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Khan A, Khan H, Faheem M, Zeb A, Badshah M, Chung YR. Isolation and Characterization of an Acidic, Salt-Tolerant Endoglucanase Cel5A from a Bacterial Strain Martelella endophytica YC6887 Genome. Mol Biotechnol 2021; 63:305-315. [PMID: 33523417 DOI: 10.1007/s12033-020-00295-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 11/29/2022]
Abstract
A Martelella endophytica (M. endophytica) strain YC6887 was previously isolated from the roots of a halophyte, Rosa rugosa, which was sequenced and characterized. The genomic and proteomic analysis showed a carbohydrate-degrading enzyme, endoglucanase Cel5A which was further characterized. The protein analysis revealed that this endoglucanase belongs to glycosidic hydrolase family 5 (GH5) with catalytic domain. This gene encodes 349-residue polypeptide and shows closest similarity with cellulases of other Martelella species. The protein was purified to homogeneity and shown that it was a 39 kDa protein. The purified recombinant Cel5A endoglucanase exhibited maximum activity at 50 °C and pH 4.5. The enzyme was salt tolerant and retained more than 50% residual activity up to 15% NaCl. The homology model structure of Cel5A displayed that it is stable and compact protein structure consisting of eleven α-helical structures and eight β-sheets. According to the predicted ligand binding site after superimposition with Pseudomonas stutzeri endoglucanase Cel5A (PDB ID: 4LX4), it consisted of five amino acid Asn157, Tyr116, Glu158, Glu270 and Trp303 that may be the expected active site of Cel5A from YC6887. This presented that our strain M. endophytica YC6887 that produces cellulase partially degrade the insoluble polysaccharides into reducing sugars.
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Affiliation(s)
- Ajmal Khan
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Centre, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea. .,Department of Biotechnology, Bacha Khan University, Charsada, KPK, Pakistan.
| | - Haji Khan
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Centre, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.,Centre for Biotechnology and Microbiology, University of Swat, Swat, KPK, 19200, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, 46000, Pakistan
| | - Amir Zeb
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Malik Badshah
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Young Ryun Chung
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Centre, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Yadav S, Pandey AK, Dubey SK. Molecular modeling, docking and simulation dynamics of β-glucosidase reveals high-efficiency, thermo-stable, glucose tolerant enzyme in Paenibacillus lautus BHU3 strain. Int J Biol Macromol 2020; 168:371-382. [PMID: 33310096 DOI: 10.1016/j.ijbiomac.2020.12.059] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
The enzyme β-glucosidase mediates the rate limiting step of conversion of cellobiose to glucose and thus plays a vital role in the process of cellulose degradation. The present study deals with analysis of the effective novel strain of Paenibacillus lautus BHU3 for identifying high-efficiency thermostable, glucose tolerant β-glucosidases. Seven counterparts with elevated Tm values ranging from 64.6 to 75.8 °C with high thermo-stability, were revealed through this analysis. The blind molecular docking of the model enzymes structures with cellobiose and pNPG gave high negative interaction energies ranging from -11.33 to -13.29 and -6.43 to -9.054 (kcal mol-1), respectively. The enzyme WP_096774744.1 effectively formed 5 hydrogen bonds with the highest interaction energy (-13.29 kcal mol-1) with cellobiose at its catalytic site. Molecular dynamics simulation analysis performed for the WP_096774744.1-pNPG complex predicted Glu5, Arg7, Lue68, Gly69 and Phe325 as the major contributing residues for accomplishing hydrolysis of β-1-4-linkage. Further, the molecular docking of WP_096774744.1 enzyme with glucose revealed a distinct glucose-binding site distant from the substrate-binding site, thus confirming the deficient competitive inhibition by glucose. Hence, WP_096774744.1 β-glucosidase appears to be an efficient enzyme with enhanced activity to biodegrade the cellulosic materials and highly relevant for waste management and various industrial applications.
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Affiliation(s)
- Suman Yadav
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, 284128, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Dar MA, Pawar KD, Rajput BP, Rahi P, Pandit RS. Purification of a cellulase from cellulolytic gut bacterium, Bacillus tequilensis G9 and its evaluation for valorization of agro-wastes into added value byproducts. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Irfan M, Tayyab A, Hasan F, Khan S, Badshah M, Shah AA. Production and Characterization of Organic Solvent-Tolerant Cellulase from Bacillus amyloliquefaciens AK9 Isolated from Hot Spring. Appl Biochem Biotechnol 2017; 182:1390-1402. [DOI: 10.1007/s12010-017-2405-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
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Attigani A, Sun L, Wang Q, Liu Y, Bai D, Li S, Huang X. The crystal structure of the endoglucanase Cel10, a family 8 glycosyl hydrolase from Klebsiella pneumoniae. Acta Crystallogr F Struct Biol Commun 2016; 72:870-876. [PMID: 27917834 PMCID: PMC5137463 DOI: 10.1107/s2053230x16017891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/08/2016] [Indexed: 02/04/2023] Open
Abstract
Cellulases are produced by microorganisms that grow on cellulose biomass. Here, a cellulase, Cel10, was identified in a strain of Klebsiella pneumoniae isolated from Chinese bamboo rat gut. Analysis of substrate specificity showed that Cel10 is able to hydrolyze amorphous carboxymethyl cellulose (CMC) and crystalline forms of cellulose (Avicel and xylan) but is unable to hydrolyze p-nitrophenol β-D-glucopyranoside (p-NPG), proving that Cel10 is an endoglucanase. A phylogenetic tree analysis indicates that Cel10 belongs to the glycoside hydrolase 8 (GH8) subfamily. In order to further understanding of its substrate specificity, the structure of Cel10 was solved by molecular replacement and refined to 1.76 Å resolution. The overall fold is distinct from those of most other enzymes belonging to the GH8 subfamily. Although it forms the typical (α/α)6-barrel motif fold, like Acetobacterxylinum CMCax, one helix is missing. Structural comparisons with Clostridium thermocellum CelA (CtCelA), the best characterized GH8 endoglucanase, revealed that sugar-recognition subsite -3 is completely missing in Cel10. The absence of this subsite correlates to a more open substrate-binding cleft on the cellooligosaccharide reducing-end side.
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Affiliation(s)
- Ayman Attigani
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
| | - Lifang Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Qing Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Yadan Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Dingping Bai
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
| | - Shengping Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Xiaohong Huang
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
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Kanchanadumkerng P, Sakka M, Sakka K, Wiwat C. Characterization of endoglucanase fromPaenibacillussp. M33, a novel isolate from a freshwater swamp forest. J Basic Microbiol 2016; 57:121-131. [DOI: 10.1002/jobm.201600225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/11/2016] [Indexed: 11/06/2022]
Affiliation(s)
| | - Makiko Sakka
- Applied Microbiology Laboratory; Graduate School of Bioresources; Mie University; Mie Japan
| | - Kazuo Sakka
- Applied Microbiology Laboratory; Graduate School of Bioresources; Mie University; Mie Japan
| | - Chanpen Wiwat
- Faculty of Pharmacy, Department of Microbiology; Mahidol University; Bangkok Thailand
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Dhar H, Kasana RC, Gulati A. Heterologous expression and characterization of detergent stable endoglucanase EG5B from Paenibacillus sp. IHB B 3084. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Gastelum-Arellanez A, Paredes-López O, Olalde-Portugal V. Extracellular endoglucanase activity from Paenibacillus polymyxa BEb-40: production, optimization and enzymatic characterization. World J Microbiol Biotechnol 2014; 30:2953-65. [DOI: 10.1007/s11274-014-1723-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
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Valencia A, Alves AP, Siegfried BD. Molecular cloning and functional characterization of an endogenous endoglucanase belonging to GHF45 from the western corn rootworm, Diabrotica virgifera virgifera. Gene 2012; 513:260-7. [PMID: 23137634 DOI: 10.1016/j.gene.2012.10.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 09/14/2012] [Accepted: 10/10/2012] [Indexed: 11/30/2022]
Abstract
A novel insect β-1,4-endoglucanase (DvvENGaseI) gene belonging to the glycoside hydrolase family (GHF) 45 was identified from the western corn rootworm, Diabrotica virgifera virgifera. The cDNA of the DvvENGaseI consisted of a 720 bp open reading frame encoding a 239 amino-acid protein. Analysis of the amino acid sequence revealed that DvvENGaseI exhibits 60% protein sequence identity when compared with an endoglucanase belonging to GHF45 from another beetle, Leptinotarsa decemlineata. Western blot analyses using a polyclonal antiserum developed from a partial peptide sequence revealed that DvvENGaseI expression coincided with body regions corresponding to the fore-, mid- and hindgut, although regions corresponding to the midgut and hindgut were the primary sites for DvvENGaseI expression. Functional analysis of the DvvENGaseI by RNA interference (RNAi) indicated that nearly complete knock-down of gene expression could be obtained by injection of dsRNA based on qRT-PCR and western blot analysis. However, suppression only resulted in slight developmental delays suggesting that this gene may be part of a larger system of cellulose degrading enzymes.
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Affiliation(s)
- Arnubio Valencia
- Departamento de Producción Agropecuaria, Facultad de Ciencias Agropecuarias, Universidad de Caldas, Calle 65#26-10, Manizales, Colombia
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Characterization of Paenibacillus curdlanolyticus B-6 Xyn10D, a xylanase that contains a family 3 carbohydrate-binding module. Appl Environ Microbiol 2011; 77:4260-3. [PMID: 21498754 DOI: 10.1128/aem.00226-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paenibacillus curdlanolyticus B-6 Xyn10D is a xylanase containing a family 3 carbohydrate-binding module (CBM3). Biochemical analyses using recombinant proteins derived from Xyn10D suggested that the CBM3 polypeptide has an affinity for cellulose and xylan and that CBM3 in Xyn10D is important for hydrolysis of insoluble arabinoxylan and natural biomass.
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Molecular cloning, purification, and characterization of a novel, acidic, pH-stable endoglucanase from Martelella mediterranea. J Microbiol 2010; 48:393-8. [PMID: 20571959 DOI: 10.1007/s12275-010-9361-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 03/03/2010] [Indexed: 10/19/2022]
Abstract
A novel gene encoding an endoglucanase designated Cel5D was cloned from a marine bacterium Martelella mediterranea by genomic library. The gene had a 1,113 bp opening reading frame encoding a 371-amino-acid protein with a molecular mass of 40,508 Da and containing a putative signal peptide (41 amino acids). Cel5D had low similarity (48-51% identity) with other known endoglucanases and consisted of one single catalytic domain, which belonged to the glycosyl hydrolase family 5. The maximum activity of Cel5D was observed at 60 degrees C and pH 5.0. Cel5D displayed broad pH stability within the range of pH 3.0-11.0 and retained hydrolytic activity in the presence of a wide variety of metal ions and some chemical reagents. These characteristics suggest that the enzyme has considerable potential in industrial applications.
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Feng Y, Jiang JX, Zhu LW. Recent developments in activities, utilization and sources of cellulase. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11632-009-0028-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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A Novel Endoglucanase (Cel9P) From a Marine Bacterium Paenibacillus sp. BME-14. Appl Biochem Biotechnol 2009; 160:1627-36. [DOI: 10.1007/s12010-009-8648-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Accepted: 04/12/2009] [Indexed: 11/27/2022]
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Li W, Huan X, Zhou Y, Ma Q, Chen Y. Simultaneous cloning and expression of two cellulase genes from Bacillus subtilis newly isolated from Golden Takin (Budorcas taxicolor Bedfordi). Biochem Biophys Res Commun 2009; 383:397-400. [PMID: 19366617 DOI: 10.1016/j.bbrc.2009.04.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
A bacterial strain with high cellulase activity was isolated of feces sample of Golden Takin (Budorcas taxicolor Bedfordi). The bacterium was classified and designated Bacillus subtilis LN by morphological and 16SrDNA gene sequence analysis. Two putative cellulase genes, CelL15 and CelL73, were simultaneously cloned from the isolated strain by PCR. The putative gene CelL15 consisted of an open reading frame (ORF) of 1470 nucleotides and encoded a protein of 490 amino acids with a molecular weight of 54kDa. The CelL73 gene consisted of an open reading frame (ORF) of 741 nucleotides and encoded a protein of 247 amino acids with a molecular weight of 27kDa. Both genes were purified and cloned into pET-28a for expression in Escherichia coli BL21 (DE3). The ability of E. coli to degrade cellulose was enhanced when the two recombinants were cultured together.
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Affiliation(s)
- Wang Li
- College of Animal Science, North-West Science and Technology University of A&F, Xinong Road 22, Yangling 712100, PR China
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Ogawa A, Sumitomo N, Hakamada Y, Saeki K, Ozaki K, Kobayashi T. Nucleotide Sequence of a Paenibacillus Endoglucanase Gene and Characterization of the Recombinant Enzyme. J Appl Glycosci (1999) 2009. [DOI: 10.5458/jag.56.253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Wang CM, Shyu CL, Ho SP, Chiou SH. Characterization of a novel thermophilic, cellulose-degrading bacterium Paenibacillus sp. strain B39. Lett Appl Microbiol 2008; 47:46-53. [DOI: 10.1111/j.1472-765x.2008.02385.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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