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Liu K, Feng YJ, Guo JX, Wang GL, Shan LL, Gao SW, Liu Q, Sun HN, Li XY, Sun XR, Bian JY, Kwon T. Argon non-thermal plasma treatment promotes the development of rice (Oryza sativa L.) in saline alkali environments. PROTOPLASMA 2024; 261:927-936. [PMID: 38519772 DOI: 10.1007/s00709-024-01946-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Soil salinization leads to a reduction in arable land area, which seriously endangers food security. Developing saline-alkali land has become a key measure to address the contradiction between population growth and limited arable land. Rice is the most important global food crop, feeding half of the world's population and making it a suitable choice for planting on saline-alkali lands. The traditional salt-alkali improvement method has several drawbacks. Currently, non-thermal plasma (NTP) technology is being increasingly applied in agriculture. However, there are few reports on the cultivation of salt/alkali-tolerant rice. Under alkaline stress, argon NTP treatment significantly increased the germination rate of Longdao 5 (LD5) rice seeds. In addition, at 15 kV and 120 s, NTP treatment significantly increased the activity of antioxidant enzymes such as catalase and SOD. NTP treatment induced changes in genes related to salt-alkali stress in rice seedlings, such as chitinase and xylanase inhibitor proteins, which increased the tolerance of the seeds to salt-alkali stress. This experiment has expanded the application scope of NTP in agriculture, providing a more cost-effective, less harmful, and faster method for developing salt-alkali-tolerant rice and laying a theoretical foundation for cultivating NTP-enhanced salt-alkali-tolerant rice.
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Affiliation(s)
- Kai Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
- Northeast Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, 150086, Heilongjiang, China
| | - Yan-Jiang Feng
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, Heilongjiang, China
| | - Jun-Xiang Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, Heilongjiang, China
| | - Gui-Ling Wang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, Heilongjiang, China
| | - Li-Li Shan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, Heilongjiang, China
| | - Shi-Wei Gao
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, 152000, Heilongjiang, China
| | - Qing Liu
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, 152000, Heilongjiang, China
| | - Hu-Nan Sun
- College of Life Science & Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Xi-Yu Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Xing-Rong Sun
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing, 163319, Heilongjiang, China
| | - Jing-Yang Bian
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing, 163319, Heilongjiang, China.
| | - Taeho Kwon
- Primate Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 351-33 Neongme-Gil, Ibam-Myeon, , Jeongeup-Si, Jeonbuk, 56216, Republic of Korea.
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, Korea National University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Math RK, Kambiranda D, Yun HD, Ghebreiyessus Y. Binding of cloned Cel enzymes on clay minerals related to the pI of the enzymes and database survey of cellulases of soil bacteria for pI. Biosci Biotechnol Biochem 2019; 84:238-246. [PMID: 31625450 DOI: 10.1080/09168451.2019.1679613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The Cel genes from Bacillus licheniformis MSB03 were cloned and expressed to investigate binding ability on clay minerals and sea sand at pH ranging 3 to 9. FTIR analysis has been done to characterize bound enzymes on clay minerals. Subsequent, surveying of NCBI database for extracellular enzymes of soil bacteria was carried out. Among the five cloned Cel enzymes assayed for binding to clay minerals, only Cel5H enzyme had the binding ability. Enzyme Cel5H exhibited highest binding to montmorillonite followed by kaolinite and sea sand. Interestingly, Cel5H had higher pI value of 9.24 than other proteins (5.2-5.7). Cel5H binding to montmorillonite was shown to be negatively affected below pH 3 and above pH 9. Infrared absorption spectra of the Cel5H-montmorillonite complexes showed distinct peaks for clay minerals and bound proteins. Furthermore, database survey of soil bacterial extracellular enzymes revealed that Bacillus species enzymes had higher pI than other soil bacterial enzymes.
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Affiliation(s)
- Renukaradhya K Math
- Research Institute of Agriculture and Life Science, Gyeongsang National University, Chinju, Republic of Korea
| | - Devaiah Kambiranda
- Department of Agricultural Sciences, Southern University Agriculture Research and Extension Center, Baton Rouge, LA, USA
| | - Han Dae Yun
- Research Institute of Agriculture and Life Science, Gyeongsang National University, Chinju, Republic of Korea
| | - Yemane Ghebreiyessus
- Department of Agricultural Sciences, Southern University Agriculture Research and Extension Center, Baton Rouge, LA, USA
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Obeng EM, Adam SNN, Budiman C, Ongkudon CM, Maas R, Jose J. Lignocellulases: a review of emerging and developing enzymes, systems, and practices. BIORESOUR BIOPROCESS 2017. [DOI: 10.1186/s40643-017-0146-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Baek SC, Ho TH, Lee HW, Jung WK, Gang HS, Kang LW, Kim H. Improvement of enzyme activity of β-1,3-1,4-glucanase from Paenibacillus sp. X4 by error-prone PCR and structural insights of mutated residues. Appl Microbiol Biotechnol 2017; 101:4073-4083. [PMID: 28180917 DOI: 10.1007/s00253-017-8145-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/16/2017] [Accepted: 01/22/2017] [Indexed: 11/29/2022]
Abstract
β-1,3-1,4-Glucanase (BGlc8H) from Paenibacillus sp. X4 was mutated by error-prone PCR or truncated using termination primers to improve its enzyme properties. The crystal structure of BGlc8H was determined at a resolution of 1.8 Å to study the possible roles of mutated residues and truncated regions of the enzyme. In mutation experiments, three clones of EP 2-6, 2-10, and 5-28 were finally selected that exhibited higher specific activities than the wild type when measured using their crude extracts. Enzyme variants of BG2-6, BG2-10, and BG5-28 were mutated at two, two, and six amino acid residues, respectively. These enzymes were purified homogeneously by Hi-Trap Q and CHT-II chromatography. Specific activity of BG5-28 was 2.11-fold higher than that of wild-type BGwt, whereas those of BG2-6 and BG2-10 were 0.93- and 1.19-fold that of the wild type, respectively. The optimum pH values and temperatures of the variants were nearly the same as those of BGwt (pH 5.0 and 40 °C, respectively). However, the half-life of the enzyme activity and catalytic efficiency (k cat/K m) of BG5-28 were 1.92- and 2.12-fold greater than those of BGwt at 40 °C, respectively. The catalytic efficiency of BG5-28 increased to 3.09-fold that of BGwt at 60 °C. These increases in the thermostability and catalytic efficiency of BG5-28 might be useful for the hydrolysis of β-glucans to produce fermentable sugars. Of the six mutated residues of BG5-28, five residues were present in mature BGlc8H protein, and two of them were located in the core scaffold of BGlc8H and the remaining three residues were in the substrate-binding pocket forming loop regions. In truncation experiments, three forms of C-terminal truncated BGlc8H were made, which comprised 360, 286, and 215 amino acid residues instead of the 409 residues of the wild type. No enzyme activity was observed for these truncated enzymes, suggesting the complete scaffold of the α6/α6-double-barrel structure is essential for enzyme activity.
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Affiliation(s)
- Seung Cheol Baek
- Department of Pharmacy, Sunchon National University, Suncheon, 57922, Republic of Korea.,Department of Agricultural Chemistry, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hyun Woo Lee
- Department of Pharmacy, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Won Kyeong Jung
- Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Hyo-Seung Gang
- Department of Agricultural Chemistry, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Gwangjin-gu, Seoul, 05029, Republic of Korea.
| | - Hoon Kim
- Department of Pharmacy, Sunchon National University, Suncheon, 57922, Republic of Korea. .,Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea.
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Biodegradation of palm kernel cake by cellulolytic and hemicellulolytic bacterial cultures through solid state fermentation. ScientificWorldJournal 2014; 2014:729852. [PMID: 25019097 PMCID: PMC4082864 DOI: 10.1155/2014/729852] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/15/2014] [Accepted: 05/24/2014] [Indexed: 11/17/2022] Open
Abstract
Four cellulolytic and hemicellulolytic bacterial cultures were purchased from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture (DSMZ) and the American Type Culture Collection (ATCC). Two experiments were conducted; the objective of the first experiment was to determine the optimum time period required for solid state fermentation (SSF) of palm kernel cake (PKC), whereas the objective of the second experiment was to investigate the effect of combinations of these cellulolytic and hemicellulolytic bacteria on the nutritive quality of the PKC. In the first experiment, the SSF was lasted for 12 days with inoculum size of 10% (v/w) on different PKC to moisture ratios. In the second experiment, fifteen combinations were created among the four microbes with one untreated PKC as a control. The SSF lasted for 9 days, and the samples were autoclaved, dried, and analyzed for proximate analysis. Results showed that bacterial cultures produced high enzymes activities at the 4th day of SSF, whereas their abilities to produce enzymes tended to be decreased to reach zero at the 8th day of SSF. Findings in the second experiment showed that hemicellulose and cellulose was significantly (P < 0.05) decreased, whereas the amount of reducing sugars were significantly (P < 0.05) increased in the fermented PKC (FPKC) compared with untreated PKC.
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Kang YM, Kim MG, Yun HD, Cho KM. Construction and expression of a novel Paenibacillus polymyxa GS01 bifunctional xyn43A-lin16A gene through overlap extension PCR. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13765-013-3050-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kim MK, Kang TH, Kim J, Kim H, Yun HD. Evidence Showing Duplication and Recombination of cel Genes in Tandem from Hyperthermophilic Thermotoga sp. Appl Biochem Biotechnol 2012; 168:1834-48. [DOI: 10.1007/s12010-012-9901-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 09/10/2012] [Indexed: 12/01/2022]
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Molecular and biochemical analyses of the GH44 module of CbMan5B/Cel44A, a bifunctional enzyme from the hyperthermophilic bacterium Caldicellulosiruptor bescii. Appl Environ Microbiol 2012; 78:7048-59. [PMID: 22843537 DOI: 10.1128/aem.02009-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A large polypeptide encoded in the genome of the thermophilic bacterium Caldicellulosiruptor bescii was determined to consist of two glycoside hydrolase (GH) modules separated by two carbohydrate-binding modules (CBMs). Based on the detection of mannanase and endoglucanase activities in the N-terminal GH5 and the C-terminal GH44 module, respectively, the protein was designated CbMan5B/Cel44A. A GH5 module with >99% identity from the same organism was characterized previously (X. Su, R. I. Mackie, and I. K. Cann, Appl. Environ. Microbiol. 78:2230-2240, 2012); therefore, attention was focused on CbMan5A/Cel44A-TM2 (or TM2), which harbors the GH44 module and the two CBMs. On cellulosic substrates, TM2 had an optimal temperature and pH of 85°C and 5.0, respectively. Although the amino acid sequence of the GH44 module of TM2 was similar to those of other GH44 modules that hydrolyzed cello-oligosaccharides, cellulose, lichenan, and xyloglucan, it was unique that TM2 also displayed modest activity on mannose-configured substrates and xylan. The TM2 protein also degraded Avicel with higher specific activity than activities reported for its homologs. The GH44 catalytic module is composed of a TIM-like domain and a β-sandwich domain, which consists of one β-sheet at the N terminus and nine β-sheets at the C terminus. Deletion of one or more β-sheets from the β-sandwich domain resulted in insoluble proteins, suggesting that the β-sandwich domain is essential for proper folding of the polypeptide. Combining TM2 with three other endoglucanases from C. bescii led to modest synergistic activities during degradation of cellulose, and based on our results, we propose a model for cellulose hydrolysis and utilization by C. bescii.
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Kang YM, Kang TH, Yun HD, Cho KM. Enhancing the Enzymatic Activity of the Multifunctional β-Glycosyl Hydrolase (Cel44C-Man26AP558) from Paenibacillus polymyxa GS01 Using DNA Shuffling. ACTA ACUST UNITED AC 2012. [DOI: 10.7845/kjm.2012.48.2.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Chauhan PS, Puri N, Sharma P, Gupta N. Mannanases: microbial sources, production, properties and potential biotechnological applications. Appl Microbiol Biotechnol 2012; 93:1817-30. [DOI: 10.1007/s00253-012-3887-5] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/03/2012] [Accepted: 01/04/2012] [Indexed: 11/28/2022]
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Ariza A, Eklöf JM, Spadiut O, Offen WA, Roberts SM, Besenmatter W, Friis EP, Skjøt M, Wilson KS, Brumer H, Davies G. Structure and activity of Paenibacillus polymyxa xyloglucanase from glycoside hydrolase family 44. J Biol Chem 2011; 286:33890-900. [PMID: 21795708 PMCID: PMC3190823 DOI: 10.1074/jbc.m111.262345] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/12/2011] [Indexed: 11/06/2022] Open
Abstract
The enzymatic degradation of plant polysaccharides is emerging as one of the key environmental goals of the early 21st century, impacting on many processes in the textile and detergent industries as well as biomass conversion to biofuels. One of the well known problems with the use of nonstarch (nonfood)-based substrates such as the plant cell wall is that the cellulose fibers are embedded in a network of diverse polysaccharides, including xyloglucan, that renders access difficult. There is therefore increasing interest in the "accessory enzymes," including xyloglucanases, that may aid biomass degradation through removal of "hemicellulose" polysaccharides. Here, we report the biochemical characterization of the endo-β-1,4-(xylo)glucan hydrolase from Paenibacillus polymyxa with polymeric, oligomeric, and defined chromogenic aryl-oligosaccharide substrates. The enzyme displays an unusual specificity on defined xyloglucan oligosaccharides, cleaving the XXXG-XXXG repeat into XXX and GXXXG. Kinetic analysis on defined oligosaccharides and on aryl-glycosides suggests that both the -4 and +1 subsites show discrimination against xylose-appended glucosides. The three-dimensional structures of PpXG44 have been solved both in apo-form and as a series of ligand complexes that map the -3 to -1 and +1 to +5 subsites of the extended ligand binding cleft. Complex structures are consistent with partial intolerance of xylosides in the -4' subsites. The atypical specificity of PpXG44 may thus find use in industrial processes involving xyloglucan degradation, such as biomass conversion, or in the emerging exciting applications of defined xyloglucans in food, pharmaceuticals, and cellulose fiber modification.
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Affiliation(s)
- Antonio Ariza
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Jens M. Eklöf
- the Division of Glycoscience, School of Biotechnology, and
| | - Oliver Spadiut
- the Division of Glycoscience, School of Biotechnology, and
- Wallenberg Wood Science Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden, and
| | - Wendy A. Offen
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Shirley M. Roberts
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | | | | | | | - Keith S. Wilson
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Harry Brumer
- the Division of Glycoscience, School of Biotechnology, and
- Wallenberg Wood Science Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden, and
| | - Gideon Davies
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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Warner CD, Go RM, García-Salinas C, Ford C, Reilly PJ. Kinetic characterization of a glycoside hydrolase family 44 xyloglucanase/endoglucanase from Ruminococcus flavefaciens FD-1. Enzyme Microb Technol 2011; 48:27-32. [DOI: 10.1016/j.enzmictec.2010.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 08/26/2010] [Accepted: 08/31/2010] [Indexed: 11/16/2022]
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Niu D, Zhou XX, Yuan TY, Lin ZW, Ruan H, Li WF. Effect of the C-terminal domains and terminal residues of catalytic domain on enzymatic activity and thermostability of lichenase from Clostridium thermocellum. Biotechnol Lett 2010; 32:963-7. [DOI: 10.1007/s10529-010-0241-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 02/19/2010] [Indexed: 11/29/2022]
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Maki M, Leung KT, Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int J Biol Sci 2009; 5:500-16. [PMID: 19680472 PMCID: PMC2726447 DOI: 10.7150/ijbs.5.500] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/21/2009] [Indexed: 11/05/2022] Open
Abstract
Lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. However, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic pH. The extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challenges. Rapid, efficient cellulase screening techniques, using cellulase assays and metagenomic libraries, are a must. Rare cellulases with activities on soluble and crystalline cellulose have been isolated from strains of Paenibacillus and Bacillus and shown to have high thermostability and/or activity over a wide pH spectrum. While novel cellulases from strains like Cellulomonas flavigena and Terendinibacter turnerae, produce multifunctional cellulases with broader substrate utilization. These enzymes offer a framework for enhancement of cellulases including: specific activity, thermalstability, or end-product inhibition. In addition, anaerobic bacteria like the clostridia offer potential due to species capable of producing compound multienzyme complexes called cellulosomes. Cellulosomes provide synergy and close proximity of enzymes to substrate, increasing activity towards crystalline cellulose. This has lead to the construction of designer cellulosomes enhanced for specific substrate activity. Furthermore, cellulosome-producing Clostridium thermocellum and its ability to ferment sugars to ethanol; its amenability to co-culture and, recent advances in genetic engineering, offer a promising future in biofuels. The exploitation of bacteria in the search for improved enzymes or strategies provides a means to upgrade feasibility for lignocellulosic biomass conversion, ultimately providing means to a 'greener' technology.
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Affiliation(s)
- Miranda Maki
- Biorefining Research Initiative, Lakehead University, Thunder Bay, Ontario, Canada
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