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Grellier M, Moreau C, Beaugrand J, Grisel S, Berrin JG, Cathala B, Villares A. Action of AA9 lytic polysaccharide monooxygenase enzymes on different cellulose allomorphs. Int J Biol Macromol 2024:133429. [PMID: 38944074 DOI: 10.1016/j.ijbiomac.2024.133429] [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: 04/15/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Lytic polysaccharide monooxygenase (LPMO)-catalyzed oxidative processes play a major role in natural biomass conversion. Despite their oxidative cleavage at the surface of polysaccharides, understanding of their mode of action, and the impact of structural patterns of the cellulose fiber on LPMO activity is still not fully understood. In this work, we investigated the action of two different LPMOs from Podospora anserina on celluloses showing different structural patterns. For this purpose, we prepared cellulose II and cellulose III allomorphs from cellulose I cotton linters, as well as amorphous cellulose. LPMO action was monitored in terms of surface morphology, molar mass changes and monosaccharide profile. Both PaLPMO9E and PaLPMO9H were active on the different cellulose allomorphs (I, II and III), and on amorphous cellulose (PASC) whereas they displayed a different behavior, with a higher molar mass decrease observed for cellulose I. Overall, the pretreatment with LPMO enzymes clearly increased the accessibility of all types of cellulose, which was quantified by the higher carboxylate content after carboxymethylation reaction on LPMO-pretreated celluloses. This work gives more insight into the action of LPMOs as a tool for deconstructing lignocellulosic biomass to obtain new bio-based building blocks.
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Affiliation(s)
| | | | | | - Sacha Grisel
- INRAE, Aix Marseille Univ., UMR BBF, F-13009 Marseille, France; INRAE, Aix Marseille Univ., 3PE Platform, F-13009 Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., UMR BBF, F-13009 Marseille, France; INRAE, Aix Marseille Univ., 3PE Platform, F-13009 Marseille, France
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2
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Senanayake M, Lin CY, Mansfield SD, Eudes A, Davison BH, Pingali SV, O'Neill H. Ectopic Production of 3,4-Dihydroxybenzoate in Planta Affects Cellulose Structure and Organization. Biomacromolecules 2024; 25:3542-3553. [PMID: 38780531 DOI: 10.1021/acs.biomac.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Lignocellulosic biomass is a highly sustainable and largely carbon dioxide neutral feedstock for the production of biofuels and advanced biomaterials. Although thermochemical pretreatment is typically used to increase the efficiency of cell wall deconstruction, genetic engineering of the major plant cell wall polymers, especially lignin, has shown promise as an alternative approach to reduce biomass recalcitrance. Poplar trees with reduced lignin content and altered composition were previously developed by overexpressing bacterial 3-dehydroshikimate dehydratase (QsuB) enzyme to divert carbon flux from the shikimate pathway. In this work, three transgenic poplar lines with increasing QsuB expression levels and different lignin contents were studied using small-angle neutron scattering (SANS) and wide-angle X-ray scattering (WAXS). SANS showed that although the cellulose microfibril cross-sectional dimension remained unchanged, the ordered organization of the microfibrils progressively decreased with increased QsuB expression. This was correlated with decreasing total lignin content in the QsuB lines. WAXS showed that the crystallite dimensions of cellulose microfibrils transverse to the growth direction were not affected by the QsuB expression, but the crystallite dimensions parallel to the growth direction were decreased by ∼20%. Cellulose crystallinity was also decreased with increased QsuB expression, which could be related to high levels of 3,4-dihydroxybenzoate, the product of QsuB expression, disrupting microfibril crystallization. In addition, the cellulose microfibril orientation angle showed a bimodal distribution at higher QsuB expression levels. Overall, this study provides new structural insights into the impact of ectopic synthesis of small-molecule metabolites on cellulose organization and structure that can be used for future efforts aimed at reducing biomass recalcitrance.
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Affiliation(s)
- Manjula Senanayake
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Chien-Yuan Lin
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Brian H Davison
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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3
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Bharadwaj A, Holwerda EK, Regan JM, Lynd LR, Richard TL. Enhancing anaerobic digestion of lignocellulosic biomass by mechanical cotreatment. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:76. [PMID: 38831375 PMCID: PMC11149370 DOI: 10.1186/s13068-024-02521-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND The aim of this study was to increase the accessibility and accelerate the breakdown of lignocellulosic biomass to methane in an anaerobic fermentation system by mechanical cotreatment: milling during fermentation, as an alternative to conventional pretreatment prior to biological deconstruction. Effluent from a mesophilic anaerobic digester running with unpretreated senescent switchgrass as the predominant carbon source was collected and subjected to ball milling for 0.5, 2, 5 and 10 min. Following this, a batch fermentation test was conducted with this material in triplicate for an additional 18 days with unmilled effluent as the 'status quo' control. RESULTS The results indicate 0.5 - 10 min of cotreatment increased sugar solubilization by 5- 13% when compared to the unmilled control, with greater solubilization correlated with increased milling duration. Biogas concentrations ranged from 44% to 55.5% methane with the balance carbon dioxide. The total biogas production was statistically higher than the unmilled control for all treatments with 2 or more minutes of milling (α = 0.1). Cotreatment also decreased mean particle size. Energy consumption measurements of a lab-scale mill indicate that longer durations of milling offer diminishing benefits with respect to additional methane production. CONCLUSIONS Cotreatment in anaerobic digestion systems, as demonstrated in this study, provides an alternative approach to conventional pretreatments to increase biogas production from lignocellulosic grassy material.
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Affiliation(s)
- Anahita Bharadwaj
- The Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - John M Regan
- The Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Tom L Richard
- The Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
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4
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Zhuang H, Zheng F, Zhang H, Wang J, Chen J. Efficacious bioconversion of alginate/cellulose to value-added oligosaccharides by alginate-degrading GH5 endoglucanase from Trichoderma asperellum. Int J Biol Macromol 2024; 270:131968. [PMID: 38704059 DOI: 10.1016/j.ijbiomac.2024.131968] [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: 01/17/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Enzymatic degradation of lignocellulosic biomass provides an eco-friendly approach to produce value-added macromolecules, e.g., bioactive polysaccharides. A novel acidophilic GH5 β-1,4-endoglucanase (termed TaCel5) from Trichoderma asperellum ND-1 was efficiently expressed in Komagataella phaffii (∼1.5-fold increase, 38.42 U/mL). TaCel5 displayed both endoglucanase (486.3 U/mg) and alginate lyase (359.5 U/mg) enzyme activities. It had optimal pH 3.0 and strong pH stability (exceed 86 % activity retained over pH range 3.0-5.0). 80 % activity (both endoglucanase and alginate lyase) was retained in the presence of 15 % ethanol or 3.42 M NaCl. Analysis of action mode revealed that hydrolytic activity of TaCel5 required at least three glucose (cellotriose) residues, yielding mainly cellobiose. Glu241 and Glu352 are essential catalytic residues, while Asp106, Asp277 and Asp317 play auxiliary roles in cellulose degradation. TaCel5 displayed high hydrolysis efficiency for glucan and alginate substrates. ESI-MS analysis indicated that the enzymatic hydrolysates of alginate mainly contained disaccharides and heptasaccharides. This is the first detailed report of a bifunctional GH5 endoglucanase/alginate lyase enzyme from T. asperellum. Thus TaCel5 has strong potential in food and feed industries as a catalyst for bioconversion of cellulose- and alginate-containing waste materials into value-added products oligosaccharides, which was of great benefit both for the economy and environment.
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Affiliation(s)
- Huan Zhuang
- Department of ENT and Head & Neck Surgery, Children's Hospital Zhejiang University School of Medicine, Hangzhou 310051, Zhejiang, China
| | - Fengzhen Zheng
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China.
| | - Hengbin Zhang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
| | - Jiaqiang Wang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
| | - Jun Chen
- Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310021, China
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5
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Liu C, Choi B, Efimova E, Nygård Y, Santala S. Enhanced upgrading of lignocellulosic substrates by coculture of Saccharomyces cerevisiae and Acinetobacter baylyi ADP1. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:61. [PMID: 38711153 DOI: 10.1186/s13068-024-02510-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/23/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Lignocellulosic biomass as feedstock has a huge potential for biochemical production. Still, efficient utilization of hydrolysates derived from lignocellulose is challenged by their complex and heterogeneous composition and the presence of inhibitory compounds, such as furan aldehydes. Using microbial consortia where two specialized microbes complement each other could serve as a potential approach to improve the efficiency of lignocellulosic biomass upgrading. RESULTS This study describes the simultaneous inhibitor detoxification and production of lactic acid and wax esters from a synthetic lignocellulosic hydrolysate by a defined coculture of engineered Saccharomyces cerevisiae and Acinetobacter baylyi ADP1. A. baylyi ADP1 showed efficient bioconversion of furan aldehydes present in the hydrolysate, namely furfural and 5-hydroxymethylfurfural, and did not compete for substrates with S. cerevisiae, highlighting its potential as a coculture partner. Furthermore, the remaining carbon sources and byproducts of S. cerevisiae were directed to wax ester production by A. baylyi ADP1. The lactic acid productivity of S. cerevisiae was improved approximately 1.5-fold (to 0.41 ± 0.08 g/L/h) in the coculture with A. baylyi ADP1, compared to a monoculture of S. cerevisiae. CONCLUSION The coculture of yeast and bacterium was shown to improve the consumption of lignocellulosic substrates and the productivity of lactic acid from a synthetic lignocellulosic hydrolysate. The high detoxification capacity and the ability to produce high-value products by A. baylyi ADP1 demonstrates the strain to be a potential candidate for coculture to increase production efficiency and economics of S. cerevisiae fermentations.
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Affiliation(s)
- Changshuo Liu
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Tampere, Finland
| | - Bohyun Choi
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Elena Efimova
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Tampere, Finland
| | - Yvonne Nygård
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Suvi Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Tampere, Finland.
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Chou KJ, Croft T, Hebdon SD, Magnusson LR, Xiong W, Reyes LH, Chen X, Miller EJ, Riley DM, Dupuis S, Laramore KA, Keller LM, Winkelman D, Maness PC. Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose. Metab Eng 2024; 83:193-205. [PMID: 38631458 DOI: 10.1016/j.ymben.2024.03.008] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass holds promise to realize economic production of second-generation biofuels/chemicals, and Clostridium thermocellum is a leading candidate for CBP due to it being one of the fastest degraders of crystalline cellulose and lignocellulosic biomass. However, CBP by C. thermocellum is approached with co-cultures, because C. thermocellum does not utilize hemicellulose. When compared with a single-species fermentation, the co-culture system introduces unnecessary process complexity that may compromise process robustness. In this study, we engineered C. thermocellum to co-utilize hemicellulose without the need for co-culture. By evolving our previously engineered xylose-utilizing strain in xylose, an evolved clonal isolate (KJC19-9) was obtained and showed improved specific growth rate on xylose by ∼3-fold and displayed comparable growth to a minimally engineered strain grown on the bacteria's naturally preferred substrate, cellobiose. To enable full xylan deconstruction to xylose, we recombinantly expressed three different β-xylosidase enzymes originating from Thermoanaerobacterium saccharolyticum into KJC19-9 and demonstrated growth on xylan with one of the enzymes. This recombinant strain was capable of co-utilizing cellulose and xylan simultaneously, and we integrated the β-xylosidase gene into the KJC19-9 genome, creating the KJCBXint strain. The strain, KJC19-9, consumed monomeric xylose but accumulated xylobiose when grown on pretreated corn stover, whereas the final KJCBXint strain showed significantly greater deconstruction of xylan and xylobiose. This is the first reported C. thermocellum strain capable of degrading and assimilating hemicellulose polysaccharide while retaining its cellulolytic capabilities, unlocking significant potential for CBP in advancing the bioeconomy.
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Affiliation(s)
- Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA.
| | - Trevor Croft
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lauren R Magnusson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Luis H Reyes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA; Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Xiaowen Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Emily J Miller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Danielle M Riley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Sunnyjoy Dupuis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Kathrin A Laramore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lisa M Keller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Dirk Winkelman
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
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7
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Li F, Li Q, Lv J, Huang M, Ling Z, Meng Y, Chen F, Ji Z. A novel seawater hydrothermal-deep eutectic solvent pretreatment enhances the production of fermentable sugars and tailored lignin nanospheres from Pinus massoniana. Int J Biol Macromol 2024; 267:131596. [PMID: 38621560 DOI: 10.1016/j.ijbiomac.2024.131596] [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: 01/19/2024] [Revised: 03/20/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Lignocellulose biorefinery depended on effective pretreatment strategies is of great significance for solving the current global crisis of ecosystem and energy security. This study proposes a novel approach combining seawater hydrothermal pretreatment (SHP) and microwave-assisted deep eutectic solvent (MD) pretreatment to achieve an effective fractionation of Pinus massoniana into high value-added products. The results indicated that complex ions (Mg2+, Ca2+, and Cl-) in natural seawater served as Lewis acids and dramatically promoted the depolymerization of mannose and xylan into oligosaccharides with 40.17 % and 75.43 % yields, respectively. Subsequent MD treatment realized a rapid and effective lignin fractionation (~90 %) while retaining cellulose. As a result, the integrated pretreatment yielded ~85 % of enzymatic glucose, indicating an eightfold increase compared with untreated pine. Because of the increased hydrophobicity induced by the formation of acyl groups during MD treatment, uniform lignin nanospheres were successfully recovered from the DES. It exhibited low dispersibility (PDI = 2.23), small molecular weight (1889 g/mol), and excellent oxidation resistance (RSI = 5.94), demonstrating promising applications in functional materials. The mechanism of lignin depolymerization was comprehensively elucidated via FTIR, 2D-HSQC NMR, and GPC analyses. Overall, this study provides a novel and environmentally friendly strategy for lignocellulose biorefinery and lignin valorization.
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Affiliation(s)
- Fucheng Li
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qiang Li
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jiachen Lv
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Mingjun Huang
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zhe Ling
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yao Meng
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Fushan Chen
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zhe Ji
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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8
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Yu P, Zheng X, Alimi LO, Al-Babili S, Khashab NM. Metal-Organic Framework-Mediated Delivery of Nucleic Acid across Intact Plant Cells. ACS APPLIED MATERIALS & INTERFACES 2024; 16:18245-18251. [PMID: 38564422 DOI: 10.1021/acsami.3c19571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Plant synthetic biology is applied in sustainable agriculture, clean energy, and biopharmaceuticals, addressing crop improvement, pest resistance, and plant-based vaccine production by introducing exogenous genes into plants. This technique faces challenges delivering genes due to plant cell walls and intact cell membranes. Novel approaches are required to address this challenge, such as utilizing nanomaterials known for their efficiency and biocompatibility in gene delivery. This work investigates metal-organic frameworks (MOFs) for gene delivery in intact plant cells by infiltration. Hence, small-sized ZIF-8 nanoparticles (below 20 nm) were synthesized and demonstrated effective DNA/RNA delivery into Nicotiana benthamiana leaves and Arabidopsis thaliana roots, presenting a promising and simplified method for gene delivery in intact plant cells. We further demonstrate that small-sized ZIF-8 nanoparticles protect RNA from RNase degradation and successfully silence an endogenous gene by delivering siRNA in N. benthamiana leaves.
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Affiliation(s)
- Pei Yu
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Xiongjie Zheng
- The BioActives Lab, Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Lukman O Alimi
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Niveen M Khashab
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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9
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Firrincieli A, Minuti A, Cappelletti M, Ferilli M, Ajmone-Marsan P, Bani P, Petruccioli M, Harfouche AL. Structural and functional analysis of the active cow rumen's microbial community provides a catalogue of genes and microbes participating in the deconstruction of cardoon biomass. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:53. [PMID: 38589938 PMCID: PMC11003169 DOI: 10.1186/s13068-024-02495-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Ruminal microbial communities enriched on lignocellulosic biomass have shown considerable promise for the discovery of microorganisms and enzymes involved in digesting cell wall compounds, a key bottleneck in the development of second-generation biofuels and bioproducts, enabling a circular bioeconomy. Cardoon (Cynara cardunculus) is a promising inedible energy crop for current and future cellulosic biorefineries and the emerging bioenergy and bioproducts industries. The rumen microbiome can be considered an anaerobic "bioreactor", where the resident microbiota carry out the depolymerization and hydrolysis of plant cell wall polysaccharides (PCWPs) through the catalytic action of fibrolytic enzymes. In this context, the rumen microbiota represents a potential source of microbes and fibrolytic enzymes suitable for biofuel production from feedstocks. In this study, metatranscriptomic and 16S rRNA sequencing were used to profile the microbiome and to investigate the genetic features within the microbial community adherent to the fiber fractions of the rumen content and to the residue of cardoon biomass incubated in the rumen of cannulated cows. RESULTS The metatranscriptome of the cardoon and rumen fibre-adherent microbial communities were dissected in their functional and taxonomic components. From a functional point of view, transcripts involved in the methanogenesis from CO2 and H2, and from methanol were over-represented in the cardoon-adherent microbial community and were affiliated with the Methanobrevibacter and Methanosphaera of the Euryarchaeota phylum. Transcripts encoding glycoside hydrolases (GHs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), and glycoside transferases (GTs) accounted for 1.5% (6,957) of the total RNA coding transcripts and were taxonomically affiliated to major rumen fibrolytic microbes, such as Oscillospiraceae, Fibrobacteraceae, Neocallimastigaceae, Prevotellaceae, Lachnospiraceae, and Treponemataceae. The comparison of the expression profile between cardoon and rumen fiber-adherent microbial communities highlighted that specific fibrolytic enzymes were potentially responsible for the breakdown of cardoon PCWPs, which was driven by specific taxa, mainly Ruminococcus, Treponema, and Neocallimastigaceae. CONCLUSIONS Analysis of 16S rRNA and metatranscriptomic sequencing data revealed that the cow rumen microbiome harbors a repertoire of new enzymes capable of degrading PCWPs. Our results demonstrate the feasibility of using metatranscriptomics of enriched microbial RNA as a potential approach for accelerating the discovery of novel cellulolytic enzymes that could be harnessed for biotechnology. This research contributes a relevant perspective towards degrading cellulosic biomass and providing an economical route to the production of advanced biofuels and high-value bioproducts.
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Affiliation(s)
- Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Marco Ferilli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
- CREI - Romeo and Enrica Invernizzi Research Center On Sustainable Dairy Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
| | - Paolo Bani
- Department of Animal Science, Food and Nutrition, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy
| | - Antoine L Harfouche
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Via San Camillo de Lellis Snc, 01100, Viterbo, Italy.
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10
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Wang B, Wang J, Hu Z, Zhu AL, Shen X, Cao X, Wen JL, Yuan TQ. Harnessing Renewable Lignocellulosic Potential for Sustainable Wastewater Purification. RESEARCH (WASHINGTON, D.C.) 2024; 7:0347. [PMID: 38576863 PMCID: PMC10993153 DOI: 10.34133/research.0347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Utilizing renewable lignocellulosic resources for wastewater remediation is crucial to achieving sustainable social development. However, the resulting by-products and the synthetic process characterized by complexity, high cost, and environmental pollution limit the further development of lignocellulose-based materials. Here, we developed a sustainable strategy that involved a new functional deep eutectic solvent (DES) to deconstruct industrial xylose residue into cellulose-rich residue with carboxyl groups, lignin with carboxyl and quaternary ammonium salt groups, and DES effluent rich in lignin fragments. Subsequently, these fractions equipped with customized functionality were used to produce efficient wastewater remediation materials in cost-effective and environmentally sound manners, namely, photocatalyst prepared by carboxyl-modified cellulose residue, biochar-based adsorbent originated from modified lignin, and flocculant synthesized by self-catalytic in situ copolymerization of residual DES effluent at room temperature. Under the no-waste principle, this strategy upgraded the whole components of waste lignocellulose into high-value-added wastewater remediation materials with excellent universality. These materials in coordination with each other can stepwise purify high-hazardous mineral processing wastewater into drinkable water, including the removal of 99.81% of suspended solids, almost all various heavy metal ions, and 97.09% chemical oxygen demand, respectively. This work provided promising solutions and blueprints for lignocellulosic resources to alleviate water shortages while also advancing the global goal of carbon neutrality.
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Affiliation(s)
- Bin Wang
- State Key Laboratory of Efficient Production of Forest Resources,
Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory of Lignocellulosic Chemistry,
Beijing Forestry University, Beijing 100083, China
| | - Jiaming Wang
- State Key Laboratory of Efficient Production of Forest Resources,
Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory of Lignocellulosic Chemistry,
Beijing Forestry University, Beijing 100083, China
| | - Zhaohui Hu
- State Key Laboratory of Efficient Production of Forest Resources,
Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory of Lignocellulosic Chemistry,
Beijing Forestry University, Beijing 100083, China
| | - An-Ling Zhu
- Hunan Nonferrous Metals Research Institute Co. Ltd., Changsha 410000, China
| | - Xiaojun Shen
- State Key Laboratory of Efficient Production of Forest Resources,
Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory of Lignocellulosic Chemistry,
Beijing Forestry University, Beijing 100083, China
| | - Xuefei Cao
- State Key Laboratory of Efficient Production of Forest Resources,
Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory of Lignocellulosic Chemistry,
Beijing Forestry University, Beijing 100083, China
| | - Jia-Long Wen
- State Key Laboratory of Efficient Production of Forest Resources,
Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory of Lignocellulosic Chemistry,
Beijing Forestry University, Beijing 100083, China
| | - Tong-Qi Yuan
- State Key Laboratory of Efficient Production of Forest Resources,
Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory of Lignocellulosic Chemistry,
Beijing Forestry University, Beijing 100083, China
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11
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Rabi Prasad B, Polaki S, Padhi RK. Isolation of delignifying bacteria and optimization of microbial pretreatment of biomass for bioenergy. Biotechnol Lett 2024; 46:183-199. [PMID: 38252364 DOI: 10.1007/s10529-023-03463-y] [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: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/17/2023] [Indexed: 01/23/2024]
Abstract
Microbial pretreatment of lignocellulosic biomass holds significant promise for environmentally friendly biofuel production, offering an alternative to fossil fuels. This study focused on the isolation and characterization of two novel delignifying bacteria, GIET1 and GIET2, to enhance cellulose accessibility by lignin degradation. Molecular characterization confirmed their genetic identities, providing valuable microbial resources for biofuel production. Our results revealed distinct preferences for temperature, pH, and incubation period for the two bacteria. Bacillus haynesii exhibited optimal performance under moderate conditions and shorter incubation period, making it suitable for rice straw and sugarcane bagasse pretreatment. In contrast, Paenibacillus alvei thrived at higher temperatures and slightly alkaline pH, requiring a longer incubation period ideal for corn stalk pretreatment. These strain-specific requirements highlight the importance of tailoring pretreatment conditions to specific feedstocks. Structural, chemical, and morphological analyses demonstrated that microbial pretreatment reduced the amorphous lignin, increasing cellulose crystallinity and accessibility. These findings underscore the potential of microbial pretreatment to enhance biofuel production by modifying the lignocellulosic biomass. Such environmentally friendly bioconversion processes offer sustainable and cleaner energy solutions. Further research to optimize these methods for scalability and broader application is necessary in the pursuit for more efficient and greener biofuel production.
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Affiliation(s)
- B Rabi Prasad
- Department of Biotechnology, SoET, GIET University, Gunupur, Odisha, 765022, India.
| | - Suman Polaki
- Department of Biotechnology, SoET, GIET University, Gunupur, Odisha, 765022, India
| | - Radha Krushna Padhi
- Department of Chemical Engineering, SoET, GIET University, Gunupur, Odisha, 765022, India
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12
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de Araújo EA, Cortez AA, Pellegrini VDOA, Vacilotto MM, Cruz AF, Batista PR, Polikarpov I. Molecular mechanism of cellulose depolymerization by the two-domain BlCel9A enzyme from the glycoside hydrolase family 9. Carbohydr Polym 2024; 329:121739. [PMID: 38286536 DOI: 10.1016/j.carbpol.2023.121739] [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: 07/21/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/31/2024]
Abstract
Carbohydrate-active enzymes from the glycoside hydrolase family 9 (GH9) play a key role in processing lignocellulosic biomass. Although the structural features of some GH9 enzymes are known, the molecular mechanisms that drive their interactions with cellulosic substrates remain unclear. To investigate the molecular mechanisms that the two-domain Bacillus licheniformis BlCel9A enzyme utilizes to depolymerize cellulosic substrates, we used a combination of biochemical assays, X-ray crystallography, small-angle X-ray scattering, and molecular dynamics simulations. The results reveal that BlCel9A breaks down cellulosic substrates, releasing cellobiose and glucose as the major products, but is highly inefficient in cleaving oligosaccharides shorter than cellotetraose. In addition, fungal lytic polysaccharide oxygenase (LPMO) TtLPMO9H enhances depolymerization of crystalline cellulose by BlCel9A, while exhibiting minimal impact on amorphous cellulose. The crystal structures of BlCel9A in both apo form and bound to cellotriose and cellohexaose were elucidated, unveiling the interactions of BlCel9A with the ligands and their contribution to substrate binding and products release. MD simulation analysis reveals that BlCel9A exhibits higher interdomain flexibility under acidic conditions, and SAXS experiments indicate that the enzyme flexibility is induced by pH and/or temperature. Our findings provide new insights into BlCel9A substrate specificity and binding, and synergy with the LPMOs.
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Affiliation(s)
- Evandro Ares de Araújo
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Giuseppe Maximo Scolfaro, 10000, Campinas, SP 13083-970, Brazil; Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Anelyse Abreu Cortez
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | | | - Milena Moreira Vacilotto
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Amanda Freitas Cruz
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Paulo Ricardo Batista
- Oswaldo Cruz Foundation, Scientific Computing Programme, Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Igor Polikarpov
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil.
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13
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Selvaraj S, Chauhan A, Dutta V, Verma R, Rao SK, Radhakrishnan A, Ghotekar S. A state-of-the-art review on plant-derived cellulose-based green hydrogels and their multifunctional role in advanced biomedical applications. Int J Biol Macromol 2024; 265:130991. [PMID: 38521336 DOI: 10.1016/j.ijbiomac.2024.130991] [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: 12/30/2023] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
The most prevalent carbohydrate on Earth is cellulose, a polysaccharide composed of glucose units that may be found in diverse sources, such as cell walls of wood and plants and some bacterial and algal species. The inherent availability of this versatile material provides a natural pathway for exploring and identifying novel uses. This study comprehensively analyzes cellulose and its derivatives, exploring their structural and biochemical features and assessing their wide-ranging applications in tissue fabrication, surgical dressings, and pharmaceutical delivery systems. The use of diverse cellulose particles as fundamental components gives rise to materials with distinct microstructures and characteristics, fulfilling the requirements of various biological applications. Although cellulose boasts substantial potential across various sectors, its exploration has predominantly unfolded within industrial realms, leaving the biomedical domain somewhat overlooked in its initial stages. This investigation, therefore, endeavors to shed light on the contemporary strides made in synthesizing cellulose and its derivatives. These innovative techniques give rise to distinctive attributes, presenting a treasure trove of advantages for their compelling integration into the intricate tapestry of biomedical applications.
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Affiliation(s)
- Satheesh Selvaraj
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India; Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Ankush Chauhan
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India; Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India.
| | - Vishal Dutta
- University Centre for Research and Development, Department of Chemistry, Chandigarh University, Gharuan, Mohali, Punjab, India
| | - Ritesh Verma
- Department of Physics, Amity University, Gurugram, Haryana 122413, India
| | - Subha Krishna Rao
- Centre for Nanoscience and Nanotechnology, International Research Centre, Sathyabama Institute for Science and Technology, Chennai 600119, India
| | - Arunkumar Radhakrishnan
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India; Department of Pharmacology, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Suresh Ghotekar
- Department of Chemistry, Smt. Devkiba Mohansinhji Chauhan College of Commerce and Science (University of Mumbai), Silvassa 396230, UT of DNH & DD, India.
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14
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Zhu J, Yang S, Cao Q, Li X, Jiao L, Shi Y, Yan Y, Xu L, Yang M, Xie X, Madzak C, Yan J. Engineering Yarrowia lipolytica as a Cellulolytic Cell Factory for Production of p-Coumaric Acid from Cellulose and Hemicellulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5867-5877. [PMID: 38446418 DOI: 10.1021/acs.jafc.4c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
De novo biosynthesis of high-value added food additive p-coumaric acid (p-CA) direct from cellulose/hemicellulose is a more sustainable route compared to the chemical route, considering the abundant cellulose/hemicellulose resources. In this study, a novel factory was constructed for the production of p-CA in Yarrowia lipolytica using cellulose/hemicellulose as the sole carbon source. Based on multicopy integration of the TAL gene and reprogramming the shikimic acid pathway, the engineered strain produced 1035.5 ± 67.8 mg/L p-CA using glucose as a carbon source. The strains with overexpression of cellulases and hemicellulases produced 84.3 ± 2.4 and 65.3 ± 4.6 mg/L p-CA, using cellulose (carboxymethyl-cellulose) or hemicellulose (xylan from bagasse) as the carbon source, respectively. This research demonstrated the feasibility of conversion of cost-effective cellulose/hemicellulose into a value-added product and provided a sustainable cellulolytic cell factory for the utilization of cellulose/hemicellulose.
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Affiliation(s)
- Jiarui Zhu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Shu Yang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | | | - Xiaoyan Li
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Liangcheng Jiao
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Yuanxing Shi
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Yunjun Yan
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Li Xu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Min Yang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Xiaoman Xie
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Catherine Madzak
- UMR 782 SayFood, INRAE, AgroParisTech, Paris-Saclay University, Palaiseau 91400, France
| | - Jinyong Yan
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
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15
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Lenertz M, Li Q, Armstrong Z, Scheiwiller A, Ni G, Wang J, Feng L, MacRae A, Yang Z. Magnetic Multienzyme@Metal-Organic Material for Sustainable Biodegradation of Insoluble Biomass. ACS APPLIED MATERIALS & INTERFACES 2024; 16:11617-11626. [PMID: 38410049 DOI: 10.1021/acsami.4c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Biodegradation of insoluble biomass such as cellulose via carbohydrase enzymes is an effective approach to break down plant cell walls and extract valuable materials therein. Yet, the high cost and poor reusability of enzymes are practical concerns. We recently proved that immobilizing multiple digestive enzymes on metal-organic materials (MOMs) allows enzymes to be reused via gravimetric separation, improving the cost efficiency of cereal biomass degradation [ACS Appl. Mater. Interfaces 2021, 13, 36, 43085-43093]. However, this strategy cannot be adapted for enzymes whose substrates or products are insoluble (e.g., cellulose crystals). Recently, we described an alternative approach based on magnetic metal-organic frameworks (MOFs) using model enzymes/substrates [ACS Appl. Mater. Interfaces 2020, 12, 37, 41794-41801]. Here, we aim to prove the effectiveness of combining these two strategies in cellulose degradation. We immobilized multiple carbohydrase enzymes that cooperate in cellulose degradation via cocrystallization with Ca2+, a carboxylate ligand (BDC) in the absence and presence of magnetic nanoparticles (MNPs). We then compared the separation efficiency and enzyme reusability of the resultant multienzyme@Ca-BDC and multienzyme@MNP-Ca-BDC composites via gravimetric and magnetic separation, respectively, and found that, although both composites were effective in cellulose degradation in the first round, the multienzyme@MNP-Ca-BDC composites displayed significantly enhanced reusability. This work provides the first experimental demonstration of using magnetic solid supports to immobilize multiple carbohydrase enzymes simultaneously and degrade cellulose and promotes green/sustainable chemistry in three ways: (1) reusing the enzymes saves energy/sources to prepare them, (2) the synthetic conditions are "green" without generating unwanted wastes, and (3) using our composites to degrade cellulose is the first step of extracting valuable materials from sustainable biomasses such as plants whose growth does not rely on nonregeneratable resources.
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Affiliation(s)
- Mary Lenertz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Zoe Armstrong
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Allison Scheiwiller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Gigi Ni
- Department of Chemistry and Chemical Biology, Harvard University, Boston, Massachusetts 02138, United States
| | - Jien Wang
- California State University, San Marcos, San Marcos, California 92096, United States
| | - Li Feng
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
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16
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Brunecky R, Knott BC, Subramanian V, Linger JG, Beckham GT, Amore A, Taylor LE, Vander Wall TA, Lunin VV, Zheng F, Garrido M, Schuster L, Fulk EM, Farmer S, Himmel ME, Decker SR. Engineering of glycoside hydrolase family 7 cellobiohydrolases directed by natural diversity screening. J Biol Chem 2024; 300:105749. [PMID: 38354778 PMCID: PMC10943489 DOI: 10.1016/j.jbc.2024.105749] [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: 11/16/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Protein engineering and screening of processive fungal cellobiohydrolases (CBHs) remain challenging due to limited expression hosts, synergy-dependency, and recalcitrant substrates. In particular, glycoside hydrolase family 7 (GH7) CBHs are critically important for the bioeconomy and typically difficult to engineer. Here, we target the discovery of highly active natural GH7 CBHs and engineering of variants with improved activity. Using experimentally assayed activities of genome mined CBHs, we applied sequence and structural alignments to top performers to identify key point mutations linked to improved activity. From ∼1500 known GH7 sequences, an evolutionarily diverse subset of 57 GH7 CBH genes was expressed in Trichoderma reesei and screened using a multiplexed activity screening assay. Ten catalytically enhanced natural variants were identified, produced, purified, and tested for efficacy using industrially relevant conditions and substrates. Three key amino acids in CBHs with performance comparable or superior to Penicillium funiculosum Cel7A were identified and combinatorially engineered into P. funiculosum cel7a, expressed in T. reesei, and assayed on lignocellulosic biomass. The top performer generated using this combined approach of natural diversity genome mining, experimental assays, and computational modeling produced a 41% increase in conversion extent over native P. funiculosum Cel7A, a 55% increase over the current industrial standard T. reesei Cel7A, and 10% improvement over Aspergillus oryzae Cel7C, the best natural GH7 CBH previously identified in our laboratory.
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Affiliation(s)
- Roman Brunecky
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Brandon C Knott
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Venkataramanan Subramanian
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Jeffrey G Linger
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T Beckham
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Antonella Amore
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Larry E Taylor
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Todd A Vander Wall
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Vladimir V Lunin
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Fei Zheng
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Mercedes Garrido
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Logan Schuster
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Emily M Fulk
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Samuel Farmer
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Michael E Himmel
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA.
| | - Stephen R Decker
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA.
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17
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Liu Y, Zhou W, Zhao M, Ma Q, Zhang J, Zhou W, Gong Z. Combination of alkaline biodiesel-derived crude glycerol pretreated corn stover with dilute acid pretreated water hyacinth for highly-efficient single cell oil production by oleaginous yeast Cutaneotrichosporon oleaginosum. BIORESOURCE TECHNOLOGY 2024; 395:130366. [PMID: 38266783 DOI: 10.1016/j.biortech.2024.130366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/07/2024] [Accepted: 01/20/2024] [Indexed: 01/26/2024]
Abstract
Single cell oil (SCO) prepared from biodiesel-derived crude glycerol (BCG) and lignocellulosic biomass (LCB) via oleaginous yeasts is an intriguing alternative precursor of biodiesel. Here, a novel strategy combining alkaline BCG pretreated corn stover and dilute acid pretreated water hyacinth for SCO overproduction was developed. The mixed pretreatment liquors (MPLs) were naturally neutralized and adjusted to a proper carbon-to-nitrogen ratio beneficial for SCO overproduction by Cutaneotrichosporon oleaginosum. The toxicity of inhibitors was relieved by dilution detoxification. The enzymatic hydrolysate of solid fractions was suitable for SCO production either separately or simultaneously with MPLs. Fed-batch fermentation of the MPLs resulted in high cell mass, SCO content, and SCO titer of 80.7 g/L, 75.7 %, and 61.1 g/L, respectively. The fatty acid profiles of SCOs implied high-quality biodiesel characteristics. This study offers a novel BCG&LCB-to-SCO route integrating BCG-based pretreatment and BCG/LCB hydrolysates co-utilization, which provides a cost-effective technical route for micro-biodiesel production.
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Affiliation(s)
- Yantao Liu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, People's Republic of China
| | - Wenting Zhou
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, People's Republic of China
| | - Man Zhao
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, People's Republic of China
| | - Qishuai Ma
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, People's Republic of China
| | - Junlu Zhang
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, People's Republic of China
| | - Wei Zhou
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, People's Republic of China
| | - Zhiwei Gong
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, People's Republic of China; HuBei Province Key Laboratory of Coal Conversion and New Carbon Materials, Wuhan University of Science and Technology, Wuhan 430081, People's Republic of China.
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18
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Islam MT, Liu Y, Hassan MM, Abraham PE, Merlet J, Townsend A, Jacobson D, Buell CR, Tuskan GA, Yang X. Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0029. [PMID: 38435807 PMCID: PMC10905259 DOI: 10.34133/bdr.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/28/2024] [Indexed: 03/05/2024] Open
Abstract
Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings of complex plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity. Furthermore, scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology, which aims to modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational design for increasing crop yield and quality, promoting the bioeconomy and enhancing environmental sustainability. In particular, data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects. To date, scRNA-seq has been demonstrated in a limited number of plant species, including model plants (e.g., Arabidopsis thaliana), agricultural crops (e.g., Oryza sativa), and bioenergy crops (e.g., Populus spp.). It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants. In this review, we summarize current technical advancements in plant scRNA-seq, including sample preparation, sequencing, and data analysis, to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples. We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research. Finally, we discuss the challenges and opportunities for the application of scRNA-seq in plants.
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Affiliation(s)
- Md Torikul Islam
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding,
Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jean Merlet
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education,
University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Alice Townsend
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education,
University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C. Robin Buell
- Center for Applied Genetic Technologies,
University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences,
University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics, and Genomics,
University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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19
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Wang Y, Chen Y, Gao X, Wang Q, Cui M, Zhang D, Guo P. Unveiling the driving role of pH on community stability and function during lignocellulose degradation in paddy soil. Front Microbiol 2024; 15:1338842. [PMID: 38468860 PMCID: PMC10925614 DOI: 10.3389/fmicb.2024.1338842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/25/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Crop straw, a major by-product of agricultural production, is pivotal in maintaining soil health and preserving the ecological environment. While straw incorporation is widely recognized as a sustainable practice, the incomplete decomposition of crop residues poses challenges to plant growth, increasing the risk of pests and diseases. This necessitates a comprehensive investigation. Methods The current study employs a 28-day pot experiment to simulate the degradation of rice straw in paddy soils. The impacts of bioaugmentation and biostimulation on lignocellulose degradation are systematically evaluated. Results Results indicate a high lignocellulose degradation ability in paddy soil, with over 80% straw weight loss within 28 days. Bioaugmentation with a lignocellulolytic microbial consortium enhances straw degradation during the initial stage (0-14 days). In contrast, biostimulation with readily available nutrients leads to soil acidification, hindering straw degradation and reducing microbial diversity. Furthermore, pH emerges as a critical factor influencing microbial community stability and function during lignocellulose degradation. Microbial co-occurrence network analysis reveals that microorganisms occupy ecological niches associated with different cellulose components. Notably, Module M2, comprising Proteobacteria, Firmicutes, Gemmatimonadota, Actinobacteriota, Bacteroidota, Myxococcota, Halobacterota, and Acidobacteriota, positively correlates with pH and weight loss. Discussion This study significantly advances our understanding of microbial mechanisms in soil decomposition, emphasizing the pivotal role of pH in community stability and function in paddy soil. These findings can inform future strategies for managing rice straw while safeguarding soil ecosystem health.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yonglun Chen
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- Sichuan Jiahuai Biotechnology Co., Ltd., Leshan, China
| | - Xiuqing Gao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- College of Biological and Pharmaceutical Sciences, Three Gorges University, Yichang, China
| | - Qiong Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Mingyu Cui
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- College of Biological and Pharmaceutical Sciences, Three Gorges University, Yichang, China
| | - Dongdong Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, Zhejiang, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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20
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Happs R, Hanes RJ, Bartling AW, Field JL, Harman-Ware AE, Clark RJ, Pendergast TH, Devos KM, Webb EG, Missaoui A, Xu Y, Makaju S, Shrestha V, Mazarei M, Stewart CN, Millwood RJ, Davison BH. Economic and Sustainability Impacts of Yield and Composition Variation in Bioenergy Crops: Switchgrass ( Panicum virgatum L.). ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024; 12:1897-1910. [PMID: 38333206 PMCID: PMC10848292 DOI: 10.1021/acssuschemeng.3c05770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024]
Abstract
Economically viable production of biobased products and fuels requires high-yielding, high-quality, sustainable process-advantaged crops, developed using bioengineering or advanced breeding approaches. Understanding which crop phenotypic traits have the largest impact on biofuel economics and sustainability outcomes is important for the targeted feedstock crop development. Here, we evaluated biomass yield and cell-wall composition traits across a large natural variant population of switchgrass (Panicum virgatum L.) grown across three common garden sites. Samples from 331 switchgrass genotypes were collected and analyzed for carbohydrate and lignin components. Considering plant survival and biomass after multiple years of growth, we found that 84 of the genotypes analyzed may be suited for commercial production in the southeastern U.S. These genotypes show a range of growth and compositional traits across the population that are apparently independent of each other. We used these data to conduct techno-economic analyses and life cycle assessments evaluating the performance of each switchgrass genotype under a standard cellulosic ethanol process model with pretreatment, added enzymes, and fermentation. We find that switchgrass yield per area is the largest economic driver of the minimum fuel selling price (MSFP), ethanol yield per hectare, global warming potential (GWP), and cumulative energy demand (CED). At any yield, the carbohydrate content is significant but of secondary importance. Water use follows similar trends but has more variability due to an increased dependence on the biorefinery model. Analyses presented here highlight the primary importance of plant yield and the secondary importance of carbohydrate content when selecting a feedstock that is both economical and sustainable.
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Affiliation(s)
- Renee
M. Happs
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Rebecca J. Hanes
- Strategic
Energy Analysis Center, National Renewable
Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Andrew W. Bartling
- Catalytic
Carbon and Transformation Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - John L. Field
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Anne E. Harman-Ware
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Robin J. Clark
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Thomas H. Pendergast
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Department
of Plant Biology, University of Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Katrien M. Devos
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Department
of Plant Biology, University of Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Erin G. Webb
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Ali Missaoui
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Yaping Xu
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Shiva Makaju
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Vivek Shrestha
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Mitra Mazarei
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Charles Neal Stewart
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Reginald J. Millwood
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Brian H. Davison
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
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21
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Fan MZ, Cheng L, Wang M, Chen J, Fan W, Jashari F, Wang W. Monomodular and multifunctional processive endocellulases: implications for swine nutrition and gut microbiome. Anim Microbiome 2024; 6:4. [PMID: 38308359 PMCID: PMC10837961 DOI: 10.1186/s42523-024-00292-w] [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: 07/24/2023] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
Poor efficiency of dietary fibre utilization not only limits global pork production profit margin but also adversely affects utilization of various dietary nutrients. Poor efficiency of dietary nutrient utilization further leads to excessive excretion of swine manure nutrients and results in environmental impacts of emission of major greenhouse gases (GHG), odor, nitrate leaching and surface-water eutrophication. Emission of the major GHG from intensive pork production contributes to global warming and deteriorates heat stress to pigs in tropical and sub-tropical swine production. Exogenous fibre enzymes of various microbial cellulases, hemicellulases and pectinases have been well studied and used in swine production as the non-nutritive gut modifier feed enzyme additives in the past over two decades. These research efforts have aimed to improve growth performance, nutrient utilization, intestinal fermentation as well as gut physiology, microbiome and health via complementing the porcine gut symbiotic microbial fibrolytic activities towards dietary fibre degradation. The widely reported exogenous fibre enzymes include the singular use of respective cellulases, hemicellulases and pectinases as well as their multienzyme cocktails. The currently applied exogenous fibre enzymes are largely limited by their inconsistent in vivo efficacy likely due to their less defined enzyme stability and limited biochemical property. More recently characterized monomodular, multifunctional and processive endoglucanases have the potential to be more efficaciously used as the next-generation designer fibre biocatalysts. These newly emerging multifunctional and processive endoglucanases have the potential to unleash dietary fibre sugar constituents as metabolic fuels and prebiotics, to optimize gut microbiome, to maintain gut permeability and to enhance performance in pigs under a challenged environment as well as to parallelly unlock biomass to manufacture biofuels and biomaterials.
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Affiliation(s)
- Ming Z Fan
- Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada.
- One Health Institute, University of Guelph, N1G 2W1, Guelph, ON, Canada.
| | - Laurence Cheng
- Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Min Wang
- Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Jiali Chen
- Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Wenyi Fan
- Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
- Transpharmation LTD, N1M 2W3, Fergus, ON, Canada
| | - Fatmira Jashari
- Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
- Department of Human Health and Nutritional Sciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Weijun Wang
- Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
- The Canadian Food Inspection Agency Ontario Operation, N1G 4S9, Guelph, ON, Canada
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22
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Dahiya D, Koitto T, Kutvonen K, Wang Y, Haddad Momeni M, de Ruijter S, Master ER. Fungal loosenin-like proteins boost the cellulolytic enzyme conversion of pretreated wood fiber and cellulosic pulps. BIORESOURCE TECHNOLOGY 2024; 394:130188. [PMID: 38104665 DOI: 10.1016/j.biortech.2023.130188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
Microbial expansin-related proteins, including loosenins, can disrupt cellulose networks and increase enzyme accessibility to cellulosic substrates. Herein, four loosenins from Phanerochaete carnosa (PcaLOOLs), and a PcaLOOL fused to a family 63 carbohydrate-binding module, were compared for ability to boost the cellulolytic deconstruction of steam pretreated softwood (SSW) and kraft pulps from softwood (ND-BSKP) and hardwood (ND-BHKP). Amending the Cellic® CTec-2 cellulase cocktail with PcaLOOLs increased reducing products from SSW by up to 40 %, corresponding to 28 % higher glucose yield. Amending Cellic® CTec-2 with PcaLOOLs also increased the release of glucose from ND-BSKP and ND-BHKP by 82 % and 28 %, respectively. Xylose release from ND-BSKP and ND-BHKP increased by 47 % and 57 %, respectively, highlighting the potential of PcaLOOLs to enhance hemicellulose recovery. Scanning electron microscopy and fiber image analysis revealed fibrillation and curlation of ND-BSKP after PcaLOOL treatment, consistent with increasing enzyme accessibility to targeted substrates.
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Affiliation(s)
- Deepika Dahiya
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Taru Koitto
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Kim Kutvonen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Yan Wang
- Biorefining Business Development & Production, St1 Oy, Firdonkatu 2, 00520 Helsinki, Finland
| | - Majid Haddad Momeni
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Siiri de Ruijter
- Biorefining Business Development & Production, St1 Oy, Firdonkatu 2, 00520 Helsinki, Finland
| | - Emma R Master
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland; Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, M5S 3E5 Toronto, Ontario, Canada.
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23
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Tavares MP, Morgan T, Gomes RF, Mendes JPR, Castro-Borges W, Maitan-Alfenas GP, Guimarães VM. Comparative analysis of Chrysoporthe cubensis exoproteomes and their specificity for saccharification of sugarcane bagasse. Enzyme Microb Technol 2024; 173:110365. [PMID: 38043248 DOI: 10.1016/j.enzmictec.2023.110365] [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: 08/21/2023] [Revised: 10/18/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
The phytopathogenic fungus Chrysoporthe cubensis is a relevant source of lignocellulolytic enzymes. This work aimed to compare the profile of lignocellulose-degrading proteins secreted by C. cubensis grown under semi-solid state fermentation using wheat bran (WB) and sugarcane bagasse (SB). The exoproteomes of the fungus grown in wheat bran (WBE) and sugarcane bagasse (SBE) were qualitative and quantitatively analyzed by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Data are available via ProteomeXchange with identifier PXD046075. Label-free proteomic analysis of WBE and SBE showed that the fungus produced a spectrum of carbohydrate-active enzymes (CAZymes) with exclusive characteristics from each extract. While SBE resulted in an enzymatic profile directed towards the depolymerization of cellulose, the enzymes in WBE were more adaptable to the degradation of biomass rich in hemicellulose and other non-lignocellulosic polymers. Saccharification of alkaline pre-treated sugarcane bagasse with SBE promoted glucose release higher than commercial cocktails (8.11 g L-1), while WBE promoted the higher release of xylose (5.71 g L-1). Our results allowed an in-depth knowledge of the complex set of enzymes secreted by C. cubensis responsible for its high lignocellulolytic activity and still provided the identification of promising target proteins for biotechnological applications in the context of biorefinery.
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Affiliation(s)
- Murillo Peterlini Tavares
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, 36570-900 Viçosa, MG, Brazil
| | - Túlio Morgan
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, 36570-900 Viçosa, MG, Brazil
| | - Riziane Ferreira Gomes
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, 36570-900 Viçosa, MG, Brazil
| | - Jean Pierre Rocha Mendes
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, 36570-900 Viçosa, MG, Brazil
| | - William Castro-Borges
- Department of Biological Science, Universidade Federal de Ouro Preto, Campus Universitário Morro do Cruzeiro, 35400-000 Ouro Preto, MG, Brasil
| | - Gabriela Piccolo Maitan-Alfenas
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, 36570-900 Viçosa, MG, Brazil
| | - Valéria Monteze Guimarães
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, 36570-900 Viçosa, MG, Brazil.
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24
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Sarangi PK, Srivastava RK, Sahoo UK, Singh AK, Parikh J, Bansod S, Parsai G, Luqman M, Shadangi KP, Diwan D, Lanterbecq D, Sharma M. Biotechnological innovations in nanocellulose production from waste biomass with a focus on pineapple waste. CHEMOSPHERE 2024; 349:140833. [PMID: 38043620 DOI: 10.1016/j.chemosphere.2023.140833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
New materials' synthesis and utilization have shown many critical challenges in healthcare and other industrial sectors as most of these materials are directly or indirectly developed from fossil fuel resources. Environmental regulations and sustainability concepts have promoted the use of natural compounds with unique structures and properties that can be biodegradable, biocompatible, and eco-friendly. In this context, nanocellulose (NC) utility in different sectors and industries is reported due to their unique properties including biocompatibility and antimicrobial characteristics. The bacterial nanocellulose (BNC)-based materials have been synthesized by bacterial cells and extracted from plant waste materials including pineapple plant waste biomass. These materials have been utilized in the form of nanofibers and nanocrystals. These materials are found to have excellent surface properties, low density, and good transparency, and are rich in hydroxyl groups for their modifications to other useful products. These materials are well utilized in different sectors including biomedical or health care centres, nanocomposite materials, supercapacitors, and polymer matrix production. This review explores different approaches for NC production from pineapple waste residues using biotechnological interventions, approaches for their modification, and wider applications in different sectors. Recent technological developments in NC production by enzymatic treatment are critically discussed. The utilization of pineapple waste-derived NC from a bioeconomic perspective is summarized in the paper. The chemical composition and properties of nanocellulose extracted from pineapple waste may have unique characteristics compared to other sources. Pineapple waste for nanocellulose production aligns with the principles of sustainability, waste reduction, and innovation, making it a promising and novel approach in the field of nanocellulose materials.
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Affiliation(s)
- Prakash Kumar Sarangi
- College of Agriculture, Central Agricultural University, Imphal, 795004, Manipur, India
| | - Rajesh Kumar Srivastava
- Department of Biotechnology, GIT, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, 530045, India
| | | | - Akhilesh Kumar Singh
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, 845401, India
| | - Jigisha Parikh
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Shama Bansod
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Ganesh Parsai
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Mohammad Luqman
- Chemical Engineering Department, College of Engineering, Taibah University, Yanbu Al-Bahr-83, Al-Bandar District 41911, Kingdom of Saudi Arabia
| | - Krushna Prasad Shadangi
- Department of Chemical Engineering, Veer Surendra Sai University of Technology, Burla, Sambalpur, Odisha, 768018, India
| | - Deepti Diwan
- Washington University, School of Medicine, Saint Louis, MO, USA
| | - Deborah Lanterbecq
- Laboratoire de Biotechnologie et Biologie Appliquée, CARAH ASBL, Rue Paul Pastur, 11, Ath, 7800, Belgium
| | - Minaxi Sharma
- Laboratoire de Biotechnologie et Biologie Appliquée, CARAH ASBL, Rue Paul Pastur, 11, Ath, 7800, Belgium.
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25
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Nousi A, Molina GA, Schiano-di-Cola C, Sørensen TH, Borch K, Pedersen JN, Westh P, Marie R. Impact of Synergy Partner Cel7B on Cel7A Binding Rates: Insights from Single-Molecule Data. J Phys Chem B 2024; 128:635-647. [PMID: 38227769 PMCID: PMC10824242 DOI: 10.1021/acs.jpcb.3c05697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Enzymatic degradation of cellulosic biomass is a well-established route for the sustainable production of biofuels, chemicals, and materials. A strategy employed by nature and industry to achieve an efficient degradation of cellulose is that cellobiohydrolases (or exocellulases), such as Cel7A, work synergistically with endoglucanases, such as Cel7B, to achieve the complete degradation of cellulose. However, a complete mechanistic understanding of this exo-endo synergy is still lacking. Here, we used single-molecule fluorescence microscopy to quantify the binding kinetics of Cel7A on cellulose when it is acting alone on the cellulose fibrils and in the presence of its synergy partner, the endoglucanase Cel7B. To this end, we used a fluorescently tagged Cel7A and studied its binding in the presence of the unlabeled Cel7B. This provided the single-molecule data necessary for the estimation of the rate constants of association kON and dissociation kOFF of Cel7A for the substrate. We show that the presence of Cel7B does not impact the dissociation rate constant, kOFF. But, the association rate of Cel7A decreases by a factor of 2 when Cel7B is present at a molar proportion of 10:1. This ratio has previously been shown to lead to synergy. This decrease in association rate is observed in a wide range of total enzyme concentrations, from sub nM to μM concentrations. This decrease in kON is consistent with the formation of cellulase clusters recently observed by others using atomic force microscopy.
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Affiliation(s)
- Aimilia Nousi
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | | | - Kim Borch
- Novozymes
A/S, Krogshøjvej
36, 2880 Bagsværd, Denmark
| | - Jonas N. Pedersen
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
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26
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Li M, Jiang L, Feng S, Huang J, Zhang P, Zhang J. Aluminum ion intercalation in mesoporous multilayer carbocatalysts promotes the conversion of glucose to 5-hydroxymethylfurfural. Dalton Trans 2024. [PMID: 38265079 DOI: 10.1039/d3dt04000c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
In this study, an efficient modification strategy was proposed by facile loading of trace aluminum ions and p-toluene sulfonic acid (p-TSA) in carbon materials to improve their catalytic activity. p-TSA is then proven to regulate the carbonization process and promote the formation of mesoporous and multilayer structures. The hexa-coordinated aluminum structure is characterized by 1H-27Al solid-state nuclear magnetic resonance (SSNMR) and X-ray photoelectron spectroscopy, which serves as the Lewis-Brønsted acid site in carbocatalysts. Accordingly, the resulting catalyst facilitates a yield of ∼70% for converting glucose to 5-hydroxymethylfurfural (HMF) with a maximum carbon balance of around 91.4% at 150 °C in 6 h. In situ NMR, electrospray ionization mass spectrometry and isotope labeling analysis reveal that the hexa-coordinated aluminum sites promote the isomerization of glucose, and the sulfonic groups facilitate the subsequent dehydration and rehydration of fructose and levoglucosan intermediates. Kinetic models further indicate the decreased energy barrier for glucose conversion over the Al3+/p-TSA intercalated carbocatalyst. This work provides a promising strategy for engineering waste-derived carbocatalysts toward effectively converting carbohydrates to precursors of biofuels and bioplastics.
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Affiliation(s)
- Mingfu Li
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, Guangdong 510316, China.
- Guangdong Province Engineering Research Center for Green Technology of Sugar Industry, Guangzhou, Guangdong 510316, China
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang 315201, China
| | - Liqun Jiang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, Guangdong 510316, China.
| | - Sufei Feng
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang 315201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junsheng Huang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, Guangdong 510316, China.
- Guangdong Province Engineering Research Center for Green Technology of Sugar Industry, Guangzhou, Guangdong 510316, China
| | - Pingjun Zhang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, Guangdong 510316, China.
- Guangdong Province Engineering Research Center for Green Technology of Sugar Industry, Guangzhou, Guangdong 510316, China
| | - Jian Zhang
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang 315201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Ahlawat YK, Biswal AK, Harun S, Harman-Ware AE, Doeppke C, Sharma N, Joshi CP, Hankoua BB. Heterologous expression of Arabidopsis laccase2, laccase4 and peroxidase52 driven under developing xylem specific promoter DX15 improves saccharification in populus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:5. [PMID: 38218877 PMCID: PMC10787383 DOI: 10.1186/s13068-023-02452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND Secondary cell wall holds considerable potential as it has gained immense momentum to replace the lignocellulosic feedstock into fuels. Lignin one of the components of secondary cell wall tightly holds the polysaccharides thereby enhancing the recalcitrance and complexity in the biomass. Laccases (LAC) and peroxidases (PRX) are the major phenyl-oxidases playing key functions during the polymerization of monolignols into lignin. Yet, the functions of laccase and peroxidases gene families remained largely unknown. Hence, the objective of this conducted study is to understand the role of specific LAC and PRX in Populus wood formation and to further investigate how the altered Lac and Prx expression affects biomass recalcitrance and plant growth. This study of heterologous expression of Arabidopsis Lac and Prx genes was conducted in poplar to avoid any otherwise occurring co-suppression mechanism during the homologous overexpression of highly expressed native genes. In the pursuit of optimizing lignocellulosic biomass for biofuel production, the present study focuses on harnessing the enzymatic potential of Arabidopsis thaliana Laccase2, Laccase4, and Peroxidase52 through heterologous expression. RESULTS We overexpressed selected Arabidopsis laccase2 (AtLac2), laccase4 (AtLac4), and peroxidase52 (AtPrx52) genes, based on their high transcript expression respective to the differentiating xylem tissues in the stem, in hybrid poplar (cv. 717) expressed under the developing xylem tissue-specific promoter, DX15 characterized the transgenic populus for the investigation of growth phenotypes and recalcitrance efficiency. Bioinformatics analyses conducted on AtLac2 and AtLac4 and AtPrx52, revealed the evolutionary relationship between the laccase gene and peroxidase gene homologs, respectively. Transgenic poplar plant lines overexpressing the AtLac2 gene (AtLac2-OE) showed an increase in plant height without a change in biomass yield as compared to the controls; whereas, AtLac4-OE and AtPrx52-OE transgenic lines did not show any such observable growth phenotypes compared to their respective controls. The changes in the levels of lignin content and S/G ratios in the transgenic poplar resulted in a significant increase in the saccharification efficiency as compared to the control plants. CONCLUSIONS Overall, saccharification efficiency was increased by 35-50%, 21-42%, and 8-39% in AtLac2-OE, AtLac4-OE, and AtPrx52-OE transgenic poplar lines, respectively, as compared to their controls. Moreover, the bioengineered plants maintained normal growth and development, underscoring the feasibility of this approach for biomass improvement without compromising overall plant fitness. This study also sheds light on the potential of exploiting regulatory elements of DX15 to drive targeted expression of lignin-modifying enzymes, thereby providing a promising avenue for tailoring biomass for improved biofuel production. These findings contribute to the growing body of knowledge in synthetic biology and plant biotechnology, offering a sustainable solution to address the challenges associated with lignocellulosic biomass recalcitrance.
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Affiliation(s)
- Yogesh K Ahlawat
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Ajaya K Biswal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA30602, USA
| | - Sarahani Harun
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Anne E Harman-Ware
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Crissa Doeppke
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Nisha Sharma
- Microbiology Section, Department of Basic Science, Dr. Y.S Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, India
| | - Chandrashekhar P Joshi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Bertrand B Hankoua
- Human Ecology Department, College of Agriculture, Science, and Technology (CAST), Food Science and Biotechnology Program, 1200 N. DuPont Highway, Dover, DE, 19901, USA.
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28
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Jilani SB. Deletion of yghZ in Escherichia coli promotes growth in presence of furfural with xylose as carbon source. FEMS Microbiol Lett 2024; 371:fnae028. [PMID: 38664064 DOI: 10.1093/femsle/fnae028] [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: 01/07/2024] [Revised: 02/23/2024] [Accepted: 04/24/2024] [Indexed: 05/15/2024] Open
Abstract
Thermo-acidic pretreatment of lignocellulosic biomass is required to make it amenable to microbial metabolism and results in generation of furfural due to breakdown of pentose sugars. Furfural is toxic to microbial metabolism and results in reduced microbial productivity and increased production costs. This study asks if deletion of yghZ gene which encodes a NADPH-dependent aldehyde reductase enzyme results in improved furfural tolerance in Escherichia coli host. The ∆yghZ strain-SSK201-was tested for tolerance to furfural in presence of 5% xylose as a carbon source in AM1 minimal medium. At 96 h and in presence of 1.0 g/L furfural, the culture harboring strain SSK201 displayed 4.5-fold higher biomass, 2-fold lower furfural concentration and 15.75-fold higher specific growth rate (µ) as compared to the parent strain SSK42. The furfural tolerance advantage of SSK201 was retained when the carbon source was switched to glucose in AM1 medium and was lost in rich LB medium. The findings have potential to be scaled up to a hydrolysate culture medium, which contains furan inhibitors and lack nutritionally rich components, under bioreactor cultivation and observe growth advantage of the ∆yghZ host. It harbors potential to generate robust industrial strains which can convert lignocellulosic carbon into metabolites of interest in a cost-efficient manner.
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Affiliation(s)
- S Bilal Jilani
- Institute of Biotechnology, Amity University, Manesar, Haryana 122413, India
- Microbial Engineering Group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
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29
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Addison B, Bu L, Bharadwaj V, Crowley MF, Harman-Ware AE, Crowley MF, Bomble YJ, Ciesielski PN. Atomistic, macromolecular model of the Populus secondary cell wall informed by solid-state NMR. SCIENCE ADVANCES 2024; 10:eadi7965. [PMID: 38170770 PMCID: PMC10776008 DOI: 10.1126/sciadv.adi7965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried Populus wood. To enhance the utility of these findings and enable evaluation of hypotheses in a physics-based environment in silico, the NMR observables are articulated into an atomistic, macromolecular model for biopolymer assemblies within the plant SCW. Through molecular dynamics simulation, we quantitatively evaluate several variations of atomistic models to determine structural details that are corroborated by ssNMR measurements.
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Affiliation(s)
- Bennett Addison
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Lintao Bu
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Vivek Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Meagan F. Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- Chemistry Department, Colorado School of Mines, Golden, CO, USA
| | - Anne E. Harman-Ware
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Michael F. Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Peter N. Ciesielski
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
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30
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Wang G, Huang M, Li F, Li Q, Chen F, Wang S, Ling Z, Ji Z. Insights into the poplar cell wall deconstruction following deep eutectic solvent pretreatment for enhanced enzymatic saccharification and lignin valorization. Int J Biol Macromol 2024; 254:127673. [PMID: 38287581 DOI: 10.1016/j.ijbiomac.2023.127673] [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: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 01/31/2024]
Abstract
In this study, a combination of microcosmic and chemical analysis methods was used to investigate deep eutectic solvent (DES) pretreatment effects on cell wall's micromorphology and lignin's dissolution regular, in order to achieve high-performance biorefinery. The atomic force microscope observed that DES pretreatment peeled off non-cellulose components to reduced "anti-degradation barrier", resulting to improve the enzymatic saccharification from 12.36 % to 90.56 %. In addition, DES pretreatment can break the β-O-4 bond between the lignin units resulting in a decline in molecular weight from 3187 g/mol to 1112 g/mol (0-6 h). However, long pretreatment time resulted regenerated lignin samples repolymerization. Finally, DES has good recoverability which showed saccharification still can reach 51.51 % at 6 h following four recycling rounds and regenerated lignin also had a typical and well-preserved structure. In general, this work offers important information for industrial biorefinery technologies and lignin valorization.
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Affiliation(s)
- Gaomin Wang
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Mingjun Huang
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Fucheng Li
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qiang Li
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Fushan Chen
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Songlin Wang
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zhe Ling
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ji
- College of Marine Science and Bioengineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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31
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Chen T, Lu Y, Xiong X, Qiu M, Peng Y, Xu Z. Hydrolytic nanozymes: Preparation, properties, and applications. Adv Colloid Interface Sci 2024; 323:103072. [PMID: 38159448 DOI: 10.1016/j.cis.2023.103072] [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: 09/19/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Hydrolytic nanozymes, as promising alternatives to hydrolytic enzymes, can efficiently catalyze the hydrolysis reactions and overcome the operating window limitations of natural enzymes. Moreover, they exhibit several merits such as relatively low cost, easier recovery and reuse, improved operating stability, and adjustable catalytic properties. Consequently, they have found relevance in practical applications such as organic synthesis, chemical weapon degradation, and biosensing. In this review, we highlight recent works addressing the broad topic of the development of hydrolytic nanozymes. We review the preparation, properties, and applications of six types of hydrolytic nanozymes, including AuNP-based nanozymes, polymeric nanozymes, surfactant assemblies, peptide assemblies, metal and metal oxide nanoparticles, and MOFs. Last, we discuss the remaining challenges and future directions. This review will stimulate the development and application of hydrolytic nanozymes.
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Affiliation(s)
- Tianyou Chen
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China.
| | - Yizhuo Lu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Xiaorong Xiong
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Meishuang Qiu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Yan Peng
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Zushun Xu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China.
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32
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Akhlaghi Bagherjeri M, Monhemi H, Haque ANMA, Naebe M. Molecular mechanism of cellulose dissolution in N-methyl morpholine-N-oxide: A molecular dynamics simulation study. Carbohydr Polym 2024; 323:121433. [PMID: 37940258 DOI: 10.1016/j.carbpol.2023.121433] [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: 07/21/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 11/10/2023]
Abstract
N-methyl morpholine-N-oxide (NMMO) is the only commercialised solvent to dissolve cellulose and produce lyocell. However, the molecular mechanism of NMMO-induced cellulose solubilisation is unknown which limits further process development. In this work, and for the first time the complete dissolution process of a large cellulose bunch was simulated in NMMO monohydrate using long microsecond molecular dynamic simulations. The dissolution process was also simulated in 1-ethyl-3-methylimidazolium acetate (EmimAc) as an efficient ionic liquid in cellulose dissolution and the results were compared with the aqueous conditions. While the cellulose bunch showed a stable and insoluble structure in pure water, it was completely and efficiently dissolved in both NMMO monohydrate and EmimAc. It was shown that the dissolution time of cellulose in NMMO monohydrate is almost twice that in EmimAc, which is in agreement with the experimental observations. Although it is revealed that hydrogen bonding is the main driving force of cellulose dissolution in NMMO monohydrate, one cannot explain the complete molecular mechanism of NMMO-induced cellulose dissolution only by considering hydrogen bonds. A straightforward molecular mechanism was proposed, in which the interactions of NMMO molecules, not with cellulose, but with the other NMMO molecules play a critical role in the dissolution process.
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Affiliation(s)
| | - Hassan Monhemi
- Department of Chemistry, University of Neyshabur, Neyshabur, Iran
| | | | - Maryam Naebe
- Deakin University, Institute for Frontier Materials, Geelong, Victoria 3216, Australia.
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33
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Fernández-Sandoval MT, García A, Teymennet-Ramírez KV, Arenas-Olivares DY, Martínez-Morales F, Trejo-Hernández MR. Removal of phenolic inhibitors from lignocellulose hydrolysates using laccases for the production of fuels and chemicals. Biotechnol Prog 2024; 40:e3406. [PMID: 37964692 DOI: 10.1002/btpr.3406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/14/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Lignocellulose is the most abundant biopolymer in the biosphere. It is inexpensive and therefore considered an attractive feedstock to produce biofuels and other biochemicals. Thermochemical and/or enzymatic pretreatment is used to release fermentable monomeric sugars. However, a variety of inhibitory by-products such as weak acids, furans, and phenolics that inhibit cell growth and fermentation are also released. Phenolic compounds are among the most toxic components in lignocellulosic hydrolysates and slurries derived from lignin decomposition, affecting overall fermentation processes and production yields and productivity. Ligninolytic enzymes have been shown to lower inhibitor concentrations in these hydrolysates, thereby enhancing their fermentability into valuable products. Among them, laccases, which are capable of oxidizing lignin and a variety of phenolic compounds in an environmentally benign manner, have been used for biomass delignification and detoxification of lignocellulose hydrolysates with promising results. This review discusses the state of the art of different enzymatic approaches to hydrolysate detoxification. In particular, laccases are used in separate or in situ detoxification steps, namely in free enzyme processes or immobilized by cell surface display technology to improve the efficiency of the fermentative process and consequently the production of second-generation biofuels and bio-based chemicals.
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Affiliation(s)
- M T Fernández-Sandoval
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - A García
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - K V Teymennet-Ramírez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - D Y Arenas-Olivares
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - F Martínez-Morales
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - M R Trejo-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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34
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Paul M, Banerjee A, Maiti S, Mitra D, DasMohapatra PK, Thatoi H. Evaluation of substrate specificity and catalytic promiscuity of Bacillus albus cellulase: an insight into in silico proteomic study aiming at enhanced production of renewable energy. J Biomol Struct Dyn 2023:1-23. [PMID: 38126200 DOI: 10.1080/07391102.2023.2295971] [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: 05/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Cellulases are enzymes that aid in the hydrolysis of cellulosic fibers and have a wide range of industrial uses. In the present in silico study, sequence alignment between cellulases from different Bacillus species revealed that most of the residues are conserved in those aligned enzymes. Three dimensional structures of cellulase enzymes from 23 different Bacillus species have been predicted and based on the alignment between the modeled structures, those enzymes have been categorized into 7 different groups according to the homology in their conformational folds. There are two structural contents in Gr-I cellulase namely β1-α2 and β3-α5 loops which varies greatly according to their static position. Molecular docking study between the B. albus cellulase and its various cellulosic substrates including xylanoglucan oligosaccharides revealed that residues viz. Phe154, Tyr258, Tyr282, Tyr285, and Tyr376 of B. albus cellulase are significantly involved in formation stacking interaction during enzyme-substrate binding. Residue interaction network and binding energy analysis for the B. albus cellulase with different cellulosic substrates depicted the strong affinity of XylGlc3 substrate with the receptor enzyme. Molecular interaction and molecular dynamics simulation studies exhibited structural stability of enzyme-substrate complexes which are greatly influenced by the presence of catalytic promiscuity in their substrate binding sites. Screening of B. albus in carboxymethylcellulose (CMC) and xylan supplemented agar media revealed the capability of the bacterium in degrading both cellulose and xylan. Overall, the study demonstrated B. albus cellulase as an effective biocatalyst candidate with the potential role of catalytic promiscuity for possible applications in biofuel industries.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
- Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Amrita Banerjee
- Oriental Institute of Science and Technology, Midnapore, India
| | - Smarajit Maiti
- Oriental Institute of Science and Technology, Midnapore, India
| | - Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, India
| | - Pradeep K DasMohapatra
- Department of Microbiology, Raiganj University, Raiganj, India
- PAKB Environment Conservation Centre, Raiganj University, Raiganj, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
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35
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Bitew D, Tesfaye A, Andualem B. Isolation, screening and identification of ethanol producing yeasts from Ethiopian fermented beverages. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 40:e00815. [PMID: 37876548 PMCID: PMC10590766 DOI: 10.1016/j.btre.2023.e00815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/25/2023] [Accepted: 10/02/2023] [Indexed: 10/26/2023]
Abstract
The growing demand for renewable energy sources such as bioethanol is facing a lack of efficient ethanologenic microbes. This study aimed to isolate and screen ethanologenic yeasts from Ethiopian fermented beverages. A progressive screening and selection approach was employed. Selected isolates were evaluated for bioethanol production using banana peel waste as substrate. A total of 102 isolates were obtained. Sixteen isolates were selected based on their tolerance to stress conditions and carbohydrate fermentation and assimilation capacity. Most found moderately tolerant to 10 %, but slightly tolerant at 15 and 20 % (v/v) ethanol concentration. They yield 15.3 to 20.1 g/L and 9.1 ± 0.6 to 12.9 ± 1.3 g/L ethanol from 2 % (w/v) glucose and 80 g/L banana peel, respectively. Molecular characterization identified them as Saccharomyces cerevisiae strains. Results demonstrate insight about their potential role in the ethanol industry. Optimization of the fermentation conditions is recommended.
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Affiliation(s)
- Dagnew Bitew
- Department of Biology, Mizan-Tepi University, P. BOX: 260, Ethiopia
- Institute of Biotechnology, University of Gondar, P.BOX: 196, Ethiopia
| | - Anteneh Tesfaye
- Institute of Biotechnology, Addis Ababa University, P.BOX: 1176, Ethiopia
- BioTEI, Winnipeg, Manitoba, Canada
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Hackl M, Power Z, Chundawat SPS. Oriented display of cello-oligosaccharides for pull-down binding assays to distinguish binding preferences of glycan binding proteins. Carbohydr Res 2023; 534:108943. [PMID: 37783054 DOI: 10.1016/j.carres.2023.108943] [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: 02/01/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
The production of biofuels from lignocellulosic biomass using carbohydrate-active enzymes like cellulases is key to a sustainable energy production. Understanding the adsorption mechanism of cellulases and associated binding domain proteins down to the molecular level details will help in the rational design of improved cellulases. In nature, carbohydrate-binding modules (CBMs) from families 17 and 28 often appear in tandem appended to the C-terminus of several endocellulases. Both CBMs are known to bind to the amorphous regions of cellulose non-competitively and show similar binding affinity towards soluble cello-oligosaccharides. Based on the available crystal structures, these CBMs may display a uni-directional binding preference towards cello-oligosaccharides (based on how the oligosaccharide was bound within the CBM binding cleft). However, molecular dynamics (MD) simulations have indicated no such clear preference. Considering that most soluble oligosaccharides are not always an ideal substrate surrogate to study the binding of CBMs to the native cell wall or cell surface displayed glycans, it is critical to use alternative reagents or substrates. To better understand the binding of type B CBMs towards smaller cello-oligosaccharides, we have developed a simple solid-state depletion or pull-down binding assay. Here, we specifically orient azido-labeled carbohydrates from the reducing end to alkyne-labeled micron-sized bead surfaces, using click chemistry, to mimic insoluble cell wall surface-displayed glycans. Our results reveal that both family 17 and 28 CBMs displayed a similar binding affinity towards cellohexaose-modified beads, but not cellopentaose-modified beads, which helps rationalize previously reported crystal structure and MD data. This may indicate a preferred uni-directional binding of specific CBMs and could explain their co-evolution as tandem constructs appended to endocellulases to increase amorphous cellulose substrate targeting efficiency. Overall, our proposed workflow can be easily translated to measure the affinity of glycan-binding proteins to click-chemistry based immobilized surface-displayed carbohydrates or antigens.
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Affiliation(s)
- Markus Hackl
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Zachary Power
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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37
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Motycka B, Csarman F, Rupp M, Schnabel K, Nagy G, Karnpakdee K, Scheiblbrandner S, Tscheliessnig R, Oostenbrink C, Hammel M, Ludwig R. Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase. Chembiochem 2023; 24:e202300431. [PMID: 37768852 PMCID: PMC10726044 DOI: 10.1002/cbic.202300431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/31/2023] [Indexed: 09/30/2023]
Abstract
The function of cellobiose dehydrogenase (CDH) in biosensors, biofuel cells, and as a physiological redox partner of lytic polysaccharide monooxygenase (LPMO) is based on its role as an electron donor. Before donating electrons to LPMO or electrodes, an interdomain electron transfer from the catalytic FAD-containing dehydrogenase domain to the electron shuttling cytochrome domain of CDH is required. This study investigates the role of two crucial amino acids located at the dehydrogenase domain on domain interaction and interdomain electron transfer by structure-based engineering. The electron transfer kinetics of wild-type Myriococcum thermophilum CDH and its variants M309A, R698S, and M309A/R698S were analyzed by stopped-flow spectrophotometry and structural effects were studied by small-angle X-ray scattering. The data show that R698 is essential to pull the cytochrome domain close to the dehydrogenase domain and orient the heme propionate group towards the FAD, while M309 is an integral part of the electron transfer pathway - its mutation reducing the interdomain electron transfer 10-fold. Structural models and molecular dynamics simulations pinpoint the action of these two residues on the domain interaction and interdomain electron transfer.
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Affiliation(s)
- Bettina Motycka
- University of Natural Resources and Life SciencesViennaDepartment of Food Science and TechnologyInstitute of Food TechnologyMuthgasse 181190ViennaAustria
- University of Natural Resources and Life Sciences, ViennaDepartment of BiotechnologyInstitute of Bioprocess Science and EngineeringMuthgasse 181190ViennaAustria
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryCyclotron road 194720BerkeleyCaliforniaUSA
| | - Florian Csarman
- University of Natural Resources and Life SciencesViennaDepartment of Food Science and TechnologyInstitute of Food TechnologyMuthgasse 181190ViennaAustria
| | - Melanie Rupp
- University of Natural Resources and Life SciencesViennaDepartment of Food Science and TechnologyInstitute of Food TechnologyMuthgasse 181190ViennaAustria
| | - Karoline Schnabel
- University of Natural Resources and Life SciencesViennaDepartment of Food Science and TechnologyInstitute of Food TechnologyMuthgasse 181190ViennaAustria
| | - Gabor Nagy
- Max Planck Institut für Multidisciplinary SciencesDepartment of Theoretical and Computational BiophysicsAm Fassberg 1137077GöttingenGermany
| | - Kwankao Karnpakdee
- University of Natural Resources and Life SciencesViennaDepartment of Food Science and TechnologyInstitute of Food TechnologyMuthgasse 181190ViennaAustria
| | - Stefan Scheiblbrandner
- University of Natural Resources and Life SciencesViennaDepartment of Food Science and TechnologyInstitute of Food TechnologyMuthgasse 181190ViennaAustria
| | - Rupert Tscheliessnig
- University of Natural Resources and Life Sciences, ViennaDepartment of BiotechnologyInstitute of Bioprocess Science and EngineeringMuthgasse 181190ViennaAustria
- Division of BiophysicsGottfried-Schatz-Research-CenterMedical University of GrazNeue Stiftingtalstraße 68010GrazAustria
| | - Chris Oostenbrink
- University of Natural Resources and Life SciencesViennaDepartment of Material Sciences and Process EngineeringInstitute of Molecular Modeling and SimulationMuthgasse 181190ViennaAustria
| | - Michal Hammel
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryCyclotron road 194720BerkeleyCaliforniaUSA
| | - Roland Ludwig
- University of Natural Resources and Life SciencesViennaDepartment of Food Science and TechnologyInstitute of Food TechnologyMuthgasse 181190ViennaAustria
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Procópio DP, Lee JW, Shin J, Tramontina R, Ávila PF, Brenelli LB, Squina FM, Damasio A, Rabelo SC, Goldbeck R, Franco TT, Leak D, Jin YS, Basso TO. Metabolic engineering of Saccharomyces cerevisiae for second-generation ethanol production from xylo-oligosaccharides and acetate. Sci Rep 2023; 13:19182. [PMID: 37932303 PMCID: PMC10628280 DOI: 10.1038/s41598-023-46293-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023] Open
Abstract
Simultaneous intracellular depolymerization of xylo-oligosaccharides (XOS) and acetate fermentation by engineered Saccharomyces cerevisiae offers significant potential for more cost-effective second-generation (2G) ethanol production. In the present work, the previously engineered S. cerevisiae strain, SR8A6S3, expressing enzymes for xylose assimilation along with an optimized route for acetate reduction, was used as the host for expressing two β-xylosidases, GH43-2 and GH43-7, and a xylodextrin transporter, CDT-2, from Neurospora crassa, yielding the engineered SR8A6S3-CDT-2-GH34-2/7 strain. Both β-xylosidases and the transporter were introduced by replacing two endogenous genes, GRE3 and SOR1, that encode aldose reductase and sorbitol (xylitol) dehydrogenase, respectively, and catalyse steps in xylitol production. The engineered strain, SR8A6S3-CDT-2-GH34-2/7 (sor1Δ gre3Δ), produced ethanol through simultaneous XOS, xylose, and acetate co-utilization. The mutant strain produced 60% more ethanol and 12% less xylitol than the control strain when a hemicellulosic hydrolysate was used as a mono- and oligosaccharide source. Similarly, the ethanol yield was 84% higher for the engineered strain using hydrolysed xylan, compared with the parental strain. Xylan, a common polysaccharide in lignocellulosic residues, enables recombinant strains to outcompete contaminants in fermentation tanks, as XOS transport and breakdown occur intracellularly. Furthermore, acetic acid is a ubiquitous toxic component in lignocellulosic hydrolysates, deriving from hemicellulose and lignin breakdown. Therefore, the consumption of XOS, xylose, and acetate expands the capabilities of S. cerevisiae for utilization of all of the carbohydrate in lignocellulose, potentially increasing the efficiency of 2G biofuel production.
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Affiliation(s)
- Dielle Pierotti Procópio
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo (USP), São Paulo, SP, 05508-010, Brazil
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo), São Paulo, SP, 05508-900, Brazil
| | - Jae Won Lee
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABER), University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, 61801, USA
| | - Jonghyeok Shin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABER), University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, 61801, USA
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Robson Tramontina
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
- Environment and Technological Processes Program, University of Sorocaba (UNISO), Sorocaba, SP, 18023-000, Brazil
| | - Patrícia Felix Ávila
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Lívia Beatriz Brenelli
- Interdisciplinary Centre of Energy Planning, University of Campinas (UNICAMP), Campinas, SP, 13083-896, Brazil
| | - Fabio Márcio Squina
- Environment and Technological Processes Program, University of Sorocaba (UNISO), Sorocaba, SP, 18023-000, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Sarita Cândida Rabelo
- Departament of Bioprocesses and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, SP, 18618-687, Brazil
| | - Rosana Goldbeck
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Telma Teixeira Franco
- Interdisciplinary Centre of Energy Planning, University of Campinas (UNICAMP), Campinas, SP, 13083-896, Brazil
- School of Chemical Engineering, University of Campinas (UNICAMP), Campinas, SP, 13083-852, Brazil
| | - David Leak
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABER), University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, 61801, USA
| | - Thiago Olitta Basso
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo (USP), São Paulo, SP, 05508-010, Brazil.
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Cha M, Kim JH, Choi HJ, Nho SB, Kim SY, Cha YL, Song H, Lee WH, Kim SK, Kim SJ. Hydrogen Production from Barley Straw and Miscanthus by the Hyperthermophilic Bacterium, Cadicellulosirupter bescii. J Microbiol Biotechnol 2023; 33:1384-1389. [PMID: 37463861 PMCID: PMC10619549 DOI: 10.4014/jmb.2305.05022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/20/2023]
Abstract
This work aimed to evaluate the feasibility of biohydrogen production from Barley Straw and Miscanthus. The primary obstacle in plant biomass decomposition is the recalcitrance of the biomass itself. Plant cell walls consist of cellulose, hemicellulose, and lignin, which make the plant robust to decomposition. However, the hyperthermophilic bacterium, Caldicellulosiruptor bescii, can efficiently utilize lignocellulosic feedstocks (Barley Straw and Miscanthus) for energy production, and C. bescii can now be metabolically engineered or isolated to produce more hydrogen and other biochemicals. In the present study, two strains, C. bescii JWCB001 (wild-type) and JWCB018 (ΔpyrFA Δldh ΔcbeI), were tested for their ability to increase hydrogen production from Barley Straw and Miscanthus. The JWCB018 resulted in a redirection of carbon and electron (carried by NADH) flow from lactate production to acetate and hydrogen production. JWCB018 produced ~54% and 63% more acetate and hydrogen from Barley Straw, respectively than its wild-type counterpart, JWCB001. Also, 25% more hydrogen from Miscanthus was obtained by the JWCB018 strain with 33% more acetate relative to JWCB001. It was supported that the engineered C. bescii, such as the JWCB018, can be a parental strain to get more hydrogen and other biochemicals from various biomass.
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Affiliation(s)
- Minseok Cha
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jun-Ha Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyo-Jin Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soo Bin Nho
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi 17546, Republic of Korea
| | - Soo-Yeon Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Republic of Korea
| | - Young-Lok Cha
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Republic of Korea
| | - Hyoungwoon Song
- Institute for Advanced Engineering, Gyeonggi 17180, Republic of Korea
| | - Won-Heong Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi 17546, Republic of Korea
| | - Soo-Jung Kim
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
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Liu Y, Li T, Zhu H, Zhou Y, Shen Q, Liu D. Cysteine facilitates the lignocellulolytic response of Trichoderma guizhouense NJAU4742 by indirectly up-regulating membrane sugar transporters. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:159. [PMID: 37891614 PMCID: PMC10612256 DOI: 10.1186/s13068-023-02418-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Filamentous fungi possess a rich CAZymes system, which is widely studied and applied in the bio-conversion of plant biomass to alcohol chemicals. Carbon source acquisition is the fundamental driver for CAZymes-producing sustainability and secondary metabolism, therefore, a deeper insight into the regulatory network of sugar transport in filamentous fungi has become urgent. RESULTS This study reports an important linkage of sulfur assimilation to lignocellulose response of filamentous fungus. Inorganic sulfur addition facilitated biodegradation of rice straw by Trichoderma guizhouense NJAU4742. Cysteine and glutathione were revealed as major intracellular metabolites responsive to sulfur addition by metabolomics, cysteine content was increased in this process and glutathione increased correspondingly. Two membrane sugar transporter genes, Tgmst1 and Tgmst2, were identified as the critical response genes significantly up-regulated when intracellular cysteine increased. Tgmst1 and Tgmst2 were both positively regulated by the glucose regulation-related protein (GRP), up-regulation of both Tgmst1 and Tggrp can cause a significant increase in intracellular glucose. The transcriptional regulatory function of GRP mainly relied on GSH-induced glutathionylation, and the transcription activating efficiency was positively related to the glutathionylation level, furthermore, DTT-induced deglutathionylation resulted in the down-regulation of downstream genes. CONCLUSIONS Inorganic sulfur addition induces a rise in intracellular Cys content, and the conversion of cysteine to glutathione caused the increase of glutathionylation level of GRP, which in turn up-regulated Tgmst1 and Tgmst2. Subsequently, the sugar transport efficiency of single cells was improved, which facilitated the maintenance of vigorous CAZymes metabolism and the straw-to-biomass conversion.
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Affiliation(s)
- Yang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Tuo Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Han Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yihao Zhou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China.
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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Wu X, Zhao S, Tian Z, Han C, Jiang X, Wang L. Dynamics of loops surrounding the active site architecture in GH5_2 subfamily TfCel5A for cellulose degradation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:154. [PMID: 37853500 PMCID: PMC10583438 DOI: 10.1186/s13068-023-02411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant natural biomass resource for the production of biofuels and other chemicals. The efficient degradation of cellulose by cellulases is a critical step for the lignocellulose bioconversion. Understanding the structure-catalysis relationship is vital for rational design of more stable and highly active enzymes. Glycoside hydrolase (GH) family 5 is the largest and most functionally diverse group of cellulases, with a conserved TIM barrel structure. The important roles of the various loop regions of GH5 enzymes in catalysis, however, remain poorly understood. RESULTS In the present study, we investigated the relationship between the loops surrounding active site architecture and its catalytic efficiency, taking TfCel5A, an enzyme from GH5_2 subfamily of Thermobifida fusca, as an example. Large-scale computational simulations and site-directed mutagenesis experiments revealed that three loops (loop 8, 3, and 7) around active cleft played diverse roles in substrate binding, intermediate formation, and product release, respectively. The highly flexible and charged residue triad of loop 8 was responsible for capturing the ligand into the active cleft. Severe fluctuation of loop 3 led to the distortion of sugar conformation at the - 1 subsite. The wobble of loop 7 might facilitate product release, and the enzyme activity of the mutant Y361W in loop 7 was increased by approximately 40%. CONCLUSION This study unraveled the vital roles of loops in active site architecture and provided new insights into the catalytic mechanism of the GH5_2 cellulases.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhennan Tian
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Chao Han
- Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Takasuka TE, Kim H, Deng K, Bianchetti CM, Yamashita K, Beebe ET, Bergeman LF, Vander Meulen KA, Deutsch S, Ralph J, Adams PD, Northen TR, Fox BG. Quantitative Analysis of The High-Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase. Chembiochem 2023; 24:e202300357. [PMID: 37402642 DOI: 10.1002/cbic.202300357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
Kelp is an abundant, farmable biomass-containing laminarin and alginate as major polysaccharides, providing an excellent model substrate to study their deconstruction by simple enzyme mixtures. Our previous study showed strong reactivity of the glycoside hydrolase family 55 during hydrolysis of purified laminarin, raising the question of its reactivity with intact kelp. In this study, we determined that a combination of a single glycoside hydrolase family 55 β-1,3-exoglucanase with a broad-specificity alginate lyase from the polysaccharide lyase family 18 gives efficient hydrolysis of untreated kelp to a mixture of simple sugars, that is, glucose, gentiobiose, mannitol-end glucose, and mannuronic and guluronic acids and their soluble oligomers. Quantitative assignments from nanostructure initiator mass spectrometry (NIMS) and 2D HSQC NMR spectroscopy and analysis of the reaction time-course are provided. The data suggest that binary combinations of enzymes targeted to the unique polysaccharide composition of marine biomass are sufficient to deconstruct kelp into soluble sugars for microbial fermentation.
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Affiliation(s)
- Taichi E Takasuka
- Research Faculty of Agriculture and, Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
- Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hoon Kim
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Present address: U.S. Department of Agriculture, Forest Service, Forest Products Laboratory, 1 Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Kai Deng
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA 94551, USA
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
| | - Christopher M Bianchetti
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kaho Yamashita
- Research Faculty of Agriculture and, Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
| | - Emily T Beebe
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Lai F Bergeman
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Kirk A Vander Meulen
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
| | - Samuel Deutsch
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA 94551, USA
| | - John Ralph
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brian G Fox
- Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
- US Department of Energy, Great Lakes Bioenergy Research Center, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Xue H, Qin R, Liu Y, Yuan L, Li G. An aggregated understanding of the influence of aqueous ammonia pretreatment on the physical deconstruction of cell walls in sugar beet pulp. Bioprocess Biosyst Eng 2023; 46:1427-1435. [PMID: 37490146 DOI: 10.1007/s00449-023-02908-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
The underlying interplay between physicochemical property and enzymatic hydrolysis of cellulose still remains unclear. The impacts of matrix glycan composition of sugar beet pulp (SBP) on physical structure and saccharification efficiency were emphasized. The results showed that aqueous ammonia (AA) pretreatment could remove the non-cellulosic polysaccharides and destroy the linkage between the pectin and lignin. The cellulose supramolecule was changed significantly after AA pretreatment, in terms of the decline in hardness, gumminess, springiness, thickness and degree of polymerization. Furthermore, vascular cell was exposed and degraded. The highest reducing sugar yield of 355.06 mg/g was obtained from the pretreated SBP (80 °C) with enzyme loading of 30 U/g, which was 1.01 times higher than that of the untreated SBP. This research also supported the idea that recognizing and precisely removing the primary epitopes in cell walls might be an ideal strategy to accomplish the improved enzymatic hydrolysis through mild pretreatment.
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Affiliation(s)
- Huiting Xue
- Inner Mongolia Engineering Technology Research Center of Germplasm Resources Conservation and Utilization, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, People's Republic of China
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010070, People's Republic of China
| | - Renjie Qin
- Inner Mongolia Engineering Technology Research Center of Germplasm Resources Conservation and Utilization, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, People's Republic of China
| | - Yang Liu
- Inner Mongolia Engineering Technology Research Center of Germplasm Resources Conservation and Utilization, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, People's Republic of China
| | - Lin Yuan
- Inner Mongolia Engineering Technology Research Center of Germplasm Resources Conservation and Utilization, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, People's Republic of China
| | - Guanhua Li
- Inner Mongolia Engineering Technology Research Center of Germplasm Resources Conservation and Utilization, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, People's Republic of China.
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Motycka B, Csarman F, Tscheliessnig R, Hammel M, Ludwig R. Resolving domain positions of cellobiose dehydrogenase by small angle X-ray scattering. FEBS J 2023; 290:4726-4743. [PMID: 37287434 PMCID: PMC10592539 DOI: 10.1111/febs.16885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023]
Abstract
The interdomain electron transfer (IET) between the catalytic flavodehydrogenase domain and the electron-transferring cytochrome domain of cellobiose dehydrogenase (CDH) plays an essential role in biocatalysis, biosensors and biofuel cells, as well as in its natural function as an auxiliary enzyme of lytic polysaccharide monooxygenase. We investigated the mobility of the cytochrome and dehydrogenase domains of CDH, which is hypothesised to limit IET in solution by small angle X-ray scattering (SAXS). CDH from Myriococcum thermophilum (syn. Crassicarpon hotsonii, syn. Thermothelomyces myriococcoides) was probed by SAXS to study the CDH mobility at different pH and in the presence of divalent cations. By comparison of the experimental SAXS data, using pair-distance distribution functions and Kratky plots, we show an increase in CDH mobility at higher pH, indicating alterations of domain mobility. To further visualise CDH movement in solution, we performed SAXS-based multistate modelling. Glycan structures present on CDH partially masked the resulting SAXS shapes, we diminished these effects by deglycosylation and studied the effect of glycoforms by modelling. The modelling shows that with increasing pH, the cytochrome domain adopts a more flexible state with significant separation from the dehydrogenase domain. On the contrary, the presence of calcium ions decreases the mobility of the cytochrome domain. Experimental SAXS data, multistate modelling and previously reported kinetic data show how pH and divalent ions impact the closed state necessary for the IET governed by the movement of the CDH cytochrome domain.
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Affiliation(s)
- Bettina Motycka
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Technology, Muthgasse 18, 1190 Vienna, Austria
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190 Vienna, Austria
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkely, California, USA
| | - Florian Csarman
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Technology, Muthgasse 18, 1190 Vienna, Austria
| | - Rupert Tscheliessnig
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190 Vienna, Austria
- Division of Biophysics, Gottfried-Schatz-Research-Center, Medical University of Graz, Graz, Austria
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkely, California, USA
| | - Roland Ludwig
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Technology, Muthgasse 18, 1190 Vienna, Austria
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DeChellis A, Nemmaru B, Sammond D, Douglass J, Patil N, Reste O, Chundawat SPS. Supercharging carbohydrate-binding module alone enhances endocellulase thermostability, binding, and activity on cellulosic biomass. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557007. [PMID: 37745483 PMCID: PMC10515785 DOI: 10.1101/2023.09.09.557007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Lignocellulosic biomass recalcitrance to enzymatic degradation necessitates high enzyme loadings incurring large processing costs for industrial-scale biofuels or biochemicals production. Manipulating surface charge interactions to minimize non-productive interactions between cellulolytic enzymes and plant cell wall components (e.g., lignin or cellulose) via protein supercharging has been hypothesized to improve biomass biodegradability, but with limited demonstrated success to date. Here we characterize the effect of introducing non-natural enzyme surface mutations and net charge on cellulosic biomass hydrolysis activity by designing a library of supercharged family-5 endoglucanase Cel5A and its native family-2a carbohydrate binding module (CBM) originally belonging to an industrially relevant thermophilic microbe Thermobifida fusca . A combinatorial library of 33 mutant constructs containing different CBM and Cel5A designs spanning a net charge range of -52 to 37 was computationally designed using Rosetta macromolecular modelling software. Activity for all mutants was rapidly characterized as soluble cell lysates and promising mutants (containing mutations either on the CBM, Cel5A catalytic domain, or both CBM and Cel5A domains) were then purified and systematically characterized. Surprisingly, often endocellulases with mutations on the CBM domain alone resulted in improved activity on cellulosic biomass, with three top-performing supercharged CBM mutants exhibiting between 2-5-fold increase in activity, compared to native enzyme, on both pretreated biomass enriched in lignin (i.e., corn stover) and isolated crystalline/amorphous cellulose. Furthermore, we were able to clearly demonstrate that endocellulase net charge can be selectively fine-tuned using protein supercharging protocol for targeting distinct substrates and maximizing biocatalytic activity. Additionally, several supercharged CBM containing endocellulases exhibited a 5-10 °C increase in optimal hydrolysis temperature, compared to native enzyme, which enabled further increase in hydrolytic yield at higher operational reaction temperatures. This study demonstrates the first successful implementation of enzyme supercharging of cellulolytic enzymes to increase hydrolytic activity towards complex lignocellulosic biomass derived substrates.
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Mathieu Y, Raji O, Bellemare A, Di Falco M, Nguyen TTM, Viborg AH, Tsang A, Master E, Brumer H. Functional characterization of fungal lytic polysaccharide monooxygenases for cellulose surface oxidation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:132. [PMID: 37679837 PMCID: PMC10486138 DOI: 10.1186/s13068-023-02383-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Microbial lytic polysaccharide monooxygenases (LPMOs) cleave diverse biomass polysaccharides, including cellulose and hemicelluloses, by initial oxidation at C1 or C4 of glycan chains. Within the Carbohydrate-Active Enzymes (CAZy) classification, Auxiliary Activity Family 9 (AA9) comprises the first and largest group of fungal LPMOs, which are often also found in tandem with non-catalytic carbohydrate-binding modules (CBMs). LPMOs originally attracted attention for their ability to potentiate complete biomass deconstruction to monosaccharides. More recently, LPMOs have been applied for selective surface modification of insoluble cellulose and chitin. RESULTS To further explore the catalytic diversity of AA9 LPMOs, over 17,000 sequences were extracted from public databases, filtered, and used to construct a sequence similarity network (SSN) comprising 33 phylogenetically supported clusters. From these, 32 targets were produced successfully in the industrial filamentous fungus Aspergillus niger, 25 of which produced detectable LPMO activity. Detailed biochemical characterization of the eight most highly produced targets revealed individual C1, C4, and mixed C1/C4 regiospecificities of cellulose surface oxidation, different redox co-substrate preferences, and CBM targeting effects. Specifically, the presence of a CBM correlated with increased formation of soluble oxidized products and a more localized pattern of surface oxidation, as indicated by carbonyl-specific fluorescent labeling. On the other hand, LPMOs without native CBMs were associated with minimal release of soluble products and comparatively dispersed oxidation pattern. CONCLUSIONS This work provides insight into the structural and functional diversity of LPMOs, and highlights the need for further detailed characterization of individual enzymes to identify those best suited for cellulose saccharification versus surface functionalization toward biomaterials applications.
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Affiliation(s)
- Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Olanrewaju Raji
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Annie Bellemare
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Marcos Di Falco
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Thi Truc Minh Nguyen
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Adrian Tsang
- Centre for Structural & Functional Genomics, Concordia University, 7141 Sherbrooke-West Street, Montreal, H4B 1R6, Canada
| | - Emma Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Botany, University of British Columbia, 3200 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
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Jahanshahi A, Lopes M, Brandão M, De Castro EA. Development of bioenergy technologies: A scientometric analysis. Heliyon 2023; 9:e20000. [PMID: 37810100 PMCID: PMC10559684 DOI: 10.1016/j.heliyon.2023.e20000] [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: 03/23/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
Bioenergy has the potential to substitute the current demand for fossil fuels in various applications. Recovering energy from bio-based materials due to environmental considerations has been adopted as a policy objective by governments and international organizations, which led to both vast financial investment and scientific research, especially in the last two decades. So far, various feedstocks and technologies have been scrutinised by the research community, although not all of them are commercially adopted due to sustainability considerations. This study employs scientometric analysis to survey the progress of scientific development in the field of bioenergy from 1966 to 2022, using ten parameters including publication year, type of document, categories, countries, affiliations, document citations, co-authorship, author citation networks, journal citation networks, and keywords. A total of 51,905 scientific documents were collected from the Web of Science, involving more than 96,000 authors from 162 countries. The dispersion of studies followed an ascending distribution with a sharp increase in the second half of the 2000s. The evolution of keywords in terms of burst strength confirmed the advancements of technologies from primary first-generation to advanced fourth-generation bioenergies. Based on the evolution of science in this area, it is concluded that integrated sustainability assessment studies, covering technical, economical, environmental, and social aspects, are needed to bridge the gap between abundant theoretical endeavours and limited commercial use of this energy source.
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Affiliation(s)
- Akram Jahanshahi
- Department of Environment and Planning, Center for Environmental and Marine Studies, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
- Research Unit on Governance, Competitiveness and Public Policies (GOVCOPP), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Myriam Lopes
- Department of Environment and Planning, Center for Environmental and Marine Studies, CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Eduardo Anselmo De Castro
- Research Unit on Governance, Competitiveness and Public Policies (GOVCOPP), University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Social, Political and Territorial Sciences (DCSPT), University of Aveiro, 3810-193 Aveiro, Portugal
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Barik S, Dash AK, Saharay M. Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations. J Chem Inf Model 2023; 63:5192-5203. [PMID: 37590465 DOI: 10.1021/acs.jcim.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The utilization of microbial cellulase enzymes for transforming plant biomass into biofuel or bioethanol, which can serve as a substitute for fossil fuel, is a subject of growing interest. Nonetheless, large-scale production of biofuel using cellulases is not economically feasible as the extraction of these enzymes from diverse microorganisms is an expensive process. To address this issue, immobilizing the enzyme to a substrate material, e.g., carbon nanotubes (CNTs), to recycle without a significant decline in its catalytic activity is a promising solution. Due to the hydrophobic nature of CNTs, we employed molecular docking and network analysis methodologies to identify potential CNT-binding sites on the outer surface of a wild-type cellulase enzyme, CelS. Classical molecular dynamics simulations of CNT-bound CelS through one of the selected binding sites resulted in negligible changes in the secondary structure of the enzyme and its catalytic domain, implying the least possible effect on the catalytic activity post-immobilization. Furthermore, our study reveals that while the unfolding near the CNT-binding region in CelS is more pronounced when the enzyme is interacting with a wider CNT, resulting in enhanced contact area and improved binding affinity, its impact on the overall CelS structure is relatively less significant when compared to thinner CNTs. Particularly, CNTs of diameter ∼12 Å can serve as a favorable option for substrate materials in cellulase immobilization. Our study also provides critical insights into the binding mechanisms between cellulase and CNTs, which could lead to the development of more efficient biocatalysts for biofuel production.
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Affiliation(s)
- Shubhashree Barik
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500046, Telangana, India
| | - Akarsh Kumar Dash
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500046, Telangana, India
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500046, Telangana, India
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Zhang X, Fang Z, Zhao D, Kamal R, Wang X, Jin G, Gong Z, Yang X. Biorefinery of vineyard winter prunings for production of microbial lipids by the oleaginous yeast Cryptococcus curvatus. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 168:221-229. [PMID: 37311389 DOI: 10.1016/j.wasman.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/11/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
Spent biomass from agricultural and forestry industries are substantial low-cost carbon source for reducing the input of microbial lipid production. Herein, the components of the vineyard winter prunings (VWPs) from 40 grape cultivars were analyzed. The VWPs contained (w/w) cellulose ranged from 24.8% to 32.4%, hemicellulose 9.6% to 13.8%, lignin 23.7% to 32.4%. The VWPs from Cabernet Sauvignon was processed with the alkali-methanol pretreatment, and 95.8% of the sugars was released from the regenerated VWPs after enzymatic hydrolysis. The hydrolysates from the regenerated VWPs was suitable for lipid production without further treatment as a lipid content of 59% could be achieved with Cryptococcus curvatus. The regenerated VWPs was also used for lipid production via simultaneous saccharification and fermentation (SSF), which led to a lipid yield of 0.088 g/g raw VWPs, 0.126 g/g regenerated VWPs and 0.185 g/g from the reducing sugars. This work demonstrated that the VWPs can be explored for co-production of microbial lipids.
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Affiliation(s)
- Xueyuan Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhumei Fang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Di Zhao
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rasool Kamal
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Xue Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guojie Jin
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhiwei Gong
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, China
| | - Xiaobing Yang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of Northwest A&F University, Yongning, Yinchuan 750104, China.
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Zhu Z, Wu S, Qi B, Wang C, Luo J, Wan Y. High-solids enzymatic saccharification of starch-rich raw herbal biomass residues for producing high titers of glucose. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:86232-86243. [PMID: 37402046 DOI: 10.1007/s11356-023-28501-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
The bioresource utilization of herbal biomass residues (HBRs) has been receiving more attention. Herein, three different HBRs from Isatidis Radix (IR) and Sophorae Flavescentis Radix (SFR) and Ginseng Radix (GR) were subjected to batch and fed-batch enzymatic hydrolysis to produce high-concentration glucose. Compositional analysis showed the three HBRs had substantial starch content (26.36-63.29%) and relatively low cellulose contents (7.85-21.02%). Due to their high starch content, the combined action of cellulolytic and amylolytic enzymes resulted in greater release of glucose from the raw HBRs compared to using the individual enzyme alone. Batch enzymatic hydrolysis of 10% (w/v) raw HBRs with low loadings of cellulase (≤ 10 FPU/g substrate) and amylolytic enzymes (≤ 5.0 mg/g substrate) led to a high glucan conversion of ≥ 70%. The addition of PEG 6000 and Tween 20 did not contribute to glucose production. Furthermore, to achieve higher glucose concentrations, fed-batch enzymatic hydrolysis was conducted using a total solid loading of 30% (w/v). After 48-h of hydrolysis, glucose concentrations of 125 g/L and 92 g/L were obtained for IR and SFR residues, respectively. GR residue yielded an 83 g/L glucose concentration after 96 h of digestion. The high glucose concentrations produced from these raw HBRs indicate their potential as ideal substrate for a profitable biorefinery. Notably, the obvious advantage of using these HBRs is the elimination of the pretreatment step, which is typically required for agricultural and woody biomass in similar studies.
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Affiliation(s)
- Zhenzhou Zhu
- Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Sirong Wu
- National R&D Center for Se-Rich Agricultural Products Processing, College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Benkun Qi
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Caixia Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jianquan Luo
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinhua Wan
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Ganjiang Innovation Academy, Chinese Academy of Sciences, Ganzhou, 341119, China
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