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da Silva AS, Adriani PP, de Oliveira GS, Rocha ARL, Perpétuo EA, Dias MVB, Chambergo FS. Biochemical characterization of an esterase from Thermobifida fusca YX with acetyl xylan esterase activity. Mol Biol Rep 2024; 51:767. [PMID: 38878205 DOI: 10.1007/s11033-024-09601-7] [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: 02/25/2024] [Accepted: 05/01/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Esterases (EC 3.1.1.X) are enzymes that catalyze the hydrolysis ester bonds. These enzymes have large potential for diverse applications in fine industries, particularly in pharmaceuticals, cosmetics, and bioethanol production. METHODS AND RESULTS In this study, a gene encoding an esterase from Thermobifida fusca YX (TfEst) was successfully cloned, and its product was overexpressed in Escherichia coli and purified using affinity chromatography. The TfEst kinetic assay revealed catalytic efficiencies of 0.58 s-1 mM-1, 1.09 s-1 mM-1, and 0.062 s-1 mM-1 against p-Nitrophenyl acetate, p-Nitrophenyl butyrate, and 1-naphthyl acetate substrates, respectively. Furthermore, TfEst also exhibited activity in a pH range from 6.0 to 10.0, with maximum activity at pH 8.0. The enzyme demonstrated a half-life of 20 min at 70 °C. Notably, TfEst displayed acetyl xylan esterase activity as evidenced by the acetylated xylan assay. The structural prediction of TfEst using AlphaFold indicated that has an α/β-hydrolase fold, which is consistent with other esterases. CONCLUSIONS The enzyme stability over a broad pH range and its activity at elevated temperatures make it an appealing candidate for industrial processes. Overall, TfEst emerges as a promising enzymatic tool with significant implications for the advancement of biotechnology and biofuels industries.
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Affiliation(s)
- Adriana S da Silva
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil
| | - Patricia P Adriani
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel S de Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Elen A Perpétuo
- Bio4Tec, Centro de Capacitação e Pesquisa em Meio Ambiente, CEPEMA-POLI-USP, Universidade de São Paulo, Cubatão, Brazil
- Institute of Marine Sciences (IMar), Federal University of Sao Paulo, Santos, Brazil
| | - Marcio V B Dias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe S Chambergo
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil.
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2
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Nazir A, Shad M, Rehman HM, Azim N, Sajjad M. Application of SUMO fusion technology for the enhancement of stability and activity of lysophospholipase from Pyrococcus abyssi. World J Microbiol Biotechnol 2024; 40:183. [PMID: 38722449 DOI: 10.1007/s11274-024-03998-w] [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: 02/11/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
Abstract
Heterologous production of proteins in Escherichia coli has raised several challenges including soluble production of target proteins, high levels of expression and purification. Fusion tags can serve as the important tools to overcome these challenges. SUMO (small ubiquitin-related modifier) is one of these tags whose fusion to native protein sequence can enhance its solubility and stability. In current research, a simple, efficient and cost-effective method is being discussed for the construction of pET28a-SUMO vector. In order to improve the stability and activity of lysophospholipase from Pyrococcus abyssi (Pa-LPL), a 6xHis-SUMO tag was fused to N-terminal of Pa-LPL by using pET28a-SUMO vector. Recombinant SUMO-fused enzyme (6 H-S-PaLPL) works optimally at 35 °C and pH 6.5 with remarkable thermostability at 35-95 °C. Thermo-inactivation kinetics of 6 H-S-PaLPL were also studied at 35-95 °C with first order rate constant (kIN) of 5.58 × 10- 2 h-1 and half-life of 12 ± 0 h at 95 °C. Km and Vmax for the hydrolysis of 4-nitrophenyl butyrate were calculated to be 2 ± 0.015 mM and 3882 ± 22.368 U/mg, respectively. 2.4-fold increase in Vmax of Pa-LPL was observed after fusion of 6xHis-SUMO tag to its N-terminal. It is the first report on the utilization of SUMO fusion tag to enhance the overall stability and activity of Pa-LPL. Fusion of 6xHis-SUMO tag not only aided in the purification process but also played a crucial role in increasing the thermostability and activity of the enzyme. SUMO-fused enzyme, thus generated, can serve as an important candidate for degumming of vegetable oils at industrial scale.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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3
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Nazir A, Shad M, Rashid N, Azim N, Sajjad M. Recombinant production and characterization of a metal ion-independent Lysophospholipase from a hyperthermophilic archaeon Pyrococcus abyssi DSM25543. Int J Biol Macromol 2024; 259:129345. [PMID: 38219941 DOI: 10.1016/j.ijbiomac.2024.129345] [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: 10/22/2023] [Revised: 12/13/2023] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
Genome sequence of Pyrococcus abyssi DSM25543 contains a coding sequence (PAB_RS01410) for α/β hydrolase (WP_010867387.1). Structural analysis revealed the presence of a consensus motif GXSXG and a highly conserved catalytic triad in the amino acid sequence of α/β hydrolase that were characteristic features of lysophospholipases. A putative lysophospholipase from P. abyssi with its potential applications in oil degumming and starch processing was heterologously produced in E. coli Rosetta (DE3) pLysS in soluble form followed by its purification and characterization. The recombinant enzyme was found to be active at temperature of 40-90 °C and pH 5.5-7.0. However, the enzyme exhibited its optimum activity at 65 °C and pH 6.5. None of the metal ions (Mn2+, Mg2+, Ni2+, Cu2+, Fe2+, Co2+, Zn2+ and Ca2+) being tested had stimulatory effect on lysophospholipase activity. Km and Vmax for hydrolysis of 4-nitrophenyl butyrate were calculated to be 1 ± 0.089 mM and 1637 ± 24.434 U/mg, respectively. It is the first report on the soluble production and characterization of recombinant lysophospholipase from P. abyssi which exhibits its lipolytic activity in the absence of divalent metal ions. Broad substrate specificity, activity and stability at elevated temperatures make recombinant lysophospholipase an ideal candidate for potential industrial applications.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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4
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Kim SH, Cho JY, Hwang JH, Kim HJ, Oh SJ, Kim HJ, Bhatia SK, Yun J, Lee SH, Yang YH. Revealing the key gene involved in bioplastic degradation from superior bioplastic degrader Bacillus sp. JY35. Int J Biol Macromol 2023:125298. [PMID: 37315675 DOI: 10.1016/j.ijbiomac.2023.125298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
The use of bioplastics, which can alleviate environmental pollution caused by non-degradable bioplastics, has received attention. As there are many types of bioplastics, method that can treat them simultaneously is important. Therefore, Bacillus sp. JY35 which can degrade different types of bioplastics, was screened in previous study. Most types of bioplastics, such as polyhydroxybutyrate (PHB), (P(3HB-co-4HB)), poly(butylene adipate-co-terephthalate) (PBAT), polybutylene succinate (PBS), and polycaprolactone (PCL), can be degraded by esterase family enzymes. To identify the genes that are involved in bioplastic degradation, analysis with whole-genome sequencing was performed. Among the many esterase enzymes, three carboxylesterase and one triacylglycerol lipase were identified and selected based on previous studies. Esterase activity using p-nitrophenyl substrates was measured, and the supernatant of JY35_02679 showed strong emulsion clarification activity compared with others. In addition, when recombinant E. coli was applied to the clear zone test, only the JY35_02679 gene showed activity in the clear zone test with bioplastic containing solid cultures. Further quantitative analysis showed 100 % PCL degradation at 7 days and 45.7 % PBS degradation at 10 days. We identified a gene encoding a bioplastic-degrading enzyme in Bacillus sp. JY35 and successfully expressed the gene in heterologous E. coli, which secreted esterases with broad specificity.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jang Yeon Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyun Joong Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, Republic of Korea
| | - Jeonghee Yun
- Department of Forest Products and Biotechnology, Kookmin University, Seoul, Republic of Korea
| | - Sang-Ho Lee
- Department of Pharmacy, College of Pharmacy, Jeju National University, Jeju-si, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, Republic of Korea.
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Sartaj K, Patel A, Matsakas L, Prasad R. Unravelling Metagenomics Approach for Microbial Biofuel Production. Genes (Basel) 2022; 13:1942. [PMID: 36360179 PMCID: PMC9689425 DOI: 10.3390/genes13111942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
Renewable biofuels, such as biodiesel, bioethanol, and biobutanol, serve as long-term solutions to fossil fuel depletion. A sustainable approach feedstock for their production is plant biomass, which is degraded to sugars with the aid of microbes-derived enzymes, followed by microbial conversion of those sugars to biofuels. Considering their global demand, additional efforts have been made for their large-scale production, which is ultimately leading breakthrough research in biomass energy. Metagenomics is a powerful tool allowing for functional gene analysis and new enzyme discovery. Thus, the present article summarizes the revolutionary advances of metagenomics in the biofuel industry and enlightens the importance of unexplored habitats for novel gene or enzyme mining. Moreover, it also accentuates metagenomics potentials to explore uncultivable microbiomes as well as enzymes associated with them.
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Affiliation(s)
- Km Sartaj
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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Nagaroor V, Gummadi SN. An overview of mammalian and microbial hormone-sensitive lipases (lipolytic family IV): biochemical properties and industrial applications. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36154870 DOI: 10.1080/02648725.2022.2127071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/13/2022] [Indexed: 11/02/2022]
Abstract
In mammals, hormone-sensitive lipase (EC 3.1.1.79) is an intracellular lipase that significantly regulates lipid metabolism. Mammalian HSL is more active towards diacylglycerol but lacks a lid covering the active site. Dyslipidemia, hepatic steatosis, cancer, and cancer-associated cachexia are symptoms of HSL pathophysiology. Certain microbial proteins show a sequence homologous to the catalytic domain of mammalian HSL, hence called microbial HSL. They possess a funnel-shaped substrate-binding pocket and restricted length of acyl chain esters, thus known as esterases. These enzymes have broad substrate specificities and are capable of stereo, regio, and enantioselective, making them attractive biocatalysts in a wide range of industrial applications in the production of flavors, pharmaceuticals, biosensors, and fine chemicals. This review will provide insight into mammalian and microbial HSLs, their sources, structural features related to substrate specificity, thermal stability, and their applications.
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Affiliation(s)
- Vijayalakshmi Nagaroor
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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7
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Evaluation of temperature, pH and nutrient conditions in bacterial growth and extracellular hydrolytic activities of two Alicyclobacillus spp. strains. Arch Microbiol 2021; 203:4557-4570. [PMID: 34159433 DOI: 10.1007/s00203-021-02332-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 12/16/2022]
Abstract
Extremophile bacteria have developed the metabolic machinery for living in extreme temperatures, pH, and high-salt content. Two novel bacterium strains Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2, were isolated from crater lake El Chichon in Chiapas, Mexico. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2 were closely related to Alicyclobacillus species (98% identity and 94.73% identity, respectively). Both strains were Gram variable, and colonies were circular, smooth and creamy. Electron microscopy showed than Alicyclobacillus sp. PA1 has a daisy-like form and Alicyclobacillus sp. PA2 is a regular rod. Both strains can use diverse carbohydrates and triglycerides as carbon source and they also can use organic and inorganic nitrogen source. But, the two strains can grow without any carbon or nitrogen sources in the culture medium. Temperature, pH and nutrition condition affect bacterial growth. Maximum growth was produced at 65 °C for Alicyclobacillus sp. PA1 (0.732 DO600) at pH 3 and Alicyclobacillus sp. PA2 (0.725 DO600) at pH 5. Inducible extracellular extremozyme activities were determined for β-galactosidase (Alicyclobacillus sp. PA1: 88.07 ± 0.252 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), cellulose (Alicyclobacillus sp. PA1: 141.20 ± 0.585 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), lipase (Alicyclobacillus sp. PA1: 138.25 ± 0.600 U/mg, Alicyclobacillus sp. PA2: 175.75 ± 1.387 U/mg), xylanase (Alicyclobacillus sp. PA1: 174.72 ± 1.746 U/mg, Alicyclobacillus sp. PA2: 172.69 ± 0.855U/mg), and protease (Alicyclobacillus sp. PA1: 15.12 ± 0.121 U/mg, Alicyclobacillus sp. PA2: 15.33 ± 0.284 U/mg). These results provide new insights on extreme enzymatic production on Alicyclobacillus species.
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Friends or Foes-Microbial Interactions in Nature. BIOLOGY 2021; 10:biology10060496. [PMID: 34199553 PMCID: PMC8229319 DOI: 10.3390/biology10060496] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability. Abstract Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.
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Verma S, Meghwanshi GK, Kumar R. Current perspectives for microbial lipases from extremophiles and metagenomics. Biochimie 2021; 182:23-36. [PMID: 33421499 DOI: 10.1016/j.biochi.2020.12.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/21/2020] [Accepted: 12/31/2020] [Indexed: 01/21/2023]
Abstract
Microbial lipases are most broadly used biocatalysts for environmental and industrial applications. Lipases catalyze the hydrolysis and synthesis of long acyl chain esters and have a characteristic folding pattern of α/β hydrolase with highly conserved catalytic triad (Serine, Aspartic/Glutamic acid and Histidine). Mesophilic lipases (optimal activity in neutral pH range, mesophilic temperature range, atmospheric pressure, normal salinity, non-radio-resistant, and instability in organic solvents) have been in use for many industrial biotransformation reactions. However, lipases from extremophiles can be used to design biotransformation reactions with higher yields, less byproducts or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. The extremophile lipase perform activity at extremes of temperature, pH, salinity, and pressure which can be screened from metagenome and de novo lipase design using computational approaches. Despite structural similarity, they exhibit great diversity at the sequence level. This diversity is broader when lipases from the bacterial, archaeal, plant, and animal domains/kingdoms are compared. Furthermore, a great diversity of novel lipases exists and can be discovered from the analysis of the dark matter - the unexplored nucleotide/metagenomic databases. This review is an update on extremophilic microbial lipases, their diversity, structure, and classification. An overview on novel lipases which have been detected through analysis of the genomic dark matter (metagenome) has also been presented.
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Affiliation(s)
- Swati Verma
- Department of Microbiology, Maharaja Ganga Singh University, Bikaner, 334004, India
| | | | - Rajender Kumar
- Department of Clinical Microbiology, Umeå University, SE-90185, Umeå, Sweden.
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Dou Z, Xu G, Ni Y. A novel carboxylesterase from Acinetobacter sp. JNU9335 for efficient biosynthesis of Edoxaban precursor with high substrate to catalyst ratio. BIORESOURCE TECHNOLOGY 2020; 317:123984. [PMID: 32827974 DOI: 10.1016/j.biortech.2020.123984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
A novel carboxylesterase AcEst1 was identified from Acinetobacter sp. JNU9335 with high efficiency in the biosynthesis of chiral precursor of Edoxaban through kinetic resolution of methyl 3-cyclohexene-1-carboxylate (CHCM). Sequence analysis revealed AcEst1 belongs to family IV of esterolytic enzymes and exhibits <40% identities with known carboxylesterases. The optimum pH and temperature of recombinant AcEst1 are 8.0 and 40 °C. Substrate spectrum analysis indicated that AcEst1 prefers substrates with short acyl and alcohol groups. AcEst1 was highly active in the hydrolysis of CHCM with kcat of 1153 s-1 and displayed high substrate tolerance. As much as 2.0 M (280 g·L-1) CHCM could be enantioselectively hydrolyzed into (S)-CHCM by merely 0.08 g·L-1AcEst1 with ees of >99% (S) and substrate to catalyst ratio (S/C) of 3500 g·g-1. These results indicate that the novel AcEst1 is a promising biocatalyst in the synthesis of chiral carboxylic acids.
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Affiliation(s)
- Zhe Dou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
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Characterization of XtjR8: A novel esterase with phthalate-hydrolyzing activity from a metagenomic library of lotus pond sludge. Int J Biol Macromol 2020; 164:1510-1518. [DOI: 10.1016/j.ijbiomac.2020.07.317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 11/21/2022]
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12
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Kirubakaran R, ArulJothi KN, Revathi S, Shameem N, Parray JA. Emerging priorities for microbial metagenome research. BIORESOURCE TECHNOLOGY REPORTS 2020; 11:100485. [PMID: 32835181 PMCID: PMC7319936 DOI: 10.1016/j.biteb.2020.100485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.
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Affiliation(s)
| | - K N ArulJothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, India
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | | | - Nowsheen Shameem
- Department of Environmental Science, Cluster University Srinagar, J&K, India
| | - Javid A Parray
- Department of Environmental Science, Govt SAM Degree College Budgam, J&K, India
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Krüger A, Schäfers C, Busch P, Antranikian G. Digitalization in microbiology - Paving the path to sustainable circular bioeconomy. N Biotechnol 2020; 59:88-96. [PMID: 32750680 DOI: 10.1016/j.nbt.2020.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022]
Abstract
The transition to a sustainable bio-based circular economy requires cutting edge technologies that ensure economic growth with environmentally responsible action. This transition will only be feasible when the opportunities of digitalization are also exploited. Digital methods and big data handling have already found their way into life sciences and generally offer huge potential in various research areas. While computational analyses of microbial metagenome data have become state of the art, the true potential of bioinformatics remains mostly untapped so far. In this article we present challenges and opportunities of digitalization including multi-omics approaches in discovering and exploiting the microbial diversity of the planet with the aim to identify robust biocatalysts for application in sustainable bioprocesses as part of the transition from a fossil-based to a bio-based circular economy. This will contribute to solving global challenges, including utilization of natural resources, food supply, health, energy and the environment.
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Affiliation(s)
- Anna Krüger
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Christian Schäfers
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Philip Busch
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
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Rade LL, da Silva MNP, Vieira PS, Milan N, de Souza CM, de Melo RR, Klein BC, Bonomi A, de Castro HF, Murakami MT, Zanphorlin LM. A Novel Fungal Lipase With Methanol Tolerance and Preference for Macaw Palm Oil. Front Bioeng Biotechnol 2020; 8:304. [PMID: 32435636 PMCID: PMC7218172 DOI: 10.3389/fbioe.2020.00304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/20/2020] [Indexed: 11/18/2022] Open
Abstract
Macaw palm is a highly oil-producing plant, which presents high contents of free fatty acids, being a promising feedstock for biofuel production. The current chemical routes are costly and complex, involving highly harsh industrial conditions. Enzymatic processing is a potential alternative; however, it is hampered by the scarce knowledge on biocatalysts adapted to this acidic feedstock. This work describes a novel lipase isolated from the thermophilic fungus Rasamsonia emersonii (ReLip), which tolerates extreme conditions such as the presence of methanol, high temperatures, and acidic medium. Among the tested feedstocks, the enzyme showed the highest preference for macaw palm oil, producing a hydrolyzate with a final free fatty acid content of 92%. Crystallographic studies revealed a closed conformation of the helical amphipathic lid that typically undergoes conformational changes in a mechanism of interfacial activation. Such conformation of the lid is stabilized by a salt bridge, not observed in other structurally characterized homologs, which is likely involved in the tolerance to organic solvents. Moreover, the lack of conservation of the aromatic cluster IxxWxxxxxF in the lid of ReLip with the natural mutation of the phenylalanine by an alanine might be correlated with the preference of short acyl chains, although preserving catalytic activity on insoluble substrates. In addition, the presence of five acidic amino acids in the lid of ReLip, a rare property reported in other lipases, may have contributed to its ability to tolerate and be effective in acidic environments. Therefore, our work describes a new fungal biocatalyst capable of efficiently hydrolyzing macaw oil, an attractive feedstock for the production of "drop-in" biofuels, with high desirable feature for industrial conditions such as thermal and methanol tolerance, and optimum acidic pH. Moreover, the crystallographic structure was elucidated, providing a structural basis for the enzyme substrate preference and tolerance to organic solvents.
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Affiliation(s)
- Letícia L. Rade
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Melque N. P. da Silva
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Plínio S. Vieira
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Natalia Milan
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Department of Chemical Engineering, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Claudia M. de Souza
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Ricardo R. de Melo
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Bruno C. Klein
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Antonio Bonomi
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Heizir F. de Castro
- Department of Chemical Engineering, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Mário T. Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Leticia M. Zanphorlin
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
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15
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Won SJ, Jeong HB, Kim HK. Characterization of Novel Salt-Tolerant Esterase Isolated from the Marine Bacterium Alteromonas sp. 39-G1. J Microbiol Biotechnol 2020; 30:216-225. [PMID: 31838795 PMCID: PMC9728341 DOI: 10.4014/jmb.1907.07057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An esterase gene, estA1, was cloned from Alteromonas sp. 39-G1 isolated from the Beaufort Sea. The gene is composed of 1,140 nucleotides and codes for a 41,190 Da protein containing 379 amino acids. As a result of a BLAST search, the protein sequence of esterase EstA1 was found to be identical to Alteromonas sp. esterase (GenBank: PHS53692). As far as we know, no research on this enzyme has yet been conducted. Phylogenetic analysis showed that esterase EstA1 was a member of the bacterial lipolytic enzyme family IV (hormone sensitive lipases). Two deletion mutants (Δ20 and Δ54) of the esterase EstA1 were produced in Escherichia coli BL21 (DE3) cells with part of the N-terminal of the protein removed and His-tag attached to the C-terminal. These enzymes exhibited the highest activity toward p-nitrophenyl (pNP) acetate (C2) and had little or no activity towards pNP-esters with acyl chains longer than C6. Their optimum temperature and pH of the catalytic activity were 45°C and pH 8.0, respectively. As the NaCl concentration increased, their enzyme activities continued to increase and the highest enzyme activities were measured in 5 M NaCl. These enzymes were found to be stable for up to 8 h in the concentration of 3-5 M NaCl. Moreover, they have been found to be stable for various metal ions, detergents and organic solvents. These salt-tolerant and chemical-resistant properties suggest that the enzyme esterase EstA1 is both academically and industrially useful.
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Affiliation(s)
- Seok-Jae Won
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Han Byeol Jeong
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Hyung-Kwoun Kim
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea,Corresponding author Phone: +82-2-2164-4890 Fax: +82-2-2164-4865 E-mail:
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16
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Park JM, Kang CH, Won SM, Oh KH, Yoon JH. Characterization of a Novel Moderately Thermophilic Solvent-Tolerant Esterase Isolated From a Compost Metagenome Library. Front Microbiol 2020; 10:3069. [PMID: 32038535 PMCID: PMC6993047 DOI: 10.3389/fmicb.2019.03069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
A novel esterase, EstCS1, was isolated from a compost metagenomics library. The EstCS1 protein, which consists of 309 amino acid residues with an anticipated molecular mass of 34 kDa, showed high amino acid sequence identities to predicted esterases and alpha/beta hydrolases (59%) from some cultured bacteria and to predicted lipases/esterases from uncultured bacteria. The phylogenetic analysis suggested that the EstCS1 belongs to the hormone-sensitive lipase family of lipolytic enzyme classification and contains a catalytic triad including Ser155–Asp255–His285. The Ser155 residue of the catalytic triad in the EstCS1 was located in the consensus active-site motif, GXSXG. Besides, a conserved HGGG motif placed in an oxyanion hole of the hormone-sensitive lipase family was discovered, too. The EstCS1 demonstrated the highest activity toward p-nitrophenyl propionate (C3) and caproate (C6) and was normally stable up to 60°C with optimal activity at 50°C. In addition, an optimal activity was observed at pH 8, and the EstCS1 possessed its stability within the pH range between 5 and 10. Interestingly, EstCS1 had an outstanding stability in up to 30% (v/v) organic solvents and activity over 50% in the presence of 50% (v/v) acetone, ethanol, dimethyl sulfoxide (DMSO), and N,N-dimethylformamide. The EstCS1 hydrolyzed sterically hindered tertiary alcohol esters of t-butyl acetate and linalyl acetate. Considering the properties, such as the moderate thermostability, stability against organic solvents, and activity toward esters of tertiary alcohols, the EstCS1 will be worthwhile to be used for organic synthesis and related industrial applications.
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Affiliation(s)
- Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Chul-Hyung Kang
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, South Korea.,Green Chemistry and Environmental Biotechnology Program, School of Science, University of Science and Technology, Daejeon, South Korea
| | - Sung-Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Ki-Hoon Oh
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, South Korea
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17
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Xu X, Wang J, Yu T, Nian H, Zhang H, Wang G, Li F. Characterization of a novel aryloxyphenoxypropionate herbicide-hydrolyzing carboxylesterase with R-enantiomer preference from Brevundimonas sp. QPT-2. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives. Mol Biotechnol 2019; 61:579-601. [DOI: 10.1007/s12033-019-00187-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Characterization of esterase activity from an Acetomicrobium hydrogeniformans enzyme with high structural stability in extreme conditions. Extremophiles 2018; 22:781-793. [DOI: 10.1007/s00792-018-1038-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 01/06/2023]
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20
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Lee MH, Khan R, Tao W, Choi K, Lee SY, Lee JW, Hwang EC, Lee SW. Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum. J Biotechnol 2018; 270:30-38. [PMID: 29407418 DOI: 10.1016/j.jbiotec.2018.01.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
Abstract
Autoinducers are indispensable for bacterial cell-cell communication. However, due to the reliance on culture-based techniques, few autoinducer-hydrolyzing enzymes are known. In this study, we characterized soil metagenome-derived unique enzymes capable of hydrolyzing 3-hydroxypalmitic acid methyl ester (3-OH PAME), an autoinducer of the plant pathogenic bacterium Ralstonia solanacearum. Among 146 candidate lipolytic clones from a soil metagenome library, 4 unique enzymes capable of hydrolyzing the autoinducer 3-OH PAME, termed ELP86, ELP96, ELP104, and EstDL33, were selected and characterized. Phylogenetic analysis revealed that metagenomic enzymes were novel esterase/lipase candidates as they clustered as novel subfamilies of family I, V, X, and family XI. The purified enzymes displayed various levels of hydrolytic activities towards 3-OH PAME with optimum activity at 40-50 °C and pH 7-10. Interestingly, ELP104 also displayed N-(3-oxohexanoyl)-L-homoserine lactone hydrolysis activity. Heterologous expression of the gene encoding 3-OH PAME hydrolase in R. solanacearum significantly decreased exopolysaccharide production without affecting bacterial growth. mRNA transcription analysis revealed that genes regulated by quorum-sensing, such as phcA and xpsR, were significantly down-regulated in the stationary growth phase of R. solanacearum. Therefore, metagenomic enzymes are capable of quorum-quenching by hydrolyzing the autoinducer 3-OH PAME, which could be used as a biocontrol strategy against bacterial wilt.
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Affiliation(s)
- Myung Hwan Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Wuhan University, Wuhan, 430072, China
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Jae Wook Lee
- Department of Chemistry, Dong-A University, Busan 49315, Republic of Korea
| | - Eul Chul Hwang
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea.
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21
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Boddu RS, Divakar K. Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry. Microb Biotechnol 2018. [DOI: 10.1007/978-981-10-7140-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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22
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Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting. Appl Biochem Biotechnol 2017; 183:636-651. [PMID: 28815469 DOI: 10.1007/s12010-017-2568-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/24/2017] [Indexed: 01/05/2023]
Abstract
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body and ocean water. This review article describes the state-of-the-art techniques and tools in metagenomics and discusses the potential of metagenomic approaches for the bioprospecting of industrial enzymes from various environmental samples. We also describe the unusual novel enzymes discovered via metagenomic approaches and discuss the future prospects for metagenome technologies.
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23
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Tang L, Xia Y, Wu X, Chen X, Zhang X, Li H. Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil. Gene 2017; 625:64-71. [DOI: 10.1016/j.gene.2017.04.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
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24
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Identification of lipolytic enzymes isolated from bacteria indigenous to Eucalyptus wood species for application in the pulping industry. ACTA ACUST UNITED AC 2017; 15:114-124. [PMID: 28794998 PMCID: PMC5545822 DOI: 10.1016/j.btre.2017.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/21/2017] [Accepted: 07/11/2017] [Indexed: 11/20/2022]
Abstract
Phenol red screening plates is the best method for detecting lipolytic activity. Substrate specificity is affected by temperature and pH. Essential to test substrates at various pH and temperature to determine optima. Lipolytic enzymes indigenous to Eucalyptus sp. can assist in pitch control.
This study highlights the importance of determining substrate specificity at variable experimental conditions. Lipases and esterases were isolated from microorganisms cultivated from Eucalyptus wood species and then concentrated (cellulases removed) and characterized. Phenol red agar plates supplemented with 1% olive oil or tributyrin was ascertained to be the most favourable method of screening for lipolytic activity. Lipolytic activity of the various enzymes were highest at 45–61 U/ml at the optimum temperature and pH of between at 30–35 °C and pH 4–5, respectively. Change in pH influenced the substrate specificity of the enzymes tested. The majority of enzymes tested displayed a propensity for longer aliphatic acyl chains such as dodecanoate (C12), myristate (C14), palmitate (C16) and stearate (C18) indicating that they could be characterised as potential lipases. Prospective esterases were also detected with specificity towards acetate (C2), butyrate (C4) and valerate (C5). Enzymes maintained up to 95% activity at the optimal pH and temperature for 2–3 h. It is essential to test substrates at various pH and temperature when determining optimum activity of lipolytic enzymes, a method rarely employed. The stability of the enzymes at acidic pH and moderate temperatures makes them excellent candidates for application in the treatment of pitch during acid bi-sulphite pulping, which would greatly benefit the pulp and paper industry.
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25
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Khan M, Sathya TA. Extremozymes from metagenome: Potential applications in food processing. Crit Rev Food Sci Nutr 2017; 58:2017-2025. [PMID: 28605203 DOI: 10.1080/10408398.2017.1296408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The long-established use of enzymes for food processing and product formulation has resulted in an increased enzyme market compounding to 7.0% annual growth rate. Advancements in molecular biology and recognition that enzymes with specific properties have application for industrial production of infant, baby and functional foods boosted research toward sourcing the genes of microorganisms for enzymes with distinctive properties. In this regard, functional metagenomics for extremozymes has gained attention on the premise that such enzymes can catalyze specific reactions. Hence, metagenomics that can isolate functional genes of unculturable extremophilic microorganisms has expanded attention as a promising tool. Developments in this field of research in relation to food sector are reviewed.
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Affiliation(s)
- Mahejibin Khan
- a CSIR-Central Food Technological Research Institute-Resource Centre Lucknow , India.,c Academy of Scientific and Innovative Research , New Delhi , India
| | - T A Sathya
- b CSIR-Central Food Technological Research Institute , Mysore , India.,c Academy of Scientific and Innovative Research , New Delhi , India
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26
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Zhang H, Li M, Li J, Wang G, Li F, Xu D, Liu Y, Xiong M. A key esterase required for the mineralization of quizalofop-p-ethyl by a natural consortium of Rhodococcus sp. JT-3 and Brevundimonas sp. JT-9. JOURNAL OF HAZARDOUS MATERIALS 2017; 327:1-10. [PMID: 28027504 DOI: 10.1016/j.jhazmat.2016.12.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
A natural consortium, named L1, of Rhodococcus sp. JT-3 and Brevundimonas sp. JT-9 was obtained from quizalofop-p-ethyl (QE) polluted soil. The consortium was able to use QE as a sole carbon source for growth and degraded 100mgL-1 of QE in 60h. Strain JT-3 initiated the catabolism of QE to quizalofop acid (QA), which was used by strain JT-9 as carbon source for growth and to simultaneously feed strain JT-3. A novel esterase EstS-JT, which was responsible for the transformation of QE to QA and essential for the mineralization of QE by the consortium, was cloned from strain JT-3. EstS-JT showed low amino acid identity to other reported esterases from esterase family VIII and represents a new member of this family. The deduced amino acid sequence contained the esterase family VIII conserved motifs S-X-X-K, YSV and WAG. The purified recombinant EstS-JT displayed maximal esterase activity at 35°C and pH 7.5. An inhibitor assay, site-directed mutagenesis and 3D modeling analysis revealed that S64, K67 and Y175 were essential for catalysis and probably comprised the catalytic center of EstS-JT. Additionally, EstS-JT had broad substrate specificity and was capable of hydrolyzing p-nitrophenyl esters (C2-C8) and various AOPP herbicides.
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Affiliation(s)
- Hui Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
| | - Mengya Li
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
| | - Jie Li
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
| | - Guangli Wang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Feng Li
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
| | - Dayong Xu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
| | - Yuan Liu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
| | - Minghua Xiong
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
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27
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Pereira MR, Maester TC, Mercaldi GF, de Macedo Lemos EG, Hyvönen M, Balan A. From a metagenomic source to a high-resolution structure of a novel alkaline esterase. Appl Microbiol Biotechnol 2017; 101:4935-4949. [PMID: 28331945 DOI: 10.1007/s00253-017-8226-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 02/27/2017] [Accepted: 03/05/2017] [Indexed: 10/19/2022]
Abstract
Esterases catalyze the cleavage and formation of ester bonds and are members of the diverse family of α/β hydrolase fold. They are useful in industries from different sectors, such as food, detergent, fine chemicals, and biofuel production. In a previous work, 30 positive clones for lipolytic activity were identified from a metagenomic library of a microbial consortium specialized in diesel oil degradation. In this study, a putative gene encoding an esterase/lipase, denominated est8, has been cloned and the corresponding protein expressed recombinantly, purified to homogeneity and characterized functional and structurally. We show that the protein codified by est8 gene, denominated Est8, is an alkaline esterase with high catalytic efficiency against p-nitrophenyl acetate and stable in the presence of up to 10% dimethyl sulfoxide. The three-dimensional structure of Est8 was determined at 1.85-Ǻ resolution, allowing the characterization of the substrate-binding pocket and features that rationalize the preference of Est8 for short-chain substrates. In an attempt to increase the size of ligand-binding pocket and enzyme activity against distinct substrates of long chain, we mutated two residues (Met213 and Phe217) that block the substrate channel. A small increase in the reaction velocity for p-nitrophenyl butyrate and p-nitrophenyl valerate hydrolysis was observed. Activity against p-nitrophenyl acetate was reduced. The functional and structural characterization of Est8 is explored in comparison with orthologues.
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Affiliation(s)
- Mariana Rangel Pereira
- National Laboratory of Biosciences (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo State, Brazil.,University of São Paulo (USP), São Paulo, São Paulo State, Brazil.,Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State, Brazil
| | - Thaís Carvalho Maester
- University of São Paulo (USP), São Paulo, São Paulo State, Brazil.,Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State, Brazil
| | - Gustavo Fernando Mercaldi
- National Laboratory of Biosciences (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo State, Brazil.,Institute of Biology, University of Campinas, Campinas, São Paulo State, Brazil
| | | | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Balan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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28
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A novel, versatile family IV carboxylesterase exhibits high stability and activity in a broad pH spectrum. Biotechnol Lett 2017; 39:577-587. [DOI: 10.1007/s10529-016-2282-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
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29
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Hong DK, Jang SH, Lee C. Gene cloning and characterization of a psychrophilic phthalate esterase with organic solvent tolerance from an Arctic bacterium Sphingomonas glacialis PAMC 26605. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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DeCastro ME, Rodríguez-Belmonte E, González-Siso MI. Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. Front Microbiol 2016; 7:1521. [PMID: 27729905 PMCID: PMC5037290 DOI: 10.3389/fmicb.2016.01521] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/12/2016] [Indexed: 11/24/2022] Open
Abstract
Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.
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Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
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31
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Liu J, Jia Z, Li S, Li Y, You Q, Zhang C, Zheng X, Xiong G, Zhao J, Qi C, Yang J. Identification and characterization of a chitin deacetylase from a metagenomic library of deep-sea sediments of the Arctic Ocean. Gene 2016; 590:79-84. [DOI: 10.1016/j.gene.2016.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/11/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
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32
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Truongvan N, Jang SH, Lee C. Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK. Biochemistry 2016; 55:3542-9. [DOI: 10.1021/acs.biochem.6b00177] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ngoc Truongvan
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - Sei-Heon Jang
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - ChangWoo Lee
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
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Guo H, Zhang Y, Shao Y, Chen W, Chen F, Li M. Cloning, expression and characterization of a novel cold-active and organic solvent-tolerant esterase from Monascus ruber M7. Extremophiles 2016; 20:451-9. [DOI: 10.1007/s00792-016-0835-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 05/15/2016] [Indexed: 01/27/2023]
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Petrovskaya LE, Novototskaya-Vlasova KA, Spirina EV, Durdenko EV, Lomakina GY, Zavialova MG, Nikolaev EN, Rivkina EM. Expression and characterization of a new esterase with GCSAG motif from a permafrost metagenomic library. FEMS Microbiol Ecol 2016; 92:fiw046. [PMID: 26929439 DOI: 10.1093/femsec/fiw046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2016] [Indexed: 11/14/2022] Open
Abstract
As a result of construction and screening of a metagenomic library prepared from a permafrost-derived microcosm, we have isolated a novel gene coding for a putative lipolytic enzyme that belongs to the hormone-sensitive lipase family. It encodes a polypeptide of 343 amino acid residues whose amino acid sequence displays maximum likelihood with uncharacterized proteins from Sphingomonas species. A putative catalytic serine residue of PMGL2 resides in a new variant of a recently discovered GTSAG sequence in which a Thr residue is replaced by a Cys residue (GCSAG). The recombinant PMGL2 was produced in Escherichia coli cells and purified by Ni-affinity chromatography. The resulting protein preferably utilizes short-chain p-nitrophenyl esters (C4 and C8) and therefore is an esterase. It possesses maximum activity at 45°C in slightly alkaline conditions and has limited thermostability at higher temperatures. Activity of PMGL2 is stimulated in the presence of 0.25-1.5 M NaCl indicating the good salt tolerance of the new enzyme. Mass spectrometric analysis demonstrated that N-terminal methionine in PMGL2 is processed and cysteine residues do not form a disulfide bond. The results of the study demonstrate the significance of the permafrost environment as a unique genetic reservoir and its potential for metagenomic exploration.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997, Moscow, Russia
| | - Ksenia A Novototskaya-Vlasova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya str., 2, 142290, Pushchino, Moscow Region, Russia
| | - Elena V Spirina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya str., 2, 142290, Pushchino, Moscow Region, Russia
| | - Ekaterina V Durdenko
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya str., 2, 142290, Pushchino, Moscow Region, Russia
| | - Galina Yu Lomakina
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory, 1/3, 119991, Moscow, Russia
| | - Maria G Zavialova
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121, Moscow, Russia
| | - Evgeny N Nikolaev
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121, Moscow, Russia Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
| | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya str., 2, 142290, Pushchino, Moscow Region, Russia
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Mirete S, Morgante V, González-Pastor JE. Functional metagenomics of extreme environments. Curr Opin Biotechnol 2016; 38:143-9. [PMID: 26901403 DOI: 10.1016/j.copbio.2016.01.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 10/22/2022]
Abstract
The bioprospecting of enzymes that operate under extreme conditions is of particular interest for many biotechnological and industrial processes. Nevertheless, there is a considerable limitation to retrieve novel enzymes as only a small fraction of microorganisms derived from extreme environments can be cultured under standard laboratory conditions. Functional metagenomics has the advantage of not requiring the cultivation of microorganisms or previous sequence information to known genes, thus representing a valuable approach for mining enzymes with new features. In this review, we summarize studies showing how functional metagenomics was employed to retrieve genes encoding for proteins involved not only in molecular adaptation and resistance to extreme environmental conditions but also in other enzymatic activities of biotechnological interest.
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Affiliation(s)
- Salvador Mirete
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Verónica Morgante
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - José Eduardo González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain.
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Gao W, Wu K, Chen L, Fan H, Zhao Z, Gao B, Wang H, Wei D. A novel esterase from a marine mud metagenomic library for biocatalytic synthesis of short-chain flavor esters. Microb Cell Fact 2016; 15:41. [PMID: 26892801 PMCID: PMC4758151 DOI: 10.1186/s12934-016-0435-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
Background Marine mud is an abundant and largely unexplored source of enzymes with unique properties that may be useful for industrial and biotechnological purposes. However, since most microbes cannot be cultured in the laboratory, a cultivation-independent metagenomic approach would be advantageous for the identification of novel enzymes. Therefore, with the objective of screening novel lipolytic enzymes, a metagenomic library was constructed using the total genomic DNA extracted from marine mud. Results Based on functional heterologous expression, 34 clones that showed lipolytic activity were isolated. The five clones with the largest halos were identified, and the corresponding genes were successfully overexpressed in Escherichia coli. Molecular analysis revealed that these encoded proteins showed 48–79 % similarity with other proteins in the GenBank database. Multiple sequence alignment and phylogenetic tree analysis classified these five protein sequences as new members of known families of bacterial lipolytic enzymes. Among them, EST4, which has 316 amino acids with a predicted molecular weight of 33.8 kDa, was further studied in detail due to its strong hydrolytic activity. Characterization of EST4 indicated that it is an alkaline esterase that exhibits highest hydrolytic activity towards p-nitrophenyl butyrate (specific activity: 1389 U mg−1) at 45 °C and pH 8.0. The half-life of EST4 is 55 and 46 h at 40 and 45 °C, respectively, indicating a relatively high thermostability. EST4 also showed remarkable stability in organic solvents, retaining 90 % of its initial activity when incubated for 12 h in the presence of hydrophobic alkanes. Furthermore, EST4 was used as an efficient whole-cell biocatalyst for the synthesis of short-chain flavor esters, showing high conversion rate and good tolerance for high substrate concentrations (up to 3.0 M). These results demonstrate a promising potential for industrial scaling-up to produce short-chain flavor esters at high substrate concentrations in non-aqueous media. Conclusions This manuscript reports unprecedented alcohol tolerance and conversion of an esterase biocatalyst identified from a marine mud metagenomic library. The high organic solvent tolerance and thermostability of EST4 suggest that it has great potential as a biocatalyst. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0435-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenyuan Gao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Kai Wu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Lifeng Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Haiyang Fan
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Zhiqiang Zhao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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Conserved tyrosine 182 residue in hyperthermophilic esterase EstE1 plays a critical role in stabilizing the active site. Extremophiles 2016; 20:187-93. [DOI: 10.1007/s00792-016-0812-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/15/2016] [Indexed: 12/12/2022]
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38
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Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics. Appl Microbiol Biotechnol 2016; 100:4435-46. [PMID: 26758295 DOI: 10.1007/s00253-015-7254-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 09/13/2015] [Accepted: 12/12/2015] [Indexed: 02/06/2023]
Abstract
Cutinases are esterases of industrial importance for applications in recycling and surface modification of polyesters. The cutinase from Thielavia terrestris (TtC) is distinct in terms of its ability to retain its stability and activity in acidic pH. Stability and activity in acidic pHs are desirable for esterases as the pH of the reaction tends to go down with the generation of acid. The pH stability and activity are governed by the charged state of the residues involved in catalysis or in substrate binding. In this study, we performed the detailed structural and biochemical characterization of TtC coupled with surface charge analysis to understand its acidic tolerance. The stability of TtC in acidic pH was rationalized by evaluating the contribution of charge interactions to the Gibbs free energy of unfolding at varying pHs. The activity of TtC was found to be limited by substrate binding affinity, which is a function of the surface charge. Additionally, the presence of glycosylation affects the biochemical characteristics of TtC owing to steric interactions with residues involved in substrate binding.
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de Barros M, Celligoi MAPC, Macedo GA. Kinetics of Denaturation and Effects of Surfactants and Polyethylene Glycol on Soybean Esterase (Glycine max L) Stability. J AM OIL CHEM SOC 2015. [DOI: 10.1007/s11746-015-2755-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sayer C, Szabo Z, Isupov MN, Ingham C, Littlechild JA. The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta terrifontis Reveals an Open Active Site Due to a Minimal 'Cap' Domain. Front Microbiol 2015; 6:1294. [PMID: 26635762 PMCID: PMC4655241 DOI: 10.3389/fmicb.2015.01294] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 11/29/2022] Open
Abstract
A carboxyl esterase (TtEst2) has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterized biochemically and shown to have activity toward small p-nitrophenyl (pNP) carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 min at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate, and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalized based upon the properties of their active site pockets.
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Affiliation(s)
- Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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Metagenomics: Retrospect and Prospects in High Throughput Age. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2015; 2015:121735. [PMID: 26664751 PMCID: PMC4664791 DOI: 10.1155/2015/121735] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/26/2015] [Indexed: 01/30/2023]
Abstract
In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.
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Masuch T, Kusnezowa A, Nilewski S, Bautista JT, Kourist R, Leichert LI. A combined bioinformatics and functional metagenomics approach to discovering lipolytic biocatalysts. Front Microbiol 2015; 6:1110. [PMID: 26528261 PMCID: PMC4602143 DOI: 10.3389/fmicb.2015.01110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/25/2015] [Indexed: 11/30/2022] Open
Abstract
The majority of protein sequence data published today is of metagenomic origin. However, our ability to assign functions to these sequences is often hampered by our general inability to cultivate the larger part of microbial species and the sheer amount of sequence data generated in these projects. Here we present a combination of bioinformatics, synthetic biology, and Escherichia coli genetics to discover biocatalysts in metagenomic datasets. We created a subset of the Global Ocean Sampling dataset, the largest metagenomic project published to date, by removing all proteins that matched Hidden Markov Models of known protein families from PFAM and TIGRFAM with high confidence (E-value > 10-5). This essentially left us with proteins with low or no homology to known protein families, still encompassing ~1.7 million different sequences. In this subset, we then identified protein families de novo with a Markov clustering algorithm. For each protein family, we defined a single representative based on its phylogenetic relationship to all other members in that family. This reduced the dataset to ~17,000 representatives of protein families with more than 10 members. Based on conserved regions typical for lipases and esterases, we selected a representative gene from a family of 27 members for synthesis. This protein, when expressed in E. coli, showed lipolytic activity toward para-nitrophenyl (pNP) esters. The Km-value of the enzyme was 66.68 μM for pNP-butyrate and 68.08 μM for pNP-palmitate with kcat/Km values at 3.4 × 106 and 6.6 × 105 M-1s-1, respectively. Hydrolysis of model substrates showed enantiopreference for the R-form. Reactions yielded 43 and 61% enantiomeric excess of products with ibuprofen methyl ester and 2-phenylpropanoic acid ethyl ester, respectively. The enzyme retains 50% of its maximum activity at temperatures as low as 10°C, its activity is enhanced in artificial seawater and buffers with higher salt concentrations with an optimum osmolarity of 3,890 mosmol/l.
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Affiliation(s)
- Thorsten Masuch
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum Bochum, Germany
| | - Anna Kusnezowa
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum Bochum, Germany
| | - Sebastian Nilewski
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum Bochum, Germany
| | - José T Bautista
- Junior Research Group for Microbial Biotechnology - Department for Biology and Biotechnology, Ruhr University Bochum Bochum, Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology - Department for Biology and Biotechnology, Ruhr University Bochum Bochum, Germany
| | - Lars I Leichert
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum Bochum, Germany
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Probing role of key residues in the divergent evolution of Yarrowia lipolytica lipase 2 and Aspergillus niger eruloyl esterase A. Microbiol Res 2015; 178:27-34. [DOI: 10.1016/j.micres.2015.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/09/2015] [Accepted: 05/16/2015] [Indexed: 11/19/2022]
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44
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Molecular cloning of rhodanese gene from soil metagenome of cold desert of North-West Himalayas: sequence and structural features of the rhodanese enzyme. 3 Biotech 2015; 5:513-521. [PMID: 28324556 PMCID: PMC4522728 DOI: 10.1007/s13205-014-0249-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/26/2014] [Indexed: 11/25/2022] Open
Abstract
Rhodanese is a multifunctional, sulfur transferase that catalyzes the detoxification of cyanide by sulphuration in a double displacement (ping pong) mechanistic reaction. In the present study, small-insert metagenomic library from soil sample collected from Ladakh (3,000–3,600 m.a.s.l) in northwestern Himalayas, India was constructed. Function-driven screening of ~8,500 colonies led to the isolation of one esterase-positive clone (clone-est) harboring 2.43 kb insert. Sequence analysis of the insert identified two ORF’s, phosM encoding phosphoesterase and rodM encoding rhodanese. The 800 bp rodM gene encoded a polypeptide of 227 amino acids (RodM). The RodM showed maximum homology with the rhodanese-like protein from Cyanobacterium synechococcus species with a score identity of only 51 %. Putative 3D structure of RodM developed by homology modeling resembles to homodimeric protein of SUD sulfur transferase of Wolinellasuccinogenes with properly structured active-site cysteine (Cys) residue. Rhodanese has been reported from few culturable microorganisms.
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45
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Singh R, Chopra C, Gupta VK, Akhlaq B, Verma V, Rasool S. Purification and characterization of CHpro1, a thermotolerant, alkali-stable and oxidation-resisting protease of Chumathang hotspring. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0834-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Leis B, Heinze S, Angelov A, Pham VTT, Thürmer A, Jebbar M, Golyshin PN, Streit WR, Daniel R, Liebl W. Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon. Front Bioeng Biotechnol 2015; 3:95. [PMID: 26191525 PMCID: PMC4486847 DOI: 10.3389/fbioe.2015.00095] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/17/2015] [Indexed: 01/27/2023] Open
Abstract
Extreme habitats serve as a source of enzymes that are active under extreme conditions and are candidates for industrial applications. In this work, six large-insert mixed genomic libraries were screened for hydrolase activities in a broad temperature range (8-70°C). Among a variety of hydrolytic activities, one fosmid clone, derived from a library of pooled isolates of hyperthermophilic archaea from deep sea vents, displayed hydrolytic activity on carboxymethyl cellulose substrate plates at 70°C but not at lower temperatures. Sequence analysis of the fosmid insert revealed a gene encoding a novel glycoside hydrolase family 12 (GHF12) endo-1,4-β-glucanase, termed Cel12E. The enzyme shares 45% sequence identity with a protein from the archaeon Thermococcus sp. AM4 and displays a unique multidomain architecture. Biochemical characterization of Cel12E revealed a remarkably thermostable protein, which appears to be of archaeal origin. The enzyme displayed maximum activity at 92°C and was active on a variety of linear 1,4-β-glucans like carboxymethyl cellulose, β-glucan, lichenan, and phosphoric acid swollen cellulose. The protein is able to bind to various insoluble β-glucans. Product pattern analysis indicated that Cel12E is an endo-cleaving β-glucanase. Cel12E expands the toolbox of hyperthermostable archaeal cellulases with biotechnological potential.
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Affiliation(s)
- Benedikt Leis
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Simon Heinze
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Angel Angelov
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Vu Thuy Trang Pham
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Georg-August University Göttingen, Göttingen, Germany
| | - Mohamed Jebbar
- Laboratoire de Microbiologie des Environnements Extrêmes-UMR 6197 (CNRS-Ifremer-UBO), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, Plouzané, France
| | | | - Wolfgang R. Streit
- Fakultät für Mathematik, Informatik und Naturwissenschaften Biologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Georg-August University Göttingen, Göttingen, Germany
| | - Wolfgang Liebl
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
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Coughlan LM, Cotter PD, Hill C, Alvarez-Ordóñez A. Biotechnological applications of functional metagenomics in the food and pharmaceutical industries. Front Microbiol 2015; 6:672. [PMID: 26175729 PMCID: PMC4485178 DOI: 10.3389/fmicb.2015.00672] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/19/2015] [Indexed: 12/31/2022] Open
Abstract
Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.
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Affiliation(s)
| | - Paul D Cotter
- Teagasc Food Research Centre Cork, Ireland ; Alimentary Pharmabiotic Centre Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre Cork, Ireland ; School of Microbiology, University College Cork Cork, Ireland
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López-López O, Cerdán ME, González Siso MI. New extremophilic lipases and esterases from metagenomics. Curr Protein Pept Sci 2015; 15:445-55. [PMID: 24588890 PMCID: PMC4093774 DOI: 10.2174/1389203715666140228153801] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 01/21/2014] [Accepted: 02/25/2014] [Indexed: 11/22/2022]
Abstract
Lipolytic enzymes catalyze the hydrolysis of ester bonds in the presence of water. In media with low water content or in organic solvents, they can catalyze synthetic reactions such as esterification and transesterification. Lipases and esterases, in particular those from extremophilic origin, are robust enzymes, functional under the harsh conditions of industrial processes owing to their inherent thermostability and resistance towards organic solvents, which combined with their high chemo-, regio- and enantioselectivity make them very attractive biocatalysts for a variety of industrial applications. Likewise, enzymes from extremophile sources can provide additional features such as activity at extreme temperatures, extreme pH values or high salinity levels, which could be interesting for certain purposes. New lipases and esterases have traditionally been discovered by the isolation of microbial strains producing lipolytic activity. The Genome Projects Era allowed genome mining, exploiting homology with known lipases and esterases, to be used in the search for new enzymes. The Metagenomic Era meant a step forward in this field with the study of the metagenome, the pool of genomes in an environmental microbial community. Current molecular biology techniques make it possible to construct total environmental DNA libraries, including the genomes of unculturable organisms, opening a new window to a vast field of unknown enzymes with new and unique properties. Here, we review the latest advances and findings from research into new extremophilic lipases and esterases, using metagenomic approaches, and their potential industrial and biotechnological applications.
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Affiliation(s)
| | | | - Maria I González Siso
- University of A Coruna, Faculty of Sciences, Department of Cellular and Molecular Biology, Biochemistry and Molecular Biology Area. Campus A Zapateira s/n, 15071, A Coruna, Spain.
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De Santi C, Ambrosino L, Tedesco P, Zhai L, Zhou C, Xue Y, Ma Y, de Pascale D. Identification and characterization of a novel salt-tolerant esterase from a Tibetan glacier metagenomic library. Biotechnol Prog 2015; 31:890-9. [PMID: 25920073 DOI: 10.1002/btpr.2096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/23/2015] [Indexed: 12/12/2022]
Abstract
A salt-tolerant esterase, designated H9Est, was identified from a metagenomic library of the Karuola glacier. H9Est gene comprised 1071 bp and encoded a polypeptide of 357 amino acids with a molecular mass of 40 kDa. Sequence analysis revealed that H9Est belonged to the family IV of bacterial lypolitic enzyme. H9Est was overexpressed in Escherichia coli and the purified enzyme showed hydrolytic activity towards p-nitrophenyl esters with carbon chain from 2 to 8. The optimal esterase activity was at 40°C and pH 8.0 and the enzyme retained its activity towards some miscible organic solvents such as polyethylene glycol. A three-dimensional model of H9Est revealed that S200, D294, and H324 formed the H9Est catalytic triad. Circular Dichroism spectra and molecular dynamic simulation indicated that the esterase had a wide denaturation temperature range and flexible loops that would be beneficial for H9Est performance at low temperatures while retaining heat-resistant features.
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Affiliation(s)
- Concetta De Santi
- Inst. of Protein Biochemistry, National Research Council, Naples, I-80131, Italy
| | - Luca Ambrosino
- Inst. of Protein Biochemistry, National Research Council, Naples, I-80131, Italy
| | - Pietro Tedesco
- Inst. of Protein Biochemistry, National Research Council, Naples, I-80131, Italy
| | | | | | | | - Yanhe Ma
- State Key Laboratory of Microbial Resources and National Engineering Laboratory for Industrial Enzymes, Inst. of Microbiology, CAS, Beijing, 100101, China
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Rodríguez MC, Loaces I, Amarelle V, Senatore D, Iriarte A, Fabiano E, Noya F. Est10: A Novel Alkaline Esterase Isolated from Bovine Rumen Belonging to the New Family XV of Lipolytic Enzymes. PLoS One 2015; 10:e0126651. [PMID: 25973851 PMCID: PMC4431682 DOI: 10.1371/journal.pone.0126651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 04/04/2015] [Indexed: 11/18/2022] Open
Abstract
A metagenomic fosmid library from bovine rumen was used to identify clones with lipolytic activity. One positive clone was isolated. The gene responsible for the observed phenotype was identified by in vitro transposon mutagenesis and sequencing and was named est10. The 367 amino acids sequence harbors a signal peptide, the conserved secondary structure arrangement of alpha/beta hydrolases, and a GHSQG pentapeptide which is characteristic of esterases and lipases. Homology based 3D-modelling confirmed the conserved spatial orientation of the serine in a nucleophilic elbow. By sequence comparison, Est10 is related to hydrolases that are grouped into the non-specific Pfam family DUF3089 and to other characterized esterases that were recently classified into the new family XV of lipolytic enzymes. Est10 was heterologously expressed in Escherichia coli as a His-tagged fusion protein, purified and biochemically characterized. Est10 showed maximum activity towards C4 aliphatic chains and undetectable activity towards C10 and longer chains which prompted its classification as an esterase. However, it was able to efficiently catalyze the hydrolysis of aryl esters such as methyl phenylacetate and phenyl acetate. The optimum pH of this enzyme is 9.0, which is uncommon for esterases, and it exhibits an optimal temperature at 40°C. The activity of Est10 was inhibited by metal ions, detergents, chelating agents and additives. We have characterized an alkaline esterase produced by a still unidentified bacterium belonging to a recently proposed new family of esterases.
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Affiliation(s)
- María Cecilia Rodríguez
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Inés Loaces
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Vanesa Amarelle
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Daniella Senatore
- Laboratorio de Ecología Microbiana, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Andrés Iriarte
- Departamento de Genómica, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Francisco Noya
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
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