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Chaudhari YB, Várnai A, Sørlie M, Horn SJ, Eijsink VGH. Engineering cellulases for conversion of lignocellulosic biomass. Protein Eng Des Sel 2023; 36:gzad002. [PMID: 36892404 PMCID: PMC10394125 DOI: 10.1093/protein/gzad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.
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Affiliation(s)
- Yogesh B Chaudhari
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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Photodynamic treatment affects the secreted antioxidant and glycoside hydrolases activities produced by Humicola grisea var. thermoidea and Penicillium echinulatum in agro-industrial substrates. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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3
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Kim IJ, Jeong D, Kim SR. Upstream processes of citrus fruit waste biorefinery for complete valorization. BIORESOURCE TECHNOLOGY 2022; 362:127776. [PMID: 35970501 DOI: 10.1016/j.biortech.2022.127776] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Citrus fruit waste (CW) is a useful biomass and its valorization into fuels and biochemicals has received much attention. For economic feasibility, increased efficiency of the preceding extraction and enzyme saccharification processes is necessary. However, at present, there is a lack of systematic reviews addressing these two integral upstream processes in concert for CW biorefinery. Here, the state-of-the-art advancements in enzyme extraction and saccharification processes-using which relevant essential oils, flavonoids, and sugars can be obtained-are reviewed. Specifically, the extraction options for two commercially available CW-derived products, essential oils and pectin, are discussed. With respect to enzyme saccharification, the use of an undefined commercial mixture routinely results in suboptimal sugar production. In this respect, applicable strategies for enzyme mixture customization are suggested for maximizing the hydrolytic efficiency of CW. The enzyme degradation system for CW-derived carbohydrates and its extensive application for sugar production are also discussed.
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Affiliation(s)
- In Jung Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; Research Institute of Tailored Food Technology, Kyungpook National University, Daegu 41566, Korea.
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Bhalla A, Arce J, Ubanwa B, Singh G, Sani RK, Balan V. Thermophilic Geobacillus WSUCF1 Secretome for Saccharification of Ammonia Fiber Expansion and Extractive Ammonia Pretreated Corn Stover. Front Microbiol 2022; 13:844287. [PMID: 35694290 PMCID: PMC9176393 DOI: 10.3389/fmicb.2022.844287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
A thermophilic Geobacillus bacterial strain, WSUCF1 contains different carbohydrate-active enzymes (CAZymes) capable of hydrolyzing hemicellulose in lignocellulosic biomass. We used proteomic, genomic, and bioinformatic tools, and genomic data to analyze the relative abundance of cellulolytic, hemicellulolytic, and lignin modifying enzymes present in the secretomes. Results showed that CAZyme profiles of secretomes varied based on the substrate type and complexity, composition, and pretreatment conditions. The enzyme activity of secretomes also changed depending on the substrate used. The secretomes were used in combination with commercial and purified enzymes to carry out saccharification of ammonia fiber expansion (AFEX)-pretreated corn stover and extractive ammonia (EA)-pretreated corn stover. When WSUCF1 bacterial secretome produced at different conditions was combined with a small percentage of commercial enzymes, we observed efficient saccharification of EA-CS, and the results were comparable to using a commercial enzyme cocktail (87% glucan and 70% xylan conversion). It also opens the possibility of producing CAZymes in a biorefinery using inexpensive substrates, such as AFEX-pretreated corn stover and Avicel, and eliminates expensive enzyme processing steps that are used in enzyme manufacturing. Implementing in-house enzyme production is expected to significantly reduce the cost of enzymes and biofuel processing cost.
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Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
| | - Jessie Arce
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Bryan Ubanwa
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, India
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkatesh Balan
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
- *Correspondence: Venkatesh Balan,
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Arnthong J, Siamphan C, Chuaseeharonnachai C, Boonyuen N, Suwannarangsee S. Towards a Miniaturized Culture Screening for Cellulolytic Fungi and Their Agricultural Lignocellulosic Degradation. J Microbiol Biotechnol 2020; 30:1670-1679. [PMID: 32876068 PMCID: PMC9728337 DOI: 10.4014/jmb.2007.07005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022]
Abstract
The substantial use of fungal enzymes to degrade lignocellulosic plant biomass has widely been attributed to the extensive requirement of powerful enzyme-producing fungal strains. In this study, a two-step screening procedure for finding cellulolytic fungi, involving a miniaturized culture method with shake-flask fermentation, was proposed and demonstrated. We isolated 297 fungal strains from several cellulose-containing samples found in two different locations in Thailand. By using this screening strategy, we then selected 9 fungal strains based on their potential for cellulase production. Through sequence-based identification of these fungal isolates, 4 species in 4 genera were identified: Aspergillus terreus (3 strains: AG466, AG438 and AG499), Penicillium oxalicum (4 strains: AG452, AG496, AG498 and AG559), Talaromyces siamensis (1 strain: AG548) and Trichoderma afroharzianum (1 strain: AG500). After examining their lignocellulose degradation capacity, our data showed that P. oxalicum AG452 exhibited the highest glucose yield after saccharification of pretreated sugarcane trash, cassava pulp and coffee silverskin. In addition, Ta. siamensis AG548 produced the highest glucose yield after hydrolysis of pretreated sugarcane bagasse. Our study demonstrated that the proposed two-step screening strategy can be further applied for discovering potential cellulolytic fungi isolated from various environmental samples. Meanwhile, the fungal strains isolated in this study will prove useful in the bioconversion of agricultural lignocellulosic residues into valuable biotechnological products.
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Affiliation(s)
- Jantima Arnthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Chatuphon Siamphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Charuwan Chuaseeharonnachai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Surisa Suwannarangsee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand,Corresponding author Phone: +66-2564 6700 Fax: +66-2564-6700 E-mail:
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Abstract
A crucial factor that determines the development of production and consumption markets for biofuels is the choice of raw materials that can ensure the highest possible production efficiency, the lowest cost and the smallest emission of harmful substances to the atmosphere during all production stages. Considerations underlying the development of biofuel production have been discussed as well as the theoretical mechanisms linking the generation of biofuels to the level of production and the variability of prices of agricultural raw products. The aim of this study has been to identify the scale at which energy raw materials originating from agriculture are used for liquid biofuels production and to explore their impact on food security. The study used public statistical data (OECD-FAO and IndexMundi). The time span of the analysis was from 2005 to 2018. First-generation biofuels based on food raw materials (cereal grains, root crops, sugarcane and vegetable oils) are becoming increasingly competitive with food production recent years have been a period of the dynamic growth in production of liquid biofuels. In 2018, the global production of these substances reached 167.9 billion litres (bioethanol and biodiesel together), consuming 16.1% of maize grain, 1.7% of wheat grain, 3.3% of grain of other feed grains and 13.5% of vegetable oil.
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Liew YX, Chan YJ, Manickam S, Chong MF, Chong S, Tiong TJ, Lim JW, Pan GT. Enzymatic pretreatment to enhance anaerobic bioconversion of high strength wastewater to biogas: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136373. [PMID: 31954239 DOI: 10.1016/j.scitotenv.2019.136373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/24/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
Oil and grease, carbohydrate, protein, and lignin are the main constituents of high strength wastewaters such as dairy wastewater, cheese whey wastewater, distillery wastewater, pulp and paper mill wastewater, and slaughterhouse wastewaters. These constituents have contributed to various operational problems faced by the high-rate anaerobic bioreactor (HRAB). During the hydrolysis stage of anaerobic digestion (AD), these constituents can be hydrolyzed. Since hydrolysis is known to be the rate-limiting step of AD, the overall AD can be enhanced by improving the hydrolysis stage. This can be done by introducing pretreatment that targets the degradation of these constituents. This review mainly focuses on the biological pretreatment on various high-strength wastewaters by using different types of enzymes namely lipase, amylase, protease, and ligninolytic enzymes which are responsible for catalyzing the degradation of oil and grease, carbohydrate, protein, and lignin respectively. This review provides a summary of enzymatic systems involved in enhancing the hydrolysis stage and consequently improve biogas production. The results show that the use of enzymes improves the biogas production in the range of 7 to 76%. Though these improvements are highly dependent on the operating conditions of pretreatment and the types of substrates. Therefore, the critical parameters that would affect the effectiveness of pretreatment are also discussed. This review paper will serve as a useful piece of information to those industries that face difficulties in treating their high-strength wastewaters for the appropriate process, equipment selection, and design of an anaerobic enzymatic system. However, more intensive studies on the optimum operating conditions of pretreatment in a larger-scale and synergistic effects between enzymes are necessary to make the enzymatic pretreatment economically feasible.
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Affiliation(s)
- Yuh Xiu Liew
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia
| | - Yi Jing Chan
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Sivakumar Manickam
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Mei Fong Chong
- 28, Jalan Pulau Tioman U10/94, Taman Greenhill, Shah Alam 40170, Selangor Darul Ehsan, Malaysia
| | - Siewhui Chong
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Timm Joyce Tiong
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Jun Wei Lim
- Department of Fundamental and Applied Sciences, Centre for Biofuel and Biochemical Research, Institute of Self-Sustainable Building, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Guan-Ting Pan
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No. 1, Section 3, Zhongxiao E Rd, Da'an District, 106 Taipei City, Taiwan, ROC.
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High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates. Appl Microbiol Biotechnol 2020; 104:3379-3389. [PMID: 32114675 PMCID: PMC7089899 DOI: 10.1007/s00253-020-10469-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/12/2019] [Accepted: 02/12/2020] [Indexed: 11/08/2022]
Abstract
Carbohydrate degradation by microbes plays an important role in global nutrient cycling, human nutrition, and biotechnological applications. Studies that focus on the degradation of complex recalcitrant polysaccharides are challenging because of the insolubility of these substrates as found in their natural contexts. Specifically, current methods to examine carbohydrate-based biomass degradation using bacterial strains or purified enzymes are not compatible with high-throughput screening using complex insoluble materials. In this report, we developed a small 3D printed filter device that fits inside a microplate well that allows for the free movement of bacterial cells, media, and enzymes while containing insoluble biomass. These devices do not interfere with standard microplate readers and can be used for both short- (24–48 h) and long-duration (> 100 h) experiments using complex insoluble substrates. These devices were used to quantitatively screen in a high-throughput manner environmental isolates for their ability to grow using lignocellulose or rice grains as a sole nutrient source. Additionally, we determined that the microplate-based containment devices are compatible with existing enzymatic assays to measure activity against insoluble biomass. Overall, these microplate containment devices provide a platform to study the degradation of complex insoluble materials in a high-throughput manner and have the potential to help uncover ecologically important aspects of bacterial metabolism as well as to accelerate biotechnological innovation.
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Bussamra BC, Gomes JC, Freitas S, Mussatto SI, da Costa AC, van der Wielen L, Ottens M. A robotic platform to screen aqueous two-phase systems for overcoming inhibition in enzymatic reactions. BIORESOURCE TECHNOLOGY 2019; 280:37-50. [PMID: 30754004 DOI: 10.1016/j.biortech.2019.01.136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/27/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Aqueous two-phase systems (ATPS) can be applied to enzymatic reactions that are affected by product inhibition. In the biorefinery context, sugars inhibit the cellulolytic enzymes in charge of converting the biomass. Here, we present a strategy to select an ATPS (formed by polymer and salt) that can separate sugar and enzymes. This automated and miniaturized method is able to determine phase diagrams and partition coefficients of solutes in these. Tailored approaches to quantify the solutes are presented, taking into account the limitations of techniques that can be applied with ATPS due to the interference of phase forming components with the analytics. The developed high-throughput (HT) platform identifies suitable phase forming components and the tie line of operation. This fast methodology proposes to screen up to six different polymer-salt systems in eight days and supplies the results to understand the influence of sugar and protein concentrations on their partition coefficients.
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Affiliation(s)
- Bianca Consorti Bussamra
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands; Development of Processes and Products (DDPP), University of Campinas, Av. Albert Einstein, 500, 6066 Campinas, Brazil.
| | - Joana Castro Gomes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Sindelia Freitas
- Development of Processes and Products (DDPP), University of Campinas, Av. Albert Einstein, 500, 6066 Campinas, Brazil
| | - Solange I Mussatto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark.
| | - Aline Carvalho da Costa
- Development of Processes and Products (DDPP), University of Campinas, Av. Albert Einstein, 500, 6066 Campinas, Brazil.
| | - Luuk van der Wielen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands; Bernal Institute, University of Limerick, Castletroy, Limerick, Ireland.
| | - Marcel Ottens
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands.
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Analytical Enzymatic Saccharification of Lignocellulosic Biomass for Conversion to Biofuels and Bio-Based Chemicals. ENERGIES 2018. [DOI: 10.3390/en11112936] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lignocellulosic feedstocks are an important resource for biorefining of renewables to bio-based fuels, chemicals, and materials. Relevant feedstocks include energy crops, residues from agriculture and forestry, and agro-industrial and forest-industrial residues. The feedstocks differ with respect to their recalcitrance to bioconversion through pretreatment and enzymatic saccharification, which will produce sugars that can be further converted to advanced biofuels and other products through microbial fermentation processes. In analytical enzymatic saccharification, the susceptibility of lignocellulosic samples to pretreatment and enzymatic saccharification is assessed in analytical scale using high-throughput or semi-automated techniques. This type of analysis is particularly relevant for screening of large collections of natural or transgenic varieties of plants that are dedicated to production of biofuels or other bio-based chemicals. In combination with studies of plant physiology and cell wall chemistry, analytical enzymatic saccharification can provide information about the fundamental reasons behind lignocellulose recalcitrance as well as about the potential of collections of plants or different fractions of plants for industrial biorefining. This review is focused on techniques used by researchers for screening the susceptibility of plants to pretreatment and enzymatic saccharification, and advantages and disadvantages that are associated with different approaches.
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Zhou L, da Costa Sousa L, Dale BE, Feng JX, Balan V. The effect of alkali-soluble lignin on purified core cellulase and hemicellulase activities during hydrolysis of extractive ammonia-pretreated lignocellulosic biomass. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171529. [PMID: 30110471 PMCID: PMC6030313 DOI: 10.1098/rsos.171529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 05/14/2018] [Indexed: 05/31/2023]
Abstract
Removing alkali-soluble lignin using extractive ammonia (EA) pretreatment of corn stover (CS) is known to improve biomass conversion efficiency during enzymatic hydrolysis. In this study, we investigated the effect of alkali-soluble lignin on six purified core glycosyl hydrolases and their enzyme synergies, adopting 31 enzyme combinations derived by a five-component simplex centroid model, during EA-CS hydrolysis. Hydrolysis experiment was carried out using EA-CS(-) (approx. 40% lignin removed during EA pretreatment) and EA-CS(+) (where no lignin was extracted). Enzymatic hydrolysis experiments were done at three different enzyme mass loadings (7.5, 15 and 30 mg protein g-1 glucan), using a previously developed high-throughput microplate-based protocol, and the sugar yields of glucose and xylose were detected. The optimal enzyme combinations (based on % protein mass loading) of six core glycosyl hydrolases for EA-CS(-) and EA-CS(+) were determined that gave high sugar conversion. The inhibition of lignin on optimal enzyme ratios was studied, by adding fixed amount of alkali-soluble lignin fractions to EA-CS(-), and pure Avicel, beechwood xylan and evaluating their sugar conversion. The optimal enzyme ratios that gave higher sugar conversion for EA-CS(-) were CBH I: 27.2-28.2%, CBH II: 18.2-22.2%, EG I: 29.2-34.3%, EX: 9.0-14.1%, βX: 7.2-10.2%, βG: 1.0-5.0% (at 7.5-30 mg g-1 protein mass loading). Endoglucanase was inhibited to a greater extent than other core cellulases and xylanases by lignin during enzyme hydrolysis. We also found that alkali-soluble lignin inhibits cellulase more strongly than hemicellulase during the course of enzyme hydrolysis.
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Affiliation(s)
- Linchao Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, People's Republic of China
| | - Leonardo da Costa Sousa
- DOE Great Lakes Bioenergy Research Center (GLBRC), Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48910, USA
| | - Bruce E. Dale
- DOE Great Lakes Bioenergy Research Center (GLBRC), Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48910, USA
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, People's Republic of China
| | - Venkatesh Balan
- DOE Great Lakes Bioenergy Research Center (GLBRC), Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48910, USA
- Department of Engineering Technology, Biotechnology Division, School of Technology, University of Houston, Houston, TX 77004, USA
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Abstract
Testing of cellulases on real biomass samples is required to do a true assessment of their efficacy for biomass degradation. Cellulase enzymes belong to a number of different glycosyl hydrolase families, all with different activity, specificity and modes of action. The concerted and synergistic action of these different cellulases determines the efficacy for plant cell wall deconstruction and cellulose hydrolysis. However, the plant cell wall of lignocellulosic materials is a very complex matrix and the efficacy of a cellulase preparation to degrade lignocellulosic materials is influenced by many factors. In this chapter, two protocols for testing efficacy of cellulases on pretreated biomass samples are described. The first protocol describes a small-scale setup employing low solids concentration that easily enables the testing of a larger number of samples. The second protocol describes a method for testing the efficacy of cellulases at conditions more closely resembling industrial conditions, i.e., high solids concentrations. Both protocols can be used to test the cellulases under a variety of substrate types, substrate concentrations, enzyme loadings and process conditions. The protocols can also be used to evaluate different feedstocks.
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Affiliation(s)
- Henning Jørgensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
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Selekman JA, Qiu J, Tran K, Stevens J, Rosso V, Simmons E, Xiao Y, Janey J. High-Throughput Automation in Chemical Process Development. Annu Rev Chem Biomol Eng 2017; 8:525-547. [DOI: 10.1146/annurev-chembioeng-060816-101411] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua A. Selekman
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Jun Qiu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Kristy Tran
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Jason Stevens
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Victor Rosso
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Eric Simmons
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Yi Xiao
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Jacob Janey
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
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14
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Yu X, Liu Y, Cui Y, Cheng Q, Zhang Z, Lu JH, Meng Q, Teng L, Ren X. Measurement of filter paper activities of cellulase with microplate-based assay. Saudi J Biol Sci 2016; 23:S93-8. [PMID: 26858572 PMCID: PMC4705267 DOI: 10.1016/j.sjbs.2015.06.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 06/19/2015] [Accepted: 06/20/2015] [Indexed: 11/05/2022] Open
Abstract
It is always a challenge to determine the total cellulase activity efficiently without reducing accuracy. The most common total cellulase activity assay is the filter paper assay (FPA) established by the International Union of Pure and Applied Chemistry (IUPAC). A new procedure to measure the FPA with microplate-based assay was studied in this work, which followed the main idea of IUPAC to dilute cellulase preparation to get fixed glucose release. FPAs of six cellulase preparations were determined with the microplate-based assay. It is shown that FPAs of cellulase Youtell, RCconc, R-10, Lerkam, Yishui and Sinopharm were 67.9, 46.0, 46.1, 27.4, 7.6 and 8.0 IU/ml respectively. There was no significant difference at the 95% confidence level between the FPA determined with IUPAC and the microplate-based assay. It could be concluded that the FPA could be determined by the microplate-based assay with the same accuracy and much more efficiency compared with that by IUPAC.
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Affiliation(s)
- Xiaoxiao Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, China
| | - Yan Liu
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Yuxiao Cui
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Qiyue Cheng
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Zaixiao Zhang
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Jia Hui Lu
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Qingfan Meng
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Lirong Teng
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Xiaodong Ren
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
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15
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Chundawat SPS, Paavola CD, Raman B, Nouailler M, Chan SL, Mielenz JR, Receveur-Brechot V, Trent JD, Dale BE. Saccharification of thermochemically pretreated cellulosic biomass using native and engineered cellulosomal enzyme systems. REACT CHEM ENG 2016. [DOI: 10.1039/c6re00172f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Tethering hydrolytic enzymes (e.g., cellulases) to protein scaffolds enhances biomass saccharification to sugars.
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Affiliation(s)
- Shishir P. S. Chundawat
- Department of Chemical & Biochemical Engineering
- The State University of New Jersey
- Piscataway
- USA
- DOE Great Lakes Bioenergy Research Center (GLBRC)
| | | | - Babu Raman
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Matthieu Nouailler
- LISM-UMR 7255 Institut De Microbiologie De La Mediterranee
- CNRS and Aix-Marseille University
- 13402 Marseille Cedex 20
- France
| | | | - Jonathan R. Mielenz
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | | | - Jonathan D. Trent
- Bioengineering Branch
- NASA Ames
- Moffett Field
- USA
- Biomolecular Engineering Department
| | - Bruce E. Dale
- DOE Great Lakes Bioenergy Research Center (GLBRC)
- Michigan State University
- East Lansing
- USA
- Chemical Engineering and Materials Science
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16
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Conroy N, Tebble I, Lye GJ. Creation of an ultra scale-down bioreactor mimic for rapid development of lignocellulosic enzymatic hydrolysis processes. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2015; 90:1983-1990. [PMID: 27594729 PMCID: PMC4989448 DOI: 10.1002/jctb.4801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/18/2015] [Accepted: 08/18/2015] [Indexed: 06/06/2023]
Abstract
BACKGROUND Cellulosic bioethanol processes involve several steps, all of which require experimental optimisation. A significant aid to this research would be a validated ultra scale-down (USD) model that could be used to perform rapid, wide ranging screening and optimisation experiments using limited materials under process relevant conditions. RESULTS In this work, the use of 30 mL shaken conical tubes as a USD model for an enzymatic hydrolysis process is established. The approach is demonstrated for the hydrolysis of distillers' dried grains with solubles (DDGS). Results from the USD tubes closely mimic those obtained from 4 L stirred tanks, in terms of the rate, composition and concentrations of sugars released, representing an 80-fold scale reduction. The utility of the USD approach is illustrated by investigating factors that may be limiting hydrolysis yields at high solids loadings. Washing the residual solids periodically during hydrolysis allowed 100% of the available sugar to be hydrolysed using commercially available enzymes. CONCLUSION The results demonstrate that the USD system reported successfully mimics the performance of conventional stirred tanks under industrially relevant conditions. The utility of the system was confirmed through its use to investigate performance limitation using a commercially relevant feedstock. © 2015 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Neil Conroy
- ReBio Technologies LtdUnit 59 Dunsfold ParkCranleighSurreyGU6 8TBUK; The Advanced Centre for Biochemical Engineering, Department of Biochemical EngineeringUniversity College LondonGordon StreetLondonWC1H 0AHUK
| | - Ian Tebble
- ReBio Technologies Ltd Unit 59 Dunsfold Park Cranleigh Surrey GU6 8TB UK
| | - Gary J Lye
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering University College London Gordon Street London WC1H 0AH UK
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17
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Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol 2015; 3:165. [PMID: 26579511 PMCID: PMC4621489 DOI: 10.3389/fbioe.2015.00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022] Open
Abstract
Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential removal of glucose by the β-glucosidase and a progressive increase in specificity of reaction from endoglucanases to cellobiohydrolase. Time-dependent reactions of these polysaccharide-selective enzymes were modeled by numerical integration, which provides a quantitative basis to make functional distinctions among a continuum of naturally evolved catalytic properties. Consequently, our method, which combines automated protein translation with high-sensitivity and time-dependent detection of multiple products, provides a new approach to annotate glycoside hydrolase phylogenetic trees with functional measurements.
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Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Christopher M Bianchetti
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Chemistry, University of Wisconsin-Oshkosh , Oshkosh, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin-Madison , Madison, WI , USA
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18
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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19
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Improvement in Saccharification Yield of Mixed Rumen Enzymes by Identification of Recalcitrant Cell Wall Constituents Using Enzyme Fingerprinting. BIOMED RESEARCH INTERNATIONAL 2015; 2015:562952. [PMID: 26180803 PMCID: PMC4477221 DOI: 10.1155/2015/562952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 11/17/2022]
Abstract
Identification of recalcitrant factors that limit digestion of forages and the development of enzymatic approaches that improve hydrolysis could play a key role in improving the efficiency of meat and milk production in ruminants. Enzyme fingerprinting of barley silage fed to heifers and total tract indigestible fibre residue (TIFR) collected from feces was used to identify cell wall components resistant to total tract digestion. Enzyme fingerprinting results identified acetyl xylan esterases as key to the enhanced ruminal digestion. FTIR analysis also suggested cross-link cell wall polymers as principal components of indigested fiber residues in feces. Based on structural information from enzymatic fingerprinting and FTIR, enzyme pretreatment to enhance glucose yield from barley straw and alfalfa hay upon exposure to mixed rumen-enzymes was developed. Prehydrolysis effects of recombinant fungal fibrolytic hydrolases were analyzed using microassay in combination with statistical experimental design. Recombinant hemicellulases and auxiliary enzymes initiated degradation of plant structural polysaccharides upon application and improved the in vitro saccharification of alfalfa and barley straw by mixed rumen enzymes. The validation results showed that microassay in combination with statistical experimental design can be successfully used to predict effective enzyme pretreatments that can enhance plant cell wall digestion by mixed rumen enzymes.
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20
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Malinowska KH, Rind T, Verdorfer T, Gaub HE, Nash MA. Quantifying Synergy, Thermostability, and Targeting of Cellulolytic Enzymes and Cellulosomes with Polymerization-Based Amplification. Anal Chem 2015; 87:7133-40. [DOI: 10.1021/acs.analchem.5b00936] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Klara H. Malinowska
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Thomas Rind
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Tobias Verdorfer
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Hermann E. Gaub
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Michael A. Nash
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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21
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Enhanced Biological Straw Saccharification Through Coculturing of Lignocellulose-Degrading Microorganisms. Appl Biochem Biotechnol 2015; 175:3709-28. [DOI: 10.1007/s12010-015-1539-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/06/2015] [Indexed: 11/26/2022]
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22
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Elliston A, Wood IP, Soucouri MJ, Tantale RJ, Dicks J, Roberts IN, Waldron KW. Methodology for enabling high-throughput simultaneous saccharification and fermentation screening of yeast using solid biomass as a substrate. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:2. [PMID: 25648300 PMCID: PMC4314751 DOI: 10.1186/s13068-014-0181-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND High-throughput (HTP) screening is becoming an increasingly useful tool for collating biological data which would otherwise require the employment of excessive resources. Second generation biofuel production is one such process. HTP screening allows the investigation of large sample sets to be undertaken with increased speed and cost effectiveness. This paper outlines a methodology that will enable solid lignocellulosic substrates to be hydrolyzed and fermented at a 96-well plate scale, facilitating HTP screening of ethanol production, whilst maintaining repeatability similar to that achieved at a larger scale. RESULTS The results showed that utilizing sheets of biomass of consistent density (handbills), for paper, and slurries of pretreated biomass that could be pipetted allowed standardized and accurate transfers to 96-well plates to be achieved (±3.1 and 1.7%, respectively). Processing these substrates by simultaneous saccharification and fermentation (SSF) at various volumes showed no significant difference on final ethanol yields, either at standard shake flask (200 mL), universal bottle (10 mL) or 96-well plate (1 mL) scales. Substrate concentrations of up to 10% (w/v) were trialed successfully for SSFs at 1 mL volume. The methodology was successfully tested by showing the effects of steam explosion pretreatment on both oilseed rape and wheat straws. CONCLUSIONS This methodology could be used to replace large shake flask reactions with comparatively fast 96-well plate SSF assays allowing for HTP experimentation. Additionally this method is compatible with a number of standardized assay techniques such as simple colorimetric, High-performance liquid chromatography (HPLC) and Nuclear magnetic resonance (NMR) spectroscopy. Furthermore this research has practical uses in the biorefining of biomass substrates for second generation biofuels and novel biobased chemicals by allowing HTP SSF screening, which should allow selected samples to be scaled up or studied in more detail.
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Affiliation(s)
- Adam Elliston
- />The Biorefinery Centre, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA UK
| | - Ian P Wood
- />The Biorefinery Centre, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA UK
| | - Marie J Soucouri
- />The Biorefinery Centre, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA UK
- />École supérieure d’ingénieurs Réunion Océan Indien, Génie Biologique, Université de La Réunion, Parc Technologique Universitaire, 2 Rue Joseph Wetzell, 97490 Sainte-Clotilde, La Réunion France
| | - Rachelle J Tantale
- />The Biorefinery Centre, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA UK
- />Institut Universitaire de Technologie, Universite de la Reunion, 40 avenue de Soweto, BP 373, 97455 Saint-Pierre Cedex, La Réunion France
| | - Jo Dicks
- />The National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA UK
| | - Ian N Roberts
- />The National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA UK
| | - Keith W Waldron
- />The Biorefinery Centre, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA UK
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23
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Analytical Methods for Lignocellulosic Biomass Structural Polysaccharides. POLYSACCHARIDES 2015. [DOI: 10.1007/978-3-319-16298-0_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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24
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Payne CE, Wolfrum EJ. Rapid analysis of composition and reactivity in cellulosic biomass feedstocks with near-infrared spectroscopy. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:43. [PMID: 25834638 PMCID: PMC4381445 DOI: 10.1186/s13068-015-0222-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/04/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Obtaining accurate chemical composition and reactivity (measures of carbohydrate release and yield) information for biomass feedstocks in a timely manner is necessary for the commercialization of biofuels. Our objective was to use near-infrared (NIR) spectroscopy and partial least squares (PLS) multivariate analysis to develop calibration models to predict the feedstock composition and the release and yield of soluble carbohydrates generated by a bench-scale dilute acid pretreatment and enzymatic hydrolysis assay. Major feedstocks included in the calibration models are corn stover, sorghum, switchgrass, perennial cool season grasses, rice straw, and miscanthus. RESULTS We present individual model statistics to demonstrate model performance and validation samples to more accurately measure predictive quality of the models. The PLS-2 model for composition predicts glucan, xylan, lignin, and ash (wt%) with uncertainties similar to primary measurement methods. A PLS-2 model was developed to predict glucose and xylose release following pretreatment and enzymatic hydrolysis. An additional PLS-2 model was developed to predict glucan and xylan yield. PLS-1 models were developed to predict the sum of glucose/glucan and xylose/xylan for release and yield (grams per gram). The release and yield models have higher uncertainties than the primary methods used to develop the models. CONCLUSION It is possible to build effective multispecies feedstock models for composition, as well as carbohydrate release and yield. The model for composition is useful for predicting glucan, xylan, lignin, and ash with good uncertainties. The release and yield models have higher uncertainties; however, these models are useful for rapidly screening sample populations to identify unusual samples.
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Affiliation(s)
- Courtney E Payne
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Edward J Wolfrum
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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25
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Gao D, Haarmeyer C, Balan V, Whitehead TA, Dale BE, Chundawat SPS. Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:175. [PMID: 25530803 PMCID: PMC4272552 DOI: 10.1186/s13068-014-0175-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/27/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Non-productive binding of enzymes to lignin is thought to impede the saccharification efficiency of pretreated lignocellulosic biomass to fermentable sugars. Due to a lack of suitable analytical techniques that track binding of individual enzymes within complex protein mixtures and the difficulty in distinguishing the contribution of productive (binding to specific glycans) versus non-productive (binding to lignin) binding of cellulases to lignocellulose, there is currently a poor understanding of individual enzyme adsorption to lignin during the time course of pretreated biomass saccharification. RESULTS In this study, we have utilized an FPLC (fast protein liquid chromatography)-based methodology to quantify free Trichoderma reesei cellulases (namely CBH I, CBH II, and EG I) concentration within a complex hydrolyzate mixture during the varying time course of biomass saccharification. Three pretreated corn stover (CS) samples were included in this study: Ammonia Fiber Expansion(a) (AFEX™-CS), dilute acid (DA-CS), and ionic liquid (IL-CS) pretreatments. The relative fraction of bound individual cellulases varied depending not only on the pretreated biomass type (and lignin abundance) but also on the type of cellulase. Acid pretreated biomass had the highest levels of non-recoverable cellulases, while ionic liquid pretreated biomass had the highest overall cellulase recovery. CBH II has the lowest thermal stability among the three T. reesei cellulases tested. By preparing recombinant family 1 carbohydrate binding module (CBM) fusion proteins, we have shown that family 1 CBMs are highly implicated in the non-productive binding of full-length T. reesei cellulases to lignin. CONCLUSIONS Our findings aid in further understanding the complex mechanisms of non-productive binding of cellulases to pretreated lignocellulosic biomass. Developing optimized pretreatment processes with reduced or modified lignin content to minimize non-productive enzyme binding or engineering pretreatment-specific, low-lignin binding cellulases will improve enzyme specific activity, facilitate enzyme recycling, and thereby permit production of cheaper biofuels.
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Affiliation(s)
- Dahai Gao
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
| | - Carolyn Haarmeyer
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
| | - Venkatesh Balan
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
| | - Timothy A Whitehead
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824 USA
| | - Bruce E Dale
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
| | - Shishir PS Chundawat
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
- />Department of Chemical & Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Room C-150A, Piscataway, NJ 08854 USA
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26
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Takasuka TE, Walker JA, Bergeman LF, Vander Meulen KA, Makino SI, Elsen NL, Fox BG. Cell-free translation of biofuel enzymes. Methods Mol Biol 2014; 1118:71-95. [PMID: 24395410 DOI: 10.1007/978-1-62703-782-2_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In nature, bacteria and fungi are able to utilize recalcitrant plant materials by secreting a diverse set of enzymes. While genomic sequencing efforts offer exhaustive lists of genes annotated as potential polysaccharide-degrading enzymes, biochemical and functional characterizations of the encoded proteins are still needed to realize the full potential of this natural genomic diversity. This chapter outlines an application of wheat germ cell-free translation to the study of biofuel enzymes using genes from Clostridium thermocellum, a model cellulolytic organism. Since wheat germ extract lacks enzymatic activities that can hydrolyze insoluble polysaccharide substrates and is likewise devoid of enzymes that consume the soluble sugar products, the cell-free translation reactions provide a clean background for production and study of the reactions of biofuel enzymes. Examples of assays performed with individual enzymes or with small sets of enzymes obtained directly from cell-free translation are provided.
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Affiliation(s)
- Taichi E Takasuka
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
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27
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Badhan A, Wang Y, Gruninger R, Patton D, Powlowski J, Tsang A, McAllister T. Formulation of enzyme blends to maximize the hydrolysis of alkaline peroxide pretreated alfalfa hay and barley straw by rumen enzymes and commercial cellulases. BMC Biotechnol 2014; 14:31. [PMID: 24766728 PMCID: PMC4022426 DOI: 10.1186/1472-6750-14-31] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efficient conversion of lignocellulosic biomass to fermentable sugars requires the synergistic action of multiple enzymes; consequently enzyme mixtures must be properly formulated for effective hydrolysis. The nature of an optimal enzyme blends depends on the type of pretreatment employed as well the characteristics of the substrate. In this study, statistical experimental design was used to develop mixtures of recombinant glycosyl hydrolases from thermophilic and anaerobic fungi that enhanced the digestion of alkaline peroxide treated alfalfa hay and barley straw by mixed rumen enzymes as well as commercial cellulases (Accelerase 1500, A1500; Accelerase XC, AXC). RESULTS Combinations of feruloyl and acetyl xylan esterases (FAE1a; AXE16A_ASPNG), endoglucanase GH7 (EGL7A_THITE) and polygalacturonase (PGA28A_ASPNG) with rumen enzymes improved straw digestion. Inclusion of pectinase (PGA28A_ASPNG), endoxylanase (XYN11A_THITE), feruloyl esterase (FAE1a) and β-glucosidase (E-BGLUC) with A1500 or endoglucanase GH7 (EGL7A_THITE) and β-xylosidase (E-BXSRB) with AXC increased glucose release from alfalfa hay. Glucose yield from straw was improved when FAE1a and endoglucanase GH7 (EGL7A_THITE) were added to A1500, while FAE1a and AXE16A_ASPNG enhanced the activity of AXC on straw. Xylose release from alfalfa hay was augmented by supplementing A1500 with E-BGLUC, or AXC with EGL7A_THITE and XYN11A_THITE. Adding arabinofuranosidase (ABF54B_ASPNG) and esterases (AXE16A_ASPNG; AXE16B_ASPNG) to A1500, or FAE1a and AXE16A_ASPNG to AXC enhanced xylose release from barley straw, a response confirmed in a scaled up assay. CONCLUSION The efficacy of commercial enzyme mixtures as well as mixed enzymes from the rumen was improved through formulation with synergetic recombinant enzymes. This approach reliably identified supplemental enzymes that enhanced sugar release from alkaline pretreated alfalfa hay and barley straw.
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Affiliation(s)
| | | | | | | | | | | | - Tim McAllister
- Agriculture and Agri food Canada, Lethbridge research Centre, Lethbridge, Alberta, Canada.
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28
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Goacher RE, Selig MJ, Master ER. Advancing lignocellulose bioconversion through direct assessment of enzyme action on insoluble substrates. Curr Opin Biotechnol 2014; 27:123-33. [PMID: 24525082 DOI: 10.1016/j.copbio.2014.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/16/2014] [Accepted: 01/17/2014] [Indexed: 11/26/2022]
Abstract
Microbial utilization of lignocellulose from plant cell walls is integral to carbon cycling on Earth. Correspondingly, secreted enzymes that initiate lignocellulose depolymerization serve a crucial step in the bioconversion of lignocellulosic biomass to fuels and chemicals. Genome and metagenome sequencing efforts that span the past decade reveal the diversity of enzymes that have evolved to transform lignocellulose from wood, herbaceous plants and grasses. Nevertheless, there are relatively few examples where 'omic' technologies have identified novel enzyme activities or combinations thereof that dramatically improve the economics of lignocellulose bioprocessing and utilization. A likely factor contributing to the discrepancy between sequence-based enzyme discovery and enzyme application is the common practice to screen enzyme candidates based on activity measurements using soluble model compounds. In this context, the development and application of imaging, physicochemical, and spectromicroscopic techniques that allow direct assessment of enzyme action on relevant lignocellulosic substrates is reviewed.
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Affiliation(s)
- Robyn E Goacher
- Department of Biochemistry, Chemistry and Physics, Niagara University, NY, USA
| | - Michael J Selig
- Department of Geoscience and Natural Resource Management, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
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Lupoi JS. Analytical Methods for Lignocellulosic Biomass Structural Polysaccharides. POLYSACCHARIDES 2014. [DOI: 10.1007/978-3-319-03751-6_30-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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30
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Gao X, Kumar R, Singh S, Simmons BA, Balan V, Dale BE, Wyman CE. Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX™, and ionic liquid pretreatments. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:71. [PMID: 24910713 PMCID: PMC4029885 DOI: 10.1186/1754-6834-7-71] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/20/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND Pretreatment is essential to realize high product yields from biological conversion of naturally recalcitrant cellulosic biomass, with thermochemical pretreatments often favored for cost and performance. In this study, enzymatic digestion of solids from dilute sulfuric acid (DA), ammonia fiber expansion (AFEX™), and ionic liquid (IL) thermochemical pretreatments of corn stover were followed over time for the same range of total enzyme protein loadings to provide comparative data on glucose and xylose yields of monomers and oligomers from the pretreated solids. The composition of pretreated solids and enzyme adsorption on each substrate were also measured to determine. The extent glucose release could be related to these features. RESULTS Corn stover solids from pretreatment by DA, AFEX, and IL were enzymatically digested over a range of low to moderate loadings of commercial cellulase, xylanase, and pectinase enzyme mixtures, the proportions of which had been previously optimized for each pretreatment. Avicel® cellulose, regenerated amorphous cellulose (RAC), and beechwood xylan were also subjected to enzymatic hydrolysis as controls. Yields of glucose and xylose and their oligomers were followed for times up to 120 hours, and enzyme adsorption was measured. IL pretreated corn stover displayed the highest initial glucose yields at all enzyme loadings and the highest final yield for a low enzyme loading of 3 mg protein/g glucan in the raw material. However, increasing the enzyme loading to 12 mg/g glucan or more resulted in DA pretreated corn stover attaining the highest longer-term glucose yields. Hydrolyzate from AFEX pretreated corn stover had the highest proportion of xylooligomers, while IL produced the most glucooligomers. However, the amounts of both oligomers dropped with increasing enzyme loadings and hydrolysis times. IL pretreated corn stover had the highest enzyme adsorption capacity. CONCLUSIONS Initial hydrolysis yields were highest for substrates with greater lignin removal, a greater degree of change in cellulose crystallinity, and high enzyme accessibility. Final glucose yields could not be clearly related to concentrations of xylooligomers released from xylan during hydrolysis. Overall, none of these factors could completely account for differences in enzymatic digestion performance of solids produced by AFEX, DA, and IL pretreatments.
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Affiliation(s)
- Xiadi Gao
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California (UCR), Riverside, CA 92521, USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, CA 92507, USA
| | - Rajeev Kumar
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, CA 92507, USA
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA
- Sandia National Laboratories, Livermore, CA 94551, USA
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA
- Sandia National Laboratories, Livermore, CA 94551, USA
| | - Venkatesh Balan
- DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA
- Biomass Conversion Research Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, MBI Building, Lansing, MI 48910, USA
| | - Bruce E Dale
- DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA
- Biomass Conversion Research Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, MBI Building, Lansing, MI 48910, USA
| | - Charles E Wyman
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California (UCR), Riverside, CA 92521, USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, CA 92507, USA
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Humpula JF, Uppugundla N, Vismeh R, Sousa L, Chundawat SPS, Jones AD, Balan V, Dale BE, Cheh AM. Probing the nature of AFEX-pretreated corn stover derived decomposition products that inhibit cellulase activity. BIORESOURCE TECHNOLOGY 2014; 152:38-45. [PMID: 24275024 DOI: 10.1016/j.biortech.2013.10.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/22/2013] [Accepted: 10/25/2013] [Indexed: 05/18/2023]
Abstract
Sequential fractionation of AFEX-pretreated corn stover extracts was carried out using ultra-centrifugation, ultra-filtration, and solid phase extraction to isolate various classes of pretreatment products to evaluate their inhibitory effect on cellulases. Ultra-centrifugation removed dark brown precipitates that caused no appreciable enzyme inhibition. Ultra-filtration of ultra-centrifuged AFEX-pretreated corn stover extractives using a 10 kDa molecular weight cutoff (MWCO) membrane removed additional high molecular weight components that accounted for 24-28% of the total observed enzyme inhibition while a 3 kDa MWCO membrane removed 60-65%, suggesting significant inhibition is caused by oligomeric materials. Solid phase extraction (SPE) of AFEX-pretreated corn stover extractives after ultra-centrifugation removed 34-43% of the inhibition; ultra-filtration with a 5 kDa membrane removed 44-56% of the inhibition and when this ultra-filtrate was subjected to SPE a total of 69-70% of the inhibition were removed. Mass spectrometry found several phenolic compounds among the hydrophobic inhibition removed by SPE adsorption.
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Affiliation(s)
- James F Humpula
- Biomass Conversion Research Laboratory, Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48824, USA; DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA
| | - Nirmal Uppugundla
- Biomass Conversion Research Laboratory, Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48824, USA; DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA
| | - Ramin Vismeh
- DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Leonardo Sousa
- Biomass Conversion Research Laboratory, Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48824, USA; DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA
| | - Shishir P S Chundawat
- Biomass Conversion Research Laboratory, Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48824, USA; DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - A Daniel Jones
- DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Venkatesh Balan
- Biomass Conversion Research Laboratory, Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48824, USA; DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA
| | - Bruce E Dale
- Biomass Conversion Research Laboratory, Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48824, USA; DOE-Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, USA
| | - Albert M Cheh
- Department of Environmental Science, American University, Washington, DC 20016, USA.
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Martin AP, Palmer WM, Byrt CS, Furbank RT, Grof CPL. A holistic high-throughput screening framework for biofuel feedstock assessment that characterises variations in soluble sugars and cell wall composition in Sorghum bicolor. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:186. [PMID: 24365407 PMCID: PMC3892131 DOI: 10.1186/1754-6834-6-186] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/10/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND A major hindrance to the development of high yielding biofuel feedstocks is the ability to rapidly assess large populations for fermentable sugar yields. Whilst recent advances have outlined methods for the rapid assessment of biomass saccharification efficiency, none take into account the total biomass, or the soluble sugar fraction of the plant. Here we present a holistic high-throughput methodology for assessing sweet Sorghum bicolor feedstocks at 10 days post-anthesis for total fermentable sugar yields including stalk biomass, soluble sugar concentrations, and cell wall saccharification efficiency. RESULTS A mathematical method for assessing whole S. bicolor stalks using the fourth internode from the base of the plant proved to be an effective high-throughput strategy for assessing stalk biomass, soluble sugar concentrations, and cell wall composition and allowed calculation of total stalk fermentable sugars. A high-throughput method for measuring soluble sucrose, glucose, and fructose using partial least squares (PLS) modelling of juice Fourier transform infrared (FTIR) spectra was developed. The PLS prediction was shown to be highly accurate with each sugar attaining a coefficient of determination (R2) of 0.99 with a root mean squared error of prediction (RMSEP) of 11.93, 5.52, and 3.23 mM for sucrose, glucose, and fructose, respectively, which constitutes an error of <4% in each case. The sugar PLS model correlated well with gas chromatography-mass spectrometry (GC-MS) and brix measures. Similarly, a high-throughput method for predicting enzymatic cell wall digestibility using PLS modelling of FTIR spectra obtained from S. bicolor bagasse was developed. The PLS prediction was shown to be accurate with an R2 of 0.94 and RMSEP of 0.64 μg.mgDW-1.h-1. CONCLUSIONS This methodology has been demonstrated as an efficient and effective way to screen large biofuel feedstock populations for biomass, soluble sugar concentrations, and cell wall digestibility simultaneously allowing a total fermentable yield calculation. It unifies and simplifies previous screening methodologies to produce a holistic assessment of biofuel feedstock potential.
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Affiliation(s)
- Antony P Martin
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan NSW 2308, Australia
| | - William M Palmer
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan NSW 2308, Australia
| | - Caitlin S Byrt
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan NSW 2308, Australia
- Australian Research Council Centre of Excellence in Plant Cell Walls, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Robert T Furbank
- CSIRO Plant Industry, High Resolution Plant Phenomics Centre, GPO Box 1600, Canberra ACT 2601, Australia
| | - Christopher PL Grof
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan NSW 2308, Australia
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Oakey H, Shafiei R, Comadran J, Uzrek N, Cullis B, Gomez LD, Whitehead C, McQueen-Mason SJ, Waugh R, Halpin C. Identification of crop cultivars with consistently high lignocellulosic sugar release requires the use of appropriate statistical design and modelling. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:185. [PMID: 24359577 PMCID: PMC3878416 DOI: 10.1186/1754-6834-6-185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/06/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND In this study, a multi-parent population of barley cultivars was grown in the field for two consecutive years and then straw saccharification (sugar release by enzymes) was subsequently analysed in the laboratory to identify the cultivars with the highest consistent sugar yield. This experiment was used to assess the benefit of accounting for both the multi-phase and multi-environment aspects of large-scale phenotyping experiments with field-grown germplasm through sound statistical design and analysis. RESULTS Complementary designs at both the field and laboratory phases of the experiment ensured that non-genetic sources of variation could be separated from the genetic variation of cultivars, which was the main target of the study. The field phase included biological replication and plot randomisation. The laboratory phase employed re-randomisation and technical replication of samples within a batch, with a subset of cultivars chosen as duplicates that were randomly allocated across batches. The resulting data was analysed using a linear mixed model that incorporated field and laboratory variation and a cultivar by trial interaction, and ensured that the cultivar means were more accurately represented than if the non-genetic variation was ignored. The heritability detected was more than doubled in each year of the trial by accounting for the non-genetic variation in the analysis, clearly showing the benefit of this design and approach. CONCLUSIONS The importance of accounting for both field and laboratory variation, as well as the cultivar by trial interaction, by fitting a single statistical model (multi-environment trial, MET, model), was evidenced by the changes in list of the top 40 cultivars showing the highest sugar yields. Failure to account for this interaction resulted in only eight cultivars that were consistently in the top 40 in different years. The correspondence between the rankings of cultivars was much higher at 25 in the MET model. This approach is suited to any multi-phase and multi-environment population-based genetic experiment.
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Affiliation(s)
- Helena Oakey
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Reza Shafiei
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jordi Comadran
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Nicola Uzrek
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Brian Cullis
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
- Computational Informatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2600, Australia
| | - Leonardo D Gomez
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Caragh Whitehead
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Simon J McQueen-Mason
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Robbie Waugh
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Claire Halpin
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Liu G, Qin Y, Li Z, Qu Y. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era. Biotechnol Adv 2013; 31:962-75. [PMID: 23507038 DOI: 10.1016/j.biotechadv.2013.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/09/2013] [Accepted: 03/10/2013] [Indexed: 11/19/2022]
Abstract
The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.
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Affiliation(s)
- Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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35
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Gao X, Kumar R, DeMartini JD, Li H, Wyman CE. Application of high throughput pretreatment and co-hydrolysis system to thermochemical pretreatment. Part 1: Dilute acid. Biotechnol Bioeng 2012; 110:754-62. [DOI: 10.1002/bit.24751] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 11/10/2022]
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36
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Luterbacher JS, Parlange JY, Walker LP. A pore-hindered diffusion and reaction model can help explain the importance of pore size distribution in enzymatic hydrolysis of biomass. Biotechnol Bioeng 2012; 110:127-36. [PMID: 22811319 DOI: 10.1002/bit.24614] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/08/2012] [Accepted: 07/09/2012] [Indexed: 11/06/2022]
Abstract
Until now, most efforts to improve monosaccharide production from biomass through pretreatment and enzymatic hydrolysis have used empirical optimization rather than employing a rational design process guided by a theory-based modeling framework. For such an approach to be successful a modeling framework that captures the key mechanisms governing the relationship between pretreatment and enzymatic hydrolysis must be developed. In this study, we propose a pore-hindered diffusion and kinetic model for enzymatic hydrolysis of biomass. When compared to data available in the literature, this model accurately predicts the well-known dependence of initial cellulose hydrolysis rates on surface area available to a cellulase-size molecule. Modeling results suggest that, for particles smaller than 5 × 10(-3) cm, a key rate-limiting step is the exposure of previously unexposed cellulose occurring after cellulose on the surface has hydrolyzed, rather than binding or diffusion. However, for larger particles, according to the model, diffusion plays a more significant role. Therefore, the proposed model can be used to design experiments that produce results that are either affected or unaffected by diffusion. Finally, by using pore size distribution data to predict the biomass fraction that is accessible to degradation, this model can be used to predict cellulose hydrolysis with time using only pore size distribution and initial composition data.
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Affiliation(s)
- Jeremy S Luterbacher
- Department of Chemical and Biomolecular Engineering, Olin Hall, Cornell University, Ithaca, New York 14850, USA
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37
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Zhang T, Wyman CE, Jakob K, Yang B. Rapid selection and identification of Miscanthus genotypes with enhanced glucan and xylan yields from hydrothermal pretreatment followed by enzymatic hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:56. [PMID: 22863302 PMCID: PMC3494522 DOI: 10.1186/1754-6834-5-56] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/20/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Because many Miscanthus genotypes can be cultivated with relatively high productivity and carbohydrate content, Miscanthus has great potential as an energy crop that can support large scale biological production of biofuels. RESULTS In this study, batch hydrothermal pretreatment at 180°C for 35 min followed by enzymatic hydrolysis was shown to give the highest total sugar yields for Miscanthus x giganteus cv. Illinois planted in Illinois. High throughput pretreatment at 180°C for 35 min and 17.5 min followed by co-hydrolysis in a multi-well batch reactor identified two varieties out of 80 that had significantly higher sugar yields from pretreatment and enzymatic hydrolysis than others. The differences in performance were then related to compositions of the 80 varieties to provide insights into desirable traits for Miscanthus that enhance sugar yields. CONCLUSIONS High throughput pretreatment and co-hydrolysis (HTPH) rapidly identified promising genotypes from a wide range of Miscanthus genotypes, including hybrids of Miscanthus sacchariflorus/M. sinensis and Miscanthus lutarioriparius, differentiating the more commercially promising species from the rest. The total glucan plus xylan content in Miscanthus appeared to influence both mass and theoretical yields, while lignin and ash contents did not have a predictable influence on performance.
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Affiliation(s)
- Taiying Zhang
- Center for Environmental Research and Technology, Bourns College of Engineering, University of California, 1084 Columbia Avenue, Riverside, CA, 92507, USA
| | - Charles E Wyman
- Center for Environmental Research and Technology, Bourns College of Engineering, University of California, 1084 Columbia Avenue, Riverside, CA, 92507, USA
- Chemical and Environmental Engineering Department, Bourns College of Engineering, University of California, Riverside, CA, 92521, USA
| | - Katrin Jakob
- Mendel Biotechnology Inc., 3935 Point Eden Way, Hayward, CA, 94545, USA
| | - Bin Yang
- Center for Environmental Research and Technology, Bourns College of Engineering, University of California, 1084 Columbia Avenue, Riverside, CA, 92507, USA
- Center for Bioproducts and Bioenergy, Washington State University, 2710 University Drive, Richland, WA, 99354, USA
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38
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Davison BH. The Increasing Importance and Capabilities of Biomass Characterization. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.1527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN
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39
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Foston M, Ragauskas AJ. Biomass Characterization: Recent Progress in Understanding Biomass Recalcitrance. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.0015] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marcus Foston
- BioEnergy Science Center, School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, Atlanta, GA
| | - Arthur J. Ragauskas
- BioEnergy Science Center, School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, Atlanta, GA
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40
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Liu HQ, Feng Y, Zhao DQ, Jiang JX. Influence of cellulose content on the enzyme activity in the saccharification digests of furfural residues. ASIA-PAC J CHEM ENG 2012. [DOI: 10.1002/apj.1644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- H. Q. Liu
- Department of Chemistry and Chemical Engineering; Beijing Forestry University; Beijing; 100083; China
| | - Y. Feng
- Department of Chemistry and Chemical Engineering; Beijing Forestry University; Beijing; 100083; China
| | - D. Q. Zhao
- Department of Chemistry and Chemical Engineering; Beijing Forestry University; Beijing; 100083; China
| | - J. X. Jiang
- Department of Chemistry and Chemical Engineering; Beijing Forestry University; Beijing; 100083; China
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41
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Wang M, Si T, Zhao H. Biocatalyst development by directed evolution. BIORESOURCE TECHNOLOGY 2012; 115:117-25. [PMID: 22310212 PMCID: PMC3351540 DOI: 10.1016/j.biortech.2012.01.054] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 05/13/2023]
Abstract
Biocatalysis has emerged as a great addition to traditional chemical processes for production of bulk chemicals and pharmaceuticals. To overcome the limitations of naturally occurring enzymes, directed evolution has become the most important tool for improving critical traits of biocatalysts such as thermostability, activity, selectivity, and tolerance towards organic solvents for industrial applications. Recent advances in mutant library creation and high-throughput screening have greatly facilitated the engineering of novel and improved biocatalysts. This review provides an update of the recent developments in the use of directed evolution to engineer biocatalysts for practical applications.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tong Si
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Departments of Chemistry, Biochemistry, and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- To whom correspondence should be addressed. Phone: (217) 333-2631. Fax: (217) 333-5052.
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Abstract
The biological production of fuels from renewable sources has been regarded as a feasible solution to the energy and environmental problems in the foreseeable future. Recently, the biofuel product spectrum has expanded from ethanol and fatty acid methyl esters (biodiesel) to other molecules, such as higher alcohols and alkanes, with more desirable fuel properties. In general, biosynthesis of these fuel molecules can be divided into two phases: carbon chain elongation and functional modification. In addition to natural fatty acid and isoprenoid chain elongation pathways, keto acid-based chain elongation followed by decarboxylation and reduction has been explored for higher alcohol production. Other issues such as metabolic balance, strain robustness, and industrial production process efficiency have also been addressed. These successes may provide both scientific insights into and practical applications toward the ultimate goal of sustainable fuel production.
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Affiliation(s)
- Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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43
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Goacher RE, Edwards EA, Yakunin AF, Mims CA, Master ER. Application of Time-of-Flight-Secondary Ion Mass Spectrometry for the Detection of Enzyme Activity on Solid Wood Substrates. Anal Chem 2012; 84:4443-51. [DOI: 10.1021/ac3005346] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robyn E. Goacher
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Charles A. Mims
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Emma R. Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
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44
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Van Dyk JS, Pletschke BI. A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes--factors affecting enzymes, conversion and synergy. Biotechnol Adv 2012; 30:1458-80. [PMID: 22445788 DOI: 10.1016/j.biotechadv.2012.03.002] [Citation(s) in RCA: 477] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/10/2012] [Accepted: 03/06/2012] [Indexed: 02/04/2023]
Abstract
Lignocellulose is a complex substrate which requires a variety of enzymes, acting in synergy, for its complete hydrolysis. These synergistic interactions between different enzymes have been investigated in order to design optimal combinations and ratios of enzymes for different lignocellulosic substrates that have been subjected to different pretreatments. This review examines the enzymes required to degrade various components of lignocellulose and the impact of pretreatments on the lignocellulose components and the enzymes required for degradation. Many factors affect the enzymes and the optimisation of the hydrolysis process, such as enzyme ratios, substrate loadings, enzyme loadings, inhibitors, adsorption and surfactants. Consideration is also given to the calculation of degrees of synergy and yield. A model is further proposed for the optimisation of enzyme combinations based on a selection of individual or commercial enzyme mixtures. The main area for further study is the effect of and interaction between different hemicellulases on complex substrates.
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Affiliation(s)
- J S Van Dyk
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, PO Box 94, Grahamstown, 6140, South Africa
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Lee SJ, Warnick TA, Pattathil S, Alvelo-Maurosa JG, Serapiglia MJ, McCormick H, Brown V, Young NF, Schnell DJ, Smart LB, Hahn MG, Pedersen JF, Leschine SB, Hazen SP. Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:5. [PMID: 0 PMCID: PMC3348094 DOI: 10.1186/1754-6834-5-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 02/08/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND There is currently considerable interest in developing renewable sources of energy. One strategy is the biological conversion of plant biomass to liquid transportation fuel. Several technical hurdles impinge upon the economic feasibility of this strategy, including the development of energy crops amenable to facile deconstruction. Reliable assays to characterize feedstock quality are needed to measure the effects of pre-treatment and processing and of the plant and microbial genetic diversity that influence bioconversion efficiency. RESULTS We used the anaerobic bacterium Clostridium phytofermentans to develop a robust assay for biomass digestibility and conversion to biofuels. The assay utilizes the ability of the microbe to convert biomass directly into ethanol with little or no pre-treatment. Plant samples were added to an anaerobic minimal medium and inoculated with C. phytofermentans, incubated for 3 days, after which the culture supernatant was analyzed for ethanol concentration. The assay detected significant differences in the supernatant ethanol from wild-type sorghum compared with brown midrib sorghum mutants previously shown to be highly digestible. Compositional analysis of the biomass before and after inoculation suggested that differences in xylan metabolism were partly responsible for the differences in ethanol yields. Additionally, we characterized the natural genetic variation for conversion efficiency in Brachypodium distachyon and shrub willow (Salix spp.). CONCLUSION Our results agree with those from previous studies of lignin mutants using enzymatic saccharification-based approaches. However, the use of C. phytofermentans takes into consideration specific organismal interactions, which will be crucial for simultaneous saccharification fermentation or consolidated bioprocessing. The ability to detect such phenotypic variation facilitates the genetic analysis of mechanisms underlying plant feedstock quality.
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Affiliation(s)
- Scott J Lee
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Thomas A Warnick
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Sivakumar Pattathil
- BioEnergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | | | | | - Heather McCormick
- BioEnergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Virginia Brown
- BioEnergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Naomi F Young
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | - Danny J Schnell
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | | | - Michael G Hahn
- BioEnergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Jeffrey F Pedersen
- USDA-ARS, Grain, Forage, and Bioenergy Research, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Susan B Leschine
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, USA
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Riedlberger P, Weuster-Botz D. New miniature stirred-tank bioreactors for parallel study of enzymatic biomass hydrolysis. BIORESOURCE TECHNOLOGY 2012; 106:138-146. [PMID: 22206921 DOI: 10.1016/j.biortech.2011.12.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 12/02/2011] [Accepted: 12/03/2011] [Indexed: 05/31/2023]
Abstract
Many factors strongly influence the enzymatic hydrolysis of biomass to fermentable sugars (feedstock composition, pretreatment, enzymes and enzyme loading). In order to optimize the reaction conditions for the hydrolysis of biomass, an accurate high-throughput bioprocess development tool is mandatory, which enables a parallelization and an easy scale-up. New S-shaped impellers were developed for magnetically inductive driven stirred-tank bioreactors at a 10mL-scale. An efficient and reproducible homogenization was shown at 20% w/w solids loading of microcrystalline cellulose and at, 4-10% with wheat straw in 48 parallel operated stirred-tank bioreactors. The scale-up was successfully validated for the enzymatic hydrolysis of wheat straw suspensions and microcrystalline cellulose mixtures by application of a cellulase complex at a milliliter- and liter-scale. As an example, the parallel stirred-tank bioreactor system was applied for the evaluation of enzymatic batch hydrolyses of plant materials with varying pretreatments.
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Affiliation(s)
- Peter Riedlberger
- Lehrstuhl für Bioverfahrenstechnik, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany
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Himmel ME, Decker SR, Johnson DK. Challenges for assessing the performance of biomass degrading biocatalysts. Methods Mol Biol 2012; 908:1-8. [PMID: 22843384 DOI: 10.1007/978-1-61779-956-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Common analytical challenges impact current work to estimate the cost of converting plant biomass to fermentable sugars. The most noteworthy are measuring cellulase and hemicellulase activities, cellulase and hemicellulase protein, biomass compositions (before and after pretreatment), and the products formed. The use of high-throughput (HTP) methods has shown considerable promise for improving both analytical precision and technician efficiency, but can also present pitfalls regarding experimental accuracy and relevance. Recent work demonstrates that HTP systems which include biomass composition analysis, thermal chemical pretreatment, and biomass saccharification can be realized.
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Affiliation(s)
- Michael E Himmel
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA.
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Foston M, Samuel R, Ragauskas AJ. 13C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall. Analyst 2012; 137:3904-9. [DOI: 10.1039/c2an35344j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wang D, Sun J, Yu HL, Li CX, Bao J, Xu JH. Maximum Saccharification of Cellulose Complex by an Enzyme Cocktail Supplemented with Cellulase from Newly Isolated Aspergillus fumigatus ECU0811. Appl Biochem Biotechnol 2011; 166:176-86. [DOI: 10.1007/s12010-011-9414-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 10/18/2011] [Indexed: 11/30/2022]
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Lucena SA, Lima LS, Cordeiro LSA, Sant'Anna C, Constantino R, Azambuja P, de Souza W, Garcia ES, Genta FA. High throughput screening of hydrolytic enzymes from termites using a natural substrate derived from sugarcane bagasse. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:51. [PMID: 22081987 PMCID: PMC3245446 DOI: 10.1186/1754-6834-4-51] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/14/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND The description of new hydrolytic enzymes is an important step in the development of techniques which use lignocellulosic materials as a starting point for fuel production. Sugarcane bagasse, which is subjected to pre-treatment, hydrolysis and fermentation for the production of ethanol in several test refineries, is the most promising source of raw material for the production of second generation renewable fuels in Brazil. One problem when screening hydrolytic activities is that the activity against commercial substrates, such as carboxymethylcellulose, does not always correspond to the activity against the natural lignocellulosic material. Besides that, the macroscopic characteristics of the raw material, such as insolubility and heterogeneity, hinder its use for high throughput screenings. RESULTS In this paper, we present the preparation of a colloidal suspension of particles obtained from sugarcane bagasse, with minimal chemical change in the lignocellulosic material, and demonstrate its use for high throughput assays of hydrolases using Brazilian termites as the screened organisms. CONCLUSIONS Important differences between the use of the natural substrate and commercial cellulase substrates, such as carboxymethylcellulose or crystalline cellulose, were observed. This suggests that wood feeding termites, in contrast to litter feeding termites, might not be the best source for enzymes that degrade sugarcane biomass.
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Affiliation(s)
- Severino A Lucena
- Directory of Programs; National Institute of Metrology, Quality and Technology; Avenida Nossa Senhora das Graças, 50 - Xerém, Duque de Caxias, 25250-020, Brazil
| | - Leile S Lima
- Directory of Programs; National Institute of Metrology, Quality and Technology; Avenida Nossa Senhora das Graças, 50 - Xerém, Duque de Caxias, 25250-020, Brazil
| | - Luís SA Cordeiro
- Directory of Programs; National Institute of Metrology, Quality and Technology; Avenida Nossa Senhora das Graças, 50 - Xerém, Duque de Caxias, 25250-020, Brazil
| | - Celso Sant'Anna
- Directory of Programs; National Institute of Metrology, Quality and Technology; Avenida Nossa Senhora das Graças, 50 - Xerém, Duque de Caxias, 25250-020, Brazil
| | - Reginaldo Constantino
- Zoology Department, University of Brasília, Campus Universitário Darcy Ribeiro - Instituto Central de Ciências Room AT-116, Brasília, 70910-900, Brazil
| | - Patricia Azambuja
- Laboratory of Insect Biochemistry and Physiology, Oswaldo Cruz Institute, Avenida Brasil 4365, Leônidas Deane Building Room 207, Rio de Janeiro, 21040-360, Brazil
- Department of Molecular Entomology, National Institute of Science and Technology, Avenida Brigadeiro Trompowsky, Centro de Ciências da Saúde, Building D-SS room 05, Rio de Janeiro, 21941-590, Brazil
| | - Wanderley de Souza
- Directory of Programs; National Institute of Metrology, Quality and Technology; Avenida Nossa Senhora das Graças, 50 - Xerém, Duque de Caxias, 25250-020, Brazil
| | - Eloi S Garcia
- Directory of Programs; National Institute of Metrology, Quality and Technology; Avenida Nossa Senhora das Graças, 50 - Xerém, Duque de Caxias, 25250-020, Brazil
- Laboratory of Insect Biochemistry and Physiology, Oswaldo Cruz Institute, Avenida Brasil 4365, Leônidas Deane Building Room 207, Rio de Janeiro, 21040-360, Brazil
- Department of Molecular Entomology, National Institute of Science and Technology, Avenida Brigadeiro Trompowsky, Centro de Ciências da Saúde, Building D-SS room 05, Rio de Janeiro, 21941-590, Brazil
| | - Fernando A Genta
- Laboratory of Insect Biochemistry and Physiology, Oswaldo Cruz Institute, Avenida Brasil 4365, Leônidas Deane Building Room 207, Rio de Janeiro, 21040-360, Brazil
- Department of Molecular Entomology, National Institute of Science and Technology, Avenida Brigadeiro Trompowsky, Centro de Ciências da Saúde, Building D-SS room 05, Rio de Janeiro, 21941-590, Brazil
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