Generation of Ionic Liquid Tolerant Pseudomonas putida KT2440 Strains via Adaptive Laboratory Evolution
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ABSTRACT:
PROVIDER: PRJNA630234 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11684953_1.fastq.gz | Fastqsanger.gz | |||
| SRR11684953_2.fastq.gz | Fastqsanger.gz | |||
| SRR11684954_1.fastq.gz | Fastqsanger.gz | |||
| SRR11684954_2.fastq.gz | Fastqsanger.gz | |||
| SRR11684955_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome of the wildtype or evolved Pseudomonas putida KT2440
2020-07-08 | GSE149827 | GEO
Project description:BackgroundThere is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass.MethodsTo generate strains capable of tolerating residual ILs present in treated feedstocks, a tolerance adaptive laboratory evolution (TALE) approach was developed and utilized to improve growth of two different Escherichia coli strains, DH1 and K-12 MG1655, in the presence of two different ionic liquids, 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]) and 1-butyl-3-methylimidazolium chloride ([C4C1Im]Cl). For multiple parallel replicate populations of E. coli, cells were repeatedly passed to select for improved fitness over the course of approximately 40 days. Clonal isolates were screened and the best performing isolates were subjected to whole genome sequencing.ResultsThe most prevalent mutations in tolerant clones occurred in transport processes related to the functions of mdtJI, a multidrug efflux pump, and yhdP, an uncharacterized transporter. Additional mutations were enriched in processes such as transcriptional regulation and nucleotide biosynthesis. Finally, the best-performing strains were compared to previously characterized tolerant strains and showed superior performance in tolerance of different IL and media combinations (i.e., cross tolerance) with robust growth at 8.5% (w/v) and detectable growth up to 11.9% (w/v) [C2C1Im][OAc].ConclusionThe generated strains thus represent the best performing platform strains available for bioproduction utilizing IL-treated renewable substrates, and the TALE method was highly successful in overcoming the general issue of substrate toxicity and has great promise for use in tolerance engineering.
| S-EPMC5691611 | biostudies-literature
Project description:The study aims essentially in the analysis of the transcriptomic and metabolomic profiles induced by the presence of the tested ionic liquids in the metabolism of Aspergillus nidulans. Focusing specially on the secondary metabolism, which genes are clustered.
2016-04-18 | GSE65946 | GEO
Project description:Changes in the Gut Microbiota of Mice Orally Exposed to Methylimidazolium Ionic Liquids: an Observational Study
| PRJEB33735 | ENA
Project description:The completely sequenced catabolic plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon the recipient strain Pseudomonas putida KT2440. To study the coordinated expression of pCAR1 with its host chromosome, transcriptome of the transconjugant strain KT2440(pCAR1) was analyzed at growth with carbazole as the sole carbon source compared to succinate as an alternative carbon source. Next, horizontal gene transfer of a plasmid potentially alters the transcriptome of its host chromosome. Transcriptome of the transconjugant strain KT2440(pCAR1) was compared to the parental strain KT2440 at the same growth conditions. Furthermore, pCAR1 encodes a possible global regulator designated ORF70, which belongs to the MvaT family of H-NS-like nucleoid-associated proteins in Pseudomonas. To investigate the regulon under the control of ORF70, transcriptome of KT2440(pCAR1deltaORF70) was compared to the parental strain KT2440(pCAR1) at the same growth conditions. Keywords: Comparative transcriptome analysis
2007-05-01 | GSE7650 | GEO
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida KT2440 and DOT-T1E in the presence of toluene with the aim to study in more detail the mechanisms involved in toluene response in a toluene-sensitive and a toluene-tolerant strains.
2017-06-04 | GSE86321 | GEO
Project description:Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium (M9 with glucose) saturated with naphthalene.
2012-07-27 | E-MEXP-3411 | biostudies-arrayexpress
Project description:We have employed molecular dynamics to investigate the differences in ionic liquid tolerance among three distinct family 5 cellulases from Trichoderma viride, Thermogata maritima, and Pyrococcus horikoshii. Simulations of the three cellulases were conducted at a range of temperatures in various binary mixtures of the ionic liquid 1-ethyl-3-methyl-imidazolium acetate with water. Our analysis demonstrates that the effects of ionic liquids on the enzymes vary in each individual case from local structural disturbances to loss of much of one of the enzyme's secondary structure. Enzymes with more negatively charged surfaces tend to resist destabilization by ionic liquids. Specific and unique structural changes in the enzymes are induced by the presence of ionic liquids. Disruption of the secondary structure, changes in dynamical motion, and local changes in the binding pocket are observed in less tolerant enzymes. Ionic-liquid-induced denaturation of one of the enzymes is indicated over the 500 ns timescale. In contrast, the most tolerant cellulase behaves similarly in water and in ionic-liquid-containing mixtures. Unlike the heuristic approaches that attempt to predict enzyme stability using macroscopic properties, molecular dynamics allows us to predict specific atomic-level structural and dynamical changes in an enzyme's behavior induced by ionic liquids and other mixed solvents. Using these insights, we propose specific experimentally testable hypotheses regarding the origin of activity loss for each of the systems investigated in this study.
| S-EPMC4336362 | biostudies-literature
Project description:Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using E. coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above ~1.0 Os kg-1 causes a dose-dependent K+ leak from the cell, resulting in a substantial decrease in cytosolic K+ content and a concurrent accumulation of Na+ in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K+ uptake. Ion flux data is consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K+ uptake to efflux. Microarray experiments reveal that about 40% of up-regulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic- and non-ionic osmotica The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K+ transporters for bacterial adaptation to hyperosmotic stress. Experiment Overall Design: Two biological replicates per treatment with microarray analysis using the Affymetrix GeneChip E. coli Genome array. Treatments used included: Experiment Overall Design: Control - E. coli Frag1, grown to early stationary growth phase in a mineral salts medium with 0.1% glucose at 25 C Experiment Overall Design: Sucrose hyperosmotic treatment - 1.25 M sucrose added to control culture Experiment Overall Design: for 10 min. Experiment Overall Design: NaCl hyperosmotic treatment - 1.37 M NaCl added to control culture Experiment Overall Design: For microarray data comparisons the sucrose and NaCl hyperosmotic treatment data was compared to the no treatment control data separately. The sucrose to control and NaCL to control comparison data tables are linked below.
2008-10-21 | E-GEOD-12190 | biostudies-arrayexpress
Project description:Our first aim was understand whole genome expression dynamics of Pseudomonas putida KT2440 surface colonies under water stress. Therefore, we wanted to identify significantly differentially expressed genes of at -0.4 MPa matric potential relative to the -0.5 kPa (near saturation condition) at different stress durations. Aliquots of overnight grown P. putida KT2440 cells were inoculated (approx. 100 µl and 1x107 cells) on the surface of ceramic plates. Prior to matric stress, the cells were incubated for 120, 116, 96, and 48 hr at-0.5 kPa to allow formation of a mature cell loan. -0.4 MPa matric potential was applied for the last 0 (control), 4, 24, and 72 hr of incubation periods, respectively, so that the total incubation time (at (-0.5 kPa) and (-0.4 MPa)) was kept constant as 5 days. Our second aim was to find out how the gene expression profile would change when we use PEG-8000 to simulate matric stress. To that effect, similar incubations were performed where the direct matric potential was -0.5 kPa, but supplemented with PEG-8000 to set a matric potential equivalent of -0.5 or -1.0 MPa. Incubations were again 5 days. In addition, we tested the effect of gas pressure on gene expression profile of cells in liquid medium. 20 ml of overnight grown KT2440 cells were exposed to 0.4 MPa (gauge) and 0.1 MPa (atmospheric) pressures.
2010-11-24 | GSE25512 | GEO