Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2014 |
| Outros Autores: | , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/10162 |
Resumo: | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil. |
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Dumaresq, Aline S. RomãoFróes, Adriana MCuadrat, Rafael R. CSilva Jr., Floriano PaesDávila, Alberto M. R.2015-05-04T16:34:31Z2015-05-04T16:34:31Z2014DUMARESQ, Aline S. Romão et al. Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases. Natural Science, v.6, n.5, p.323-337, 2014.2150-4091https://www.arca.fiocruz.br/handle/icict/1016210.4236/ns.2014.65034engScientific Research Publishing, Inc,Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databasesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Polo de Biologia Computacional e Sistemas. Laboratório de Bioquímica de Proteínas e Peptídeos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Pólo de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Chitinases catalyze the hydrolysis of chitin, a linear homopolymer of β-(1,4)-linked N-acetylglucosamine. The broad range of applications of chitinolytic enzymes makes their identification and study very promising. Metagenomic approaches offer access to functional genes in uncultured representatives of the microbiota and hold great potential in the discovery of novel enzymes, but tools to extensively explore these data are still scarce. In this study, we develop a chitinase mining pipeline to facilitate the comprehensive search of these enzymes in environmental metagenomic databases and also to explore phylogenetic relationships among the retrieved sequences. In order to perform the analyses, UniprotKB fungal and bacterial chitinases sequences belonging to the glycoside hydrolases (GH) family-18, 19 and 20 were used to generate 15 reference datasets, which were then used to generate high quality seed alignments with the MAFFT program. Profile Hidden Markov Models (pHMMs) were built from each seed alignment using the hmmbuild program of HMMER v3.0 package. The best-hit sequences returned by hmmsearch against two environmental metagenomic databases (Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis—CAMERA and Integrated Microbial Genomes—IMG/M) were retrieved and further analyzed. The NJ trees generated for each chitinase dataset showed some variability in the catalytic domain region of the metagenomic sequences and revealed common sequence patterns among all the trees. The scanning of the retrieved metagenomic sequences for chitinase conserved domains/signatures using both the InterPro and the RPS-BLAST tools confirmed the efficacy and sensitivity of our pHMM-based approach in detecting putative chitinases sequences. These analyses provide insight into the potential reservoir of novel molecules in metagenomic databases while supporting the chitinase mining pipeline developed in this work. By using our chitinase mining pipeline, a larger number of previously unannotated metagenomic chitinase sequences can be classified, enabling further studies on these enzymes.ChitinaseMetagenomepHMMSequence SearchCiências Biológicasinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txttext/plain1914https://www.arca.fiocruz.br/bitstream/icict/10162/1/license.txt7d48279ffeed55da8dfe2f8e81f3b81fMD51ORIGINALfloriano_silva2jretal_IOC_2014.pdfapplication/pdf1479033https://www.arca.fiocruz.br/bitstream/icict/10162/2/floriano_silva2jretal_IOC_2014.pdf565fc72f13375bdcb8c10a29d58cd594MD52TEXTfloriano_silva2jretal_IOC_2014.pdf.txtfloriano_silva2jretal_IOC_2014.pdf.txtExtracted texttext/plain62176https://www.arca.fiocruz.br/bitstream/icict/10162/3/floriano_silva2jretal_IOC_2014.pdf.txt25d09a9ee1bc037ebe9d069dc4fee755MD53icict/101622023-09-14 16:02:28.741oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-09-14T19:02:28Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
| dc.title.pt_BR.fl_str_mv |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases |
| title |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases |
| spellingShingle |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases Dumaresq, Aline S. Romão Chitinase Metagenome pHMM Sequence Search Ciências Biológicas |
| title_short |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases |
| title_full |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases |
| title_fullStr |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases |
| title_full_unstemmed |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases |
| title_sort |
Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases |
| author |
Dumaresq, Aline S. Romão |
| author_facet |
Dumaresq, Aline S. Romão Fróes, Adriana M Cuadrat, Rafael R. C Silva Jr., Floriano Paes Dávila, Alberto M. R. |
| author_role |
author |
| author2 |
Fróes, Adriana M Cuadrat, Rafael R. C Silva Jr., Floriano Paes Dávila, Alberto M. R. |
| author2_role |
author author author author |
| dc.contributor.author.fl_str_mv |
Dumaresq, Aline S. Romão Fróes, Adriana M Cuadrat, Rafael R. C Silva Jr., Floriano Paes Dávila, Alberto M. R. |
| dc.subject.en.pt_BR.fl_str_mv |
Chitinase Metagenome pHMM Sequence Search |
| topic |
Chitinase Metagenome pHMM Sequence Search Ciências Biológicas |
| dc.subject.decs.pt_BR.fl_str_mv |
Ciências Biológicas |
| description |
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil. |
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2014 |
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2014 |
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2015-05-04T16:34:31Z |
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2015-05-04T16:34:31Z |
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DUMARESQ, Aline S. Romão et al. Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases. Natural Science, v.6, n.5, p.323-337, 2014. |
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10.4236/ns.2014.65034 |
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DUMARESQ, Aline S. Romão et al. Towards a Comprehensive Search of Putative Chitinases Sequences in Environmental Metagenomic Databases. Natural Science, v.6, n.5, p.323-337, 2014. 2150-4091 10.4236/ns.2014.65034 |
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