Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Outros Autores: | |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/51383 |
Resumo: | Pseudomonas sp. M1 is able to mineralize several unusual substrates of natural and xenobiotic origin, contributing to its competence to thrive in different ecological niches. In this work, the genome of M1 strain was resequenced by Illumina MiSeq to refine the quality of a published draft by resolving the majority of repeat-rich regions. In silico genome analysis led to the prediction of metabolic pathways involved in biotransformation of several unusual substrates (e.g., plant-derived volatiles), providing clues on the genomic complement required for such biodegrading/biotransformation functionalities. Pseudomonas sp. M1 exhibits a particular sensory and biotransformation/biocatalysis potential toward β-myrcene, a terpene vastly used in industries worldwide. Therefore, the genomic responsiveness of M1 strain toward β-myrcene was investigated, using an RNA sequencing approach. M1 cells challenged with β-myrcene(compared with cells grown in lactate) undergo an extensive alteration of the transcriptome expression profile, including 1,873 genes evidencing at least 1.5-fold of altered expression (627 upregulated and 1,246 downregulated), toward β-myrcene-imposed molecular adaptation and cellular specialization. A thorough data analysis identified a novel 28-kb genomic island, whose expression was strongly stimulated in β-myrcene-supplemented medium, that is essential for β-myrcene catabolism. This island includes β-myrcene-induced genes whose products are putatively involved in 1) substrate sensing, 2) gene expression regulation, and 3) β-myrcene oxidation and bioconversion of β-myrcene derivatives into central metabolism intermediates. In general, this locus does not show high homology with sequences available in databases and seems to have evolved through the assembly of several functional blocks acquired from different bacteria, probably, at different evolutionary stages. |
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Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformationBiodegradation, EnvironmentalGene Expression Regulation, BacterialGenomicsHigh-Throughput Nucleotide SequencingMetabolic Networks and PathwaysMonoterpenesPseudomonasGenome, Bacterialgenome sequencingbiocatalysisterpenesRNA-seqgenomic islandCiências Naturais::Ciências BiológicasScience & TechnologyPseudomonas sp. M1 is able to mineralize several unusual substrates of natural and xenobiotic origin, contributing to its competence to thrive in different ecological niches. In this work, the genome of M1 strain was resequenced by Illumina MiSeq to refine the quality of a published draft by resolving the majority of repeat-rich regions. In silico genome analysis led to the prediction of metabolic pathways involved in biotransformation of several unusual substrates (e.g., plant-derived volatiles), providing clues on the genomic complement required for such biodegrading/biotransformation functionalities. Pseudomonas sp. M1 exhibits a particular sensory and biotransformation/biocatalysis potential toward β-myrcene, a terpene vastly used in industries worldwide. Therefore, the genomic responsiveness of M1 strain toward β-myrcene was investigated, using an RNA sequencing approach. M1 cells challenged with β-myrcene(compared with cells grown in lactate) undergo an extensive alteration of the transcriptome expression profile, including 1,873 genes evidencing at least 1.5-fold of altered expression (627 upregulated and 1,246 downregulated), toward β-myrcene-imposed molecular adaptation and cellular specialization. A thorough data analysis identified a novel 28-kb genomic island, whose expression was strongly stimulated in β-myrcene-supplemented medium, that is essential for β-myrcene catabolism. This island includes β-myrcene-induced genes whose products are putatively involved in 1) substrate sensing, 2) gene expression regulation, and 3) β-myrcene oxidation and bioconversion of β-myrcene derivatives into central metabolism intermediates. In general, this locus does not show high homology with sequences available in databases and seems to have evolved through the assembly of several functional blocks acquired from different bacteria, probably, at different evolutionary stages.Acknowledgments This work was supported by FEDER through POFC— COMPETE and by national funds from Foundation for Science and Technology (Portugal) through the projects PEst-C/BIA/UI4050/2011, PTDC/EBB-BIO/104980/2008 and PTDC/BIA-MIC/113733/09, and through a PhD grant (grant number SFRH/BD/76894/2011) to P.S.-C.info:eu-repo/semantics/publishedVersionOxford University PressUniversidade do MinhoCastro, Pedro Miguel SoaresSantos, Pedro M.20152015-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/51383eng1759-665310.1093/gbe/evu25425503374info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:41:46Zoai:repositorium.sdum.uminho.pt:1822/51383Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:38:49.937345Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation |
title |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation |
spellingShingle |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation Castro, Pedro Miguel Soares Biodegradation, Environmental Gene Expression Regulation, Bacterial Genomics High-Throughput Nucleotide Sequencing Metabolic Networks and Pathways Monoterpenes Pseudomonas Genome, Bacterial genome sequencing biocatalysis terpenes RNA-seq genomic island Ciências Naturais::Ciências Biológicas Science & Technology |
title_short |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation |
title_full |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation |
title_fullStr |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation |
title_full_unstemmed |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation |
title_sort |
Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-Myrcene biotransformation |
author |
Castro, Pedro Miguel Soares |
author_facet |
Castro, Pedro Miguel Soares Santos, Pedro M. |
author_role |
author |
author2 |
Santos, Pedro M. |
author2_role |
author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Castro, Pedro Miguel Soares Santos, Pedro M. |
dc.subject.por.fl_str_mv |
Biodegradation, Environmental Gene Expression Regulation, Bacterial Genomics High-Throughput Nucleotide Sequencing Metabolic Networks and Pathways Monoterpenes Pseudomonas Genome, Bacterial genome sequencing biocatalysis terpenes RNA-seq genomic island Ciências Naturais::Ciências Biológicas Science & Technology |
topic |
Biodegradation, Environmental Gene Expression Regulation, Bacterial Genomics High-Throughput Nucleotide Sequencing Metabolic Networks and Pathways Monoterpenes Pseudomonas Genome, Bacterial genome sequencing biocatalysis terpenes RNA-seq genomic island Ciências Naturais::Ciências Biológicas Science & Technology |
description |
Pseudomonas sp. M1 is able to mineralize several unusual substrates of natural and xenobiotic origin, contributing to its competence to thrive in different ecological niches. In this work, the genome of M1 strain was resequenced by Illumina MiSeq to refine the quality of a published draft by resolving the majority of repeat-rich regions. In silico genome analysis led to the prediction of metabolic pathways involved in biotransformation of several unusual substrates (e.g., plant-derived volatiles), providing clues on the genomic complement required for such biodegrading/biotransformation functionalities. Pseudomonas sp. M1 exhibits a particular sensory and biotransformation/biocatalysis potential toward β-myrcene, a terpene vastly used in industries worldwide. Therefore, the genomic responsiveness of M1 strain toward β-myrcene was investigated, using an RNA sequencing approach. M1 cells challenged with β-myrcene(compared with cells grown in lactate) undergo an extensive alteration of the transcriptome expression profile, including 1,873 genes evidencing at least 1.5-fold of altered expression (627 upregulated and 1,246 downregulated), toward β-myrcene-imposed molecular adaptation and cellular specialization. A thorough data analysis identified a novel 28-kb genomic island, whose expression was strongly stimulated in β-myrcene-supplemented medium, that is essential for β-myrcene catabolism. This island includes β-myrcene-induced genes whose products are putatively involved in 1) substrate sensing, 2) gene expression regulation, and 3) β-myrcene oxidation and bioconversion of β-myrcene derivatives into central metabolism intermediates. In general, this locus does not show high homology with sequences available in databases and seems to have evolved through the assembly of several functional blocks acquired from different bacteria, probably, at different evolutionary stages. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015 2015-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/51383 |
url |
http://hdl.handle.net/1822/51383 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1759-6653 10.1093/gbe/evu254 25503374 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Oxford University Press |
publisher.none.fl_str_mv |
Oxford University Press |
dc.source.none.fl_str_mv |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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