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Kholousi Adab F, Mehdi Yaghoobi M, Gharechahi J. Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme. Sci Rep 2024; 14:8560. [PMID: 38609443 PMCID: PMC11014956 DOI: 10.1038/s41598-024-59256-4] [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: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.
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Affiliation(s)
- Faezeh Kholousi Adab
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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2
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Andrade VB, Tomazetto G, Almeida DV, Tramontina R, Squina FM, Garcia W. Enzymatic and biophysical characterization of a novel modular cellulosomal GH5 endoglucanase multifunctional from the anaerobic gut fungus Piromyces finnis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140963. [PMID: 37690538 DOI: 10.1016/j.bbapap.2023.140963] [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: 06/26/2023] [Revised: 08/14/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
Cellulases from anaerobic fungi are enzymes less-studied biochemically and structurally than cellulases from bacteria and aerobic fungi. Currently, only thirteen GH5 cellulases from anaerobic fungi were biochemically characterized and two crystal structures were reported. In this context, here, we report the functional and biophysical characterization of a novel multi-modular cellulosomal GH5 endoglucanase from the anaerobic gut fungus Piromyces finnis (named here PfGH5). Multiple sequences alignments indicate that PfGH5 is composed of a GH5 catalytic domain and a CBM1 carbohydrate-binding module connected through a CBM10 dockerin module. Our results showed that PfGH5 is an endoglucanase from anaerobic fungus with a large spectrum of activity. PfGH5 exhibited preference for hydrolysis of oat β-glucan, followed by galactomannan, carboxymethyl cellulose, mannan, lichenan and barley β-glucan, therefore displaying multi-functionality. For oat β-glucan, PfGH5 reaches its optimum enzymatic activity at 40 °C and pH 5.5, with Km of 7.1 μM. Ion exchange chromatography analyzes revealed the production of oligosaccharides with a wide degree of polymerization indicated that PfGH5 has endoglucanase activity. The ability to bind and cleave different types of carbohydrates evidence the potential of PfGH5 for use in biotechnology and provide a useful basis for future investigation and application of new anaerobic fungi enzymes.
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Affiliation(s)
- Viviane Brito Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Geizecler Tomazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, 8200 Aarhus, Denmark
| | - Dnane Vieira Almeida
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Robson Tramontina
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil.
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Biswas S, Bhattar AVK, Bhatta R, Rahman H. Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet. Microorganisms 2023; 12:47. [PMID: 38257874 PMCID: PMC10818812 DOI: 10.3390/microorganisms12010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
A study was undertaken to compare the rumen microbial community composition, methane yield, rumen fermentation, and CAZyme profiles between cattle and buffaloes. The primary aim of this study was to ascertain the impact of the host species on the above when diet and environmental factors are fixed. A total of 43 phyla, 200 orders, 458 families, and 1722 microbial genera were identified in the study. Bacteroidetes was the most prominent bacterial phylum and constituted >1/3rd of the ruminal microbiota; however, their abundances were comparable between cattle and buffaloes. Firmicutes were the second most abundant bacteria, found to be negatively correlated with the Bacteroidetes. The abundances of Firmicutes as well as the F/B ratio were not different between the two host species. In this study, archaea affiliated with the nine phyla were identified, with Euryarchaeota being the most prominent. Like bacterial phyla, the abundances of Euryarchaeota methanogens were also similar between the cattle and buffaloes. At the order level, Methanobacteriales dominated the archaea. Methanogens from the Methanosarcinales, Methanococcales, Methanomicrobiales, and Methanomassiliicoccales groups were also identified, but at a lower frequency. Methanobrevibacter was the most prevalent genus of methanogens, accounting for approximately three percent of the rumen metagenome. However, their distribution was not different between the two host species. CAZymes affiliated with five classes, namely CBM, CE, GH, GT, and PL, were identified in the metagenome, where the GH class was the most abundant and constituted ~70% of the total CAZymes. The protozoal numbers, including Entodiniomorphs and Holotrichs, were also comparable between the cattle and buffaloes. Results from the study did not reveal any significant difference in feed intake, nutrient digestibility, and rumen fermentation between cattle and buffaloes fed on the same diet. As methane yield due to the similar diet composition, feed ingredients, rumen fermentation, and microbiota composition did not vary, these results indicate that the microbiota community structure and methane emissions are under the direct influence of the diet and environment, and the host species may play only a minor role until the productivity does not vary. More studies are warranted to investigate the effect of different diets and environments on microbiota composition and methane yield. Further, the impact of variable productivity on both the cattle and buffaloes when the diet and environmental factors are fixed needs to be ascertained.
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Affiliation(s)
- Pradeep K. Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Shraddha Trivedi
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110012, India
| | - Atul P. Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Siddharth Biswas
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Ashwin V. K. Bhattar
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Habibar Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110012, India
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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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Gharechahi J, Vahidi MF, Sharifi G, Ariaeenejad S, Ding XZ, Han JL, Salekdeh GH. Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses. ENVIRONMENTAL RESEARCH 2023; 229:115925. [PMID: 37086884 DOI: 10.1016/j.envres.2023.115925] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/26/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Animal Science Research Department, Qom Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Qom, Iran
| | - Golandam Sharifi
- Department of Basic Sciences, Encyclopedia Research Center, Institute for Humanities and Cultural Studies, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), 00100, Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
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6
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Jeilu O, Simachew A, Alexandersson E, Johansson E, Gessesse A. Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics. Front Microbiol 2022; 13:1059061. [PMID: 36569080 PMCID: PMC9768486 DOI: 10.3389/fmicb.2022.1059061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.
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Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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Singh R, Pal DB, Alkhanani MF, Almalki AH, Areeshi MY, Haque S, Srivastava N. Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155966. [PMID: 35584752 DOI: 10.1016/j.scitotenv.2022.155966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.
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Affiliation(s)
- Rajeev Singh
- Department of Environmental Studies, Satyawati College, University of Delhi, Delhi, 110052, India
| | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, Taif 21944, Saudi Arabia
| | - Mohammed Yahya Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University, Faculty of Medicine, Görükle Campus, 16059 Nilüfer, Bursa, Turkey
| | - Neha Srivastava
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, India.
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Heterologous expression and characterization of two novel glucanases derived from sheep rumen microbiota. World J Microbiol Biotechnol 2022; 38:87. [DOI: 10.1007/s11274-022-03269-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022]
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Understanding microbial networks of farm animals through genomics, metagenomics and other meta-omic approaches for livestock wellness and sustainability. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms.
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Identification and characterization of a novel endo-β-1,4-glucanase from a soil metagenomic library. Carbohydr Res 2021; 510:108460. [PMID: 34700218 DOI: 10.1016/j.carres.2021.108460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 10/08/2021] [Accepted: 10/17/2021] [Indexed: 11/23/2022]
Abstract
A cosmid clone cZFYN1413 with CMCase activity was identified from a soil metagenomic library. The sequence analysis of a subclone of cZFYN1413 revealed an endo-β-1,4-glucanase gene ZFYN1413 belonging to glycoside hydrolase family 6 and a transmembrane region in the N-terminal of ZFYN1413. Expression of ZFYN1413 in Escherichia coli BL21 (DE3) resulted in ZFYN1413-87, which was a truncated protein cleaved in transmembrane region of ZFYN1413. ZFYN1413-87 was expressed and its enzyme properties were studied. ZFYN1413-87 possessed strong endo-β-1,4-glucanase activity, and 52% of the activity could be retained after the protein was treated in buffer of pH 3.0 for 2 h. The study provided a special example of endo-β-1,4-glucanase in GH6 family.
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11
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2021; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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12
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Eberhardt MF, Irazoqui JM, Amadio AF. β-Galactosidases from a Sequence-Based Metagenome: Cloning, Expression, Purification and Characterization. Microorganisms 2020; 9:microorganisms9010055. [PMID: 33379234 PMCID: PMC7823827 DOI: 10.3390/microorganisms9010055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022] Open
Abstract
Stabilization ponds are a common treatment technology for wastewater generated by dairy industries. Large proportions of cheese whey are thrown into these ponds, creating an environmental problem because of the large volume produced and the high biological and chemical oxygen demands. Due to its composition, mainly lactose and proteins, it can be considered as a raw material for value-added products, through physicochemical or enzymatic treatments. β-Galactosidases (EC 3.2.1.23) are lactose modifying enzymes that can transform lactose in free monomers, glucose and galactose, or galactooligosacharides. Here, the identification of novel genes encoding β-galactosidases, identified via whole-genome shotgun sequencing of the metagenome of dairy industries stabilization ponds is reported. The genes were selected based on the conservation of catalytic domains, comparing against the CAZy database, and focusing on families with β-galactosidases activity (GH1, GH2 and GH42). A total of 394 candidate genes were found, all belonging to bacterial species. From these candidates, 12 were selected to be cloned and expressed. A total of six enzymes were expressed, and five cleaved efficiently ortho-nitrophenyl-β-galactoside and lactose. The activity levels of one of these novel β-galactosidase was higher than other enzymes reported from functional metagenomics screening and higher than the only enzyme reported from sequence-based metagenomics. A group of novel mesophilic β-galactosidases from diary stabilization ponds' metagenomes was successfully identified, cloned and expressed. These novel enzymes provide alternatives for the production of value-added products from dairy industries' by-products.
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Pabbathi NPP, Velidandi A, Gandam PK, Koringa P, Parcha SR, Baadhe RR. Novel buffalo rumen metagenome derived acidic cellulase Cel-3.1 cloning, characterization, and its application in saccharifying rice straw and corncob biomass. Int J Biol Macromol 2020; 170:239-250. [PMID: 33316338 DOI: 10.1016/j.ijbiomac.2020.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022]
Abstract
Lignocellulosic biomass (LCB) is a prominent option for second-generation biofuels production. Cellulase hydrolyses cellulose, a component of LCB by attacking the β-1,4-glycosidic bonds, thus liberating mono, di, and oligosaccharides, which subsequently, can be converted to biofuel. In this study, a novel cellulase (Cel-3.1) of 1593 bp which encodes a 530 amino acid protein was identified from buffalo rumen metagenomic fosmid library, and functional expression was achieved through transformation into Escherichia coli. The molecular weight was estimated as 58 kDa on SDS-PAGE. Cel-3.1 belongs to glycosyl hydrolase family-5 (GH-5) and is predicted to have 14 α-helices and 15 β-strands. The optimal temperature and pH for Cel-3.1 were experimentally determined as 5.0 and 50 °C respectively. The synergistic effect of Ca2+ with K+ ions improved Cel-3.1 activity significantly (25%) and 1% Polyethylene Glycol (PEG-400), 1% β-mercaptoethanol enhanced the relative activity Cel-3.1 by 31.68%, 12.03% respectively. Further, the enzymatic (Cel-3.1) hydrolysis of pretreated rice straw and corncob released 13.41 ± 0.26 mg/mL and 15.04 ± 0.08 mg/mL reducing sugars respectively. High Performance Liquid Chromatography (HPLC), Scanning Electron Microscope (SEM), and Fourier Transformation Infrared spectroscopy (FTIR) analysis revealed the capability of Cel-3.1 for the breakdown and hydrolysis of both rice straw and corncob to generate various fermentable sugars.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Aditya Velidandi
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Prakash Koringa
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India
| | - Sreenivasa Rao Parcha
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India.
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Patel M, Patel HM, Dave S. Determination of bioethanol production potential from lignocellulosic biomass using novel Cel-5m isolated from cow rumen metagenome. Int J Biol Macromol 2020; 153:1099-1106. [DOI: 10.1016/j.ijbiomac.2019.10.240] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/13/2019] [Accepted: 10/25/2019] [Indexed: 11/17/2022]
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15
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Directed modification of a ruminal cellulase gene (CMC-1) from a metagenomic library isolated from Yunnan gayal (Bos frontalis). Arch Microbiol 2020; 202:1117-1126. [PMID: 32060600 DOI: 10.1007/s00203-020-01812-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/21/2022]
Abstract
Gayal (Bos frontalis) of the Yunnan region is well adapted to harsh environmental conditions. Its diet consists predominantly of bamboo, reeds, and woody plants, suggesting that the rumen of this species contains many fiber-degrading bacteria and cellulases. The aim of this study was to identify and modify specific cellulases found in the gayal rumen. In the present study, a directed evolution strategy of error-prone PCR was employed to improve the activity or optimal temperature of a cellulase gene (CMC-1) isolated from gayal rumen. The CMC-1 gene was heterologously expressed in Escherichia coli (E. coli) BL21, and the recombinant CMC-1 protein hydrolyzed carboxyl methyl cellulose (CMC) with an optimal activity at pH 5.0 and 50 °C. A library of mutated ruminal CMC-1 genes was constructed and a mutant EP-15 gene was identified. Sequencing analysis revealed that EP-15 and CMC-1 belonged to the glycosyl hydrolase family 5 (GHF5) and had the highest homology to a cellulase (Accession No. WP_083429257.1) from Prevotellaceae bacterium, HUN156. There were similar predicted GH5 domains in EP-15 and CMC-1. The EP-15 gene was heterologously expressed and exhibited cellulase activity in E. coli BL21 at pH 5.0, but the optimum temperature for its activity was reduced from that of CMC-1 (50 °C) to 45 °C, which was closer to the physiological temperature of the rumen (40 °C). The cellulase activity of EP-15 was about two times higher than CMC-1 at 45 °C or PH 5.0, and also was more stable in response to temperature and pH changes compared to CMC-1. This study successfully isolated and modified a ruminal cellulase gene from metagenomics library of Yunnan gayal. Our findings may obtain a useful cellulase in future applications and present the first evidence of modified cellulases in the gayal rumen.
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Souza RC, Cantão ME, Nogueira MA, Vasconcelos ATR, Hungria M. Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach. Braz J Microbiol 2018; 49:723-730. [PMID: 29636299 PMCID: PMC6175745 DOI: 10.1016/j.bjm.2018.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 11/23/2022] Open
Abstract
The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases>laccases>cellulases>proteases>amylases>pectinases. Statistically significant differences were attributed to the tillage system, with the NT showing about five times more hydrolases than the CT system. The outstanding differences can be attributed to the management of crop residues, left on the soil surface in the NT, and mechanically broken and incorporated into the soil in the CT. Differences between the CS and the CR were slighter, 10% higher for the CS, but not statistically different. Most of the sequences belonged to fungi (Verticillium, and Colletotrichum for lipases and laccases, and Aspergillus for proteases), and to the archaea Sulfolobus acidocaldarius for amylases. Our results indicate that agricultural soils under conservative managements may represent a hotspot for bioprospection of hydrolases.
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Affiliation(s)
- Renata Carolini Souza
- Embrapa Soja, C.P. 231, 86001-970 Londrina, PN, Brazil; CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil
| | | | - Marco Antonio Nogueira
- Embrapa Soja, C.P. 231, 86001-970 Londrina, PN, Brazil; CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil
| | - Ana Tereza Ribeiro Vasconcelos
- CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil; Laboratório Nacional de Computação Científica, Labinfo, Av. Getúlio Vargas 333, 25651-071 Petrópolis, RJ, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, PN, Brazil; CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, DF, Brazil.
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Kim HB, Lee KT, Kim MJ, Lee JS, Kim KS. Identification and characterization of a novel KG42 xylanase (GH10 family) isolated from the black goat rumen-derived metagenomic library. Carbohydr Res 2018; 469:1-9. [PMID: 30170217 DOI: 10.1016/j.carres.2018.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 11/18/2022]
Abstract
This study was conducted to isolate and functionally characterize a novel xylan-degrading enzyme from the microbial metagenomes of black goat rumens. A novel gene, KG42, was isolated from one of the 17 xylan-degrading metagenomic fosmid clones obtained from black goat rumens. The KG42 gene, comprising a 1107 bp open reading frame, encodes a protein composed of 368 amino acids (41 kDa) with a glycosyl hydrolase family 10 (GH10) domain, consisting of a "salad-bowl" shaped tertiary structure (a typical 8-fold α/β barrel (α/β)8) and two catalytic residues. KG42 xylanase protein has at best 40% sequence identity with other homologous GH10 xylanase proteins. The enzyme displayed its optimum activity at pH 5.0 and 50 °C. The enzyme was thermally stable at pH and temperature ranges of 5.0-10.0 and 20-60 °C, respectively. Substrate specificity and hydrolytic patterns implied that the KG42 xylanase functions as an endo-β-1,4-xylanase (EC 3.2.1.8). The KG42 xylanase was also used for the preparation of bifidogenic xylan hydrolysates, demonstrating its potential applications toward preparing prebiotic xylooligosaccharides.
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Affiliation(s)
- Hye-Bin Kim
- Department of Food Science and Technology, Chung-Ang University, Ansung, 456-756, South Korea
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, South Korea
| | - Min-Ju Kim
- Department of Food Science and Technology, Chung-Ang University, Ansung, 456-756, South Korea
| | - Jin-Sung Lee
- Department of Biological Sciences, Kyonggi University, Suwon, 442-760, South Korea
| | - Keun-Sung Kim
- Department of Food Science and Technology, Chung-Ang University, Ansung, 456-756, South Korea.
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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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Duque E, Daddaoua A, Cordero BF, Udaondo Z, Molina‐Santiago C, Roca A, Solano J, Molina‐Alcaide E, Segura A, Ramos J. Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production. Microb Biotechnol 2018; 11:781-787. [PMID: 29663699 PMCID: PMC6011990 DOI: 10.1111/1751-7915.13269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/01/2022] Open
Abstract
The success of second-generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with β-xylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase and β-xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active β-xylosidase was at least 10-fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue.
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Affiliation(s)
- Estrella Duque
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Abdelali Daddaoua
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Faculty of PharmacyDepartment of PharmacologyUniversity of Granada18071GranadaSpain
| | - Baldo F. Cordero
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Zulema Udaondo
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Carlos Molina‐Santiago
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Amalia Roca
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | - Jennifer Solano
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | | | - Ana Segura
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Juan‐Luis Ramos
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
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Isolation and characterization of a novel endo-β-1,4-glucanase from a metagenomic library of the black-goat rumen. Braz J Microbiol 2017; 48:801-808. [PMID: 28689814 PMCID: PMC5628298 DOI: 10.1016/j.bjm.2017.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 02/06/2017] [Accepted: 03/01/2017] [Indexed: 11/21/2022] Open
Abstract
The various types of lignocellulosic biomass found in plants comprise the most abundant renewable bioresources on Earth. In this study, the ruminal microbial ecosystem of black goats was explored because of their strong ability to digest lignocellulosic forage. A metagenomic fosmid library containing 115,200 clones was prepared from the black-goat rumen and screened for a novel cellulolytic enzyme. The KG35 gene, containing a novel glycosyl hydrolase family 5 cellulase domain, was isolated and functionally characterized. The novel glycosyl hydrolase family 5 cellulase gene is composed of a 963-bp open reading frame encoding a protein of 320 amino acid residues (35.1 kDa). The deduced amino acid sequence showed the highest sequence identity (58%) for sequences from the glycosyl hydrolase family 5 cellulases. The novel glycosyl hydrolase family 5 cellulase gene was overexpressed in Escherichia coli. Substrate specificity analysis revealed that this recombinant glycosyl hydrolase family 5 cellulase functions as an endo-β-1,4-glucanase. The recombinant KG35 endo-β-1,4-glucanase showed optimal activity within the range of 30–50 °C at a pH of 6–7. The thermostability was retained and the pH was stable in the range of 30–50 °C at a pH of 5–7.
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Isolation and characterization of a novel glycosyl hydrolase family 74 (GH74) cellulase from the black goat rumen metagenomic library. Folia Microbiol (Praha) 2016; 62:175-181. [PMID: 27866354 DOI: 10.1007/s12223-016-0486-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/13/2016] [Indexed: 10/20/2022]
Abstract
This study aimed to isolate and characterize a novel cellulolytic enzyme from black goat rumen by using a culture-independent approach. A metagenomic fosmid library was constructed from black goat rumen contents and screened for a novel cellulase. The KG37 gene encoding a protein of 858 amino acid residues (92.7 kDa) was isolated. The deduced protein contained a glycosyl hydrolase family 74 (GH74) domain and showed 77% sequence identity to two endo-1,4-β-glucanases from Fibrobacter succinogenes. The novel GH74 cellulase gene was overexpressed in Escherichia coli, and its protein product was functionally characterized. The recombinant GH74 cellulase showed a broad substrate spectrum. The enzyme exhibited its optimum activity at pH 5.0 and temperature range of 20-50 °C. The enzyme was thermally stable at pH 5.0 and at a temperature of 20-40 °C. The novel GH74 cellulase can be practically exploited to convert lignocellulosic biomass to value-added products in various industrial applications in future.
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Maruthamuthu M, Jiménez DJ, Stevens P, van Elsas JD. A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes. BMC Genomics 2016; 17:86. [PMID: 26822785 PMCID: PMC4730625 DOI: 10.1186/s12864-016-2404-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/18/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered. RESULTS Here, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 °C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 °C and pH 10.0. CONCLUSIONS This study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two clones, 10BT and T4-1, required the presence of multiple substrates for detectable activity, indicating a new avenue in library activity screening. Finally, clones NT2-2, T5-5 and NT18-17 were found to encode putative novel thermo-alkaline enzymes, which could represent a starting point for further biotechnological applications.
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Affiliation(s)
- Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Diego Javier Jiménez
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Patricia Stevens
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
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Identification of a novel family of carbohydrate-binding modules with broad ligand specificity. Sci Rep 2016; 6:19392. [PMID: 26765840 PMCID: PMC4725902 DOI: 10.1038/srep19392] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/03/2015] [Indexed: 11/13/2022] Open
Abstract
Most enzymes that act on carbohydrates include non-catalytic carbohydrate-binding modules (CBMs) that recognize and target carbohydrates. CBMs bring their appended catalytic modules into close proximity with the target substrate and increase the hydrolytic rate of enzymes acting on insoluble substrates. We previously identified a novel CBM (CBMC5614-1) at the C-terminus of endoglucanase C5614-1 from an uncultured microorganism present in buffalo rumen. In the present study, that the functional region of CBMC5614-1 involved in ligand binding was localized to 134 amino acids. Two representative homologs of CBMC5614-1, sharing the same ligand binding profile, targeted a range of β-linked polysaccharides that adopt very different conformations. Targeted substrates included soluble and insoluble cellulose, β-1,3/1,4-mixed linked glucans, xylan, and mannan. Mutagenesis revealed that three conserved aromatic residues (Trp-380, Tyr-411, and Trp-423) play an important role in ligand recognition and targeting. These results suggest that CBMC5614-1 and its homologs form a novel CBM family (CBM72) with a broad ligand-binding specificity. CBM72 members can provide new insight into CBM-ligand interactions and may have potential in protein engineering and biocatalysis.
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Kim SC, Kang SH, Choi EY, Hong YH, Bok JD, Kim JY, Lee SS, Choi YJ, Choi IS, Cho KK. Cloning and Characterization of an Endoglucanase Gene from Actinomyces sp. Korean Native Goat 40. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:126-33. [PMID: 26732336 PMCID: PMC4698679 DOI: 10.5713/ajas.15.0616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 10/09/2015] [Accepted: 11/14/2015] [Indexed: 11/27/2022]
Abstract
A gene from Actinomyces sp. Korean native goat (KNG) 40 that encodes an endo-β-1,4-glucanase, EG1, was cloned and expressed in Escherichia coli (E. coli) DH5α. Recombinant plasmid DNA from a positive clone with a 3.2 kb insert hydrolyzing carboxyl methyl-cellulose (CMC) was designated as pDS3. The entire nucleotide sequence was determined, and an open-reading frame (ORF) was deduced. The ORF encodes a polypeptide of 684 amino acids. The recombinant EG1 produced in E. coli DH5α harboring pDS3 was purified in one step using affinity chromatography on crystalline cellulose and characterized. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis/zymogram analysis of the purified enzyme revealed two protein bands of 57.1 and 54.1 kDa. The amino terminal sequences of these two bands matched those of the deduced ones, starting from residue 166 and 208, respectively. Putative signal sequences, a Shine–Dalgarno-type ribosomal binding site, and promoter sequences related to the consensus sequences were deduced. EG1 has a typical tripartite structure of cellulase, a catalytic domain, a serine-rich linker region, and a cellulose-binding domain. The optimal temperature for the activity of the purified enzyme was 55°C, but it retained over 90% of maximum activity in a broad temperature range (40°C to 60°C). The optimal pH for the enzyme activity was 6.0. Kinetic parameters, Km and Vmax of rEG1 were 0.39% CMC and 143 U/mg, respectively.
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Affiliation(s)
- Sung Chan Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 200-702, Korea
| | - Seung Ha Kang
- CSIRO Animal, Food and Health Science, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | - Eun Young Choi
- Department of Biological Science, Silla University, Busan 617-736, Korea
| | - Yeon Hee Hong
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 200-702, Korea
| | - Jin Duck Bok
- Institute of Green-Bio Science and Technology, Seoul National University, Pyungchang 25354, Korea
| | - Jae Yeong Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 200-702, Korea
| | - Sang Suk Lee
- Department of Animal Science and Technology, Sunchon National University, Sunchon 540-742, Korea
| | - Yun Jaie Choi
- Institute of Green-Bio Science and Technology, Seoul National University, Pyungchang 25354, Korea
| | - In Soon Choi
- Department of Biological Science, Silla University, Busan 617-736, Korea
| | - Kwang Keun Cho
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 200-702, Korea
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Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN. Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 2016; 9:22-34. [PMID: 26275154 PMCID: PMC4720405 DOI: 10.1111/1751-7915.12309] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53,000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Mónica Martínez-Martínez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststraße 18, D-22609, Hamburg, Germany
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
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26
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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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27
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Montella S, Amore A, Faraco V. Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development. Crit Rev Biotechnol 2015; 36:998-1009. [PMID: 26381035 DOI: 10.3109/07388551.2015.1083939] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.
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Affiliation(s)
- Salvatore Montella
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Antonella Amore
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Vincenza Faraco
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
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28
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Loaces I, Amarelle V, Muñoz-Gutierrez I, Fabiano E, Martinez A, Noya F. Improved ethanol production from biomass by a rumen metagenomic DNA fragment expressed in Escherichia coli MS04 during fermentation. Appl Microbiol Biotechnol 2015; 99:9049-60. [DOI: 10.1007/s00253-015-6801-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
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29
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Kawulok J, Deorowicz S. CoMeta: classification of metagenomes using k-mers. PLoS One 2015; 10:e0121453. [PMID: 25884504 PMCID: PMC4401624 DOI: 10.1371/journal.pone.0121453] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 02/15/2015] [Indexed: 02/07/2023] Open
Abstract
Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (Classification of metagenomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepared groups may contain sequences having various functions. In CoMeta, we used the exact method for read classification using short subsequences (k-mers) and fast program for indexing large set of k-mers. In contrast to the most popular methods based on BLAST, where the query is compared with each reference sequence, we begin the classification from the top of the taxonomy tree to reduce the number of comparisons. The presented experimental study confirms that CoMeta outperforms other programs used in this context. CoMeta is available at https://github.com/jkawulok/cometa under a free GNU GPL 2 license.
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Affiliation(s)
- Jolanta Kawulok
- Institute of Informatics, Silesian University of Technology, Gliwice, Poland
| | - Sebastian Deorowicz
- Institute of Informatics, Silesian University of Technology, Gliwice, Poland
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30
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Identification of glycosyl hydrolases from a metagenomic library of microflora in sugarcane bagasse collection site and their cooperative action on cellulose degradation. J Biosci Bioeng 2015; 119:384-91. [DOI: 10.1016/j.jbiosc.2014.09.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/12/2014] [Accepted: 09/13/2014] [Indexed: 11/19/2022]
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31
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Kim HJ, Kim MJ, Turner TL, Kim BS, Song KM, Yi SH, Lee MK. Pyrosequencing analysis of microbiota reveals that lactic acid bacteria are dominant in Korean flat fish fermented food, gajami-sikhae. Biosci Biotechnol Biochem 2014; 78:1611-8. [DOI: 10.1080/09168451.2014.921560] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
The gajami-sikhae, traditional Korean cuisine fermented with flat fish, samples were collected from eight different manufacturers (GS1–GS8). We employed pyrosequencing method to analyze the bacterial communities of the gajami-sikhae samples. Family- and genus-level analyses indicated that the bacterial community compositions of GS3 and GS6 were distinct from those of the rest. The species-level structures of bacterial communities of the gajami-sikhae samples except for GS3 and GS6 featured Lactobacillus sakei as the most abundant species. Leuconostoc mesenteroides was revealed as the most dominant species among the bacterial community of GS6 and the bacterial community of GS3 was composed of various lactic acid bacteria. We employed a culture-based method to isolate beneficial strains from the gajami-sikhae samples. However, most of the 47 selected colonies were identified as Bacillus subtilis and Bacillus amyloliquefaciens. This study indicated that gajami-sikhae was mainly composed of many beneficial lactic acid bacteria.
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Affiliation(s)
- Hyo Jin Kim
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam-Si, Republic of Korea
| | - Min-Jeong Kim
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam-Si, Republic of Korea
| | - Timothy Lee Turner
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bong-Soo Kim
- ChunLab, Inc., Seoul National University, Seoul, Republic of Korea
| | - Kyung-Mo Song
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam-Si, Republic of Korea
| | - Sung Hun Yi
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam-Si, Republic of Korea
| | - Myung-Ki Lee
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam-Si, Republic of Korea
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32
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Alvarez TM, Paiva JH, Ruiz DM, Cairo JPLF, Pereira IO, Paixão DAA, de Almeida RF, Tonoli CCC, Ruller R, Santos CR, Squina FM, Murakami MT. Structure and function of a novel cellulase 5 from sugarcane soil metagenome. PLoS One 2013; 8:e83635. [PMID: 24358302 PMCID: PMC3866126 DOI: 10.1371/journal.pone.0083635] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/04/2013] [Indexed: 11/26/2022] Open
Abstract
Cellulases play a key role in enzymatic routes for degradation of plant cell-wall polysaccharides into simple and economically-relevant sugars. However, their low performance on complex substrates and reduced stability under industrial conditions remain the main obstacle for the large-scale production of cellulose-derived products and biofuels. Thus, in this study a novel cellulase with unusual catalytic properties from sugarcane soil metagenome (CelE1) was isolated and characterized. The polypeptide deduced from the celE1 gene encodes a unique glycoside hydrolase domain belonging to GH5 family. The recombinant enzyme was active on both carboxymethyl cellulose and β-glucan with an endo-acting mode according to capillary electrophoretic analysis of cleavage products. CelE1 showed optimum hydrolytic activity at pH 7.0 and 50 °C with remarkable activity at alkaline conditions that is attractive for industrial applications in which conventional acidic cellulases are not suitable. Moreover, its three-dimensional structure was determined at 1.8 Å resolution that allowed the identification of an insertion of eight residues in the β8-α8 loop of the catalytic domain of CelE1, which is not conserved in its psychrophilic orthologs. This 8-residue-long segment is a prominent and distinguishing feature of thermotolerant cellulases 5 suggesting that it might be involved with thermal stability. Based on its unconventional characteristics, CelE1 could be potentially employed in biotechnological processes that require thermotolerant and alkaline cellulases.
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Affiliation(s)
- Thabata M Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Joice H Paiva
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Diego M Ruiz
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - João Paulo L F Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Isabela O Pereira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Douglas A A Paixão
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Rodrigo F de Almeida
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Celisa C C Tonoli
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Camila R Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Mario T Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
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