Pseudomonas putida KT2440
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR093244.fastq.gz | Fastqsanger.gz | |||
| DRR093245.fastq.gz | Fastqsanger.gz | |||
| DRR093246.fastq.gz | Fastqsanger.gz | |||
| DRR093247.fastq.gz | Fastqsanger.gz | |||
| DRR093248.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We analyzed gene expression during conjugative transfer of plasmid RP4. Pairs of rifampicin-susceptible (RifS) and -resistance (RifR) strains of Pseudomonas putida KT2440 were conjugated for 10 minute on filter membrane in the presence of rifampicin to discriminate the expression changes in the donor and recipient cells.
2020-03-13 | GSE146879 | GEO
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007089.
2018-11-21 | PXD007133 | Pride
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007090.
2018-11-21 | PXD007722 | Pride
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the proteome, acetylome, and succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis.
2018-09-24 | PXD007089 | Pride
Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the proteome, acetylome, and succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis.
2018-11-22 | PXD007090 | Pride
Project description:The role of the MfsR repressor on the transcriptome of the integrative and conjugative element ICEclc in Pseudomonas putida UWC1
| PRJNA222864 | ENA
Project description:D-Amino acids have been shown to play an increasingly diverse role in bacterial physiology, yet much remains to be learned about their synthesis and catabolism. Here we used the model soil- and rhizosphere-dwelling organism Pseudomonas putida KT2440 to elaborate on the genomics and enzymology of d-amino acid metabolism. P. putida KT2440 catabolized the d-stereoisomers of lysine, phenylalanine, arginine, alanine, and hydroxyproline as the sole carbon and nitrogen sources. With the exception of phenylalanine, each of these amino acids was racemized by P. putida KT2440 enzymes. Three amino acid racemases were identified from a genomic screen, and the enzymes were further characterized in vitro. The putative biosynthetic alanine racemase Alr showed broad substrate specificity, exhibiting measurable racemase activity with 9 of the 19 chiral amino acids. Among these amino acids, activity was the highest with lysine, and the k(cat)/K(m) values with l- and d-lysine were 3 orders of magnitude greater than the k(cat)/K(m) values with l- and d-alanine. Conversely, the putative catabolic alanine racemase DadX showed narrow substrate specificity, clearly preferring only the alanine stereoisomers as the substrates. However, DadX did show 6- and 9-fold higher k(cat)/K(m) values than Alr with l- and d-alanine, respectively. The annotated proline racemase ProR of P. putida KT2440 showed negligible activity with either stereoisomer of the 19 chiral amino acids but exhibited strong epimerization activity with hydroxyproline as the substrate. Comparative genomic analysis revealed differences among pseudomonads with respect to alanine racemase genes that may point to different roles for these genes among closely related species.
| S-EPMC3811597 | biostudies-literature
Project description:Plastics, in all forms, are a ubiquitous cornerstone of modern civilization. Although humanity undoubtedly benefits from the versatility and durability of plastics, they also cause a tremendous burden for the environment. Bio-upcycling is a promising approach to reduce this burden, especially for polymers that are currently not amenable to mechanical recycling. Wildtype P. putida KT2440 is able to grow on 1,4-butanediol as sole carbon source, but only very slowly. Adaptive laboratory evolution (ALE) led to the isolation of several strains with significantly enhanced growth rate and yield. Genome re-sequencing and proteomic analysis were applied to characterize the genomic and metabolic basis of efficient 1,4-butanediol metabolism. Initially, 1,4-butanediol is oxidized to 4-hydroxybutyrate, in which the highly expressed dehydrogenase enzymes encoded within the PP_2674-2680 ped gene cluster play an essential role. The resulting 4-hydroxybutyrate can be metabolized through three possible pathways: (i) oxidation to succinate, (ii) CoA activation and subsequent oxidation to succinyl-CoA, and (iii) beta oxidation to glycolyl-CoA and acetyl-CoA. The evolved strains were both mutated in a transcriptional regulator (PP_2046) of an operon encoding both beta-oxidation related genes and an alcohol dehydrogenase. When either the regulator or the alcohol dehydrogenase is deleted, no 1,4-butanediol uptake or growth could be detected. Using a reverse engineering approach, PP_2046 was replaced by a synthetic promotor (14g) to overexpress the downstream operon (PP_2047-2051), thereby enhancing growth on 1,4-butanediol. This work provides a deeper understanding of microbial 1,4-butanediol metabolism in P. putida, which is also expandable to other aliphatic alpha-omega diols. It enables the more efficient metabolism of these diols, thereby enabling biotechnological valorization of plastic monomers in a bio-upcycling approach.
| S-EPMC7090098 | biostudies-literature
Project description:Pseudomonas putida is rapidly becoming a workhorse for industrial production due to its metabolic versatility, genetic accessibility and stress-resistance properties. The P. putida strain KT2440 is often described as Generally Regarded as Safe, or GRAS, indicating the strain is safe to use as food additive. This description is incorrect. P. putida KT2440 is classified by the FDA as HV1 certified, indicating it is safe to use in a P1 or ML1 environment.
| S-EPMC6680625 | biostudies-literature
Project description:Targeted gene regulation is indispensable for reprogramming a cellular network to modulate a microbial phenotype. Here, we adopted the type II CRISPR interference (CRISPRi) system for simple and efficient regulation of target genes in Pseudomonas putida KT2440. A single CRISPRi plasmid was generated to express a nuclease-deficient Cas9 gene and a designed single guide RNA, under control of l-rhamnose-inducible Prha BAD and the constitutive Biobrick J23119 promoter respectively. Two target genes were selected to probe the CRISPRi-mediated gene regulation: exogenous green fluorescent protein on the multicopy plasmid and endogenous glpR on the P. putida KT2440 chromosome, encoding GlpR, a transcriptional regulator that represses expression of the glpFKRD gene cluster for glycerol utilization. The CRISPRi system successfully repressed the two target genes, as evidenced by a reduction in the fluorescence intensity and the lag phase of P. putida KT2440 cell growth on glycerol. Furthermore, CRISPRi-mediated repression of glpR improved both the cell growth and glycerol utilization, resulting in the enhanced production of mevalonate in an engineered P. putida KT2440 harbouring heterologous genes for the mevalonate pathway. CRISPRi is expected to become a robust tool to reprogram P. putida KT2440 for the development of microbial cell factories producing industrially valuable products.
| S-EPMC6922533 | biostudies-literature