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Lipase metagenomic

Lifeng Zhu, Qi Wu, Cao Deng, Mengjie Zhang, Chenglin Zhang, Hua Chen, Guoqing Lu, Fuwen Wei
Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.g., Felidae, Canidae) clustered in the same clade, and other clades comprised omnivorous and herbivorous Carnivora (e.g., badgers, bears and pandas)...
May 2018: Environmental Microbiology
Patrick T West, Alexander J Probst, Igor V Grigoriev, Brian C Thomas, Jillian F Banfield
Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential...
April 2018: Genome Research
Ping Lu, Xinwei Gao, Hao Dong, Zhen Liu, Francesco Secundo, Changhu Xue, Xiangzhao Mao
Astaxanthin is a pigment with various functions. Free astaxanthin is obtained mainly through saponification methods, which could result in many byproducts. Enzymatic methods using lipases have been used in a few cases, while there are no reports on the use of esterases for the production of free astaxanthin. Herein we present the screening and identification of a novel esterase (Est3-14) from a marine mud metagenomic library. Est3-14 is pH-sensitive and keeps good stability in alkaline buffers (residual activity 94%, pH 8...
March 21, 2018: Journal of Agricultural and Food Chemistry
Myung Hwan Lee, Raees Khan, Weixin Tao, Kihyuck Choi, Seung Yeup Lee, Jae Wook Lee, Eul Chul Hwang, Seon-Woo Lee
Autoinducers are indispensable for bacterial cell-cell communication. However, due to the reliance on culture-based techniques, few autoinducer-hydrolyzing enzymes are known. In this study, we characterized soil metagenome-derived unique enzymes capable of hydrolyzing 3-hydroxypalmitic acid methyl ester (3-OH PAME), an autoinducer of the plant pathogenic bacterium Ralstonia solanacearum. Among 146 candidate lipolytic clones from a soil metagenome library, 4 unique enzymes capable of hydrolyzing the autoinducer 3-OH PAME, termed ELP86, ELP96, ELP104, and EstDL33, were selected and characterized...
March 20, 2018: Journal of Biotechnology
Abhijit Poddar, Subrata K Das
The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates...
January 2018: Archives of Microbiology
Anna Kusnezowa, Lars I Leichert
BACKGROUND: With the development of Next Generation Sequencing technologies, the number of predicted proteins from entire (meta-) genomes has risen exponentially. While for some of these sequences protein functions can be inferred from homology, an experimental characterization is still a requirement for the determination of protein function. However, functional characterization of proteins cannot keep pace with our capabilities to generate more and more sequence data. RESULTS: Here, we present an approach to reduce the number of proteins from entire (meta-) genomes to a reasonably small number for further experimental characterization without loss of important information...
May 22, 2017: BMC Bioinformatics
Daniel Borda-Molina, José Salvador Montaña, María Mercedes Zambrano, Sandra Baena
Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes...
August 2017: Antonie Van Leeuwenhoek
Wei Yan, Furong Li, Li Wang, Yaxin Zhu, Zhiyang Dong, Linhan Bai
A new gene encoding a lipase (designated as Lip-1) was identified from a metagenomic bacterial artificial chromosome(BAC) library prepared from a concentrated water sample collected from a hot spring field in Niujie, Eryuan of Yunnan province in China. The open reading frame of this gene encoded 622 amino acid residues. It was cloned, fused with the oleosin gene and over expressed in Escherichia coli to prepare immobilized lipase artificial oil body AOB-sole-lip-1. The monomeric Sole-lip-1 fusion protein presented a molecular mass of 102...
March 2017: Biotechnology Reports
Leli Tang, Yulin Xia, Xiuling Wu, Xiaoli Chen, Xueling Zhang, He Li
One clone (Lip906) exhibiting lipase activity was screened from a metagenomic library by using a medium containing tricaprylin. A novel lipase gene from the inserted fragment of Lip906 was obtained by sequencing. The phylogenetic analysis of Lip906 lipase exhibited 34% and 32% homologue to lipases from Streptomyces sp. MspMP-M5 and Rhodopirellula europaea. This gene was expressed in Escherichia coli (E. coli) BL21 (DE3), and the recombinant protein was purified and characterized. The best substrate of the recombinant Lip906 lipase was p-nitrophenyl myristate (C14)...
August 20, 2017: Gene
Mariana Rangel Pereira, Thaís Carvalho Maester, Gustavo Fernando Mercaldi, Eliana Gertrudes de Macedo Lemos, Marko Hyvönen, Andrea Balan
Esterases catalyze the cleavage and formation of ester bonds and are members of the diverse family of α/β hydrolase fold. They are useful in industries from different sectors, such as food, detergent, fine chemicals, and biofuel production. In a previous work, 30 positive clones for lipolytic activity were identified from a metagenomic library of a microbial consortium specialized in diesel oil degradation. In this study, a putative gene encoding an esterase/lipase, denominated est8, has been cloned and the corresponding protein expressed recombinantly, purified to homogeneity and characterized functional and structurally...
June 2017: Applied Microbiology and Biotechnology
Ana Popovic, Tran Hai, Anatoly Tchigvintsev, Mahbod Hajighasemi, Boguslaw Nocek, Anna N Khusnutdinova, Greg Brown, Julia Glinos, Robert Flick, Tatiana Skarina, Tatyana N Chernikova, Veronica Yim, Thomas Brüls, Denis Le Paslier, Michail M Yakimov, Andrzej Joachimiak, Manuel Ferrer, Olga V Golyshina, Alexei Savchenko, Peter N Golyshin, Alexander F Yakunin
Metagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone...
March 8, 2017: Scientific Reports
Amélie Dukunde, Dominik Schneider, Mingji Lu, Silja Brady, Rolf Daniel
OBJECTIVES: To investigate the properties of a novel metagenome-derived member of the hormone-sensitive lipase family of lipolytic enzymes. RESULTS: A forest soil metagenome-derived gene encoding an esterase (Est06) belonging to the hormone-sensitive lipase family of lipolytic enzymes was subcloned, heterologously expressed and characterized. Est06 is a polypeptide of 295 amino acids with a molecular mass of 31 kDa. The deduced protein sequence shares 61% similarity with a hypothetical protein from the marine symbiont Candidatus Entotheonella sp...
April 2017: Biotechnology Letters
Rakesh Kumar, Linga Banoth, Uttam Chand Banerjee, Jagdeep Kaur
In the present study, efficient enzymatic methods were developed using a recombinant metagenomic lipase (LipR1) for the synthesis of corresponding esters by the transesterification of five different pharmaceutically important secondary alcohols. The recombinant lipase (specific activity=87m6U/mg) showed maximum conversion in presence of ionic liquid with Naphthyl-ethanol (eeP=99%), Indanol and Methyl-4 pyridine methanol (eeS of 98% and 99%) respectively in 1h. Vinyl acetate was found as suitable acyl donor in transesterification reactions...
February 2017: International Journal of Biological Macromolecules
Rajesh Kumar Sahoo, Mohit Kumar, Lala Behari Sukla, Enketeswara Subudhi
Screening of metagenomic library from Taptapani Hot Spring (Odisha) yielded a positive lipase clone (pUC-lip479). Sequence analysis showed an ORF (RK-lip479) of 416 amino acid residues which was overexpressed in Escherichia coli BL21 (DE3). Optimum pH and temperature of purified lipase RK-lip479 were 8.0 and 65 °C, respectively, and found to be stable over a pH range of 7.0-9.0 and temperatures 55-75 °C. RK-lip479 could hydrolyse a wide range of 4-nitrophenyl esters (4-nitrophenyoctanoate, 4-nitrophenyldodecanoate, 4-nitrophenylpalmitate, 4-nitrophenylmyristate and 4-nitrophenylstearate), and maximum activity was observed with 4-nitrophenyldodecanoate...
February 2017: Environmental Science and Pollution Research International
Mahejibin Khan, Amit Kumar
The understanding of the 3-dimensional enzyme structure is important for the point of protein engineering and applications. Computer-based molecular modelling is a vital tool for theoretical predication of enzyme activities and finding their substrates and inhibitors. SMlipA lipase was cloned from forest soil metagenome and characterized as broad spectrum enzyme with high stability in various organic solvents. In the present study, to understand the mechanism of SMlipA lipase and to identify the key residues involved in enzyme-substrate interaction, three dimensional-computational model of SMlipA has been generated and validated for stereo-chemical and amino-acid environment quality using appropriate programs, and further validation of the active-site architecture was achieved by performing docking studies with different ligand...
November 2016: Journal of Molecular Graphics & Modelling
Lada E Petrovskaya, Ksenia A Novototskaya-Vlasova, Sultan Sh Gapizov, Elena V Spirina, Ekaterina V Durdenko, Elizaveta M Rivkina
Siberian permafrost is a unique environment inhabited with diverse groups of microorganisms. Among them, there are numerous producers of biotechnologically relevant enzymes including lipases and esterases. Recently, we have constructed a metagenomic library from a permafrost sample and identified in it several genes coding for potential lipolytic enzymes. In the current work, properties of the recombinant esterases obtained from this library are compared with the previously characterized lipase from Psychrobacter cryohalolentis and other representatives of the hormone-sensitive lipase family...
July 4, 2017: Bioengineered
Haseong Kim, Kil Koang Kwon, Wonjae Seong, Seung-Goo Lee
The recent development of a high-throughput single-cell assay technique enables the screening of novel enzymes based on functional activities from a large-scale metagenomic library(1). We previously proposed a genetic enzyme screening system (GESS) that uses dimethylphenol regulator activated by phenol or p-nitrophenol. Since a vast amount of natural enzymatic reactions produce these phenolic compounds from phenol deriving substrates, this single genetic screening system can be theoretically applied to screen over 200 different enzymes in the BRENDA database...
August 8, 2016: Journal of Visualized Experiments: JoVE
Jing Huang, Ying-Yi Huo, Rui Ji, Siyun Kuang, Chaoneng Ji, Xue-Wei Xu, Jixi Li
Hormone sensitive lipase (HSL) catalyzes the hydrolysis of triacylglycerols into fatty acids and glycerol, thus playing key roles in energy homeostasis. However, the application of HSL serving as a pharmaceutical target and an industrial biocatalyst is largely hampered due to the lack of high-resolution structural information. Here we report biochemical properties and crystal structures of a novel HSL homologue esterase Est22 from a deep-sea metagenomic library. Est22 prefers short acyl chain esters and has a very high activity with substrate p-nitrophenyl butyrate...
2016: Scientific Reports
Stephan Thies, Sonja Christina Rausch, Filip Kovacic, Alexandra Schmidt-Thaler, Susanne Wilhelm, Frank Rosenau, Rolf Daniel, Wolfgang Streit, Jörg Pietruszka, Karl-Erich Jaeger
DNA derived from environmental samples is a rich source of novel bioactive molecules. The choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. We have constructed a metagenomic library in Escherichia coli DH10b with environmental DNA (eDNA) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from the family Flavobacteriaceae...
2016: Scientific Reports
Tayvich Vorapreeda, Chinae Thammarongtham, Kobkul Laoteng
Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach...
July 2016: World Journal of Microbiology & Biotechnology
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