1
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Ashoor S, Mathew GM, Sukumaran RK. Rice straw hydrolysis using in-situ produced enzymes: Feedstock influences fungal enzyme composition and hydrolytic efficiency. Prep Biochem Biotechnol 2024; 54:967-973. [PMID: 38327105 DOI: 10.1080/10826068.2024.2312458] [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] [Indexed: 02/09/2024]
Abstract
Trichoderma reesei RUT-C30 was cultivated on differentially pretreated rice straw and pure cellulose as a carbon source/inducer for cellulase production, and the enzymes were evaluated for hydrolysis of sequential acid and alkali pretreated rice straw. Growth on pretreated rice straw enhanced protein secretion and cellulase activities compared to pure cellulose as a carbon source. The yield of cellulolytic enzymes was higher for alkali pretreated rice straw (ALP-RS), while H2O2-treated (HP-RS) could not induce cellulases to a larger level compared to pure cellulose. Protein concentration was 3.5-fold higher on ALP-RS as compared to pure cellulose, with a maximum filter-paper cellulase (FPase) activity of 1.76 IU/ml and carboxy-methyl cellulase (CMCase) activity of 40.16 IU/ml (2.18 fold higher). Beta-glucosidase (BGL) activity was more or less the same with the different substrates and supplementation of heterologous BGL could result in a quantum jump in hydrolytic efficiencies, which in the case of ALP-RS induced enzymes was 34% (increased from 69.26% to 92.51%). The use of lignocellulosic biomass (LCB) itself as a substrate for the production of cellulase is advantageous not only in terms of raw material costs but also for obtaining a more suitable enzyme profile for biomass hydrolysis.
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Affiliation(s)
- Selim Ashoor
- Department of Agricultural Microbiology, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Gincy Marina Mathew
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, India
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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2
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Lojananan N, Cheirsilp B, Intasit R, Billateh A, Srinuanpan S, Suyotha W, Boonsawang P. Successive process for efficient biovalorization of Brewers' spent grain to lignocellulolytic enzymes and lactic acid production through simultaneous saccharification and fermentation. BIORESOURCE TECHNOLOGY 2024; 397:130490. [PMID: 38403168 DOI: 10.1016/j.biortech.2024.130490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
This study aimed to increase the value of brewers' spent grain (BSG) by using it as feedstock to produce lignocellulolytic enzymes and lactic acid (LA). Twenty-two fungal strains were screened for lignocellulolytic enzyme production from BSG. Among them, Trichoderma sp. showed the highest cellulase activity (35.84 ± 0.27 U/g-BSG) and considerably high activities of xylanase (599.61 ± 23.09 U/g-BSG) and β-glucosidase (16.97 ± 0.77 U/g-BSG) under successive solid-state and submerged fermentation. The processes were successfully scaled up in a bioreactor. The enzyme cocktail was recovered and characterized. The maximum cellulase and xylanase activities were found at pH 5.0 and 50 °C, and the activities were highly stable at pH 4-8 and 30-50 °C. The enzyme cocktail was applied in simultaneous saccharification and fermentation of acid-pretreated BSG for LA production. The maximum LA obtained was 59.3 ± 1.0 g/L. This study has shown the efficient biovalorization of BSG, and this approach may also be applicable to other agro-industrial wastes.
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Affiliation(s)
- Nattha Lojananan
- Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources, International Program of Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Benjamas Cheirsilp
- Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources, International Program of Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
| | - Rawitsara Intasit
- Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources, International Program of Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Asma Billateh
- Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources, International Program of Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Sirasit Srinuanpan
- Center of Excellence of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wasana Suyotha
- Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources, International Program of Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Piyarat Boonsawang
- Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources, International Program of Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
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3
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Mou L, Pan R, Liu Y, Jiang W, Zhang W, Jiang Y, Xin F, Jiang M. Isolation of a newly Trichoderma asperellum LYS1 with abundant cellulase-hemicellulase enzyme cocktail for lignocellulosic biomass degradation. Enzyme Microb Technol 2023; 171:110318. [PMID: 37683573 DOI: 10.1016/j.enzmictec.2023.110318] [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: 03/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
As the most abundant and renewable natural resource in the world, lignocellulose is a promising alternative to fossil energy to relieve environmental concerns and resource depletion. However, due to its recalcitrant structure, strains with efficient degradation capability still need exploring. In this study, a fungus was successfully isolated from decayed wood and named as Trichoderma asperellum LYS1 by phylogenetic and draft genomic analysis. The further investigations showed that strain LYS1 had an outstanding performance on lignocellulose degradation, especially for hemicellulose-rich biomass. After the analysis of encoded CAZymes, mainly on GH family, a large amount of genes coding β-glucosidase and xylanase may contribute to the high degradation of cellulose and hemicellulose. Collectively, the results generated in this study demonstrated that T. asperellum LYS1 is a potential cell factory for lignocellulose biorefinery.
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Affiliation(s)
- Lu Mou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Runze Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Yansong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu Academy of Chemical Inherent Safety, Nanjing 211800, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu Academy of Chemical Inherent Safety, Nanjing 211800, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu Academy of Chemical Inherent Safety, Nanjing 211800, PR China
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4
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Zhang Y, Wang R, Liu L, Wang E, Yang J, Yuan H. Distinct lignocellulolytic enzymes produced by Trichoderma harzianum in response to different pretreated substrates. BIORESOURCE TECHNOLOGY 2023; 378:128990. [PMID: 37003454 DOI: 10.1016/j.biortech.2023.128990] [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: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
In order to optimize the composition of enzyme cocktail for improving the hydrolytic efficiency of lignocellulose, different substrates were tested as inducers for producing lignocellulolytic enzymes by Trichoderma harzianum EM0925 in this study. As results, ultrafine grinding or steam explosion pretreated substrates can induce T. harzianum EM0925 to secret holo lignocellulolytic enzymes; acid treated substrate can induce cellobiohydrolase; while alkali or sodium chlorite treated substrates can induce β-xylosidase specifically. Furthermore, the combination of enzyme cocktails with different hydrolysis characteristics can further improve the hydrolysis efficiency, since 100% yields of glucose and xylose were obtained simultaneously from ultrafine grinding treated corn stover at low enzyme dosage (1.2 mg proteins/g substrate). This study for the first time demonstrated an effective solution that specific-pretreated substrates can be used as inducers for specific enzyme production by T. harzianum, which provided new idea and potential strategy for the construction of highly-efficient lignocellulolytic enzyme cocktails.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China; Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Ruonan Wang
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liang Liu
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jinshui Yang
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China.
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5
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Rosolen RR, Horta MAC, de Azevedo PHC, da Silva CC, Sforca DA, Goldman GH, de Souza AP. Whole-genome sequencing and comparative genomic analysis of potential biotechnological strains of Trichoderma harzianum, Trichoderma atroviride, and Trichoderma reesei. Mol Genet Genomics 2023; 298:735-754. [PMID: 37017807 DOI: 10.1007/s00438-023-02013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/24/2023] [Indexed: 04/06/2023]
Abstract
Trichoderma atroviride and Trichoderma harzianum are widely used as commercial biocontrol agents against plant diseases. Recently, T. harzianum IOC-3844 (Th3844) and T. harzianum CBMAI-0179 (Th0179) demonstrated great potential in the enzymatic conversion of lignocellulose into fermentable sugars. Herein, we performed whole-genome sequencing and assembly of the Th3844 and Th0179 strains. To assess the genetic diversity within the genus Trichoderma, the results of both strains were compared with strains of T. atroviride CBMAI-00020 (Ta0020) and T. reesei CBMAI-0711 (Tr0711). The sequencing coverage value of all genomes evaluated in this study was higher than that of previously reported genomes for the same species of Trichoderma. The resulting assembly revealed total lengths of 40 Mb (Th3844), 39 Mb (Th0179), 36 Mb (Ta0020), and 32 Mb (Tr0711). A genome-wide phylogenetic analysis provided details on the relationships of the newly sequenced species with other Trichoderma species. Structural variants revealed genomic rearrangements among Th3844, Th0179, Ta0020, and Tr0711 relative to the T. reesei QM6a reference genome and showed the functional effects of such variants. In conclusion, the findings presented herein allow the visualization of genetic diversity in the evaluated strains and offer opportunities to explore such fungal genomes in future biotechnological and industrial applications.
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Affiliation(s)
- Rafaela Rossi Rosolen
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil
| | - Maria Augusta Crivelente Horta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Paulo Henrique Campiteli de Azevedo
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Danilo Augusto Sforca
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Gustavo Henrique Goldman
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil.
- Department of Plant Biology, Institute of Biology, UNICAMP, Cidade Universitária Zeferino Vaz, Rua Monteiro Lobato, Campinas, SP, Brazil.
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Naitam MG, Tomar GS, Kaushik R. Optimization and production of holocellulosic enzyme cocktail from fungi Aspergillus nidulans under solid-state fermentation for the production of poly(3-hydroxybutyrate). Fungal Biol Biotechnol 2022; 9:17. [PMID: 36527155 PMCID: PMC9758824 DOI: 10.1186/s40694-022-00147-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022] Open
Abstract
The production of petroleum-based plastics increased dramatically following industrialization. Because of multifaceted properties such as durability, thermostability, water resistance, and many others, these plastics have become an indispensable part of daily life. However, while improving people's quality of life, indiscriminate use of plastics has caused pollution and raised environmental concerns. To address this situation and reduce environmental risks, microbially produced biopolymers such as poly-3-hydroxyalkanoates can be used to make bioplastics that are completely biodegradable under normal environmental conditions. At the moment, the cost of bioplastic production is high when compared to petroleum-based plastics, so alternate strategies for making the bioplastic process economical are urgently needed. Agricultural waste is abundant around the world and can be efficiently used as a low-cost renewable feedstock after pretreatment and enzymatic hydrolysis. Fungi are well known as primary degraders of lignocellulosic waste, and this property was used in the current study to enzymatically hydrolyze the pretreated paddy straw for the production of reducing sugars, which were then used in the microbial fermentation for the production of PHB. In this study, Aspergillus nidulans was used to advance a low-cost and efficient enzyme hydrolysis system for the generation of reducing sugars from lignocellulosic biomass. For the production of the holocellulosic enzyme complex, the fungus was grown on wheat straw with Reese mineral medium as a wetting agent. After 216 h of solid-state fermentation at 30 °C, pH 6.0, the enzyme extract from A. nidulans demonstrated the highest activity, CMCase 68.58 (± 0.55), FPase 12.0 (± 0.06), Xylanase 27.17 (± 0.83), and β-glucosidase 1.89 (± 0.037). The initial pH, incubation temperature, and time all had a significant impact on final enzyme activity. Enzymatic hydrolysis of pretreated paddy straw produced reducing sugars (8.484 to 30.91 gL-1) that were then used to produce poly(3-hydroxybutyrate) using halophilic bacterial isolates. Burkholderia gladioli 2S4R1 and Bacillus cereus LB7 accumulated 26.80% and 20.47% PHB of the cell dry weight, respectively. This suggests that the holocellulosic enzyme cocktail could play a role in the enzymatic hydrolysis of lignocellulosic materials and the production of PHA from less expensive feedstocks such as agricultural waste.
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Affiliation(s)
- Mayur G. Naitam
- grid.418196.30000 0001 2172 0814Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Govind Singh Tomar
- grid.418196.30000 0001 2172 0814Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Rajeev Kaushik
- grid.418196.30000 0001 2172 0814Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Integrating 1G with 2G Bioethanol Production by Using Distillers’ Dried Grains with Solubles (DDGS) as the Feedstock for Lignocellulolytic Enzyme Production. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
First-generation (1G) bioethanol is one of the most used liquid biofuels in the transport industry. It is generated by using sugar- or starch-based feedstocks, while second-generation (2G) bioethanol is generated by using lignocellulosic feedstocks. Distillers’ dried grains with solubles (DDGS) is a byproduct of first-generation bioethanol production with a current annual production of 22.6 million tons in the USA. DDGS is rich in fiber and valuable nutrients contents, which can be used to produce lignocellulolytic enzymes such as cellulases and hemicellulases for 2G bioethanol production. However, DDGS needs a pretreatment method such as dilute acid, ammonia soaking, or steam hydrolysis to release monosaccharides and short-length oligosaccharides as fermentable sugars for use in microbial media. These fermentable sugars can then induce microbial growth and enzyme production compared to only glucose or xylose in the media. In addition, selection of one or more suitable microbial strains, which work best with the DDGS for enzyme production, is also needed. Media optimization and fermentation process optimization strategies can then be applied to find the optimum conditions for the production of cellulases and hemicellulases needed for 2G bioethanol production. Therefore, in this review, a summary of all such techniques is compiled with a special focus on recent findings obtained in previous pieces of research conducted by the authors and by others in the literature. Furthermore, a comparison of such techniques applied to other feedstocks and process improvement strategies is also provided. Overall, dilute acid pretreatment is proven to be better than other pretreatment methods, and fermentation optimization strategies can enhance enzyme production by considerable folds with a suitable feedstock such as DDGS. Future studies can be further enhanced by the technoeconomic viability of DDGS as the on-site enzyme feedstock for the manufacture of second-generation bioethanol (2G) in first-generation (1G) ethanol plants, thus bridging the two processes for the efficient production of bioethanol using corn or other starch-based lignocellulosic plants.
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Shangdiar S, Lin YC, Ponnusamy VK, Wu TY. Pretreatment of lignocellulosic biomass from sugar bagasse under microwave assisted dilute acid hydrolysis for biobutanol production. BIORESOURCE TECHNOLOGY 2022; 361:127724. [PMID: 35917859 DOI: 10.1016/j.biortech.2022.127724] [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: 06/19/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Alternative renewable energy sources are the future potential energy that will benefit the country's overall energy shortage and demand. The efficient biofuel production depends on the viability of the raw material used. The holistic approach of this study is to establish an integrated bioprocess from lignocellulosic material for biofuel synthesis. Sugar bagasse as one of the waste material, can be economically process for sugar extraction used in biofuel production. In this study, the optimum saccharification rate obtained was 43.62% when the biomass was pretreated at microwave temperature of 100 °C for 15 min with 2.5 g catalyst concentration. The results attained shows that hydrolysis time reduces to approximately 40-50% in compare with other traditional heating method. The sample was analyzed by using UV spectrophotometer and HPLC and computed by using Response Surface Method in MINITAB 17, whereas the structural changes of the residue was detected by using ATR-FTIR and ESEM.
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Affiliation(s)
- Sumarlin Shangdiar
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung 804, Taiwan; Center for Emerging Contaminants Research, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Yuan-Chung Lin
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung 804, Taiwan; Center for Emerging Contaminants Research, National Sun Yat-sen University, Kaohsiung 804, Taiwan; Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan.
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung City, Taiwan; Department of Chemistry, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Tzi-Yi Wu
- Department of Chemical Engineering and Materials Engineering, National Yunlin University of Science and Technology, Yunlin 64002, Taiwan
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Steering the formation of cellobiose and oligosaccharides during enzymatic hydrolysis of asparagus fibre. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Rosolen RR, Aono AH, Almeida DA, Ferreira Filho JA, Horta MAC, De Souza AP. Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1. Front Genet 2022; 13:807243. [PMID: 35281818 PMCID: PMC8912865 DOI: 10.3389/fgene.2022.807243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/04/2022] [Indexed: 12/24/2022] Open
Abstract
Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis of T. harzianum IOC-3844 and T. harzianum CBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences among Trichoderma spp. The results of the T. harzianum strains were compared with those of Trichoderma atroviride CBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed with cre1 or xyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of the cre1 and xyr1 groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts in cre1 and xyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluated T. harzianum strains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related to xyr1 and cre1 differed, suggesting that each T. harzianum strain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluated T. harzianum strains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.
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Affiliation(s)
- Rafaela Rossi Rosolen
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Déborah Aires Almeida
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Jaire Alves Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Anete Pereira De Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Anete Pereira De Souza,
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11
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Abstract
The booming demand for energy across the world, especially for petroleum-based fuels, has led to the search for a long-term solution as a perfect source of sustainable energy. Lignocellulosic biomass resolves this obstacle as it is a readily available, inexpensive, and renewable fuel source that fulfills the criteria of sustainability. Valorization of lignocellulosic biomass and its components into value-added products maximizes the energy output and promotes the approach of lignocellulosic biorefinery. However, disruption of the recalcitrant structure of lignocellulosic biomass (LCB) via pretreatment technologies is costly and power-/heat-consuming. Therefore, devising an effective pretreatment method is a challenge. Likewise, the thermochemical and biological lignocellulosic conversion poses problems of efficiency, operational costs, and energy consumption. The advent of integrated technologies would probably resolve this problem. However, it is yet to be explored how to make it applicable at a commercial scale. This article will concisely review basic concepts of lignocellulosic composition and the routes opted by them to produce bioenergy. Moreover, it will also discuss the pros and cons of the pretreatment and conversion methods of lignocellulosic biomass. This critical analysis will bring to light the solutions for efficient and cost-effective conversion of lignocellulosic biomass that would pave the way for the development of sustainable energy systems.
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Dodge N, Russo DA, Blossom BM, Singh RK, van Oort B, Croce R, Bjerrum MJ, Jensen PE. Water-soluble chlorophyll-binding proteins from Brassica oleracea allow for stable photobiocatalytic oxidation of cellulose by a lytic polysaccharide monooxygenase. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:192. [PMID: 33292428 PMCID: PMC7708235 DOI: 10.1186/s13068-020-01832-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/16/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are indispensable redox enzymes used in industry for the saccharification of plant biomass. LPMO-driven cellulose oxidation can be enhanced considerably through photobiocatalysis using chlorophyll derivatives and light. Water soluble chlorophyll binding proteins (WSCPs) make it is possible to stabilize and solubilize chlorophyll in aqueous solution, allowing for in vitro studies on photostability and ROS production. Here we aim to apply WSCP-Chl a as a photosensitizing complex for photobiocatalysis with the LPMO, TtAA9. RESULTS We have in this study demonstrated how WSCP reconstituted with chlorophyll a (WSCP-Chl a) can create a stable photosensitizing complex which produces controlled amounts of H2O2 in the presence of ascorbic acid and light. WSCP-Chl a is highly reactive and allows for tightly controlled formation of H2O2 by regulating light intensity. TtAA9 together with WSCP-Chl a shows increased cellulose oxidation under low light conditions, and the WSCP-Chl a complex remains stable after 24 h of light exposure. Additionally, the WSCP-Chl a complex demonstrates stability over a range of temperatures and pH conditions relevant for enzyme activity in industrial settings. CONCLUSION With WSCP-Chl a as the photosensitizer, the need to replenish Chl is greatly reduced, enhancing the catalytic lifetime of light-driven LPMOs and increasing the efficiency of cellulose depolymerization. WSCP-Chl a allows for stable photobiocatalysis providing a sustainable solution for biomass processing.
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Affiliation(s)
- N Dodge
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg, Denmark
| | - D A Russo
- Department of Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - B M Blossom
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - R K Singh
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - B van Oort
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - R Croce
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M J Bjerrum
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - P E Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg, Denmark.
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Delabona PDS, Codima CA, Ramoni J, Zubieta MP, de Araújo BM, Farinas CS, Pradella JGDC, Seiboth B. The impact of putative methyltransferase overexpression on the Trichoderma harzianum cellulolytic system for biomass conversion. BIORESOURCE TECHNOLOGY 2020; 313:123616. [PMID: 32563792 DOI: 10.1016/j.biortech.2020.123616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Trichoderma harzianum has attracting attention for its potential alternative use in biofuel production, due to a recognized competence for high diversity glycoside hydrolases (GH) enzyme complex, including higher β-glucosidases and auxiliary proteins, using low-cost carbon sources. This strain constitutively overexpressed the global regulator putative methyltransferase - LAE1, in order to improve the GHs production. The recombinant strain achieved 79-fold increase in lae1 expression and high GHs productivity. The evaluation of the LAE1 impact to induce the GHs used soluble and lignocellulose inexpensive carbon sources in a stirred-tank bioreactor. Using sugarcane bagasse with sucrose, the overexpression of lae1 resulted in significantly increment of gh61b (31x), cel7a (25x), bgl1(20x) and xyn3 (20x) genes expression. Reducing sugar released from pretreated sugarcane bagasse, which hydrolyzed by recombinant crude enzyme cocktail, achieved 41% improvement. Therefore, lae1 overexpression effectively is a promising improving GHs target for biomass degradation by T. harzianum.
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Affiliation(s)
- Priscila da Silva Delabona
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil; Synthetic Biology and Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1a, A-1060 Vienna, Austria; Federal University of Goiás (UFG), Samambaia Campus, Goiânia, GO, Brazil.
| | - Carla Aloia Codima
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil
| | - Jonas Ramoni
- Synthetic Biology and Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1a, A-1060 Vienna, Austria
| | - Mariane Paludetti Zubieta
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil
| | | | | | - José Geraldo da Cruz Pradella
- National Centre of Research in Energy and Materials, High-tech Pole II, 10000 Giuseppe Maximo Scolfaro St, P.O Box 6192, Campinas, SP, Brazil
| | - Bernhard Seiboth
- Synthetic Biology and Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1a, A-1060 Vienna, Austria
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15
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Carbohydrate-Active Enzymes: Structure, Activity, and Reaction Products. Int J Mol Sci 2020; 21:ijms21082727. [PMID: 32326403 PMCID: PMC7215940 DOI: 10.3390/ijms21082727] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/11/2020] [Indexed: 12/18/2022] Open
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16
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Contreras F, Pramanik S, M. Rozhkova A, N. Zorov I, Korotkova O, P. Sinitsyn A, Schwaneberg U, D. Davari M. Engineering Robust Cellulases for Tailored Lignocellulosic Degradation Cocktails. Int J Mol Sci 2020; 21:E1589. [PMID: 32111065 PMCID: PMC7084875 DOI: 10.3390/ijms21051589] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/11/2022] Open
Abstract
Lignocellulosic biomass is a most promising feedstock in the production of second-generation biofuels. Efficient degradation of lignocellulosic biomass requires a synergistic action of several cellulases and hemicellulases. Cellulases depolymerize cellulose, the main polymer of the lignocellulosic biomass, to its building blocks. The production of cellulase cocktails has been widely explored, however, there are still some main challenges that enzymes need to overcome in order to develop a sustainable production of bioethanol. The main challenges include low activity, product inhibition, and the need to perform fine-tuning of a cellulase cocktail for each type of biomass. Protein engineering and directed evolution are powerful technologies to improve enzyme properties such as increased activity, decreased product inhibition, increased thermal stability, improved performance in non-conventional media, and pH stability, which will lead to a production of more efficient cocktails. In this review, we focus on recent advances in cellulase cocktail production, its current challenges, protein engineering as an efficient strategy to engineer cellulases, and our view on future prospects in the generation of tailored cellulases for biofuel production.
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Affiliation(s)
- Francisca Contreras
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Aleksandra M. Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan N. Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Korotkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Arkady P. Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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