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Thapa S, Zhou S, O'Hair J, Al Nasr K, Ropelewski A, Li H. Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach. BMC Biotechnol 2023; 23:51. [PMID: 38049781 PMCID: PMC10696843 DOI: 10.1186/s12896-023-00821-6] [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: 03/17/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities. RESULTS Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity. CONCLUSIONS In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.
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Affiliation(s)
- Santosh Thapa
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
- Vanderbilt University Medical Center, 2215 Garland Ave, Nashville, TN, 37232, USA
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Joshua O'Hair
- Department of Biological Sciences, College of Life & Physical Sciences, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Kamal Al Nasr
- Department of Computer Sciences, College of Engineering, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Alexander Ropelewski
- Pittsburgh Supercomputing Center, 300 S. Craig Street, Pittsburgh, PA, 15213, USA
| | - Hui Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA.
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Cloning, molecular modeling and characterization of acidic cellulase from buffalo rumen and its applicability in saccharification of lignocellulosic biomass. Int J Biol Macromol 2018; 113:73-81. [DOI: 10.1016/j.ijbiomac.2018.02.100] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 11/21/2022]
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Shah RK, Patel AK, Davla DM, Parikh IK, Subramanian RB, Patel KC, Jakhesara SJ, Joshi CG. Molecular cloning, heterologous expression, and functional characterization of a cellulolytic enzyme (Cel PRII) from buffalo rumen metagenome. 3 Biotech 2017; 7:257. [PMID: 28733938 DOI: 10.1007/s13205-017-0895-2] [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: 03/27/2017] [Accepted: 07/12/2017] [Indexed: 01/02/2023] Open
Abstract
A cellulase encoding gene, Cel PRII, was identified from Mehsani buffalo rumen metagenome, and cloned and expressed in Escherichia coli BL21(DE3)pLysS. The 1170 bp full length gene encodes a 389 residue polypeptide (Cel PRII) containing a catalytic domain belonging to glycosyl hydrolase (GH) 5 family. The fusion protein consisting of the Cel PRII, thioredoxin tag and 6x Histidine tag with predicted molecular weight of 63 kDa when recovered from inclusion bodies under denaturing conditions, exhibited cellulolytic activity against carboxymethyl cellulose (CMC). Recombinant Cel PRII was stable in the pH range 4.0-10.0 with pH optima 6.0. The optimal reaction temperature of Cel PRII was 30 °C with more than 50% of its activity retained at the temperatures ranging from 0 to 50 °C. Cel PRII exhibited enhanced enzymatic activity in the presence of Mn2+ ions and was inhibited in the presence of chelating agent EDTA. The K m and V max values for CMC were found to be 166 mg/mL and 1292 IU/mg, respectively. Cel PRII identified in the present study may act as an excellent candidate for industrial applications, and may aid in lignocellulosic biomass conversion because of its potential cellulolytic activity, thermostability, and excellent pH stability.
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Affiliation(s)
- Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388110, India
- P. G. Department of Biosciences, Sardar Patel University, Bakrol, 388315, India
| | - Amrutlal K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388110, India
- Hester Biosciences Ltd., Merda-Adraj, Kadi, 382728, India
| | - Deepti M Davla
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388110, India
| | - Ishan K Parikh
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388110, India
- Zydus Vaccine Technology Centre, Changodar, Ahmedabad, 382213, India
| | | | - Kamlesh C Patel
- P. G. Department of Biosciences, Sardar Patel University, Bakrol, 388315, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388110, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388110, India.
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Prospects of Metagenomic Cellulases for Converting Lignocellulosic Biomass into Bio-ethanol. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.2.51] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Sriariyanun M, Tantayotai P, Yasurin P, Pornwongthong P, Cheenkachorn K. Production, purification and characterization of an ionic liquid tolerant cellulase from Bacillus sp. isolated from rice paddy field soil. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2015.11.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Pandey S, Gulati S, Goyal E, Singh S, Kumar K, Nain L, Saxena A. Construction and screening of metagenomic library derived from soil for β-1, 4-endoglucanase gene. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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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Mai Z, Su H, Yang J, Huang S, Zhang S. Cloning and characterization of a novel GH44 family endoglucanase from mangrove soil metagenomic library. Biotechnol Lett 2014; 36:1701-9. [DOI: 10.1007/s10529-014-1531-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/31/2014] [Indexed: 11/30/2022]
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Sae-Lee R, Boonmee A. Newly derived GH43 gene from compost metagenome showing dual xylanase and cellulase activities. Folia Microbiol (Praha) 2014; 59:409-17. [PMID: 24737296 DOI: 10.1007/s12223-014-0313-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
A metagenomic fosmid library was constructed from compost microbial communities that were collected from various farms throughout the Khon Kaen province, Thailand. The library was enriched in carboxymethylcellulose (CM-cellulose)--containing media prior to the screening of clones capable of degrading cellulosic materials. Two clones were selected for further subcloning and sequencing based on different patterns from restriction analysis. Deduced amino acid analysis of possible ORFs revealed one novel gene encoding an enzyme belonging to glycosyl hydrolase family 43 (GH43), which is a GH family rarely found in metagenomic studies. The most notable finding is that this enzyme, designated as Biof1_09, shows dual activities, namely endocellulase and endoxylanase activities. Biof1_09 showed greater than 50% of its activity under acidic conditions ranging from pH 3.5 to 5.5 with a pH optimum of 4.5. The optimum temperature of this enzyme was between 45 and 55 °C with an optimum of 50 °C. The properties of Biof1_09 make this enzyme an attractive candidate for large-scale expression for use in lignocellulose degradation for various bioprocess applications, including bioethanol fermentation.
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Affiliation(s)
- Ritthironk Sae-Lee
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
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Cheema TA, Jirajaroenrat K, Sirinarumitr T, Rakshit SK. Isolation of a Gene Encoding a Cellulolytic Enzyme from Swamp Buffalo Rumen Metagenomes and Its Cloning and Expression inEscherichia Coli. Anim Biotechnol 2012; 23:261-77. [DOI: 10.1080/10495398.2012.722156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome-host models and inform strategies promoting less-polluting, more robust and efficient ruminants.
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Identification and Characterization of a Cellulase-Encoding Gene from the Buffalo Rumen Metagenomic Library. Biosci Biotechnol Biochem 2012; 76:1075-84. [DOI: 10.1271/bbb.110786] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Bao L, Huang Q, Chang L, Zhou J, Lu H. Screening and characterization of a cellulase with endocellulase and exocellulase activity from yak rumen metagenome. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.08.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang G, Li S, Xue Y, Mao L, Ma Y. Effects of salts on activity of halophilic cellulase with glucomannanase activity isolated from alkaliphilic and halophilic Bacillus sp. BG-CS10. Extremophiles 2011; 16:35-43. [PMID: 22012583 DOI: 10.1007/s00792-011-0403-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 10/05/2011] [Indexed: 10/16/2022]
Abstract
Alkaliphilic and halophilic Bacillus sp. BG-CS10 was isolated from Zabuye Salt Lake, Tibet. The gene celB, encoding a halophilic cellulase was identified from the genomic library of BG-CS10. CelB belongs to the cellulase superfamily and DUF291 superfamily, with an unknown function domain and less than 58% identity to other cellulases in GenBank. The purified recombinant protein (molecular weight: 62 kDa) can hydrolyze soluble cellulose substrates containing beta-1,4-linkages, such as carboxylmethyl cellulose and konjac glucomannan, but has no exoglucanase and β-glucosidase activities. Thus, CelB is a cellulase with an endo mode of action and glucomannanase activity. Interestingly, the enzyme activity was increased approximately tenfold with 2.5 M NaCl or 3 M KCl. Furthermore, the optimal temperatures were 55°C with 2.5 M NaCl and 35°C without NaCl, respectively. This indicates that NaCl can improve enzyme thermostability. The K ( m ) and k (cat) values of CelB for CMC with 2.5 M NaCl were 3.18 mg mL(-1) and 26 s(-1), while the K ( m ) and k (cat) values of CelB without NaCl were 6.6 mg mL(-1) and 2.1 s(-1). Thus, this thermo-stable, salt and pH-tolerant cellulase is a promising candidate for industrial applications, and provides a new model to study salt effects on the structure of protein.
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Affiliation(s)
- Guimin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Duan CJ, Feng JX. Mining metagenomes for novel cellulase genes. Biotechnol Lett 2010; 32:1765-75. [PMID: 20640872 DOI: 10.1007/s10529-010-0356-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/09/2010] [Indexed: 11/26/2022]
Abstract
Cellulases hydrolyze the β-1,4 linkages of cellulose and are widely used in food, brewing and wine, animal feed, textiles and laundry, and pulp and paper industries, especially for hydrolyzing cellulosic materials into sugars, which can be fermented to produce useful products such as ethanol. Metagenomics has become an alternative approach to conventional culture-dependent methods as it allows exhaustive mining of microbial genomes in their natural environments. This review covers the current state of research and challenges in mining novel cellulase genes from the metagenomes of various environments, and discusses the potential biotechnological applications of metagenome-derived cellulases.
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Affiliation(s)
- Cheng-Jie Duan
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
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