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Rai R, Samanta D, Goh KM, Chadha BS, Sani RK. Biochemical unravelling of the endoxylanase activity in a bifunctional GH39 enzyme cloned and expressed from thermophilic Geobacillus sp. WSUCF1. Int J Biol Macromol 2024; 257:128679. [PMID: 38072346 DOI: 10.1016/j.ijbiomac.2023.128679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024]
Abstract
The glycoside hydrolase family 39 (GH39) proteins are renowned for their extremophilic and multifunctional enzymatic properties, yet the molecular mechanisms underpinning these unique characteristics continue to be an active subject of research. In this study, we introduce WsuXyn, a GH39 protein with a molecular weight of 58 kDa, originating from the thermophilic Geobacillus sp. WSUCF1. Previously reported for its exceptional thermostable β-xylosidase activity, WsuXyn has recently demonstrated a significant endoxylanase activity (3752 U·mg-1) against beechwood xylan, indicating towards its bifunctional nature. Physicochemical characterization revealed that WsuXyn exhibits optimal endoxylanase activity at 70 °C and pH 7.0. Thermal stability assessments revealed that the enzyme is resilient to elevated temperatures, with a half-life of 168 h. Key kinetic parameters highlight the exceptional catalytic efficiency and strong affinity of the protein for xylan substrate. Moreover, WsuXyn-mediated hydrolysis of beechwood xylan has achieved 77 % xylan conversion, with xylose as the primary product. Structural analysis, amalgamated with docking simulations, has revealed strong binding forces between xylotetraose and the protein, with key amino acid residues, including Glu278, Tyr230, Glu160, Gly202, Cys201, Glu324, and Tyr283, playing pivotal roles in these interactions. Therefore, WsuXyn holds a strong promise for biodegradation and value-added product generation through lignocellulosic biomass conversion.
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Affiliation(s)
- Rohit Rai
- Faculty of Applied Medical Sciences, Lovely Professional University, Phagwara 144411, India.
| | - Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia
| | | | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; BuG ReMeDEE consortium and Composite and Nanocomposite Advanced Manufacturing Centre/Biomaterials (CNAM/Bio), Rapid City, SD 57701, USA.
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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Gadallah EE, El-Borai AM, El-Aassar SA, Beltagy EA. Purification, characterization, immobilization and applications of an enzybiotic β-1,3-1,4-glucanase produced from halotolerant marine Halomonas meridiana ES021. World J Microbiol Biotechnol 2023; 39:89. [PMID: 36740637 PMCID: PMC9899757 DOI: 10.1007/s11274-023-03527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023]
Abstract
Extracellular β-1,3-1,4-glucanase-producing strain Halomonas meridiana ES021 was isolated from Gabal El-Zeit off shore, Red Sea, Egypt. The Extracellular enzyme was partially purified by precipitation with 75% acetone followed by anion exchange chromatography on DEAE-cellulose, where a single protein band was determined with molecular mass of approximately 72 kDa. The Km value was 0.62 mg β-1,3-1,4-glucan/mL and Vmax value was 7936 U/mg protein. The maximum activity for the purified enzyme was observed at 40 °C, pH 5.0, and after 10 min of the reaction. β-1,3-1,4-glucanase showed strong antibacterial effect against Bacillus subtilis, Streptococcus agalactiae and Vibrio damsela. It also showed antifungal effect against Penicillium sp. followed by Aspergillus niger. No toxicity was observed when tested on Artemia salina. Semi-purified β-1,3-1,4-glucanase was noticed to be effective in clarification of different juices at different pH values and different time intervals. The maximum clarification yields were 51.61% and 66.67% on mango juice at 40 °C and pH 5.3 for 2 and 4 h, respectively. To our knowledge, this is the first report of β-1,3-1,4-glucanase enzyme from halotolerant Halomonas species.
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Affiliation(s)
- Eman E Gadallah
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt.
| | - Aliaa M El-Borai
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Samy A El-Aassar
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Ehab A Beltagy
- National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt
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Lisov AV, Kiselev SS, Trubitsina LI, Belova OV, Andreeva-Kovalevskaya ZI, Trubitsin IV, Shushkova TV, Leontievsky AA. Multifunctional Enzyme with Endoglucanase and Alginase/Glucuronan Lyase Activities from Bacterium Cellulophaga lytica. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:617-627. [PMID: 36154882 DOI: 10.1134/s0006297922070045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 06/16/2023]
Abstract
Cellulophaga lytica is a Gram-negative aerobic bacterium in the genome of which there are many genes encoding polysaccharide degrading enzymes. One of the enzymes named ClGP contains a glycoside hydrolase domain from the GH5 family and a polysaccharide lyase domain from the PL31 family. The enzyme also contains the TAT signaling peptide and the TIGR04183 domain that indicates extracellular nature of the enzyme. Phylogenetic analysis has shown that the enzymes most closely related to ClGP and containing all four domains (TAT, GH5, PL31, TIGR04183) are widespread among bacterial species belonging to the Flavobacteriaceae family. ClGP produced by the recombinant strain of E. coli was purified and characterized. ClGP exhibited activity of endoglucanase (EC 3.2.1.4) and catalyzed hydrolysis of β-D-glucan, carboxymethyl cellulose sodium salt (CMC-Na), and amorphous cellulose, but failed to hydrolyze microcrystalline cellulose and xylan. Products of CMC hydrolysis were cellobiose and cellotriose, whereas β-D-glucan was hydrolyzed to glucose, cellobiose, cellotetraose, and cellopentaose. ClGP was more active against the poly-β-D-mannuronate blocks than against the poly-α-L-glucuronate blocks of alginic acid. This indicates that the enzyme is a polyM lyase (EC 4.2.2.3). ClGP was active against polyglucuronic acid, so it displayed a glucuronan lyase (EC 4.2.2.14) activity. The enzyme had a neutral pH-optimum, was stable in the pH range 6.0-8.0, and displayed moderate thermal stability. ClGP effectively saccharified two species of brown algae, Saccharina latissima and Laminaria digitata, that suggests its potential for use in the production of biofuel from macroalgae.
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Affiliation(s)
- Alexander V Lisov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Sergei S Kiselev
- Institute of Cell Biophysics, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Liubov I Trubitsina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Oxana V Belova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Zhanna I Andreeva-Kovalevskaya
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Ivan V Trubitsin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Tatyana V Shushkova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexey A Leontievsky
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Huang Z, Ni G, Wang F, Zhao X, Chen Y, Zhang L, Qu M. Characterization of a Thermostable Lichenase from Bacillus subtilis B110 and Its Effects on β-Glucan Hydrolysis. J Microbiol Biotechnol 2022; 32:484-492. [PMID: 34949743 PMCID: PMC9628817 DOI: 10.4014/jmb.2111.11017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
Lichenase is an enzyme mainly implicated in the degradation of polysaccharides in the cell walls of grains. Emerging evidence shows that a highly efficient expression of a thermostable recombinant lichenase holds considerable promise for application in the beer-brewing and animal feed industries. Herein, we cloned a lichenase gene (CelA203) from Bacillus subtilis B110 and expressed it in E. coli. This gene contains an ORF of 729 bp, encoding a protein with 242 amino acids and a calculated molecular mass of 27.3 kDa. According to the zymogram results, purified CelA203 existed in two forms, a monomer, and a tetramer, but only the tetramer had potent enzymatic activity. CelA203 remained stable over a broad pH and temperature range and retained 40% activity at 70°C for 1 h. The Km and Vmax of CelA203 towards barley β-glucan and lichenan were 3.98 mg/ml, 1017.17 U/mg, and 2.78 mg/ml, 198.24 U/mg, respectively. Furthermore, trisaccharide and tetrasaccharide were the main products obtained from CelA203-mediated hydrolysis of deactivated oat bran. These findings demonstrate a promising role for CelA203 in the production of oligosaccharides in animal feed and brewing industries.
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Affiliation(s)
- Zhen Huang
- Key Laboratory of Animal Nutrition of Jiangxi Province, Nutritional Feed Development Engineering Research Center, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Guorong Ni
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China,Corresponding authors F. Wang E-mail:
| | - Xiaoyan Zhao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Yunda Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Lixia Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Mingren Qu
- Key Laboratory of Animal Nutrition of Jiangxi Province, Nutritional Feed Development Engineering Research Center, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China,
M. Qu Phone/Fax: +86 791 83813459 E-mail:
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Mondal S, Thakur A, Fontes CMGA, Goyal A. A trimodular family 16 glycoside hydrolase from the cellulosome of Ruminococcus flavefaciens displays highly specific licheninase (EC 3.2.1.73) activity. MICROBIOLOGY-SGM 2021; 167. [PMID: 34297654 DOI: 10.1099/mic.0.001055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cellulosomes are highly complex cell-bound multi-enzymatic nanomachines used by anaerobes to break down plant carbohydrates. The genome sequence of Ruminococcus flavefaciens revealed a remarkably diverse cellulosome composed of more than 200 cellulosomal enzymes. Here we provide a detailed biochemical characterization of a highly elaborate R. flavefaciens cellulosomal enzyme containing an N-terminal dockerin module, which anchors the enzyme into the multi-enzyme complex through binding of cohesins located in non-catalytic cell-bound scaffoldins, and three tandemly repeated family 16 glycoside hydrolase (GH16) catalytic domains. The DNA sequence encoding the three homologous catalytic domains was cloned and hyper-expressed in Escherichia coli BL21 (DE3) cells. SDS-PAGE analysis of purified His6 tag containing RfGH16_21 showed a single soluble protein of molecular size ~89 kDa, which was in agreement with the theoretical size, 89.3 kDa. The enzyme RfGH16_21 exhibited activity over a wide pH range (pH 5.0-8.0) and a broad temperature range (50-70 °C), displaying maximum activity at an optimum pH of 7.0 and optimum temperature of 55 °C. Substrate specificity analysis of RfGH16_21 revealed maximum activity against barley β-d-glucan (257 U mg-1) followed by lichenan (247 U mg-1), but did not show significant activity towards other tested polysaccharides, suggesting that it is specifically a β-1,3-1,4-endoglucanase. TLC analysis revealed that RfGH16_21 hydrolyses barley β-d-glucan to cellotriose, cellotetraose and a higher degree of polymerization of gluco-oligosaccharides indicating an endo-acting catalytic mechanism. This study revealed a fairly high, active and thermostable bacterial endo-glucanase which may find considerable biotechnological potentials.
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Affiliation(s)
- Sunetra Mondal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Abhijeet Thakur
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
- NZYTech - Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E - R/C, 1649-038 Lisbon, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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Pech-Cervantes AA, Muhammad I, Ogunade IM, Jiang Y, Kim DH, Gonzalez CF, Hackmann TJ, Oliveira AS, Vyas D, Adesogan AT. Exogenous fibrolytic enzymes and recombinant bacterial expansins synergistically improve hydrolysis and in vitro digestibility of bermudagrass haylage. J Dairy Sci 2019; 102:8059-8073. [PMID: 31326164 DOI: 10.3168/jds.2019-16339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 05/07/2019] [Indexed: 11/19/2022]
Abstract
Four experiments were conducted to examine the effects of a recombinant bacterial expansin-like protein (BsEXLX1) from Bacillus subtilis and a commercial exogenous fibrolytic enzyme (EFE) preparation for ruminants on hydrolysis of pure substrates (cellulose and xylan) and in vitro digestibility of bermudagrass haylage (BMH). Recombinant Escherichia coli BL21 strain was used to express BsEXLX1; the protein was purified using an affinity column. In experiment 1, carboxymethylcellulose, Whatman #1 filter paper (General Electric, Boston, MA) and oat-spelt xylan substrates were subjected to 4 treatments (1) sodium citrate buffer (control), (2) BsEXLX1 (162 µg/g of substrate), (3) EFE (2.3 mg/g of substrate), and (4) EFE + BsELX1 in 3 independent runs. Samples were incubated at optimal conditions for both additives (pH 5 and 50°C) or at ruminal (pH 6 and 39°C) or ambient (pH 6 and 25°C) conditions for 24 h and sugar release was measured. In experiment 2, digestibility in vitro of BMH was examined after treatment with the following: (1) control (buffer only), (2) BsEXLX1 (162 µg/g of dry matter), (3) EFE (2.2 mg/g of dry matter), and (4) EFE + BsEXLX1 in 3 independent runs at 39°C for 24 h. Experiment 3 examined effects of EFE and BsEXLX1 on simulated preingestive hydrolysis and profile of released sugars from BMH after samples were suspended in deionized water with sodium azide at 25°C for 24 h in 2 independent runs. In experiment 4, the sequence of the BsEXLX1 purified protein was compared with 447 ruminal bacterial genomes to identify similar proteins from the rumen. In experiment 1, compared with EFE alone, EFE and BsEXLX1 synergistically increased sugar release from carboxymethylcellulose and Whatman #1 filter paper under all simulated conditions; however, hydrolysis of xylan was not improved. In experiment 2, compared with EFE alone, treatment with EFE and BsEXLX1 increased neutral detergent fiber and acid detergent fiber digestibility of bermudagrass haylage (by 5.5 and 15%, respectively) and total volatile fatty acid concentrations, and decreased acetate-propionate ratio. In experiment 3, compared with EFE alone. The EFE and BsEXLX1 synergistically reduced concentrations of neutral detergent fiber and acid detergent fiber and increased release of sugars by 9.3%, particularly cellobiose (72.5%). In experiment 4, a similar sequence to that of BsEXLX1 was identified in Bacillus licheniformis, and similar hypothetical protein sequences were identified in Ruminococcus flavefaciens strains along with different protein structures in E. xylanophilum and Lachnospiraceae. This study showed that an expansin-like protein synergistically increased the hydrolysis of pure cellulose substrates and the hydrolysis and digestibility in vitro of BMH.
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Affiliation(s)
| | - I Muhammad
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32603
| | - I M Ogunade
- Department of Animal Sciences, University of Florida, Gainesville 32611; Division of Food and Animal Science, Kentucky State University, Frankfort 40601
| | - Y Jiang
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - D H Kim
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - C F Gonzalez
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32603
| | - T J Hackmann
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - A S Oliveira
- Institute of Agriculture and Environmental Sciences, Federal University of Mato Grosso, Campus Sinop, Sinop, MT, Brazil, 78890
| | - D Vyas
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - A T Adesogan
- Department of Animal Sciences, University of Florida, Gainesville 32611.
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Ghadikolaei KK, Sangachini ED, Vahdatirad V, Noghabi KA, Zahiri HS. An extreme halophilic xylanase from camel rumen metagenome with elevated catalytic activity in high salt concentrations. AMB Express 2019; 9:86. [PMID: 31209584 PMCID: PMC6579805 DOI: 10.1186/s13568-019-0809-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 06/06/2019] [Indexed: 11/22/2022] Open
Abstract
An extreme halophilic xylanase, designated as XylCMS, was characterized by cloning and expression of the encoding gene from a camel rumen metagenome. XylCMS proved to be a GH11 xylanase with high identity to a hypothetical glycosyl hydrolase from Ruminococcus flavefaciens. XylCMS with a molecular weight of about 47 kDa showed maximum activity at pH 6 and 55 °C. The enzyme activity was significantly stimulated by NaCl in 1–5 M concentrations. Interestingly, the optimum temperature was not influenced by NaCl but the Kcat of the enzyme was enhanced by 2.7-folds at 37 °C and 1.2-folds at 55 °C. The Km value was decreased with NaCl by 4.3-folds at 37 °C and 3.7-folds at 55 °C resulting in a significant increase in catalytic efficiency (Kcat/Km) by 11.5-folds at 37 °C and 4.4-folds at 55 °C. Thermodynamic analysis indicated that the activation energy (Ea) and enthalpy (∆H) of the reaction were decreased with NaCl by 2.4 and threefold, respectively. From the observations and the results of fluorescence spectroscopy, it was concluded that NaCl at high concentrations improves both the flexibility and substrate affinity of XylCMS that are crucial for catalytic activity by influencing substrate binding, product release and the energy barriers of the reaction. XylCMS as an extreme halophilic xylanase with stimulated activity in artificial seawater and low water activity conditions has potentials for application in industrial biotechnology.
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Zhang B, Liu Y, Yang H, Yan Q, Yang S, Jiang ZQ, Li S. Biochemical properties and application of a novel β-1,3-1,4-glucanase from Paenibacillus barengoltzii. Food Chem 2017; 234:68-75. [DOI: 10.1016/j.foodchem.2017.04.162] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/25/2017] [Accepted: 04/25/2017] [Indexed: 11/30/2022]
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A review on chimeric xylanases: methods and conditions. 3 Biotech 2017; 7:67. [PMID: 28452014 DOI: 10.1007/s13205-017-0660-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/14/2017] [Indexed: 12/30/2022] Open
Abstract
Multi-functional enzymes are one of the nature's solutions to facilitate metabolic pathways, thus several reactions are regulated and performed simultaneously on one polypeptide chain. Inspired by nature, artificial chimeric proteins have been designed to reduce the production costs and improve the performance. One of the interesting applications of this method is in the plant-based industries such as feed additive, waste treatment, biofuel production, and pulp and paper bleaching. In fact, the heterogeneous texture of plants needs using a combination of different enzymes to achieve an optimal quality in the manufacturing process. Given that xylans are the most abundant non-cellulosic polysaccharides in nature, xylanases are widely utilized in the mentioned industries. In this regard, several studies have been conducted to develop the relevant chimeric enzymes. Despite the successes that have been attained in this field, misfolding, functional or structural interference, and linker breakage have been reported in some cases. The present paper reviews the research to introduce the prerequisites to design an appropriate chimeric xylanase.
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Improvement of anti-nutritional effect resulting from β-glucanase specific expression in the parotid gland of transgenic pigs. Transgenic Res 2016; 26:1-11. [DOI: 10.1007/s11248-016-9984-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 09/29/2016] [Indexed: 01/12/2023]
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Fusion of agarase and neoagarobiose hydrolase for mono-sugar production from agar. Appl Microbiol Biotechnol 2016; 101:1573-1580. [PMID: 27888333 DOI: 10.1007/s00253-016-8011-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
In enzymatic saccharification of agar, endo- and exo-agarases together with neoagarobiose hydrolase (NABH) are important key enzymes for the sequential hydrolysis reactions. In this study, a bifunctional endo/exo-agarase was fused with NABH for production of mono-sugars (D-galactose and 3,6-anhydro-L-galactose) from agar using only one fusion enzyme. Two fusion enzymes with either bifunctional agarase (Sco3476) or NABH (Zg4663) at the N-terminus, Sco3476-Zg4663 (SZ) and Zg4663-Sco3476 (ZS), were constructed. Both fusion enzymes exhibited their optimal agarase and NABH activities at 40 and 35 °C, respectively. Fusions SZ and ZS enhanced the thermostability of the NABH activity, while only fusion SZ showed a slight enhancement in the NABH catalytic efficiency (K cat/K M) from 14.8 (mg/mL)-1 s-1 to 15.8 (mg/mL)-1 s-1. Saccharification of agar using fusion SZ resulted in 2-fold higher mono-sugar production and 3-fold lower neoagarobiose accumulation when compared to the physical mixture of Sco3476 and Zg4663. Therefore, this fusion has the potential to reduce enzyme production cost, decrease intermediate accumulation, and increase mono-sugar yield in agar saccharification.
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Cheng J, Huang S, Jiang H, Zhang Y, Li L, Wang J, Fan C. Isolation and characterization of a non-specific endoglucanase from a metagenomic library of goat rumen. World J Microbiol Biotechnol 2015; 32:12. [DOI: 10.1007/s11274-015-1957-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
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Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. PLoS One 2014; 9:e99221. [PMID: 24992679 PMCID: PMC4081043 DOI: 10.1371/journal.pone.0099221] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 05/12/2014] [Indexed: 12/20/2022] Open
Abstract
Background A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels. Methodology/Principal Findings Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37). Conclusions/Significance Our comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.
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Abstract
Mammals rely entirely on symbiotic microorganisms within their digestive tract to gain energy from plant biomass that is resistant to mammalian digestive enzymes. Especially in herbivorous animals, specialized organs (the rumen, cecum, and colon) have evolved that allow highly efficient fermentation of ingested plant biomass by complex anaerobic microbial communities. We consider here the two most intensively studied, representative gut microbial communities involved in degradation of plant fiber: those of the rumen and the human large intestine. These communities are dominated by bacteria belonging to the Firmicutes and Bacteroidetes phyla. In Firmicutes, degradative capacity is largely restricted to the cell surface and involves elaborate cellulosome complexes in specialized cellulolytic species. By contrast, in the Bacteroidetes, utilization of soluble polysaccharides, encoded by gene clusters (PULs), entails outer membrane binding proteins, and degradation is largely periplasmic or intracellular. Biomass degradation involves complex interplay between these distinct groups of bacteria as well as (in the rumen) eukaryotic microorganisms.
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Affiliation(s)
- Bryan A White
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801;
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16
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Tu T, Bai Y, Luo H, Ma R, Wang Y, Shi P, Yang P, Meng K, Yao B. A novel bifunctional pectinase from Penicillium oxalicum SX6 with separate pectin methylesterase and polygalacturonase catalytic domains. Appl Microbiol Biotechnol 2014; 98:5019-28. [DOI: 10.1007/s00253-014-5533-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/07/2014] [Accepted: 01/12/2014] [Indexed: 01/28/2023]
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17
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Bhardwaj A, Mahanta P, Ramakumar S, Ghosh A, Leelavathi S, Reddy VS. Emerging role of N- and C-terminal interactions in stabilizing (β/α)8 fold with special emphasis on Family 10 xylanases. Comput Struct Biotechnol J 2012; 2:e201209014. [PMID: 24688655 PMCID: PMC3962208 DOI: 10.5936/csbj.201209014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/24/2012] [Accepted: 10/24/2012] [Indexed: 11/22/2022] Open
Abstract
Xylanases belong to an important class of industrial enzymes. Various xylanases have been purified and characterized from a plethora of organisms including bacteria, marine algae, plants, protozoans, insects, snails and crustaceans. Depending on the source, the enzymatic activity of xylanases varies considerably under various physico-chemical conditions such as temperature, pH, high salt and in the presence of proteases. Family 10 or glycosyl hydrolase 10 (GH10) xylanases are one of the well characterized and thoroughly studied classes of industrial enzymes. The TIM-barrel fold structure which is ubiquitous in nature is one of the characteristics of family 10 xylanases. Family 10 xylanases have been used as a “model system” due to their TIM-barrel fold to dissect and understand protein stability under various conditions. A better understanding of structure-stability-function relationships of family 10 xylanases allows one to apply these governing molecular rules to engineer other TIM-barrel fold proteins to improve their stability and retain function(s) under adverse conditions. In this review, we discuss the implications of N-and C-terminal interactions, observed in family 10 xylanases on protein stability under extreme conditions. The role of metal binding and aromatic clusters in protein stability is also discussed. Studying and understanding family 10 xylanase structure and function, can contribute to our protein engineering knowledge.
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Affiliation(s)
- Amit Bhardwaj
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34149, Trieste, Italy
| | - Pranjal Mahanta
- Department of Physics, Indian Institute of Science, Bangalore, India
| | | | - Amit Ghosh
- National Institute of Cholera and Enteric diseases, Kolkata, India
| | - Sadhu Leelavathi
- Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Vanga Siva Reddy
- Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi - 110067, India
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18
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Moraïs S, Barak Y, Lamed R, Wilson DB, Xu Q, Himmel ME, Bayer EA. Paradigmatic status of an endo- and exoglucanase and its effect on crystalline cellulose degradation. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:78. [PMID: 23095278 PMCID: PMC3502487 DOI: 10.1186/1754-6834-5-78] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/19/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Microorganisms employ a multiplicity of enzymes to efficiently degrade the composite structure of plant cell wall cellulosic polysaccharides. These remarkable enzyme systems include glycoside hydrolases (cellulases, hemicellulases), polysaccharide lyases, and the carbohydrate esterases. To accomplish this challenging task, several strategies are commonly observed either separately or in combination. These include free enzyme systems, multifunctional enzymes, and multi-enzyme self-assembled designer cellulosome complexes. RESULTS In order to compare these different paradigms, we employed a synthetic biology approach to convert two different cellulases from the free enzymatic system of the well-studied bacterium, Thermobifida fusca, into bifunctional enzymes with different modular architectures. We then examined their performance compared to those of the combined parental free-enzyme and equivalent designer-cellulosome systems. The results showed that the cellulolytic activity displayed by the different architectures of the bifunctional enzymes was somewhat inferior to that of the wild-type free enzyme system. CONCLUSIONS The activity exhibited by the designer cellulosome system was equal or superior to that of the free system, presumably reflecting the combined proximity of the enzymes and high flexibility of the designer cellulosome components, thus enabling efficient enzymatic activity of the catalytic modules.
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Affiliation(s)
- Sarah Moraïs
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
- Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100, Israel
| | - Yoav Barak
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - David B Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory (NREL) and BioEnergy Science Center (BESC), Golden, CO, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory (NREL) and BioEnergy Science Center (BESC), Golden, CO, USA
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Specific fusion of β-1,4-endoglucanase and β-1,4-glucosidase enhances cellulolytic activity and helps in channeling of intermediates. Appl Environ Microbiol 2012; 78:7447-54. [PMID: 22904050 DOI: 10.1128/aem.01386-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identification and design of new cellulolytic enzymes with higher catalytic efficiency are a key factor in reducing the production cost of lignocellulosic bioalcohol. We report here identification of a novel β-glucosidase (Gluc1C) from Paenibacillus sp. strain MTCC 5639 and construction of bifunctional chimeric proteins based on Gluc1C and Endo5A, a β-1,4-endoglucanase isolated from MTCC 5639 earlier. The 448-amino-acid-long Gluc1C contained a GH superfamily 1 domain and hydrolyzed cellodextrin up to a five-sugar chain length, with highest efficiency toward cellobiose. Addition of Gluc1C improved the ability of Endo5A to release the reducing sugars from carboxymethyl cellulose. We therefore constructed six bifunctional chimeric proteins based on Endo5A and Gluc1C varying in the positions and sizes of linkers. One of the constructs, EG5, consisting of Endo5A-(G(4)S)(3)-Gluc1C, demonstrated 3.2- and 2-fold higher molar specific activities for β-glucosidase and endoglucanase, respectively, than Gluc1C and Endo5A alone. EG5 also showed 2-fold higher catalytic efficiency than individual recombinant enzymes. The thermal denaturation monitored by circular dichroism (CD) spectroscopy demonstrated that the fusion of Gluc1C with Endo5A resulted in increased thermostability of both domains by 5°C and 9°C, respectively. Comparative hydrolysis experiments done on alkali-treated rice straw and CMC indicated 2-fold higher release of product by EG5 than that by the physical mixture of Endo5A and Gluc1C, providing a rationale for channeling of intermediates. Addition of EG5 to a commercial enzyme preparation significantly enhanced release of reducing sugars from pretreated biomass, indicating its commercial applicability.
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20
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In-fusion expression and characterization of β-xylanase and β-1,3-1,4-glucanase in Pichia pastoris. Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0056-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Abstract
Bacteria that colonize the mammalian intestine collectively possess a far larger repertoire of degradative enzymes and metabolic capabilities than their hosts. Microbial fermentation of complex non-digestible dietary carbohydrates and host-derived glycans in the human intestine has important consequences for health. Certain dominant species, notably among the Bacteroidetes, are known to possess very large numbers of genes that encode carbohydrate active enzymes and can switch readily between different energy sources in the gut depending on availability. Nevertheless, more nutritionally specialized bacteria appear to play critical roles in the community by initiating the degradation of complex substrates such as plant cell walls, starch particles and mucin. Examples are emerging from the Firmicutes, Actinobacteria and Verrucomicrobium phyla, but more information is needed on these little studied groups. The impact of dietary carbohydrates, including prebiotics, on human health requires understanding of the complex relationship between diet composition, the gut microbiota and metabolic outputs.
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Affiliation(s)
- Harry J. Flint
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK,Correspondence to: Harry J. Flint,
| | - Karen P. Scott
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK
| | - Sylvia H. Duncan
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK
| | - Petra Louis
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK
| | - Evelyne Forano
- INRA; UR454 Microbiologie; Saint-Genès Champanelle, France
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22
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Warner CD, Camci-Unal G, Pohl NLB, Ford C, Reilly PJ. Substrate Binding by the Catalytic Domain and Carbohydrate Binding Module ofRuminococcus flavefaciensFD-1 Xyloglucanase/Endoglucanase. Ind Eng Chem Res 2012. [DOI: 10.1021/ie202988a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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Functional analyses of multiple lichenin-degrading enzymes from the rumen bacterium Ruminococcus albus 8. Appl Environ Microbiol 2011; 77:7541-50. [PMID: 21890664 DOI: 10.1128/aem.06088-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ruminococcus albus 8 is a fibrolytic ruminal bacterium capable of utilization of various plant cell wall polysaccharides. A bioinformatic analysis of a partial genome sequence of R. albus revealed several putative enzymes likely to hydrolyze glucans, including lichenin, a mixed-linkage polysaccharide of glucose linked together in β-1,3 and β-1,4 glycosidic bonds. In the present study, we demonstrate the capacity of four glycoside hydrolases (GHs), derived from R. albus, to hydrolyze lichenin. Two of the genes encoded GH family 5 enzymes (Ra0453 and Ra2830), one gene encoded a GH family 16 enzyme (Ra0505), and the last gene encoded a GH family 3 enzyme (Ra1595). Each gene was expressed in Escherichia coli, and the recombinant protein was purified to near homogeneity. Upon screening on a wide range of substrates, Ra0453, Ra2830, and Ra0505 displayed different hydrolytic properties, as they released unique product profiles. The Ra1595 protein, predicted to function as a β-glucosidase, preferred cleavage of a nonreducing end glucose when linked by a β-1,3 glycosidic bond to the next glucose residue. The major product of Ra0505 hydrolysis of lichenin was predicted to be a glucotriose that was degraded only by Ra0453 to glucose and cellobiose. Most importantly, the four enzymes functioned synergistically to hydrolyze lichenin to glucose, cellobiose, and cellotriose. This lichenin-degrading enzyme mix should be of utility as an additive to feeds administered to monogastric animals, especially those high in fiber.
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25
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Synthesis and characterization of chimeric proteins based on cellulase and xylanase from an insect gut bacterium. Appl Environ Microbiol 2011; 77:4859-66. [PMID: 21642416 DOI: 10.1128/aem.02808-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Insects living on wood and plants harbor a large variety of bacterial flora in their guts for degrading biomass. We isolated a Paenibacillus strain, designated ICGEB2008, from the gut of a cotton bollworm on the basis of its ability to secrete a variety of plant-hydrolyzing enzymes. In this study, we cloned, expressed, and characterized two enzymes, β-1,4-endoglucanase (Endo5A) and β-1,4-endoxylanase (Xyl11D), from the ICGEB2008 strain and synthesized recombinant bifunctional enzymes based on Endo5A and Xyl11D. The gene encoding Endo5A was obtained from the genome of the ICGEB2008 strain by shotgun cloning. The gene encoding Xyl11D was obtained using primers for conserved xylanase sequences, which were identified by aligning xylanase sequences in other species of Paenibacillus. Endo5A and Xyl11D were overexpressed in Escherichia coli, and their optimal activities were characterized. Both Endo5A and Xyl11D exhibited maximum specific activity at 50°C and pH 6 to 7. To take advantage of this feature, we constructed four bifunctional chimeric models of Endo5A and Xyl11D by fusing the encoding genes either end to end or through a glycine-serine (GS) linker. We predicted three-dimensional structures of the four models using the I-TASSER server and analyzed their secondary structures using circular dichroism (CD) spectroscopy. The chimeric model Endo5A-GS-Xyl11D, in which a linker separated the two enzymes, yielded the highest C-score on the I-TASSER server, exhibited secondary structure properties closest to the native enzymes, and demonstrated 1.6-fold and 2.3-fold higher enzyme activity than Endo5A and Xyl11D, respectively. This bifunctional enzyme could be effective for hydrolyzing plant biomass owing to its broad substrate range.
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Characterization of a bifunctional xylanase/endoglucanase from yak rumen microorganisms. Appl Microbiol Biotechnol 2011; 90:1933-42. [DOI: 10.1007/s00253-011-3182-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/01/2011] [Accepted: 02/02/2011] [Indexed: 11/25/2022]
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27
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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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Abstract
Industrial production of solvents such as EtOH and BuOH from cellulosic biomass has the potential to provide a sustainable energy source that is relatively cheap, abundant, and environmentally sound, but currently production costs are driven up by expensive enzymes, which are necessary to degrade cellulose into fermentable sugars. These costs could be significantly reduced if a microorganism could be engineered to efficiently and quickly convert cellulosic biomass directly to product in a one-step process. There is a large amount of biodiversity in the number of existing microorganisms that naturally possess the enzymes necessary to convert cellulose to usable sugars, and many of these microorganisms can directly ferment sugars to EtOH or other solvents. Currently, the vast majority of cellulolytic organisms are poorly understood and have complex metabolic networks. In this review, we survey the current state of knowledge on different cellulases and metabolic capabilities found in various cellulolytic microorganisms. We also propose that the use of large-scale metabolic models (and associated analyses) is potentially an ideal means for improving our understanding of basic metabolic network function and directing metabolic engineering efforts for cellulolytic microorganisms.
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Affiliation(s)
- Christopher M Gowen
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284-3028, USA
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29
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Rincon MT, Dassa B, Flint HJ, Travis AJ, Jindou S, Borovok I, Lamed R, Bayer EA, Henrissat B, Coutinho PM, Antonopoulos DA, Berg Miller ME, White BA. Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1. PLoS One 2010; 5:e12476. [PMID: 20814577 PMCID: PMC2930009 DOI: 10.1371/journal.pone.0012476] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 08/03/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The cellulosome is a multi-enzyme machine, which plays a key role in the breakdown of plant cell walls in many anaerobic cellulose-degrading microorganisms. Ruminococcus flavefaciens FD-1, a major fiber-degrading bacterium present in the gut of herbivores, has the most intricate cellulosomal organization thus far described. Cellulosome complexes are assembled through high-affinity cohesin-dockerin interactions. More than two-hundred dockerin-containing proteins have been identified in the R. flavefaciens genome, yet the reason for the expansion of these crucial cellulosomal components is yet unknown. METHODOLOGY/PRINCIPAL FINDINGS We have explored the full spectrum of 222 dockerin-containing proteins potentially involved in the assembly of cellulosome-like complexes of R. flavefaciens. Bioinformatic analysis of the various dockerin modules showed distinctive conservation patterns within their two Ca(2+)-binding repeats and their flanking regions. Thus, we established the conceptual framework for six major groups of dockerin types, according to their unique sequence features. Within this framework, the modular architecture of the parent proteins, some of which are multi-functional proteins, was evaluated together with their gene expression levels. Specific dockerin types were found to be associated with selected groups of functional components, such as carbohydrate-binding modules, numerous peptidases, and/or carbohydrate-active enzymes. In addition, members of other dockerin groups were linked to structural proteins, e.g., cohesin-containing proteins, belonging to the scaffoldins. CONCLUSIONS/SIGNIFICANCE This report profiles the abundance and sequence diversity of the R. flavefaciens FD-1 dockerins, and provides the molecular basis for future understanding of the potential for a wide array of cohesin-dockerin specificities. Conserved differences between dockerins may be reflected in their stability, function or expression within the context of the parent protein, in response to their role in the rumen environment.
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Affiliation(s)
- Marco T. Rincon
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Harry J. Flint
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Anthony J. Travis
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Sadanari Jindou
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bernard Henrissat
- Architecture et Fonction des Macromolecules Biologiques, CNRS and Universites d'Aix-Marseille I & II, Marseille, France
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolecules Biologiques, CNRS and Universites d'Aix-Marseille I & II, Marseille, France
| | - Dion A. Antonopoulos
- Division of Nutritional Sciences, Department of Animal Sciences, North American Consortium for Genomics of Fibrolytic Ruminal Bacteria, University of Illinois, Urbana, Illinois, United States of America
| | - Margret E. Berg Miller
- Division of Nutritional Sciences, Department of Animal Sciences, North American Consortium for Genomics of Fibrolytic Ruminal Bacteria, University of Illinois, Urbana, Illinois, United States of America
| | - Bryan A. White
- Division of Nutritional Sciences, Department of Animal Sciences, North American Consortium for Genomics of Fibrolytic Ruminal Bacteria, University of Illinois, Urbana, Illinois, United States of America
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Paenibacillus sp. strain E18 bifunctional xylanase-glucanase with a single catalytic domain. Appl Environ Microbiol 2010; 76:3620-4. [PMID: 20382811 DOI: 10.1128/aem.00345-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylanases are utilized in a variety of industries for the breakdown of plant materials. Most native and engineered bifunctional/multifunctional xylanases have separate catalytic domains within the same polypeptide chain. Here we report a new bifunctional xylanase (XynBE18) produced by Paenibacillus sp. E18 with xylanase and beta-1,3-1,4-glucanase activities derived from the same active center by substrate competition assays and site-directed mutagenesis of xylanase catalytic Glu residues (E129A and E236A). The gene consists of 981 bp, encodes 327 amino acids, and comprises only one catalytic domain that is highly homologous to the glycoside hydrolase family 10 xylanase catalytic domain. Recombinant XynBE18 purified from Escherichia coli BL21(DE3) showed specificity toward oat spelt xylan and birchwood xylan and beta-1,3-1,4-glucan (barley beta-glucan and lichenin). Homology modeling and molecular dynamic simulation were used to explore structure differences between XynBE18 and the monofunctional xylanase XynE2, which has enzymatic properties similar to those of XynBE18 but does not hydrolyze beta-1,3-1,4-glucan. The cleft containing the active site of XynBE18 is larger than that of XynE2, suggesting that XynBE18 is able to bind larger substrates such as barley beta-glucan and lichenin. Further molecular docking studies revealed that XynBE18 can accommodate xylan and beta-1,3-1,4-glucan, but XynE2 is only accessible to xylan. These results indicate a previously unidentified structure-function relationship for substrate specificities among family 10 xylanases.
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Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 2009; 4:e6650. [PMID: 19680555 PMCID: PMC2721979 DOI: 10.1371/journal.pone.0006650] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 07/07/2009] [Indexed: 11/19/2022] Open
Abstract
Background Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels. Methodology/Principal Findings The R. flavefaciens FD-1 genome was sequenced to 29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into 119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs), polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated, 135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three multi-modular xylanases (ORF01222, ORF03896, and ORF01315) exhibited the highest levels of up-regulation. Conclusions/Significance The genomic evidence indicates that R. flavefaciens FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a cellulosome architecture. Functional analysis of the genome has revealed that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components.
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Affiliation(s)
- Margret E. Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Dionysios A. Antonopoulos
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Marco T. Rincon
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Mark Band
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Albert Bari
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Tatsiana Akraiko
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Alvaro Hernandez
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jyothi Thimmapuram
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités Aix-Marseille I & II, Marseille, France
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités Aix-Marseille I & II, Marseille, France
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Sadanari Jindou
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Harry J. Flint
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bryan A. White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Lin YS, Tsai LC, Lee SH, Yuan HS, Shyur LF. Structural and catalytic roles of residues located in β13 strand and the following β-turn loop in Fibrobacter succinogenes 1,3-1,4-β-d-glucanase. Biochim Biophys Acta Gen Subj 2009; 1790:231-9. [DOI: 10.1016/j.bbagen.2009.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Cellulosomes are intricate multienzyme systems produced by several cellulolytic bacteria, the first example of which was discovered in the anaerobic thermophilic bacterium, Clostridium thermocellum. Cellulosomes are designed for efficient degradation of plant cell wall polysaccharides, notably cellulose--the most abundant renewable polymer on earth. The component parts of the multicomponent complex are integrated by virtue of a unique family of integrating modules, the cohesins and the dockerins, whose distribution and specificity dictate the overall cellulosome architecture. A full generation of research has elapsed since the original publications that documented the cellulosome concept. In this review, we provide a personal account on the discovery process, while describing how divergent cellulosome systems were identified and investigated, culminating in the collaboration of several labs worldwide to tackle together the challenging field of cellulosome genomics and metagenomics.
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Affiliation(s)
- Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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34
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Engineering of a multifunctional hemicellulase. Biotechnol Lett 2009; 31:751-7. [DOI: 10.1007/s10529-009-9926-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 12/23/2008] [Accepted: 01/05/2009] [Indexed: 11/25/2022]
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35
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Yang S, Wang Y, Jiang Z, Hua C. Crystallization and preliminary X-ray analysis of a 1,3-1,4-beta-glucanase from Paecilomyces thermophila. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:754-6. [PMID: 18678950 DOI: 10.1107/s1744309108021064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2008] [Accepted: 07/08/2008] [Indexed: 11/10/2022]
Abstract
In this study, the crystallization and preliminary X-ray analysis of a thermostable 1,3-1,4-beta-glucanase produced by Paecilomyces thermophila is described. The purified 1,3-1,4-beta-glucanase was crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the hexagonal space group P6(3)22, with unit-cell parameters a = b = 154.54, c = 87.62 A. X-ray diffraction data were collected to a resolution of 2.54 A and gave a data set with an overall R(merge) of 7.3% and a completeness of 94.6%. The Matthews coefficient (V(M)) and the solvent content are 2.38 A(3) Da(-1) and 48%, respectively.
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Affiliation(s)
- Shaoqing Yang
- Department of Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
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36
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Lu P, Feng MG. Bifunctional enhancement of a β-glucanase-xylanase fusion enzyme by optimization of peptide linkers. Appl Microbiol Biotechnol 2008; 79:579-87. [PMID: 18415095 DOI: 10.1007/s00253-008-1468-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 03/20/2008] [Accepted: 03/23/2008] [Indexed: 11/29/2022]
Affiliation(s)
- Ping Lu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China
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37
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Pérez-Avalos O, Sánchez-Herrera LM, Salgado LM, Ponce-Noyola T. A bifunctional endoglucanase/endoxylanase from Cellulomonas flavigena with potential use in industrial processes at different pH. Curr Microbiol 2008; 57:39-44. [PMID: 18379842 DOI: 10.1007/s00284-008-9149-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Accepted: 06/07/2007] [Indexed: 11/30/2022]
Abstract
Cellulomonas flavigena CDBB-531 was found to secrete a bifunctional cellulase/xylanase with a molecular mass of 49 kDa and pI 4.3. This enzyme was active on Remazol brilliant blue-carboxymethylcellulose (RBB-CMC) and Remazol brilliant blue-xylan (RBB-X). Based on thin-layer chromatographic analysis of the degradation products, the cellulase activity produced glucose, cellobiose, cellotriose, and cellotetraose from CMC as the substrate. When xylan from birchwood was used, end products were xylose, arabinose, and xylobiose. The bifunctional enzyme showed a pH optimum of 6 for cellulase activity and 9 for xylanase activity, which pointed out that this enzyme had separate sites for each activity. In both cases, the apparent optimum temperature was 50 degrees C. The predicted amino acid sequence of purified protein showed similarity with the catalytic domain of several glycosyl hydrolases of family 10.
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Affiliation(s)
- Odilia Pérez-Avalos
- Departamento de Biotecnologia y Bioingenieria, CINVESTAV, Zacatenco, DF, Mexico
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38
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Bifunctional xylanases and their potential use in biotechnology. J Ind Microbiol Biotechnol 2008; 35:635-44. [DOI: 10.1007/s10295-008-0342-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 03/06/2008] [Accepted: 03/06/2008] [Indexed: 10/22/2022]
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39
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Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 2008; 6:121-31. [PMID: 18180751 DOI: 10.1038/nrmicro1817] [Citation(s) in RCA: 1081] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The microbiota of the mammalian intestine depend largely on dietary polysaccharides as energy sources. Most of these polymers are not degradable by the host, but herbivores can derive 70% of their energy intake from microbial breakdown--a classic example of mutualism. Moreover, dietary polysaccharides that reach the human large intestine have a major impact on gut microbial ecology and health. Insight into the molecular mechanisms by which different gut bacteria use polysaccharides is, therefore, of fundamental importance. Genomic analyses of the gut microbiota could revolutionize our understanding of these mechanisms and provide new biotechnological tools for the conversion of polysaccharides, including lignocellulosic biomass, into monosaccharides.
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40
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Anish R, Rao M. Biochemical characterization of a novel β-1–3, 1–4 glucan 4-glucanohydrolase from Thermomonospora sp. having a single active site for lichenan and xylan. Biochimie 2007; 89:1489-97. [PMID: 17689169 DOI: 10.1016/j.biochi.2007.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 06/19/2007] [Indexed: 11/30/2022]
Abstract
A bifunctional high molecular weight (Mr, 64,500 Da) beta-1-3, 1-4 glucan 4-glucanohydrolase was purified to homogeneity from Thermomonospora sp., exhibiting activity towards lichenan and xylan. A kinetic method was used to analyze the active site that hydrolyzes lichenan and xylan. The experimental data was in agreement with the theoretical values calculated for a single active site. Probing the conformation and microenvironment at active site of the enzyme by fluorescent chemo-affinity label, OPTA resulted in the formation of an isoindole derivative with complete inactivation of the enzyme to hydrolyse both lichenan and xylan confirmed the results of kinetic method. OPTA forms an isoindole derivative by cross-linking the proximal thiol and amino groups. The modification of cysteine and lysine residues by DTNB and TNBS respectively abolished the ability of the enzyme to form an isoindole derivative with OPTA, indicating the participation of cysteine and lysine in the formation of isoindole complex.
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Affiliation(s)
- Ramakrishnan Anish
- Biochemical Sciences Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
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41
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Ozkose E, Akyol I, Ekinci MS. Molecular study on cloned endoglucanase gene from rumen bacterium. J Mol Microbiol Biotechnol 2005; 8:111-6. [PMID: 15925902 DOI: 10.1159/000084566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An endoglucanase gene was subcloned from anaerobic rumen bacterium Ruminococcus flavefaciens strain 17. To express endoglucanase gene in Escherichia coli and Streptococcus bovis JB1, an endoglucanase gene fragment was inserted into pVA838-based shuttle vectors. Removal of endoglucanase gene promoter and expression of endoglucanase by promoter of S. bovis JB1 alpha-amylase gene (pACMCS) was also achieved. Survival of constructs pVACMCI, pTACMC and pACMCS, which carry endoglucanase gene, and stability of endoglucanase gene in S. bovis JB1, were observed. Maximal endoglucanase activities from S. bovis JB1/pVACMCI were 2- to 3-fold higher than from E. coli/pVACMCI. Specific cell activity of E. coli/pACMCS was found to be approximately 2- to -3 fold higher than the both E. coli/pVACMCI and E. coli/pTACMC. Specific cell activity of S. bovis JB1/pACMCS was also found to be approximately 2-fold higher than the both S. bovis/pVACMCI and S. bovis JB1/pTACMC.
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Affiliation(s)
- Emin Ozkose
- Department of Animal Science, Faculty of Agriculture, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
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42
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Han SO, Yukawa H, Inui M, Doi RH. Isolation and expression of the xynB gene and its product, XynB, a consistent component of the Clostridium cellulovorans cellulosome. J Bacteriol 2005; 186:8347-55. [PMID: 15576784 PMCID: PMC532426 DOI: 10.1128/jb.186.24.8347-8355.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of the Clostridium cellulovorans xynB gene, which encodes the XynB xylanase, consists of 1,821 bp and encodes a protein of 607 amino acids with a molecular weight of 65,976. XynB contains a typical N-terminal signal peptide of 29 amino acid residues, followed by a 147-amino-acid sequence that is homologous to the family 4-9 (subfamily 9 in family 4) carbohydrate-binding domain. Downstream of this domain is a family 10 catalytic domain of glycosyl hydrolase. The C terminus separated from the catalytic domain by a short linker sequence contains a dockerin domain responsible for cellulosome assembly. The XynB sequence from mass spectrometry and N-terminal amino acid sequence analyses agreed with that deduced from the nucleotide sequence. XynB was highly active toward xylan, but not active toward carboxymethyl cellulose. The enzyme was optimally active at 40 degrees C and pH 5.0. Northern hybridizations revealed that xynB is transcribed as a monocistronic 1.9-kb mRNA. RNA ligase-mediated rapid amplification of 5' cDNA ends by PCR (RLM-5'RACE PCR) analysis of C. cellulovorans RNA identified a single transcriptional start site of xynB located 47 bp upstream from the first nucleotide of the translation initiation codon. Alignment of the xynB promoter region provided evidence for highly conserved sequences that exhibited strong similarity to the sigmaA consensus promoter sequences of gram-positive bacteria. Expression of xynB mRNA increased from early to middle exponential phase and decreased during the early stationary phase when the cells were grown on cellobiose. No alternative promoter was observed by RLM-5'RACE PCR and reverse transcriptase PCR analyses during expression. The analysis of the products from xylan hydrolysis by thin-layer chromatography indicated its endoxylanase activity. The results suggest that XynB is a consistent and major cellulosomal enzyme during growth on cellulose or xylan.
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Affiliation(s)
- Sung Ok Han
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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43
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Collins T, Gerday C, Feller G. Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev 2005; 29:3-23. [PMID: 15652973 DOI: 10.1016/j.femsre.2004.06.005] [Citation(s) in RCA: 1036] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2003] [Revised: 06/10/2004] [Accepted: 06/14/2004] [Indexed: 11/28/2022] Open
Abstract
Xylanases are hydrolytic enzymes which randomly cleave the beta 1,4 backbone of the complex plant cell wall polysaccharide xylan. Diverse forms of these enzymes exist, displaying varying folds, mechanisms of action, substrate specificities, hydrolytic activities (yields, rates and products) and physicochemical characteristics. Research has mainly focused on only two of the xylanase containing glycoside hydrolase families, namely families 10 and 11, yet enzymes with xylanase activity belonging to families 5, 7, 8 and 43 have also been identified and studied, albeit to a lesser extent. Driven by industrial demands for enzymes that can operate under process conditions, a number of extremophilic xylanases have been isolated, in particular those from thermophiles, alkaliphiles and acidiphiles, while little attention has been paid to cold-adapted xylanases. Here, the diverse physicochemical and functional characteristics, as well as the folds and mechanisms of action of all six xylanase containing families will be discussed. The adaptation strategies of the extremophilic xylanases isolated to date and the potential industrial applications of these enzymes will also be presented.
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Affiliation(s)
- Tony Collins
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium.
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44
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Howard MB, Ekborg NA, Taylor LE, Weiner RM, Hutcheson SW. Chitinase B of "Microbulbifer degradans" 2-40 contains two catalytic domains with different chitinolytic activities. J Bacteriol 2004; 186:1297-303. [PMID: 14973034 PMCID: PMC344425 DOI: 10.1128/jb.186.5.1297-1303.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chitinase B of "Microbulbifer degradans" 2-40 is a modular protein that is predicted to contain two glycoside hydrolase family 18 (GH18) catalytic domains, two polyserine domains, and an acidic repeat domain. Each of the GH18 domains was shown to be catalytically active against chitin. Activity assays reveal that the amino-terminal catalytic domain (GH18(N)) releases methylumbelliferone from 4'-methylumbelliferyl-N,N'-diacetylchitobiose 13.6-fold faster than the carboxy-terminal catalytic domain (GH18(C)) and releases chitobiose from the nonreducing end of chitooligosaccharides, therefore functioning as an exochitinase. GH18(C) releases methylumbelliferone from 4'-methylumbelliferyl-N,N',N"-triacetylchitotriose 2.7-fold faster than GH18(N) and cleaves chitooligosaccharides at multiple bonds, consistent with endochitinolytic activity. Each domain was maximally active from 30 to 37 degrees C and from pH 7.2 to 8.0 and was not affected by Mg(2+), Mn(2+), Ca(2+), K(+), EDTA, EGTA, or 1.0 M NaCl. The activity of each domain was moderately inhibited by Ni(2+), Sr(2+), and Cu(2+), while Hg(2+) completely abolished activity. When the specific activities of various recombinant portions of ChiB were calculated by using native chitin as a substrate, the polypeptide containing the endo-acting domain was twofold more active on native chitin than the other containing the exo-acting domain. The presence of both domains in a single reaction increased the amount of reducing sugars released from native chitin to 140% above the theoretical combined rate, indicating that the domains function cooperatively to degrade chitin. These data demonstrate that the GH18 domains of ChiB have different activities on the same substrate and function cooperatively to enhance chitin depolymerization.
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Affiliation(s)
- Michael B Howard
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
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45
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Flint HJ. Polysaccharide Breakdown by Anaerobic Microorganisms Inhabiting the Mammalian Gut. ADVANCES IN APPLIED MICROBIOLOGY 2004; 56:89-120. [PMID: 15566977 DOI: 10.1016/s0065-2164(04)56003-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Harry J Flint
- Microbial Genetics Group Rowett Research Institute Bucksburn, Aberdeen, AB21 9SB, United Kingdom.
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46
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Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS. Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev 2003; 27:663-93. [PMID: 14638418 DOI: 10.1016/s0168-6445(03)00072-x] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as developing world. Rumen fermentation is unique in that efficient plant cell wall degradation relies on the cooperation between microorganisms that produce fibrolytic enzymes and the host animal that provides an anaerobic fermentation chamber. Increasing the efficiency with which the rumen microbiota degrades fiber has been the subject of extensive research for at least the last 100 years. Fiber digestion in the rumen is not optimal, as is supported by the fact that fiber recovered from feces is fermentable. This view is confirmed by the knowledge that mechanical and chemical pretreatments improve fiber degradation, as well as more recent research, which has demonstrated increased fiber digestion by rumen microorganisms when plant lignin composition is modified by genetic manipulation. Rumen microbiologists have sought to improve fiber digestion by genetic and ecological manipulation of rumen fermentation. This has been difficult and a number of constraints have limited progress, including: (a) a lack of reliable transformation systems for major fibrolytic rumen bacteria, (b) a poor understanding of ecological factors that govern persistence of fibrolytic bacteria and fungi in the rumen, (c) a poor understanding of which glycolyl hydrolases need to be manipulated, and (d) a lack of knowledge of the functional genomic framework within which fiber degradation operates. In this review the major fibrolytic organisms are briefly discussed. A more extensive discussion of the enzymes involved in fiber degradation is included. We also discuss the use of plant genetic manipulation, application of free-living lignolytic fungi and the use of exogenous enzymes. Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen.
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Affiliation(s)
- Denis O Krause
- CSIRO Australia, Queensland Bioscience Precinct, St. Lucia, Qld 4067, Australia.
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47
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Tsai LC, Shyur LF, Lee SH, Lin SS, Yuan HS. Crystal structure of a natural circularly permuted jellyroll protein: 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes. J Mol Biol 2003; 330:607-20. [PMID: 12842475 DOI: 10.1016/s0022-2836(03)00630-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes (Fsbeta-glucanase) is classified as one of the family 16 glycosyl hydrolases. It hydrolyzes the glycosidic bond in the mixed-linked glucans containing beta-1,3- and beta-1,4-glycosidic linkages. We constructed a truncated form of recombinant Fsbeta-glucanase containing the catalytic domain from amino acid residues 1-258, which exhibited a higher thermal stability and enzymatic activity than the full-length enzyme. The crystal structure of the truncated Fsbeta-glucanase was solved at a resolution of 1.7A by the multiple wavelength anomalous dispersion (MAD) method using the anomalous signals from the seleno-methionine-labeled protein. The overall topology of the truncated Fsbeta-glucanase consists mainly of two eight-stranded anti-parallel beta-sheets arranged in a jellyroll beta-sandwich, similar to the fold of many glycosyl hydrolases and carbohydrate-binding modules. Sequence comparison with other bacterial glucanases showed that Fsbeta-glucanase is the only naturally occurring circularly permuted beta-glucanase with reversed sequences. Structural comparison shows that the engineered circular-permuted Bacillus enzymes are more similar to their parent enzymes with which they share approximately 70% sequence identity, than to the naturally occurring Fsbeta-glucanase of similar topology with 30% identity. This result suggests that protein structure relies more on sequence identity than topology. The high-resolution structure of Fsbeta-glucanase provides a structural rationale for the different activities obtained from a series of mutant glucanases and a basis for the development of engineered enzymes with increased activity and structural stability.
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Affiliation(s)
- Li-Chu Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
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48
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Rincon MT, Ding SY, McCrae SI, Martin JC, Aurilia V, Lamed R, Shoham Y, Bayer EA, Flint HJ. Novel organization and divergent dockerin specificities in the cellulosome system of Ruminococcus flavefaciens. J Bacteriol 2003; 185:703-13. [PMID: 12533446 PMCID: PMC142803 DOI: 10.1128/jb.185.3.703-713.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Accepted: 09/30/2002] [Indexed: 11/20/2022] Open
Abstract
The DNA sequence coding for putative cellulosomal scaffolding protein ScaA from the rumen cellulolytic anaerobe Ruminococcus flavefaciens 17 was completed. The mature protein exhibits a calculated molecular mass of 90,198 Da and comprises three cohesin domains, a C-terminal dockerin, and a unique N-terminal X domain of unknown function. A novel feature of ScaA is the absence of an identifiable cellulose-binding module. Nevertheless, native ScaA was detected among proteins that attach to cellulose and appeared as a glycosylated band migrating at around 130 kDa. The ScaA dockerin was previously shown to interact with the cohesin-containing putative surface-anchoring protein ScaB. Here, six of the seven cohesins from ScaB were overexpressed as histidine-tagged products in E. coli; despite their considerable sequence differences, each ScaB cohesin specifically recognized the native 130-kDa ScaA protein. The binding specificities of dockerins found in R. flavefaciens plant cell wall-degrading enzymes were examined next. The dockerin sequences of the enzymes EndA, EndB, XynB, and XynD are all closely related but differ from those of XynE and CesA. A recombinant ScaA cohesin bound selectively to dockerin-containing fragments of EndB, but not to those of XynE or CesA. Furthermore, dockerin-containing EndB and XynB, but not XynE or CesA, constructs bound specifically to native ScaA. XynE- and CesA-derived probes did however bind a number of alternative R. flavefaciens bands, including an approximately 110-kDa supernatant protein expressed selectively in cultures grown on xylan. Our findings indicate that in addition to the ScaA dockerin-ScaB cohesin interaction, at least two distinct dockerin-binding specificities are involved in the novel organization of plant cell wall-degrading enzymes in this species and suggest that different scaffoldins and perhaps multiple enzyme complexes may exist in R. flavefaciens.
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Affiliation(s)
- Marco T Rincon
- Gut Microbiology Group, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, United Kingdom
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Hernández A, Copa-Patiño JL, Soliveri J. xln23 from Streptomyces chattanoogensis UAH23 encodes a putative enzyme with separate xylanase and arabinofuranosidase catalytic domains. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 2002; 12:167-77. [PMID: 11762192 DOI: 10.3109/10425170109080771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The xylanase gene xysA of Streptomyces halstedii JM8 was used to isolate a DNA fragment from a gene library of Pstl-digested chromosomal DNA of the lignocellulolytic actinomycete Streptomyces chattanoogensis CECT-3336. Nucleotide sequence analysis revealed a gene (xln23) encoding a bifunctional multimodular enzyme bearing two independent xylanase and alpha-L-arabinofuranosidase domains separated by a Ser/Gly-rich linker. The N terminus of the predicted protein showed high homology to family F xylanases. The C terminus was homologous to amino acid sequences found in enzymes included in the glycosyl hydrolase family 62 and, in particular, to those of alpha-L-arabinofuranosidase AbsB from Streptomyces lividans. PCR and RT-PCR experiments showed that the nucleotide sequences corresponding to each domain are arranged as expected on the chromosomal DNA and that they are cotranscribed. To our knowledge, this is the first description of xylanase and arabinofuranosidase domains in a same open reading frame.
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Affiliation(s)
- A Hernández
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Alcalá, 28871-Alcalá de Henares, Spain
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Sapag A, Wouters J, Lambert C, de Ioannes P, Eyzaguirre J, Depiereux E. The endoxylanases from family 11: computer analysis of protein sequences reveals important structural and phylogenetic relationships. J Biotechnol 2002; 95:109-31. [PMID: 11911922 DOI: 10.1016/s0168-1656(02)00002-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eighty-two amino acid sequences of the catalytic domains of mature endoxylanases belonging to family 11 have been aligned using the programs MATCHBOX and CLUSTAL. The sequences range in length from 175 to 233 residues. The two glutamates acting as catalytic residues are conserved in all sequences. A very good correlation is found between the presence (at position 100) of an asparagine in the so-called 'alkaline' xylanases, or an aspartic acid in those with a more acidic pH optimum. Four boxes defining segments of highest similarity were detected; they correspond to regions of defined secondary structure: B5, B6, B8 and the carboxyl end of the alpha helix, respectively. Cysteine residues are not common in these sequences (0.7% of all residues), and disulfide bridges are not important in explaining the stability of several thermophilic xylanases. The alignment allows the classification of the enzymes in groups according to sequence similarity. Fungal and bacterial enzymes were found to form mostly separate clusters of higher similarity.
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Affiliation(s)
- Amalia Sapag
- Laboratorio de Bioquímica, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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