Prediction of novel non-coding RNAs relevant for the growth of Pseudomonas putida in a bioreactor

Pobre, Vânia; Graça-Lopes, Gil; Saramago, Margarida; Ankenbauer, Andreas; Arraiano, Cecília M.; Viegas, Sandra C.

doi:10.1099/mic.0.000875

Cited by 7 publications

(6 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Other promising deletions may comprise the knock-out of non-necessary carbon uptake and processing pathway which are numerously present in the degrading microbe P. putida and which are not necessary when the cell is growing in well-defined synthetic media. Moreover, the knowledge of numerous non-coding RNAs that were recently discovered in repeatedly starving P. putida KT2440 (Pobre et al, 2020) targets to genetically optimize this strain for large-scale application.…”

Section: Transient Carbon Starvation Intensifies Catabolic Reactionsmentioning

confidence: 99%

Pseudomonas putida KT2440 is naturally endowed to withstand industrial‐scale stress conditions

Ankenbauer

Schäfer

Viegas

et al. 2020

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

Pseudomonas putida is recognized as a very promising strain for industrial application due to its high redox capacity and frequently observed tolerance towards organic solvents. In this research, we studied the metabolic and transcriptional response of P. putida KT2440 exposed to large-scale heterogeneous mixing conditions in the form of repeated glucose shortage. Cellular responses were mimicked in an experimental setup comprising a stirred tank reactor and a connected plug flow reactor. We deciphered that a stringent response-like transcriptional regulation programme is frequently induced, which seems to be linked to the intracellular pool of 3-hydroxyalkanoates (3-HA) that are known to serve as precursors for polyhydroxyalkanoates (PHA). To be precise, P. putida is endowed with a survival strategy likely to access cellular PHA, amino acids and glycogen in few seconds under glucose starvation to obtain ATP from respiration, thereby replenishing the reduced ATP levels and the adenylate energy charge. Notably, cells only need 0.4% of glucose uptake to build those 3-HA-based energy buffers. Concomitantly, genes that are related to amino acid catabolism and b-oxidation are upregulated during the transient absence of glucose. Furthermore, we provide a detailed list of transcriptional short-and long-term responses that increase the cellular maintenance by about 17% under the industrial-like conditions tested.

show abstract

Section: Transient Carbon Starvation Intensifies Catabolic Reactionsmentioning

confidence: 99%

Pseudomonas putida KT2440 is naturally endowed to withstand industrial‐scale stress conditions

Ankenbauer

Schäfer

Viegas

et al. 2020

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Adapter contamination and low-quality and ambiguous nucleotides were trimmed from the remaining reads. The overall quality assessment of each corrected data set was carried out using FastQC 77 . Single-end reads from the Next-Seq500 were mapped against the de novo assemblies with Bowtie2 and SAMtools v.0.1.19 was used for format file conversion 77 .…”

Section: Transcriptomic Analysismentioning

confidence: 99%

“…The overall quality assessment of each corrected data set was carried out using FastQC 77 . Single-end reads from the Next-Seq500 were mapped against the de novo assemblies with Bowtie2 and SAMtools v.0.1.19 was used for format file conversion 77 . Differential expression analyses were performed with the R package edgeR 78 , after identified features with zero reads in every conditions were removed.…”

Section: Transcriptomic Analysismentioning

confidence: 99%

Genipin prevents alpha-synuclein aggregation and toxicity by affecting endocytosis, metabolism and lipid storage

et al. 2023

View full text Add to dashboard Cite

Parkinson’s Disease (PD) is a common neurodegenerative disorder affecting millions of people worldwide for which there are only symptomatic therapies. Small molecules able to target key pathological processes in PD have emerged as interesting options for modifying disease progression. We have previously shown that a (poly)phenol-enriched fraction (PEF) of Corema album L. leaf extract modulates central events in PD pathogenesis, namely α-synuclein (αSyn) toxicity, aggregation and clearance. PEF was now subjected to a bio-guided fractionation with the aim of identifying the critical bioactive compound. We identified genipin, an iridoid, which relieves αSyn toxicity and aggregation. Furthermore, genipin promotes metabolic alterations and modulates lipid storage and endocytosis. Importantly, genipin was able to prevent the motor deficits caused by the overexpression of αSyn in a Drosophila melanogaster model of PD. These findings widens the possibility for the exploitation of genipin for PD therapeutics.

show abstract

“…We named the compendium putidaPRECISE321, for putida Precision RNA-seq Expression Compendium for Independent Signal Exploration. It consists of 321 samples from 118 unique experimental conditions across 21 projects [22][23][24][25][26][27][28][29][30][31] . We centered each project to a baseline condition in order to remove batch effects (Supplementary Fig.…”

Section: Ica Reveals 84 Independently Modulated Groups Of Genes In P ...mentioning

confidence: 99%

Machine-learning fromPseudomonas putidaTranscriptomes Reveals Its Transcriptional Regulatory Network

Lim

Rychel

Sastry

et al. 2022

Preprint

View full text Add to dashboard Cite

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1,993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

show abstract

Prediction of novel non-coding RNAs relevant for the growth of Pseudomonas putida in a bioreactor

Cited by 7 publications

References 38 publications

Pseudomonas putida KT2440 is naturally endowed to withstand industrial‐scale stress conditions

Pseudomonas putida KT2440 is naturally endowed to withstand industrial‐scale stress conditions

Genipin prevents alpha-synuclein aggregation and toxicity by affecting endocytosis, metabolism and lipid storage

Machine-learning fromPseudomonas putidaTranscriptomes Reveals Its Transcriptional Regulatory Network

Contact Info

Product

Resources

About