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De PS, Theilmann J, Raguin A. A detailed sensitivity analysis identifies the key factors influencing the enzymatic saccharification of lignocellulosic biomass. Comput Struct Biotechnol J 2024; 23:1005-1015. [PMID: 38420218 PMCID: PMC10900831 DOI: 10.1016/j.csbj.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/09/2024] [Accepted: 01/14/2024] [Indexed: 03/02/2024] Open
Abstract
Corn stover is the most abundant form of crop residue that can serve as a source of lignocellulosic biomass in biorefinery approaches, for instance for the production of bioethanol. In such biorefinery processes, the constituent polysaccharide biopolymers are typically broken down into simple monomeric sugars by enzymatic saccharification, for further downstream fermentation into bioethanol. However, the recalcitrance of this material to enzymatic saccharification invokes the need for innovative pre-treatment methods to increase sugar conversion yield. Here, we focus on experimental glucose conversion time-courses for corn stover lignocellulose that has been pre-treated with different acid-catalysed processes and intensities. We identify the key parameters that determine enzymatic saccharification dynamics by performing a Sobol's sensitivity analysis on the comparison between the simulation results from our complex stochastic biophysical model, and the experimental data that we accurately reproduce. We find that the parameters relating to cellulose crystallinity and those associated with the cellobiohydrolase activity are predominantly driving the enzymatic saccharification dynamics. We confirm our computational results using mathematical calculations for a purely cellulosic substrate. On the one hand, having identified that only five parameters drastically influence the saccharification dynamics allows us to reduce the dimensionality of the parameter space (from nineteen to five parameters), which we expect will significantly speed up our fitting algorithm for comparison of experimental and simulated saccharification time-courses. On the other hand, these parameters directly highlight key targets for experimental endeavours in the optimisation of pre-treatment and saccharification conditions. Finally, this systematic and two-fold theoretical study, based on both mathematical and computational approaches, provides experimentalists with key insights that will support them in rationalising their complex experimental results.
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Affiliation(s)
- Partho Sakha De
- Institute for Computational Cell Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, NRW, Germany
| | - Jasmin Theilmann
- Institute for Computational Cell Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
| | - Adélaïde Raguin
- Institute for Computational Cell Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, NRW, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
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2
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Dickwella Widanage MC, Gautam I, Sarkar D, Mentink-Vigier F, Vermaas JV, Ding SY, Lipton AS, Fontaine T, Latgé JP, Wang P, Wang T. Adaptative survival of Aspergillus fumigatus to echinocandins arises from cell wall remodeling beyond β-1,3-glucan synthesis inhibition. Nat Commun 2024; 15:6382. [PMID: 39085213 PMCID: PMC11291495 DOI: 10.1038/s41467-024-50799-8] [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: 05/13/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024] Open
Abstract
Antifungal echinocandins inhibit the biosynthesis of β-1,3-glucan, a major and essential polysaccharide component of the fungal cell wall. However, the efficacy of echinocandins against the pathogen Aspergillus fumigatus is limited. Here, we use solid-state nuclear magnetic resonance (ssNMR) and other techniques to show that echinocandins induce dynamic changes in the assembly of mobile and rigid polymers within the A. fumigatus cell wall. The reduction of β-1,3-glucan induced by echinocandins is accompanied by a concurrent increase in levels of chitin, chitosan, and highly polymorphic α-1,3-glucans, whose physical association with chitin maintains cell wall integrity and modulates water permeability. The rearrangement of the macromolecular network is dynamic and controls the permeability and circulation of the drug throughout the cell wall. Thus, our results indicate that echinocandin treatment triggers compensatory rearrangements in the cell wall that may help A. fumigatus to tolerate the drugs' antifungal effects.
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Affiliation(s)
- Malitha C Dickwella Widanage
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - Isha Gautam
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | | | | | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory, East Lansing, MI, USA
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Shi-You Ding
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Andrew S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thierry Fontaine
- Institut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, F-, 75015, Paris, France
| | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology, University of Crete, Heraklion, Greece
| | - Ping Wang
- Departments of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA.
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3
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Ponnuchamy V, Sandak A, Sandak J. Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures. ACS OMEGA 2024; 9:25646-25654. [PMID: 38911769 PMCID: PMC11191132 DOI: 10.1021/acsomega.3c08853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/28/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024]
Abstract
Understanding the atomic-scale structure of wood microfibrils is essential for establishing fundamental properties in various wood-based research aspects, including moisture impact, wood modification, and pretreatment. In this study, we employed molecular dynamics simulations to investigate the arrangement of wood polymers, including cellulose, hemicellulose, and lignin, with a primary focus on the composition of softwood, specifically Norway Spruce wood. We assessed the accuracy of our molecular dynamics model by comparing it with available experimental data, such as density, Young's modulus, and glass transition temperature, which ensures the reliability of our approach. A key aspect of our study involved modeling the active sorption site for water interaction with wood polymers. Our findings revealed that the interaction between water and hemicellulose, particularly within the hemicellulose-cellulose interphase, was the most prominent binding site. This observation aligns with prior research in this field, further strengthening the validity of our results.
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Affiliation(s)
- Veerapandian Ponnuchamy
- InnoRenew
CoE, Livade 6a, 6310 Izola, Slovenia
- University
of Primorska, Andrej Marušič Institute, Muzejski trg 2, 6000 Koper, Slovenia
| | - Anna Sandak
- InnoRenew
CoE, Livade 6a, 6310 Izola, Slovenia
- University
of Primorska, Andrej Marušič Institute, Muzejski trg 2, 6000 Koper, Slovenia
- Faculty
of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Jakub Sandak
- InnoRenew
CoE, Livade 6a, 6310 Izola, Slovenia
- University
of Primorska, Andrej Marušič Institute, Muzejski trg 2, 6000 Koper, Slovenia
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4
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Fülöp L. Carbohydrate polymer degradation derivatives as possible natural mannanase inhibitors. Int J Biol Macromol 2024; 269:132033. [PMID: 38702000 DOI: 10.1016/j.ijbiomac.2024.132033] [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: 02/17/2024] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
The role of mannanases is diverse and they are used in many industrial applications, in animal feed, in the food industry and in healthcare. They are also applied in biomass processing, because they play an important role in the breakdown of hemicellulose. Among the mannanase inhibitors, heavy metal ions and general enzyme inhibitors are mainly mentioned. Unfortunately, almost no data are available on carbohydrate-based natural inhibitors of mannanases. According to the literature, carbohydrates do not play an important role in the inhibition of mannanases, so neither do oligosaccharides. This is in contrast to the action and inhibition of other O-glycosyl hydrolases. My hypothesis is that mannanases, like other polysaccharide-degrading enzymes, work in the same way and can be inhibited by oligosaccharides. Evidence from docking and modeling results supports and makes probable the hypothesis that oligosaccharides can inhibit the activity of mannanases, similar to the inhibition of other O-glycosyl hydrolases. Among natural carbohydrate oligomers, several potential mannanase inhibitors have been identified and characterized. In addition to expensive research, it is very important to use research based on cheaper modeling to explore the processes. The results obtained are novel and forward-looking, enabling in-depth and targeted research to be carried out.
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Chen Z, Shi Q, Zhao T, Liu Y, Hao J, Li Z, Ning L. Molecular insights into inhibiting effects of lignin on cellulase investigated by molecular dynamics simulation. J Biomol Struct Dyn 2024:1-13. [PMID: 38497800 DOI: 10.1080/07391102.2024.2328738] [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: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024]
Abstract
The hydrolysis of lignocellulose into fermentable monosaccharides using cellulases represents a critical stage in lignocellulosic bioconversion. However, the inactivation of cellulase in the presence of lignin is attributed to the high cost of biofinery. To address this challenge, a comprehensive investigation into the structure-function relationship underlying lignin-driven cellulase inactivation is essential. In this study, molecular docking and molecular dynamics (MD) simulations were employed to explore the impacts of lignin fragments on the catalytic efficiency of cellulase at the atomic level. The findings revealed that soluble lignin fragments and cellulose could spontaneously form stable complexes with cellulase, indicating a competitive binding scenario. The enzyme's structure remained unchanged upon binding to lignin. Furthermore, specific amino acid residues have been identified as involved in interactions with lignin and cellulose. Hydrophobic interactions were found to dominate the binding of lignin to cellulase. Based on the mechanisms underlying the interactions between lignin fragments and cellulase, decreased hydrophobicity and change in the charge of lignin may mitigate the inhibition of cellulase. Furthermore, site mutations and chemical modification are also feasible to improve the efficiency of cellulase. This study may contribute valuable insights into the design of more lignin-resistant enzymes and the optimization of lignocellulosic pretreatment technologies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhenjuan Chen
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Qingwen Shi
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Tengfei Zhao
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Yuxi Liu
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Jinhong Hao
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Zhijian Li
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Lulu Ning
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
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6
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Barragán-Trinidad M, Buitrón G. Pretreatment of agave bagasse with ruminal fluid to improve methane recovery. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 175:52-61. [PMID: 38159368 DOI: 10.1016/j.wasman.2023.12.041] [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: 09/06/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Agave bagasse, a lignocellulosic waste that results from the milling and juice extraction of Agave tequilana var azul pineapples, is a suitable substrate for the production of methane through anaerobic digestion. However, it is necessary to apply a pretreatment to convert the bagasse into energy. In this context, this paper proposes using ruminal microorganisms to hydrolyze agave bagasse. This study evaluated the effect of the initial agave bagasse to ruminal fluid (S0/X0) ratio (0.33, 0.5, 1, and 2) on the hydrolysis efficiency. Subsequently, the supernatant was used for methane production. The hydrolysis efficiency increased as the S0/X0 ratio decreased. A hydrolysis efficiency of 60 % was achieved using an S0/X0 ratio of 0.33. The S0/X0 ratio of 0.33 optimally improved the specific methane production and energy recovery (155 ± 2 mL CH4/g TS and 6.1 ± 0.1 kJ/g TS) compared to raw biomass. The most abundant hydrolytic bacteria were Prevotella, Ruminococcus and Fibrobacter, and Engyodontium was the most abundant proteolytic fungus.
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Affiliation(s)
- Martín Barragán-Trinidad
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico.
| | - Germán Buitrón
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico.
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7
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Peracchi LM, Panahabadi R, Barros-Rios J, Bartley LE, Sanguinet KA. Grass lignin: biosynthesis, biological roles, and industrial applications. FRONTIERS IN PLANT SCIENCE 2024; 15:1343097. [PMID: 38463570 PMCID: PMC10921064 DOI: 10.3389/fpls.2024.1343097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/06/2024] [Indexed: 03/12/2024]
Abstract
Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.
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Affiliation(s)
- Luigi M. Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Rahele Panahabadi
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Jaime Barros-Rios
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karen A. Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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8
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Porninta K, Khemacheewakul J, Techapun C, Phimolsiripol Y, Jantanasakulwong K, Sommanee S, Mahakuntha C, Feng J, Htike SL, Moukamnerd C, Zhuang X, Wang W, Qi W, Li FL, Liu T, Kumar A, Nunta R, Leksawasdi N. Pretreatment and enzymatic hydrolysis optimization of lignocellulosic biomass for ethanol, xylitol, and phenylacetylcarbinol co-production using Candida magnoliae. Front Bioeng Biotechnol 2024; 11:1332185. [PMID: 38304106 PMCID: PMC10830760 DOI: 10.3389/fbioe.2023.1332185] [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: 11/02/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024] Open
Abstract
Cellulosic bioethanol production generally has a higher operating cost due to relatively expensive pretreatment strategies and low efficiency of enzymatic hydrolysis. The production of other high-value chemicals such as xylitol and phenylacetylcarbinol (PAC) is, thus, necessary to offset the cost and promote economic viability. The optimal conditions of diluted sulfuric acid pretreatment under boiling water at 95°C and subsequent enzymatic hydrolysis steps for sugarcane bagasse (SCB), rice straw (RS), and corn cob (CC) were optimized using the response surface methodology via a central composite design to simplify the process on the large-scale production. The optimal pretreatment conditions (diluted sulfuric acid concentration (% w/v), treatment time (min)) for SCB (3.36, 113), RS (3.77, 109), and CC (3.89, 112) and the optimal enzymatic hydrolysis conditions (pretreated solid concentration (% w/v), hydrolysis time (h)) for SCB (12.1, 93), RS (10.9, 61), and CC (12.0, 90) were achieved. CC xylose-rich and CC glucose-rich hydrolysates obtained from the respective optimal condition of pretreatment and enzymatic hydrolysis steps were used for xylitol and ethanol production. The statistically significant highest (p ≤ 0.05) xylitol and ethanol yields were 65% ± 1% and 86% ± 2% using Candida magnoliae TISTR 5664. C. magnoliae could statistically significantly degrade (p ≤ 0.05) the inhibitors previously formed during the pretreatment step, including up to 97% w/w hydroxymethylfurfural, 76% w/w furfural, and completely degraded acetic acid during the xylitol production. This study was the first report using the mixed whole cells harvested from xylitol and ethanol production as a biocatalyst in PAC biotransformation under a two-phase emulsion system (vegetable oil/1 M phosphate (Pi) buffer). PAC concentration could be improved by 2-fold compared to a single-phase emulsion system using only 1 M Pi buffer.
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Affiliation(s)
- Kritsadaporn Porninta
- Program in Biotechnology, Multidisciplinary and Interdisciplinary School, Chiang Mai University, Chiang Mai, Thailand
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Julaluk Khemacheewakul
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Charin Techapun
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Yuthana Phimolsiripol
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Jantanasakulwong
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Sumeth Sommanee
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchadaporn Mahakuntha
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Juan Feng
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Su Lwin Htike
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | | | - Xinshu Zhuang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, China
| | - Wen Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, China
| | - Wei Qi
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, China
| | - Fu-Li Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Tianzhong Liu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Anbarasu Kumar
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Department of Biotechnology, Periyar Maniammai Institute of Science & Technology (Deemed to be University), Thanjavur, India
| | - Rojarej Nunta
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Division of Food Innovation and Business, Faculty of Agricultural Technology, Lampang Rajabhat University, Lampang, Thailand
| | - Noppol Leksawasdi
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
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De PS, Glass T, Stein M, Spitzlei T, Raguin A. PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall. Comput Struct Biotechnol J 2023; 21:5463-5475. [PMID: 38022701 PMCID: PMC10663758 DOI: 10.1016/j.csbj.2023.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Enzymatic digestion of lignocellulosic plant biomass is a key step in bio-refinery approaches for the production of biofuels and other valuable chemicals. However, the recalcitrance of this material in conjunction with its variability and heterogeneity strongly hampers the economic viability and profitability of biofuel production. To complement both academic and industrial experimental research in the field, we designed an advanced web application that encapsulates our in-house developed complex biophysical model of enzymatic plant cell wall degradation. PREDIG (https://predig.cs.hhu.de/) is a user-friendly, free, and fully open-source web application that allows the user to perform in silico experiments. Specifically, it uses a Gillespie algorithm to run stochastic simulations of the enzymatic saccharification of a lignocellulose microfibril, at the mesoscale, in three dimensions. Such simulations can for instance be used to test the action of distinct enzyme cocktails on the substrate. Additionally, PREDIG can fit the model parameters to uploaded experimental time-course data, thereby returning values that are intrinsically difficult to measure experimentally. This gives the user the possibility to learn which factors quantitatively explain the recalcitrance to saccharification of their specific biomass material.
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Affiliation(s)
- Partho Sakha De
- Institute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Torben Glass
- Institute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Merle Stein
- Institute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Thomas Spitzlei
- Institute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Adélaïde Raguin
- Institute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
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10
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Sarkar D, Santiago IJ, Vermaas JV. Atomistic Origins of Biomass Recalcitrance in Organosolv Pretreatment. Chem Eng Sci 2023. [DOI: 10.1016/j.ces.2023.118587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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11
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Wang L, Li X, Wan C, Zhang K, Wu Z, Hu F, Zhang R, Fu X, Yu H. Enhanced production of sugars and UV-shielded lignin/PAN fiber mats from chemi-mechanical pulps. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:161090. [PMID: 36586767 DOI: 10.1016/j.scitotenv.2022.161090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
This study investigated poplar pretreatments by chemi-mechanical pulping (CMP) under different beating degrees and alkali concentrations. The enzyme-mediated hydrolysis of pretreated poplar was enhanced by deacetylation and delignification. Meanwhile, the remaining lignin residues were used to produce lignin/polyacrylonitrile (PAN) fiber mats by electrospinning. These mats exhibited excellent mechanical and UV-blocking performance when the lignin was obtained from pulps under milder alkali concentrations (5 g/L). 31P nuclear magnetic resonance (31P NMR) and two-dimensional heteronuclear single-quantum correlation nuclear magnetic resonance (2D HSQC NMR) data revealed that increasing the beating degree at low alkali concentration during the CMP process led to the cleavage of β-O-4' interunit linkages and re-condensation in lignin, releasing several phenolic groups. Lignin with more linear β-O-4' interunit linkages and lesser phenolic groups, obtained from treatment of CMP with lower alkali concentration (5 g/L) and beating degree (20°SR), resulted in the corresponding lignin/PAN fiber mats exhibiting better mechanical performance. Further, lignin, along with the increased phenolic-OH and COOH, and p-hydroxybenzoate (PB) units with a more extended conjugate structure, derived from CMP under lower alkali concentration (5 g/L) and higher beating degree (45°SR), led to a stronger ultraviolet (UV) absorption in the corresponding lignin/PAN mats. To summarize, this study reports a mild and low-pollution biomass pretreatment method (CMP) that can efficiently regulate the lignin structure and exhibit efficient anti-ultraviolet properties. The corresponding UV-blocking fiber mats can be potentially used as materials for wearable fabrics.
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Affiliation(s)
- Lei Wang
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan 430068, China
| | - Xiaohan Li
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan 430068, China
| | - Chenzhong Wan
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan 430068, China
| | - Kesheng Zhang
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan 430068, China
| | - Zhao Wu
- Hubei Key Laboratory of Biomass Fibers and Eco-dyeing and Finishing, College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan 430073, Hubei, China
| | - Fen Hu
- Hubei Key Laboratory of Biomass Fibers and Eco-dyeing and Finishing, College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan 430073, Hubei, China
| | - Ran Zhang
- Hubei Key Laboratory of Biomass Fibers and Eco-dyeing and Finishing, College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan 430073, Hubei, China.
| | - Xiao Fu
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Hongbo Yu
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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12
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Raza S, Miller M, Hamberger B, Vermaas JV. Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations. J Phys Chem B 2023; 127:1144-1157. [PMID: 36717085 PMCID: PMC9923751 DOI: 10.1021/acs.jpcb.2c07209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Plants synthesize small molecule diterpenes composed of 20 carbons from precursor isopentenyl diphosphate and dimethylallyl disphosphate, manufacturing diverse compounds used for defense, signaling, and other functions. Industrially, diterpenes are used as natural aromas and flavoring, as pharmaceuticals, and as natural insecticides or repellents. Despite diterpene ubiquity in plant systems, it remains unknown how plants control diterpene localization and transport. For many other small molecules, plant cells maintain transport proteins that control compound compartmentalization. However, for most diterpene compounds, specific transport proteins have not been identified, and so it has been hypothesized that diterpenes may cross biological membranes passively. Through molecular simulation, we study membrane transport for three complex diterpenes from among the many made by members of the Lamiaceae family to determine their permeability coefficient across plasma membrane models. To facilitate accurate simulation, the intermolecular interactions for leubethanol, abietic acid, and sclareol were parametrized through the standard CHARMM methodology for incorporation into molecular simulations. To evaluate the effect of membrane composition on permeability, we simulate the three diterpenes in two membrane models derived from sorghum and yeast lipidomics data. We track permeation events within our unbiased simulations, and compare implied permeation coefficients with those calculated from Replica Exchange Umbrella Sampling calculations using the inhomogeneous solubility diffusion model. The diterpenes are observed to permeate freely through these membranes, indicating that a transport protein may not be needed to export these small molecules from plant cells. Moreover, the permeability is observed to be greater for plant-like membrane compositions when compared against animal-like membrane models. Increased permeability for diterpene molecules in plant membranes suggest that plants have tailored their membranes to facilitate low-energy transport processes for signaling molecules.
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Affiliation(s)
- Saad Raza
- Plant
Research Laboratory, College of Natural Science, Michigan State University, East LansingMichigan48824, United States
| | - Mykayla Miller
- Department
of Chemistry and Biochemistry, California
State University, Fullerton, Fullerton, California92831, United States
| | - Björn Hamberger
- Department
Of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East LansingMichigan48824, United States
| | - Josh V. Vermaas
- Plant
Research Laboratory, College of Natural Science, Michigan State University, East LansingMichigan48824, United States,Department
Of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East LansingMichigan48824, United States,E-mail: . Phone: +1 (517) 884-6937
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13
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Mohan M, Simmons BA, Sale KL, Singh S. Multiscale molecular simulations for the solvation of lignin in ionic liquids. Sci Rep 2023; 13:271. [PMID: 36609448 PMCID: PMC9822913 DOI: 10.1038/s41598-022-25372-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/29/2022] [Indexed: 01/09/2023] Open
Abstract
Lignin, the second most abundant biopolymer found in nature, has emerged as a potential source of sustainable fuels, chemicals, and materials. Finding suitable solvents, as well as technologies for efficient and affordable lignin dissolution and depolymerization, are major obstacles in the conversion of lignin to value-added products. Certain ionic liquids (ILs) are capable of dissolving and depolymerizing lignin but designing and developing an effective IL for lignin dissolution remains quite challenging. To address this issue, the COnductor-like Screening MOdel for Real Solvents (COSMO-RS) model was used to screen 5670 ILs by computing logarithmic activity coefficients (ln(γ)) and excess enthalpies (HE) of lignin, respectively. Based on the COSMO-RS computed thermodynamic properties (ln(γ) and HE) of lignin, anions such as acetate, methyl carbonate, octanoate, glycinate, alaninate, and lysinate in combination with cations like tetraalkylammonium, tetraalkylphosphonium, and pyridinium are predicted to be suitable solvents for lignin dissolution. The dissolution properties such as interaction energy between anion and cation, viscosity, Hansen solubility parameters, dissociation constants, and Kamlet-Taft parameters of selected ILs were evaluated to assess their propensity for lignin dissolution. Furthermore, molecular dynamics (MD) simulations were performed to understand the structural and dynamic properties of tetrabutylammonium [TBA]+-based ILs and lignin mixtures and to shed light on the mechanisms involved in lignin dissolution. MD simulation results suggested [TBA]+-based ILs have the potential to dissolve lignin because of their higher contact probability and interaction energies with lignin when compared to cholinium lysinate.
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Affiliation(s)
- Mood Mohan
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Bioresource and Environmental Security Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
| | - Blake A. Simmons
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Kenneth L. Sale
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Department of Computational Biology and Biophysics, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
| | - Seema Singh
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Bioresource and Environmental Security Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
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14
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Ramakrishna P, Cesarino I. Loosen up! How lignin manipulations affect biomass molecular assembly and deconstruction. PLANT PHYSIOLOGY 2023; 191:3-5. [PMID: 36303327 PMCID: PMC9806552 DOI: 10.1093/plphys/kiac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Priya Ramakrishna
- Laboratory for Biological Geochemistry, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, São Paulo, Brazil
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15
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Madadi M, Song G, Sun F, Sun C, Xia C, Zhang E, Karimi K, Tu M. Positive role of non-catalytic proteins on mitigating inhibitory effects of lignin and enhancing cellulase activity in enzymatic hydrolysis: Application, mechanism, and prospective. ENVIRONMENTAL RESEARCH 2022; 215:114291. [PMID: 36103929 DOI: 10.1016/j.envres.2022.114291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/18/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Fermentable sugar production from lignocellulosic biomass has received considerable attention and has been dramatic progress recently. However, due to low enzymatic hydrolysis (EH) yields and rates, a high dosage of the costly enzyme is required, which is a bottleneck for commercial applications. Over the last decades, various strategies have been developed to reduce cellulase enzyme costs. The progress of the non-catalytic additive proteins in mitigating inhibition in EH is discussed in detail in this review. The low efficiency of EH is mostly due to soluble lignin compounds, insoluble lignin, and harsh thermal and mechanical conditions of the EH process. Adding non-catalytic proteins into the EH is considered a simple and efficient approach to boost hydrolysis yield. This review discussed the multiple mechanical steps involved in the EH process. The effect of physicochemical properties of modified lignin on EH and its interaction with cellulase and cellulose are identified and discussed, which include hydrogen bonding, hydrophobic, electrostatic, and cation-π interactions, as well as physical barriers. Moreover, the effects of different conditions of EH that lead to cellulase deactivation by thermal and mechanical mechanisms are also explained. Finally, recent advances in the development, potential mechanisms, and economic feasibility of non-catalytic proteins on EH are evaluated and perspectives are presented.
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Affiliation(s)
- Meysam Madadi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guojie Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Chihe Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Changlei Xia
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Ezhen Zhang
- Institute of Agro-Products Processing Science and Technology, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Keikhosro Karimi
- Department of Chemical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Maobing Tu
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221, United States
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16
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Vermaas JV, Crowley MF, Beckham GT. Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes. J Biol Chem 2022; 298:102627. [PMID: 36273587 PMCID: PMC9720347 DOI: 10.1016/j.jbc.2022.102627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 12/12/2022] Open
Abstract
Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.
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Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA,National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA,For correspondence: Josh V. Vermaas; Michael F. Crowley; Gregg T. Beckham
| | - Michael F. Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy, Laboratory, Golden, Colorado, USA,For correspondence: Josh V. Vermaas; Michael F. Crowley; Gregg T. Beckham
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy, Laboratory, Golden, Colorado, USA,For correspondence: Josh V. Vermaas; Michael F. Crowley; Gregg T. Beckham
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17
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Characterization of lignin and lignin-derivatives from biomass. Application as expander of Lead-acid battery. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Jomura M, Yoshida R, Michalčíková L, Tláskal V, Baldrian P. Factors Controlling Dead Wood Decomposition in an Old-Growth Temperate Forest in Central Europe. J Fungi (Basel) 2022; 8:jof8070673. [PMID: 35887430 PMCID: PMC9325057 DOI: 10.3390/jof8070673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Dead wood represents an important pool of carbon and nitrogen in forest ecosystems. This source of soil organic matter has diverse ecosystem functions that include, among others, carbon and nitrogen cycling. However, information is limited on how deadwood properties such as chemical composition, decomposer abundance, community composition, and age correlate and affect decomposition rate. Here, we targeted coarse dead wood of beech, spruce, and fir, namely snags and tree trunks (logs) in an old-growth temperate forest in central Europe; measured their decomposition rate as CO2 production in situ; and analyzed their relationships with other measured variables. Respiration rate of dead wood showed strong positive correlation with acid phosphatase activity and negative correlation with lignin content. Fungal biomass (ergosterol content) and moisture content were additional predictors. Our results indicate that dead wood traits, including tree species, age, and position (downed/standing), affected dead wood chemical properties, microbial biomass, moisture condition, and enzyme activity through changes in fungal communities and ultimately influenced the decomposition rate of dead wood.
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Affiliation(s)
- Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Kanagawa, Japan;
- Correspondence:
| | - Riki Yoshida
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Kanagawa, Japan;
| | - Lenka Michalčíková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
- Department of Biology, Faculty of Science, University of Hradec Kralove, Hradecká 1285, 500-03 Hradec Králové, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
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19
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Cheng L, Wang W, Fan MZ. Characterization of in vitro stability for two processive endoglucanases as exogenous fibre biocatalysts in pig nutrition. Sci Rep 2022; 12:9135. [PMID: 35650308 PMCID: PMC9160044 DOI: 10.1038/s41598-022-13124-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Development of highly efficacious exogenous fibre degradation enzymes can enhance efficiency of dietary fibre utilization and sustainability of global pork production. The objectives of this study were to investigate in vitro stability for two processive endoglucanases, referred to as GH5-tCel5A1 and GH5-p4818Cel5_2A that were overexpressed in CLEARCOLIBL21(DE3). Three-dimensional models predicted presence of Cys residues on the catalytic site surfaces of GH5-tCel5A1 and GH5-p4818Cel5_2A; and time course experimental results shown that both cellulases were susceptible to auto-oxidation by airborne O2 and were unstable. Furthermore, we examined these endoglucanases' stability under the mimicked in vitro porcine gastric and the small intestinal pH and proteases' conditions. Eadie-Hofstee inhibition kinetic analyses showed that GH5-tCel5A1 and GH5-p4818Cel5_2A respectively lost 18 and 68% of their initial activities after 2-h incubations under the gastric conditions and then lost more than 90% of their initial activities after 2-3 h of incubations under the small intestinal conditions. Therefore, further enzyme protein engineering to improve resistance and alternatively post-fermentation enzyme processing such as coating to bypass the gastric-small intestinal environment will be required to enable these two processive endoglucanases as efficacious exogenous fibre enzymes in pig nutrition application.
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Affiliation(s)
- Laurence Cheng
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Weijun Wang
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Canadian Food Inspection Agency (CFIA) - Ontario Operation, Guelph, ON, N1G 2W1, Canada
| | - Ming Z Fan
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- One Health Institute, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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20
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Reppke MJ, Gerstner R, Windeisen-Holzhauser E, Richter K, Benz JP. Press water from the mechanical drying of Douglas-fir wood chips has multiple beneficial effects on lignocellulolytic fungi. Fungal Biol Biotechnol 2022; 9:10. [PMID: 35606847 PMCID: PMC9128199 DOI: 10.1186/s40694-022-00141-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/10/2022] [Indexed: 12/05/2022] Open
Abstract
Background The mechanical drying of wood chips is an innovative method that improves the heating value of sawmill by-products in an energy-efficient continuous process. The liquid that comes out of the wood chips as press water (PW), however, contains a variety of undissolved as well as dissolved organic substances. The disposal of the PW as wastewater would generate additional costs due to its high organic load, offsetting the benefits in energy costs associated with the enhanced heating value of the wood chips. Our research explored if the organic load in PW could be utilized as a substrate by cellulolytic filamentous fungi. Hence, using the industrially relevant Ascomycete Trichoderma reesei RUT-C30 as well as several Basidiomycete wood-rotting fungi, we examined the potential of press water obtained from Douglas-fir wood chips to be used in the growth and enzyme production media. Results The addition of PW supernatant to liquid cultures of T. reesei RUT-C30 resulted in a significant enhancement of the endoglucanase and endoxylanase activities with a substantially shortened lag-phase. A partial replacement of Ca2+, Mg2+, K+, as well as a complete replacement of Fe2+, Mn2+, Zn2+ by supplementing PW of the liquid media was achieved without negative effects on enzyme production. Concentrations of PW above 50% showed no adverse effects regarding the achievable endoglucanase activity but affected the endoxylanase activity to some extent. Exploring the enhancing potential of several individual PW components after chemical analysis revealed that the observed lag-phase reduction of T. reesei RUT-C30 was not caused by the dissolved sugars and ions, nor the wood particles in the PW sediment, suggesting that other, so far non-identified, compounds are responsible. However, also the growth rate of several basidiomycetes was significantly enhanced by the supplementation of raw PW to the agar medium. Moreover, their cultivation in liquid cultures reduced the turbidity of the PW substantially. Conclusions PW was identified as a suitable media supplement for lignocellulolytic fungi, including the cellulase and xylanase producer T. reesei RUT-C30 and several wood-degrading basidiomycetes. The possibility to replace several minerals, trace elements and an equal volume of fresh water in liquid media with PW and the ability of fungal mycelia to filter out the suspended solids is a promising way to combine biological wastewater treatment with value-adding biotechnological applications. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-022-00141-y.
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21
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Enzymatic Conversion of Different Qualities of Refined Softwood Hemicellulose Recovered from Spent Sulfite Liquor. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103207. [PMID: 35630684 PMCID: PMC9143570 DOI: 10.3390/molecules27103207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022]
Abstract
Spent sulfite liquor (SSL) from softwood processing is rich in hemicellulose (acetyl galactoglucomannan, AcGGM), lignin, and lignin-derived compounds. We investigated the effect of sequential AcGGM purification on the enzymatic bioconversion of AcGGM. SSL was processed through three consecutive purification steps (membrane filtration, precipitation, and adsorption) to obtain AcGGM with increasing purity. Significant reduction (~99%) in lignin content and modest loss (~18%) of polysaccharides was observed during purification from the least pure preparation (UFR), obtained by membrane filtration, compared to the purest preparation (AD), obtained by adsorption. AcGGM (~14.5 kDa) was the major polysaccharide in the preparations; its enzymatic hydrolysis was assessed by reducing sugar and high-performance anion-exchange chromatography analysis. The hydrolysis of the UFR preparation with Viscozyme L or Trichoderma reesei β-mannanase TrMan5A (1 mg/mL) resulted in less than ~50% bioconversion of AcGGM. The AcGGM in the AD preparation was hydrolyzed to a higher degree (~67% with TrMan5A and 80% with Viscozyme L) and showed the highest conversion rate. This indicates that SSL contains enzyme-inhibitory compounds (e.g., lignin and lignin-derived compounds such as lignosulfonates) which were successfully removed.
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22
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Cellulosic Ethanol Production Using a Dual Functional Novel Yeast. Int J Microbiol 2022; 2022:7853935. [PMID: 35295685 PMCID: PMC8920679 DOI: 10.1155/2022/7853935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Reducing the cost of cellulosic ethanol production, especially for cellulose hydrolytic enzymes, is vital to growing a sustainable and efficient cellulosic ethanol industry and bio-based economy. Using an ethanologenic yeast able to produce hydrolytic enzymes, such as Clavispora NRRL Y-50464, is one solution. NRRL Y-50464 is fast-growing and robust, and tolerates inhibitory compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) associated with lignocellulose-to-fuel conversion. It produces three forms of β-glucosidase isozymes, BGL1, BGL2, and BGL3, and ferment cellobiose as the sole carbon source. These β-glucosidases exhibited desirable enzyme kinetic parameters and high levels of enzyme-specific activity toward cellobiose and many oligosaccharide substrates. They tolerate the product inhibition of glucose and ethanol, and are stable to temperature and pH conditions. These characteristics are desirable for more efficient cellulosic ethanol production by simultaneous saccharification and fermentation. NRRL Y-50464 provided the highest cellulosic ethanol titers and conversion rates at lower cellulase loadings, using either pure cellulose or agricultural residues, as so far reported in the literature. This review summarizes NRRL Y-50464 performance on cellulosic ethanol production from refined cellulose, rice straw, and corn stover processed in various ways, in the presence or absence of furfural and HMF. This dual functional yeast has potential to serve as a prototype for the development of next-generation biocatalysts. Perspectives on continued strain development and process engineering improvements for more efficient cellulosic ethanol production from lignocellulosic materials are also discussed.
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23
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Vermaas JV, Mayne CG, Shinn E, Tajkhorshid E. Assembly and Analysis of Cell-Scale Membrane Envelopes. J Chem Inf Model 2022; 62:602-617. [PMID: 34910495 PMCID: PMC8903035 DOI: 10.1021/acs.jcim.1c01050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms─a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.
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Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401,;
| | - Christopher G. Mayne
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Shinn
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,;
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Banu Jamaldheen S, Kurade MB, Basak B, Yoo CG, Oh KK, Jeon BH, Kim TH. A review on physico-chemical delignification as a pretreatment of lignocellulosic biomass for enhanced bioconversion. BIORESOURCE TECHNOLOGY 2022; 346:126591. [PMID: 34929325 DOI: 10.1016/j.biortech.2021.126591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Effective pretreatment of lignocellulosic biomass (LCB) is one of the most important steps in biorefinery, ensuring the quality and commercial viability of the overall bioprocess. Lignin recalcitrance in LCB is a major bottleneck in biological conversion as the polymerization of lignin with hemicellulose hinders enzyme accessibility and further bioconversion to fuels and chemicals. Therefore, there is a need to delignify LCB to ease further bioprocessing. The efficiency of delignification, quality and quantity of the desired products, and generation of inhibitors depend upon the type of pretreatment employed. This review summarizes different single and integrated physicochemical pretreatments for delignification. Additionally, conditions required for effective delignification and the advantages and drawbacks of each method were evaluated. Advances in overcoming the recalcitrance of residual lignin to saccharification and the methods to recover lignin after delignification are also discussed. Efficient lignin recovery and valorization strategies provide an avenue for the sustainable lignocellulose biorefinery.
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Affiliation(s)
- Sumitha Banu Jamaldheen
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Bikram Basak
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Chang Geun Yoo
- Department of Chemical Engineering, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Kyeong Keun Oh
- Department of Chemical Engineering, Dankook University, Youngin 16890, Gyeonggi-do, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Tae Hyun Kim
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea.
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Liu T, Wang P, Tian J, Guo J, Zhu W, Jin Y, Xiao H, Song J. Polystyrene sulfonate is effective for enhancing biomass enzymatic saccharification under green liquor pretreatment in bioenergy poplar. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:10. [PMID: 35418140 PMCID: PMC8783513 DOI: 10.1186/s13068-022-02108-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/08/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Water-soluble lignin (particularly lignosulfonate, LS) has been well documented for its significance on enzymatic saccharification of lignocellulose, though the promotion mechanism has not been fully understood. Much attention has been paid to natural lignin or its derivatives. The disadvantage of using natural lignin-based polymers as promoting agents lies in the difficulty in tailor-incorporating functional groups due to their complex 3D structures. To further improve our understanding on the promotion mechanism of water-soluble lignin in the bioconversion of lignocellulose and to pursue better alternatives with different skeleton structures other than natural lignin, herein we reported a synthetic soluble linear aromatic polymer, sodium polystyrene sulfonate (PSS), to mimic LS for enhancing the efficiency of enzymatic saccharification. RESULTS The role of PSS in enzymatic saccharification of pure cellulose and green liquor-pretreated poplar (GL-P) was explored by analyzing substrate enzymatic digestibility (SED) under different addition dosages and various pH media, along with LS for comparison. At the cellulase loading of 13.3 FPU/g-glucan, the glucose yield of GL-P increased from 53% for the control to 81.5% with PSS addition of 0.1 g/g-substrate. It outperformed LS with the addition of 0.2 g/g-substrate by 6.3%. In the pH range from 4.5 to 6, PSS showed a positive effect on lignocellulose saccharification with the optimum pH at 4.8, where the most pronounced SED of GL-P was achieved. The underlying mechanism was unveiled by measuring zeta potential and using Quartz Crystal Microbalance (QCM) and Multi-parametric Surface Plasmon Resonance (MP-SPR). The results confirmed that the complexes of cellulase and PSS were conjugated and the negatively supercharged complexes reduced non-productive binding effectively along with the improved saccharification efficiency. The thickness of PSS required to block the binding sites of cellulase film was less than half of that of LS, and the PSS adlayer on cellulase film is also more hydrated and with a much lower shear modulus than LS adlayer. CONCLUSIONS PSS as LS analogue is effective for enhancing the biomass enzymatic saccharification of GL-pretreated poplar. PSS exhibited a severer inhibition on the enzymatic saccharification of pure cellulose, while a more positive effect on bioconversion of lignocellulose (GL-P) than LS. In addition, a much lower dosage is required by PSS. The dynamic enzymatic hydrolysis indicated PSS could prolong the processive activity of cellulase. The valid data stemmed from QCM and SPR expressed that PSS bound to cellulases and the as-formed complexes reduced the non-productive adsorption of cellulase onto substrate lignin more efficiently than LS due to its flexible skeleton and highly hydrated structure. Therefore, PSS is a promising alternative promoting agent for lignocellulose saccharification. From another perspective, the synthetic lignin mimics with controllable structures enable us to reach an in-depth understanding of the promotion mechanism of soluble lignins on enzymatic saccharification.
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Affiliation(s)
- Tian Liu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Peipei Wang
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Jing Tian
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiaqi Guo
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China.
| | - Wenyuan Zhu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Yongcan Jin
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
| | - Junlong Song
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China.
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Li M, Jiang B, Wu W, Wu S, Yang Y, Song J, Ahmad M, Jin Y. Current understanding and optimization strategies for efficient lignin-enzyme interaction: A review. Int J Biol Macromol 2022; 195:274-286. [PMID: 34883164 DOI: 10.1016/j.ijbiomac.2021.11.188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
From energy perspective, with abundant polysaccharides (45-85%), the renewable lignocellulosic is recognized as the 2nd generation feedstock for bioethanol and bio-based products production. Enzymatic hydrolysis is a critical pathway to yield fermentable monosaccharides from pretreated substrates of lignocellulose. Nevertheless, the lignin presence in lignocellulosic substrates leads to the low substrate enzymatic digestibility ascribed to the nonproductive adsorption. It has been reported that the water-soluble lignin (low molecular weight, sulfonated/sulfomethylated and graft polymer) enhance the rate of enzymatic digestibility, however, the catalytic mechanism of lignin-enzyme interaction remains elusive. In this review, optimization strategies for enzymatic hydrolysis based on the lignin structural modification, enzyme engineering, and different additives are critically reviewed. Lignin-enzyme interaction mechanism is also discussed (lignin and various cellulases). In addition, the mathematical models and simulation of lignin, cellulose and enzyme aims for promoting an integrated biomass-conversion process for sustainable production of value-added biofuels.
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Affiliation(s)
- Mohan Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, China
| | - Bo Jiang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, China; Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjuan Wu
- Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Shufang Wu
- Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Yiqin Yang
- Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Junlong Song
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, China; Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Mehraj Ahmad
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, China; Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Yongcan Jin
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, China; Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China.
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Lee DS, Song Y, Lee YG, Bae HJ. Comparative Evaluation of Adsorption of Major Enzymes in a Cellulase Cocktail Obtained from Trichoderma reesei onto Different Types of Lignin. Polymers (Basel) 2022; 14:polym14010167. [PMID: 35012188 PMCID: PMC8747337 DOI: 10.3390/polym14010167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 02/04/2023] Open
Abstract
Cellulase adsorption onto lignin decreases the productivity of enzymatic hydrolysis of lignocellulosic biomass. Here, adsorption of enzymes onto different types of lignin was investigated, and the five major enzymes—cellobiohydrolases (CBHs), endoglucanase (Cel7B), β-glucosidase (Cel3A), xylanase (XYNIV), and mannanase (Man5A)—in a cellulase cocktail obtained from Trichoderma reesei were individually analyzed through SDS-PAGE and zymogram assay. Lignin was isolated from woody (oak and pine lignin) and herbaceous (rice straw and kenaf lignin) plants. The relative adsorption of CBHs compared to the control was in the range of 14.15–18.61%. The carbohydrate binding motif (CBM) of the CBHs contributed to higher adsorption levels in oak and kenaf lignin, compared to those in pine and rice lignin. The adsorption of endoglucanase (Cel7B) by herbaceous plant lignin was two times higher than that of woody lignin, whereas XYNIV showed the opposite pattern. β-glucosidase (Cel3A) displayed the highest and lowest adsorption ratios on rice straw and kenaf lignin, respectively. Mannanase (Man5A) was found to have the lowest adsorption ratio on pine lignin. Our results showed that the hydrophobic properties of CBM and the enzyme structures are key factors in adsorption onto lignin, whereas the properties of specific lignin types indirectly affect adsorption.
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Affiliation(s)
- Dae-Seok Lee
- Bio-Energy Research Center, Chonnam National University, Gwangju 500-575, Korea; (D.-S.L.); (Y.S.)
| | - Younho Song
- Bio-Energy Research Center, Chonnam National University, Gwangju 500-575, Korea; (D.-S.L.); (Y.S.)
| | - Yoon-Gyo Lee
- Department of Wood Science and Landscape Architecture, Chonnam National University, Gwangju 500-757, Korea;
| | - Hyeun-Jong Bae
- Bio-Energy Research Center, Chonnam National University, Gwangju 500-575, Korea; (D.-S.L.); (Y.S.)
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Korea
- Correspondence: ; Tel.: +81-62-530-2097
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Paul M, Mohapatra S, Kumar Das Mohapatra P, Thatoi H. Microbial cellulases - An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. BIORESOURCE TECHNOLOGY 2021; 340:125710. [PMID: 34365301 DOI: 10.1016/j.biortech.2021.125710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The inherent resistance of lignocellulosic biomass makes it impervious for industrially important enzymes such as cellulases to hydrolyze cellulose. Further, the competitive absorption behavior of lignin and hemicellulose for cellulases, due to their electron-rich surfaces augments the inappropriate utilization of these enzymes. Hence, modification of the surface charge of the cellulases to reduce its non-specific binding to lignin and enhance its affinity for cellulose is an urgent necessity. Further, maintaining the stability of cellulases by the preservation of their secondary structures using immobilization techniques will also play an integral role in its industrial production. In silico approaches for increasing the catalytic activity of cellulase enzymes is also significant along with a range of substrate specificity. In addition, enhanced productivity of cellulases by tailoring the related genes through the process of genetic engineering and higher cellulase recovery after saccharification seems to be promising areas for efficient and large-scale enzyme production concepts.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India
| | - Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Bhubaneswar 751003, Odisha, India
| | - Pradeep Kumar Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India; PAKB Environment Conservation Centre, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India.
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Swetha A, ShriVigneshwar S, Gopinath KP, Sivaramakrishnan R, Shanmuganathan R, Arun J. Review on hydrothermal liquefaction aqueous phase as a valuable resource for biofuels, bio-hydrogen and valuable bio-chemicals recovery. CHEMOSPHERE 2021; 283:131248. [PMID: 34182640 DOI: 10.1016/j.chemosphere.2021.131248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Hydrothermal liquefaction (HTL) of biomass results in the formation of bio-oil, aqueous phase (HTL-AP), bio-char, and gaseous products. Safer disposal of HTL-AP is difficult on an industrial scale since it comprises low molecular acid compounds. This review provides a comprehensive note on the recent articles published on the effective usage of HTL-AP for the recovery of valuable compounds. Thermo-chemical and biological processes are the preferred techniques for the recovery of biofuel, platform chemicals from HTL-AP. From this review, it was evident that the composition of HTL-AP and product recovery are the integrated pathways, which depend on each other. Substitute as reaction medium in HTL process, growth medium for algae and microbes are the most common mode of reuse and recycle of HTL-AP. Future research is needed to depict the mechanism of HTL process when HTL-AP is used as a reaction medium on an industrial scale. Need to find a solution for the hindrance in commercializing HTL process and recovery of value-added compounds from HTL-AP from lab scale to industry level. Integrated pathways on reuse and HTL-AP recycle helps in reduced environmental concerns and sustainable production of bio-products.
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Affiliation(s)
- Authilingam Swetha
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, 603110, Tamil Nadu, India
| | - Sivakumar ShriVigneshwar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, 603110, Tamil Nadu, India
| | | | - Ramachandran Sivaramakrishnan
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rajasree Shanmuganathan
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Jayaseelan Arun
- Center for Waste Management - 'International Research Centre', Sathyabama Institute of Science and Technology, Jeppiaar Nagar (OMR), Chennai, 603119, Tamil Nadu, India.
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Yuan Y, Jiang B, Chen H, Wu W, Wu S, Jin Y, Xiao H. Recent advances in understanding the effects of lignin structural characteristics on enzymatic hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:205. [PMID: 34670604 PMCID: PMC8527784 DOI: 10.1186/s13068-021-02054-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/10/2021] [Indexed: 05/19/2023]
Abstract
Enzymatic hydrolysis of lignocellulose for bioethanol production shows a great potential to remit the rapid consumption of fossil fuels, given the fact that lignocellulose feedstocks are abundant, cost-efficient, and renewable. Lignin results in low enzymatic saccharification by forming the steric hindrance, non-productive adsorption of cellulase onto lignin, and deactivating the cellulase. In general, the non-productive binding of cellulase on lignin is widely known as the major cause for inhibiting the enzymatic hydrolysis. Pretreatment is an effective way to remove lignin and improve the enzymatic digestibility of lignocellulose. Along with removing lignin, the pretreatment can modify the lignin structure, which significantly affects the non-productive adsorption of cellulase onto lignin. To relieve the inhibitory effect of lignin on enzymatic hydrolysis, enormous efforts have been made to elucidate the correlation of lignin structure with lignin-enzyme interactions but with different views. In addition, contrary to the traditional belief that lignin inhibits enzymatic hydrolysis, in recent years, the addition of water-soluble lignin such as lignosulfonate or low molecular-weight lignin exerts a positive effect on enzymatic hydrolysis, which gives a new insight into the lignin-enzyme interactions. For throwing light on their structure-interaction relationship during enzymatic hydrolysis, the effect of residual lignin in substrate and introduced lignin in hydrolysate on enzymatic hydrolysis are critically reviewed, aiming at realizing the targeted regulation of lignin structure for improving the saccharification of lignocellulose. The review is also focused on exploring the lignin-enzyme interactions to mitigate the negative impact of lignin and reducing the cost of enzymatic hydrolysis of lignocellulose.
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Affiliation(s)
- Yufeng Yuan
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Bo Jiang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Hui Chen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Wenjuan Wu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Shufang Wu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Yongcan Jin
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China.
- Laboratory of Wood Chemistry, Nanjing Forestry University, 159 Longpan Rd, Nanjing, 210037, China.
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB, E3B 11 5A3, Canada
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Behle E, Raguin A. Stochastic model of lignocellulosic material saccharification. PLoS Comput Biol 2021; 17:e1009262. [PMID: 34516546 PMCID: PMC8460048 DOI: 10.1371/journal.pcbi.1009262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 09/23/2021] [Accepted: 07/09/2021] [Indexed: 12/03/2022] Open
Abstract
The processing of agricultural wastes towards extraction of renewable resources is recently being considered as a promising alternative to conventional biofuel production. The degradation of agricultural residues is a complex chemical process that is currently time intensive and costly. Various pre-treatment methods are being investigated to determine the subsequent modification of the material and the main obstacles in increasing the enzymatic saccharification. In this study, we present a computational model that complements the experimental approaches. We decipher how the three-dimensional structure of the substrate impacts the saccharification dynamics. We model a cell wall microfibril composed of cellulose and surrounded by hemicellulose and lignin, with various relative abundances and arrangements. This substrate is subjected to digestion by different cocktails of well characterized enzymes. The saccharification dynamics is simulated in silico using a stochastic procedure based on a Gillespie algorithm. As we additionally implement a fitting procedure that optimizes the parameters of the simulation runs, we are able to reproduce experimental saccharification time courses for corn stover. Our model highlights the synergistic action of enzymes, and confirms the linear decrease of sugar conversion when either lignin content or crystallinity of the substrate increases. Importantly, we show that considering the crystallinity of cellulose in addition to the substrate composition is essential to interpret experimental saccharification data. Finally, our findings support the hypothesis of xylan being partially crystalline. Leftover wastes generated by agriculture, such as inedible leaves and stalks of plants, represent an abundant and unexploited raw material that contains energy in the form of sugar polymers. Their breakdown and processing into bio-ethanol is recently being considered as a promising candidate for renewable fuel production. However, it is still poorly understood, how the microscopic structure and composition of plant waste materials impact their enzymatic digestion. Various experimental pre-processing methods are currently being tested to determine their effect on the material composition and structure, and the sugar conversion. In this study, we present a computational model to complement such experimental approaches. We simulate a microscopic plant fragment typically found in plant waste materials, whose structure and composition can be tailored. This fragment is then subjected to enzymatic digestion, whose dynamics is tracked in silico. The model reproduces experimentally observed time courses for plant fragments of known composition. It additionally provides new hypotheses for interpreting complex experimental results.
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Affiliation(s)
- Eric Behle
- Department of Biology, Cluster of Excellence on Plant Sciences, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf, Germany
| | - Adélaïde Raguin
- Department of Biology, Cluster of Excellence on Plant Sciences, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf, Germany
- * E-mail:
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Zhao X, Meng X, Ragauskas AJ, Lai C, Ling Z, Huang C, Yong Q. Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques. Biotechnol Adv 2021; 54:107830. [PMID: 34480987 DOI: 10.1016/j.biotechadv.2021.107830] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/07/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.
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Affiliation(s)
- Xiaoxue Zhao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA; Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chenhuan Lai
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ling
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Yong
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
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Recent Advances in the Biosynthesis of Polyhydroxyalkanoates from Lignocellulosic Feedstocks. Life (Basel) 2021; 11:life11080807. [PMID: 34440551 PMCID: PMC8398495 DOI: 10.3390/life11080807] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 12/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are biodegradable polymers that are considered able to replace synthetic plastic because their biochemical characteristics are in some cases the same as other biodegradable polymers. However, due to the disadvantages of costly and non-renewable carbon sources, the production of PHA has been lower in the industrial sector against conventional plastics. At the same time, first-generation sugar-based cultivated feedstocks as substrates for PHA production threatens food security and considerably require other resources such as land and energy. Therefore, attempts have been made in pursuit of suitable sustainable and affordable sources of carbon to reduce production costs. Thus, in this review, we highlight utilising waste lignocellulosic feedstocks (LF) as a renewable and inexpensive carbon source to produce PHA. These waste feedstocks, second-generation plant lignocellulosic biomass, such as maize stoves, dedicated energy crops, rice straws, wood chips, are commonly available renewable biomass sources with a steady supply of about 150 billion tonnes per year of global yield. The generation of PHA from lignocellulose is still in its infancy, hence more screening of lignocellulosic materials and improvements in downstream processing and substrate pre-treatment are needed in the future to further advance the biopolymer sector.
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Agrawal R, Verma A, Singhania RR, Varjani S, Di Dong C, Kumar Patel A. Current understanding of the inhibition factors and their mechanism of action for the lignocellulosic biomass hydrolysis. BIORESOURCE TECHNOLOGY 2021; 332:125042. [PMID: 33813178 DOI: 10.1016/j.biortech.2021.125042] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Biorefining of lignocellulosic biomass is a relatively new concept but it has strong potential to develop and partially replace the fossil derived fuels and myriad of value products to subsequently reduce the greenhouse gas emissions. However, the energy and cost intensive process of releasing the entrapped fermentable sugars is a major challenge for its commercialization. Various factors playing a detrimental role during enzymatic hydrolysis of biomass are inherent recalcitrance of lignocellulosic biomass, expensive enzymes, sub-optimal enzyme composition, lack of synergistic activity and enzyme inhibition caused by various inhibitors. The current study investigated the mechanism of enzyme inhibition during lignocellulosic biomass saccharification especially at high solid loadings. These inhibition factors are categorized into physio-chemical factors, water-soluble and -insoluble enzyme inhibitors, oligomers and enzyme-lignin binding. Furthermore, different approaches are proposed to alleviate the challenges and improve the enzymatic hydrolysis efficiency such as supplementation with surfactants, synergistic catalytic/non-catalytic proteins, and bioprocess modifications.
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Affiliation(s)
- Ruchi Agrawal
- The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| | - Amit Verma
- College of Basic Science and Humanities, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar - 385506 (Banaskantha), Gujarat, India
| | - Reeta Rani Singhania
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, Gujarat 382010, India
| | - Cheng Di Dong
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Anil Kumar Patel
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan.
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35
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Ing N, Deng K, Chen Y, Aulitto M, Gin JW, Pham TLM, Petzold CJ, Singer SW, Bowen B, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR. A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities. Sci Rep 2021; 11:11803. [PMID: 34083602 PMCID: PMC8175421 DOI: 10.1038/s41598-021-91181-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Lignocellulosic biomass is composed of three major biopolymers: cellulose, hemicellulose and lignin. Analytical tools capable of quickly detecting both glycan and lignin deconstruction are needed to support the development and characterization of efficient enzymes/enzyme cocktails. Previously we have described nanostructure-initiator mass spectrometry-based assays for the analysis of glycosyl hydrolase and most recently an assay for lignin modifying enzymes. Here we integrate these two assays into a single multiplexed assay against both classes of enzymes and use it to characterize crude commercial enzyme mixtures. Application of our multiplexed platform based on nanostructure-initiator mass spectrometry enabled us to characterize crude mixtures of laccase enzymes from fungi Agaricus bisporus (Ab) and Myceliopthora thermophila (Mt) revealing activity on both carbohydrate and aromatic substrates. Using time-series analysis we determined that crude laccase from Ab has the higher GH activity and that laccase from Mt has the higher activity against our lignin model compound. Inhibitor studies showed a significant reduction in Mt GH activity under low oxygen conditions and increased activities in the presence of vanillin (common GH inhibitor). Ultimately, this assay can help to discover mixtures of enzymes that could be incorporated into biomass pretreatments to deconstruct diverse components of lignocellulosic biomass.
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Affiliation(s)
- Nicole Ing
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Martina Aulitto
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W Gin
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thanh Le Mai Pham
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steve W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin Bowen
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kenneth L Sale
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anup K Singh
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,University of California, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Hillman ET, Li M, Hooker CA, Englaender JA, Wheeldon I, Solomon KV. Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus. Biotechnol Prog 2021; 37:e3172. [PMID: 33960738 DOI: 10.1002/btpr.3172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/06/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.
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Affiliation(s)
- Ethan T Hillman
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA
| | - Mengwan Li
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Casey A Hooker
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| | - Jacob A Englaender
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Ian Wheeldon
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Kevin V Solomon
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
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37
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Oates NC, Abood A, Schirmacher AM, Alessi AM, Bird SM, Bennett JP, Leadbeater DR, Li Y, Dowle AA, Liu S, Tymokhin VI, Ralph J, McQueen-Mason SJ, Bruce NC. A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1. Proc Natl Acad Sci U S A 2021; 118:e2008888118. [PMID: 33903229 PMCID: PMC8106297 DOI: 10.1073/pnas.2008888118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lignocellulose, the structural component of plant cells, is a major agricultural byproduct and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities, and currently, efficient transformation requires expensive pretreatments and high loadings of enzymes. Here, we report on a fungus from the Parascedosporium genus, isolated from a wheat-straw composting community, that secretes a large and diverse array of carbohydrate-active enzymes (CAZymes) when grown on lignocellulosic substrates. We describe an oxidase activity that cleaves the major β-ether units in lignin, thereby releasing the flavonoid tricin from monocot lignin and enhancing the digestion of lignocellulose by polysaccharidase mixtures. We show that the enzyme, which holds potential for the biorefining industry, is widely distributed among lignocellulose-degrading fungi from the Sordariomycetes phylum.
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Affiliation(s)
- Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Alexandra M Schirmacher
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Anna M Alessi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Susannah M Bird
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Joseph P Bennett
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Sarah Liu
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - Vitaliy I Tymokhin
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom;
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Ning P, Yang G, Hu L, Sun J, Shi L, Zhou Y, Wang Z, Yang J. Recent advances in the valorization of plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:102. [PMID: 33892780 PMCID: PMC8063360 DOI: 10.1186/s13068-021-01949-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/07/2021] [Indexed: 05/28/2023]
Abstract
Plant biomass is a highly abundant renewable resource that can be converted into several types of high-value-added products, including chemicals, biofuels and advanced materials. In the last few decades, an increasing number of biomass species and processing techniques have been developed to enhance the application of plant biomass followed by the industrial application of some of the products, during which varied technologies have been successfully developed. In this review, we summarize the different sources of plant biomass, the evolving technologies for treating it, and the various products derived from plant biomass. Moreover, the challenges inherent in the valorization of plant biomass used in high-value-added products are also discussed. Overall, with the increased use of plant biomass, the development of treatment technologies, and the solution of the challenges raised during plant biomass valorization, the value-added products derived from plant biomass will become greater in number and more valuable.
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Affiliation(s)
- Peng Ning
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lihong Hu
- Institute of Chemical Industry of Forest Products, Key Laboratory of Biomass Energy and Material, CAF, Nanjing, China
| | - Jingxin Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Lina Shi
- Agricultural Integrated Service Center of Zhuyouguan, Longkou, Yantai, China
| | - Yonghong Zhou
- Institute of Chemical Industry of Forest Products, Key Laboratory of Biomass Energy and Material, CAF, Nanjing, China
| | - Zhaobao Wang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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Understanding the dissolution of softwood lignin in ionic liquid and water mixed solvents. Int J Biol Macromol 2021; 182:402-412. [PMID: 33838189 DOI: 10.1016/j.ijbiomac.2021.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/22/2022]
Abstract
Lignin is the most abundant heterogeneous aromatic polymer on earth to produce a large number of value-added chemicals. Besides, the separation of lignin from the lignocellulosic biomass is essential for cellulosic biofuel production. For the first time, we report a cosolvent-based approach to understand the dissolution of lignin with 61 guaiacyl subunits at the molecular level. Atomistic molecular dynamics simulations of the lignin were performed in 0%, 20%, 50%, 80%, and 100% 1-Ethyl-3-Methylimidazolium Acetate (EmimOAc) systems. The lignin structure was significantly destabilized in both 50%, and 80% EmimOAc cosolvents, and pure EmimOAc systems leading to the breakdown of intrachain hydrogen bonds. Lignin-OAc and lignin-water hydrogen bonds were formed with increasing EmimOAc concentration, signifying the dissolution process. The OAc anions mostly solvated the alkyl chains and hydroxy groups of lignin. Besides, the imidazolium head of Emim cations contributed to solvation of methoxy groups and hydroxy groups, whereas ethyl tail interacted with the benzene ring of guaiacyl subunits. Effective dissolution was obtained in both the 50% and 80% EmimOAc cosolvent systems. Overall, our study presents a molecular view of the lignin dissolution focusing on the role of both cation and anion, which will help to design efficient cosolvent-based methods for lignin dissolution.
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40
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Patri AS, Mohan R, Pu Y, Yoo CG, Ragauskas AJ, Kumar R, Kisailus D, Cai CM, Wyman CE. THF co-solvent pretreatment prevents lignin redeposition from interfering with enzymes yielding prolonged cellulase activity. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:63. [PMID: 33750435 PMCID: PMC7944909 DOI: 10.1186/s13068-021-01904-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/16/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Conventional aqueous dilute sulfuric acid (DSA) pretreatment of lignocellulosic biomass facilitates hemicellulose solubilization and can improve subsequent enzymatic digestibility of cellulose to fermentable glucose. However, much of the lignin after DSA pretreatment either remains intact within the cell wall or readily redeposits back onto the biomass surface. This redeposited lignin has been shown to reduce enzyme activity and contribute to rapid enzyme deactivation, thus, necessitating significantly higher enzyme loadings than deemed economical for biofuel production from biomass. RESULTS In this study, we demonstrate how detrimental lignin redeposition on biomass surface after pretreatment can be prevented by employing Co-solvent Enhanced Lignocellulosic Fractionation (CELF) pretreatment that uses THF-water co-solvents with dilute sulfuric acid to solubilize lignin and overcome limitations of DSA pretreatment. We first find that enzymatic hydrolysis of CELF-pretreated switchgrass can sustain a high enzyme activity over incubation periods as long as 5 weeks with enzyme doses as low as 2 mg protein/g glucan to achieve 90% yield to glucose. A modified Ninhydrin-based protein assay revealed that the free-enzyme concentration in the hydrolysate liquor, related to enzyme activity, remained unchanged over long hydrolysis times. DSA-pretreated switchgrass, by contrast, had a 40% drop in free enzymes in solution during incubation, providing evidence of enzyme deactivation. Furthermore, measurements of enzyme adsorption per gram of lignin suggested that CELF prevented lignin redeposition onto the biomass surface, and the little lignin left in the solids was mostly integral to the original lignin-carbohydrate complex (LCC). Scanning electron micrographs and NMR characterization of lignin supported this observation. CONCLUSIONS Enzymatic hydrolysis of solids from CELF pretreatment of switchgrass at low enzyme loadings was sustained for considerably longer times and reached higher conversions than for DSA solids. Analysis of solids following pretreatment and enzymatic hydrolysis showed that prolonged cellulase activity could be attributed to the limited lignin redeposition on the biomass surface making more enzymes available for hydrolysis of more accessible glucan.
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Affiliation(s)
- Abhishek S Patri
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, 1084 Columbia Ave, Riverside, CA, 92507, USA
| | - Ramya Mohan
- Materials Science & Engineering Program, Bourns College of Engineering, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Yunqiao Pu
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Chang G Yoo
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Dept. of Paper and Bioprocess Engineering, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, USA
| | - Arthur J Ragauskas
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Rajeev Kumar
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, 1084 Columbia Ave, Riverside, CA, 92507, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
| | - David Kisailus
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
- Materials Science & Engineering Program, Bourns College of Engineering, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Charles M Cai
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, 1084 Columbia Ave, Riverside, CA, 92507, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA
| | - Charles E Wyman
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA.
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA.
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, 1084 Columbia Ave, Riverside, CA, 92507, USA.
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, 37831, USA.
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41
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Wang J, Xu Y, Meng X, Pu Y, Ragauskas A, Zhang J. Production of xylo-oligosaccharides from poplar by acetic acid pretreatment and its impact on inhibitory effect of poplar lignin. BIORESOURCE TECHNOLOGY 2021; 323:124593. [PMID: 33387707 DOI: 10.1016/j.biortech.2020.124593] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Recently, efficient production of xylo-oligosaccharides (XOS) from poplar by acetic acid (AA) pretreatment was developed; but the effect of residual lignin on subsequent cellulase hydrolysis was unclear. Herein, XOS was produced from poplar by AA pretreatment and the effect of AA pretreatment on lignin inhibition to cellulase hydrolysis was investigated. The results indicated that a high XOS yield of 55.8% was obtained, and the inhibition degree of lignin in poplar increased from 1.0% to 6.8% after AA pretreatment. Lignin was acetylated and its molecular weight decreased from 12,211 to 2871 g/mol after AA pretreatment. The increase of S/G ratio, phenolic hydroxyl, and condensed units of lignin after AA pretreatment might be reasons for this intensified inhibition. The results advanced our understanding of the structural and inhibitory properties of lignin after production of XOS from poplar with AA pretreatment, and provided references for efficient cellulase hydrolysis of poplar after AA pretreatment.
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Affiliation(s)
- Jinye Wang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yong Xu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996-2200, USA
| | - Yunqiao Pu
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA
| | - Arthur Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996-2200, USA; Joint Institute for Biological Sciences, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA
| | - Junhua Zhang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China; Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing 210037, China.
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42
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Keanini RG, Dahlberg J, Tkacik PT. On the physical mechanisms underlying single molecule dynamics in simple liquids. Sci Rep 2021; 11:2528. [PMID: 33510369 PMCID: PMC7843658 DOI: 10.1038/s41598-021-82112-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/29/2020] [Indexed: 12/01/2022] Open
Abstract
Physical arguments and comparisons with published experimental data suggest that in simple liquids: (i) single-molecule-scale viscous forces are produced by temperature-dependent London dispersion forces, (ii) viscosity decay with increasing temperature reflects electron cloud compression and attendant suppression of electron screening, produced by increased nuclear agitation, and (iii) temperature-dependent self-diffusion is driven by a narrow band of phonon frequencies lying at the low-frequency end of the solid-state-like phonon spectrum. The results suggest that collision-induced electron cloud distortion plays a decisive role in single molecule dynamics: (i) electron cloud compression produces short-lived repulsive states and single molecule, self-diffusive hops, while (ii) shear-induced distortion generates viscosity and single-molecule-scale viscous drag. The results provide new insight into nonequilibrium molecular dynamics in nonpolar, nonmetallic liquids.
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Affiliation(s)
- Russell G Keanini
- Department of Mechanical Engineering, University of North Carolina at Charlotte, Charlotte, 28078, USA.
| | - Jerry Dahlberg
- Department of Mechanical Engineering, University of North Carolina at Charlotte, Charlotte, 28078, USA
| | - Peter T Tkacik
- Department of Mechanical Engineering, University of North Carolina at Charlotte, Charlotte, 28078, USA
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43
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A steady-state approach for inhibition of heterogeneous enzyme reactions. Biochem J 2020; 477:1971-1982. [PMID: 32391552 DOI: 10.1042/bcj20200083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/02/2023]
Abstract
The kinetic theory of enzymes that modify insoluble substrates is still underdeveloped, despite the prevalence of this type of reaction both in vivo and industrial applications. Here, we present a steady-state kinetic approach to investigate inhibition occurring at the solid-liquid interface. We propose to conduct experiments under enzyme excess (E0 ≫ S0), i.e. the opposite limit compared with the conventional Michaelis-Menten framework. This inverse condition is practical for insoluble substrates and elucidates how the inhibitor reduces enzyme activity through binding to the substrate. We claim that this type of inhibition is common for interfacial enzyme reactions because substrate accessibility is low, and we show that it can be analyzed by experiments and rate equations that are analogous to the conventional approach, except that the roles of enzyme and substrate have been swapped. To illustrate the approach, we investigated the major cellulases from Trichoderma reesei (Cel6A and Cel7A) acting on insoluble cellulose. As model inhibitors, we used catalytically inactive variants of Cel6A and Cel7A. We made so-called inverse Michaelis-Menten curves at different concentrations of inhibitors and found that a new rate equation accounted well for the data. In most cases, we found a mixed type of surface-site inhibition mechanism, and this probably reflected that the inhibitor both competed with the enzyme for the productive binding-sites (competitive inhibition) and hampered the processive movement on the surface (uncompetitive inhibition). These results give new insights into the complex interplay of Cel7A and Cel6A on cellulose and the approach may be applicable to other heterogeneous enzyme reactions.
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44
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Aguilera-Segura SM, Di Renzo F, Mineva T. Molecular Insight into the Cosolvent Effect on Lignin-Cellulose Adhesion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:14403-14416. [PMID: 33202139 DOI: 10.1021/acs.langmuir.0c02794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding and controlling the physical adsorption of lignin compounds on cellulose pulp are key parameters in the successful optimization of organosolv processes. The effect of binary organic-aqueous solvents on the coordination of lignin to cellulose was studied with molecular dynamics simulations, considering ethanol and acetonitrile to be organic cosolvents in aqueous solutions in comparison to their monocomponent counterparts. The structures of the solvation shells around cellulose and lignin and the energetics of lignin-cellulose adhesion indicate a more effective disruption of lignin-cellulose binding by binary solvents. The synergic effect between solvent components is explained by their preferential interactions with lignin-cellulose complexes. In the presence of pure water, long-lasting H-bonds in the lignin-cellulose complex are observed, promoted by the nonfavorable interactions of lignin with water. Ethanol and acetonitrile compete with water and lignin for cellulose oxygen binding sites, causing a nonlinear decrease in the lignin-cellulose interactions with the amount of the organic component. This effect is modulated by the water exclusion from the cellulose solvation shell by the organic solvent component. The amount and rate of water exclusion depend on the type of organic cosolvent and its concentration.
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Affiliation(s)
| | | | - Tzonka Mineva
- ICGM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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45
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Grossman AB, Rice KC, Vermerris W. Lignin solvated in zwitterionic Good's buffers displays antibacterial synergy against
Staphylococcus aureus
. J Appl Polym Sci 2020. [DOI: 10.1002/app.49107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Adam B. Grossman
- Department of Microbiology & Cell Science IFAS, University of Florida Gainesville Florida, USA
| | - Kelly C. Rice
- Department of Microbiology & Cell Science IFAS, University of Florida Gainesville Florida, USA
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science IFAS, University of Florida Gainesville Florida, USA
- UF Genetics Institute, University of Florida Gainesville Florida
- Florida Center for Renewable Chemicals and Fuels University of Florida Gainesville Florida
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46
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Jiménez-Villota DS, Acosta-Pavas JC, Betancur-Ramírez KJ, Ruiz-Colorado AA. Modeling and Kinetic Parameter Estimation of the Enzymatic Hydrolysis Process of Lignocellulosic Materials for Glucose Production. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c03047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- David Sebastián Jiménez-Villota
- Departamento de Procesos y Energı́a, Facultad de Minas, Universidad Nacional de Colombia—Sede Medellı́n, Medellı́n 050034, Colombia
| | - Juan Camilo Acosta-Pavas
- Departamento de Procesos y Energı́a, Facultad de Minas, Universidad Nacional de Colombia—Sede Medellı́n, Medellı́n 050034, Colombia
| | - Kelly Johana Betancur-Ramírez
- Departamento de Procesos y Energı́a, Facultad de Minas, Universidad Nacional de Colombia—Sede Medellı́n, Medellı́n 050034, Colombia
| | - Angela Adriana Ruiz-Colorado
- Departamento de Procesos y Energı́a, Facultad de Minas, Universidad Nacional de Colombia—Sede Medellı́n, Medellı́n 050034, Colombia
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47
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Effects of Biosurfactants on Enzymatic Saccharification and Fermentation of Pretreated Softwood. Molecules 2020; 25:molecules25163559. [PMID: 32764287 PMCID: PMC7465028 DOI: 10.3390/molecules25163559] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/21/2022] Open
Abstract
The enzymatic hydrolysis of cellulose is inhibited by non-productive adsorption of cellulases to lignin, and that is particularly problematic with lignin-rich materials such as softwood. Although conventional surfactants alleviate non-productive adsorption, using biosurfactants in softwood hydrolysis has not been reported. In this study, the effects of four biosurfactants, namely horse-chestnut escin, Pseudomonas aeruginosa rhamnolipid, and saponins from red and white quinoa varieties, on the enzymatic saccharification of steam-pretreated spruce were investigated. The used biosurfactants improved hydrolysis, and the best-performing one was escin, which led to cellulose conversions above 90%, decreased by around two-thirds lignin inhibition of Avicel hydrolysis, and improved hydrolysis of pretreated spruce by 24%. Red quinoa saponins (RQS) addition resulted in cellulose conversions above 80%, which was around 16% higher than without biosurfactants, and it was more effective than adding rhamnolipid or white quinoa saponins. Cellulose conversion improved with the increase in RQS addition up to 6 g/100 g biomass, but no significant changes were observed above that dosage. Although saponins are known to inhibit yeast growth, no inhibition of Saccharomyces cerevisiae fermentation of hydrolysates produced with RQS addition was detected. This study shows the potential of biosurfactants for enhancing the enzymatic hydrolysis of steam-pretreated softwood.
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48
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Fan S, Sun Y, Ter Heijne A, Chen WS, Buisman CJN. Effect of nitrogen, phosphorus and pH on biological wood oxidation at 42 °C. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138569. [PMID: 32344251 DOI: 10.1016/j.scitotenv.2020.138569] [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: 02/17/2020] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Biological wood oxidation (BWO) is proposed as a cleaner alternative to wood combustion for heat production and wood waste management. Currently, BWO is not extensively studied and little is known about it. Nevertheless, given the composition of wood residues, which is dominated by carbon, nutrient availability may become a limiting factor during BWO. Our objective was to study the nutrition requirements for sustaining the BWO. For this purpose, three different factors including nitrogen addition, phosphorus addition and pH, were studied. Oxygen consumption and mass loss were monitored and used to evaluate the impact of nutrition on BWO and to calculate the theoretical heat production. The result showed that nitrogen addition at a relatively low level (2.5-10 mg/g) enhanced the cumulative oxygen consumption by 60-124% and mass loss by 28-95%, when compared with the BWO without nitrogen addition. The highest nitrogen addition examined in this research (20 mg/g), on the other hand, did not enhance BWO. Different phosphorus addition (0.5-5 mg/g) and pH (4-6) had little impacts on BWO. The highest theoretical heat production rate (0.63 W/kg dry wood biomass) was achieved using 2.5 mg/g nitrogen addition with a 95-day incubation. This suggests that nitrogen addition is required and able to sustain BWO. Besides, the cumulative oxygen consumption showed a good linear relationship with mass loss. This study provides the first indication on the effective quantify of nitrogen addition for enhancing BWO, which contributes to the selection of nutrient source for BWO in future studies.
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Affiliation(s)
- Shiyang Fan
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Yue Sun
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Annemiek Ter Heijne
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Wei-Shan Chen
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Cees J N Buisman
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, Leeuwarden, the Netherlands
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49
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Enzymes to unravel bioproducts architecture. Biotechnol Adv 2020; 41:107546. [PMID: 32275940 DOI: 10.1016/j.biotechadv.2020.107546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022]
Abstract
Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materials, in both food and non-food bioprocesses. This review details the global strategy and presents the most recent investigations to prepare and use enzymes as relevant probes, with a focus on glycoside-hydrolases involved in plant deconstruction and proteases and lipases involved in food digestion. First, to expand the enzyme repertoire to fit bioproduct complexity, novel enzymes are mined from biodiversity and can be artificially engineered. Enzymes are further characterized by exploring sequence/structure/dynamics/function relationships together with the environmental factors influencing enzyme interactions with their substrates. Then, the most advanced experimental and theoretical approaches developed for exploring bioproducts at various scales (from nanometer to millimeter) using active and inactive enzymes as probes are illustrated. Overall, combining multimodal and multiscale approaches brings a better understanding of native-form or transformed bioproduct architecture and composition, and paves the way to mainstream the use of enzymes as probes.
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50
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Yoo CG, Meng X, Pu Y, Ragauskas AJ. The critical role of lignin in lignocellulosic biomass conversion and recent pretreatment strategies: A comprehensive review. BIORESOURCE TECHNOLOGY 2020; 301:122784. [PMID: 31980318 DOI: 10.1016/j.biortech.2020.122784] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 05/19/2023]
Abstract
Heterogeneity and rigidity of lignocellulose causing resistance to its deconstruction have provided technical and economic challenges in the current biomass conversion processes. Lignin has been considered as a crucial recalcitrance component in biomass utilization. An in-depth understanding of lignin properties and their influences on biomass conversion can provide clues to improve biomass utilization. Also, utilization of lignin can significantly increase the economic viability of biorefinery. Recent lignin-targeting pretreatments have aimed not only to overcome recalcitrance for biomass conversion but also to selectively fractionate lignin for lignin valorization. Numerous studies have been conducted in biomass characteristics and conversion technologies, and the role of lignin is critical for lignin valorization and biomass pretreatment development. This review provides a comprehensive review of lignin-related biomass characteristics, the impact of lignin on the biological conversion of biomass, and recent lignin-targeting pretreatment strategies. The desired lignin properties in biorefinery and future pretreatment directions are also discussed.
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Affiliation(s)
- Chang Geun Yoo
- Department of Paper and Bioprocess Engineering, State University of New York - College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996-2200, USA
| | - Yunqiao Pu
- Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA; Center for Bioenergy Innovation (CBI), Joint Institute for Biological Sciences, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996-2200, USA; Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA; Center for Bioenergy Innovation (CBI), Joint Institute for Biological Sciences, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA; Department of Forestry, Wildlife and Fisheries, Center of Renewable Carbon, The University of Tennessee, Institute of Agriculture, Knoxville, TN 37996-2200, USA.
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