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      Bacillus sp. JR3 esterase LipJ: A new mesophilic enzyme showing traces of a thermophilic past

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          Abstract

          A search for extremophile enzymes from ancient volcanic soils in El Hierro Island (Canary Islands, Spain) allowed isolation of a microbial sporulated strain collection from which several enzymatic activities were tested. Isolates were obtained after sample cultivation under several conditions of nutrient contents and temperature. Among the bacterial isolates, supernatants from the strain designated JR3 displayed high esterase activity at temperatures ranging from 30 to 100°C, suggesting the presence of at least a hyper-thermophilic extracellular lipase. Sequence alignment of known thermophilic lipases allowed design of degenerated consensus primers for amplification and cloning of the corresponding lipase, named LipJ. However, the cloned enzyme displayed maximum activity at 30°C and pH 7, showing a different profile from that observed in supernatants of the parental strain. Sequence analysis of the cloned protein showed a pentapeptide motif -GHSMG- distinct from that of thermophilic lipases, and much closer to that of esterases. Nevertheless, the 3D structural model of LipJ displayed the same folding as that of thermophilic lipases, suggesting a common evolutionary origin. A phylogenetic study confirmed this possibility, positioning LipJ as a new member of the thermophilic family of bacterial lipases I.5. However, LipJ clusters in a clade close but separated from that of Geobacillus sp. thermophilic lipases. Comprehensive analysis of the cloned enzyme suggests a common origin of LipJ and other bacterial thermophilic lipases, and highlights the most probable divergent evolutionary pathway followed by LipJ, which during the harsh past times would have probably been a thermophilic enzyme, having lost these properties when the environment changed to more benign conditions.

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          Most cited references59

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          Protein Identification and Analysis Tools on the ExPASy Server

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            16S ribosomal DNA amplification for phylogenetic study.

            A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.
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              Bacterial lipolytic enzymes: classification and properties.

              Knowledge of bacterial lipolytic enzymes is increasing at a rapid and exciting rate. To obtain an overview of this industrially very important class of enzymes and their characteristics, we have collected and classified the information available from protein and nucleotide databases. Here we propose an updated and extensive classification of bacterial esterases and lipases based mainly on a comparison of their amino acid sequences and some fundamental biological properties. These new insights result in the identification of eight different families with the largest being further divided into six subfamilies. Moreover, the classification enables us to predict (1) important structural features such as residues forming the catalytic site or the presence of disulphide bonds, (2) types of secretion mechanism and requirement for lipase-specific foldases, and (3) the potential relationship to other enzyme families. This work will therefore contribute to a faster identification and to an easier characterization of novel bacterial lipolytic enzymes.
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                Author and article information

                Contributors
                Role: InvestigationRole: Methodology
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draft
                Role: InvestigationRole: Methodology
                Role: ConceptualizationRole: Formal analysisRole: SupervisionRole: Validation
                Role: Data curationRole: Formal analysisRole: Resources
                Role: ConceptualizationRole: Funding acquisitionRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                25 July 2017
                2017
                : 12
                : 7
                : e0181029
                Affiliations
                [1 ] Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, Spain
                [2 ] Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, Barcelona, Spain
                Karl-Franzens-Universitat Graz, AUSTRIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0003-4008-0669
                Article
                PONE-D-17-13645
                10.1371/journal.pone.0181029
                5526573
                28742841
                410abad7-bdc8-4a80-84fd-45fb3b271026
                © 2017 Ribera et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 9 April 2017
                : 25 June 2017
                Page count
                Figures: 9, Tables: 3, Pages: 24
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100007136, Secretaría de Estado de Investigación, Desarrollo e Innovación;
                Award ID: CTQ2014-59632-R, CTQ2013-48995-C2-2-R
                Funded by: funder-id http://dx.doi.org/10.13039/501100004892, Agencia Española de Cooperación Internacional para el Desarrollo;
                Award ID: A203563511
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100007136, Secretaría de Estado de Investigación, Desarrollo e Innovación;
                Award ID: CTQ2013-48995-C2-2-R
                Funded by: funder-id http://dx.doi.org/10.13039/501100007136, Secretaría de Estado de Investigación, Desarrollo e Innovación;
                Award ID: AC2015-00008-00-00
                Funded by: funder-id http://dx.doi.org/10.13039/501100002943, Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya;
                Award ID: 2014SGR-534 00327
                This work was financed by the Scientific and Technological Research Council (MINECO, Spain), grants CTQ2014-59632-R, CTQ2013-48995-C2-2-R and AC2015-00008-00-00, by the Pla de Recerca de Catalunya, grants 2009SGR-819 and 2014SGR-534 00327, by PCI-AECID project A203563511, and by the Generalitat de Catalunya to the “Xarxa de Referència en Biotecnologia” (XRB).
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Hydrolases
                Lipases
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Hydrolases
                Lipases
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Motif Analysis
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                Bacillus
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