scholarly journals Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source

2005 ◽  
Vol 103 (2) ◽  
pp. 389-394 ◽  
Author(s):  
M. Ronen ◽  
D. Botstein
Keyword(s):  
Steady State ◽  
Carbon Source ◽  
Transcriptional Response ◽  
Yeast Cultures

scholarly journals Steady-state analysis of glucose repression reveals hierarchical expression of proteins under Mig1p control in Saccharomyces cerevisiae

2005 ◽  
Vol 388 (3) ◽  
pp. 843-849 ◽  
Author(s):  
Malkhey VERMA ◽  
Paike J. BHAT ◽  
K. V. VENKATESH
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Steady State ◽  
Glucose Repression ◽  
Transcriptional Response ◽  
Mitogen Activated Protein Kinase ◽  
Critical Feature ◽  
Steady State Analysis ◽  
Mitogen Activated Protein ◽  
Kinase Cascade ◽  
State Analysis

Glucose repression is a global transcriptional regulatory mechanism commonly observed in micro-organisms for the repression of enzymes that are not essential for glucose metabolism. In Saccharomyces cerevisiae, Mig1p, a homologue of Wilms' tumour protein, is a global repressor protein dedicated to glucose repression. Mig1p represses genes either by binding directly to the upstream repression sequence of structural genes or by indirectly repressing a transcriptional activator, such as Gal4p. In addition, some genes are repressed by both of the above mechanisms. This raises a fundamental question regarding the physiological relevance of the varied mechanisms of repression that exist involving Mig1p. We address this issue by comparing two well-known glucose-repression systems, that is, SUC2 and GAL gene expression systems, which encompass all the above three mechanisms. We demonstrate using steady-state analysis that these mechanisms lead to a hierarchical glucose repression profile of different family of genes. This switch over from one carbon source to another is well-calibrated as a function of glucose concentration through this hierarchical transcriptional response. The mechanisms prevailing in this repression system can achieve amplification and sensitivity, as observed in the well-characterized MAPK (mitogen-activated protein kinase) cascade system, albeit through a different structure. A critical feature of repression predicted by our steady-state model for the mutant strain of S. cerevisiae lacking Gal80p agrees well with the data reported here as well as that available in the literature.

scholarly journals Global transcriptional response of Methylorubrum extorquens to formaldehyde stress expands the role of EfgA and is distinct from antibiotic translational inhibition

2021 ◽  
Author(s):  
Jannell Bazurto ◽  
Siavash Riazi ◽  
Simon D'Alton ◽  
Daniel E. Deatherage ◽  
Eric L. Bruger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carbon Source ◽  
Transcriptional Response ◽  
Genotoxic Stress ◽  
Biological Molecules ◽  
Regulatory Control ◽  
Translation Inhibition ◽  
Translational Inhibition ◽  
Potential Carbon

The potency and indiscriminate nature of formaldehyde reactivity upon biological molecules make it a universal stressor. However, some organisms such as Methylorubrum extorquens possess means to rapidly and effectively mitigate formaldehyde-induced damage. EfgA is a recently identified formaldehyde sensor predicted to halt translation in response to elevated formaldehyde as a means to protect cells. Herein, we investigate growth and changes in gene expression to understand how M. extorquens responds to formaldehyde with and without the EfgA-formaldehyde-mediated translational response, and how this mechanism compares to antibiotic-mediated translation inhibition. These distinct mechanisms of translation inhibition have notable differences: they each involve different specific players and in addition, formaldehyde also acts as a general, multi-target stressor and a potential carbon source. We present findings demonstrating that in addition to its characterized impact on translation, functional EfgA allows for a rapid and robust transcriptional response to formaldehyde and that removal of EfgA leads to heightened proteotoxic and genotoxic stress in the presence of increased formaldehyde levels. We also found that many downstream consequences of translation inhibition were shared by EfgA-formaldehyde- and kanamycin-mediated translation inhibition. Our work uncovered additional layers of regulatory control enacted by functional EfgA upon experiencing formaldehyde stress, and further demonstrated the importance this protein plays at both transcriptional and translational levels in this model methylotroph.

Thermal hydrolysate as a carbon source for denitrification

1996 ◽  
Vol 33 (12) ◽  
pp. 99-108 ◽  
Author(s):  
John Barlindhaug ◽  
Hallvard Ødegaard
Keyword(s):  
Steady State ◽  
Carbon Source ◽  
Retention Time ◽  
Liquid Fraction ◽  
Wastewater Sludge ◽  
Treated Wastewater ◽  
Thermal Hydrolysis ◽  
Biofilm Reactors ◽  
Hydrolysis Process

Thermal hydrolysate is the liquid fraction (supernatant) of thermally treated wastewater sludge. The objective of the present study was to investigate the quality of thermal hydrolysate as a carbon source for denitrification. Steady state denitrification experiments in moving bed biofilm reactors were carried out. It was demonstrated that 2/3 of the COD in the thermal hydrolysate was utilised as a carbon source in the post denitrification step, with a retention time of 52 minutes. This degree of utilisation is about the same as reported for biological hydrolysate, which generally has been considered to be of better quality as a carbon source than thermal hydrolysate. The yield of soluble COD in the thermal hydrolysis process (180°C in 30 minutes) was found to be 28%. Typical COD-yields for biological hydrolysis are around 11%.

scholarly journals A link between gut community metabolism and pathogenesis: molecular hydrogen-stimulated glucarate catabolism aids Salmonella virulence

Open Biology ◽  
2013 ◽  
Vol 3 (12) ◽  
pp. 130146 ◽  
Author(s):  
Reena Lamichhane-Khadka ◽  
Stéphane L. Benoit ◽  
Susan E. Maier ◽  
Robert J. Maier
Keyword(s):  
Carbon Source ◽  
Molecular Hydrogen ◽  
Carbon Sources ◽  
Transcriptional Response ◽  
Hydrogen Gas ◽  
Serovar Typhimurium ◽  
Salmonella Virulence ◽  
Alternative Carbon Source ◽  
Dependent Growth ◽  
High Level

Glucarate, an oxidized product of glucose, is a major serum organic acid in humans. Still, its role as a carbon source for a pathogen colonizing hosts has not been studied. We detected high-level expression of a potential glucarate permease encoding gene gudT when Salmonella enterica serovar Typhimurium are exposed to hydrogen gas (H 2 ), a gaseous by-product of gut commensal metabolism. A gudT strain of Salmonella is deficient in glucarate-dependent growth, however, it can still use other monosaccharides, such as glucose or galactose. Complementation of the gudT mutant with a plasmid harbouring gudT restored glucarate-dependent growth to wild-type (WT) levels. The gudT mutant exhibits attenuated virulence: the mean time of death for mice inoculated with WT strain was 2 days earlier than for mice inoculated with the gudT strain. At 4 days postinoculation, liver and spleen homogenates from mice inoculated with a gudT strain contained significantly fewer viable Salmonella than homogenates from animals inoculated with the parent. The parent strain grew well H 2 -dependently in a minimal medium with amino acids and glucarate provided as the sole carbon sources, whereas the gudT strain achieved approximately 30% of the parent strain's yield. Glucarate-mediated growth of a mutant strain unable to produce H 2 was stimulated by H 2 addition, presumably owing to the positive transcriptional response to H 2 . Gut microbiota-produced molecular hydrogen apparently signals Salmonella to catabolize an alternative carbon source available in the host. Our results link a gut microbiome-produced diffusible metabolite to augmenting bacterial pathogenesis.

scholarly journals Chlamydia trachomatis Lacks an Adaptive Response to Changes in Carbon Source Availability

2004 ◽  
Vol 72 (7) ◽  
pp. 4286-4289 ◽  
Author(s):  
Tracy L. Nicholson ◽  
Karen Chiu ◽  
Richard S. Stephens
Keyword(s):  
Chlamydia Trachomatis ◽  
Carbon Source ◽  
Adaptive Response ◽  
Environmental Changes ◽  
Carbon Sources ◽  
Transcriptional Response ◽  
Free Living ◽  
Regulate Gene Expression ◽  
Obligate Intracellular ◽  
Obligate Intracellular Pathogen

ABSTRACT Most bacteria coordinately regulate gene expression as an adaptive response to a variety of environmental changes. One key environmental cue is the carbon source necessary for central metabolism. We used microarray analysis to monitor the global transcriptional response of the obligate intracellular pathogen Chlamydia trachomatis to the presence of glycolytic and gluconeogenic carbon sources. In contrast to free-living bacteria, changing the carbon source from glucose to glutamate or α-ketoglutarate had little effect on the global gene transcription of C. trachomatis.

Anti-IL-5 mepolizumab minimally influences residual blood eosinophils in severe asthma

2021 ◽  
pp. 2100935
Author(s):  
Glenn Van Hulst ◽  
Joseph Jorssen ◽  
Nathalie Jacobs ◽  
Monique Henket ◽  
Renaud Louis ◽  
...  
Keyword(s):  
Steady State ◽  
Transcriptional Response ◽  
Long Term Effects ◽  
Neutralising Antibodies ◽  
Eosinophilic Asthma ◽  
Severe Eosinophilic Asthma ◽  
Residual Blood ◽  
Blood Eosinophils

Neutralising antibodies against the cytokine interleukin (IL)-5 have become widely used for the control of severe eosinophilic asthma. Remarkably, patients receiving neutralising anti-IL5 biological therapies retain a very stable population of residual blood eosinophils. Whether these residual eosinophils are endowed with particular biological activity has not yet been studied but is of importance in predicting potential long-term effects of IL5 neutralisation in patients. To tackle the effect of IL5 depletion on residual eosinophils, we used a comparative RNA-sequencing approach and compared the gene expression program of eosinophils arising in IL5-depleted or IL5-replete human or murine hosts, at steady-state in vivo and following in vitro stimulation with the eosinophil-activating alarmin IL33. We compared blood eosinophils from patients with severe allergic eosinophilic asthma treated with anti-IL5 mepolizumab therapy to those of healthy controls and matched asthma patients receiving anti-IgE omalizumab therapy. We made similar comparisons on bone marrow eosinophils from mice genetically deficient or not for IL5. We report that restriction of IL5 availability did not elicit any detectable transcriptional response in steady-state residual eosinophils in mepolizumab-treated patients or IL5-deficient mice, and influenced only a handful of genes in their response to IL33. Together, these results support the notion that treatment with IL5 neutralising antibodies spares a pool of circulating residual eosinophils largely resembling those of healthy individuals.

Effect of oxygen and nitrate on nitrogen fixation and denitrification by Azospirillum brasilense grown in continuous culture

1978 ◽  
Vol 24 (11) ◽  
pp. 1395-1403 ◽  
Author(s):  
L. M. Nelson ◽  
R. Knowles
Keyword(s):  
Nitrogen Fixation ◽  
Steady State ◽  
Carbon Source ◽  
Acetylene Reduction ◽  
Azospirillum Brasilense ◽  
Protective Mechanism ◽  
Culture Vessel ◽  
Sole Nitrogen Source ◽  
Free Medium ◽  
Effect Of Oxygen

Azospirillum brasilense was grown continuously at various levels of dissolved oxygen (O2) in a nitrogen-free medium containing malate as the carbon source. Steady-state cultures were established only at O2 concentrations less than 0.0150 atm (1 atm = 101.325 Pa) and rates of acetylene reduction (N2 fixation) and efficiencies of N2 fixation were maximal between 0.0050–0.0075 atm dissolved O2. These cultures appeared to be O2- or N2-limited. There was no evidence of a respiratory protective mechanism in this organism. Anaerobic denitrifying steady-state cultures were established with nitrate (NO3−) as the sole nitrogen source with no detectable N2 fixation. N2 fixation, but no denitrification, was observed when NO3− was decreased to 10 μg N per millilitre at 0.003 atm dissolved O2. In samples removed from the culture vessel, either activity could be induced with a lag of approximately 120 min by incubation under appropriate conditions.

scholarly journals The Glycerol-Dependent Metabolic Persistence of Pseudomonas putida KT2440 Reflects the Regulatory Logic of the GlpR Repressor

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Pablo I. Nikel ◽  
Francisco J. Romero-Campero ◽  
Joshua A. Zeidman ◽  
Ángel Goñi-Moreno ◽  
Víctor de Lorenzo
Keyword(s):  
Carbon Source ◽  
Pseudomonas Putida ◽  
Molecular Mechanisms ◽  
Transcriptional Response ◽  
Time Dependent ◽  
Lag Phase ◽  
Gradual Change ◽  
Pseudomonas Putida Kt2440 ◽  
Genetic Changes ◽  
Content Type

ABSTRACTThe growth of the soil bacteriumPseudomonas putidaKT2440 on glycerol as the sole carbon source is characterized by a prolonged lag phase, not observed with other carbon substrates. We examined the bacterial growth in glycerol cultures while monitoring the metabolic activity of individual cells. Fluorescence microscopy and flow cytometry, as well as the analysis of the temporal start of growth in single-cell cultures, revealed that adoption of a glycerol-metabolizing regime was not the result of a gradual change in the whole population but rather reflected a time-dependent bimodal switch between metabolically inactive (i.e., nongrowing) and fully active (i.e., growing) bacteria. A transcriptional Φ(glpD-gfp) fusion (a proxy of the glycerol-3-phosphate [G3P] dehydrogenase activity) linked the macroscopic phenotype to the expression of theglpgenes. Either deletingglpR(encoding the G3P-responsive transcriptional repressor that controls the expression of theglpFKRDgene cluster) or altering G3P formation (by overexpressingglpK, encoding glycerol kinase) abolished the bimodalglpDexpression. These manipulations eliminated the stochastic growth start by shortening the otherwise long lag phase. Provision ofglpRintransrestored the phenotypes lost in theΔglpRmutant. The prolonged nongrowth regime ofP. putidaon glycerol could thus be traced to the regulatory device controlling the transcription of theglpgenes. Since the physiological agonist of GlpR is G3P, the arrangement of metabolic and regulatory components at this checkpoint merges a positive feedback loop with a nonlinear transcriptional response, a layout fostering the observed time-dependent shift between two alternative physiological states.IMPORTANCEPhenotypic variation is a widespread attribute of prokaryotes that leads,inter alia, to the emergence of persistent bacteria, i.e., live but nongrowing members within a genetically clonal population. Persistence allows a fraction of cells to avoid the killing caused by conditions or agents that destroy most growing bacteria (e.g., some antibiotics). Known molecular mechanisms underlying the phenomenon include genetic changes, epigenetic variations, and feedback-based multistability. We show that a prolonged nongrowing state of the bacterial population can be brought about by a distinct regulatory architecture of metabolic genes when cells face specific nutrients (e.g., glycerol).Pseudomonas putidamay have adopted the resulting carbon source-dependent metabolic bet hedging as an advantageous trait for exploring new chemical and nutritional landscapes. Defeating such naturally occurring adaptive features of environmental bacteria is instrumental in improving the performance of these microorganisms as whole-cell catalysts in a bioreactor setup.

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