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Lyu Y, Luo H, Chai S, Zhang Y, Fan X, Wang S, Feng Z. Discovery and characterization of a novel PKD-Fn3 domains containing GH44 endoglucanase from a Tibetan metagenomic library. J Appl Microbiol 2023; 134:lxad187. [PMID: 37596069 DOI: 10.1093/jambio/lxad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023]
Abstract
AIMS To explore novel microbial endoglucanases with unique properties derived from extreme environments by using metagenomics approach. METHODS AND RESULTS A Tibetan soil metagenomic library was applied for screening cellulase-active clones by function-based metagenomics. The candidate genes in the active clones were identified through bioinformatic analyses and heterologously expressed using an Escherichia coli system. The recombinant endoglucanases were purified and characterized using enzyme assays to determine their bioactivities, stabilities, substrate specificities, and other enzymatic properties. A novel endoglucanase gene Zfeg1907 was identified, which consisted of a glycoside hydrolase family 44 (GH44) catalytic domain along with a polycystic kidney disease (PKD) domain and a fibronectin type Ⅲ (Fn3) domain at the C terminal. Recombinant enzyme ZFEG1907 and its truncated mutant ZFEG1907t (ΔPKDΔFn3) were successfully expressed and purified. The two recombinants exhibited catalytic activities toward carboxymethyl cellulose, konjac glucomannan (KGM), and lichenan. Both enzymes had an optimal temperature of 50°C and an optimal pH value of 5.0. The catalytic activities of both recombinant enzymes were promoted by adding Zn2+ and Ca2+ at the final concentration of 10 mM. The Km value of ZFEG1907 was lower, while the kcat/Km value of ZFEG1907 was higher than those of of ZFEG1907t when using carboxymethyl cellulose, KGM, and lichenan as substrates. Structure prediction of two recombinants revealed that PKD-Fn3 domains consisted of a flexible linker and formed a β-sandwich structure. CONCLUSIONS A novel endoglucanase ZFEG1907 contained a GH44 catalytic domain and a PKD-Fn3 domain was characterized. The PKD-Fn3 domains were not indispensable for the activity but contributed to the enzyme binding of the polysaccharide substrates as a carbohydrate-binding module (CBM).
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Affiliation(s)
- Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Hao Luo
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Shumao Chai
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Ying Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Xinyu Fan
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
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2
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Dionisi HM, Lozada M, Campos E. Diversity of GH51 α-L-arabinofuranosidase homolog sequences from subantarctic intertidal sediments. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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3
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Hengge NN, Mallinson SJB, Pason P, Lunin VV, Alahuhta M, Chung D, Himmel ME, Westpheling J, Bomble YJ. Characterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticus. Int J Mol Sci 2022; 23:ijms23116070. [PMID: 35682749 PMCID: PMC9181691 DOI: 10.3390/ijms23116070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial conversion of biomass relies on a complex combination of enzyme systems promoting synergy to overcome biomass recalcitrance. Some thermophilic bacteria have been shown to exhibit particularly high levels of cellulolytic activity, making them of particular interest for biomass conversion. These bacteria use varying combinations of CAZymes that vary in complexity from a single catalytic domain to large multi-modular and multi-functional architectures to deconstruct biomass. Since the discovery of CelA from Caldicellulosiruptor bescii which was identified as one of the most active cellulase so far identified, the search for efficient multi-modular and multi-functional CAZymes has intensified. One of these candidates, GuxA (previously Acel_0615), was recently shown to exhibit synergy with other CAZymes in C. bescii, leading to a dramatic increase in growth on biomass when expressed in this host. GuxA is a multi-modular and multi-functional enzyme from Acidothermus cellulolyticus whose catalytic domains include a xylanase/endoglucanase GH12 and an exoglucanase GH6, representing a unique combination of these two glycoside hydrolase families in a single CAZyme. These attributes make GuxA of particular interest as a potential candidate for thermophilic industrial enzyme preparations. Here, we present a more complete characterization of GuxA to understand the mechanism of its activity and substrate specificity. In addition, we demonstrate that GuxA exhibits high levels of synergism with E1, a companion endoglucanase from A. cellulolyticus. We also present a crystal structure of one of the GuxA domains and dissect the structural features that might contribute to its thermotolerance.
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Affiliation(s)
- Neal N. Hengge
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Sam J. B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand;
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, GA 30602, USA;
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
- Correspondence:
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4
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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Rakitin AL, Naumoff DG, Beletsky AV, Kulichevskaya IS, Mardanov AV, Ravin NV, Dedysh SN. Complete genome sequence of the cellulolytic planctomycete Telmatocola sphagniphila SP2 T and characterization of the first cellulolytic enzyme from planctomycetes. Syst Appl Microbiol 2021; 44:126276. [PMID: 34735803 DOI: 10.1016/j.syapm.2021.126276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/05/2021] [Accepted: 09/12/2021] [Indexed: 11/26/2022]
Abstract
Planctomycetes of the family Gemmataceae are strictly aerobic chemo-organotrophs that display a number of hydrolytic capabilities. A member of this family, Telmatocola sphagniphila SP2T, is the first described planctomycete with experimentally proven ability for growth on cellulose. In this study, the complete genome sequence of strain SP2T was obtained and the genome-encoded determinants of its cellulolytic potential were analyzed. The T. sphagniphila SP2T genome was 6.59 Mb in size and contained over 5200 potential protein-coding genes. The search for enzymes that could be potentially involved in cellulose degradation identified a putative cellulase that contained a domain from the GH44 family of glycoside hydrolases. Homologous enzymes were also revealed in the genomes of two other Gemmataceae planctomycetes, Zavarzinella formosa A10T and Tuwongella immobilis MBLW1T. The gene encoding this predicted cellulase in strain SP2T was expressed in E. coli and the hydrolytic activity of the recombinant enzyme was confirmed in tests with carboxymethyl cellulose but not with crystalline cellulose, xylan, mannan or laminarin. This is the first experimentally characterized cellulolytic enzyme from planctomycetes.
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Affiliation(s)
- Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daniil G Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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Ibrahim E, Mahmoud A, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Kinetics and thermodynamics of thermal inactivation for recombinant Escherichia coli cellulases, cel12B, cel8C, and polygalacturonase, peh28; biocatalysts for biofuel precursor production. J Biochem 2021; 169:109-117. [PMID: 32810224 DOI: 10.1093/jb/mvaa097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/11/2020] [Indexed: 11/13/2022] Open
Abstract
Lignocellulosic biomass conversion using cellulases/polygalacturonases is a process that can be progressively influenced by several determinants involved in cellulose microfibril degradation. This article focuses on the kinetics and thermodynamics of thermal inactivation of recombinant Escherichia coli cellulases, cel12B, cel8C and a polygalacturonase, peh 28, derived from Pectobacterium carotovorum sub sp. carotovorum. Several consensus motifs conferring the enzymes' thermal stability in both cel12B and peh28 model structures have been detailed earlier, which were confirmed for the three enzymes through the current study of their thermal inactivation profiles over the 20-80°C range using the respective activities on carboxymethylcellulose and polygalacturonic acid. Kinetic constants and half-lives of thermal inactivation, inactivation energy, plus inactivation entropies, enthalpies and Gibbs free energies, revealed high stability, less conformational change and protein unfolding for cel12B and peh28 due to thermal denaturation compared to cel8C. The apparent thermal stability of peh28 and cel12B, along with their hydrolytic efficiency on a lignocellulosic biomass conversion as reported previously, makes these enzymes candidates for various industrial applications. Analysis of the Gibbs free energy values suggests that the thermal stabilities of cel12B and peh28 are entropy-controlled over the tested temperature range.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA.,Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Ahmed Mahmoud
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Kim D Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Keith E Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ebtesam N Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Patrick L Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Jean M Escudero
- Department of Basic Sciences, St. Louis College of Pharmacy, St. Louis, MO 63110-1088, USA
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Chai S, Zhang X, Jia Z, Xu X, Zhang Y, Wang S, Feng Z. Identification and characterization of a novel bifunctional cellulase/hemicellulase from a soil metagenomic library. Appl Microbiol Biotechnol 2020; 104:7563-7572. [DOI: 10.1007/s00253-020-10766-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 06/06/2020] [Accepted: 07/01/2020] [Indexed: 01/06/2023]
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Escuder-Rodríguez JJ, DeCastro ME, Cerdán ME, Rodríguez-Belmonte E, Becerra M, González-Siso MI. Cellulases from Thermophiles Found by Metagenomics. Microorganisms 2018; 6:microorganisms6030066. [PMID: 29996513 PMCID: PMC6165527 DOI: 10.3390/microorganisms6030066] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/05/2023] Open
Abstract
Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
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9
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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10
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Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:52. [PMID: 28413443 PMCID: PMC5327597 DOI: 10.1186/s13068-017-0732-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The high crystallinity of cellulosic biomass myofibrils as well as the complexity of their intermolecular structure is a significant impediment for biofuel production. Cloning of celB-, celC-encoded cellulases (cel12B and cel8C) and peh-encoded polygalacturonase (peh28) from Pectobacterium carotovorum subsp. carotovorum (Pcc) was carried out in our previous study using Escherichia coli as a host vector. The current study partially characterizes the enzymes' molecular structures as well as their catalytic performance on different substrates which can be used to improve their potential for lignocellulosic biomass conversion. RESULTS β-Jelly roll topology, (α/α)6 antiparallel helices and right-handed β-helices were the folds identified for cel12B, cel8C, and peh28, respectively, in their corresponding protein model structures. Purifications of 17.4-, 6.2-, and 6.0-fold, compared to crude extract, were achieved for cel12B and cel8C, and peh28, respectively, using specific membrane ultrafiltrations and size-exclusion chromatography. Avicel and carboxymethyl cellulose (CMC) were substrates for cel12B, whereas for cel8C catalytic activity was only shown on CMC. The enzymes displayed significant synergy on CMC but not on Avicel when tested for 3 h at 45 °C. No observed β-glucosidase activities were identified for cel8C and cel12B when tested on p-nitrophenyl-β-d-glucopyranoside. Activity stimulation of 130% was observed when a recombinant β-glucosidase from Pcc was added to cel8C and cel12B as tested for 3 h at 45 °C. Optimum temperature and pH of 45 °C and 5.4, respectively, were identified for all three enzymes using various substrates. Catalytic efficiencies (kcat/Km) were calculated for cel12B and cel8C on CMC as 0.141 and 2.45 ml/mg/s respectively, at 45 °C and pH 5.0 and for peh28 on polygalacturonic acid as 4.87 ml/mg/s, at 40 °C and pH 5.0. Glucose and cellobiose were the end-products identified for cel8C, cel12B, and β-glucosidase acting together on Avicel or CMC, while galacturonic acid and other minor co-products were identified for peh28 action on pectin. CONCLUSIONS This study provides some insight into which parameters should be optimized when application of cel8C, cel12B, and peh28 to biomass conversion is the goal.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Kim D. Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Keith E. Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4 Canada
| | - Ebtesam N. Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Patrick L. Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Jean M. Escudero
- Department of Basic Science, St. Louis College of Pharmacy, St. Louis, MO 63110-1088 USA
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11
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Segato F, Dias B, Berto GL, de Oliveira DM, De Souza FHM, Citadini AP, Murakami MT, Damásio ARL, Squina FM, Polikarpov I. Cloning, heterologous expression and biochemical characterization of a non-specific endoglucanase family 12 from Aspergillus terreus NIH2624. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:395-403. [PMID: 28088615 DOI: 10.1016/j.bbapap.2017.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/20/2016] [Accepted: 01/06/2017] [Indexed: 01/30/2023]
Abstract
The cellulases from Glycoside Hydrolyses family 12 (GH12) play an important role in cellulose degradation and plant cell wall deconstruction being widely used in a number of bioindustrial processes. Aiming to contribute toward better comprehension of these class of the enzymes, here we describe a high-yield secretion of a endoglucanase GH12 from Aspegillus terreus (AtGH12), which was cloned and expressed in Aspergillus nidulans strain A773. The purified protein was used for complete biochemical and functional characterization. The optimal temperature and pH of the enzyme were 55°C and 5.0 respectively, which has high activity against β-glucan and xyloglucan and also is active toward glucomannan and CMC. The enzyme retained activity up to 60°C. AtGH12 is strongly inhibited by Cu2+, Fe2+, Cd2+, Mn2+, Ca2+, Zn2+ and EDTA, whereas K+, Tween, Cs+, DMSO, Triton X-100 and Mg2+ enhanced the enzyme activity. Furthermore, SAXS data reveal that the enzyme has a globular shape and CD analysis demonstrated a prevalence of a β-strand structure corroborating with typical β-sheets fold commonly found for other endoglucanases from GH12 family.
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Affiliation(s)
- Fernando Segato
- Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil; Departamento de Biotecnologia, Escola de Engenharia de Lorena - Universidade de São Paulo, Lorena, SP, Brazil
| | - Bruno Dias
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Gabriela L Berto
- Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil; Departamento de Biotecnologia, Escola de Engenharia de Lorena - Universidade de São Paulo, Lorena, SP, Brazil
| | - Dyoni M de Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Flávio H M De Souza
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Ana Paula Citadini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Mario T Murakami
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - André R L Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fábio Márcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Igor Polikarpov
- Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil.
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12
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High-throughput pyrosequencing used for the discovery of a novel cellulase from a thermophilic cellulose-degrading microbial consortium. Biotechnol Lett 2016; 39:123-131. [DOI: 10.1007/s10529-016-2224-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 09/15/2016] [Indexed: 10/20/2022]
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13
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Goh KM, Chan KG, Lim SW, Liew KJ, Chan CS, Shamsir MS, Ee R, Adrian TGS. Genome Analysis of a New Rhodothermaceae Strain Isolated from a Hot Spring. Front Microbiol 2016; 7:1109. [PMID: 27471502 PMCID: PMC4943939 DOI: 10.3389/fmicb.2016.01109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/04/2016] [Indexed: 11/21/2022] Open
Abstract
A bacterial strain, designated RA, was isolated from water sample of a hot spring on Langkawi Island of Malaysia using marine agar. Strain RA is an aerophilic and thermophilic microorganism that grows optimally at 50–60°C and is capable of growing in marine broth containing 1–10% (w/v) NaCl. 16S rRNA gene sequence analysis demonstrated that this strain is most closely related (<90% sequence identity) to Rhodothermaceae, which currently comprises of six genera: Rhodothermus (two species), Salinibacter (three species), Salisaeta (one species), Rubricoccus (one species), Rubrivirga (one species), and Longimonas (one species). Notably, analysis of average nucleotide identity (ANI) values indicated that strain RA may represent the first member of a novel genus of Rhodothermaceae. The draft genome of strain RA is 4,616,094 bp with 3630 protein-coding gene sequences. Its GC content is 68.3%, which is higher than that of most other genomes of Rhodothermaceae. Strain RA has genes for sulfate permease and arylsulfatase to withstand the high sulfur and sulfate contents of the hot spring. Putative genes encoding proteins involved in adaptation to osmotic stress were identified which encode proteins namely Na+/H+ antiporters, a sodium/solute symporter, a sodium/glutamate symporter, trehalose synthase, malto-oligosyltrehalose synthase, choline-sulfatase, potassium uptake proteins (TrkA and TrkH), osmotically inducible protein C, and the K+ channel histidine kinase KdpD. Furthermore, genome description of strain RA and comparative genome studies in relation to other related genera provide an overview of the uniqueness of this bacterium.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Soon Wee Lim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok Jun Liew
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Tan-Guan-Sheng Adrian
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
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14
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Calzado F, Prates ET, Gonçalves TA, Rubio MV, Zubieta MP, Squina FM, Skaf MS, Damásio AR. Molecular basis of substrate recognition and specificity revealed in family 12 glycoside hydrolases. Biotechnol Bioeng 2016; 113:2577-2586. [DOI: 10.1002/bit.26036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/29/2016] [Accepted: 06/05/2016] [Indexed: 02/02/2023]
Affiliation(s)
- Felipe Calzado
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas-SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology; University of Campinas (UNICAMP); Campinas-SP 13083862 Brazil
| | - Erica T. Prates
- Institute of Chemistry; University of Campinas (UNICAMP); Campinas-SP Brazil
| | - Thiago A. Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas-SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology; University of Campinas (UNICAMP); Campinas-SP 13083862 Brazil
| | - Marcelo V. Rubio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas-SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology; University of Campinas (UNICAMP); Campinas-SP 13083862 Brazil
| | - Mariane P. Zubieta
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas-SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology; University of Campinas (UNICAMP); Campinas-SP 13083862 Brazil
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas-SP Brazil
| | - Munir S. Skaf
- Institute of Chemistry; University of Campinas (UNICAMP); Campinas-SP Brazil
| | - André R.L. Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas-SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology; University of Campinas (UNICAMP); Campinas-SP 13083862 Brazil
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15
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Wang J, Gao G, Li Y, Yang L, Liang Y, Jin H, Han W, Feng Y, Zhang Z. Cloning, Expression, and Characterization of a Thermophilic Endoglucanase, AcCel12B from Acidothermus cellulolyticus 11B. Int J Mol Sci 2015; 16:25080-95. [PMID: 26506341 PMCID: PMC4632791 DOI: 10.3390/ijms161025080] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/29/2015] [Accepted: 10/13/2015] [Indexed: 12/23/2022] Open
Abstract
The gene ABK52392 from the thermophilic bacterium Acidothermus cellulolyticus 11B was predicted to be endoglucanase and classified into glycoside hydrolase family 12. ABK52392 encodes a protein containing a catalytic domain and a carbohydrate binding module. ABK52392 was cloned and functionally expressed in Escherichia coli. After purification by Ni-NTA agarose affinity chromatography and Q-Sepharose® Fast Flow chromatography, the properties of the recombinant protein (AcCel12B) were characterized. AcCel12B exhibited optimal activity at pH 4.5 and 75 °C. The half-lives of AcCel12B at 60 and 70 °C were about 90 and 2 h, respectively, under acidic conditions. The specific hydrolytic activities of AcCel12B at 70 °C and pH 4.5 for sodium carboxymethylcellulose (CMC) and regenerated amorphous cellulose (RAC) were 118.3 and 104.0 U·mg−1, respectively. The Km and Vmax of AcCel12B for CMC were 25.47 mg·mL−1 and 131.75 U·mg−1, respectively. The time course of hydrolysis for RAC was investigated by measuring reducing ends in the soluble and insoluble phases. The total hydrolysis rate rapidly decreased after the early stage of incubation and the generation of insoluble reducing ends decreased earlier than that of soluble reducing ends. High thermostability of the cellulase indicates its potential commercial significance and it could be exploited for industrial application in the future.
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Affiliation(s)
- Junling Wang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
- Department of Biotechnology, Jilin Agricultural Science and Technology College, Jilin 132101, China.
| | - Gui Gao
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yuwei Li
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - Liangzhen Yang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yanli Liang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Hanyong Jin
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yan Feng
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Zuoming Zhang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
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16
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Okano H, Kanaya E, Ozaki M, Angkawidjaja C, Kanaya S. Structure, activity, and stability of metagenome-derived glycoside hydrolase family 9 endoglucanase with an N-terminal Ig-like domain. Protein Sci 2015; 24:408-19. [PMID: 25545469 DOI: 10.1002/pro.2632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 11/07/2022]
Abstract
A metagenome-derived glycoside hydrolase family 9 enzyme with an N-terminal immunoglobulin-like (Ig-like) domain, leaf-branch compost (LC)-CelG, was characterized and its crystal structure was determined. LC-CelG did not hydrolyze p-nitrophenyl cellobioside but hydrolyzed CM-cellulose, indicating that it is endoglucanase. LC-CelG exhibited the highest activity at 70°C and >80% of the maximal activity at a broad pH range of 5-9. Its denaturation temperature was 81.4°C, indicating that LC-CelG is a thermostable enzyme. The structure of LC-CelG resembles those of CelD from Clostridium thermocellum (CtCelD), Cel9A from Alicyclobacillus acidocaldarius (AaCel9A), and cellobiohydrolase CbhA from C. thermocellum (CtCbhA), which show relatively low (29-31%) amino acid sequence identities to LC-CelG. Three acidic active site residues are conserved as Asp194, Asp197, and Glu558 in LC-CelG. Ten of the thirteen residues that form the substrate binding pocket of AaCel9A are conserved in LC-CelG. Removal of the Ig-like domain reduced the activity and stability of LC-CelG by 100-fold and 6.3°C, respectively. Removal of the Gln40- and Asp99-mediated interactions between the Ig-like and catalytic domains destabilized LC-CelG by 5.0°C without significantly affecting its activity. These results suggest that the Ig-like domain contributes to the stabilization of LC-CelG mainly due to the Gln40- and Asp99-mediated interactions. Because the LC-CelG derivative lacking the Ig-like domain accumulated in Escherichia coli cells mostly in an insoluble form and this derivative accumulated in a soluble form exhibited very weak activity, the Ig-like domain may be required to make the conformation of the active site functional and prevent aggregation of the catalytic domain.
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Affiliation(s)
- Hiroyuki Okano
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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