulase Immobilisation on Bioinspired Silica. NANOMATERIALS 2022; 12:nano12040626. [PMID: 35214956 PMCID: PMC8880491 DOI: 10.3390/nano12040626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
Cellulases are enzymes with great potential for converting biomass to biofuels for sustainable energy. However, their commercial use is limited by their costs and low reusability. Therefore, the scientific and industrial sectors are focusing on finding better strategies to reuse enzymes and improve their performance. In this work, cellulase from Aspergillus niger was immobilised through in situ entrapment and adsorption on bio-inspired silica (BIS) supports. To the best of our knowledge, this green effect strategy has never been applied for cellulase into BIS. In situ entrapment was performed during support synthesis, applying a one-pot approach at mild conditions (room temperature, pH 7, and water solvent), while adsorption was performed after support formation. The loading efficiency was investigated on different immobilisation systems by Bradford assay and FTIR. Bovine serum albumin (BSA) was chosen as a control to optimize cellulase loading. The residual activity of cellulase was analysed by the dinitro salicylic acid (DNS) method. Activity of 90% was observed for the entrapped enzyme, while activity of ~55% was observed for the adsorbed enzyme. Moreover, the supported enzyme systems were recycled five times to evaluate their reuse potential. The thermal and pH stability tests suggested that both entrapment and adsorption strategies can increase enzyme activity. The results highlight that the entrapment in BIS is a potentially useful strategy to easily immobilise enzymes, while preserving their stability and recycle potential.
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Affiliation(s)
- Vincenzo Lombardi
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy;
- Correspondence: (V.L.); (S.V.P.); (A.B.); Tel.: +44-114-222-7593 (S.V.P.); +39-041-234-6744 (A.B.)
| | - Matteo Trande
- Department of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK;
| | - Michele Back
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy;
| | - Siddharth V. Patwardhan
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
- Correspondence: (V.L.); (S.V.P.); (A.B.); Tel.: +44-114-222-7593 (S.V.P.); +39-041-234-6744 (A.B.)
| | - Alvise Benedetti
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy;
- Correspondence: (V.L.); (S.V.P.); (A.B.); Tel.: +44-114-222-7593 (S.V.P.); +39-041-234-6744 (A.B.)
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16
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Sagarika MS, Parameswaran C, Senapati A, Barala J, Mitra D, Prabhukarthikeyan SR, Kumar A, Nayak AK, Panneerselvam P. Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150451. [PMID: 34607097 DOI: 10.1016/j.scitotenv.2021.150451] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.
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Affiliation(s)
- Mahapatra Smruthi Sagarika
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India; Indira Gandhi Agricultural University, Raipur, Chhattisgarh 492012, India
| | | | - Ansuman Senapati
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Jatiprasad Barala
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Debasis Mitra
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | | | - Anjani Kumar
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
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17
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Recent Progress in Biopolymer-Based Hydrogel Materials for Biomedical Applications. Int J Mol Sci 2022; 23:ijms23031415. [PMID: 35163339 PMCID: PMC8836285 DOI: 10.3390/ijms23031415] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 12/23/2022] Open
Abstract
Hydrogels from biopolymers are readily synthesized, can possess various characteristics for different applications, and have been widely used in biomedicine to help with patient treatments and outcomes. Polysaccharides, polypeptides, and nucleic acids can be produced into hydrogels, each for unique purposes depending on their qualities. Examples of polypeptide hydrogels include collagen, gelatin, and elastin, and polysaccharide hydrogels include alginate, cellulose, and glycosaminoglycan. Many different theories have been formulated to research hydrogels, which include Flory-Rehner theory, Rubber Elasticity Theory, and the calculation of porosity and pore size. All these theories take into consideration enthalpy, entropy, and other thermodynamic variables so that the structure and pore sizes of hydrogels can be formulated. Hydrogels can be fabricated in a straightforward process using a homogeneous mixture of different chemicals, depending on the intended purpose of the gel. Different types of hydrogels exist which include pH-sensitive gels, thermogels, electro-sensitive gels, and light-sensitive gels and each has its unique biomedical applications including structural capabilities, regenerative repair, or drug delivery. Major biopolymer-based hydrogels used for cell delivery include encapsulated skeletal muscle cells, osteochondral muscle cells, and stem cells being delivered to desired locations for tissue regeneration. Some examples of hydrogels used for drug and biomolecule delivery include insulin encapsulated hydrogels and hydrogels that encompass cancer drugs for desired controlled release. This review summarizes these newly developed biopolymer-based hydrogel materials that have been mainly made since 2015 and have shown to work and present more avenues for advanced medical applications.
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18
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Industrially Important Genes from Trichoderma. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Makowski K, Leszczewicz M, Broncel N, Lipińska-Zubrycka L, Głębski A, Komorowski P, Walkowiak B. Isolation, Biochemical Characterisation and Identification of Thermotolerant and Cellulolytic Paenibacillus lactis and Bacillus licheniformis. Food Technol Biotechnol 2021; 59:325-336. [PMID: 34759764 PMCID: PMC8542176 DOI: 10.17113/ftb.59.03.21.7096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/24/2021] [Indexed: 11/12/2022] Open
Abstract
Research background Cellulose is an ingredient of waste materials that can be converted to other valuable substances. This is possible provided that the polymer molecule is degraded to smaller particles and used as a carbon source by microorganisms. Because of the frequently applied methods of pretreatment of lignocellulosic materials, the cellulases derived from thermophilic microorganisms are particularly desirable. Experimental approach We were looking for cellulolytic microorganisms able to grow at 50 °C and we described their morphological features and biochemical characteristics based on carboxymethyl cellulase (CMCase) activity and the API® ZYM system. The growth curves during incubation at 50 °C were examined using the BioLector® microbioreactor. Results and conclusions Forty bacterial strains were isolated from fermenting hay, geothermal karst spring, hot spring and geothermal pond at 50 °C. The vast majority of the bacteria were Gram-positive and rod-shaped with the maximum growth temperature of at least 50 °C. We also demonstrated a large diversity of biochemical characteristics among the microorganisms. The CMCase activity was confirmed in 27 strains. Hydrolysis capacities were significant in bacterial strains: BBLN1, BSO6, BSO10, BSO13 and BSO14, and reached 2.74, 1.62, 1.30, 1.38 and 8.02 respectively. Rapid and stable growth was observed, among others, for BBLN1, BSO10, BSO13 and BSO14. The strains fulfilled the selection conditions and were identified based on the 16S rDNA sequences. BBLN1, BSO10, BSO13 were classified as Bacillus licheniformis, whereas BSO14 as Paenibacillus lactis. Novelty and scientific contribution We described cellulolytic activity and biochemical characteristics of many bacteria isolated from hot environments. We are also the first to report the cellulolytic activity of thermotolerant P. lactis. Described strains can be a source of new thermostable cellulases, which are extremely desirable in various branches of circular bioeconomy.
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Affiliation(s)
- Krzysztof Makowski
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Biotechnika, Tymienieckiego 25, 90-350 Lodz, Poland
| | - Martyna Leszczewicz
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland
| | - Natalia Broncel
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland
| | - Lidia Lipińska-Zubrycka
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Adrian Głębski
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland
| | - Piotr Komorowski
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-537 Lodz, Poland
| | - Bogdan Walkowiak
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-537 Lodz, Poland
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20
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Madland E, Forsberg Z, Wang Y, Lindorff-Larsen K, Niebisch A, Modregger J, Eijsink VGH, Aachmann FL, Courtade G. Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus. J Biol Chem 2021; 297:101084. [PMID: 34411561 PMCID: PMC8449059 DOI: 10.1016/j.jbc.2021.101084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022] Open
Abstract
Among the extensive repertoire of carbohydrate-active enzymes, lytic polysaccharide monooxygenases (LPMOs) have a key role in recalcitrant biomass degradation. LPMOs are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds in polysaccharides such as cellulose and chitin. Several LPMOs contain carbohydrate-binding modules (CBMs) that are known to promote LPMO efficiency. However, structural and functional properties of some CBMs remain unknown, and it is not clear why some LPMOs, like CjLPMO10A from the soil bacterium Cellvibrio japonicus, have multiple CBMs (CjCBM5 and CjCBM73). Here, we studied substrate binding by these two CBMs to shine light on their functional variation and determined the solution structures of both by NMR, which constitutes the first structure of a member of the CBM73 family. Chitin-binding experiments and molecular dynamics simulations showed that, while both CBMs bind crystalline chitin with Kd values in the micromolar range, CjCBM73 has higher affinity for chitin than CjCBM5. Furthermore, NMR titration experiments showed that CjCBM5 binds soluble chitohexaose, whereas no binding of CjCBM73 to this chitooligosaccharide was detected. These functional differences correlate with distinctly different arrangements of three conserved aromatic amino acids involved in substrate binding. In CjCBM5, these residues show a linear arrangement that seems compatible with the experimentally observed affinity for single chitin chains. On the other hand, the arrangement of these residues in CjCBM73 suggests a wider binding surface that may interact with several chitin chains. Taken together, these results provide insight into natural variation among related chitin-binding CBMs and the possible functional implications of such variation.
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Affiliation(s)
- Eva Madland
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Gaston Courtade
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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21
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Lai CY, Ng KL, Wang H, Lam CC, Wong WKR. Spontaneous Cleavages of a Heterologous Protein, the CenA Endoglucanase of Cellulomonas fimi, in Escherichia coli. Microbiol Insights 2021; 14:11786361211024637. [PMID: 34188486 PMCID: PMC8209791 DOI: 10.1177/11786361211024637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/22/2021] [Indexed: 11/26/2022] Open
Abstract
CenA is an endoglucanase secreted by the Gram-positive cellulolytic bacterium, Cellulomonas fimi, to the environment as a glycosylated protein. The role of glycosylation in CenA is unclear. However, it seems not crucial for functional activity and secretion since the unglycosylated counterpart, recombinant CenA (rCenA), is both bioactive and secretable in Escherichia coli. Using a systematic screening approach, we have demonstrated that rCenA is subjected to spontaneous cleavages (SC) in both the cytoplasm and culture medium of E. coli, under the influence of different environmental factors. The cleavages were found to occur in both the cellulose-binding (CellBD) and catalytic domains, with a notably higher occurring rate detected in the former than the latter. In CellBD, the cleavages were shown to occur close to potential N-linked glycosylation sites, suggesting that these sites might serve as ‘attributive tags’ for differentiating rCenA from endogenous proteins and the points of initiation of SC. It is hypothesized that glycosylation plays a crucial role in protecting CenA from SC when interacting with cellulose in the environment. Subsequent to hydrolysis, SC would ensure the dissociation of CenA from the enzyme-substrate complex. Thus, our findings may help elucidate the mechanisms of protein turnover and enzymatic cellulolysis.
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Affiliation(s)
- Cheuk Yin Lai
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Ka Lun Ng
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Hao Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chui Chi Lam
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Wan Keung Raymond Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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22
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Kargar F, Mortazavi M, Maleki M, Mahani MT, Ghasemi Y, Savardashtaki A. Isolation, Identification and In Silico Study of Native Cellulase Producing Bacteria. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666191127142035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
The purpose of this study was to screen the bacteria producing cellulase enzymes and
their bioinformatics studies.
Background:
Cellulose is a long-chain polymer of glucose that hydrolyzes by cellulases to glucose
molecules. In order to design the new biotechnological applications, some strategies have been used as
increasing the efficiency of enzyme production, generating cost-effective enzymes, producing stable
enzymes and identification of new strains.
Objective:
On the other hand, some bacteria special features have made them suitable candidates for the
identification of the new source of enzymes. In this regard, some native strains of bacteria were screened.
Methods:
These bacteria were grown on a culture containing the liquid M9 media containing CMC to
ensure the synthesis of cellulase. The formation of a clear area in the culture medium indicated decomposition
of cellulose. In the following, the DNA of these bacteria were extracted and their 16S rDNA
genes were amplified.
Result:
The results show that nine samples were able to synthesize cellulase. In following, these strains
were identified using 16S rDNA. The results show that these screened bacteria belonged to the Bacillus
sp., Alcaligenes sp., Alcaligenes sp., and Enterobacter sp.
Conclusion:
The enzyme activity analysis shows that the Bacillus toyonensis, Bacillus sp. strain
XA15-411 Bacillus cereus have produced the maximum yield of cellulases. However, these amounts
of enzyme production in these samples are not proportional to their growth rate. As the bacterial
growth chart within 4 consecutive days shows that the Alcaligenes sp. Bacillus cereus, Bacillus
toyonensis, Bacillus sp. strain XA15-411 have a maximum growth rate. The study of the phylogenetic
tree also shows that Bacillus species are more abundant in the production of cellulase enzyme. These
bioinformatics analyses show that the Bacillus species have different evolutionary relationships and
evolved in different evolutionary time. However, for maximum cellulase production by this bacteria,
some information as optimum temperature, optimum pH, carbon and nitrogen sources are needed for
the ideal formulation of media composition. The cellulase production is closely controlled in microorganisms
and the cellulase yields appear to depend on a variety of factors. However, the further studies
are needed for cloning, purification and application of these new microbial cellulases in the different
commercial fields as in food, detergent, and pharmaceutical, paper, textile industries and also various
chemical industries. However, these novel enzymes can be further engineered through rational design
or using random mutagenesis techniques.
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Affiliation(s)
- Farzane Kargar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Tabriz University of Medical Sciences Tabriz, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences, Shiraz, Iran
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Determining Cellulolytic Activity of Microorganisms. CHEMISTRY-DIDACTICS-ECOLOGY-METROLOGY 2021. [DOI: 10.2478/cdem-2020-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Decomposition of cellulose to glucose requires complex cooperation of glycoside hydrolase enzymes. As a result of glycoside β-1,4 bonds hydrolysis, shorter chains of cellulose, oligodextrin, cellobiose and glucose are created. A number of bacteria and fungi demonstrate the capacity to degrade cellulose. Their activity can be assessed with the use of qualitative and quantitative methods. Qualitative methods with the use of e.g. Congo red, are used in screening studies, however, they do not provide information about the quantity of the produced enzyme. Spectrophotometric methods are more accurate and they measure the quantities of reducing sugars with the use of appropriate substrates, e.g. carboxymethylcellulose is used to determine endoglucanases, avicel cellulose to determine exoglucanases and Whatman filter paper to determine total cellulolytic activity. Activity of microorganisms depends not only on their species or type but also, among others, on substratum composition, cultivation conditions and the appropriate selection of parameters of the carried out enzymatic reactions.
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24
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Molecular characterization of cellulolytic (endo- and exoglucanase) bacteria from the largest mangrove forest (Sundarbans), Bangladesh. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01606-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Cellulase, due to its massive applicability, has been used in various industrial processes such as biofuels (bioethanol, triphasic biomethanation), agricultural and plant waste management, chiral separation, and ligand binding studies. The finding of a novel cellulase-producing bacterium will benefit the industries, which rely on yeast to produce cellulase in fermentation technology, because bacteria can easily be manipulated and fermented cost-effectively.
Methods
Cellulase enzyme-secreting bacteria were isolated from different regions of the world’s largest mangrove forests, Sundarbans in Bangladesh. Biochemical, morphological, and 16S rRNA identification protocol was followed to precisely characterize the bacterial strains.
Result
We have determined that the strain T2-D2 (Bacillus sp.), E1-PT (Pseudomonas sp.), and D1-PT (Pseudomonas sp.) showed maximum endoglycolytic and strain C1-BT (Bacillus sp.), E1-BT (Bacillus sp.), and T-4 (E) showed relatively higher exoglycolytic activity during the test. So, it can be easily cultured at a normal temperature (97.7–99.5 °F). On the one hand, T2-D2 (Bacillus sp.) and E1-PT (Pseudomonas sp.) have shown the highest growth rate at pH 7 as it was neither acidic nor basic.
Conclusion
It was concluded that the strain T2-D2 (Bacillus sp.) and E1-PT (Pseudomonas sp.) would be our target cellulolytic strains wherein the experimental isolates belonged to the Enterobacteriaceae, Psuedomonacea, Bacillacea, and Morganellacea family.
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25
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Ben‐David Y, Moraïs S, Bayer EA, Mizrahi I. Rapid adaptation for fibre degradation by changes in plasmid stoichiometry within Lactobacillus plantarum at the synthetic community level. Microb Biotechnol 2020; 13:1748-1764. [PMID: 32639625 PMCID: PMC7533337 DOI: 10.1111/1751-7915.13584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 12/19/2022] Open
Abstract
The multi-enzyme cellulosome complex can mediate the valorization of lignocellulosic biomass into soluble sugars that can serve in the production of biofuels and valuable products. A potent bacterial chassis for the production of active cellulosomes displayed on the cell surface is the bacterium Lactobacillus plantarum, a lactic acid bacterium used in many applications. Here, we developed a methodological pipeline to produce improved designer cellulosomes, using a cell-consortium approach, whereby the different components self-assemble on the surface of L. plantarum. The pipeline served as a vehicle to select and optimize the secretion efficiency of potent designer cellulosome enzyme components, to screen for the most efficient enzymatic combinations and to assess attempts to grow the engineered bacterial cells on wheat straw as a sole carbon source. Using this strategy, we were able to improve the secretion efficiency of the selected enzymes and to secrete a fully functional high-molecular-weight scaffoldin component. The adaptive laboratory process served to increase significantly the enzymatic activity of the most efficient cell consortium. Internal plasmid re-arrangement towards a higher enzymatic performance attested for the suitability of the approach, which suggests that this strategy represents an efficient way for microbes to adapt to changing conditions.
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Affiliation(s)
- Yonit Ben‐David
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovot7610001Israel
| | - Sarah Moraïs
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovot7610001Israel
- Department of Life SciencesNational Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8499000Israel
| | - Edward A. Bayer
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovot7610001Israel
| | - Itzhak Mizrahi
- Department of Life SciencesNational Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8499000Israel
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26
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Nidetzky B, Zhong C. Phosphorylase-catalyzed bottom-up synthesis of short-chain soluble cello-oligosaccharides and property-tunable cellulosic materials. Biotechnol Adv 2020; 51:107633. [PMID: 32966861 DOI: 10.1016/j.biotechadv.2020.107633] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/23/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022]
Abstract
Cellulose-based materials are produced industrially in countless varieties via top-down processing of natural lignocellulose substrates. By contrast, cellulosic materials are only rarely prepared via bottom up synthesis and oligomerization-induced self-assembly of cellulose chains. Building up a cellulose chain via precision polymerization is promising, however, for it offers tunability and control of the final chemical structure. Synthetic cellulose derivatives with programmable material properties might thus be obtained. Cellodextrin phosphorylase (CdP; EC 2.4.1.49) catalyzes iterative β-1,4-glycosylation from α-d-glucose 1-phosphate, with the ability to elongate a diversity of acceptor substrates, including cellobiose, d-glucose and a range of synthetic glycosides having non-sugar aglycons. Depending on the reaction conditions leading to different degrees of polymerization (DP), short-chain soluble cello-oligosaccharides (COS) or insoluble cellulosic materials are formed. Here, we review the characteristics of CdP as bio-catalyst for synthetic applications and show advances in the enzymatic production of COS and reducing end-modified, tailored cellulose materials. Recent studies reveal COS as interesting dietary fibers that could provide a selective prebiotic effect. The bottom-up synthesized celluloses involve chains of DP ≥ 9, as precipitated in solution, and they form ~5 nm thick sheet-like crystalline structures of cellulose allomorph II. Solvent conditions and aglycon structures can direct the cellulose chain self-assembly towards a range of material architectures, including hierarchically organized networks of nanoribbons, or nanorods as well as distorted nanosheets. Composite materials are also formed. The resulting materials can be useful as property-tunable hydrogels and feature site-specific introduction of functional and chemically reactive groups. Therefore, COS and cellulose obtained via bottom-up synthesis can expand cellulose applications towards product classes that are difficult to access via top-down processing of natural materials.
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Affiliation(s)
- Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz 8010, Austria; Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, Graz 8010, Austria.
| | - Chao Zhong
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz 8010, Austria
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27
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Jiang S, Zheng X, Li L. De novo assembly of Auricularia polytricha transcriptome and discovery of genes involved in the degradation of lignocellulose. Biotechnol Appl Biochem 2020; 68:983-991. [PMID: 32786100 DOI: 10.1002/bab.2005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/27/2020] [Indexed: 11/10/2022]
Abstract
Auricularia polytricha belonging to Basidiomycota has the ability to degrade lignocellulose. However, there has been no resource in public databases examining the transcriptome of A. polytricha. In this study, high-throughput sequencing platform BGISEQ-500 was used to generate large amount of transcript sequences from A. polytricha for gene discovery and molecular marker development. A total of 28,102 unigenes were discovered from the assembly of clean reads. In addition, functional categorization of the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) metabolic pathways revealed several important biological processes. GO annotation analysis presented 47 categories, with the major subcategories being catalytic activity, binding, cellular process, metabolic process, and cell. Among the five functional categories and 21 subcategories of processes discovered from KEGG, global and overview maps, carbohydrate metabolism, transport, and catabolism are the main subcategories. Furthermore, among the unigenes related to lignocellulosic degradation discovered by KEGG pathway enrichment analysis, 2, 5, and 16 unigenes in de novo assembly of A. polytricha transcriptome were found to relate to cellulose, hemicellulose, and lignin degradation, respectively. The study provided valuable information on the degradation of lignocellulose to facilitate research on the degradation mechanism, molecular marker, functional research, gene mapping, and other multigenomic studies of species containing lignocellulose.
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Affiliation(s)
- Shiyu Jiang
- College of Grain and Food science, Henan University of Technology, Zhengzhou, Henan, People's Republic of China
| | - Xueling Zheng
- College of Grain and Food science, Henan University of Technology, Zhengzhou, Henan, People's Republic of China
| | - Li Li
- College of Grain and Food science, Henan University of Technology, Zhengzhou, Henan, People's Republic of China
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28
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One-step electrospinning cellulose nanofibers with superhydrophilicity and superoleophobicity underwater for high-efficiency oil-water separation. Int J Biol Macromol 2020; 162:1536-1545. [PMID: 32781123 DOI: 10.1016/j.ijbiomac.2020.07.175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/23/2022]
Abstract
Cellulose nanofibers have been widely applied in many fields because of its unique advantages. However, it is a challenge to prepare cellulose nanofibers by electrospinning directly owing to the special molecular structure of cellulose. This limits the practical applications of cellulose nanofibers. In this work, cellulose nanofibers were successfully prepared directly by design of new electrospinning receiving device and optimization of process parameters. The as-prepared cellulose nanofibers exhibit good oil-water separation performances. Driven solely by gravity, the separation flux of the cellulose nanofibers for mixture of oil and water reaches 34,300.6 L m-2 h-1, and the separation flux and efficiency for surfactant-stabilized emulsion of oil and water reach 2503.7 L m-2 h-1 and over 98.3%, respectively. The as-prepared cellulose nanofibers also exhibit good mechanical properties and reusability. The breaking strength of the cellulose nanofibers can reach 148.2 cN. The separation fluxes of cellulose nanofibers for mixtures and emulsions of oil and water can be maintained 99.7% and 86.3% of the initial value after being used for 20 times. Furthermore, the as-prepared cellulose nanofibers have good degradability. These properties render as-prepared cellulose nanofibers as promising materials with potential applications in oil-water separation.
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29
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Qin Y, Fu Y, Li Q, Luo F, He H. Purification and Enzymatic Properties of a Difunctional Glycoside Hydrolase from Aspergillus oryzae HML366. Indian J Microbiol 2020; 60:475-484. [PMID: 33087997 DOI: 10.1007/s12088-020-00892-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 05/30/2020] [Indexed: 01/06/2023] Open
Abstract
In the study, an extracellular enzyme HML CBH1 was purified from the fermentation solution of Aspergillus oryzae HML366, and characterized by biological and molecular analysis. Following the culturing of A. oryzae HML366 under the optimized conditions for enzyme production, an enzyme named HML CBH1 with a molecular weight of 48 kDa was purified using 3000 Da cellulose ultrafiltration column and anion exchange chromatography. The specific activity of the purified enzyme was 9.65 U/mg, and the optimum temperature and pH for the enzyme were 50 and 5.0 °C, respectively. The enzyme was stable at temperatures below 60 °C and pH ranging from 3.0 to 10.0. The partial amino acid sequence of HML CBH1 was analyzed by time-of-flight mass spectrometry, and Mascot and Blast analysis showed that the HML CBH1 sequence was identical to the protein gi:22138643, belonging to the glycoside hydrolase family 7, and had exoglucanase and endoglucanase activity.
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Affiliation(s)
- Yongling Qin
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300 China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300 China
| | - Yue Fu
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300 China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300 China
| | - Qiqian Li
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300 China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300 China
| | - Fengfeng Luo
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300 China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300 China
| | - Haiyan He
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300 China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300 China
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30
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Giovannoni M, Gramegna G, Benedetti M, Mattei B. Industrial Use of Cell Wall Degrading Enzymes: The Fine Line Between Production Strategy and Economic Feasibility. Front Bioeng Biotechnol 2020; 8:356. [PMID: 32411686 PMCID: PMC7200985 DOI: 10.3389/fbioe.2020.00356] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Cell Wall Degrading Enzymes (CWDEs) are a heterogeneous group of enzymes including glycosyl-hydrolases, oxidoreductases, lyases, and esterases. Microbes with degrading activities toward plant cell wall polysaccharides are the most relevant source of CWDEs for industrial applications. These organisms secrete a wide array of CWDEs in amounts strictly necessary for their own sustenance, nonetheless the production of CWDEs from wild type microbes can be increased at large-scale by using optimized fermentation strategies. In the last decades, advances in genetic engineering allowed the expression of recombinant CWDEs also in lab-domesticated organisms such as E. coli, yeasts and plants, dramatically increasing the available options for the large-scale production of CWDEs. The optimization of a CWDE-producing biofactory is a hard challenge that biotechnologists tackle by testing different expression strategies and expression-hosts. Although both the yield and production costs are critical factors to produce biomolecules at industrial scale, these parameters are often disregarded in basic research. This review presents the main characteristics and industrial applications of CWDEs directed toward the cell wall of plants, bacteria, fungi and microalgae. Different biofactories for CWDE expression are compared in order to highlight strengths and weaknesses of each production system and how these aspects impact the final enzyme cost and, consequently, the economic feasibility of using CWDEs for industrial applications.
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Affiliation(s)
- Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanna Gramegna
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Manuel Benedetti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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31
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Bealer EJ, Kavetsky K, Dutko S, Lofland S, Hu X. Protein and Polysaccharide-Based Magnetic Composite Materials for Medical Applications. Int J Mol Sci 2019; 21:E186. [PMID: 31888066 PMCID: PMC6981412 DOI: 10.3390/ijms21010186] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/26/2022] Open
Abstract
The combination of protein and polysaccharides with magnetic materials has been implemented in biomedical applications for decades. Proteins such as silk, collagen, and elastin and polysaccharides such as chitosan, cellulose, and alginate have been heavily used in composite biomaterials. The wide diversity in the structure of the materials including their primary monomer/amino acid sequences allow for tunable properties. Various types of these composites are highly regarded due to their biocompatible, thermal, and mechanical properties while retaining their biological characteristics. This review provides information on protein and polysaccharide materials combined with magnetic elements in the biomedical space showcasing the materials used, fabrication methods, and their subsequent applications in biomedical research.
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Affiliation(s)
- Elizabeth J. Bealer
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (K.K.); (S.D.); (S.L.)
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Kyril Kavetsky
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (K.K.); (S.D.); (S.L.)
| | - Sierra Dutko
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (K.K.); (S.D.); (S.L.)
| | - Samuel Lofland
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (K.K.); (S.D.); (S.L.)
| | - Xiao Hu
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (K.K.); (S.D.); (S.L.)
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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32
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Wei Z, Chen C, Liu YJ, Dong S, Li J, Qi K, Liu S, Ding X, Ortiz de Ora L, Muñoz-Gutiérrez I, Li Y, Yao H, Lamed R, Bayer EA, Cui Q, Feng Y. Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex. Nucleic Acids Res 2019; 47:5988-5997. [PMID: 31106374 PMCID: PMC6582324 DOI: 10.1093/nar/gkz355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/18/2022] Open
Abstract
The σ70 family alternative σI factors and their cognate anti-σI factors are widespread in Clostridia and Bacilli and play a role in heat stress response, virulence, and polysaccharide sensing. Multiple σI/anti-σI factors exist in some lignocellulolytic clostridial species, specifically for regulation of components of a multienzyme complex, termed the cellulosome. The σI and anti-σI factors are unique, because the C-terminal domain of σI (SigIC) and the N-terminal inhibitory domain of anti-σI (RsgIN) lack homology to known proteins. Here, we report structure and interaction studies of a pair of σI and anti-σI factors, SigI1 and RsgI1, from the cellulosome-producing bacterium, Clostridium thermocellum. In contrast to other known anti-σ factors that have N-terminal helical structures, RsgIN has a β-barrel structure. Unlike other anti-σ factors that bind both σ2 and σ4 domains of the σ factors, RsgIN binds SigIC specifically. Structural analysis showed that SigIC contains a positively charged surface region that recognizes the promoter -35 region, and the synergistic interactions among multiple interfacial residues result in the specificity displayed by different σI/anti-σI pairs. We suggest that the σI/anti-σI factors represent a distinctive mode of σ/anti-σ complex formation, which provides the structural basis for understanding the molecular mechanism of the intricate σI/anti-σI system.
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Affiliation(s)
- Zhen Wei
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Qi
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiyue Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Ding
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yifei Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongwei Yao
- High-Field Nuclear Magnetic Resonance Center, Xiamen University, 422 South Siming Road, Xiamen 361005, China
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- To whom correspondence should be addressed. Tel: +86 532 80662706; Fax: +86 532 80662707;
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Cao Y, Li X, Xiong J, Wang L, Yan LT, Ge J. Investigating the origin of high efficiency in confined multienzyme catalysis. NANOSCALE 2019; 11:22108-22117. [PMID: 31720641 DOI: 10.1039/c9nr07381g] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biomimetic strategies have successfully been applied to confine multiple enzymes on scaffolds to obtain higher catalytic efficiency of enzyme cascades than freely distributed enzymes. However, the origin of high efficiency is poorly understood. We developed a coarse-grained, particle-based model to understand the origin of high efficiency. We found that a reaction intermediate is the key in affecting reaction kinetics. In the case of unstable intermediates, the confinement of multiple enzymes in clusters enhanced the catalytic efficiency and a shorter distance between enzymes resulted in a higher reaction rate and yield. This understanding was verified by co-encapsulating multiple enzymes in metal-organic framework (MOF) nanocrystals as artificially confined multienzyme complexes. The activity enhancement of multiple enzymes in MOFs depended on the distance between enzymes, when the decay of intermediates existed. The finding of this study is useful for designing in vitro synthetic biology systems based on artificial multienzyme complexes.
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Affiliation(s)
- Yufei Cao
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
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Enzymatic hydrolysis of cellulose using extracts from insects. Carbohydr Res 2019; 485:107811. [PMID: 31526927 DOI: 10.1016/j.carres.2019.107811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/02/2019] [Accepted: 09/08/2019] [Indexed: 11/20/2022]
Abstract
The use of Zophobas morio extracts in the aspect of cellulose hydrolysis is presented for the first time. The aim of this study was to investigate the action of enzymes obtained from Z. morio on cellulose hydrolysis and to determine their influence on the structural properties of cellulose with use the Fourier transform infrared spectroscopy (FTIR) and gel permeation chromatography (GPC). Cellulose hydrolysis products were analyzed by high performance liquid chromatography (HPLC). This analysis indicated that microcrystalline cellulose with smaller particle size was more susceptible to enzymatically treatment. Moreover, our investigation of cellulase activity showed a different profile of the used enzyme during particular developmental stages of Z. morio. Midgut extracts obtained from adult insects are more effective in degrading cellulose than extracts from larvae. The analysis of cellulose hydrolysis confirms that the efficiency of this reaction also depends on the structure of cellulosic materials and internal conditions of enzymatic reaction. In this study the cellulolytic activity of Z. morio midgut extracts showed that these insects could be valuable sources of cellulases.
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Origin, evolution and functional characterization of the land plant glycoside hydrolase subfamily GH5_11. Mol Phylogenet Evol 2019; 138:205-218. [DOI: 10.1016/j.ympev.2019.05.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 01/20/2023]
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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Moraïs S, Mizrahi I. Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem. FEMS Microbiol Rev 2019; 43:362-379. [PMID: 31050730 PMCID: PMC6606855 DOI: 10.1093/femsre/fuz007] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/05/2019] [Indexed: 12/20/2022] Open
Abstract
The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.
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Affiliation(s)
- Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
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Wang Y, Leng L, Islam MK, Liu F, Lin CSK, Leu SY. Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization. Int J Mol Sci 2019; 20:ijms20133354. [PMID: 31288425 PMCID: PMC6651384 DOI: 10.3390/ijms20133354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks.
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Affiliation(s)
- Ying Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ling Leng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Md Khairul Islam
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Fanghua Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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Barruetabeña N, Alonso-Lerma B, Galera-Prat A, Joudeh N, Barandiaran L, Aldazabal L, Arbulu M, Alcalde M, De Sancho D, Gavira JA, Carrion-Vazquez M, Perez-Jimenez R. Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis. Commun Chem 2019. [DOI: 10.1038/s42004-019-0176-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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40
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Busch A, Danchin EGJ, Pauchet Y. Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in Phytophaga beetles. BMC Evol Biol 2019; 19:100. [PMID: 31077129 PMCID: PMC6509783 DOI: 10.1186/s12862-019-1429-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cellulose, a major polysaccharide of the plant cell wall, consists of β-1,4-linked glucose moieties forming a molecular network recalcitrant to enzymatic breakdown. Although cellulose is potentially a rich source of energy, the ability to degrade it is rare in animals and was believed to be present only in cellulolytic microbes. Recently, it has become clear that some animals encode endogenous cellulases belonging to several glycoside hydrolase families (GHs), including GH45. GH45s are distributed patchily among the Metazoa and, in insects, are encoded only by the genomes of Phytophaga beetles. This study aims to understand both the enzymatic functions and the evolutionary history of GH45s in these beetles. RESULTS To this end, we biochemically assessed the enzymatic activities of 37 GH45s derived from five species of Phytophaga beetles and discovered that beetle-derived GH45s degrade three different substrates: amorphous cellulose, xyloglucan and glucomannan. Our phylogenetic and gene structure analyses indicate that at least one gene encoding a putative cellulolytic GH45 was present in the last common ancestor of the Phytophaga, and that GH45 xyloglucanases evolved several times independently in these beetles. The most closely related clade to Phytophaga GH45s was composed of fungal sequences, suggesting this GH family was acquired by horizontal gene transfer from fungi. Besides the insects, other arthropod GH45s do not share a common origin and appear to have emerged at least three times independently. CONCLUSION The rise of functional innovation from gene duplication events has been a fundamental process in the evolution of GH45s in Phytophaga beetles. Both, enzymatic activity and ancestral origin suggest that GH45s were likely an essential prerequisite for the adaptation allowing Phytophaga beetles to feed on plants.
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Affiliation(s)
- André Busch
- Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
| | | | - Yannick Pauchet
- Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany.
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41
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Ahn JH, Kim JH, Ha WH, Park YD. Tooth wear and cleaning effect of an abrasive-free dentifrice. J Dent Sci 2019; 13:13-19. [PMID: 30895089 PMCID: PMC6388868 DOI: 10.1016/j.jds.2017.10.006] [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: 09/13/2017] [Revised: 10/12/2017] [Indexed: 11/24/2022] Open
Abstract
Background/purpose To evaluate the degree of wear on human teeth and the cleaning effect of abrasive-free dentifrice. A sodium pyrophosphate and cellulose-containing abrasive-free dentifrice and calcium carbonate-containing control dentifrice were evaluated. Materials and methods Dentin and enamel specimens were subjected to 109,500 successive double strokes and 5480 double strokes in pH-cycling condition. A profilometer measured abrasion depth. The cleaning effect of dentifrices on artificial stain was evaluated by cleaning power (modified Stookey method) and by removal of colored stain on artificial tooth. Results The experimental results were evaluated using Mann–Whitney U test. The abrasion depth in dentin specimens was 13.97–26.73 times smaller with abrasive-free dentifrice than with control dentifrice. The abrasion depth of enamel specimen was 2.17 ± 0.66 μm with control dentifrice. The values for abrasive-free dentifrice were too small to measure. In pH-cycling conditions using dentin specimens, abrasion depth was 14.28–19.00 times smaller with abrasive-free dentifrice than with control dentifrice. The cleaning power and removing effect of colored stain were statistically insignificant between abrasive-free dentifrice and control dentifrice (P > 0.05). Conclusion The abrasive-free dentifrice was as effective as control dentifrice in its cleaning effect on artificial stain and can significantly reduce tooth wear more than control dentifrice.
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Affiliation(s)
- Jae-Hyun Ahn
- Department of Oral-care, LG Household & Health Care Research Park, Daejeon, South Korea
- Corresponding author. Department of Oral-care, LG Household & Health Care Research Park, 84 Jang-dong, Yusung-gu, Daejeon, South Korea. Fax: +82 42 863 2073.
| | - Ji-Hye Kim
- Department of Oral-care, LG Household & Health Care Research Park, Daejeon, South Korea
| | - Won-Ho Ha
- Department of Oral-care, LG Household & Health Care Research Park, Daejeon, South Korea
| | - Yong-Duk Park
- Kyung Hee University, School of Dentistry, Preventive and Social Dentistry, South Korea
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Enhancing Enzymatic Properties of Endoglucanase I Enzyme from Trichoderma Reesei via Swapping from Cellobiohydrolase I Enzyme. Catalysts 2019. [DOI: 10.3390/catal9020130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Utilizing plant-based materials as a biofuel source is an increasingly popular attempt to redesign the global energy cycle. This endeavour underlines the potential of cellulase enzymes for green energy production and requires the structural and functional engineering of natural enzymes to enhance their utilization. In this work, we aimed to engineer enzymatic and functional properties of Endoglucanase I (EGI) by swapping the Ala43-Gly83 region of Cellobiohydrolase I (CBHI) from Trichoderma reesei. Herein, we report the enhanced enzymatic activity and improved thermal stability of the engineered enzyme, called EGI_swapped, compared to EGI. The difference in the enzymatic activity profile of EGI_swapped and the EGI enzymes became more pronounced upon increasing metal-ion concentrations in the reaction media. Notably, the engineered enzyme retained a considerable level of enzymatic activity after thermal incubation for 90 min at 70 °C while EGI completely lost its enzymatic activity. Circular Dichroism spectroscopy studies revealed distinctive conformational and thermal susceptibility differences between EGI_swapped and EGI enzymes, confirming the improved structural integrity of the swapped enzyme. This study highlights the importance of swapping the metal-ion coordination region in the engineering of EGI enzyme for enhanced structural and thermal stability.
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43
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Multiple Factors Influencing the Strategy of Lignin Mycodegradation. Fungal Biol 2019. [DOI: 10.1007/978-3-030-23834-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pazhang M, Younesi FS, Mehrnejad F, Najavand S, Tarinejad A, Haghi M, Rashno F, Khajeh K. Ig-like Domain in Endoglucanase Cel9A from Alicyclobacillus acidocaldarius Makes Dependent the Enzyme Stability on Calcium. Mol Biotechnol 2018; 60:698-711. [PMID: 30062637 DOI: 10.1007/s12033-018-0105-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) has an Ig-like domain and the enzyme stability is dependent to calcium. In this study the effect of calcium on the structure and stability of the wild-type enzyme and the truncated form (the wild-type enzyme without Ig-like domain, AaCel9AΔN) was investigated. Fluorescence quenching results indicated that calcium increased and decreased the rigidity of the wild-type and truncated enzymes, respectively. RMSF results indicated that AaCel9A has two flexible regions (regions A and B) and deleting the Ig-like domain increased the truncated enzyme stability by decreasing the flexibility of region B probably through increasing the hydrogen bonds. Calcium contact map analysis showed that deleting the Ig-like domain decreased the calcium contacting residues and their calcium binding affinities, especially, in region B which has a role in calcium binding site in AaCel9A. Metal depletion and activity recovering as well as stability results showed that the structure and stability of the wild-type and truncated enzymes are completely dependent on and independent of calcium, respectively. Finally, one can conclude that the deletion of Ig-like domain makes AaCel9AΔN independent of calcium via decreasing the flexibility of region B through increasing the hydrogen bonds. This suggests a new role for the Ig-like domain which makes AaCel9A structure dependent on calcium.
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Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Fereshteh S Younesi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Saeed Najavand
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Tarinejad
- Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mehrnaz Haghi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Fatemeh Rashno
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
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45
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Dvortsov IA, Lunina NA, Demidyuk IV, Kostrov SV. Disturbed processing of the carbohydrate‐binding module of family 54 significantly impairs its binding to polysaccharides. FEBS Lett 2018; 592:3414-3420. [DOI: 10.1002/1873-3468.13262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/06/2018] [Accepted: 09/21/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Igor A. Dvortsov
- Institute of Molecular Genetics Russian Academy of Sciences Moscow Russia
| | - Nataliya A. Lunina
- Institute of Molecular Genetics Russian Academy of Sciences Moscow Russia
| | - Ilya V. Demidyuk
- Institute of Molecular Genetics Russian Academy of Sciences Moscow Russia
| | - Sergey V. Kostrov
- Institute of Molecular Genetics Russian Academy of Sciences Moscow Russia
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46
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Busch A, Kunert G, Wielsch N, Pauchet Y. Cellulose degradation in Gastrophysa viridula (Coleoptera: Chrysomelidae): functional characterization of two CAZymes belonging to glycoside hydrolase family 45 reveals a novel enzymatic activity. INSECT MOLECULAR BIOLOGY 2018; 27:633-650. [PMID: 29774620 DOI: 10.1111/imb.12500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cellulose is a major component of the primary and secondary cell walls in plants. Cellulose is considered to be the most abundant biopolymer on Earth and represents a large potential source of metabolic energy. Yet, cellulose degradation is rare and mostly restricted to cellulolytic microorganisms. Recently, various metazoans, including leaf beetles, have been found to encode their own cellulases, giving them the ability to degrade cellulose independently of cellulolytic symbionts. Here, we analyzed the cellulosic capacity of the leaf beetle Gastrophysa viridula, which typically feeds on Rumex plants. We identified three putative cellulases member of two glycoside hydrolase (GH) families, namely GH45 and GH9. Using heterologous expression and functional assays, we demonstrated that both GH45 proteins are active enzymes, in contrast to the GH9 protein. One GH45 protein acted on amorphous cellulose as an endo-β-1,4-glucanase, whereas the other evolved to become an endo-β-1,4-xyloglucanase. We successfully knocked down the expression of both GH45 genes using RNAi, but no changes in weight gain or mortality were observed compared to control insects. Our data indicated that the breakdown of these polysaccharides in G. viridula may facilitate access to plant cell content, which is rich in nitrogen and simple sugars.
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Affiliation(s)
- A Busch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - G Kunert
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - N Wielsch
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Y Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
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Van de Wouwer D, Boerjan W, Vanholme B. Plant cell wall sugars: sweeteners for a bio-based economy. PHYSIOLOGIA PLANTARUM 2018; 164:27-44. [PMID: 29430656 DOI: 10.1111/ppl.12705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 05/23/2023]
Abstract
Global warming and the consequent climate change is one of the major environmental challenges we are facing today. The driving force behind the rise in temperature is our fossil-based economy, which releases massive amounts of the greenhouse gas carbon dioxide into the atmosphere. In order to reduce greenhouse gas emission, we need to scale down our dependency on fossil resources, implying that we need other sources for energy and chemicals to feed our economy. Here, plants have an important role to play; by means of photosynthesis, plants capture solar energy to split water and fix carbon derived from atmospheric carbon dioxide. A significant fraction of the fixed carbon ends up as polysaccharides in the plant cell wall. Fermentable sugars derived from cell wall polysaccharides form an ideal carbon source for the production of bio-platform molecules. However, a major limiting factor in the use of plant biomass as feedstock for the bio-based economy is the complexity of the plant cell wall and its recalcitrance towards deconstruction. To facilitate the release of fermentable sugars during downstream biomass processing, the composition and structure of the cell wall can be engineered. Different strategies to reduce cell wall recalcitrance will be described in this review. The ultimate goal is to obtain a tailor-made biomass, derived from plants with a cell wall optimized for particular industrial or agricultural applications, without affecting plant growth and development.
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Affiliation(s)
- Dorien Van de Wouwer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
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Cui J, Li L, Kou L, Rong H, Li B, Zhang X. Comparing Immobilized Cellulase Activity in a Magnetic Three-Phase Fluidized Bed Reactor under Three Types of Magnetic Field. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b02195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jun Cui
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, China
| | - Lin Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, China
- School of Chemical Engineering and Energy Technology, Dongguan University of Technology, College Road 1, Dongguan, 523808, China
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, 381 Wushan Road, Guangzhou, 510640, China
| | - Lingmei Kou
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, China
| | - Hui Rong
- Guangzhou Entry-Exit Inspection & Quarantine Bureau of the People’s Republic of China, Guangzhou 510623, China
| | - Bing Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, China
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, 381 Wushan Road, Guangzhou, 510640, China
| | - Xia Zhang
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, China
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, 381 Wushan Road, Guangzhou, 510640, China
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Schmid CAO, Schröder P, Armbruster M, Schloter M. Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis. MICROBIAL ECOLOGY 2018; 76:226-239. [PMID: 29188301 DOI: 10.1007/s00248-017-1110-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/13/2017] [Indexed: 05/09/2023]
Abstract
This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.
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Affiliation(s)
- Christoph A O Schmid
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Peter Schröder
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | | | - Michael Schloter
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
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Putative role of invariant water molecules in the X-ray structures of family G fungal endoxylanases. J Biosci 2018. [DOI: 10.1007/s12038-018-9752-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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