1
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Lv L, Lin J, Feng Y, Wang W, Li S. Coated recombinant Escherichia coli for delayed release of β-mannanase in the water-based fracturing fluid. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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2
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Weng C, Peng X, Han Y. Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:84. [PMID: 33812391 PMCID: PMC8019502 DOI: 10.1186/s13068-021-01934-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/19/2021] [Indexed: 05/23/2023]
Abstract
Lignin, the most abundant renewable aromatic compound in nature, is an excellent feedstock for value-added bioproducts manufacturing; while the intrinsic heterogeneity and recalcitrance of which hindered the efficient lignin biorefinery and utilization. Compared with chemical processing, bioprocessing with microbial and enzymatic catalysis is a clean and efficient method for lignin depolymerization and conversion. Generally, lignin bioprocessing involves lignin decomposition to lignin-based aromatics via extracellular microbial enzymes and further converted to value-added bioproducts through microbial metabolism. In the review, the most recent advances in degradation and conversion of lignin to value-added bioproducts catalyzed by microbes and enzymes were summarized. The lignin-degrading microorganisms of white-rot fungi, brown-rot fungi, soft-rot fungi, and bacteria under aerobic and anaerobic conditions were comparatively analyzed. The catalytic metabolism of the microbial lignin-degrading enzymes of laccase, lignin peroxidase, manganese peroxidase, biphenyl bond cleavage enzyme, versatile peroxidase, and β-etherize was discussed. The microbial metabolic process of H-lignin, G-lignin, S-lignin based derivatives, protocatechuic acid, and catechol was reviewed. Lignin was depolymerized to lignin-derived aromatic compounds by the secreted enzymes of fungi and bacteria, and the aromatics were converted to value-added compounds through microbial catalysis and metabolic engineering. The review also proposes new insights for future work to overcome the recalcitrance of lignin and convert it to value-added bioproducts by microbial and enzymatic catalysis.
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Affiliation(s)
- Caihong Weng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Chen X, Wang X, Liu Y, Zhang R, Zhang L, Zhan R, Wang S, Wang K. Biochemical analyses of a novel thermostable GH5 endo β-1,4-mannanase with minor β-1,4-glucosidic cleavage activity from Bacillus sp. KW1 and its synergism with a commercial α-galactosidase on galactomannan hydrolysis. Int J Biol Macromol 2020; 166:778-788. [PMID: 33144255 DOI: 10.1016/j.ijbiomac.2020.10.235] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/07/2020] [Accepted: 10/30/2020] [Indexed: 11/17/2022]
Abstract
A novel GH5 endo-1,4-β-mannanase (BaMan5A) was identified from Bacillus sp. KW1, it shares the highest sequence identity (86%) with another characterized Bacillus endo-1,4-β-mannanase. The recombinant BaMan5A displayed maximum activity at pH 7.0 and 70 °C, it was stable at a broad pH range (pH 3.5-11.0) after 12-h incubation at 25 °C, and exhibited good thermostability, retaining about 100% and 85% activity after incubating at 60 °C for 12 h and 65 °C for 8 h, respectively. The results of polysaccharide hydrolysis revealed that the enzyme can only hydrolyze mannan substrates, including carob galactomannan, konjac glucomannan, 1,4-β-D-mannan, locust bean gum, and guar gum, yielding mannose, mannobiose, mannotriose, and some other oligosaccharides. The best substrate was carob galactomannan, the corresponding specific activity and Km value were 10,886 μmol/min/μmol and 3.31 mg/mL, respectively. Interestingly, BaMan5A was capable to hydrolyze both manno-oligosaccharides and cello-oligosaccharides, including mannotetraose, mannopentaose, mannohexaose, cellopentaose and cellohexaose. Furthermore, BaMan5A acted synergistically with a commercial α-galactosidase (CbAgal) on galactomannan depolymerization, a best synergy degree of 1.58 was achieved after optimizing enzyme ratios. This study not only expands the diversity of Bacillus GH5 β-mannanase, but also discloses the potential of BaMan5A in industrial application.
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Affiliation(s)
- Xi Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, PR China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, PR China; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, PR China
| | - Xinhai Wang
- Department of General Surgery, Huashan Hospital of Fudan University, Shanghai, PR China
| | - Yun Liu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, PR China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, PR China; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, PR China
| | - Ruiqin Zhang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, PR China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, PR China; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, PR China
| | - Liang Zhang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, PR China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, PR China; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, PR China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, PR China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, PR China; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, PR China
| | - Sidi Wang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Kui Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, PR China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, PR China; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, PR China.
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4
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Kaira GS, Kapoor M. Molecular advancements on over-expression, stability and catalytic aspects of endo-β-mannanases. Crit Rev Biotechnol 2020; 41:1-15. [PMID: 33032458 DOI: 10.1080/07388551.2020.1825320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The hydrolysis of mannans by endo-β-mannanases continues to gather significance as exemplified by its commercial applications in food, feed, and a rekindled interest in biorefineries. The present review provides a comprehensive account of fundamental research and fascinating insights in the field of endo-β-mannanase engineering in order to improve over-expression and to decipher molecular determinants governing activity-stability during harsh conditions, substrate recognition, polysaccharide specificity, endo/exo mode of action and multi-functional activities in the modular polypeptide. In-depth analysis of the available literature has also been made on rational and directed evolution approaches, which have translated native endo-β-mannanases into superior biocatalysts for satisfying industrial requirements.
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Affiliation(s)
- Gaurav Singh Kaira
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mukesh Kapoor
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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5
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Hsu Y, Arioka M. In vitro and in vivo characterization of genes involved in mannan degradation in Neurospora crassa. Fungal Genet Biol 2020; 144:103441. [PMID: 32777385 DOI: 10.1016/j.fgb.2020.103441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 01/22/2023]
Abstract
To better understand the roles of genes involved in mannan degradation in filamentous fungi, in this study we searched, identified, and characterized one putative GH5 endo-β-mannanase (GH5-7) and two putative GH2 mannan-degrading enzymes (GH2-1 and GH2-4) in Neurospora crassa. Real-time RT-PCR analyses showed that the expression levels of these genes were significantly up-regulated when the cells were grown in mannan-containing media where the induction level of gh5-7 was the highest. All three proteins were heterologously expressed and purified. GH5-7 displayed a substrate preference toward galactomannan by showing 10-times higher catalytic efficiency than to linear β-mannan. In contrast, GH2-1 preferred short manno-oligosaccharides or β-mannan as substrates. Compared to the wild type strain, the growth of Δgh5-7 and Δgh5-7Δgh2-4 mutants, but not Δgh2-1, Δgh2-4, and Δgh2-1Δgh2-4 mutants, was poor in the cultures containing glucomannan or galactomannan as the sole carbon source, suggesting that GH5-7 plays a critical role in the utilization of heteromannans in vivo. On the other hand, all the mutants showed significantly slow growth when grown in the medium containing linear β-mannan. Collectively, these results indicate that N. crassa can utilize glucomannan and galactomannan without GH2-1 and GH2-4, but efficient degradation of β-mannan requires a concerted action of three enzymes, GH5-7, GH2-1, and GH2-4.
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Affiliation(s)
- Yunhan Hsu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Manabu Arioka
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Japan.
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6
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Cann I, Pereira GV, Abdel-Hamid AM, Kim H, Wefers D, Kayang BB, Kanai T, Sato T, Bernardi RC, Atomi H, Mackie RI. Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products. Appl Environ Microbiol 2020; 86:e02296-19. [PMID: 31980431 PMCID: PMC7082577 DOI: 10.1128/aem.02296-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.
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Affiliation(s)
- Isaac Cann
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Gabriel V Pereira
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel Wefers
- Karlsruhe Institute of Technology, Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe, Germany
| | - Boniface B Kayang
- Department of Animal Science, School of Agriculture, University of Ghana, Legon, Ghana
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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7
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Pareek S, Kurakawa T, Das B, Motooka D, Nakaya S, Rongsen-Chandola T, Goyal N, Kayama H, Dodd D, Okumura R, Maeda Y, Fujimoto K, Nii T, Ogawa T, Iida T, Bhandari N, Kida T, Nakamura S, Nair GB, Takeda K. Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi. NPJ Biofilms Microbiomes 2019; 5:37. [PMID: 31885873 PMCID: PMC6925221 DOI: 10.1038/s41522-019-0110-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.
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Affiliation(s)
- Siddhika Pareek
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan.,3Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, 100-0004 Japan
| | - Takashi Kurakawa
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan
| | - Bhabatosh Das
- 4Molecular Genetics Laboratory, Center for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad, 121001 India
| | - Daisuke Motooka
- 5Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
| | - Shuuichi Nakaya
- 6Global Applications Development Center, Shimadzu Corp, Kyoto, 604-8511 Japan
| | | | - Nidhi Goyal
- 7Centre for Health Research and Development, Society for Applied Studies, New Delhi, 110016 India
| | - Hisako Kayama
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan.,3Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, 100-0004 Japan
| | - Dylan Dodd
- 8Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Ryu Okumura
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan.,3Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, 100-0004 Japan
| | - Yuichi Maeda
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan.,9Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Kosuke Fujimoto
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,9Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Takuro Nii
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan.,9Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Takao Ogawa
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan.,9Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Tetsuya Iida
- 5Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan.,10Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
| | - Nita Bhandari
- 7Centre for Health Research and Development, Society for Applied Studies, New Delhi, 110016 India
| | - Toshiyuki Kida
- 11Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, 565-0871 Japan
| | - Shota Nakamura
- 5Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
| | - G Balakrish Nair
- 4Molecular Genetics Laboratory, Center for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad, 121001 India
| | - Kiyoshi Takeda
- 1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.,2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871 Japan.,3Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, 100-0004 Japan
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8
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Xie J, He Z, Wang Z, Wang B, Pan L. Efficient expression of a novel thermophilic fungal β-mannosidase from Lichtheimia ramosa with broad-range pH stability and its synergistic hydrolysis of locust bean gum. J Biosci Bioeng 2019; 128:416-423. [PMID: 31130335 DOI: 10.1016/j.jbiosc.2019.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/28/2019] [Accepted: 04/10/2019] [Indexed: 10/26/2022]
Abstract
β-Mannosidase (EC 3.2.1.25) is an exoglycosidase specific for the hydrolysis of terminal β-1,4-glycosidic linkage in mannan which can be applied in the food manufacture, animal feed, bioethanol making and coffee extraction industries. A novel β-mannosidase gene (Lrman5A) from Lichtheimia ramosa was synthesized and recombinantly expressed in Pichia pastoris X33. Lrman5A encodes 444 amino acids with a calculated molecular mass of 51.0 kDa which shares the highest identity (73%) with the β-mannosidase from Rhizomucor miehei. Purified recombinant Lrman5A showed the maximal activity at pH 6.0 and 65°C, had broad-range pH stability (retaining >65% activity after incubation at pH 3.0-8.5 at 37°C for 24 h), and was highly thermostable (retaining >80% activity after incubation at 65°C for 10 min). The specific activity, and Km of Lrman5A was 17.5 U/mg and 1.377 mM, respectively. Lrman5A and GH5 β-mannanase displayed significant synergistic effects on the degradation of locust bean gum (LBG) and released more mannose (up to 2.89 folds) by simultaneous or sequential addition. Due to its hydrolytic properties, Lrman5A may have potential applications in the area of bioenergy, feed and food processing.
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Affiliation(s)
- Jianhua Xie
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, People's Republic of China; AsiaPac (Dongguan) Bio-Technology Co., Ltd., Songshan Lake National Hi-tech Industrial Development Zone, No. 3, North Industrial Road, Dongguan City, Guangdong 523808, People's Republic of China
| | - Zhimei He
- AsiaPac (Dongguan) Bio-Technology Co., Ltd., Songshan Lake National Hi-tech Industrial Development Zone, No. 3, North Industrial Road, Dongguan City, Guangdong 523808, People's Republic of China
| | - Zheng Wang
- AsiaPac (Dongguan) Bio-Technology Co., Ltd., Songshan Lake National Hi-tech Industrial Development Zone, No. 3, North Industrial Road, Dongguan City, Guangdong 523808, People's Republic of China
| | - Bin Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, People's Republic of China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Guangzhou, Guangdong 510006, People's Republic of China.
| | - Li Pan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, People's Republic of China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Guangzhou, Guangdong 510006, People's Republic of China
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9
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Extremely thermoactive archaeal endoglucanase from a shallow marine hydrothermal vent from Vulcano Island. Appl Microbiol Biotechnol 2018; 103:1267-1274. [DOI: 10.1007/s00253-018-9542-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/19/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023]
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10
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Ueda M, Hirano Y, Fukuhara H, Naka Y, Nakazawa M, Sakamoto T, Ogata Y, Tamada T. Gene cloning, expression, and X-ray crystallographic analysis of a β-mannanase from Eisenia fetida. Enzyme Microb Technol 2018; 117:15-22. [DOI: 10.1016/j.enzmictec.2018.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/16/2018] [Accepted: 05/25/2018] [Indexed: 10/16/2022]
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11
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Lee KT, Toushik SH, Baek JY, Kim JE, Lee JS, Kim KS. Metagenomic Mining and Functional Characterization of a Novel KG51 Bifunctional Cellulase/Hemicellulase from Black Goat Rumen. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9034-9041. [PMID: 30085665 DOI: 10.1021/acs.jafc.8b01449] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A novel KG51 gene was isolated from a metagenomic library of Korean black goat rumen and its recombinant protein was characterized as a bifunctional enzyme (cellulase/hemicellulase). In silico sequence and domain analyses revealed that the KG51 gene encodes a novel carbohydrate-active enzyme that possesses a salad-bowl-like shaped glycosyl hydrolase family 5 (GH5) catalytic domain but, at best, 41% sequence identity with other homologous GH5 proteins. Enzymatic profiles (optimum pH values and temperatures, as well as pH and thermal stabilities) of the recombinant KG51 bifunctional enzyme were also determined. On the basis of the substrate specificity data, the KG51 enzyme exhibited relatively strong cellulase (endo-β-1,4-glucanase [EC 3.2.1.4]) and hemicellulase (mannan endo-β-1,4-mannosidase [EC 3.2.1.78] and endo-β-1,4-xylanase [EC 3.2.1.8]) activities, but no exo-β-1,4-glucanase (EC 3.2.1.74), exo-β-1,4-glucan cellobiohydrolase (EC 3.2.1.91), and exo-1,4-β-xylosidase (EC 3.2.1.37) activities. Finally, the potential industrial applicability of the KG51 enzyme was tested in the preparation of prebiotic konjac glucomannan hydrolysates.
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Affiliation(s)
- Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division , National Institute of Animal Science , Rural Development Administration, Wanju 565-851 , South Korea
| | - Sazzad Hossen Toushik
- Department of Food Science and Technology , Chung-Ang University , Ansung 456-756 , South Korea
| | - Jin-Young Baek
- Department of Food Science and Technology , Chung-Ang University , Ansung 456-756 , South Korea
| | - Ji-Eun Kim
- Department of Food Science and Technology , Chung-Ang University , Ansung 456-756 , South Korea
| | - Jin-Sung Lee
- Department of Biological Sciences , Kyonggi University , Suwon 442-760 , South Korea
| | - Keun-Sung Kim
- Department of Food Science and Technology , Chung-Ang University , Ansung 456-756 , South Korea
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12
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Fusco FA, Ronca R, Fiorentino G, Pedone E, Contursi P, Bartolucci S, Limauro D. Biochemical characterization of a thermostable endomannanase/endoglucanase from Dictyoglomus turgidum. Extremophiles 2017; 22:131-140. [DOI: 10.1007/s00792-017-0983-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/20/2017] [Indexed: 11/21/2022]
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13
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Chu Y, Tu T, Penttinen L, Xue X, Wang X, Yi Z, Gong L, Rouvinen J, Luo H, Hakulinen N, Yao B, Su X. Insights into the roles of non-catalytic residues in the active site of a GH10 xylanase with activity on cellulose. J Biol Chem 2017; 292:19315-19327. [PMID: 28974575 PMCID: PMC5702671 DOI: 10.1074/jbc.m117.807768] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/20/2017] [Indexed: 11/06/2022] Open
Abstract
Bifunctional glycoside hydrolases have potential for cost-savings in enzymatic decomposition of plant cell wall polysaccharides for biofuels and bio-based chemicals. The N-terminal GH10 domain of a bifunctional multimodular enzyme CbXyn10C/Cel48B from Caldicellulosiruptor bescii is an enzyme able to degrade xylan and cellulose simultaneously. However, the molecular mechanism underlying its substrate promiscuity has not been elucidated. Herein, we discovered that the binding cleft of CbXyn10C would have at least six sugar-binding subsites by using isothermal titration calorimetry analysis of the inactive E140Q/E248Q mutant with xylo- and cello-oligosaccharides. This was confirmed by determining the catalytic efficiency of the wild-type enzyme on these oligosaccharides. The free form and complex structures of CbXyn10C with xylose- or glucose-configured oligosaccharide ligands were further obtained by crystallographic analysis and molecular modeling and docking. CbXyn10C was found to have a typical (β/α)8-TIM barrel fold and "salad-bowl" shape of GH10 enzymes. In complex structures with xylo-oligosaccharides, seven sugar-binding subsites were found, and many residues responsible for substrate interactions were identified. Site-directed mutagenesis indicated that 6 and 10 amino acid residues were key residues for xylan and cellulose hydrolysis, respectively. The most important residues are centered on subsites -2 and -1 near the cleavage site, whereas residues playing moderate roles could be located at more distal regions of the binding cleft. Manipulating the residues interacting with substrates in the distal regions directly or indirectly improved the activity of CbXyn10C on xylan and cellulose. Most of the key residues for cellulase activity are conserved across GH10 xylanases. Revisiting randomly selected GH10 enzymes revealed unreported cellulase activity, indicating that the dual function may be a more common phenomenon than has been expected.
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Affiliation(s)
- Yindi Chu
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Tu
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Leena Penttinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland
| | - Xianli Xue
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyu Wang
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhuolin Yi
- the Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China, and
| | - Li Gong
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- the Key Laboratory of Molecular Animal Nutrition and Feed Sciences, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Juha Rouvinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland
| | - Huiying Luo
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nina Hakulinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland,
| | - Bin Yao
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China,
| | - Xiaoyun Su
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China,
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Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus. Appl Environ Microbiol 2017; 83:AEM.00794-17. [PMID: 28710263 DOI: 10.1128/aem.00794-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/05/2017] [Indexed: 12/21/2022] Open
Abstract
The plant cell wall polysaccharide arabinan provides an important supply of arabinose, and unraveling arabinan-degrading strategies by microbes is important for understanding its use as a source of energy. Here, we explored the arabinan-degrading enzymes in the thermophilic bacterium Caldanaerobius polysaccharolyticus and identified a gene cluster encoding two glycoside hydrolase (GH) family 51 α-l-arabinofuranosidases (CpAbf51A, CpAbf51B), a GH43 endoarabinanase (CpAbn43A), a GH27 β-l-arabinopyranosidase (CpAbp27A), and two GH127 β-l-arabinofuranosidases (CpAbf127A, CpAbf127B). The genes were expressed as recombinant proteins, and the functions of the purified proteins were determined with para-nitrophenyl (pNP)-linked sugars and naturally occurring pectin structural elements as the substrates. The results demonstrated that CpAbn43A is an endoarabinanase while CpAbf51A and CpAbf51B are α-l-arabinofuranosidases that exhibit diverse substrate specificities, cleaving α-1,2, α-1,3, and α-1,5 linkages of purified arabinan-oligosaccharides. Furthermore, both CpAbf127A and CpAbf127B cleaved β-arabinofuranose residues in complex arabinan side chains, thus providing evidence of the function of this family of enzymes on such polysaccharides. The optimal temperatures of the enzymes ranged between 60°C and 75°C, and CpAbf43A and CpAbf51A worked synergistically to release arabinose from branched and debranched arabinan. Furthermore, the hydrolytic activity on branched arabinan oligosaccharides and degradation of pectic substrates by the endoarabinanase and l-arabinofuranosidases suggested a microbe equipped with diverse activities to degrade complex arabinan in the environment. Based on our functional analyses of the genes in the arabinan degradation cluster and the substrate-binding studies on a component of the cognate transporter system, we propose a model for arabinan degradation and transport by C. polysaccharolyticusIMPORTANCE Genomic DNA sequencing and bioinformatic analysis allowed the identification of a gene cluster encoding several proteins predicted to function in arabinan degradation and transport in C. polysaccharolyticus The analysis of the recombinant proteins yielded detailed insights into the putative arabinan metabolism of this thermophilic bacterium. The use of various branched arabinan oligosaccharides provided a detailed understanding of the substrate specificities of the enzymes and allowed assignment of two new GH127 polypeptides as β-l-arabinofuranosidases able to degrade pectic substrates, thus expanding our knowledge of this rare group of glycoside hydrolases. In addition, the enzymes showed synergistic effects for the degradation of arabinans at elevated temperatures. The enzymes characterized from the gene cluster are, therefore, of utility for arabinose production in both the biofuel and food industries.
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15
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Wefers D, Cavalcante JJ, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie RI, Koropatkin NM, Cann I. Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases. J Mol Biol 2017; 429:2509-2527. [DOI: 10.1016/j.jmb.2017.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/25/2017] [Accepted: 06/26/2017] [Indexed: 11/17/2022]
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16
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Ladevèze S, Laville E, Despres J, Mosoni P, Potocki-Véronèse G. Mannoside recognition and degradation by bacteria. Biol Rev Camb Philos Soc 2016; 92:1969-1990. [PMID: 27995767 DOI: 10.1111/brv.12316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/01/2016] [Accepted: 11/11/2016] [Indexed: 11/29/2022]
Abstract
Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein-protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them. This review focuses on the various mannosides that can be found in nature and details their structure. It underlines their involvement in cellular interactions and finally describes the latest discoveries regarding the catalytic machinery and metabolic pathways that bacteria have developed to metabolize them.
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Affiliation(s)
- Simon Ladevèze
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Elisabeth Laville
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Jordane Despres
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
| | - Pascale Mosoni
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
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17
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Rashamuse K, Sanyika Tendai W, Mathiba K, Ngcobo T, Mtimka S, Brady D. Metagenomic mining of glycoside hydrolases from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) and the characterization of a multimodular β-1,4-xylanase (GH11). Biotechnol Appl Biochem 2016; 64:174-186. [DOI: 10.1002/bab.1480] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/19/2015] [Indexed: 11/06/2022]
Affiliation(s)
| | - Walter Sanyika Tendai
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
- Department of Biotechnology; Chinhoyi University of Technology; Chinhoyi Zimbabwe
| | - Kgama Mathiba
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
| | - Thobile Ngcobo
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
| | - Sibongile Mtimka
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
| | - Dean Brady
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
- Molecular Sciences Institute; School of Chemistry; University of the Witwatersrand; Johannesburg South Africa
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18
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Conway JM, Pierce WS, Le JH, Harper GW, Wright JH, Tucker AL, Zurawski JV, Lee LL, Blumer-Schuette SE, Kelly RM. Multidomain, Surface Layer-associated Glycoside Hydrolases Contribute to Plant Polysaccharide Degradation by Caldicellulosiruptor Species. J Biol Chem 2016; 291:6732-47. [PMID: 26814128 DOI: 10.1074/jbc.m115.707810] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 01/08/2023] Open
Abstract
The genome of the extremely thermophilic bacterium Caldicellulosiruptor kronotskyensisencodes 19 surface layer (S-layer) homology (SLH) domain-containing proteins, the most in any Caldicellulosiruptorspecies genome sequenced to date. These SLH proteins include five glycoside hydrolases (GHs) and one polysaccharide lyase, the genes for which were transcribed at high levels during growth on plant biomass. The largest GH identified so far in this genus, Calkro_0111 (2,435 amino acids), is completely unique toC. kronotskyensisand contains SLH domains. Calkro_0111 was produced recombinantly inEscherichia colias two pieces, containing the GH16 and GH55 domains, respectively, as well as putative binding and spacer domains. These displayed endo- and exoglucanase activity on the β-1,3-1,6-glucan laminarin. A series of additional truncation mutants of Calkro_0111 revealed the essential architectural features required for catalytic function. Calkro_0402, another of the SLH domain GHs inC. kronotskyensis, when produced inE. coli, was active on a variety of xylans and β-glucans. Unlike Calkro_0111, Calkro_0402 is highly conserved in the genus Caldicellulosiruptorand among other biomass-degrading Firmicutes but missing from Caldicellulosiruptor bescii As such, the gene encoding Calkro_0402 was inserted into the C. besciigenome, creating a mutant strain with its S-layer extensively decorated with Calkro_0402. This strain consequently degraded xylans more extensively than wild-typeC. bescii The results here provide new insights into the architecture and role of SLH domain GHs and demonstrate that hemicellulose degradation can be enhanced through non-native SLH domain GHs engineered into the genomes of Caldicellulosiruptorspecies.
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Affiliation(s)
- Jonathan M Conway
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - William S Pierce
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Jaycee H Le
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - George W Harper
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - John H Wright
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Allyson L Tucker
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Jeffrey V Zurawski
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Laura L Lee
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Sara E Blumer-Schuette
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Robert M Kelly
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
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19
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A review of the enzymatic hydrolysis of mannans and synergistic interactions between β-mannanase, β-mannosidase and α-galactosidase. World J Microbiol Biotechnol 2015; 31:1167-75. [DOI: 10.1007/s11274-015-1878-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 05/23/2015] [Indexed: 10/23/2022]
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20
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Distinct roles for carbohydrate-binding modules of glycoside hydrolase 10 (GH10) and GH11 xylanases from Caldicellulosiruptor sp. strain F32 in thermostability and catalytic efficiency. Appl Environ Microbiol 2015; 81:2006-14. [PMID: 25576604 DOI: 10.1128/aem.03677-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylanases are crucial for lignocellulosic biomass deconstruction and generally contain noncatalytic carbohydrate-binding modules (CBMs) accessing recalcitrant polymers. Understanding how multimodular enzymes assemble can benefit protein engineering by aiming at accommodating various environmental conditions. Two multimodular xylanases, XynA and XynB, which belong to glycoside hydrolase families 11 (GH11) and GH10, respectively, have been identified from Caldicellulosiruptor sp. strain F32. In this study, both xylanases and their truncated mutants were overexpressed in Escherichia coli, purified, and characterized. GH11 XynATM1 lacking CBM exhibited a considerable improvement in specific activity (215.8 U nmol(-1) versus 94.7 U nmol(-1)) and thermal stability (half-life of 48 h versus 5.5 h at 75°C) compared with those of XynA. However, GH10 XynB showed higher enzyme activity and thermostability than its truncated mutant without CBM. Site-directed mutagenesis of N-terminal amino acids resulted in a mutant, XynATM1-M, with 50% residual activity improvement at 75°C for 48 h, revealing that the disordered region influenced protein thermostability negatively. The thermal stability of both xylanases and their truncated mutants were consistent with their melting temperature (Tm), which was determined by using differential scanning calorimetry. Through homology modeling and cross-linking analysis, we demonstrated that for XynB, the resistance against thermoinactivation generally was enhanced through improving both domain properties and interdomain interactions, whereas for XynA, no interdomain interactions were observed. Optimized intramolecular interactions can accelerate thermostability, which provided microbes a powerful evolutionary strategy to assemble catalysts that are adapted to various ecological conditions.
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21
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Chekan JR, Kwon IH, Agarwal V, Dodd D, Revindran V, Mackie RI, Cann I, Nair SK. Structural and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17. J Biol Chem 2014; 289:34965-77. [PMID: 25342756 DOI: 10.1074/jbc.m114.579904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hemicelluloses, the polysaccharide component of plant cell walls, represent one of the most abundant biopolymers in nature. The most common hemicellulosic constituents of softwoods, such as conifers and cycads, are mannans consisting of a 1,4-linked β-mannopyranosyl main chain with branch decorations. Efforts toward the utilization of hemicellulose for bioconversion into cellulosic biofuels have resulted in the identification of several families of glycoside hydrolases that can degrade mannan. However, effective biofermentation of manno-oligosaccharides is limited by a lack of appropriate uptake route in ethanologenic organisms. Here, we used transcriptome sequencing to gain insights into mannan degradation by the thermophilic anaerobic bacterium Caldanaerobius polysaccharolyticus. The most highly up-regulated genes during mannan fermentation occur in a cluster containing several genes encoding enzymes for efficient mannan hydrolysis as well as a solute-binding protein (CpMnBP1) that exhibits specificity for short mannose polymers but exhibited the flexibility to accommodate branched polysaccharide decorations. Co-crystal structures of CpMnBP1 in complex with mannobiose (1.4-Å resolution) and mannotriose (2.2-Å resolution) revealed the molecular rationale for chain length and oligosaccharide specificity. Calorimetric analysis of several active site variants confirmed the roles of residues critical to the function of CpMnBP1. This work represents the first biochemical characterization of a mannose-specific solute-binding protein and provides a framework for engineering mannan utilization capabilities for microbial fermentation.
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Affiliation(s)
| | | | | | - Dylan Dodd
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology
| | - Vanessa Revindran
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Isaac Cann
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology,
| | - Satish K Nair
- From the Departments of Biochemistry, Institute for Genomic Biology, Center for Biophysics and Computational Biology, and
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22
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Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes. Proc Natl Acad Sci U S A 2014; 111:E3708-17. [PMID: 25136124 DOI: 10.1073/pnas.1406156111] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes that degrade dietary and host-derived glycans represent the most abundant functional activities encoded by genes unique to the human gut microbiome. However, the biochemical activities of a vast majority of the glycan-degrading enzymes are poorly understood. Here, we use transcriptome sequencing to understand the diversity of genes expressed by the human gut bacteria Bacteroides intestinalis and Bacteroides ovatus grown in monoculture with the abundant dietary polysaccharide xylan. The most highly induced carbohydrate active genes encode a unique glycoside hydrolase (GH) family 10 endoxylanase (BiXyn10A or BACINT_04215 and BACOVA_04390) that is highly conserved in the Bacteroidetes xylan utilization system. The BiXyn10A modular architecture consists of a GH10 catalytic module disrupted by a 250 amino acid sequence of unknown function. Biochemical analysis of BiXyn10A demonstrated that such insertion sequences encode a new family of carbohydrate-binding modules (CBMs) that binds to xylose-configured oligosaccharide/polysaccharide ligands, the substrate of the BiXyn10A enzymatic activity. The crystal structures of CBM1 from BiXyn10A (1.8 Å), a cocomplex of BiXyn10A CBM1 with xylohexaose (1.14 Å), and the CBM from its homolog in the Prevotella bryantii B14 Xyn10C (1.68 Å) reveal an unanticipated mode for ligand binding. A minimal enzyme mix, composed of the gene products of four of the most highly up-regulated genes during growth on wheat arabinoxylan, depolymerizes the polysaccharide into its component sugars. The combined biochemical and biophysical studies presented here provide a framework for understanding fiber metabolism by an important group within the commensal bacterial population known to influence human health.
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23
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Biochemical characterization of a thermophilic β-mannanase from Talaromyces leycettanus JCM12802 with high specific activity. Appl Microbiol Biotechnol 2014; 99:1217-28. [DOI: 10.1007/s00253-014-5979-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 11/27/2022]
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24
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Bernardi RC, Cann I, Schulten K. Molecular dynamics study of enhanced Man5B enzymatic activity. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:83. [PMID: 24976862 PMCID: PMC4074406 DOI: 10.1186/1754-6834-7-83] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/21/2014] [Indexed: 05/25/2023]
Abstract
BACKGROUND Biofuels are a well-known alternative to the largely used fossil-derived fuels, however the competition with food production is an ethical dilemma. Fortunately a solution is offered by second-generation biofuels which can be produced from agricultural waste or, more specifically, from plant cell wall polysaccharides. The conversion process involves typically enzymatic hydrolysis of lignocellulosic biomass and then separation of its constituent sugars that are further fermented to produce ethanol. Over the years several technologies have been developed that allow this conversion process to occur and the objective is now to make this process cost-competitive in today's markets. RESULTS We observe that reduction of enzymatic efficiency in the presence of gluco-oligosaccharides is associated with a loss of the enzyme's flexibility, the latter being required to bind new substrate, while the presence of manno-oligosaccharides does not pose this problem. Molecular dynamics simulations identify key contacts between substrates and the enzyme catalytic pocket that might be modified through site-directed mutagenesis to prevent loss of enzymatic efficiency. CONCLUSIONS Based on previous experimental studies and the new molecular dynamics data, we suggest that cellohexaose in the active site pocket slows down or even inhibits Man5B enzymatic activity. The assumption of such a mechanism is reasonable since when the gluco-oligosaccharide substrate is attached to the catalytic pocket it takes much longer to leave the pocket and thus prevents other substrates from reaching the active site. The insight is of crucial importance since the inhibition of enzymes by the enzymatic product or by an unsuitable substrate is a major technological problem in reducing the competitiveness of second-generation biofuel production.
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Affiliation(s)
- Rafael C Bernardi
- Beckman Institute, University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801, USA
| | - Isaac Cann
- Energy Biosciences Institute, University of Illinois, 1206 W. Gregory Dr, Urbana, IL 61801, USA
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL 61801, USA
- Department of Animal Science, University of Illinois, 1207 W. Gregory Dr, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Dr, Urbana, IL 61801, USA
| | - Klaus Schulten
- Beckman Institute, University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801, USA
- Department of Physics, University of Illinois, 1110 W. Green St, Urbana, IL 61801, USA
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25
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Tsukagoshi H, Nakamura A, Ishida T, Touhara KK, Otagiri M, Moriya S, Samejima M, Igarashi K, Fushinobu S, Kitamoto K, Arioka M. Structural and biochemical analyses of glycoside hydrolase family 26 β-mannanase from a symbiotic protist of the termite Reticulitermes speratus. J Biol Chem 2014; 289:10843-10852. [PMID: 24570006 DOI: 10.1074/jbc.m114.555383] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Termites and their symbiotic protists have established a prominent dual lignocellulolytic system, which can be applied to the biorefinery process. One of the major components of lignocellulose from conifers is glucomannan, which comprises a heterogeneous combination of β-1,4-linked mannose and glucose. Mannanases are known to hydrolyze the internal linkage of the glucomannan backbone, but the specific mechanism by which they recognize and accommodate heteropolysaccharides is currently unclear. Here, we report biochemical and structural analyses of glycoside hydrolase family 26 mannanase C (RsMan26C) from a symbiotic protist of the termite Reticulitermes speratus. RsMan26C was characterized based on its catalytic efficiency toward glucomannan, compared with pure mannan. The crystal structure of RsMan26C complexed with gluco-manno-oligosaccharide(s) explained its specificities for glucose and mannose at subsites -5 and -2, respectively, in addition to accommodation of both glucose and mannose at subsites -3 and -4. RsMan26C has a long open cleft with a hydrophobic platform of Trp(94) at subsite -5, facilitating enzyme binding to polysaccharides. Notably, a unique oxidized Met(85) specifically interacts with the equatorial O-2 of glucose at subsite -3. Our results collectively indicate that specific recognition and accommodation of glucose at the distal negative subsites confers efficient degradation of the heteropolysaccharide by mannanase.
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Affiliation(s)
- Hikaru Tsukagoshi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Akihiko Nakamura
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takuya Ishida
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kouki K Touhara
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Masato Otagiri
- Biomass Engineering Program Cooperation Division, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shigeharu Moriya
- Laboratory of Environmental Molecular Biology, Graduate School of Yokohama City University, Yokohama, Kanagawa 230-0045, Japan; Molecular and Informative Life Science Unit, RIKEN Advanced Science Institute, Yokohama, Kanagawa 230-0045, Japan
| | - Masahiro Samejima
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Katsuhiko Kitamoto
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Manabu Arioka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
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Oyama T, Schmitz GE, Dodd D, Han Y, Burnett A, Nagasawa N, Mackie RI, Nakamura H, Morikawa K, Cann I. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases. PLoS One 2013; 8:e80448. [PMID: 24278284 PMCID: PMC3835425 DOI: 10.1371/journal.pone.0080448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022] Open
Abstract
CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.
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Affiliation(s)
- Takuji Oyama
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - George E. Schmitz
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Alanna Burnett
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Naoko Nagasawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kosuke Morikawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Isaac Cann
- Institute for Protein Research, Osaka University, Osaka, Japan
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Reconstitution of a thermostable xylan-degrading enzyme mixture from the bacterium Caldicellulosiruptor bescii. Appl Environ Microbiol 2012; 79:1481-90. [PMID: 23263957 DOI: 10.1128/aem.03265-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylose, the major constituent of xylans, as well as the side chain sugars, such as arabinose, can be metabolized by engineered yeasts into ethanol. Therefore, xylan-degrading enzymes that efficiently hydrolyze xylans will add value to cellulases used in hydrolysis of plant cell wall polysaccharides for conversion to biofuels. Heterogeneous xylan is a complex substrate, and it requires multiple enzymes to release its constituent sugars. However, the components of xylan-degrading enzymes are often individually characterized, leading to a dearth of research that analyzes synergistic actions of the components of xylan-degrading enzymes. In the present report, six genes predicted to encode components of the xylan-degrading enzymes of the thermophilic bacterium Caldicellulosiruptor bescii were expressed in Escherichia coli, and the recombinant proteins were investigated as individual enzymes and also as a xylan-degrading enzyme cocktail. Most of the component enzymes of the xylan-degrading enzyme mixture had similar optimal pH (5.5 to ∼6.5) and temperature (75 to ∼90°C), and this facilitated their investigation as an enzyme cocktail for deconstruction of xylans. The core enzymes (two endoxylanases and a β-xylosidase) exhibited high turnover numbers during catalysis, with the two endoxylanases yielding estimated k(cat) values of ∼8,000 and ∼4,500 s(-1), respectively, on soluble wheat arabinoxylan. Addition of side chain-cleaving enzymes to the core enzymes increased depolymerization of a more complex model substrate, oat spelt xylan. The C. bescii xylan-degrading enzyme mixture effectively hydrolyzes xylan at 65 to 80°C and can serve as a basal mixture for deconstruction of xylans in bioenergy feedstock at high temperatures.
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Aspeborg H, Coutinho PM, Wang Y, Brumer H, Henrissat B. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol 2012; 12:186. [PMID: 22992189 PMCID: PMC3526467 DOI: 10.1186/1471-2148-12-186] [Citation(s) in RCA: 325] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 09/13/2012] [Indexed: 12/02/2022] Open
Abstract
Background The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at
http://www.cazy.org/GH5.html.
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Affiliation(s)
- Henrik Aspeborg
- Division of Glycoscience, School of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, Stockholm SE-106 91, Sweden
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Han Y, Hawkins AS, Adams MWW, Kelly RM. Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle. Appl Environ Microbiol 2012; 78:6194-202. [PMID: 22752162 PMCID: PMC3416614 DOI: 10.1128/aem.01312-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/20/2012] [Indexed: 11/20/2022] Open
Abstract
Crenarchaeotal genomes encode the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle for carbon dioxide fixation. Of the 13 enzymes putatively comprising the cycle, several of them, including methylmalonyl-coenzyme A (CoA) epimerase (MCE) and methylmalonyl-CoA mutase (MCM), which convert (S)-methylmalonyl-CoA to succinyl-CoA, have not been confirmed and characterized biochemically. In the genome of Metallosphaera sedula (optimal temperature [T(opt)], 73°C), the gene encoding MCE (Msed_0639) is adjacent to that encoding the catalytic subunit of MCM-α (Msed_0638), while the gene for the coenzyme B(12)-binding subunit of MCM (MCM-β) is located remotely (Msed_2055). The expression of all three genes was significantly upregulated under autotrophic compared to heterotrophic growth conditions, implying a role in CO(2) fixation. Recombinant forms of MCE and MCM were produced in Escherichia coli; soluble, active MCM was produced only if MCM-α and MCM-β were coexpressed. MCE is a homodimer and MCM is a heterotetramer (α(2)β(2)) with specific activities of 218 and 2.2 μmol/min/mg, respectively, at 75°C. The heterotetrameric MCM differs from the homo- or heterodimeric orthologs in other organisms. MCE was activated by divalent cations (Ni(2+), Co(2+), and Mg(2+)), and the predicted metal binding/active sites were identified through sequence alignments with less-thermophilic MCEs. The conserved coenzyme B(12)-binding motif (DXHXXG-SXL-GG) was identified in M. sedula MCM-β. The two enzymes together catalyzed the two-step conversion of (S)-methylmalonyl-CoA to succinyl-CoA, consistent with their proposed role in the 3-HP/4-HB cycle. Based on the highly conserved occurrence of single copies of MCE and MCM in Sulfolobaceae genomes, the M. sedula enzymes are likely to be representatives of these enzymes in the 3-HP/4-HB cycle in crenarchaeal thermoacidophiles.
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Affiliation(s)
- Yejun Han
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Aaron S. Hawkins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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Su X, Zhang J, Mackie RI, Cann IKO. Supplementing with non-glycoside hydrolase proteins enhances enzymatic deconstruction of plant biomass. PLoS One 2012; 7:e43828. [PMID: 22952777 PMCID: PMC3428283 DOI: 10.1371/journal.pone.0043828] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 07/30/2012] [Indexed: 11/19/2022] Open
Abstract
The glycoside hydrolases (GH) of Caldicellulosiruptor bescii are thermophilic enzymes, and therefore they can hydrolyze plant cell wall polysaccharides at high temperatures. Analyses of two C. bescii glycoside hydrolases, CbCelA-TM1 and CbXyn10A with cellulase and endoxylanase activity, respectively, demonstrated that each enzyme is highly thermostable under static incubation at 70°C. Both enzymes, however, rapidly lost their enzymatic activities when incubated at 70°C with end-over-end shaking. Since crowding conditions, even at low protein concentrations, seem to influence enzymatic properties, three non-glycoside hydrolase proteins were tested for their capacity to stabilize the thermophilic proteins at high temperatures. The three proteins investigated were a small heat shock protein CbHsp18 from C. bescii, a histone MkHistone1 from Methanopyrus kandleri, and bovine RNase A, from a commercial source. Fascinatingly, each of these proteins increased the thermostability of the glycoside hydrolases at 70°C during end-over-end shaking incubation, and this property translated into increases in hydrolysis of several substrates including the bioenergy feedstock Miscanthus. Furthermore, MkHistone1 and RNase A also altered the initial products released from the cello-oligosaccharide cellopentaose during hydrolysis with the cellodextrinase CbCdx1A, which further demonstrated the capacity of the three non-GH proteins to influence hydrolysis of substrates by the thermophilic glycoside hydrolases. The non-GH proteins used in the present report were small proteins derived from each of the three lineages of life, and therefore expand the space from which different polypeptides can be tested for their influence on plant cell wall hydrolysis, a critical step in the emerging biofuel industry.
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Affiliation(s)
- Xiaoyun Su
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Jing Zhang
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Isaac K. O. Cann
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Han Y, Agarwal V, Dodd D, Kim J, Bae B, Mackie RI, Nair SK, Cann IKO. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus. J Biol Chem 2012; 287:34946-34960. [PMID: 22918832 DOI: 10.1074/jbc.m112.391532] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.
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Affiliation(s)
- Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Vinayak Agarwal
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801
| | - Jason Kim
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801
| | - Brian Bae
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Satish K Nair
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.
| | - Isaac K O Cann
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801.
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Biochemical and mutational analyses of a multidomain cellulase/mannanase from Caldicellulosiruptor bescii. Appl Environ Microbiol 2012; 78:2230-40. [PMID: 22247178 DOI: 10.1128/aem.06814-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Thermophilic cellulases and hemicellulases are of significant interest to the biofuel industry due to their perceived advantages over their mesophilic counterparts. We describe here biochemical and mutational analyses of Caldicellulosiruptor bescii Cel9B/Man5A (CbCel9B/Man5A), a highly thermophilic enzyme. As one of the highly secreted proteins of C. bescii, the enzyme is likely to be critical to nutrient acquisition by the bacterium. CbCel9B/Man5A is a modular protein composed of three carbohydrate-binding modules flanked at the N terminus and the C terminus by a glycoside hydrolase family 9 (GH9) module and a GH5 module, respectively. Based on truncational analysis of the polypeptide, the cellulase and mannanase activities within CbCel9B/Man5A were assigned to the N- and C-terminal modules, respectively. CbCel9B/Man5A and its truncational mutants, in general, exhibited a pH optimum of ∼5.5 and a temperature optimum of 85°C. However, at this temperature, thermostability was very low. After 24 h of incubation at 75°C, the wild-type protein maintained 43% activity, whereas a truncated mutant, TM1, maintained 75% activity. The catalytic efficiency with phosphoric acid swollen cellulose as a substrate for the wild-type protein was 7.2 s(-1) ml/mg, and deleting the GH5 module led to a mutant (TM1) with a 2-fold increase in this kinetic parameter. Deletion of the GH9 module also increased the apparent k(cat) of the truncated mutant TM5 on several mannan-based substrates; however, a concomitant increase in the K(m) led to a decrease in the catalytic efficiencies on all substrates. These observations lead us to postulate that the two catalytic activities are coupled in the polypeptide.
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Su X, Agarwal V, Dodd D, Bae B, Mackie RI, Nair SK, Cann IKO. Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modules. J Biol Chem 2010; 285:34665-76. [PMID: 20739280 DOI: 10.1074/jbc.m110.168302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbohydrate binding modules (CBMs) are specialized proteins that bind to polysaccharides and oligosaccharides. Caldanaerobius polysaccharolyticus Man5ACBM16-1/CBM16-2 bind to glucose-, mannose-, and glucose/mannose-configured substrates. The crystal structures of the two proteins represent the only examples in CBM family 16, and studies that evaluate the roles of amino acid residues in ligand binding in this family are lacking. In this study, we probed the roles of amino acids (selected based on CBM16-1/ligand co-crystal structures) on substrate binding. Two tryptophan (Trp-20 and Trp-125) and two glutamine (Gln-81 and Gln-93) residues are shown to be critical in ligand binding. Additionally, several polar residues that flank the critical residues also contribute to ligand binding. The CBM16-1 Q121E mutation increased affinity for all substrates tested, whereas the Q21G and N97R mutants exhibited decreased substrate affinity. We solved CBM/substrate co-crystal structures to elucidate the molecular basis of the increased substrate binding by CBM16-1 Q121E. The Gln-121, Gln-21, and Asn-97 residues can be manipulated to fine-tune ligand binding by the Man5A CBMs. Surprisingly, none of the eight residues investigated was absolutely conserved in CBM family 16. Thus, the critical residues in the Man5A CBMs are either not essential for substrate binding in the other members of this family or the two CBMs are evolutionarily distinct from the members available in the current protein database. Man5A is dependent on its CBMs for robust activity, and insights from this study should serve to enhance our understanding of the interdependence of its catalytic and substrate binding modules.
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Affiliation(s)
- Xiaoyun Su
- Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
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