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Xiao Y, Dong S, Liu YJ, You C, Feng Y, Cui Q. Key roles of β-glucosidase BglA for the catabolism of both laminaribiose and cellobiose in the lignocellulolytic bacterium Clostridium thermocellum. Int J Biol Macromol 2023; 250:126226. [PMID: 37558019 DOI: 10.1016/j.ijbiomac.2023.126226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
The thermophilic bacterium Clostridium thermocellum efficiently degrades polysaccharides into oligosaccharides. The metabolism of β-1,4-linked cello-oligosaccharides is initiated by three enzymes, i.e., the cellodextrin phosphorylase (Cdp), the cellobiose phosphorylase (Cbp), and the β-glucosidase A (BglA), in C. thermocellum. In comparison, how the oligosaccharides containing other kinds of linkage are utilized is rarely understood. In this study, we found that BglA could hydrolyze the β-1,3-disaccharide laminaribiose with much higher activity than that against the β-1,4-disaccharide cellobiose. The structural basis of the substrate specificity was analyzed by crystal structure determination and molecular docking. Genetic deletions of BglA and Cbp, respectively, and enzymatic analysis of cell extracts demonstrated that BglA is the key enzyme responsible for laminaribiose metabolism. Furthermore, the deletion of BglA can suppress the expression of Cbp and the deletion of Cbp can up-regulate the expression of BglA, indicating that BglA and Cbp have cross-regulation and BglA is also critical for cellobiose metabolism. These insights pave the way for both a fundamental understanding of metabolism and regulation in C. thermocellum and emphasize the importance of the degradation and utilization of polysaccharides containing β-1,3-linked glycosidic bonds in lignocellulose biorefinery.
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Affiliation(s)
- Yan Xiao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
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2
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Uke A, Sornyotha S, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A. Genomic analysis of Paenibacillus macerans strain I6, which can effectively saccharify oil palm empty fruit bunches under nutrient-free conditions. J Biosci Bioeng 2023:S1389-1723(23)00111-1. [PMID: 37095007 DOI: 10.1016/j.jbiosc.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
The improper disposal of palm oil industrial waste has led to serious environmental pollution. In this study, we isolated Paenibacillus macerans strain I6, which can degrade oil palm empty fruit bunches generated by the palm oil industry in nutrient-free water, from bovine manure biocompost and sequenced its genome on PacBio RSII and Illumina NovaSeq 6000 platforms. We obtained 7.11 Mbp of genomic sequences with 52.9% GC content from strain I6. Strain I6 was phylogenetically closely related to P. macerans strains DSM24746 and DSM24 and was positioned close to the head of the branch containing strains I6, DSM24746, and DSM24 in the phylogenetic tree. We used the RAST (rapid annotation using subsystem technology) server to annotate the strain I6 genome and discovered genes related to biological saccharification; 496 genes were related to carbohydrate metabolism and 306 genes were related to amino acids and derivatives. Among them were carbohydrate-active enzymes (CAZymes), including 212 glycoside hydrolases. Up to 23.6% of the oil palm empty fruit bunches was degraded by strain I6 under anaerobic and nutrient-free conditions. Evaluation of the enzymatic activity of extracellular fractions of strain I6 showed that amylase and xylanase activity was highest when xylan was the carbon source. The high enzyme activity and the diversity in the associated genes may contribute to the efficient degradation of oil palm empty fruit bunches by strain I6. Our results indicate the potential utility of P. macerans strain I6 for lignocellulosic biomass degradation.
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Affiliation(s)
- Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Somphit Sornyotha
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan; Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - Sirilak Baramee
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan.
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3
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Liu GL, Bu XY, Chen C, Fu C, Chi Z, Kosugi A, Cui Q, Chi ZM, Liu YJ. Bioconversion of non-food corn biomass to polyol esters of fatty acid and single-cell oils. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:9. [PMID: 36650607 PMCID: PMC9844004 DOI: 10.1186/s13068-023-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND Lignocellulose is a valuable carbon source for the production of biofuels and biochemicals, thus having the potential to substitute fossil resources. Consolidated bio-saccharification (CBS) is a whole-cell-based catalytic technology previously developed to produce fermentable sugars from lignocellulosic agricultural wastes. The deep-sea yeast strain Rhodotorula paludigena P4R5 can produce extracellular polyol esters of fatty acids (PEFA) and intracellular single-cell oils (SCO) simultaneously. Therefore, the integration of CBS and P4R5 fermentation processes would achieve high-value-added conversion of lignocellulosic biomass. RESULTS The strain P4R5 could co-utilize glucose and xylose, the main monosaccharides from lignocellulose, and also use fructose and arabinose for PEFA and SCO production at high levels. By regulating the sugar metabolism pathways for different monosaccharides, the strain could produce PEFA with a single type of polyol head. The potential use of PEFA as functional micelles was also determined. Most importantly, when sugar-rich CBS hydrolysates derived from corn stover or corncob residues were used to replace grain-derived pure sugars for P4R5 fermentation, similar PEFA and SCO productions were obtained, indicating the robust conversion of non-food corn plant wastes to high-value-added glycolipids and lipids. Since the produced PEFA could be easily collected from the culture via short-time standing, we further developed a semi-continuous process for PEFA production from corncob residue-derived CBS hydrolysate, and the PEFA titer and productivity were enhanced up to 41.1 g/L and 8.22 g/L/day, respectively. CONCLUSIONS Here, we integrated the CBS process and the P4R5 fermentation for the robust production of high-value-added PEFA and SCO from non-food corn plant wastes. Therefore, this study suggests a feasible way for lignocellulosic agro-waste utilization and the potential application of P4R5 in industrial PEFA production.
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Affiliation(s)
- Guang-Lei Liu
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266101 China
| | - Xian-Ying Bu
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China
| | - Chaoyang Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Chunxiang Fu
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Chi
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266101 China
| | - Akihiko Kosugi
- grid.452611.50000 0001 2107 8171Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki Japan
| | - Qiu Cui
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Zhen-Ming Chi
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266101 China
| | - Ya-Jun Liu
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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Cousin E, Namhaed K, Pérès Y, Cognet P, Delmas M, Hermansyah H, Gozan M, Alaba PA, Aroua MK. Towards efficient and greener processes for furfural production from biomass: A review of the recent trends. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157599. [PMID: 35901885 DOI: 10.1016/j.scitotenv.2022.157599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
As mentioned in several recent reviews, biomass-based furfural is attracting increasing interest as a feasible alternative for the synthesis of a wide range of non-petroleum-derived compounds. However, the lack of environmentally friendly, cost-effective, and sustainable industrial procedures is still evident. This review describes the chemical and biological routes for furfural production. The mechanisms proposed for the chemical transformation of xylose to furfural are detailed, as are the current advances in the manufacture of furfural from biomass. The main goal is to overview the different ways of improving the furfural synthesis process. A pretreatment process, particularly chemical and physico-chemical, enhances the digestibility of biomass, leading to the production of >70 % of available sugars for the production of valuable products. The combination of heterogeneous (zeolite and polymeric solid) catalyst and biphasic solvent system (water/GVL and water/CPME) is regarded as an attractive approach, affording >75 % furfural yield for over 80 % of selectivity with the possibility of catalyst reuse. Microwave heating as an activation technique reduces reaction time at least tenfold, making the process more sustainable. The state of the art in industrial processes is also discussed. It shows that, when sulfuric acid is used, the furfural yields do not exceed 55 % for temperatures close to 180 °C. However, the MTC process recently achieved an 83 % yield by continuously removing furfural from the liquid phase. Finally, the CIMV process, using a formic acid/acetic acid mixture, has been developed. The economic aspects of furfural production are then addressed. Future research will be needed to investigate scaling-up and biological techniques that produce acceptable yields and productivities to become commercially viable and competitive in furfural production from biomass.
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Affiliation(s)
- Elsa Cousin
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Kritsana Namhaed
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Yolande Pérès
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Patrick Cognet
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Michel Delmas
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Heri Hermansyah
- Biorefinery Lab, Bioprocess Engineering Program, Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Depok 16424, Indonesia.
| | - Misri Gozan
- Biorefinery Lab, Bioprocess Engineering Program, Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Depok 16424, Indonesia.
| | - Peter Adeniyi Alaba
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Mohamed Kheireddine Aroua
- Centre for Carbon Dioxide Capture and Utilization (CCDCU), School of Science and Technology, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, 47500 Petaling Jaya, Malaysia; Department of Engineering, Lancaster University, Lancaster LA1 4YW, United Kingdom; Sunway Materials Smart Science & Engineering Research Cluster (SMS2E), Sunway University, No. 5 Jalan Universiti, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia
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5
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Nhim S, Waeonukul R, Uke A, Baramee S, Ratanakhanokchai K, Tachaapaikoon C, Pason P, Liu YJ, Kosugi A. Biological cellulose saccharification using a coculture of Clostridium thermocellum and Thermobrachium celere strain A9. Appl Microbiol Biotechnol 2022; 106:2133-2145. [PMID: 35157106 PMCID: PMC8930880 DOI: 10.1007/s00253-022-11818-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/30/2021] [Accepted: 01/30/2022] [Indexed: 11/29/2022]
Abstract
Abstract An anaerobic thermophilic bacterial strain, A9 (NITE P-03545), that secretes β-glucosidase was newly isolated from wastewater sediments by screening using esculin. The 16S rRNA gene sequence of strain A9 had 100% identity with that of Thermobrachium celere type strain JW/YL-NZ35. The complete genome sequence of strain A9 showed 98.4% average nucleotide identity with strain JW/YL-NZ35. However, strain A9 had different physiological properties from strain JW/YL-NZ35, which cannot secrete β-glucosidases or grow on cellobiose as the sole carbon source. The key β-glucosidase gene (TcBG1) of strain A9, which belongs to glycoside hydrolase family 1, was characterized. Recombinant β-glucosidase (rTcBG1) hydrolyzed cellooligosaccharides to glucose effectively. Furthermore, rTcBG1 showed high thermostability (at 60°C for 2 days) and high glucose tolerance (IC50 = 0.75 M glucose), suggesting that rTcBG1 could be used for biological cellulose saccharification in cocultures with Clostridium thermocellum. High cellulose degradation was observed when strain A9 was cocultured with C. thermocellum in a medium containing 50 g/l crystalline cellulose, and glucose accumulation in the culture supernatant reached 35.2 g/l. In contrast, neither a monoculture of C. thermocellum nor coculture of C. thermocellum with strain JW/YL-NZ35 realized efficient cellulose degradation or high glucose accumulation. These results show that the β-glucosidase secreted by strain A9 degrades cellulose effectively in combination with C. thermocellum cellulosomes and has the potential to be used in a new biological cellulose saccharification process that does not require supplementation with β-glucosidases. Key points • Strain A9 can secrete a thermostable β-glucosidase that has high glucose tolerance • A coculture of strain A9 and C. thermocellum showed high cellulose degradation • Strain A9 achieves biological saccharification without addition of β-glucosidase Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11818-0.
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Affiliation(s)
- Sreyneang Nhim
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.,Shandong Energy Institute, Qingdao, 266101, People's Republic of China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, People's Republic of China
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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6
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Ichikawa S, Ito D, Asaoka S, Abe R, Katsuo N, Ito T, Ito D, Karita S. The expression of alternative sigma-I7 factor induces the transcription of cellulosomal genes in the cellulolytic bacterium Clostridium thermocellum. Enzyme Microb Technol 2022; 156:110002. [DOI: 10.1016/j.enzmictec.2022.110002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
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7
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Qi K, Chen C, Yan F, Feng Y, Bayer EA, Kosugi A, Cui Q, Liu YJ. Coordinated β-glucosidase activity with the cellulosome is effective for enhanced lignocellulose saccharification. BIORESOURCE TECHNOLOGY 2021; 337:125441. [PMID: 34182347 DOI: 10.1016/j.biortech.2021.125441] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Consolidated bio-saccharification (CBS) technology employs cellulosome-producing bacterial cells, rather than fungal cellulases, as biocatalysts for cost-effective production of lignocellulosic sugars. Extracellular β-glucosidase (BGL) expression in the whole-cell arsenal is indispensable, due to severe cellobiose inhibition of the cellulosome. However, high-level BGL expression in Clostridium thermocellum is challenging, and the optimal BGL production level for efficient cellulose saccharification is currently unknown. Herein, we obtained new CBS biocatalysts by transforming BGL-expressing plasmids into C. thermocellum, which produced abundant BGL proteins and hydrolyzed cellulose effectively. The optimal ratio of extracellular BGL-to-cellulosome activity was determined to be in a range of 5.5 to 21.6. Despite the critical impact of BGL, both excessive BGL expression and its assembly on the cellulosome via type I cohesin-dockerin interaction led to reduced cellulosomal activity, which further confirmed the importance of coordinated BGL expression with the cellulosome. This study will further promote industrial CBS application in lignocellulose conversion.
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Affiliation(s)
- Kuan Qi
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Engineering Laboratory for Single Cell Oil, Qingdao Engineering Laboratory for Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Dalian National Laboratory for Clean Energy, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Engineering Laboratory for Single Cell Oil, Qingdao Engineering Laboratory for Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Dalian National Laboratory for Clean Energy, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fei Yan
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Engineering Laboratory for Single Cell Oil, Qingdao Engineering Laboratory for Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Dalian National Laboratory for Clean Energy, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Engineering Laboratory for Single Cell Oil, Qingdao Engineering Laboratory for Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Dalian National Laboratory for Clean Energy, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel; Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8499000, Israel
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Engineering Laboratory for Single Cell Oil, Qingdao Engineering Laboratory for Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Dalian National Laboratory for Clean Energy, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Engineering Laboratory for Single Cell Oil, Qingdao Engineering Laboratory for Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Dalian National Laboratory for Clean Energy, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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8
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Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution. Microorganisms 2021; 9:microorganisms9071445. [PMID: 34361881 PMCID: PMC8303734 DOI: 10.3390/microorganisms9071445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium for consolidated bioprocessing with a robust ability to degrade lignocellulosic biomass through a multienzyme cellulosomal complex. The bacterium uses the released cellodextrins, glucose polymers of different lengths, as its primary carbon source and energy. In contrast, the bacterium exhibits poor growth on monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on hexose sugars have been relatively poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium in hexose sugars-based media, and genome resequencing was used to detect the genes that got mutated during adaptation period. RNA-seq data of the first culture growing on either fructose or glucose revealed that several glycolytic genes in the Embden–Mayerhof–Parnas pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After seven consecutive transfer events on fructose and glucose (~42 generations for fructose-adapted cells and ~40 generations for glucose-adapted cells), several genes in the EMP glycolysis of the evolved strains increased the levels of mRNA expression, accompanied by a faster growth, a greater biomass yield, a higher ethanol titer than those in their parent strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in those responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as potential targets for further metabolic engineering to improve this bacterium for bio-industrial usage.
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9
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Yayo J, Kuil T, Olson DG, Lynd LR, Holwerda EK, van Maris AJA. Laboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and Fructose. Appl Environ Microbiol 2021; 87:e03017-20. [PMID: 33608285 PMCID: PMC8091016 DOI: 10.1128/aem.03017-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/10/2021] [Indexed: 02/04/2023] Open
Abstract
The native ability of Clostridium thermocellum to efficiently solubilize cellulose makes it an interesting platform for sustainable biofuel production through consolidated bioprocessing. Together with other improvements, industrial implementation of C. thermocellum, as well as fundamental studies into its metabolism, would benefit from improved and reproducible consumption of hexose sugars. To investigate growth of C. thermocellum on glucose or fructose, as well as the underlying molecular mechanisms, laboratory evolution was performed in carbon-limited chemostats with increasing concentrations of glucose or fructose and decreasing cellobiose concentrations. Growth on both glucose and fructose was achieved with biomass yields of 0.09 ± 0.00 and 0.18 ± 0.00 gbiomass gsubstrate-1, respectively, compared to 0.15 ± 0.01 gbiomass gsubstrate-1 for wild type on cellobiose. Single-colony isolates had no or short lag times on the monosaccharides, while wild type showed 42 ± 4 h on glucose and >80 h on fructose. With good growth on glucose, fructose, and cellobiose, the fructose isolates were chosen for genome sequence-based reverse metabolic engineering. Deletion of a putative transcriptional regulator (Clo1313_1831), which upregulated fructokinase activity, reduced lag time on fructose to 12 h with a growth rate of 0.11 ± 0.01 h-1 and resulted in immediate growth on glucose at 0.24 ± 0.01 h-1 Additional introduction of a G-to-V mutation at position 148 in cbpA resulted in immediate growth on fructose at 0.32 ± 0.03 h-1 These insights can guide engineering of strains for fundamental studies into transport and the upper glycolysis, as well as maximizing product yields in industrial settings.IMPORTANCEC. thermocellum is an important candidate for sustainable and cost-effective production of bioethanol through consolidated bioprocessing. In addition to unsurpassed cellulose deconstruction, industrial application and fundamental studies would benefit from improvement of glucose and fructose consumption. This study demonstrated that C. thermocellum can be evolved for reproducible constitutive growth on glucose or fructose. Subsequent genome sequencing, gene editing, and physiological characterization identified two underlying mutations with a role in (regulation of) transport or metabolism of the hexose sugars. In light of these findings, such mutations have likely (and unknowingly) also occurred in previous studies with C. thermocellum using hexose-based media with possible broad regulatory consequences. By targeted modification of these genes, industrial and research strains of C. thermocellum can be engineered to (i) reduce glucose accumulation, (ii) study cellodextrin transport systems in vivo, (iii) allow experiments at >120 g liter-1 soluble substrate concentration, or (iv) reduce costs for labeling studies.
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Affiliation(s)
- Johannes Yayo
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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10
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Ichikawa S, Tsuge Y, Karita S. Metabolome Analysis of Constituents in Membrane Vesicles for Clostridium thermocellum Growth Stimulation. Microorganisms 2021; 9:microorganisms9030593. [PMID: 33805707 PMCID: PMC8002186 DOI: 10.3390/microorganisms9030593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 11/24/2022] Open
Abstract
The cultivation of the cellulolytic bacterium, Clostridium thermocellum, can have cost-effective cellulosic biomass utilizations, such as consolidated bioprocessing, simultaneous biological enzyme production and saccharification. However, these processes require a longer cultivation term of approximately 1 week. We demonstrate that constituents of the C. thermocellum membrane vesicle fraction significantly promoted the growth rate of C. thermocellum. Similarly, cell-free Bacillus subtilis broth was able to increase C. thermocellum growth rate, while several B. subtilis single-gene deletion mutants, e.g., yxeJ, yxeH, ahpC, yxdK, iolF, decreased the growth stimulation ability. Metabolome analysis revealed signal compounds for cell–cell communication in the C. thermocellum membrane vesicle fraction (ethyl 2-decenoate, ethyl 4-decenoate, and 2-dodecenoic acid) and B. subtilis broth (nicotinamide, indole-3-carboxaldehyde, urocanic acid, nopaline, and 6-paradol). These findings suggest that the constituents in membrane vesicles from C. thermocellum and B. subtilis could promote C. thermocellum growth, leading to improved efficiency of cellulosic biomass utilization.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
- Correspondence: ; Tel.: +89-59-231-9254; Fax: +89-59-231-9352
| | - Yoichiro Tsuge
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
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11
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Langsdorf A, Volkmar M, Holtmann D, Ulber R. Material utilization of green waste: a review on potential valorization methods. BIORESOUR BIOPROCESS 2021; 8:19. [PMID: 38650228 PMCID: PMC10991214 DOI: 10.1186/s40643-021-00367-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/03/2021] [Indexed: 01/09/2023] Open
Abstract
Considering global developments like climate change and the depletion of fossil resources, the use of new and sustainable feedstocks such as lignocellulosic biomass becomes inevitable. Green waste comprises heterogeneous lignocellulosic biomass with low lignin content, which does not stem from agricultural processes or purposeful cultivation and therefore mainly arises in urban areas. So far, the majority of green waste is being composted or serves as feedstock for energy production. Here, the hitherto untapped potential of green waste for material utilization instead of conventional recycling is reviewed. Green waste is a promising starting material for the direct extraction of valuable compounds, the chemical and fermentative conversion into basic chemicals as well as the manufacturing of functional materials like electrodes for electro-biotechnological applications through carbonization. This review serves as a solid foundation for further work on the valorization of green waste.
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Affiliation(s)
- Alexander Langsdorf
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
| | - Marianne Volkmar
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Strasse 49, 67663, Kaiserslautern, Germany
| | - Dirk Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany.
| | - Roland Ulber
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Strasse 49, 67663, Kaiserslautern, Germany
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12
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Park H, Patel A, Hunt KA, Henson MA, Carlson RP. Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis. NPJ Biofilms Microbiomes 2020; 6:59. [PMID: 33268782 PMCID: PMC7710750 DOI: 10.1038/s41522-020-00170-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/23/2020] [Indexed: 01/03/2023] Open
Abstract
Planktonic cultures, of a rationally designed consortium, demonstrated emergent properties that exceeded the sums of monoculture properties, including a >200% increase in cellobiose catabolism, a >100% increase in glycerol catabolism, a >800% increase in ethanol production, and a >120% increase in biomass productivity. The consortium was designed to have a primary and secondary-resource specialist that used crossfeeding with a positive feedback mechanism, division of labor, and nutrient and energy transfer via necromass catabolism. The primary resource specialist was Clostridium phytofermentans (a.k.a. Lachnoclostridium phytofermentans), a cellulolytic, obligate anaerobe. The secondary-resource specialist was Escherichia coli, a versatile, facultative anaerobe, which can ferment glycerol and byproducts of cellobiose catabolism. The consortium also demonstrated emergent properties of enhanced biomass accumulation when grown as biofilms, which created high cell density communities with gradients of species along the vertical axis. Consortium biofilms were robust to oxic perturbations with E. coli consuming O2, creating an anoxic environment for C. phytofermentans. Anoxic/oxic cycling further enhanced biomass productivity of the biofilm consortium, increasing biomass accumulation ~250% over the sum of the monoculture biofilms. Consortium emergent properties were credited to several synergistic mechanisms. E. coli consumed inhibitory byproducts from cellobiose catabolism, driving higher C. phytofermentans growth and higher cellulolytic enzyme production, which in turn provided more substrate for E. coli. E. coli necromass enhanced C. phytofermentans growth while C. phytofermentans necromass aided E. coli growth via the release of peptides and amino acids, respectively. In aggregate, temporal cycling of necromass constituents increased flux of cellulose-derived resources through the consortium. The study establishes a consortia-based, bioprocessing strategy built on naturally occurring interactions for improved conversion of cellulose-derived sugars into bioproducts.
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Affiliation(s)
- Heejoon Park
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Engineering and Technology, University of North Alabama, Florence, AL, USA
| | - Ayushi Patel
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kristopher A Hunt
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Michael A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA. .,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
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Qin Y, Li Q, Luo F, Fu Y, He H. One-step purification of two novel thermotolerant β-1,4-glucosidases from a newly isolated strain of Fusarium chlamydosporum HML278 and their characterization. AMB Express 2020; 10:182. [PMID: 33030626 PMCID: PMC7544787 DOI: 10.1186/s13568-020-01116-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/24/2020] [Indexed: 01/07/2023] Open
Abstract
A newly identified cellulase-producing Fusarium chlamydosporum HML278 was cultivated under solid-state fermentation of sugarcane bagasse, and two new β-glucosides enzymes (BG FH1, BG FH2) were recovered from fermentation solution by modified non-denaturing active gel electrophoresis and gel filtration chromatography. SDS-PAGE analysis showed that the molecular weight of BG FH1 and BG FH2 was 93 kDa and 52 kDa, respectively, and the enzyme activity was 5.6 U/mg and 11.5 U/mg, respectively. The optimal reaction temperature of the enzymes was 60 ℃, and the enzymes were stable with a temperature lower than 70 ℃. The optimal pH of the purified enzymes was 6.0, and the enzymes were stable between pH 4–10. Km and Vmax values were 2.76 mg/mL and 20.6 U/mg for pNPG, respectively. Thin-layer chromatography and high-performance liquid chromatography analysis showed that BG FH1and BG FH2 had hydrolysis activity toward cellobiose and could hydrolyze cellobiose into glucose. In addition, both enzymes exhibited transglycoside activity, which could use glucose to synthesize cellobiose and cellotriose, and preferentially synthesize alcohol. In conclusion, our study demonstrated that F. chlamydosporum HML278 produces heat-resistant β-glucosidases with both hydrolytic activity and transglycosidic activity, and these β-glucosidases have potential application in bioethanol and papermaking industries.
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14
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Mutturi S, Ike M, Yamagishi K, Tokuyasu K. Isolation, characterization, and application of thermotolerant Streptomyces sp. K5 for efficient conversion of cellobiose to chitinase using pulse- feeding strategy. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Consolidated bio-saccharification: Leading lignocellulose bioconversion into the real world. Biotechnol Adv 2020; 40:107535. [DOI: 10.1016/j.biotechadv.2020.107535] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 11/22/2022]
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16
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Blumer-Schuette SE. Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology. Microorganisms 2020; 8:E385. [PMID: 32164310 PMCID: PMC7142884 DOI: 10.3390/microorganisms8030385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.
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17
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Ou J, Bao T, Ernst P, Si Y, Prabhu SD, Wu H, Zhang J(J, Zhou L, Yang ST, Liu X(M. Intracellular metabolism analysis of Clostridium cellulovorans via modeling integrating proteomics, metabolomics and fermentation. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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Hu B, Zhu M. Reconstitution of cellulosome: Research progress and its application in biorefinery. Biotechnol Appl Biochem 2019; 66:720-730. [DOI: 10.1002/bab.1804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/03/2019] [Indexed: 09/01/2023]
Affiliation(s)
- Bin‐Bin Hu
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals School of Biology and Biological Engineering South China University of Technology, Guangzhou Higher Education Mega Center Panyu Guangzhou People's Republic of China
- Yunnan Academy of Tobacco Agricultural Sciences Kunming People's Republic of China
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou People's Republic of China
| | - Ming‐Jun Zhu
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals School of Biology and Biological Engineering South China University of Technology, Guangzhou Higher Education Mega Center Panyu Guangzhou People's Republic of China
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou People's Republic of China
- College of Life and Geographic Sciences Kashi University Kashi People's Republic of China
- The Key Laboratory of Ecology and Biological Resources in Yarkand Oasis at Colleges & Universities under the Department of Education of Xinjiang Uygur Autonomous Region Kashi University Kashi People's Republic of China
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19
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Nakazono-Nagaoka E, Fujikawa T, Shikata A, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A. Draft genome sequence data of Clostridium thermocellum PAL5 possessing high cellulose-degradation ability. Data Brief 2019; 25:104274. [PMID: 31406903 PMCID: PMC6685675 DOI: 10.1016/j.dib.2019.104274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 12/25/2022] Open
Abstract
Clostridium thermocellum is a potent cellulolytic bacterium. C. thermocellum strain PAL5, was derived from strain S14 that was isolated from bagasse paper sludge, possesses higher cellulose-degradation ability than representative strains ATCC27405 and DSM1313. In this work, we determined the draft genome sequence of C. thermocellum PAL5. Genomic DNA was used for whole-genome sequencing using the Illumina HiSeq 2500. We obtained 215 contigs of >200 bp (N50, 78,366 bp; mean length, 17,378 bp). The assembled data were subjected to the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline, and 3198 protein-coding sequences, 53 tRNA genes, and 4 rRNA genes were identified. The data are accessible at NCBI (the accession number SBHL00000000). Our data resource will facilitate further studies of efficient cellulose-degradation using C. thermocellum.
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Affiliation(s)
- Eiko Nakazono-Nagaoka
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan
| | - Takashi Fujikawa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Japan
| | - Ayumi Shikata
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan
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20
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Nguyen SN, Flores A, Talamantes D, Dar F, Valdez A, Schwans J, Berlemont R. GeneHunt for rapid domain-specific annotation of glycoside hydrolases. Sci Rep 2019; 9:10137. [PMID: 31300677 PMCID: PMC6626019 DOI: 10.1038/s41598-019-46290-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
The identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this "gene to enzyme pipeline" provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.
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Affiliation(s)
- S N Nguyen
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Flores
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - D Talamantes
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - F Dar
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Valdez
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - J Schwans
- Department of Chemistry and Biochemistry, California State University Long Beach, Long Beach, California, USA
| | - R Berlemont
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA.
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21
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Ichikawa S, Ogawa S, Nishida A, Kobayashi Y, Kurosawa T, Karita S. Cellulosomes localise on the surface of membrane vesicles from the cellulolytic bacterium Clostridium thermocellum. FEMS Microbiol Lett 2019; 366:5526221. [DOI: 10.1093/femsle/fnz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
ABSTRACTMembrane vesicles released from bacteria contribute to cell–cell communication by carrying various cargos such as proteins, nucleic acids and signaling molecules. Cellulolytic bacteria have been isolated from many environments, yet the function of membrane vesicles for cellulolytic ability has been rarely described. Here, we show that a Gram-positive cellulolytic bacterium Clostridium thermocellum released membrane vesicles, each approximately 50–300 nm in diameter, into the broth. The observations with immunoelectron microscopy also revealed that cellulosomes, which are carbohydrate-active enzyme complexes that give C. thermocellum high cellulolytic activity, localized on the surface of the membrane vesicles. The membrane vesicles collected by ultracentrifugation maintained the cellulolytic activity. Supplementation with the biosurfactant surfactin or sonication treatment disrupted the membrane vesicles in the exoproteome of C. thermocellum and significantly decreased the degradation activity of the exoproteome for microcrystalline cellulose. However, these did not affect the degradation activity for soluble carboxymethyl cellulose. These results suggest a novel function of membrane vesicles: C. thermocellum releases cellulolytic enzymes on the surface of membrane vesicles to enhance the cellulolytic activity of C. thermocellum for crystalline cellulose.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Satoru Ogawa
- Faculty of Medicine, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Ayami Nishida
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Yuzuki Kobayashi
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Toshihito Kurosawa
- Advanced Science Research Promotion Center, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
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22
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Passoth V, Sandgren M. Biofuel production from straw hydrolysates: current achievements and perspectives. Appl Microbiol Biotechnol 2019; 103:5105-5116. [PMID: 31081521 PMCID: PMC6570699 DOI: 10.1007/s00253-019-09863-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 12/15/2022]
Abstract
Straw is an agricultural residue of the production of e.g. cereals, rapeseed or sunflowers. It includes dried stalks, leaves, and empty ears and corncobs, which are separated from the grains during harvest. Straw is a promising lignocellulosic feedstock with a beneficial greenhouse gas balance for the production of biofuels and chemicals. Like all lignocellulosic materials, straw is recalcitrant and requires thermochemical and enzymatic pretreatment to enable access to the three major biopolymers of straw-the polysaccharides cellulose and hemicellulose and the polyaromatic compound lignin. Straw is used for commercial ethanol and biogas production. Considerable research has also been conducted to produce biobutanol, biodiesel and biochemicals from this raw material, but more research is required to establish them on a commercial scale. The major hindrance for launching industrial biofuel and chemicals' production from straw is the high cost necessitated by pretreatment of the material. Improvements of microbial strains, production and extraction technologies, as well as co-production of high-value compounds represent ways of establishing straw as feedstock for the production of biofuels, chemicals and food.
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Affiliation(s)
- Volkmar Passoth
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden.
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
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Glucose production from cellulose through biological simultaneous enzyme production and saccharification using recombinant bacteria expressing the β-glucosidase gene. J Biosci Bioeng 2019; 127:340-344. [DOI: 10.1016/j.jbiosc.2018.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 12/18/2022]
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Liu S, Liu YJ, Feng Y, Li B, Cui Q. Construction of consolidated bio-saccharification biocatalyst and process optimization for highly efficient lignocellulose solubilization. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:35. [PMID: 30820245 PMCID: PMC6378752 DOI: 10.1186/s13068-019-1374-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The industrial conversion of biomass to high-value biofuels and biochemical is mainly restricted by lignocellulose solubilization. Consolidated bio-saccharification (CBS) is considered a promising process for lignocellulose solubilization depending on whole-cell biocatalysts that simultaneously perform effective cellulase production and hydrolysis. However, it usually takes a long time to reach a high saccharification level using the current CBS biocatalyst and process. RESULTS To promote the saccharification efficiency and reduce the cost, a Clostridium thermocellum recombinant strain ∆pyrF::KBm was constructed as a new CBS biocatalyst in this study. The key CBS factors, including the medium, inoculum size and cultivation, and substrate load, were investigated and optimized. The saccharification process was also stimulated by adding free hemicellulases, suggesting the need to further enhance hemicellulase activity of the whole-cell catalyst. Under the optimal conditions, the CBS process was shortened by 50% with pretreated wheat straw as the substrate. The sugar yield reached 0.795 g/g and the saccharification level was 89.3%. CONCLUSIONS This work provided a new biocatalyst and an optimized process of CBS and confirmed that CBS is a feasible strategy for cost-efficient solubilization of lignocellulose, which will greatly promote the industrial utilization of lignocellulosic biomass.
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Affiliation(s)
- Shiyue Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Bin Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
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Xin F, Dong W, Zhang W, Ma J, Jiang M. Biobutanol Production from Crystalline Cellulose through Consolidated Bioprocessing. Trends Biotechnol 2019; 37:167-180. [DOI: 10.1016/j.tibtech.2018.08.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 01/08/2023]
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Li X, Xiao Y, Feng Y, Li B, Li W, Cui Q. The spatial proximity effect of beta-glucosidase and cellulosomes on cellulose degradation. Enzyme Microb Technol 2018; 115:52-61. [PMID: 29859603 DOI: 10.1016/j.enzmictec.2018.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/30/2018] [Accepted: 04/23/2018] [Indexed: 01/05/2023]
Abstract
Low-cost saccharification is one of the key bottlenecks hampering the further application of lignocellulosic biomass. Clostridium thermocellum is a naturally ideal cellulose degrading bacterium armed with cellulosomes, which are multienzyme complexes that are capable of efficiently degrading cellulose. However, under controlled condition, the inhibition effect of hydrolysate cellobiose severely restricts the hydrolytic ability of cellulosomes. Although the addition of beta-glucosidase (Bgl) could effectively relieve this inhibition, the spatial proximity effect of Bgl and cellulosomes on cellulose degradation is still unclear. To address this issue, free Bgl from Caldicellulosiruptor sp. F32 (CaBglA), carbohydrate-binding module (CBM) fused CaBglA (CaBglA-CBM) and cellulosomal type II cohesin module (CohII) fused to CaBglA (CaBglA-CohII) were successfully constructed, and their enzymatic activities, binding abilities and saccharification efficiencies were systematically investigated in vitro and in vivo. In vivo, with the adjacency of CaBglA to cellulosomes, the saccharification efficiency of microcrystalline cellulose increased from 40% to 50%. For the pretreated wheat straw, the degradation rate of the combination of cells and the CaBglA-CohII or the CaBglA-CBM was as efficient as that of the free CaBglA (approximately 60%). This study demonstrated that the proximity of CaBglA to cellulosomes had a positive effect on microcrystalline cellulose but not on pretreated wheat straw, which may result from the nonproductive adsorption of lignin and the decreased thermostability of CaBglA-CBM and CaBglA-CohII compared to that of CaBglA. The above results will contribute to the design of cost-effective Bgls for industrial cellulose degradation.
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Affiliation(s)
- Xiaoyi Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China
| | - Yan Xiao
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Bin Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China.
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Widyasti E, Shikata A, Hashim R, Sulaiman O, Sudesh K, Wahjono E, Kosugi A. Biodegradation of fibrillated oil palm trunk fiber by a novel thermophilic, anaerobic, xylanolytic bacterium Caldicoprobacter sp. CL-2 isolated from compost. Enzyme Microb Technol 2018; 111:21-28. [DOI: 10.1016/j.enzmictec.2017.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 10/18/2022]
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Liu YJ, Liu S, Dong S, Li R, Feng Y, Cui Q. Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:6. [PMID: 29344087 PMCID: PMC5766998 DOI: 10.1186/s13068-017-1009-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum is considered one of the most efficient natural cellulose degraders because of its cellulosomal system. As the major exoglucanase of cellulosome in C. thermocellum, Cel48S plays key roles and influences the activity and features of cellulosome to a great extent. Thus, it is of great importance to reveal the enzymatic features of Cel48S. However, Cel48S has not been well performed due to difficulties in purifying either recombinant or native Cel48S proteins. RESULTS We observed that the soluble fraction of the catalytic domain of Cel48S (Cel48S_CD) obtained by heterologous expression in Escherichia coli and denaturation-refolding treatment contained a large portion of incorrectly folded proteins with low activity. Using a previously developed seamless genome-editing system for C. thermocellum, we achieved direct purification of Cel48S_CD from the culture supernatant of C. thermocellum DSM1313 by inserting a sequence encoding 12 successive histidine residues and a TAA stop codon immediately behind the GH domain of Cel48S. Based on the fully active protein, biochemical and structural analyses were performed to reveal its innate characteristics. The native Cel48S_CD showed high activity of 117.61 ± 2.98 U/mg and apparent substrate preference for crystalline cellulose under the assay conditions. The crystal structure of the native GH48 protein revealed substrate-coupled changes in the residue conformation, indicating induced-fit effects between Cel48S_CD and substrates. Mass spectrum and crystal structural analyses suggested no significant posttranslational modification in the native Cel48S_CD protein. CONCLUSION Our results confirmed that the high activity and substrate specificity of Cel48S_CD from C. thermocellum were consistent with its importance in the cellulosome. The structure of the native Cel48S_CD protein revealed evidence of conformational changes during substrate binding. In addition, our study provided a reliable method for in situ purification of cellulosomal and other secretive proteins from C. thermocellum.
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Affiliation(s)
- Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Shiyue Liu
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Sheng Dong
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Renmin Li
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
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Tiwari R, Singh PK, Singh S, Nain PKS, Nain L, Shukla P. Bioprospecting of novel thermostable β-glucosidase from Bacillus subtilis RA10 and its application in biomass hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:246. [PMID: 29093750 PMCID: PMC5663093 DOI: 10.1186/s13068-017-0932-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 10/19/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Saccharification is the most crucial and cost-intensive process in second generation biofuel production. The deficiency of β-glucosidase in commercial enzyme leads to incomplete biomass hydrolysis. The decomposition of biomass at high temperature environments leads us to isolate thermotolerant microbes with β-glucosidase production potential. RESULTS A total of 11 isolates were obtained from compost and cow dung samples that were able to grow at 50 °C. On the basis of qualitative and quantitative estimation of β-glucosidase enzyme production, Bacillus subtilis RA10 was selected for further studies. The medium components and growth conditions were optimized and β-glucosidase enzyme production was enhanced up to 19.8-fold. The β-glucosidase from B. subtilis RA10 retained 78% of activity at 80 °C temperature and 68.32% of enzyme activity was stable even at 50 °C after 48 h of incubation. The supplementation of β-glucosidase from B. subtilis RA10 into commercial cellulase enzyme resulted in 1.34-fold higher glucose release. Furthermore, β-glucosidase was also functionally elucidated by cloning and overexpression of full length GH1 family β-glucosidase gene from B. subtilis RA10. The purified protein was characterized as thermostable β-glucosidase enzyme. CONCLUSIONS The thermostable β-glucosidase enzyme from B. subtilis RA10 would facilitate efficient saccharification of cellulosic biomass into fermentable sugar. Consequently, after saccharification, thermostable β-glucosidase enzyme would be recovered and reused to reduce the cost of overall bioethanol production process.
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Affiliation(s)
- Rameshwar Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012 India
- Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110 016 India
| | - Puneet Kumar Singh
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Surender Singh
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Pawan K. S. Nain
- Design and Mechatronic Division, School of Civil and Mechanical Engineering, Galgotias University, Noida, Uttar Pradesh 201312 India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii. Appl Environ Microbiol 2017. [PMID: 28625990 DOI: 10.1128/aem.00969-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates to C. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(-) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15% (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance.IMPORTANCE Key to a microbial process for solubilization of plant biomass is the organism's access to the carbohydrate content of lignocellulose. Economically viable routes will characteristically minimize physical, chemical, and biological pretreatment such that microbial steps contribute to the greatest extent possible. Recently, transgenic versions of plants and trees have been developed with the intention of lowering the barrier to lignocellulose conversion, with particular focus on lignin content and composition. Here, the extremely thermophilic bacterium Caldicellulosiruptor bescii was used to solubilize natural and genetically modified switchgrass lines, with and without the aid of hydrothermal treatment. For lignocellulose conversion, it is clear that the microorganism, plant biomass substrate, and processing steps must all be considered simultaneously to achieve optimal results. Whether switchgrass lines engineered for low lignin or natural variants with desirable properties are used, conversion will depend on microbial access to crystalline cellulose in the plant cell wall.
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Albino Gomes A, Pazinatto Telli E, Miletti LC, Skoronski E, Gomes Ghislandi M, Felippe da Silva G, Borba Magalhães MDL. Improved enzymatic performance of graphene-immobilized β-glucosidase A in the presence of glucose-6-phosphate. Biotechnol Appl Biochem 2017. [DOI: 10.1002/bab.1569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anderson Albino Gomes
- Department of Food and Animal Science; Center of Agroveterinary Sciences; State University of Santa Catarina; Lages Brazil
- Department of Environmental Engineering; Center of Agroveterinary Sciences; State University of Santa Catarina; Lages Brazil
| | - Elisa Pazinatto Telli
- Department of Food and Animal Science; Center of Agroveterinary Sciences; State University of Santa Catarina; Lages Brazil
| | - Luiz Claudio Miletti
- Department of Food and Animal Science; Center of Agroveterinary Sciences; State University of Santa Catarina; Lages Brazil
| | - Everton Skoronski
- Department of Environmental Engineering; Center of Agroveterinary Sciences; State University of Santa Catarina; Lages Brazil
| | - Marcos Gomes Ghislandi
- Department of Materials Engineering; Academic Unit at Cabo de Santo Agostinho; Rural Federal University of Pernambuco; Cabo de Santo Agostinho Brazil
| | - Gustavo Felippe da Silva
- Department of Forest Engineering; Center of Agroveterinary Sciences; State University of Santa Catarina; Lages Brazil
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Zhang J, Liu S, Li R, Hong W, Xiao Y, Feng Y, Cui Q, Liu YJ. Efficient whole-cell-catalyzing cellulose saccharification using engineered Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:124. [PMID: 28507596 PMCID: PMC5429504 DOI: 10.1186/s13068-017-0796-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/19/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cost-efficient saccharification is one of the main bottlenecks for industrial lignocellulose conversion. Clostridium thermocellum naturally degrades lignocellulose efficiently using the cellulosome, a multiprotein supermolecular complex, and thus can be potentially used as a low-cost catalyst for lignocellulose saccharification. The industrial use of C. thermocellum is restrained due largely to the inhibition of the hydrolysate cellobiose to its cellulosome. Although the supplementation of beta-glucosidase may solve the problem, the production of the enzymes greatly complicates the process and may also increase the cost of saccharification. RESULTS To conquer the feedback inhibition and establish an efficient whole-cell catalyst for highly efficient cellulose saccharification, we constructed a recombinant strain of C. thermocellum ∆pyrF::CaBglA which produced a secretory exoglucanase CelS-bearing heterologous BGL using a newly developed seamless genome editing system. Without the extra addition of enzymes, the relative saccharification level of ∆pyrF::CaBglA was stimulated by over twofolds compared to its parent strain ∆pyrF through a two-stage saccharification process with 100 g/L Avicel as the carbon source. The production of reducing sugars and the relative saccharification level were further enhanced to 490 mM and 79.4%, respectively, with increased cell density. CONCLUSIONS The high cellulose-degrading ability and sugar productivity suggested that the whole-cell-catalysis strategy for cellulose saccharification is promising, and the C. thermocellum strain ∆pyrF::CaBglA could be potentially used as an efficient whole-cell catalyst for industrial cellulose saccharification.
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Affiliation(s)
- Jie Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Shiyue Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Renmin Li
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Wei Hong
- Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University), Ministry of Education, Guiyang, 550000 People’s Republic of China
| | - Yan Xiao
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
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Hu BB, Zhu MJ. Enhanced hydrogen production and biological saccharification from spent mushroom compost by Clostridium thermocellum 27405 supplemented with recombinant β-glucosidases. INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 2017; 42:7866-7874. [DOI: 10.1016/j.ijhydene.2017.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Qu XS, Hu BB, Zhu MJ. Enhanced saccharification of cellulose and sugarcane bagasse by Clostridium thermocellum cultures with Triton X-100 and β-glucosidase/Cellic®CTec2 supplementation. RSC Adv 2017; 7:21360-21365. [DOI: 10.1039/c7ra02477k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Increased saccharification and utilization of biomass directly byC. thermocellumcultures with Triton X-100 and β-glucosidase supplementation.
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Affiliation(s)
- Xiao-Su Qu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou Higher Education Mega Center
- Guangzhou 510006
- People's Republic of China
| | - Bin-Bin Hu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou Higher Education Mega Center
- Guangzhou 510006
- People's Republic of China
| | - Ming-Jun Zhu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou Higher Education Mega Center
- Guangzhou 510006
- People's Republic of China
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Sheng T, Zhao L, Gao LF, Liu WZ, Cui MH, Guo ZC, Ma XD, Ho SH, Wang AJ. Lignocellulosic saccharification by a newly isolated bacterium, Ruminiclostridium thermocellum M3 and cellular cellulase activities for high ratio of glucose to cellobiose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:172. [PMID: 27525041 PMCID: PMC4982309 DOI: 10.1186/s13068-016-0585-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/27/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Lignocellulosic biomass is one of earth's most abundant resources, and it has great potential for biofuel production because it is renewable and has carbon-neutral characteristics. Lignocellulose is mainly composed of carbohydrate polymers (cellulose and hemicellulose), which contain approximately 75 % fermentable sugars for biofuel fermentation. However, saccharification by cellulases is always the main bottleneck for commercialization. Compared with the enzyme systems of fungi, bacteria have evolved distinct systems to directly degrade lignocellulose. However, most reported bacterial saccharification is not efficient enough without help from additional β-glucosidases. Thus, to enhance the economic feasibility of using lignocellulosic biomass for biofuel production, it will be extremely important to develop a novel bacterial saccharification system that does not require the addition of β-glucosidases. RESULTS In this study, a new thermophilic bacterium named Ruminiclostridium thermocellum M3, which could directly saccharify lignocellulosic biomass, was isolated from horse manure. The results showed that R. thermocellum M3 can grow at 60 °C on a variety of carbon polymers, including microcrystalline cellulose, filter paper, and xylan. Upon utilization of these substrates, R. thermocellum M3 achieved an oligosaccharide yield of 481.5 ± 16.0 mg/g Avicel, and a cellular β-glucosidase activity of up to 0.38 U/mL, which is accompanied by a high proportion (approximately 97 %) of glucose during the saccharification. R. thermocellum M3 also showed potential in degrading natural lignocellulosic biomass, without additional pretreatment, to oligosaccharides, and the oligosaccharide yields using poplar sawdust, corn cobs, rice straw, and cornstalks were 52.7 ± 2.77, 77.8 ± 5.9, 89.4 ± 9.3, and 107.8 ± 5.88 mg/g, respectively. CONCLUSIONS The newly isolated strain R. thermocellum M3 degraded lignocellulose and accumulated oligosaccharides. R. thermocellum M3 saccharified lignocellulosic feedstock without the need to add β-glucosidases or control the pH, and the high proportion of glucose production distinguishes it from all other known monocultures of cellulolytic bacteria. R. thermocellum M3 is a potential candidate for lignocellulose saccharification, and it is a valuable choice for the refinement of bioproducts.
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Affiliation(s)
- Tao Sheng
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Lei Zhao
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090 China
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Ling-Fang Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wen-Zong Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Min-Hua Cui
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Ze-Chong Guo
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Xiao-Dan Ma
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Shih-Hsin Ho
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Ai-Jie Wang
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090 China
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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Rabemanolontsoa H, Saka S. Various pretreatments of lignocellulosics. BIORESOURCE TECHNOLOGY 2016; 199:83-91. [PMID: 26316403 DOI: 10.1016/j.biortech.2015.08.029] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/09/2015] [Accepted: 08/10/2015] [Indexed: 05/09/2023]
Abstract
Biomass pretreatment for depolymerizing lignocellulosics to fermentable sugars has been studied for nearly 200 years. Researches have aimed at high sugar production with minimal degradation to inhibitory compounds. Chemical, physico-chemical and biochemical conversions are the most promising technologies. This article reviews the advances and current trends in the pretreatment of lignocellulosics for a prosperous biorefinery.
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Affiliation(s)
- Harifara Rabemanolontsoa
- Department of Socio-Environmental Energy Science, Graduate School of Energy Science, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shiro Saka
- Department of Socio-Environmental Energy Science, Graduate School of Energy Science, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
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Xia W, Xu X, Qian L, Shi P, Bai Y, Luo H, Ma R, Yao B. Engineering a highly active thermophilic β-glucosidase to enhance its pH stability and saccharification performance. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:147. [PMID: 27446236 PMCID: PMC4955127 DOI: 10.1186/s13068-016-0560-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/11/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND β-Glucosidase is an important member of the biomass-degrading enzyme system, and plays vital roles in enzymatic saccharification for biofuels production. Candidates with high activity and great stability over high temperature and varied pHs are always preferred in industrial practice. To achieve cost-effective biomass conversion, exploring natural enzymes, developing high level expression systems and engineering superior mutants are effective approaches commonly used. RESULTS A newly identified β-glucosidase of GH3, Bgl3A, from Talaromyces leycettanus JCM12802, was overexpressed in yeast strain Pichia pastoris GS115, yielding a crude enzyme activity of 6000 U/ml in a 3 L fermentation tank. The purified enzyme exhibited outstanding enzymatic properties, including favorable temperature and pH optima (75 °C and pH 4.5), good thermostability (maintaining stable at 60 °C), and high catalytic performance (with a specific activity and catalytic efficiency of 905 U/mg and 9096/s/mM on pNPG, respectively). However, the narrow stability of Bgl3A at pH 4.0-5.0 would limit its industrial applications. Further site-directed mutagenesis indicated the role of excessive O-glycosylation in pH liability. By removing the potential O-glycosylation sites, two mutants showed improved pH stability over a broader pH range (3.0-10.0). Besides, with better stability under pH 5.0 and 50 °C compared with wild type Bgl3A, saccharification efficiency of mutant M1 was improved substantially cooperating with cellulase Celluclast 1.5L. And mutant M1 reached approximately equivalent saccharification performance to commercial β-glucosidase Novozyme 188 with identical β-glucosidase activity, suggesting its great prospect in biofuels production. CONCLUSIONS In this study, we overexpressed a novel β-glucosidase Bgl3A with high specific activity and high catalytic efficiency in P. pastoris. We further proved the negative effect of excessive O-glycosylation on the pH stability of Bgl3A, and enhanced the pH stability by reducing the O-glycosylation. And the enhanced mutants showed much better application prospect with substantially improved saccharification efficiency on cellulosic materials.
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Affiliation(s)
- Wei Xia
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
- />College of Animal Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Xinxin Xu
- />Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 People’s Republic of China
| | - Lichun Qian
- />College of Animal Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Pengjun Shi
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Yingguo Bai
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Huiying Luo
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Rui Ma
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Bin Yao
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
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Weiss PHE, Álvares ACM, Gomes AA, Miletti LC, Skoronski E, da Silva GF, de Freitas SM, Magalhães MLB. Beta glucosidase from Bacillus polymyxa is activated by glucose-6-phosphate. Arch Biochem Biophys 2015; 580:50-6. [PMID: 26116788 DOI: 10.1016/j.abb.2015.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/19/2015] [Accepted: 06/21/2015] [Indexed: 01/10/2023]
Abstract
Optimization of cellulose enzymatic hydrolysis is crucial for cost effective bioethanol production from lignocellulosic biomass. Enzymes involved in cellulose hydrolysis are often inhibited by their end-products, cellobiose and glucose. Efforts have been made to produce more efficient enzyme variants that are highly tolerant to product accumulation; however, further improvements are still necessary. Based on an alternative approach we initially investigated whether recently formed glucose could be phosphorylated into glucose-6-phosphate to circumvent glucose accumulation and avoid inhibition of beta-glucosidase from Bacillus polymyxa (BGLA). The kinetic properties and structural analysis of BGLA in the presence of glucose-6-phosphate (G6P) were investigated. Kinetic studies demonstrated that enzyme was not inhibited by G6P. In contrast, the presence of G6P activated the enzyme, prevented beta glucosidase feedback inhibition by glucose accumulation and improved protein stability. G6P binding was investigated by fluorescence quenching experiments and the respective association constant indicated high affinity binding of G6P to BGLA. Data reported here are of great impact for future design strategies for second-generation bioethanol production.
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Affiliation(s)
- Paulo H E Weiss
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Alice C M Álvares
- Biophysics Laboratory, Department of Cellular Biology, University of Brasília, Brasília 70910-900, Brazil
| | - Anderson A Gomes
- Water Treatment Laboratory, Department of Environmental Engineering, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Luiz C Miletti
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Everton Skoronski
- Water Treatment Laboratory, Department of Environmental Engineering, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Gustavo F da Silva
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Sonia M de Freitas
- Biophysics Laboratory, Department of Cellular Biology, University of Brasília, Brasília 70910-900, Brazil
| | - Maria L B Magalhães
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil.
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Aburaya S, Esaka K, Morisaka H, Kuroda K, Ueda M. Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis. AMB Express 2015; 5:29. [PMID: 26020016 PMCID: PMC4441647 DOI: 10.1186/s13568-015-0115-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/08/2015] [Indexed: 02/04/2023] Open
Abstract
Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading and metabolizing various types of substrates, including cellulose, hemicellulose (xylan and galactomannan), and pectin. Among Clostridia, this ability to degrade and metabolize a wide range of hemicellulose and pectin substrates is a unique feature; however, the mechanisms are currently unknown. To clarify the mechanisms of hemicelluloses and pectin recognition and metabolism, we carried out a quantitative proteome analysis of C. cellulovorans cultured with these substrates. C. cellulovorans was cultured in the medium of glucose (control), xylan, galactomannan (Locus bean gum, LBG), or pectin for 36 h. Xylan and galactomannan were used to search for the common recognition mechanisms of hemicellulose, and pectin was used to search for unique recognition systems in C. cellulovorans. Using an isobaric tag method and liquid chromatograph/mass spectrometer equipped with a long monolithic silica capillary column, we identified 734 intracellular proteins from all substrates. We performed KEGG analyses and cluster analyses of the resulting proteins. In the KEGG analyses, we found common degradation mechanisms for hemicellulose and pectin. In the cluster analysis corresponding to the genome analysis, we detected substrate-specific clusters that include genes involved in substrate recognition, substrate degradation, and metabolism. Combining the results of the KEGG analyses and cluster analyses, we propose the mechanisms involved in the recognition and metabolism of hemicellulose and pectin in C. cellulovorans.
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Holwerda EK, Thorne PG, Olson DG, Amador-Noguez D, Engle NL, Tschaplinski TJ, van Dijken JP, Lynd LR. The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:155. [PMID: 25379055 PMCID: PMC4207885 DOI: 10.1186/s13068-014-0155-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 10/03/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Clostridium thermocellum is a model thermophilic organism for the production of biofuels from lignocellulosic substrates. The majority of publications studying the physiology of this organism use substrate concentrations of ≤10 g/L. However, industrially relevant concentrations of substrate start at 100 g/L carbohydrate, which corresponds to approximately 150 g/L solids. To gain insight into the physiology of fermentation of high substrate concentrations, we studied the growth on, and utilization of high concentrations of crystalline cellulose varying from 50 to 100 g/L by C. thermocellum. RESULTS Using a defined medium, batch cultures of C. thermocellum achieved 93% conversion of cellulose (Avicel) initially present at 100 g/L. The maximum rate of substrate utilization increased with increasing substrate loading. During fermentation of 100 g/L cellulose, growth ceased when about half of the substrate had been solubilized. However, fermentation continued in an uncoupled mode until substrate utilization was almost complete. In addition to commonly reported fermentation products, amino acids - predominantly L-valine and L-alanine - were secreted at concentrations up to 7.5 g/L. Uncoupled metabolism was also accompanied by products not documented previously for C. thermocellum, including isobutanol, meso- and RR/SS-2,3-butanediol and trace amounts of 3-methyl-1-butanol, 2-methyl-1-butanol and 1-propanol. We hypothesize that C. thermocellum uses overflow metabolism to balance its metabolism around the pyruvate node in glycolysis. CONCLUSIONS C. thermocellum is able to utilize industrially relevant concentrations of cellulose, up to 93 g/L. We report here one of the highest degrees of crystalline cellulose utilization observed thus far for a pure culture of C. thermocellum, the highest maximum substrate utilization rate and the highest amount of isobutanol produced by a wild-type organism.
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Affiliation(s)
- Evert K Holwerda
- />Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
| | | | - Daniel G Olson
- />Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
| | - Daniel Amador-Noguez
- />Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Nancy L Engle
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Timothy J Tschaplinski
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Johannes P van Dijken
- />Emeritus Industrial Biotechnology of Delft University of Technology, Delft, BC 2628 The Netherlands
| | - Lee R Lynd
- />Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- />BioEnergy Science Center, Oak Ridge, TN 37830 USA
- />Mascoma Corporation, Lebanon, NH 03766 USA
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