RNA‐seq transcriptome analysis of a
            <i>Pseudomonas</i>
            strain with diversified catalytic properties growth under different culture medium

Yang, Jiawei; Zheng, Daijun; Cui, Bao‐Dong; Yang, Min; Chen, Yong‐Zheng

doi:10.1002/mbo3.357

Cited by 20 publications

(10 citation statements)

References 37 publications

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“…As previously described (Ramos et al ., ; Segura et al ., ; Volkers et al ., ; Yang et al ., ), one of the central characteristics of P. putida strains such as DOT‐T1E is that they bear genes encoding proteins involved in the degradation of toluene and other aromatic compounds. In this study we detected the induction of all of the genes involved toluene degradation in DOT‐T1E (from T1E_4262 to T1E_4274), confirming that cells sensed toluene.…”

Section: Resultsmentioning

confidence: 99%

Global transcriptional response of solvent‐sensitive and solvent‐tolerant Pseudomonas putida strains exposed to toluene

Molina‐Santiago

Udaondo

Gómez-Lozano

et al. 2016

Environmental Microbiology

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Summary Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan‐genome analysis has revealed that 30% of genes belong to the core‐genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA‐seq analysis compared the short‐ and long‐term responses of the toluene‐sensitive KT2440 strain and the highly tolerant DOT‐T1E strain. The sensitive strain activates a larger number of genes in a higher magnitude than DOT‐T1E. This is expected because KT2440 bears one toluene tolerant pump, while DOT‐T1E encodes three of these pumps. Both strains activate membrane modifications to reduce toluene membrane permeability. The KT2440 strain activates the TCA cycle to generate energy, while avoiding energy‐intensive processes such as flagellar biosynthesis. This suggests that KT2440 responds to toluene by focusing on survival mechanisms. The DOT‐T1E strain activates toluene degradation pathways, using toluene as source of energy. Among the unique genes encoded by DOT‐T1E is a 70 kb island composed of genes of unknown function induced in response to toluene.

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Section: Resultsmentioning

confidence: 99%

Global transcriptional response of solvent‐sensitive and solvent‐tolerant Pseudomonas putida strains exposed to toluene

Molina‐Santiago

Udaondo

Gómez-Lozano

et al. 2016

Environmental Microbiology

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“…RNA-Seq data are commonly used to define the genome-wide transcript expression profiling and the identification of differentially expressed genes (DEGs) among different biological or experimental conditions (Han et al, 2015; Pereira, Imada & Guedes, 2017). RNA-Seq has emerged as a powerful tool for transcriptomic analysis in the field of environmental microbiology, which has especially been applied in the assessment of the microbial diversity in polluted sites (Yan et al, 2017), as well as in the discovery and characterization of genes implicated in the tolerance, biodegradation, and bioremediation of xenobiotics by different microorganisms (Zhang et al, 2015; Yang et al, 2016; Albers et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional analysis reveals the metabolic state ofBurkholderia zhejiangensisCEIB S4-3 during methyl parathion degradation

Castrejón-Godínez

Ortiz-Hernández

Salazar

et al. 2019

PeerJ

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Burkholderia zhejiangensis CEIB S4-3 has the ability to degrade methyl parathion (MP) and its main hydrolysis byproduct p-nitrophenol (PNP). According to genomic data, several genes related with metabolism of MP and PNP were identified in this strain. However, the metabolic state of the strain during the MP degradation has not been evaluated. In the present study, we analyzed gene expression changes during MP hydrolysis and PNP degradation through a transcriptomic approach. The transcriptional analysis revealed differential changes in the expression of genes involved in important cellular processes, such as energy production and conversion, transcription, amino acid transport and metabolism, translation, ribosomal structure and biogenesis, among others. Transcriptomic data also exhibited the overexpression of both PNP-catabolic gene clusters (pnpABA′E1E2FDC and pnpE1E2FDC) present in the strain. We found and validated by quantitative reverse transcription polymerase chain reaction the expression of the methyl parathion degrading gene, as well as the genes responsible for PNP degradation contained in two clusters. This proves the MP degradation pathway by the strain tested in this work. The exposure to PNP activates, in the first instance, the expression of the transcriptional regulators multiple antibiotic resistance regulator and Isocitrate Lyase Regulator (IclR), which are important in the regulation of genes from aromatic compound catabolism, as well as the expression of genes that encode transporters, permeases, efflux pumps, and porins related to the resistance to multidrugs and other xenobiotics. In the presence of the pesticide, 997 differentially expressed genes grouped in 104 metabolic pathways were observed. This report is the first to describe the transcriptomic analysis of a strain of B. zhejiangensis during the biodegradation of PNP.

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“…(R)-sulfoxides preparation through reductive resolution of racsulfoxides. In our previous reports, [22,29] an MsrA gene from Pseudomonas monteilii CCTCCM 2013 683 (pmMsrA)h as been screened and recombinant expressed in E. coli. Several( R)-sulfoxides with ee > 93 %w ere prepared under substrate concentration of 2-5 mm using whole-cells ystem expressing pmMsrA protein.…”

Section: Introductionmentioning

confidence: 99%

Biocatalytic Preparation of Chiral Sulfoxides through Asymmetric Reductive Resolution by Methionine Sulfoxide Reductase A

et al. 2018

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Here we report an environmentally friendly method for the preparation of chiral sulfoxides under high substrate concentration using recombinant methionine sulfoxide reductase A from Pseudomonas monteilii (pmMsrA) as a biocatalyst. Our results show that this enzyme can effectively accomplish the preparation of (R)‐sulfoxides with approximately 50 % yield and 94–99 % enantiomeric excess through asymmetric reductive resolution of racemic sulfoxide. With the establishment of the enzyme regeneration system, the initial substrate concentration could be increased 40–100 times compared to our original report. The (R)‐sulfoxides were obtained with high enantioselectivity under the substrate concentration up to 200 mm (approximately 32 g L−1), representing a quite high substrate concentration in biocatalytic preparation of chiral sulfoxides. Moreover, this system showed fairly good activity and enantioselectivity towards a series of ortho‐ and para‐substituted phenyl methyl sulfoxides under high substrate concentration.

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RNA‐seq transcriptome analysis of a Pseudomonas strain with diversified catalytic properties growth under different culture medium

Cited by 20 publications

References 37 publications

Global transcriptional response of solvent‐sensitive and solvent‐tolerant Pseudomonas putida strains exposed to toluene

Global transcriptional response of solvent‐sensitive and solvent‐tolerant Pseudomonas putida strains exposed to toluene

Transcriptional analysis reveals the metabolic state ofBurkholderia zhejiangensisCEIB S4-3 during methyl parathion degradation

Biocatalytic Preparation of Chiral Sulfoxides through Asymmetric Reductive Resolution by Methionine Sulfoxide Reductase A

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