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Deciphering the genome repertoire of Pseudomonas sp. M1 toward ?-myrcene biotransformation.

ABSTRACT: 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 ?-myrcene, a terpene vastly used in industries worldwide. Therefore, the genomic responsiveness of M1 strain toward ?-myrcene was investigated, using an RNA sequencing approach. M1 cells challenged with ?-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 ?-myrcene-imposed molecular adaptation and cellular specialization. A thorough data analysis identified a novel 28-kb genomic island, whose expression was strongly stimulated in ?-myrcene-supplemented medium, that is essential for ?-myrcene catabolism. This island includes ?-myrcene-induced genes whose products are putatively involved in 1) substrate sensing, 2) gene expression regulation, and 3) ?-myrcene oxidation and bioconversion of ?-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.

SUBMITTER: Soares-Castro P

PROVIDER: S-EPMC4316614 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-myrcene biotransformation.

Soares-Castro Pedro P Santos Pedro M PM

Genome biology and evolution 20141212 1

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 ...[more]

PMID: 25503374

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Project description:Pseudomonas sp. strain M1 is able to mineralize highly hydrophobic and recalcitrant compounds, such as benzene, phenol, and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such a spectrum of compounds as the sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of strain M1 regarding ?-myrcene catabolism was elucidated in this work, with a focus on the biocatalytical potential of the ?-myrcene-associated core code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units. Functional characterization of this locus with promoter probes and analytical approaches validated the genetic organization predicted in silico and associated the ?-myrcene-induced promoter activity to the production of ?-myrcene derivatives. Notably, by using a whole-genome mutagenesis strategy, different genotypes of the 28-kb GI were generated, resulting in the identification of a novel putative ?-myrcene hydroxylase, responsible for the initial oxidation of ?-myrcene into myrcen-8-ol, and a sensor-like regulatory protein, whose inactivation abolished the myr+ trait of M1 cells. Moreover, it was demonstrated that the range of monoterpene substrates of the M1 enzymatic repertoire, besides ?-myrcene, also includes other acyclic (e.g., ?-linalool) and cyclic [e.g., R-(+)-limonene and (-)-?-pinene] molecules. Our findings are the cornerstone for following metabolic engineering approaches and hint at a major role of the 28-kb GI in the biotransformation of a broad monoterpene backbone spectrum for its future biotechnological applications.IMPORTANCE Information regarding microbial systems able to biotransform monoterpenes, especially ?-myrcene, is limited and focused mainly on nonsystematic metabolite identification. Complete and detailed knowledge at the genetic, protein, metabolite, and regulatory levels is essential in order to set a model organism or a catabolic system as a biotechnology tool. Moreover, molecular characterization of reported systems is scarce, almost nonexistent, limiting advances in the development of optimized cell factories with strategies based on the new generation of metabolic engineering platforms. This study provides new insights into the intricate molecular functionalities associated with ?-myrcene catabolism in Pseudomonas, envisaging the production of a molecular knowledge base about the underlying catalytic and regulatory mechanisms of plant-derived volatile catabolic pathways.

Dataset Information

Deciphering the genome repertoire of Pseudomonas sp. M1 toward ?-myrcene biotransformation.

Publications

Deciphering the genome repertoire of Pseudomonas sp. M1 toward β-myrcene biotransformation.

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