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González-Hernández JC, Ramírez-Conejo JD, García-Aguirre YP. Comparative analysis of β-glucosidase activity in non-conventional yeasts. AN ACAD BRAS CIENC 2023; 95:e20221118. [PMID: 38055563 DOI: 10.1590/0001-3765202320221118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/08/2022] [Indexed: 12/08/2023] Open
Abstract
The objective of this study was to evaluate the β-glucosidase activity in the non-conventional yeasts under cellulose, glucose and sucrose substrates. The participation of the enzyme β-glucosidase and its contribution to the enzymatic degradation of tannins is known. Within the classification of tannins are ellagitannins, molecules of gallic acid and ellagic acid, which are considered as nutraceutical compounds due to the properties that they present and that they can be used in the design of food and new drugs, synthesis of materials with antimicrobial capacity. The extracellular β-glucosidase activity was mainly presented in the Candida and Pichia strains, being the glucose and sucrose media the most capable for inducing the activity that showed maximum values with P. pastoris in glucose (0.1682±0.00 µmol/min mg protein), and C. utilis in cellulose (0.1129±0.1349 µmol/min mg of protein), and sucrose (0.0657±0.0214 µmol/min mg protein). Additionally, I. terricola and P. kluyvery stood out in a qualitative cellulose degradation approach measured by Congo red method (9.60±0.04 mm and 9.20±0.05 mm respectively). These indicate that P. pastoris and C. utilis have potential as β-glucosidase producers, especially when growing under complex carbon sources for biomass conversion, new biofuels production and polyphenol degradation with more manageable bioreactor process.
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Affiliation(s)
- Juan Carlos González-Hernández
- Tecnológico Nacional de México/Instituto Tecnológico de Morelia, Av. Tecnológico 1500, Col. Lomas de Santiaguito, C.P. 58120, Morelia, Michoacán, México
| | - Juan David Ramírez-Conejo
- Tecnológico Nacional de México/Instituto Tecnológico de Morelia, Av. Tecnológico 1500, Col. Lomas de Santiaguito, C.P. 58120, Morelia, Michoacán, México
| | - Yolanda Patricia García-Aguirre
- Tecnológico Nacional de México/Instituto Tecnológico de Morelia, Av. Tecnológico 1500, Col. Lomas de Santiaguito, C.P. 58120, Morelia, Michoacán, México
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Li H, Lu Z, Hao MS, Kvammen A, Inman AR, Srivastava V, Bulone V, McKee LS. Family 92 carbohydrate-binding modules specific for β-1,6-glucans increase the thermostability of a bacterial chitinase. Biochimie 2023; 212:153-160. [PMID: 37121306 DOI: 10.1016/j.biochi.2023.04.019] [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: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 05/02/2023]
Abstract
In biomass-processing industries there is a need for enzymes that can withstand high temperatures. Extensive research efforts have been dedicated to finding new thermostable enzymes as well as developing new means of stabilising existing enzymes. The attachment of a stable non-catalytic domain to an enzyme can, in some instances, protect a biocatalyst from thermal denaturation. Carbohydrate-binding modules (CBMs) are non-catalytic domains typically found appended to biomass-degrading or modifying enzymes, such as glycoside hydrolases (GHs). Most often, CBMs interact with the same polysaccharide as their enzyme partners, leading to an enhanced reaction rate via the promotion of enzyme-substrate interactions. Contradictory to this general concept, we show an example of a chitin-degrading enzyme from GH family 18 that is appended to two CBM domains from family 92, both of which bind preferentially to the non-substrate polysaccharide β-1,6-glucan. During chitin hydrolysis, the CBMs do not contribute to enzyme-substrate interactions but instead confer a 10-15 °C increase in enzyme thermal stability. We propose that CBM92 domains may have a natural enzyme stabilisation role in some cases, which may be relevant to enzyme design for high-temperature applications in biorefinery.
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Affiliation(s)
- He Li
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Meng-Shu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Alma Kvammen
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden; College of Medicine & Public Health, Flinders University, Bedford Park Campus, Sturt Road, SA, 5042, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden; Wallenberg Wood Science Center, Teknikringen 56-58, 100 44, Stockholm, Sweden.
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Zhou HY, Chen Q, Zhang YF, Chen DD, Yi XN, Chen DS, Cheng XP, Li M, Wang HY, Chen KQ, Liu ZQ, Zheng YG. Improving the catalytic activity of β-glucosidase from Coniophora puteana via semi-rational design for efficient biomass cellulose degradation. Enzyme Microb Technol 2023; 164:110188. [PMID: 36584665 DOI: 10.1016/j.enzmictec.2022.110188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
In order to improve the degradation activity of β-glucosidase (CpBgl) from Coniophora puteana, the structural modification was conducted. The enzyme activity of mutants CpBgl-Q20C and CpBgl-A240S was increased by 65.75% and 58.58%, respectively. These mutants exhibited maximum activity under the same conditions as wild-type CpBgl (65 ℃ and pH 5.0), slightly improved stabilities compared that of the wild-type, and remarkably enhanced activities in the presence of Mn2+ or Fe2+. The Vmax of CpBgl-Q20C and CpBgl-A240S was increased to 138.18 and 125.14 μmol/mg/min, respectively, from 81.34 μmol/mg/min of the wild-type, and the catalysis efficiency (kcat/Km) of CpBgl-Q20C (335.79 min-1/mM) and CpBgl-A240S (281.51 min-1/mM) was significantly improved compared with that of the wild-type (149.12 min-1/mM). When the mutant CpBgl-Q20C were used in the practical degradation of different biomasses, the glucose yields of filter paper, corncob residue, and fungi mycelia residue were increased by 17.68%, 25.10%, and 20.37%, respectively. The spatial locations of the mutation residues in the architecture of CpBgl and their unique roles in the enzyme-substrate binding and catalytic efficiency were probed in this work. These results laid a foundation for evolution of other glycoside hydrolases and the industrial bio-degradation of cellulosic biomass in nature.
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Affiliation(s)
- Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Qi Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Yi-Feng Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Dou-Dou Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Xiao-Nan Yi
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - De-Shui Chen
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Xin-Ping Cheng
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Hong-Yan Wang
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Kai-Qian Chen
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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Bioethanol Production from Lignocellulosic Biomass-Challenges and Solutions. Molecules 2022; 27:molecules27248717. [PMID: 36557852 PMCID: PMC9785513 DOI: 10.3390/molecules27248717] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Regarding the limited resources for fossil fuels and increasing global energy demands, greenhouse gas emissions, and climate change, there is a need to find alternative energy sources that are sustainable, environmentally friendly, renewable, and economically viable. In the last several decades, interest in second-generation bioethanol production from non-food lignocellulosic biomass in the form of organic residues rapidly increased because of its abundance, renewability, and low cost. Bioethanol production fits into the strategy of a circular economy and zero waste plans, and using ethanol as an alternative fuel gives the world economy a chance to become independent of the petrochemical industry, providing energy security and environmental safety. However, the conversion of biomass into ethanol is a challenging and multi-stage process because of the variation in the biochemical composition of biomass and the recalcitrance of lignin, the aromatic component of lignocellulose. Therefore, the commercial production of cellulosic ethanol has not yet become well-received commercially, being hampered by high research and production costs, and substantial effort is needed to make it more widespread and profitable. This review summarises the state of the art in bioethanol production from lignocellulosic biomass, highlights the most challenging steps of the process, including pretreatment stages required to fragment biomass components and further enzymatic hydrolysis and fermentation, presents the most recent technological advances to overcome the challenges and high costs, and discusses future perspectives of second-generation biorefineries.
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Papoutsidakis GI, Buckin V. Real-time monitoring of enzymatic hydrolysis of 1,3(4)-β-glucan with high-resolution ultrasonic spectroscopy. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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7
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Ashwini S, Bhavani PV, Deepa N, Sowmya N, Raghavendra MP. Development of sequence-characterized amplified region (SCAR) markers for accurate and differential identification of multienzyme-producing and non-enzymatic Aspergillus strains of industrial importance. Arch Microbiol 2022; 205:2. [PMID: 36436138 DOI: 10.1007/s00203-022-03340-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/25/2022] [Accepted: 11/16/2022] [Indexed: 11/28/2022]
Abstract
Aspergillus strains are known to produce multiple enzymes of industrial importance. To screen Aspergillus isolates and select a strain with the ability to produce multiple enzymes and discriminate it from non-enzymatic strains, a rapid and accurate approach is required. With this background, a DNA fingerprinting-based study was conducted to develop a simple but accurate molecular detection method with the potential to discriminate multienzyme-producing Aspergillus strains from non-enzymatic strains, irrespective of species. To achieve this, Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR was employed to derive group-specific Sequence Characterized Amplified Region (SCAR) markers (i.e., markers corresponding to PCR amplicons of known DNA sequence). To this end, both group-specific (multienzyme-producing and non-enzymatic Aspergillus group) SCAR markers were sought by comparing the ERIC fingerprint profiles and used to develop primers for use in specific and differential identification of multienzyme-producing Aspergillus isolates. As an outcome, the two SCAR-PCR formats were developed. One format is for specific identification of multienzyme-producing Aspergillus strains (SCAR-PCR1), and the other for identifying non-enzymatic Aspergillus strains (SCAR-PCR2). Both SCAR-PCRs were able to discriminate between these two contrasting groups. These formats are simple but accurate and rapid compared to the time-consuming and laborious conventional methods. Therefore, they could be efficient as an alternative strategy for the high-throughput screening of industrially important Aspergillus strains.
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Affiliation(s)
- Shankar Ashwini
- Postgraduate Department of Microbiology, Maharani's Science College for Women, JLB Road, Mysuru, Karnataka, 570005, India.,Department of Microbiology, Bharathiyar University, Coimbatore, Tamil Nadu, 641046, India
| | | | - Nagaraj Deepa
- Department of Studies in Microbiology, University of Mysore, Manasagangothri, Mysuru, 570006, India
| | - Nagaraj Sowmya
- Pentavalent Bio Sciences Private Limited, Electronic City, Phase 1, Bengaluru, Karnataka, 560100, India
| | - Maddur Puttaswamy Raghavendra
- Postgraduate Department of Microbiology, Maharani's Science College for Women, JLB Road, Mysuru, Karnataka, 570005, India.
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Singh R, Pal DB, Alkhanani MF, Almalki AH, Areeshi MY, Haque S, Srivastava N. Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155966. [PMID: 35584752 DOI: 10.1016/j.scitotenv.2022.155966] [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: 02/14/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.
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Affiliation(s)
- Rajeev Singh
- Department of Environmental Studies, Satyawati College, University of Delhi, Delhi, 110052, India
| | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, Taif 21944, Saudi Arabia
| | - Mohammed Yahya Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University, Faculty of Medicine, Görükle Campus, 16059 Nilüfer, Bursa, Turkey
| | - Neha Srivastava
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, India.
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Areeshi MY. Microbial cellulase production using fruit wastes and its applications in biofuels production. Int J Food Microbiol 2022; 378:109814. [DOI: 10.1016/j.ijfoodmicro.2022.109814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/06/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
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Srivastava A, Nagar P, Rathore S, Adlakha N. The Linker Region Promotes Activity and Binding Efficiency of Modular LPMO towards Polymeric Substrate. Microbiol Spectr 2022; 10:e0269721. [PMID: 35080440 PMCID: PMC8791183 DOI: 10.1128/spectrum.02697-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 12/03/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) mediate oxidative degradation of plant polysaccharides. The genes encoding LPMOs are most commonly arranged with one catalytic domain, while a few are found tethered to additional noncatalytic units, i.e., cellulase linker and carbohydrate-binding module (CBM). The presence of CBM is known to facilitate catalysis by directing the enzymes toward cellulosic polymer, while the role of linkers is poorly understood. Based on limited experimental evidence, linkers are believed to serve merely as flexible spacers between the structured domains. Thus, this study aims to unravel the role of the linker regions present in LPMO sequences. For this, we analyzed the genome of Botrytis cinerea and found 9 genes encoding cellulose lytic monooxygenases (AA9 family), of which BcAA9C was overexpressed in cellulose-inducible conditions. We designed variants of flLPMO (full-length enzyme) with truncation of either linker or CBM to examine the role of linker in activity, binding, and thermal stability of the associated monooxygenase. Biochemical assays predicted that the deletion of linker does not impact the potential of flLPMO for catalyzing the oxidation of Amplex Red, but that it does have a major influence on the capability of flLPMO to degrade recalcitrant polysaccharide substrate. Langmuir isotherm and SEM analysis demonstrated that linker domain aids in polysaccharide binding during flLPMO-mediated deconstruction of plant cell wall. Interestingly, linker domain was also found to contribute toward the thermostability of flLPMO. Overall, our study reveals that linker is not merely a spacer, but plays a key role in LPMO-mediated biomass fibrillation; these findings are broadly applicable to other polysaccharide-degrading enzymes. IMPORTANCE The polysaccharide-disintegrating carbohydrate-active enzymes (CAZymes) are often found with multimodular architecture, where the catalytic domain is connected to an accessory CBM domain with the help of a flexible linker region. So far, the linker has been understood merely as a flexible spacer between the two domains. Therefore, the current study is designed to determine the role of linker in polysaccharide fibrillation. To conceive this study, we have selected LPMO as a model enzyme, as it is not only an industrially relevant enzyme but it also harbors a catalytic domain, linker region, and CBM domain. The present study highlighted the crucial and indispensable role of the linker region in mediating polysaccharide disintegration. Considering its role in binding, thermostability, and activity toward polysaccharide substrate, we propose linker as a potential candidate for future CAZyme engineering.
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Affiliation(s)
- Aishwarya Srivastava
- Synthetic Biology and Bioprocessing Laboratory, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, Haryana, India
| | - Pragya Nagar
- Synthetic Biology and Bioprocessing Laboratory, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, Haryana, India
| | - Sumit Rathore
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Nidhi Adlakha
- Synthetic Biology and Bioprocessing Laboratory, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, Haryana, India
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Elsababty ZE, Abdel-Aziz SH, Ibrahim AM, Guirgis AA, Dawwam GE. Purification, biochemical characterization, and molecular cloning of cellulase from Bacillus licheniformis strain Z9 isolated from soil. J Genet Eng Biotechnol 2022; 20:34. [PMID: 35192092 PMCID: PMC8864052 DOI: 10.1186/s43141-022-00317-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/11/2022] [Indexed: 12/03/2022]
Abstract
Background Cellulose is the most prevalent biomass and renewable energy source in nature. The hydrolysis of cellulosic biomass to glucose units is essential for the economic exploitation of this natural resource. Cellulase enzyme, which is largely generated by bacteria and fungus, is commonly used to degrade cellulose. Cellulases are used in a variety of industries, including bioethanol manufacturing, textiles, detergents, drugs, food, and paper. As part of our quest to find an efficient biocatalyst for the hydrolysis of cellulosic biomass, we describe the amplification, cloning, and sequencing of cellulase (cel9z) from Bacillus licheniformis strain Z9, as well as the characterization of the resulting enzyme. Results Cellulase was partially purified from B. licheniformis strain Z9 using (NH4)2SO4 precipitation and Sephadex G-100 gel column chromatography with 356.5 U/mg specific activity, 2.1-purification fold, and 3.07 % yield. The nucleotide sequence of the cellulase gene was deposited to the GenBank, B. licheniformis strain Z9 cellulase (cel9z) gene, under accession number MK814929. This corresponds to 1453 nucleotides gene and encodes for a protein composed of 484 amino acids. Comparison of deduced amino acids sequence to other related cellulases showed that the enzyme cel9z can be classified as a glycoside hydrolase family 9. SDS-PAGE analysis of the purified enzyme revealed that the molecular mass was 54.5 kDa. The optimal enzyme activity was observed at pH 7.4 and 30 °C. The enzyme was found to be strongly inhibited by Mg2+ and Na+, whereas strongly activated by Fe3+, Cu2+, and Ca2+. Conclusions B. licheniformis strain Z9 and its cellulase gene can be further utilized for recombinant production of cellulases for industrial application. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00317-4.
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Ajeje SB, Hu Y, Song G, Peter SB, Afful RG, Sun F, Asadollahi MA, Amiri H, Abdulkhani A, Sun H. Thermostable Cellulases / Xylanases From Thermophilic and Hyperthermophilic Microorganisms: Current Perspective. Front Bioeng Biotechnol 2021; 9:794304. [PMID: 34976981 PMCID: PMC8715034 DOI: 10.3389/fbioe.2021.794304] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The bioconversion of lignocellulose into monosaccharides is critical for ensuring the continual manufacturing of biofuels and value-added bioproducts. Enzymatic degradation, which has a high yield, low energy consumption, and enhanced selectivity, could be the most efficient and environmentally friendly technique for converting complex lignocellulose polymers to fermentable monosaccharides, and it is expected to make cellulases and xylanases the most demanded industrial enzymes. The widespread nature of thermophilic microorganisms allows them to proliferate on a variety of substrates and release substantial quantities of cellulases and xylanases, which makes them a great source of thermostable enzymes. The most significant breakthrough of lignocellulolytic enzymes lies in lignocellulose-deconstruction by enzymatic depolymerization of holocellulose into simple monosaccharides. However, commercially valuable thermostable cellulases and xylanases are challenging to produce in high enough quantities. Thus, the present review aims at giving an overview of the most recent thermostable cellulases and xylanases isolated from thermophilic and hyperthermophilic microbes. The emphasis is on recent advancements in manufacturing these enzymes in other mesophilic host and enhancement of catalytic activity as well as thermostability of thermophilic cellulases and xylanases, using genetic engineering as a promising and efficient technology for its economic production. Additionally, the biotechnological applications of thermostable cellulases and xylanases of thermophiles were also discussed.
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Affiliation(s)
- Samaila Boyi Ajeje
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guojie Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Sunday Bulus Peter
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Richmond Godwin Afful
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hamid Amiri
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Ali Abdulkhani
- Department of Wood and Paper Science and Technology, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Haiyan Sun
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Mukwevho VO, Dreyer LL, Roets F. Early colonization of Protea flowers enable dominance of competitively weak saprobic fungi in seed cones, benefitting their hosts. Fungal Biol 2021; 126:122-131. [DOI: 10.1016/j.funbio.2021.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 11/04/2022]
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14
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Improved saccharification of Chlorella vulgaris biomass by fungal secreted enzymes for bioethanol production. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Pimentel PSSR, de Oliveira JB, Astolfi-Filho S, Pereira N. Enzymatic Hydrolysis of Lignocellulosic Biomass Using an Optimized Enzymatic Cocktail Prepared from Secretomes of Filamentous Fungi Isolated from Amazonian Biodiversity. Appl Biochem Biotechnol 2021; 193:3915-3935. [PMID: 34410613 DOI: 10.1007/s12010-021-03642-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022]
Abstract
The use of lignocellulosic biomass (LCB) has emerged as one of the main strategies for generating renewable biofuels. For the efficient use of such feedstock, pre-treatments are essential. The hydrolysis of cellulose - major component of LCB - demands enzymatic cocktails with improved efficiency to generate fermentable sugars. In this scenario, lignocellulolytic fungi have enormous potential for the development of efficient enzyme platforms. In this study, two enzymatic cocktails were developed for hydrolysis of two lignocellulosic biomasses: industrial cellulose pulp and cassava peel. The solid biomass ratio in relation to the protein content of the enzyme cocktail was performed by experimental design. The optimized cocktail for the hydrolysis of cellulose pulp (AMZ 1) was composed, in protein base, by 43% of Aspergillus sp. LMI03 enzyme extract and 57% of T. reesei QM9414, while the optimal enzyme cocktail for cassava peel hydrolysis (AMZ 2) was composed by 50% of Aspergillus sp. LMI03 enzyme extract, 25% of the extract of P. citrinum LMI01 and 25% of T. reesei. The ratio between solids and protein loading for AMZ 1 cocktail performance was 52 g/L solids and 30 mg protein/g solids, resulting in a hydrolytic efficiency of 93%. For the AMZ 2 cocktail, the hydrolytic efficiency was 78% for an optimized ratio of 78 g/L solids and 19 mg protein/g solids. These results indicate that cocktails formulated with enzymatic extracts of P. citrinum LMI01, Aspergillus sp. LMI03, and T. reesei QM9414 are excellent alternatives for efficient hydrolysis of plant biomass and for other processes that depend on biocatalysis.
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Affiliation(s)
| | - Jessica Batista de Oliveira
- Multi Institutional Biotechnology Graduate Program, Federal University of Amazonas, Manaus, 69067-005, Brazil
| | - Spartaco Astolfi-Filho
- Centro de Apoio Multidisciplinar (CAM), Federal University of Amazonas, Manaus, 69067-005, Brazil
| | - Nei Pereira
- Laboratory of Bioprocess Development, Center of Biofuels, Oil and Derivatives, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-594, Brazil
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16
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Marasinghe SD, Jo E, Hettiarachchi SA, Lee Y, Eom TY, Gang Y, Kang YH, Oh C. Characterization of glycoside hydrolase family 11 xylanase from Streptomyces sp. strain J103; its synergetic effect with acetyl xylan esterase and enhancement of enzymatic hydrolysis of lignocellulosic biomass. Microb Cell Fact 2021; 20:129. [PMID: 34238305 PMCID: PMC8265113 DOI: 10.1186/s12934-021-01619-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Xylanase-containing enzyme cocktails are used on an industrial scale to convert xylan into value-added products, as they hydrolyse the β-1,4-glycosidic linkages between xylopyranosyl residues. In the present study, we focused on xynS1, the glycoside hydrolase (GH) 11 xylanase gene derived from the Streptomyces sp. strain J103, which can mediate XynS1 protein synthesis and lignocellulosic material hydrolysis. Results xynS1 has an open reading frame with 693 base pairs that encodes a protein with 230 amino acids. The predicted molecular weight and isoelectric point of the protein were 24.47 kDa and 7.92, respectively. The gene was cloned into the pET-11a expression vector and expressed in Escherichia coli BL21(DE3). Recombinant XynS1 (rXynS1) was purified via His-tag affinity column chromatography. rXynS1 exhibited optimal activity at a pH of 5.0 and temperature of 55 °C. Thermal stability was in the temperature range of 50–55 °C. The estimated Km and Vmax values were 51.4 mg/mL and 898.2 U/mg, respectively. One millimolar of Mn2+ and Na+ ions stimulated the activity of rXynS1 by up to 209% and 122.4%, respectively, and 1 mM Co2+ and Ni2+ acted as inhibitors of the enzyme. The mixture of rXynS1, originates from Streptomyces sp. strain J103 and acetyl xylan esterase (AXE), originating from the marine bacterium Ochrovirga pacifica, enhanced the xylan degradation by 2.27-fold, compared to the activity of rXynS1 alone when Mn2+ was used in the reaction mixture; this reflected the ability of both enzymes to hydrolyse the xylan structure. The use of an enzyme cocktail of rXynS1, AXE, and commercial cellulase (Celluclast® 1.5 L) for the hydrolysis of lignocellulosic biomass was more effective than that of commercial cellulase alone, thereby increasing the relative activity 2.3 fold. Conclusion The supplementation of rXynS1 with AXE enhanced the xylan degradation process via the de-esterification of acetyl groups in the xylan structure. Synergetic action of rXynS1 with commercial cellulase improved the hydrolysis of pre-treated lignocellulosic biomass; thus, rXynS1 could potentially be used in several industrial applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01619-x.
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Affiliation(s)
- Svini Dileepa Marasinghe
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Eunyoung Jo
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Sachithra Amarin Hettiarachchi
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - Youngdeuk Lee
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Tae-Yang Eom
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yehui Gang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Hyeok Kang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chulhong Oh
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea. .,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.
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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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18
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Gong X, Sui L, Morton J, Brennan MA, Brennan CS. Investigation of nutritional and functional effects of rice bran protein hydrolysates by using Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines: A review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.01.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Bacterial valorization of pulp and paper industry process streams and waste. Appl Microbiol Biotechnol 2021; 105:1345-1363. [PMID: 33481067 DOI: 10.1007/s00253-021-11107-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
The pulp and paper industry is a major source of lignocellulose-containing streams. The components of lignocellulose material are lignin, hemicellulose, and cellulose that may be hydrolyzed into their smaller components and used as feedstocks for valorization efforts. Much of this material is contained in underutilized streams and waste products, such as black liquor, pulp and paper sludge, and wastewater. Bacterial fermentation strategies have suitable potential to upgrade lignocellulosic biomass contained in these streams to value-added chemicals. Bacterial conversion allows for a sustainable and economically feasible approach to valorizing these streams, which can bolster and expand applications of the pulp and paper industry. This review discusses the composition of pulp and paper streams, bacterial isolates from process streams that can be used for lignocellulose biotransformations, and technological approaches for improving valorization efforts. KEY POINTS: • Reviews the conversion of pulp and paper industry waste by bacterial isolates. • Metabolic pathways for the breakdown of lignocellulose components. • Methods for isolating bacteria, determining value-added products, and increasing product yields.
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20
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Naicker JE, Govinden R, Lekha P, Sithole B. Transformation of pulp and paper mill sludge (PPMS) into a glucose-rich hydrolysate using green chemistry: Assessing pretreatment methods for enhanced hydrolysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 270:110914. [PMID: 32721348 DOI: 10.1016/j.jenvman.2020.110914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/30/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Pulp and paper mill sludge is a waste stream derived from the pulp and paper making industry, comprised of organic and inorganic material in the form of cellulose, hemicellulose, lignin and ash. In South Africa, approximately fivefour hundred thousand wet tonnes are produced per annum and is currently disposed via landfilling or incineration. However, these disposal methods raise environmental and financial concerns. This waste stream is an attractive feedstock for fermentable sugars, mainly glucose, recovery and can be redirected for valorisation as a feedstock for microbial fermentation to produce value-added products. Sugar recovery by enzymatic hydrolysis, as opposed to acidic hydrolysis, is a promising approach but is hampered by the lignin and inorganic material found in pulp and paper mill sludge. Several treatment steps to reduce or remove these components prior to enzymatic hydrolysis are assessed in this review. Pretreatment improves hydrolysis of cellulosic fibres and ensures a substantial yield of sugars.
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Affiliation(s)
- Justin Emmanuel Naicker
- University of KwaZulu-Natal (Westville Campus), Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Sciences, University Road, Westville, Private Bag X 54001, Durban, 4000, South Africa.
| | - Roshini Govinden
- University of KwaZulu-Natal (Westville Campus), Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Sciences, University Road, Westville, Private Bag X 54001, Durban, 4000, South Africa
| | - Prabashni Lekha
- Council for Scientific and Industrial Research, Biorefinery Industry Development Facility, PO Box 59081, Umbilo, 4075, South Africa
| | - Bruce Sithole
- Council for Scientific and Industrial Research, Biorefinery Industry Development Facility, PO Box 59081, Umbilo, 4075, South Africa; University of KwaZulu-Natal (Howard Campus), Discipline of Chemical Engineering, College of Agriculture, Engineering and Sciences, Private Bag X 54001, Durban, 4000, South Africa
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21
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Hebal H, Parviainen A, Anbarasan S, Li H, Makkonen L, Bankar S, King AW, Kilpeläinen I, Benallaoua S, Turunen O. Inhibition of hyperthermostable xylanases by superbase ionic liquids. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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22
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A novel thermostable cellulase cocktail enhances lignocellulosic bioconversion and biorefining in a broad range of pH. Int J Biol Macromol 2020; 154:349-360. [DOI: 10.1016/j.ijbiomac.2020.03.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 11/22/2022]
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23
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Cripwell RA, Favaro L, Viljoen-Bloom M, van Zyl WH. Consolidated bioprocessing of raw starch to ethanol by Saccharomyces cerevisiae: Achievements and challenges. Biotechnol Adv 2020; 42:107579. [PMID: 32593775 DOI: 10.1016/j.biotechadv.2020.107579] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/05/2020] [Accepted: 06/14/2020] [Indexed: 12/30/2022]
Abstract
Recent advances in amylolytic strain engineering for starch-to-ethanol conversion have provided a platform for the development of raw starch consolidated bioprocessing (CBP) technologies. Several proof-of-concept studies identified improved enzyme combinations, alternative feedstocks and novel host strains for evaluation and application under fermentation conditions. However, further research efforts are required before this technology can be scaled up to an industrial level. In this review, different CBP approaches are defined and discussed, also highlighting the role of auxiliary enzymes for a supplemented CBP process. Various achievements in the development of amylolytic Saccharomyces cerevisiae strains for CBP of raw starch and the remaining challenges that need to be tackled/pursued to bring yeast raw starch CBP to industrial realization, are described. Looking towards the future, it provides potential solutions to develop more cost-effective processes that include cheaper substrates, integration of the 1G and 2G economies and implementing a biorefinery concept where high-value products are also derived from starchy substrates.
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Affiliation(s)
- Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
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Akram F, Haq IU. Overexpression and characterization of TnCel12B, a hyperthermophilic GH12 endo-1,4-β-glucanase cloned from Thermotoga naphthophila RKU-10 T. Anal Biochem 2020; 599:113741. [PMID: 32339490 DOI: 10.1016/j.ab.2020.113741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 11/26/2022]
Abstract
A putative cellulolytic gene (825 bp) from Thermotoga naphthophila RKU-10T was overexpressed as an active soluble endo-1,4-β-glucanase (TnCel12B), belongs to glycoside hydrolase family 12 (GH12), in a mesophilic expression host. Heterologous expression and engineered bacterial cell mass was improved through specific strategies (induction and cultivation). Hence, intracellular activity of TnCel12B was enhanced in ZYBM9 modified medium (pH 7.0) by 8.38 and 6.25 fold with lactose (200 mM) and IPTG (0.5 mM) induction, respectively; and 6.95 fold was increased in ZYP-5052 auto-inducing medium after 8 h incubation at 26 °C (200 rev min-1). Purified TnCel12B with a molecular weight of ~32 kDa, was optimally active at 90 °C and pH 6.0; and exhibited prodigious stability over a wide range of temperature (50-85 °C) and pH (5.0-9.0) for 8 h TnCel12B displayed great resistance towards different chemical modulators, though activity was improved by Mg2+, Zn2+, Pb2+ and Ca2+. Purified TnCel12B had affinity with various substrates but peak activity was observed toward barley β-glucan (1664 U mg-1) and carboxymethyl cellulose (736 U mg-1). The values of Km, Vmax, kcat, and kcatKm-1 were found to be 4.63 mg mL-1, 916 μmol mg-1min-1, 1326.7 s-1 and 286.54 mL mg-1 s-1, respectively using CMC substrate. All noteworthy features of TnCel12B make it an appropriate industrial candidate for bioethanol production and various other potential applications.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, GC University, Lahore, 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore, 54000, Pakistan.
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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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Puentes-Téllez PE, Salles JF. Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass. MICROBIAL ECOLOGY 2020; 79:312-325. [PMID: 31286170 PMCID: PMC7033055 DOI: 10.1007/s00248-019-01403-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 06/02/2023]
Abstract
Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization. We verified the importance of pre-selection by using two sources of microbial inoculum: soil samples from a sugarcane field with history of straw addition (St15) and control samples, from the same field, without amendments (St0). We found similitudes in terms of stabilization between the abundant and rare fractions. We also found positive correlations of both abundant and rare taxa (like Caulobacteraceae and Alcaligenaceae) and the degradation of lignocellulosic fractions. Differences in the inocula's initial diversity rapidly decreased during the enrichment resulting in comparable richness levels at the end of the process; however, the legacy of the St15 inoculum and its specialization positively influenced the degradation capacities of the community. Analysis of specialization of the final communities revealed increased straw degradation capacity in the communities enriched in bagasse, which could be potentially used as a strategy for improving lignocellulose waste degradation on the sugarcane fields. This work highlights the importance of including the rare fraction of bacterial communities during investigations involving the screening and assessment of effective degrading communities.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Baral P, Jain L, Kurmi AK, Kumar V, Agrawal D. Augmented hydrolysis of acid pretreated sugarcane bagasse by PEG 6000 addition: a case study of Cellic CTec2 with recycling and reuse. Bioprocess Biosyst Eng 2019; 43:473-482. [DOI: 10.1007/s00449-019-02241-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/23/2019] [Indexed: 12/01/2022]
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Matrix Discriminant Analysis Evidenced Surface-Lithium as an Important Factor to Increase the Hydrolytic Saccharification of Sugarcane Bagasse. Molecules 2019; 24:molecules24193614. [PMID: 31597244 PMCID: PMC6804010 DOI: 10.3390/molecules24193614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/10/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022] Open
Abstract
Statistical evidence pointing to the very soft change in the ionic composition on the surface of the sugar cane bagasse is crucial to improve yields of sugars by hydrolytic saccharification. Removal of Li+ by pretreatments exposing -OH sites was the most important factor related to the increase of saccharification yields using enzyme cocktails. Steam Explosion and Microwave:H2SO4 pretreatments produced unrelated structural changes, but similar ionic distribution patterns. Both increased the saccharification yield 1.74-fold. NaOH produced structural changes related to Steam Explosion, but released surface-bounded Li+ obtaining 2.04-fold more reducing sugars than the control. In turn, the higher amounts in relative concentration and periodic structures of Li+ on the surface observed in the control or after the pretreatment with Ethanol:DMSO:Ammonium Oxalate, blocked -OH and O- available for ionic sputtering. These changes correlated to 1.90-fold decrease in saccharification yields. Li+ was an activator in solution, but its presence and distribution pattern on the substrate was prejudicial to the saccharification. Apparently, it acts as a phase-dependent modulator of enzyme activity. Therefore, no correlations were found between structural changes and the efficiency of the enzymatic cocktail used. However, there were correlations between the Li+ distribution patterns and the enzymatic activities that should to be shown.
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Mardones W, Callegari E, Eyzaguirre J. Corncob and sugar beet pulp induce specific sets of lignocellulolytic enzymes in Penicillium purpurogenum. Mycology 2019; 10:118-125. [PMID: 31069125 PMCID: PMC6493289 DOI: 10.1080/21501203.2018.1517830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/26/2018] [Indexed: 01/19/2023] Open
Abstract
Penicillium purpurogenum is a filamentous fungus, which grows on a variety of natural carbon sources and secretes a large number of enzymes involved in cellulose, hemicelluloses and pectin biodegradation. The purpose of this work has been to identify potential lignocellulolytic enzymes and to compare the secreted enzymes produced when the fungus is grown on sugar beet pulp (rich in cellulose and pectin) and corn cob (rich in cellulose and xylan). Culture supernatants were subjected to two-dimensional nano-liquid chromatography/tandem mass spectrometry. Using MASCOT and a genome-derived protein database, the proteins present in the supernatant were identified. The putative function in the degradation of the polysaccharides was determined using dbCAN software. The results show that there is a good correlation between the polysaccharide composition of the carbon sources and the function of the secreted enzymes: both cultures are rich in cellulases, while sugar beet pulp induces pectinases and corncob, xylanases. The eventual biochemical characterisation of these enzymes will be of value for a better understanding of the biodegradation process performed by the fungus and increase the availability of enzymes for biotechnological methods associated with this process.
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Affiliation(s)
- Wladimir Mardones
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Eduardo Callegari
- BRIN-USDSSOM Proteomics Facility, University of South Dakota, Vermillion, SD, USA
| | - Jaime Eyzaguirre
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
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Fortune B, Mhlongo S, van Zyl LJ, Huddy R, Smart M, Trindade M. Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome. BMC Biotechnol 2019; 19:22. [PMID: 30999885 PMCID: PMC6472066 DOI: 10.1186/s12896-019-0510-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The importance of the accessory enzymes such as α-L-arabinofuranosidases (AFases) in synergistic interactions within cellulolytic mixtures has introduced a paradigm shift in the search for hydrolytic enzymes. The aim of this study was to characterize novel AFase genes encoding enzymes with differing temperature optima and thermostabilities for use in hydrolytic cocktails. RESULTS Three fosmids, pFos-H4, E3 and D3 were selected from the cloned metagenome of high temperature compost, expressed in Escherichia coli and subsequently purified to homogeneity from cell lysate. All the AFases were clustered within the GH51 AFase family and shared a homo-hexameric structure. Both AFase-E3 and H4 showed optimal activity at 60 °C while AFase-D3 had unique properties as it showed optimal activity at 25 °C as well as the ability to maintain substantial activity at temperatures as high as 90 °C. However, AFase-E3 was the most thermostable amongst the three AFases showing full activity even at 70 °C. The maximum activity was observed at a pH profile between pH 4.0-6.0 for all three AFases with optimal activity for AFase H4, D3 and E3 at pH 5.0, 4.5 and 4.0, respectively. All the AFases showed KM range between 0.31 mM and 0.43 mM, Kcat range between 131 s- 1 and 219 s- 1 and the specific activity for AFase-H4, AFases-E3 and was 143, 228 and 175 U/mg, respectively. AFases-E3 and D3 displayed activities against pNP-β-L-arabinopyranoside and pNP-β-L-mannopyranoside respectively, and both hydrolysed pNP-β-D-glucopyranoside. CONCLUSION All three AFases displayed different biochemical characteristics despite all showing conserved overall structural similarity with typical domains of AFases belonging to GH51 family. The hydrolysis of cellobiose by a GH51 family AFase is demonstrated for the first time in this study.
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Affiliation(s)
- Brent Fortune
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Sizwe Mhlongo
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Robert Huddy
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Mariette Smart
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.
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de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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Hooker CA, Hillman ET, Overton JC, Ortiz-Velez A, Schacht M, Hunnicutt A, Mosier NS, Solomon KV. Hydrolysis of untreated lignocellulosic feedstock is independent of S-lignin composition in newly classified anaerobic fungal isolate, Piromyces sp. UH3-1. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:293. [PMID: 30386430 PMCID: PMC6203967 DOI: 10.1186/s13068-018-1292-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/15/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as anaerobic gut fungi. These gut fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. RESULTS We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classified the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops. Importantly, UH3-1 hydrolyzes high syringyl lignin-containing poplar that is inhibitory to many fungi with efficiencies equal to that of low syringyl lignin-containing poplar with no reduction in fungal growth. This behavior is correlated with slight remodeling of the fungal secretome whose composition adapts with substrate to express an enzyme cocktail optimized to degrade the available biomass. CONCLUSIONS Piromyces sp. UH3-1, a newly isolated anaerobic gut fungus, grows on diverse untreated substrates through production of a broad range of carbohydrate active enzymes that are robust to variations in substrate composition. Additionally, UH3-1 and potentially other anaerobic fungi are resistant to inhibitory lignin composition possibly due to changes in enzyme secretion with substrate. Thus, anaerobic fungi are an attractive platform for the production of enzymes that efficiently use mixed feedstocks of variable composition for second generation biofuels. More importantly, our work suggests that the study of anaerobic fungi may reveal naturally evolved strategies to circumvent common hydrolytic inhibitors that hinder biomass usage.
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Affiliation(s)
- Casey A. Hooker
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
| | - Jonathan C. Overton
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Adrian Ortiz-Velez
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Makayla Schacht
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Abigail Hunnicutt
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Nathan S. Mosier
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Kevin V. Solomon
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
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Characterization of a New Glyoxal Oxidase from the Thermophilic Fungus Myceliophthora thermophila M77: Hydrogen Peroxide Production Retained in 5-Hydroxymethylfurfural Oxidation. Catalysts 2018. [DOI: 10.3390/catal8100476] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Myceliophthora thermophyla is a thermophilic industrially relevant fungus that secretes an assortment of hydrolytic and oxidative enzymes for lignocellulose degradation. Among them is glyoxal oxidase (MtGLOx), an extracellular oxidoreductase that oxidizes several aldehydes and α-hydroxy carbonyl substrates coupled to the reduction of O2 to H2O2. This copper metalloprotein belongs to a class of enzymes called radical copper oxidases (CRO) and to the “auxiliary activities” subfamily AA5_1 that is based on the Carbohydrate-Active enZYmes (CAZy) database. Only a few members of this family have been characterized to date. Here, we report the recombinant production, characterization, and structure-function analysis of MtGLOx. Electron Paramagnetic Resonance (EPR) spectroscopy confirmed MtGLOx to be a radical-coupled copper complex and small angle X-ray scattering (SAXS) revealed an extended spatial arrangement of the catalytic and four N-terminal WSC domains. Furthermore, we demonstrate that methylglyoxal and 5-hydroxymethylfurfural (HMF), a fermentation inhibitor, are substrates for the enzyme.
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Second-Generation Bioethanol from Coconut Husk. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4916497. [PMID: 30363680 PMCID: PMC6180963 DOI: 10.1155/2018/4916497] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/12/2018] [Accepted: 09/03/2018] [Indexed: 11/18/2022]
Abstract
Coconut palm (Cocos nucifera) is an important commercial crop in many tropical countries, but its industry generates large amounts of residue. One way to address this problem is to use this residue, coconut husk, to produce second-generation (2G) ethanol. The aim of this review is to describe the methods that have been used to produce bioethanol from coconut husk and to suggest ways to improve different steps of the process. The analysis performed in this review determined that alkaline pretreatment is the best choice for its delignification potential. It was also observed that although most reported studies use enzymes to perform hydrolysis, acid hydrolysis is a good alternative. Finally, ethanol production using different microorganisms and fermentation strategies is discussed and the possibility of obtaining other added-value products from coconut husk components by using a biorefinery scheme is addressed.
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Midorikawa GEO, Correa CL, Noronha EF, Filho EXF, Togawa RC, Costa MMDC, Silva-Junior OB, Grynberg P, Miller RNG. Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse. Front Bioeng Biotechnol 2018; 6:123. [PMID: 30280097 PMCID: PMC6153317 DOI: 10.3389/fbioe.2018.00123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq transcriptome profiling was conducted on a strain of Aspergillus tamarii, efficient in biomass polysaccharide degradation, in order to identify genes encoding proteins involved in plant biomass saccharification. Enzyme production and gene expression was compared following growth in liquid and semi-solid culture with steam-exploded sugarcane bagasse (SB) (1% w/v) and glucose (1% w/v) employed as contrasting sole carbon sources. Enzyme production following growth in liquid minimum medium supplemented with SB resulted in 0.626 and 0.711 UI.mL-1 xylanases after 24 and 48 h incubation, respectively. Transcriptome profiling revealed expression of over 7120 genes, with groups of genes modulated according to solid or semi-solid culture, as well as according to carbon source. Gene ontology analysis of genes expressed following SB hydrolysis revealed enrichment in xyloglucan metabolic process and xylan, pectin and glucan catabolic process, indicating up-regulation of genes involved in xylanase secretion. According to carbohydrate-active enzyme (CAZy) classification, 209 CAZyme-encoding genes were identified with significant differential expression on liquid or semi-solid SB, in comparison to equivalent growth on glucose as carbon source. Up-regulated CAZyme-encoding genes related to cellulases (CelA, CelB, CelC, CelD) and hemicellulases (XynG1, XynG2, XynF1, XylA, AxeA, arabinofuranosidase) showed up to a 10-fold log2FoldChange in expression levels. Five genes from the AA9 (GH61) family, related to lytic polysaccharide monooxygenase (LPMO), were also identified with significant expression up-regulation. The transcription factor gene XlnR, involved in induction of hemicellulases, showed up-regulation on liquid and semi-solid SB culture. Similarly, the gene ClrA, responsible for regulation of cellulases, showed increased expression on liquid SB culture. Over 150 potential transporter genes were also identified with increased expression on liquid and semi-solid SB culture. This first comprehensive analysis of the transcriptome of A. tamarii contributes to our understanding of genes and regulatory systems involved in cellulose and hemicellulose degradation in this fungus, offering potential for application in improved enzymatic cocktail development for plant biomass degradation in biorefinery applications.
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Affiliation(s)
| | - Camila Louly Correa
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | | | | | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
| | | | | | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
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Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Tovar-Herrera OE, Martha-Paz AM, Pérez-LLano Y, Aranda E, Tacoronte-Morales JE, Pedroso-Cabrera MT, Arévalo-Niño K, Folch-Mallol JL, Batista-García RA. Schizophyllum commune: An unexploited source for lignocellulose degrading enzymes. Microbiologyopen 2018; 7:e00637. [PMID: 29785766 PMCID: PMC6011954 DOI: 10.1002/mbo3.637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 02/01/2023] Open
Abstract
Lignocellulose represents the most abundant source of carbon in the Earth. Thus, fraction technology of the biomass turns up as an emerging technology for the development of biorefineries. Saccharification and fermentation processes require the formulation of enzymatic cocktails or the development of microorganisms (naturally or genetically modified) with the appropriate toolbox to produce a cost‐effective fermentation technology. Therefore, the search for microorganisms capable of developing effective cellulose hydrolysis represents one of the main challenges in this era. Schizophyllum commune is an edible agarical with a great capability to secrete a myriad of hydrolytic enzymes such as xylanases and endoglucanases that are expressed in a high range of substrates. In addition, a large number of protein‐coding genes for glycoside hydrolases, oxidoreductases like laccases (Lacs; EC 1.10.3.2), as well as some sequences encoding for lytic polysaccharide monooxygenases (LPMOs) and expansins‐like proteins demonstrate the potential of this fungus to be applied in different biotechnological process. In this review, we focus on the enzymatic toolbox of S. commune at the genetic, transcriptomic, and proteomic level, as well as the requirements to be employed for fermentable sugars production in biorefineries. At the end the trend of its use in patent registration is also reviewed.
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Affiliation(s)
- Omar Eduardo Tovar-Herrera
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Adriana Mayrel Martha-Paz
- Laboratorio de Micología y Fitopatología, Unidad de manipulación genética, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Yordanis Pérez-LLano
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Elisabet Aranda
- Instituto del Agua, Universidad de Granada, Granada, Granada, Spain
| | | | | | - Katiushka Arévalo-Niño
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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Kushwaha D, Srivastava N, Mishra I, Upadhyay SN, Mishra PK. Recent trends in biobutanol production. REV CHEM ENG 2018. [DOI: 10.1515/revce-2017-0041] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abstract
Finite availability of conventional fossil carbonaceous fuels coupled with increasing pollution due to their overexploitation has necessitated the quest for renewable fuels. Consequently, biomass-derived fuels are gaining importance due to their economic viability and environment-friendly nature. Among various liquid biofuels, biobutanol is being considered as a suitable and sustainable alternative to gasoline. This paper reviews the present state of the preprocessing of the feedstock, biobutanol production through fermentation and separation processes. Low butanol yield and its toxicity are the major bottlenecks. The use of metabolic engineering and integrated fermentation and product recovery techniques has the potential to overcome these challenges. The application of different nanocatalysts to overcome the existing challenges in the biobutanol field is gaining much interest. For the sustainable production of biobutanol, algae, a third-generation feedstock has also been evaluated.
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Affiliation(s)
- Deepika Kushwaha
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU) , Varanasi 221005 , India
| | - Neha Srivastava
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU) , Varanasi 221005 , India
| | - Ishita Mishra
- Green Brick Eco Solutions, Okha Industrial Area , New Delhi 110020 , India
| | - Siddh Nath Upadhyay
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU) , Varanasi 221005 , India
| | - Pradeep Kumar Mishra
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU) , Varanasi 221005 , India
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39
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Effects of mutations of non-catalytic aromatic residues on substrate specificity of Bacillus licheniformis endocellulase cel12A. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Godoy AS, Pereira CS, Ramia MP, Silveira RL, Camilo CM, Kadowaki MA, Lange L, Busk PK, Nascimento AS, Skaf MS, Polikarpov I. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members. Sci Rep 2018; 8:3678. [PMID: 29487297 PMCID: PMC5829257 DOI: 10.1038/s41598-018-21798-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the "Newton's cradle" catalytic mechanism recently proposed for this subfamily.
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Affiliation(s)
- Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Caroline S Pereira
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Marina Paglione Ramia
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Rodrigo L Silveira
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Cesar M Camilo
- Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970, Piracicaba, São Paulo, Brazil
| | - Marco A Kadowaki
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Lene Lange
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark
| | - Peter K Busk
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark
| | - Alessandro S Nascimento
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.
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41
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Production of thermostable β-glucosidase and CMCase by Penicillium sp. LMI01 isolated from the Amazon region. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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42
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Pinar O, Karaosmanoğlu K, Sayar NA, Kula C, Kazan D, Sayar AA. Assessment of hazelnut husk as a lignocellulosic feedstock for the production of fermentable sugars and lignocellulolytic enzymes. 3 Biotech 2017; 7:367. [PMID: 29062677 DOI: 10.1007/s13205-017-1002-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/26/2017] [Indexed: 12/22/2022] Open
Abstract
The present work focuses firstly on the evaluation of the effect of laccase on enzymatic hydrolysis of hazelnut husk which is one of the most abundant lignocellulosic agricultural residues generated in Turkey. In this respect, the co-enzymatic treatment of hazelnut husk by cellulase and laccase, without a conventional pretreatment step is evaluated. Using 2.75 FPU/g substrate (40 g/L substrate) and a ratio of 131 laccase U/FPU achieved the highest reducing sugars concentration. Gas chromatography mass spectrometry confirmed that the hydrolysate was composed of glucose, xylose, mannose, arabinose and galactose. The inclusion of laccase in the enzyme mixture [carboxymethyl cellulase (CMCase) and β-glucosidase] increased the final glucose content of the reducing sugars from 20 to 50%. Therefore, a very significant increase in glucose content of the final reducing sugars concentration was obtained by laccase addition. Furthermore, the production of cellulases and laccase by Pycnoporus sanguineus DSM 3024 using hazelnut husk as substrate was also investigated. Among the hazelnut husk concentrations tested (1.5, 6, 12, 18 g/L), the highest CMCase concentration was obtained using 12 g/L husk concentration on the 10th day of fermentation. Besides CMCase, P. sanguineus DSM 3024 produced β-glucosidase and laccase using hazelnut husk as carbon source. In addition to CMCase and β-glucosidase, the highest laccase activity measured was 2240 ± 98 U/L (8.89 ± 0.39 U/mg). To the best of our knowledge, this is the first study to report hazelnut husk hydrolysis in the absence of pretreatment procedures.
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Affiliation(s)
- Orkun Pinar
- Department of Bioengineering, Faculty of Engineering, Marmara University, Göztepe Campus, Kadıköy, 34722 Istanbul, Turkey
| | - Kübra Karaosmanoğlu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Göztepe Campus, Kadıköy, 34722 Istanbul, Turkey
| | - Nihat Alpagu Sayar
- Department of Bioengineering, Faculty of Engineering, Marmara University, Göztepe Campus, Kadıköy, 34722 Istanbul, Turkey
| | - Ceyda Kula
- Department of Bioengineering, Faculty of Engineering, Marmara University, Göztepe Campus, Kadıköy, 34722 Istanbul, Turkey
| | - Dilek Kazan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Göztepe Campus, Kadıköy, 34722 Istanbul, Turkey
| | - Ahmet Alp Sayar
- Department of Bioengineering, Faculty of Engineering, Marmara University, Göztepe Campus, Kadıköy, 34722 Istanbul, Turkey
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Singhania RR, Patel AK, Pandey A, Ganansounou E. Genetic modification: A tool for enhancing beta-glucosidase production for biofuel application. BIORESOURCE TECHNOLOGY 2017; 245:1352-1361. [PMID: 28596076 DOI: 10.1016/j.biortech.2017.05.126] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 05/25/2023]
Abstract
Beta-glucosidase (BGL) is a rate-limiting enzyme for cellulose hydrolysis as it acts in the final step of lignocellulosic biomass conversion to convert cellobiose into glucose, the final end product. Most of the fungal strains used for cellulase production are deficient in BGL hence BGL is supplemented into cellulases to have an efficient biomass conversion. Genetic engineering has enabled strain modification to produce BGL optimally with desired properties to be employed for biofuel applications. It has been cloned either directly into the host strains lacking BGL or into another expression system, to be overexpressed so as to be blended into BGL deficient cellulases. In this article, role of genetic engineering to overcome BGL limitations in the cellulase cocktail and its significance for biofuel applications has been critically reviewed.
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Affiliation(s)
- Reeta Rani Singhania
- DBT-IOC Advanced Bio-Energy Research Centre, Indian Oil Corporation; R&D Centre, Sector-13, Faridabad 121007, India
| | - Anil Kumar Patel
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu 96822, HI, United States.
| | - Ashok Pandey
- Center of Innovative and Applied Bioprocessing, Sector 81, Knowledge City PO Manauli, SAS Nagar, Mohali 140306, Punjab, India
| | - Edgard Ganansounou
- Bioenergy and Energy Planning Research Group, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Tiwari R, Singh PK, Singh S, Nain PKS, Nain L, Shukla P. Bioprospecting of novel thermostable β-glucosidase from Bacillus subtilis RA10 and its application in biomass hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:246. [PMID: 29093750 PMCID: PMC5663093 DOI: 10.1186/s13068-017-0932-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 10/19/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Saccharification is the most crucial and cost-intensive process in second generation biofuel production. The deficiency of β-glucosidase in commercial enzyme leads to incomplete biomass hydrolysis. The decomposition of biomass at high temperature environments leads us to isolate thermotolerant microbes with β-glucosidase production potential. RESULTS A total of 11 isolates were obtained from compost and cow dung samples that were able to grow at 50 °C. On the basis of qualitative and quantitative estimation of β-glucosidase enzyme production, Bacillus subtilis RA10 was selected for further studies. The medium components and growth conditions were optimized and β-glucosidase enzyme production was enhanced up to 19.8-fold. The β-glucosidase from B. subtilis RA10 retained 78% of activity at 80 °C temperature and 68.32% of enzyme activity was stable even at 50 °C after 48 h of incubation. The supplementation of β-glucosidase from B. subtilis RA10 into commercial cellulase enzyme resulted in 1.34-fold higher glucose release. Furthermore, β-glucosidase was also functionally elucidated by cloning and overexpression of full length GH1 family β-glucosidase gene from B. subtilis RA10. The purified protein was characterized as thermostable β-glucosidase enzyme. CONCLUSIONS The thermostable β-glucosidase enzyme from B. subtilis RA10 would facilitate efficient saccharification of cellulosic biomass into fermentable sugar. Consequently, after saccharification, thermostable β-glucosidase enzyme would be recovered and reused to reduce the cost of overall bioethanol production process.
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Affiliation(s)
- Rameshwar Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012 India
- Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110 016 India
| | - Puneet Kumar Singh
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Surender Singh
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Pawan K. S. Nain
- Design and Mechatronic Division, School of Civil and Mechanical Engineering, Galgotias University, Noida, Uttar Pradesh 201312 India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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45
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Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction. PLoS One 2017; 12:e0186355. [PMID: 29023528 PMCID: PMC5638507 DOI: 10.1371/journal.pone.0186355] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/01/2017] [Indexed: 12/04/2022] Open
Abstract
The gastrointestinal (GI) habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk) and a domesticated goat (Black Bengal) were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF) of D2 (alkaline pretreated pulpy biomass) using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL) and FPase (0.5 U/mL) activities (55°C, pH 8). The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.
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46
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Malgas S, Thoresen M, van Dyk JS, Pletschke BI. Time dependence of enzyme synergism during the degradation of model and natural lignocellulosic substrates. Enzyme Microb Technol 2017; 103:1-11. [DOI: 10.1016/j.enzmictec.2017.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 10/19/2022]
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47
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Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME JOURNAL 2017; 11:2538-2551. [PMID: 28731473 DOI: 10.1038/ismej.2017.108] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
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Affiliation(s)
- Olov Svartström
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Alneberg
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Ino de Bruijn
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jonas Malmsten
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.,Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Marie Dalin
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilie El Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pranjul Shah
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Henrik Aspeborg
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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48
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Borin GP, Sanchez CC, de Santana ES, Zanini GK, Dos Santos RAC, de Oliveira Pontes A, de Souza AT, Dal'Mas RMMTS, Riaño-Pachón DM, Goldman GH, Oliveira JVDC. Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei. BMC Genomics 2017; 18:501. [PMID: 28666414 PMCID: PMC5493111 DOI: 10.1186/s12864-017-3857-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Background Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source. Results Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated. Conclusions This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3857-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Camila Cristina Sanchez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Eliane Silva de Santana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Guilherme Keppe Zanini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Renato Augusto Corrêa Dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Angélica de Oliveira Pontes
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Aline Tieppo de Souza
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Roberta Maria Menegaldo Tavares Soares Dal'Mas
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.,Current address: Laboratório de Biologia de Sistemas Regulatórios, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748 - Butantã - São Paulo - SP, São Paulo, CEP 05508-000, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, Ribeirão Preto, CEP, São Paulo, 14040-903, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.
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Maruthamuthu M, van Elsas JD. Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:142. [PMID: 28588643 PMCID: PMC5457731 DOI: 10.1186/s13068-017-0808-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance. RESULTS Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli. Four of the eight enzymes had significant activities on either pNP-β-d-galactopyranoside, pNP-β-d-xylopyranoside, pNP-α-l-arabinopyranoside or pNP-α-d-glucopyranoside. These proteins, denoted as proteins 1, 2, 5 and 6, were his-tag purified and their nature and activities further characterized using molecular and activity screens with the pNP-labeled substrates. Proteins 1 and 2 showed high homologies with (1) a β-galactosidase (74%) and (2) a β-xylosidase (84%), whereas the remaining two (5 and 6) were homologous with proteins reported as a diguanylate cyclase and an aquaporin, respectively. The β-galactosidase- and β-xylosidase-like proteins 1 and 2 were confirmed as being responsible for previously found thermo-alkaliphilic glycosidase activities of extracts of E. coli carrying the respective source fosmids. Remarkably, the β-xylosidase-like protein 2 showed activities with both pNP-Xyl and pNP-Ara in the temperature range 40-50 °C and pH range 8.0-10.0. Moreover, proteins 5 and 6 showed thermotolerant α-glucosidase activity at pH 10.0. In silico structure prediction of protein 5 revealed the presence of a potential "GGDEF" catalytic site, encoding α-glucosidase activity, whereas that of protein 6 showed a "GDSL" site, encoding a 'new family' α-glucosidase activity. CONCLUSION Using a rational screening approach, we identified and characterized four thermo-alkaliphilic glycosyl hydrolases that have the potential to serve as constituents of enzyme cocktails that produce sugars from lignocellulosic plant remains.
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Affiliation(s)
- Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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Brognaro H, Almeida VM, de Araujo EA, Piyadov V, Santos MAM, Marana SR, Polikarpov I. Biochemical Characterization and Low-Resolution SAXS Molecular Envelope of GH1 β-Glycosidase from Saccharophagus degradans. Mol Biotechnol 2017; 58:777-788. [PMID: 27670285 DOI: 10.1007/s12033-016-9977-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The marine bacteria Saccharophagus degradans (also known as Microbulbifer degradans), are rod-shaped and gram-negative motile γ-proteobacteria, capable of both degrading a variety of complex polysaccharides and fermenting monosaccharides into ethanol. In order to obtain insights into structure-function relationships of the enzymes, involved in these biochemical processes, we characterized a S. degradans β-glycosidase from glycoside hydrolase family 1 (SdBgl1B). SdBgl1B has the optimum pH of 6.0 and a melting temperature T m of approximately 50 °C. The enzyme has high specificity toward short D-glucose saccharides with β-linkages with the following preferences β-1,3 > β-1,4 ≫ β-1,6. The enzyme kinetic parameters, obtained using artificial substrates p-β-NPGlu and p-β-NPFuc and also the disaccharides cellobiose, gentiobiose and laminaribiose, revealed SdBgl1B preference for p-β-NPGlu and laminaribiose, which indicates its affinity for glucose and also preference for β-1,3 linkages. To better understand structural basis of the enzyme activity its 3D model was built and analysed. The 3D model fits well into the experimentally retrieved low-resolution SAXS-based envelope of the enzyme, confirming monomeric state of SdBgl1B in solution.
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Affiliation(s)
- Hevila Brognaro
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Vitor Medeiros Almeida
- Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 748, Bloco 10, Sala 1054, São Paulo, SP, 05508-900, Brazil
| | - Evandro Ares de Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Vasily Piyadov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Maria Auxiliadora Morim Santos
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Sandro Roberto Marana
- Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 748, Bloco 10, Sala 1054, São Paulo, SP, 05508-900, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil.
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