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Adjeroud M, Kecha M, Escuder-Rodríguez JJ, Becerra M, González-Siso MI. AMWEst, a new thermostable and detergent-tolerant esterase retrieved from the Albian aquifer. Appl Microbiol Biotechnol 2024; 108:114. [PMID: 38204131 PMCID: PMC10781878 DOI: 10.1007/s00253-023-12844-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/12/2024]
Abstract
A fosmid library was constructed with the metagenomic DNA from the high-temperature sediment-rich water of the Albian aquifer (Algeria). Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. We identified a novel gene named AMWEst (1209 base pairs) encoding a protein of 402 amino acids with a predicted molecular weight of 43.44 kDa and conferring esterase activity. AMWEst was successfully overexpressed in the yeast mesophilic host Saccharomyces cerevisiae, and the expression system used proved to be efficient and produced sufficient activity for its biochemical characterization. Multiple sequence alignment indicated that AMWEst contained a conserved pentapeptide motif (Gly120-His121-Ser122-Gln123-Gly124). The optimum pH and temperature of the recombinant esterase AMWEst were 8 and 80 °C, respectively. Additionally, AMWEst showed higher activity towards short carbon substrates and showed maximum activity for p-nitrophenyl hexanoate (C6). Notably, AMWEst has a remarkable thermostability, and the enzyme retains almost maximum activity at 70 °C after incubation for 1 h. Moreover, enzyme activity was enhanced by high concentrations of SDS and Triton X-100 detergents. KEY POINTS: • A novel thermostable esterase has been retrieved through functional metagenomics • The esterase is detergent-tolerant, which is attractive for some applications • The esterase can be expressed in a yeast mesophilic host to enhance its yield.
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Affiliation(s)
- Moussa Adjeroud
- Laboratoire de Mycologie, Département de Biologie Appliquée, de Biotechnologie Et de L'Activité Microbienne (LaMyBAM), Faculté Des Sciences de La Nature Et de La Vie, Université Des Frères Mentouri Constantine 1, 25000, Constantine, Algeria
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée, Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université de Bejaia, Campus Targa Ouzemmour, 6000, Bejaia, Algeria
| | - Juan-José Escuder-Rodríguez
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Manuel Becerra
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
| | - María-Isabel González-Siso
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
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2
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Vinces TC, de Souza AS, Carvalho CF, Visnardi AB, Teixeira RD, Llontop EE, Bismara BAP, Vicente EJ, Pereira JO, de Souza RF, Yonamine M, Marana SR, Farah CS, Guzzo CR. Monomeric Esterase: Insights into Cooperative Behavior, Hysteresis/Allokairy. Biochemistry 2024; 63:1178-1193. [PMID: 38669355 DOI: 10.1021/acs.biochem.3c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Herein, we present a novel esterase enzyme, Ade1, isolated from a metagenomic library of Amazonian dark earths soils, demonstrating its broad substrate promiscuity by hydrolyzing ester bonds linked to aliphatic groups. The three-dimensional structure of the enzyme was solved in the presence and absence of substrate (tributyrin), revealing its classification within the α/β-hydrolase superfamily. Despite being a monomeric enzyme, enzymatic assays reveal a cooperative behavior with a sigmoidal profile (initial velocities vs substrate concentrations). Our investigation brings to light the allokairy/hysteresis behavior of Ade1, as evidenced by a transient burst profile during the hydrolysis of substrates such as p-nitrophenyl butyrate and p-nitrophenyl octanoate. Crystal structures of Ade1, coupled with molecular dynamics simulations, unveil the existence of multiple conformational structures within a single molecular state (E̅1). Notably, substrate binding induces a loop closure that traps the substrate in the catalytic site. Upon product release, the cap domain opens simultaneously with structural changes, transitioning the enzyme to a new molecular state (E̅2). This study advances our understanding of hysteresis/allokairy mechanisms, a temporal regulation that appears more pervasive than previously acknowledged and extends its presence to metabolic enzymes. These findings also hold potential implications for addressing human diseases associated with metabolic dysregulation.
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Affiliation(s)
- Tania Churasacari Vinces
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Cecília F Carvalho
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Aline Biazola Visnardi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Raphael D Teixeira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Edgar E Llontop
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Beatriz Aparecida Passos Bismara
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Elisabete J Vicente
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - José O Pereira
- Biotechnology Group, Federal University of Amazonas, Amazonas CEP 69077-000, Brazil
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Mauricio Yonamine
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Sandro Roberto Marana
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Chuck Shaker Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
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Sahlin J, Wu C, Buscemi A, Schärer C, Nazemi SA, S K R, Herrera-Reinoza N, Jung TA, Shahgaldian P. Nanobiocatalysts with inbuilt cofactor recycling for oxidoreductase catalysis in organic solvents. NANOSCALE ADVANCES 2023; 5:5036-5044. [PMID: 37705789 PMCID: PMC10496889 DOI: 10.1039/d3na00413a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
The major stumbling block in the implementation of oxidoreductase enzymes in continuous processes is their stark dependence on costly cofactors that are insoluble in organic solvents. We describe a chemical strategy that allows producing nanobiocatalysts, based on an oxidoreductase enzyme, that performs biocatalytic reactions in hydrophobic organic solvents without external cofactors. The chemical design relies on the use of a silica-based carrier nanoparticle, of which the porosity can be exploited to create an aqueous reservoir containing the cofactor. The nanoparticle core, possessing radial-centred pore channels, serves as a cofactor reservoir. It is further covered with a layer of reduced porosity. This layer serves as a support for the immobilisation of the selected enzyme yet allowing the diffusion of the cofactor from the nanoparticle core. The immobilised enzyme is, in turn, shielded by an organosilica layer of controlled thickness fully covering the enzyme. Such produced nanobiocatalysts are shown to catalyse the reduction of a series of relevant ketones into the corresponding secondary alcohols, also in a continuous flow fashion.
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Affiliation(s)
- Jenny Sahlin
- Institute of Chemistry and Bioanalytics, School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland Hofackerstrasse 30 Muttenz CH-4132 Switzerland
| | - Congyu Wu
- Institute of Chemistry and Bioanalytics, School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland Hofackerstrasse 30 Muttenz CH-4132 Switzerland
| | - Andrea Buscemi
- Institute of Chemistry and Bioanalytics, School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland Hofackerstrasse 30 Muttenz CH-4132 Switzerland
| | - Claude Schärer
- Institute of Chemistry and Bioanalytics, School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland Hofackerstrasse 30 Muttenz CH-4132 Switzerland
| | - Seyed Amirabbas Nazemi
- Institute of Chemistry and Bioanalytics, School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland Hofackerstrasse 30 Muttenz CH-4132 Switzerland
| | - Rejaul S K
- Institute of Physics, University of Basel Klingelbergstrasse 82 Basel CH-4056 Switzerland
| | - Nataly Herrera-Reinoza
- Laboratory for X-ray Nanoscience and Technologies, Paul Scherrer Institute Forschungsstrasse 111 Villigen CH-5232 Switzerland
| | - Thomas A Jung
- Institute of Physics, University of Basel Klingelbergstrasse 82 Basel CH-4056 Switzerland
- Laboratory for X-ray Nanoscience and Technologies, Paul Scherrer Institute Forschungsstrasse 111 Villigen CH-5232 Switzerland
| | - Patrick Shahgaldian
- Institute of Chemistry and Bioanalytics, School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland Hofackerstrasse 30 Muttenz CH-4132 Switzerland
- Swiss Nanoscience Institute Klingelbergstrasse 82 Basel CH-4056 Switzerland
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4
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Papanikolaou A, Chatzikonstantinou AV, Zarafeta D, Kourkoumelis N, Skretas G, Pavlidis ΙV, Stamatis H. Substrate Specificity of the Highly Thermostable Esterase EstDZ3. Chembiochem 2023; 24:e202200642. [PMID: 36545817 DOI: 10.1002/cbic.202200642] [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: 11/08/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Esterases are among the most studied enzymes, and their applications expand into several branches of industrial biotechnology. Yet, despite the fact that information on their substrate specificity is crucial for selecting or designing the best fitted biocatalyst for the desired application, it cannot be predicted from their amino acid sequence. In this work, we studied the substrate scope of the newly discovered hydrolytic extremozyme, EstDZ3, against a library of esters with variable carbon chain lengths in an effort to understand the crucial amino acids for the substrate selectivity of this enzyme. EstDZ3 appears to be active against a wide range of esters with high selectivity towards medium- to long-carbon chain vinyl esters. In-silico studies of its 3D structure revealed that the selectivity might arise from the mainly hydrophobic nature of the active site's environment.
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Affiliation(s)
- Angelos Papanikolaou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandra V Chatzikonstantinou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110, Ioannina, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Nikolaos Kourkoumelis
- Department of Medical Physics, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635, Athens, Greece.,Institute for Bio-innovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Ιoannis V Pavlidis
- Department of Chemistry, University of Crete Voutes, University Campus, 70013, Heraklion, Greece
| | - Haralambos Stamatis
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110, Ioannina, Greece
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5
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Biochemical characterization, substrate and stereoselectivity of an outer surface putative α/β hydrolase from the pathogenic Leptospira. Int J Biol Macromol 2023; 229:803-813. [PMID: 36587638 DOI: 10.1016/j.ijbiomac.2022.12.283] [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: 10/21/2022] [Revised: 12/13/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
The genome of pathogenic leptospira encodes a plethora of outer surface and secretory proteins. The outer surface or secreted α/β hydrolases in a few pathogenic organisms are crucial virulent factors. They hydrolyze host immune factors and pathogen's immune-activating ligands, which help pathogens to evade the host's innate immunity. In this study, we report biochemical characterizations, substrate and stereoselectivity of one of the leptospiral outer surface putative α/β hydrolases, IQB77_09235 (LABH). Purified LABH displayed better kinetic parameters towards small water-soluble esters such as p-nitrophenyl acetate and p-nitrophenyl butyrate. The LABH exhibited moderate thermostability and displayed a pH optimum of 8.5. Remarkably, a phylogenetic study suggested that LABH does not cluster with other characterized bacterial esterases or lipases. Protein structural modeling revealed that some structural features are closely associated with Staphylococcus hycus lipase (SAH), a triacylglycerol hydrolase. The hydrolytic activity of the protein was found to be inhibited by a lipase inhibitor, orlistat. Biocatalytic application of the protein in the kinetic resolution of racemic 1-phenylethyl acetate reveals excellent enantioselectivity (E > 500) in the production of (R)-1-phenylethanol, a valuable chiral synthon in several industries. To our knowledge, this is the first detailed characterization of outer surface α/β hydrolases from leptospiral spp.
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6
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Li QQ, Zhu ZR, Liu QG, An YT, Wang YX, Zhang SB, Li G. Characterization of a novel thermostable alkaline lipase derived from a compost metagenomic library and its potential application in the detergent industry. Front Microbiol 2022; 13:1088581. [PMID: 36620038 PMCID: PMC9817002 DOI: 10.3389/fmicb.2022.1088581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/25/2022] Open
Abstract
Using composted soil samples, a metagenomic library consisting of 36,000 clones was constructed. Then, a novel lipase, Lip54q, which belongs to the VIII family of lipolytic enzymes, was identified from the metagenomic library by functional screening. To explore the enzymatic properties of Lip54q, lip54q was heterologous expressed in Escherichia coli with a high expression level of recombinant protein up to 720 mg/L. The recombinant enzyme showed the highest activity (28,160 U/mg) against a C10 substrate at pH 9.0 and 47°C, and was stable at temperatures ≤50°C and pH 8.0-11.0. Of particular interest, the surfactants, Tween-20, Tween-80 and Tritonx-100, exhibited strong promoting effects on Lip54q activities regardless of whether low concentrations (0.1%) or high concentrations (10%) were used. Application studies of Lip54q using six commercial detergents indicated that the enzyme had strong tolerance and immersion resistance to all six detergents. The results of oil-stain removal experiments suggested that addition of the enzyme to various commercial detergents could significantly improve the abilities of these detergents to remove oil-stains. Furthermore, the results of a molecular docking analysis of Lip54q showed that both the C10 substrate and linoleic acid molecules could form hydrogen bond interactions with the catalytic amino acids, Ser-268, Glu-168, and Asp-192, in the catalytic center of the enzyme, and the hydrogen bond distances were shorter. The electrostatic attraction between the enzyme and the substrate formed by the hydrogen bond with a shorter distance is stronger, which is conducive to the formation of a more stable complex between the enzyme and the substrate, thus increasing the activity of the enzyme to such substrate. These results 1ay a good foundation for application of this enzyme in the detergent industry in the future.
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Affiliation(s)
- Qing-Qing Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zi-Ran Zhu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qing-Gang Liu
- Guang Zhou Liby Enterprise Group Co., Ltd., Guangzhou, China
| | - Yu-Ting An
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yi-Xiang Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shu-Bin Zhang
- Guang Zhou Liby Enterprise Group Co., Ltd., Guangzhou, China
| | - Gang Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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7
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Molecular Cloning and Characterization of a New Family VI Esterase from an Activated Sludge Metagenome. Microorganisms 2022; 10:microorganisms10122403. [PMID: 36557656 PMCID: PMC9786865 DOI: 10.3390/microorganisms10122403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
A new esterase gene, est6, was discovered in an activated sludge metagenomic library. The 729-bp gene encodes a 242-amino acid protein (designated Est6) with a molecular mass of 26.1 kDa. Est6 shared only a moderate identity to a putative hydrolase with the highest BLASTP analysis score. Most of the closely related proteins are uncharacterized and are predicted from genome sequencing data of microorganisms or metagenomic DNA sequences. The phylogenetic analysis of Est6 showed that the protein was assigned to family VI esterases/lipases. The catalytic triad of Est6 was predicted to be Ser135, Asp188, and His219, with Ser135 in a typically conserved pentapeptide (GFSQG) of family VI members, which was further confirmed by site-directed mutagenesis. The est6 gene was overexpressed successfully in its soluble form in Escherichia coli and then purified to its tag-free form and homogeneity by affinity chromatography. The purified Est6 in pH 8.0 buffer was active as a monomer. The optimal conditions for Est6 activity were at a temperature of 45 °C and pH of 8.0 when using p-nitrophenyl acetate as a substrate. The enzyme was stable over wide temperature and pH ranges, and it exhibited activity in the presence of organic solvents, metal cations, or detergents. Furthermore, the enzyme showed significant regioselectivity in the spectrophotometric analysis. In conclusion, Est6 might have the potential for applications in biotechnological processes.
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8
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Abstract
Many enzymes possess high catalytic efficiency and selectivity that far surpass classical organic or organometallic catalysts. However, the initial starting enzyme for a given transformation does not always possess the right properties needed for broad utilization. Searching in genome/protein sequence libraries for homologs, aided with powerful bioinformatic tools developed in recent years, provides an avenue to identify superior biocatalysts. Herein, we highlight several case studies to illustrate the power of this concept. A brief discussion on its complementarity with contemporary approaches in protein engineering (such as directed evolution) and possible future developments is also provided.
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Affiliation(s)
- Yanlong Jiang
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX,77005, USA
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX,77005, USA
- Lead Contact
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9
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Nazarian Z, Arab SS. Discovery of carboxylesterases via metagenomics: Putative enzymes that contribute to chemical kinetic resolution. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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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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11
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Lu M, Schneider D, Daniel R. Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern. Front Microbiol 2022; 13:851969. [PMID: 35756004 PMCID: PMC9226776 DOI: 10.3389/fmicb.2022.851969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
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Affiliation(s)
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
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12
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Liu X, Zhou M, Sun R, Xing S, Wu T, He H, Chen J, Bielicki JK. Characterization of a Novel Esterase Est33 From an Antarctic Bacterium: A Representative of a New Esterase Family. Front Microbiol 2022; 13:855658. [PMID: 35655995 PMCID: PMC9152352 DOI: 10.3389/fmicb.2022.855658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/18/2022] [Indexed: 11/26/2022] Open
Abstract
Studies of microorganisms from extreme environments can sometimes reveal novel proteins with unique properties. Here, we identified a novel esterase gene (Est33) from an Antarctic bacterium. The protein was expressed and purified for biochemical characterizations. Site-mutation variants including S94A, D205A, and H233A were constructed to explore the structure–function relationship of the catalytic triad of Est33, and we found mutating Ser94, Asp205, and His233 residues lead to a complete loss of enzyme activity. In addition, the catalytic Ser94 located in a conserved pentapeptide motif GVSWG. Phylogenetic analysis showed that Est33 and its closely related homologs belonged to an independent group apart from other known family members, indicating that Est33 represented a new family of esterase. The Est33 enzyme was found to be a cold-active esterase retaining 25%–100% activity from 10°C to 30°C and to have optimal catalytic activity toward p-nitrophenol acetate (30°C and pH7.5). The serine modifying reagent phenylmethylsulfonyl fluoride inhibited the activity of Est33 by 77.34%, while thiol reagents such as dithiol threitol (DTT) activated the enzyme by 3-fold. Metal chelating reagents EDTA had no effects, indicating that Est33 is not a metalloenzyme. Collectively, these results indicate that Est33 constitutes the first member of a novel esterase family XXI that has been identified.
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Affiliation(s)
- Xiaoyu Liu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Mingyang Zhou
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Rui Sun
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shu Xing
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Tao Wu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Hailun He
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jianbin Chen
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.,Shandong Provincial Key Laboratory of Molecular Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - John Kevin Bielicki
- Lawrence Berkeley National Laboratory, University of California at Berkeley, Berkeley, CA, United States
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13
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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14
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Farihan Afnan Mohd Rozi M, Noor Zaliha Raja Abd Rahman R, Thean Chor Leow A, Shukuri Mohamad Ali M. Ancestral Sequence Reconstruction of Ancient Lipase from Family I.3 Bacterial Lipolytic Enzymes. Mol Phylogenet Evol 2021; 168:107381. [PMID: 34968679 DOI: 10.1016/j.ympev.2021.107381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 01/14/2023]
Abstract
Family I.3 lipase is distinguished from other families by the amino acid sequence and secretion mechanism. Little is known about the evolutionary process driving these differences. This study attempt to understand how the diverse temperature stabilities of bacterial lipases from family I.3 evolved. To achieve that, eighty-three protein sequences sharing a minimum 30% sequence identity with Antarctic Pseudomonas sp. AMS8 lipase were used to infer phylogenetic tree. Using ancestral sequence reconstruction (ASR) technique, the last universal common ancestor (LUCA) sequence of family I.3 was reconstructed. A gene encoding LUCA was synthesized, cloned and expressed as inclusion bodies in E. coli system. Insoluble form of LUCA was refolded using urea dilution method and then purified using affinity chromatography. The purified LUCA exhibited an optimum temperature and pH at 70℃ and 10 respectively. Various metal ions increased or retained the activity of LUCA. LUCA also demonstrated tolerance towards various organic solvents in 25% v/v concentration. The finding from this study could support the understanding on temperature and environment during ancient time. In overall, reconstructed ancestral enzymes have improved physicochemical properties that make them suitable for industrial applications and ASR technique can be employed as a general technique for enzyme engineering.
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Affiliation(s)
- Mohamad Farihan Afnan Mohd Rozi
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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15
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Thermostable lipases and their dynamics of improved enzymatic properties. Appl Microbiol Biotechnol 2021; 105:7069-7094. [PMID: 34487207 DOI: 10.1007/s00253-021-11520-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 10/20/2022]
Abstract
Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed. KEY POINTS: • The dynamics of lipases contributes to their non-covalent interactions and structural stability. • Thermostability can be enhanced by well-established genetic tools for improved kinetic efficiency. • Molecular dynamics greatly provides structure-function insights on thermodynamics of lipase.
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16
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An integrated overview of bacterial carboxylesterase: Structure, function and biocatalytic applications. Colloids Surf B Biointerfaces 2021; 205:111882. [PMID: 34087776 DOI: 10.1016/j.colsurfb.2021.111882] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022]
Abstract
Carboxylesterases (CEs) are members of prominent esterase, and as their name imply, they catalyze the cleavage of ester linkages. By far, a considerable number of novel CEs have been identified to investigate their exquisite physiological and biochemical properties. They are abundant enzymes in nature, widely distributed in relatively broad temperature range and in various sources; both macroorganisms and microorganisms. Given the importance of these enzymes in broad industries, interest in the study of their mechanisms and structural-based engineering are greatly increasing. This review presents the current state of knowledge and understanding about the structure and functions of this ester-metabolizing enzyme, primarily from bacterial sources. In addition, the potential biotechnological applications of bacterial CEs are also encompassed. This review will be useful in understanding the molecular basis and structural protein of bacterial CEs that are significant for the advancement of enzymology field in industries.
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17
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Du H, Hu RW, Zhao HM, Huang HB, Xiang L, Liu BL, Feng NX, Li H, Li YW, Cai QY, Mo CH. Mechanistic insight into esterase-catalyzed hydrolysis of phthalate esters (PAEs) based on integrated multi-spectroscopic analyses and docking simulation. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124901. [PMID: 33360702 DOI: 10.1016/j.jhazmat.2020.124901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/01/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
A novel PAE-hydrolyzing esterase (named Hyd) gene was screened from the genomic library of Rhodococcus sp. 2G and was successfully expressed in heterologous E. coli, which was defined as a new family of esterolytic enzymes. The purified Hyd could efficiently degrade various PAEs, displaying high activity and stability with a broad range of pH (4-10) and temperature (20-60 °C). Interaction mechanism of Hyd with dibutyl phthalate (DBP) was investigated by integrated multi-spectroscopic and docking simulation methods. Fluorescence and UV-vis spectra revealed that DBP could quench the fluorescence of Hyd through a static quenching mechanism. The results from synchronous fluorescence and CD spectra confirmed that the DBP binding to Hyd triggered conformational and micro-environmental changes of Hyd, which were characterized by increased stretching extent and random coil, and decreased α-helix and β-sheet. Molecular docking study showed that DBP could be bound to the cavity of Hyd with hydrogen bonding and hydrophobic interaction. A novel and distinctive catalytic mechanism was proposed: two key residues Thr190 and Ser191 might catalyze the hydrolysis of DBP, instead of the conserved catalytic triad (Ser-His-Asp) reported elsewhere, which was confirmed by site-directed mutagenesis.
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Affiliation(s)
- Huan Du
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Rui-Wen Hu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - He-Biao Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Bai-Lin Liu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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18
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Suharti, Mahardika G, Raissa, Dewi L, Yohandini H, Widhiastuty MP, Sakti RAW, Wahyudi ST, Akhmaloka. Cloning, heterologous expression, and characterization of a novel thioesterase from natural sample. Heliyon 2021; 7:e06542. [PMID: 33851045 PMCID: PMC8024609 DOI: 10.1016/j.heliyon.2021.e06542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
A novel thioesterse gene was successfully cloned and sequenced directly from natural sample of Domas Hot Spring, West Java, Indonesia. Homological analysis of the sequence showed that the gene appeared high homology to thioesterase genes with the highest to a putative thioesterase gene from uncultured Acidilobus sp. JCHS at 66% identity. However, phylogenetic analysis showed that the protein was separated from the branch with other known thioesterases. The size of the gene is around 500 base pairs, lied into 2 kb DNA fragment from a random PCR amplicon. The gene was overexpressed in Escherichia coli, a dominant band appeared at 17 kDa in SDS-PAGE with expression level at around 32% of total proteins. The activity of the purified protein using acetyl-CoA as substrate showed that the protein exhibited thioesterase activity. Furthermore, the enzyme also showed esterase activity on p-nitrophenyl ester as substrate. Detail characterization of esterolytic activity showed that the enzyme preferred p-nitrophenyl decanoate as substrate. The optimum activity of the enzyme was at 80 °C and pH 8. Activity of the enzyme was maintained after incubation at 80 °C up to 24 h. In addition, the enzyme was favorable on polar organic solvents. All the data obtained suggested that the enzyme is a novel alkaline thermostable thioesterase.
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Affiliation(s)
- Suharti
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Gita Mahardika
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
| | - Raissa
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Laksmi Dewi
- Department of Chemical Engineering, Faculty of Industrial Engineering, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Heni Yohandini
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Sriwijaya, Jl. Raya Palembang Prabumulih KM 32, Indralaya-Ogan Ilir, Indonesia
| | - Made Puspasari Widhiastuty
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
| | - Raden Aditya Wibawa Sakti
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Setyanto Tri Wahyudi
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Physics, IPB University, Bogor, 16680, Indonesia
| | - Akhmaloka
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
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19
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Sysoev M, Grötzinger SW, Renn D, Eppinger J, Rueping M, Karan R. Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods. Front Microbiol 2021; 12:630013. [PMID: 33643258 PMCID: PMC7902512 DOI: 10.3389/fmicb.2021.630013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.
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Affiliation(s)
- Maksim Sysoev
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan W. Grötzinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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20
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Chang X, Wu S, Chen J, Xiong S, Wang P, Shi X, Wang A, Wang B. Characterization of a carboxylesterase with hyper-thermostability and alkali-stability from Streptomyces lividans TK24. Extremophiles 2021; 25:115-128. [PMID: 33515353 DOI: 10.1007/s00792-021-01215-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/06/2021] [Indexed: 01/14/2023]
Abstract
A gene (estA', 804 bp) from Streptomyces lividans TK24 was artificially synthesized and successfully overexpressed as a 6His-tagged fusion protein in Escherichia coli. It encoded a carboxylesterase (EstA) that composed of 267 amino acids with a predicted molecular weight of 28.56 kDa. Multiple sequence alignment indicated that EstA has typical characteristics of esterases, including a catalytic triad (Ser93-Asp194-His224) and a conserved pentapeptide motif (Gly91-Leu92-Ser93-Met94-Gly95). Simultaneously, phylogenetic analysis indicated that EstA belongs to family VI. Biochemical characterization displayed its optimum enzyme activity was at 55 ℃ and pH 8.5. Additionally, EstA exhibited higher activity towards short carbon substrates and showed the outstanding catalytic efficiency for pNPA2 with kcat/Km of 2296.14 ± 10.35 s-1 mM-1. Notably, EstA has hyper-thermostability and good alkali stability. The activity of EstA did not change obviously when incubated at 50 and 100 ℃ for 337 and 1 h, independently. Besides, by incubating at 100 ℃ for 6 h, EstA remained about half of its initial activity. Moreover, EstA showed stability at pH ranging from 8.0 to 11.0, and about 90% residual enzyme activity was reserved by being treated at pH 8.0 or 9.0 for 80 h, especially. Such multiple features prepare EstA for a potential candidate in the field of biological catalysis of some industrial applications under harsh conditions.
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Affiliation(s)
- Xin Chang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Shuang Wu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Jie Chen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Shengqi Xiong
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xueqin Shi
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Ao Wang
- College of Physical Education, Anhui Normal University, Wuhu, 241000, Anhui, China.
| | - Baojuan Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
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21
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Recazens E, Mouisel E, Langin D. Hormone-sensitive lipase: sixty years later. Prog Lipid Res 2020; 82:101084. [PMID: 33387571 DOI: 10.1016/j.plipres.2020.101084] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 12/24/2020] [Indexed: 12/19/2022]
Abstract
Hormone-sensitive lipase (HSL) was initially characterized as the hormonally regulated neutral lipase activity responsible for the breakdown of triacylglycerols into fatty acids in adipose tissue. This review aims at providing up-to-date information on structural properties, regulation of expression, activity and function as well as therapeutic potential. The lipase is expressed as different isoforms produced from tissue-specific alternative promoters. All isoforms are composed of an N-terminal domain and a C-terminal catalytic domain within which a regulatory domain containing the phosphorylation sites is embedded. Some isoforms possess additional N-terminal regions. The catalytic domain shares similarities with bacteria, fungus and vascular plant proteins but not with other mammalian lipases. HSL singularity is provided by regulatory and N-terminal domains sharing no homology with other proteins. HSL has a broad substrate specificity compared to other neutral lipases. It hydrolyzes acylglycerols, cholesteryl and retinyl esters among other substrates. A novel role of HSL, independent of its enzymatic function, has recently been described in adipocytes. Clinical studies revealed dysregulations of HSL expression and activity in disorders, such as lipodystrophy, obesity, type 2 diabetes and cancer-associated cachexia. Development of specific inhibitors positions HSL as a pharmacological target for the treatment of metabolic complications.
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Affiliation(s)
- Emeline Recazens
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France
| | - Etienne Mouisel
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France
| | - Dominique Langin
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France; Franco-Czech Laboratory for Clinical Research on Obesity, Third Faculty of Medicine, Prague and Paul Sabatier University, Toulouse, France; Toulouse University Hospitals, Laboratory of Clinical Biochemistry, Toulouse, France.
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22
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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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23
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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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24
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Wang B, Wu S, Chang X, Chen J, Ma J, Wang P, Zhu G. Characterization of a novel hyper-thermostable and chlorpyrifos-hydrolyzing carboxylesterase EstC: A representative of the new esterase family XIX. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 170:104704. [PMID: 32980065 DOI: 10.1016/j.pestbp.2020.104704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 08/05/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Carboxylesterases have widely been used in a series of industrial applications, especially, the detoxification of pesticide residues. In the present study, EstC, a novel carboxylesterase from Streptomyces lividans TK24, was successfully heterogeneously expressed, purified and characterized. Phylogenetic analysis showed that EstC can be assigned as the first member of a novel family XIX. Multiple sequence alignment indicated that EstC has highly conserved structural features, including a catalytic triad formed by Ser155, Asp248 and His278, as well as a canonical Gly-His-Ser-Ala-Gly pentapeptide. Biochemical characterization indicated that EstC exhibited maximal activity at pH 9.0 (Tris-HCl buffer) and 55 °C. It also showed higher activity towards short-chain substrates, with the highest activity for p-nitrophenyl acetate (pNPA2) (Km = 0.31 ± 0.02 mM, kcat/Km = 1923.35 ± 9.62 s-1 mM-1) compared to other pNP esters used in this experiment. Notably, EstC showed hyper-thermostability and good alkali stability. The activity of EstC had no significant changes when it was incubated under 55 °C for 100 h and reached half-life after incubation at 100 °C for 8 h. Beyond that, EstC also showed stability at pH ranging from 6.0 to 11.0 and about 90% residual activity still reserved after treatment at pH 8.0 or 9.0 for 26 h, especially. Furthermore, EstC had outstanding potential for bioremediation of chlorpyrifos-contaminated environment. The recombinant enzyme (0.5 U mL-1) could hydrolyze 79.89% chlorpyrifos (5 mg L-1) at 37 °C within 80 min. These properties will make EstC have a potential application value in various industrial productions and detoxification of chlorpyrifos residues.
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Affiliation(s)
- Baojuan Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Shuang Wu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Xin Chang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Jie Chen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Jinxue Ma
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
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25
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Myrtollari K, Katsoulakis N, Zarafeta D, Pavlidis IV, Skretas G, Smonou I. Activity and specificity studies of the new thermostable esterase EstDZ2. Bioorg Chem 2020; 104:104214. [PMID: 32927128 DOI: 10.1016/j.bioorg.2020.104214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
In this paper, we study the activity and specificity of EstDZ2, a new thermostable carboxyl esterase of unknown function, which was isolated from a metagenome library from a Russian hot spring. The biocatalytic reaction employing EstDZ2 proved to be an efficient method for the hydrolysis of aryl p-, o- or m-substituted esters of butyric acid and esters of secondary alcohols. Docking studies revealed structural features of the enzyme that led to activity differences among the different substrates.
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Affiliation(s)
- Kamela Myrtollari
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Nikolaos Katsoulakis
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Ioannis V Pavlidis
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Ioulia Smonou
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece.
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26
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Zarafeta D, Galanopoulou AP, Leni ME, Kaili SI, Chegkazi MS, Chrysina ED, Kolisis FN, Hatzinikolaou DG, Skretas G. XynDZ5: A New Thermostable GH10 Xylanase. Front Microbiol 2020; 11:545. [PMID: 32390953 PMCID: PMC7193231 DOI: 10.3389/fmicb.2020.00545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)8 TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia P Galanopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Evangelia Leni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Stavroula I Kaili
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Magda S Chegkazi
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitris G Hatzinikolaou
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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27
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Qiu J, Zhang Y, Shi Y, Jiang J, Wu S, Li L, Shao Y, Xin Z. Identification and characterization of a novel phthalate-degrading hydrolase from a soil metagenomic library. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 190:110148. [PMID: 31911388 DOI: 10.1016/j.ecoenv.2019.110148] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/27/2019] [Accepted: 12/28/2019] [Indexed: 06/10/2023]
Abstract
Phthalate esters have raised public concerns owing to their effects on the environment and human health. We identified a novel phthalate-degrading hydrolase, EstJ6, from a metagenomic library using function-driven screening. Phylogenetic analysis indicated that EstJ6 is a member of family IV esterases. EstJ6 hydrolyzed various dialkyl and monoalkyl phthalate esters, and exhibited high hydrolytic activity (128 U/mg) toward dibutyl phthalate at 40 °C and pH 7.5. EstJ6 hydrolyzed not only common phthalate esters with simple side chains but also diethylhexyl phthalate and monoethylhexyl phthalate, which have complex and long side chains. Site-directed mutagenesis indicated that the catalytic triad residues of EstJ6 consists of Ser146, Glu240, and His270. EstJ6 is therefore a promising biodegradation enzyme, and our study illustrates the advantages of a metagenomic approach in identifying enzyme-coding genes for agricultural, food, and biotechnological applications.
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Affiliation(s)
- Jiarong Qiu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yueqi Zhang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yaning Shi
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Junwei Jiang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shenglu Wu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Longxiang Li
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China.
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28
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Biochemical characterization of an esterase from Clostridium acetobutylicum with novel GYSMG pentapeptide motif at the catalytic domain. J Ind Microbiol Biotechnol 2019; 47:169-181. [PMID: 31807968 DOI: 10.1007/s10295-019-02253-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
Gene CA_C0816 codes for a serine hydrolase protein from Clostridium acetobutylicum (ATCC 824) a member of hormone-sensitive lipase of lipolytic family IV. This gene was overexpressed in E. coli strain BL21and purified using Ni2+-NTA affinity chromatography. Size exclusion chromatography revealed that the protein is a dimer in solution. Optimum pH and temperature for recombinant Clostridium acetobutylicum esterase (Ca-Est) were found to be 7.0 and 60 °C, respectively. This enzyme exhibited high preference for p-nitrophenyl butyrate. KM and kcat/KM of the enzyme were 24.90 µM and 25.13 s-1 µM-1, respectively. Sequence analysis of Ca-Est predicts the presence of catalytic amino acids Ser 89, His 224, and Glu 196, presence of novel GYSMG conserved sequence (instead of GDSAG and GTSAG motif), and undescribed variation of HGSG motif. Site-directed mutagenesis confirmed that Ser 89 and His 224 play a major role in catalysis. This study reports that Ca-Est is hormone-sensitive lipase with novel GYSMG pentapeptide motif at a catalytic domain.
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29
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Almeida JM, Alnoch RC, Souza EM, Mitchell DA, Krieger N. Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140320. [PMID: 31756433 DOI: 10.1016/j.bbapap.2019.140320] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
In recent years, metagenomic strategies have been widely used to isolate and identify new enzymes from uncultivable components of microbial communities. Among these enzymes, various lipases have been obtained from metagenomic libraries from different environments and characterized. Although many of these lipases have characteristics that could make them interesting for application in biocatalysis, relatively little work has been done to evaluate their potential to catalyze industrially important reactions. In the present article, we highlight the latest research on lipases obtained through metagenomic tools, focusing on studies of activity and stability and investigations of application in biocatalysis. We also discuss the challenges of metagenomic approaches for the bioprospecting of new lipases.
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Affiliation(s)
- Janaina Marques Almeida
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - Robson Carlos Alnoch
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - Emanuel Maltempi Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - David Alexander Mitchell
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - Nadia Krieger
- Departamento de Química, Universidade Federal do Paraná, Cx.P. 19032 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil.
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30
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Hitch TCA, Clavel T. A proposed update for the classification and description of bacterial lipolytic enzymes. PeerJ 2019; 7:e7249. [PMID: 31328034 PMCID: PMC6622161 DOI: 10.7717/peerj.7249] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/03/2019] [Indexed: 11/23/2022] Open
Abstract
Bacterial lipolytic enzymes represent an important class of proteins: they provide their host species with access to additional resources and have multiple applications within the biotechnology sector. Since the formalisation of lipolytic enzymes into families and subfamilies, advances in molecular biology have led to the discovery of lipolytic enzymes unable to be classified via the existing system. Utilising sequence-based comparison methods, we have integrated these novel families within the classification system so that it now consists of 35 families and 11 true lipase subfamilies. Representative sequences for each family and subfamily have been defined as well as methodology for accurate comparison of novel sequences against the reference proteins, facilitating the future assignment of novel proteins. Both the code and protein sequences required for integration of additional families are available at: https://github.com/thh32/Lipase_reclassification.
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Affiliation(s)
- Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
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31
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Koutsandreas T, Ladoukakis E, Pilalis E, Zarafeta D, Kolisis FN, Skretas G, Chatziioannou AA. ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. Front Genet 2019; 10:469. [PMID: 31178894 PMCID: PMC6543708 DOI: 10.3389/fgene.2019.00469] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/01/2019] [Indexed: 01/27/2023] Open
Abstract
Metagenomic analysis of environmental samples provides deep insight into the enzymatic mixture of the corresponding niches, capable of revealing peptide sequences with novel functional properties exploiting the high performance of next-generation sequencing (NGS) technologies. At the same time due to their ever increasing complexity, there is a compelling need for ever larger computational configurations to ensure proper bioinformatic analysis, and fine annotation. With the aiming to address the challenges of such an endeavor, we have developed a novel web-based application named ANASTASIA (automated nucleotide aminoacid sequences translational plAtform for systemic interpretation and analysis). ANASTASIA provides a rich environment of bioinformatic tools, either publicly available or novel, proprietary algorithms, integrated within numerous automated algorithmic workflows, and which enables versatile data processing tasks for (meta)genomic sequence datasets. ANASTASIA was initially developed in the framework of the European FP7 project HotZyme, whose aim was to perform exhaustive analysis of metagenomes derived from thermal springs around the globe and to discover new enzymes of industrial interest. ANASTASIA has evolved to become a stable and extensible environment for diversified, metagenomic, functional analyses for a range of applications overarching industrial biotechnology to biomedicine, within the frames of the ELIXIR-GR project. As a showcase, we report the successful in silico mining of a novel thermostable esterase termed “EstDZ4” from a metagenomic sample collected from a hot spring located in Krisuvik, Iceland.
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Affiliation(s)
- Theodoros Koutsandreas
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
| | - Efthymios Ladoukakis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Eleftherios Pilalis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis A Chatziioannou
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
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32
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Gupta V, Singh I, Kumar P, Rasool S, Verma V. A hydrolase with esterase activity expressed from a fosmid gene bank prepared from DNA of a North West Himalayan glacier frozen soil sample. 3 Biotech 2019; 9:107. [PMID: 30863691 DOI: 10.1007/s13205-019-1621-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/08/2019] [Indexed: 01/26/2023] Open
Abstract
Screening of 20,000 clones of a fosmid gene bank, constructed from DNA extracted from North West Himalaya (NWH) glacier soil sample, using functional approach identified 10 esterase/lipase-producing clones. Of these, a clone designated pFG43 with an insert size of 45 kb which produced the highest concentration of enzyme (467.43 U/mg) was sequenced. Clone pFG43 contained 61 open reading frames (ORF) and of these an ORF of 1155 bp designated ME-003, was found to be closely related to a hydrolase from Acidobacteria sps (77% sequence identity and E value = 1e-164) and subsequently identified as a putative cocaine esterase. ORF ME-003 was amplified and sub-cloned using a TA vector system into E. coli (DH5α). The purified recombinant enzyme with a molecular weight of 43 kDa had optimal activity at 40 °C, pH 6 and the highest activity with shorter chain fatty acids than with higher chain length fatty acids. There is insignificant effect of inhibitors on the enzyme activity of ME-003, except PMSF which completely inhibited its activity. ME-003 activity was also inhibited in the presence of copper oxide but remained stable in presence of other metal ions. The enzyme activity was also inhibited in the presence of organic solvents; however, in the presence of 10% isopropanol, 12% of enzymatic activity was retained. Among various detergents, SDS completely inhibited enzymatic activity. The recombinant enzyme also shows enantio-specific activity against the racemic drug intermediates/precursors and exhibited 90% ee against racemic 1-phenyl ethanol and fluoxetine.
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Affiliation(s)
- Verruchi Gupta
- 1School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Katra, Jammu and Kashmir 182320 India
| | - Inderpal Singh
- 1School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Katra, Jammu and Kashmir 182320 India.,2Bioinformatics Infrastructure Facility (BIF), School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Katra, Jammu and Kashmir 182320 India
| | - Paramdeep Kumar
- 3Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Shafaq Rasool
- 1School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Katra, Jammu and Kashmir 182320 India
| | - Vijeshwar Verma
- 1School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Katra, Jammu and Kashmir 182320 India.,2Bioinformatics Infrastructure Facility (BIF), School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Katra, Jammu and Kashmir 182320 India
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33
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Wilkins LGE, Ettinger CL, Jospin G, Eisen JA. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Sci Rep 2019; 9:3059. [PMID: 30816235 PMCID: PMC6395817 DOI: 10.1038/s41598-019-39576-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.
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Affiliation(s)
- Laetitia G E Wilkins
- Department of Environmental Sciences, Policy & Management, University of California, Berkeley, CA, 94720, USA. .,Genome Center, University of California, Davis, CA, 95616, USA.
| | | | | | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, 95616, USA.,Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.,Department of Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA
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34
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Lu M, Dukunde A, Daniel R. Biochemical profiles of two thermostable and organic solvent-tolerant esterases derived from a compost metagenome. Appl Microbiol Biotechnol 2019; 103:3421-3437. [PMID: 30809711 DOI: 10.1007/s00253-019-09695-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022]
Abstract
Owing to the functional versatility and potential applications in industry, interest in lipolytic enzymes tolerant to organic solvents is increasing. In this study, functional screening of a compost soil metagenome resulted in identification of two lipolytic genes, est1 and est2, encoding 270 and 389 amino acids, respectively. The two genes were heterologously expressed and characterized. Est1 and Est2 are thermostable enzymes with optimal enzyme activities at 80 and 70 °C, respectively. A second-order rotatable design, which allows establishing the relationship between multiple variables with the obtained responses, was used to explore the combined effects of temperature and pH on esterase stability. The response curve indicated that Est1, and particularly Est2, retained high stability within a broad range of temperature and pH values. Furthermore, the effects of organic solvents on Est1 and Est2 activities and stabilities were assessed. Notably, Est2 activity was significantly enhanced (two- to tenfold) in the presence of ethanol, methanol, isopropanol, and 1-propanol over a concentration range between 6 and 30% (v/v). For the short-term stability (2 h of incubation), Est2 exhibited high tolerance against 60% (v/v) of ethanol, methanol, isopropanol, DMSO, and acetone, while Est1 activity resisted these solvents only at lower concentrations (below 30%, v/v). Est2 also displayed high stability towards some water-immiscible organic solvents, such as ethyl acetate, diethyl ether, and toluene. With respect to long-term stability, Est2 retained most of its activity after 26 days of incubation in the presence of 30% (v/v) ethanol, methanol, isopropanol, DMSO, or acetone. All of these features indicate that Est1 and Est2 possess application potential.
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Affiliation(s)
- Mingji Lu
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Amélie Dukunde
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany.
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35
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Gricajeva A, Bikutė I, Kalėdienė L. Atypical organic-solvent tolerant bacterial hormone sensitive lipase-like homologue EstAG1 from Staphylococcus saprophyticus AG1: Synthesis and characterization. Int J Biol Macromol 2019; 130:253-265. [PMID: 30797006 DOI: 10.1016/j.ijbiomac.2019.02.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022]
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Some of the most industrially relevant enzymes of this type are lipolytic and their market is predicted to uphold leadership up till 2024. In this study, a novel bacterial hormone-sensitive lipase-like (bHSL) family homologue, designated EstAG1, was discovered by mining gDNA of bacteria isolated from fat contaminated soil in Lithuania. Putative lipolytic enzyme was cloned, overexpressed in E. coli, purified and characterized determining its biochemical properties. While the true physiological role of the discovered leaderless, ~36 kDa enzyme is unknown, metal-activated EstAG1 possessed optima at 45-47.5 °C, pH 7.5-8, with a generally intermediate activity profile between esterases and lipases. Furthermore, EstAG1 was hyperactivated by ethanol, dioxane and DMSO, implicating that it could be industrially applicable enzyme for the synthesis of valuable products such as biodiesel, flavor esters, etc. Sequence analysis and structure modeling revealed that the highest sequence homology of EstAG1 with the closest structurally and functionally described protein makes up only 26%. It was also revealed that EstAG1 has some differences in the bHSL family-characteristic conserved sequence motives. Therefore, EstAG1 presents interest both in terms of biotechnological applications and basic research.
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Affiliation(s)
- Alisa Gricajeva
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Ingrida Bikutė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Lilija Kalėdienė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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36
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Korzhenkov AA, Teplyuk AV, Lebedinsky AV, Khvashchevskaya AA, Kopylova YG, Arakchaa KD, Golyshin PN, Lunev EA, Golyshina OV, Kublanov IV, Toshchakov SV, Gavrilov SN. Members of the Uncultured Taxon OP1 (“Acetothermia”) Predominate in the Microbial Community of an Alkaline Hot Spring at East-Tuvinian Upland. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718060115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Mahajan R, Verma S, Kushwaha M, Singh D, Akhter Y, Chatterjee S. Biodegradation of di‑n‑butyl phthalate by psychrotolerant Sphingobium yanoikuyae strain P4 and protein structural analysis of carboxylesterase involved in the pathway. Int J Biol Macromol 2018; 122:806-816. [PMID: 30395899 DOI: 10.1016/j.ijbiomac.2018.10.225] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 02/07/2023]
Abstract
A priority pollutant Phthalate Esters (PAEs) are widely used as plasticizers and are responsible mainly for carcinogenicity and endocrine disruption in human. For the bioremediation of PAEs, a psychrotolerant Sphingobium yanoikuyae strain P4, capable of utilizing many phthalates di‑methyl phthalate (DMP), di‑ethyl phthalate (DEP), di‑n‑butyl phthalate (DBP), di‑isobutyl phthalate (DIBP), butyl benzyl phthalate (BBP), and few Polycyclic Aromatic Hydrocarbons as the sole source of carbon and energy was isolated from Palampur, Kangra, Himachal Pradesh, India. 100% utilization of DBP (1 g L-1) by the strain was observed within 24 h of incubation at 28 °C. Interestingly the strain also degraded DBP completely at 20 °C and 15 °C within 36 h and 60 h, respectively. Esterase involved in DBP degradation was found to be inducible in nature and intracellular. Comparative sequence analysis of carboxylesterase enzyme sequences revealed conserved motifs: G-X-S-X-G and -HGG- which were the characteristic peptide motifs reported in different esterases. Structural analysis showed that the enzyme belongs to serine hydrolase superfamily, which has an α/β hydrolase fold. Interaction and binding of DBP to a catalytic Ser184 residue in the esterase enzyme were also analysed. In conclusion, carboxylesterase possess the required active site which may be involved in the catabolism of DBP.
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Affiliation(s)
- Rishi Mahajan
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Temporary Academic Block-Shahpur, District-Kangra, Himachal Pradesh 176206, India; Department of Chemistry and Chemical Sciences, Central University of Himachal Pradesh, Temporary Academic Block-Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Shalini Verma
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Temporary Academic Block-Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Madhulika Kushwaha
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Temporary Academic Block-Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Dharam Singh
- Molecular and Microbial Genetics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, District-Kangra, Himachal Pradesh 176061, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India.
| | - Subhankar Chatterjee
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Temporary Academic Block-Shahpur, District-Kangra, Himachal Pradesh 176206, India; Department of Chemistry and Chemical Sciences, Central University of Himachal Pradesh, Temporary Academic Block-Shahpur, District-Kangra, Himachal Pradesh 176206, India.
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Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2018; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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Discovering novel hydrolases from hot environments. Biotechnol Adv 2018; 36:2077-2100. [PMID: 30266344 DOI: 10.1016/j.biotechadv.2018.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022]
Abstract
Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.
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Ranjan R, Yadav MK, Suneja G, Sharma R. Discovery of a diverse set of esterases from hot spring microbial mat and sea sediment metagenomes. Int J Biol Macromol 2018; 119:572-581. [PMID: 30059741 DOI: 10.1016/j.ijbiomac.2018.07.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022]
Abstract
Esterases are an important group of biocatalysts for synthetic organic chemistry. Functional metagenomics allows discovery of novel biocatalysts by providing access to the gene pool of the microbial community of a habitat. Two metagenomic libraries representing the gene pool of sea sediment and hot spring microbial mat were constructed. Functional screening of these libraries resulted in the isolation of total 8 clones with tributyrin hydrolytic activity. Sequence analysis revealed 10 putative lipolytic proteins with 42-99% homology to the protein sequences in the databases, nine of which represented six known esterase families. Four of the encoded proteins represented Family V and amongst others, one each represented the Family VIII, pectin acetylesterase, enterobactin esterase, G-D-S-L family and OsmC domain containing esterase. One unusual lipolytic protein possessed poly-(3-hydroxybutyrate) depolymerase domain fused to lipase/esterase domain. Two phylogenetically related esterases (MLC3 and SLC5) belonging to family V were expressed and purified to homogeneity. The enzymes exhibited environment-adapted temperature optimum and thermostability. MLC3 was able to stereoselectively hydrolyze R-methyl mandelate to produce R-mandelic acid, an important chiral building block, which suggests MLC3 has potential commercial application.
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Affiliation(s)
- Ravi Ranjan
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India
| | - Manish Kumar Yadav
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Mathura Road, New Delhi 110025, India
| | - Garima Suneja
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Mathura Road, New Delhi 110025, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Mathura Road, New Delhi 110025, India.
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Chandra Mohana N, Yashavantha Rao H, Rakshith D, Mithun P, Nuthan B, Satish S. Omics based approach for biodiscovery of microbial natural products in antibiotic resistance era. J Genet Eng Biotechnol 2018; 16:1-8. [PMID: 30647697 PMCID: PMC6296576 DOI: 10.1016/j.jgeb.2018.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 01/01/2023]
Abstract
The need for a new antibiotic pipeline to confront threat imposed by resistant pathogens has become a major global concern for human health. To confront the challenge there is a need for discovery and development of new class of antibiotics. Nature which is considered treasure trove, there is re-emerged interest in exploring untapped microbial to yield novel molecules, due to their wide array of negative effects associated with synthetic drugs. Natural product researchers have developed many new techniques over the past few years for developing diverse compounds of biopotential. Taking edge in the advancement of genomics, genetic engineering, in silico drug design, surface modification, scaffolds, pharmacophores and target-based approach is necessary. These techniques have been economically sustainable and also proven efficient in natural product discovery. This review will focus on recent advances in diverse discipline approach from integrated Bioinformatics predictions, genetic engineering and medicinal chemistry for the synthesis of natural products vital for the discovery of novel antibiotics having potential application.
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Affiliation(s)
- N. Chandra Mohana
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - H.C. Yashavantha Rao
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - D. Rakshith
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - P.R. Mithun
- Department of Life Sciences, Christ University, Bengaluru 560029, Karnataka, India
| | - B.R. Nuthan
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
| | - S. Satish
- Microbial Drugs Laboratory, Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysore 570006, Karnataka, India
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Parapouli M, Foukis A, Stergiou PY, Koukouritaki M, Magklaras P, Gkini OA, Papamichael EM, Afendra AS, Hatziloukas E. Molecular, biochemical and kinetic analysis of a novel, thermostable lipase (LipSm) from Stenotrophomonas maltophilia Psi-1, the first member of a new bacterial lipase family (XVIII). ACTA ACUST UNITED AC 2018; 25:4. [PMID: 29456971 PMCID: PMC5806266 DOI: 10.1186/s40709-018-0074-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/27/2018] [Indexed: 11/10/2022]
Abstract
Background Microbial lipases catalyze a broad spectrum of reactions and are enzymes of considerable biotechnological interest. The focus of this study was the isolation of new lipase genes, intending to discover novel lipases whose products bear interesting biochemical and structural features and may have a potential to act as valuable biocatalysts in industrial applications. Results A novel lipase gene (lipSm), from a new environmental Stenotrophomonas maltophilia strain, Psi-1, originating from a sludge sample from Psittaleia (Greece), was cloned and sequenced. lipSm was further overexpressed in E. coli BL21(DE3) and the overproduced enzyme LipSm was purified and analyzed in respect to its biochemical and kinetic properties. In silico analysis of LipSm revealed that it is taxonomically related to several uncharacterized lipases from different genera, which constitute a unique clade, markedly different from all other previously described bacterial lipase families. All members of this clade displayed identical, conserved consensus sequence motifs, i.e. the catalytic triad (S, D, H), and an unusual, amongst bacterial lipases, Y-type oxyanion hole. 3D-modeling revealed the presence of a lid domain structure, which allows LipSm to act on small ester substrates without interfacial activation. In addition, the high percentage of alanine residues along with the occurrence of the AXXXA motif nine times in LipSm suggest that it is a thermostable lipase, a feature verified experimentally, since LipSm was still active after heating at 70 °C for 30 min. Conclusions The phylogenetic analysis of LipSm suggests the establishment of a new bacterial lipase family (XVIII) with LipSm being its first characterized member. Furthermore, LipSm is alkaliphilic, thermostable and lacks the requirement for interfacial activation, when small substrates are used. These properties make LipSm a potential advantageous biocatalyst in industry and biotechnology.
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Affiliation(s)
- Maria Parapouli
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece
| | - Athanasios Foukis
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece
| | | | - Maria Koukouritaki
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece
| | - Panagiotis Magklaras
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece
| | - Olga A Gkini
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece
| | - Emmanuel M Papamichael
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece
| | - Amalia-Sofia Afendra
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece
| | - Efstathios Hatziloukas
- 1Enzyme Biotechnology and Genetic Engineering Group, University of Ioannina, 451 10 Ioannina, Greece.,2Department of Biological Applications & Technologies, University of Ioannina, University Campus, 451 10 Ioannina, Greece
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Cloning, expression and characterization of the esterase estUT1 from Ureibacillus thermosphaericus which belongs to a new lipase family XVIII. Extremophiles 2018; 22:271-285. [PMID: 29330648 DOI: 10.1007/s00792-018-0996-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/23/2017] [Indexed: 10/18/2022]
Abstract
A new esterase gene from thermophilic bacteria Ureibacillus thermosphaericus was cloned into the pET32b vector and expressed in Escherichia coli BL21(DE3). Alignment of the estUT1 amino acid sequence revealed the presence of a novel canonical pentapeptide (GVSLG) and 41-47% identity to the closest family of the bacterial lipases XIII. Thus the esterase estUT1 from U. thermosphaericus was assigned as a member of the novel family XVIII. It also showed a strong activity toward short-chain esters (C2-C8), with the highest activity for C2. When p-nitrophenyl butyrate is used as a substrate, the temperature and pH optimum of the enzyme were 70-80 °C and 8.0, respectively. EstUT1 showed high thermostability and 68.9 ± 2.5% residual activity after incubation at 70 °C for 6 h. Homology modeling of the enzyme structure showed the presence of a putative catalytic triad Ser93, Asp192, and His222. The activity of estUT1 was inhibited by PMSF, suggesting that the serine residue is involved in the catalytic activity of the enzyme. The purified enzyme exhibited high stability in organic solvents. EstUT1 retained 85.8 ± 2.4% residual activity in 30% methanol at 50 °C for 6 h. Stability at high temperature and tolerance to organic solvents make estUT1 a promising enzyme for biotechnology application.
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Bonch-Osmolovskaya E, Elcheninov A, Zayulina K, Kublanov I. New thermophilic prokaryotes with hydrolytic activities. MICROBIOLOGY AUSTRALIA 2018. [DOI: 10.1071/ma18038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Thermophilic microorganisms are capable of growing on polymeric substrates and have been intensively studied for their enzymes, thermostable hydrolases (glycosidases, proteinases, lipases), which have important applications in many fields of bioindustry: production of detergents, food processing, paper and textile industry, biofuel formation from organic wastes, etc.1. The advantages of thermostable enzymes application are in their higher stability not only against temperature, but also against high or low pH, presence of detergents, etc. High temperature increases solubility of substrates2, thus making them more available, and significantly decreases the contamination risks. Many highly stable hydrolases, produced by thermophilic bacteria and archaea have been discovered3–6; however, due to continuous industrial demand and our knowledge that natural environments are a significant reservoir of genetic and hence functional diversity7, new thermophilic organisms producing hydrolytic enzymes are still of high interest. Here we present our achievements in isolation of novel thermophilic bacteria and archaea with various hydrolytic activities.
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Foong CP, Lakshmanan M, Abe H, Taylor TD, Foong SY, Sudesh K. A novel and wide substrate specific polyhydroxyalkanoate (PHA) synthase from unculturable bacteria found in mangrove soil. JOURNAL OF POLYMER RESEARCH 2017. [DOI: 10.1007/s10965-017-1403-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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