scholarly journals Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium

2019 ◽  
Vol 21 (11) ◽  
pp. 4446-4459 ◽  
Author(s):  
Lázaro Molina ◽  
Ruggero La Rosa ◽  
Juan Nogales ◽  
Fernando Rojo
Keyword(s):  
Pseudomonas Putida ◽  
Complete Medium ◽  
Substrate Uptake ◽  
Global Regulator ◽  
Pseudomonas Putida Kt2440 ◽  
Metabolic Fluxes ◽  
Uptake Rates

scholarly journals The Target for the Pseudomonas putida Crc Global Regulator in the Benzoate Degradation Pathway Is the BenR Transcriptional Regulator

2007 ◽  
Vol 190 (5) ◽  
pp. 1539-1545 ◽  
Author(s):  
Renata Moreno ◽  
Fernando Rojo
Keyword(s):  
Pseudomonas Putida ◽  
Target Genes ◽  
Carbon Sources ◽  
Degradation Pathway ◽  
Complete Medium ◽  
Mrna Levels ◽  
Global Regulator ◽  
Benzoate Degradation ◽  
Transcriptional Units ◽  
Degradation Intermediates

ABSTRACT Crc protein is a global regulator involved in catabolite repression control of several pathways for the assimilation of carbon sources in pseudomonads when other preferred substrates are present. In Pseudomonas putida cells growing exponentially in a complete medium containing benzoate, Crc strongly inhibits the expression of the benzoate degradation genes. These genes are organized into several transcriptional units. We show that Crc directly inhibits the expression of the peripheral genes that transform benzoate into catechol (the ben genes) but that its effect on genes corresponding to further steps of the pathway (the cat and pca genes of the central catechol and β-ketoadipate pathways) is indirect, since these genes are not induced because the degradation intermediates, which act as inducers, are not produced. Crc inhibits the translation of target genes by binding to mRNA. The expression of the ben, cat, and pca genes requires the BenR, CatR, and PcaR transcriptional activators, respectively. Crc significantly reduced benABCD mRNA levels but did not affect those of benR. Crc bound to the 5′ end of benR mRNA but not to equivalent regions of catR and pcaR mRNAs. A translational fusion of the benR and lacZ genes was sensitive to Crc, but a transcriptional fusion was not. We propose that Crc acts by reducing the translation of benR mRNA, decreasing BenR levels below those required for the full expression of the benABCD genes. This strategy provides great metabolic flexibility, allowing the hierarchical assimilation of different structurally related compounds that share a common central pathway by selectively regulating the entry of each substrate into the central pathway.

scholarly journals Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan

2018 ◽  
Author(s):  
Simeon Leupold ◽  
Georg Hubmann ◽  
Athanasios Litsios ◽  
Anne C. Meinema ◽  
Alexandros Papagiannakis ◽  
...  
Keyword(s):  
Metabolic Changes ◽  
Cellular Aging ◽  
Substrate Uptake ◽  
Comprehensive Description ◽  
Cellular Processes ◽  
Metabolic Fluxes ◽  
Age Related ◽  
Uptake Rates ◽  
Inference Methods ◽  
Holistic Description

A comprehensive description of the phenotypic changes during cellular aging is key towards unraveling its causal forces. Using recently developed experimental tools, which previously had enabled us to map age related changes in proteome and transcriptome (Janssens et al., 2015), and model-based inference methods, here, we generated a comprehensive account of the metabolic changes during the entire replicative life of Saecharomyces cerevisiae. With age, we found decreasing metabolite levels, decreasing growth and substrate uptake rates accompanied by a switch from aerobic fermentation to a respiratory metabolism, with increased glycerol and acetate production. The identification of intracellular metabolic fluxes revealed an increase in redox cofactor turnover, likely to combat the increased production of reactive oxygen species. The identified metabolic changes possibly reflect a dynamic adaptation to the age-associated, non- homeostatic increase in volume. With metabolism being an important factor of the cellular phenotype, this work complements our recent mapping of the transcriptomic and proteomic changes towards a holistic description of the cellular processes during aging.

The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: Evidence from proteomic and genomic analyses

PROTEOMICS ◽  
2009 ◽  
Vol 9 (11) ◽  
pp. 2910-2928 ◽  
Author(s):  
Renata Moreno ◽  
Montserrat Martínez-Gomariz ◽  
Luis Yuste ◽  
Concha Gil ◽  
Fernando Rojo
Keyword(s):  
Amino Acids ◽  
Pseudomonas Putida ◽  
Complete Medium ◽  
Global Regulator ◽  
Genomic Analyses

scholarly journals Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Simeon Leupold ◽  
Georg Hubmann ◽  
Athanasios Litsios ◽  
Anne C Meinema ◽  
Vakil Takhaveev ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Metabolic Changes ◽  
Cellular Aging ◽  
Substrate Uptake ◽  
Cellular Phenotype ◽  
Experimental Procedure ◽  
Metabolic Fluxes ◽  
Age Related ◽  
Uptake Rates ◽  
Holistic Description

A comprehensive description of the phenotypic changes during cellular aging is key towards unraveling its causal forces. Previously, we mapped age-related changes in the proteome and transcriptome (Janssens et al., 2015). Here, employing the same experimental procedure and model-based inference, we generate a comprehensive account of metabolic changes during the replicative life of Saccharomyces cerevisiae. With age, we found decreasing metabolite levels, decreasing growth and substrate uptake rates accompanied by a switch from aerobic fermentation to respiration, with glycerol and acetate production. The identified metabolic fluxes revealed an increase in redox cofactor turnover, likely to combat increased production of reactive oxygen species. The metabolic changes are possibly a result of the age-associated decrease in surface area per cell volume. With metabolism being an important factor of the cellular phenotype, this work complements our recent mapping of the transcriptomic and proteomic changes towards a holistic description of the cellular phenotype during aging.

scholarly journals The exopolysaccharide gene cluster pea is transcriptionally controlled by RpoS and repressed by AmrZ in Pseudomonas putida KT2440

2019 ◽  
Vol 218 ◽  
pp. 1-11 ◽  
Author(s):  
Huizhong Liu ◽  
Huaduo Yan ◽  
Yujie Xiao ◽  
Hailing Nie ◽  
Qiaoyun Huang ◽  
...  
Keyword(s):  
Pseudomonas Putida ◽  
Gene Cluster ◽  
Pseudomonas Putida Kt2440

scholarly journals Conversion and assimilation of furfural and 5-(hydroxymethyl)furfural by Pseudomonas putida KT2440

2017 ◽  
Vol 4 ◽  
pp. 22-28 ◽  
Author(s):  
Michael T. Guarnieri ◽  
Mary Ann Franden ◽  
Christopher W. Johnson ◽  
Gregg T. Beckham
Keyword(s):  
Pseudomonas Putida ◽  
Pseudomonas Putida Kt2440 ◽  
Hydroxymethyl Furfural

scholarly journals Formation of trans Fatty Acids Is Not Involved in Growth-Linked Membrane Adaptation of Pseudomonas putida

2005 ◽  
Vol 71 (4) ◽  
pp. 1915-1922 ◽  
Author(s):  
Claus Härtig ◽  
Norbert Loffhagen ◽  
Hauke Harms
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Pseudomonas Putida ◽  
De Novo ◽  
Isomerization Reaction ◽  
Cyclopropane Fatty Acid ◽  
Substrate Uptake ◽  
Resting Cells ◽  
Saturation Degree ◽  
Fatty Acid Compositions

ABSTRACT Fatty acid compositions in growing and resting cells of several strains of Pseudomonas putida (P8, NCTC 10936, and KT 2440) were studied, with a focus on alterations of the saturation degree, cis-trans isomerization, and cyclopropane formation. The fatty acid compositions of the strains were very similar under comparable growth conditions, but surprisingly, and contrary to earlier reports, trans fatty acids were not found in either exponentially growing cells or stationary-phase cells. During the transition from growth to the starvation state, cyclopropane fatty acids were preferentially formed, an increase in the saturation degree of fatty acids was observed, and larger amounts of hydroxy fatty acids were detected. A lowered saturation degree and concomitant higher membrane fluidity seemed to be optimal for substrate uptake and growth. The incubation of cells under nongrowth conditions rapidly led to the formation of trans fatty acids. We show that harvesting and sample preparation for analysis could provoke the enzyme-catalyzed formation of trans fatty acids. Freeze-thawing of resting cells and increased temperatures accelerated the formation of trans fatty acids. We demonstrate that cis-trans isomerization only occurred in cells that were subjected to an abrupt disturbance without having the possibility of adapting to the changed conditions by the de novo synthesis of fatty acids. The cis-trans isomerization reaction was in competition with the cis-to-cyclopropane fatty acid conversion. The potential for the formation of trans fatty acids depended on the cyclopropane content that was already present.

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