scholarly journals Ribosome provisioning activates a bistable switch coupled to fast exit from stationary phase

2018 ◽  
Author(s):  
P. Remigi ◽  
G.C. Ferguson ◽  
S. De Monte ◽  
P.B. Rainey
Keyword(s):  
Stationary Phase ◽  
Phenotypic Switch ◽  
Activation Threshold ◽  
Bistable Switch ◽  
Genetic Components ◽  
Colanic Acid ◽  
Stochastic Entry ◽  
Molecular Bases ◽  
Ribosome Biosynthesis ◽  
Selective Regime

AbstractObservations of bacteria at the single-cell level have revealed many instances of phenotypic heterogeneity within otherwise clonal populations, but the selective causes, molecular bases and broader ecological relevance remain poorly understood. In an earlier experiment in which the bacteriumPseudomonas fluorescensSBW25 was propagated under a selective regime that mimicked the host immune response, a genotype evolved that stochastically switched between capsulation states. The genetic cause was a mutation incarBthat decreased the pyrimidine pool (and growth rate), lowering the activation threshold of a pre-existing but hitherto unrecognised phenotypic switch. Genetic components surrounding bifurcation of UTP flux towards DNA/RNA or UDP-glucose (a precursor of colanic acid forming the capsules) were implicated as key components. Extending these molecular analyses – and based on a combination of genetics, transcriptomics, biochemistry and mathematical modelling – we show that pyrimidine limitation triggers an increase in ribosome biosynthesis and that switching is caused by competition between ribosomes and CsrA/RsmA proteins for the mRNA transcript of a feed-forward regulator of colanic acid biosynthesis. We additionally show that in the ancestral bacterium the switch is part of a programme that determines stochastic entry into the semi-quiescent capsulated state, ensures that such cells are provisioned with excess ribosomes, and enables provisioned cells to exit rapidly from stationary phase under permissive conditions.

scholarly journals Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase

2019 ◽  
Vol 36 (5) ◽  
pp. 1056-1070 ◽  
Author(s):  
Philippe Remigi ◽  
Gayle C Ferguson ◽  
Ellen McConnell ◽  
Silvia De Monte ◽  
David W Rogers ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Activation Threshold ◽  
Bistable Switch ◽  
Genetic Components ◽  
Colanic Acid ◽  
Stochastic Entry ◽  
Pseudomonas Fluorescens Sbw25 ◽  
Molecular Bases ◽  
Ribosome Biosynthesis ◽  
Selective Regime

Abstract Observations of bacteria at the single-cell level have revealed many instances of phenotypic heterogeneity within otherwise clonal populations, but the selective causes, molecular bases, and broader ecological relevance remain poorly understood. In an earlier experiment in which the bacterium Pseudomonas fluorescens SBW25 was propagated under a selective regime that mimicked the host immune response, a genotype evolved that stochastically switched between capsulation states. The genetic cause was a mutation in carB that decreased the pyrimidine pool (and growth rate), lowering the activation threshold of a preexisting but hitherto unrecognized phenotypic switch. Genetic components surrounding bifurcation of UTP flux toward DNA/RNA or UDP-glucose (a precursor of colanic acid forming the capsules) were implicated as key components. Extending these molecular analyses—and based on a combination of genetics, transcriptomics, biochemistry, and mathematical modeling—we show that pyrimidine limitation triggers an increase in ribosome biosynthesis and that switching is caused by competition between ribosomes and CsrA/RsmA proteins for the mRNA transcript of a positively autoregulated activator of colanic acid biosynthesis. We additionally show that in the ancestral bacterium the switch is part of a program that determines stochastic entry into a semiquiescent capsulated state, ensures that such cells are provisioned with excess ribosomes, and enables provisioned cells to exit rapidly from stationary phase under permissive conditions.

scholarly journals Combinations of 4 mutations (FV R506Q, FV H1299R, FV Y1702C, PT 20210G/A) affecting the prothrombinase complex in a thrombophilic family

Blood ◽  
2000 ◽  
Vol 96 (4) ◽  
pp. 1443-1448 ◽  
Author(s):  
Elisabetta Castoldi ◽  
Paolo Simioni ◽  
Michael Kalafatis ◽  
Barbara Lunghi ◽  
Daniela Tormene ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Family Members ◽  
Causative Role ◽  
Laboratory Findings ◽  
Prothrombinase Complex ◽  
Apc Resistance ◽  
Genetic Components ◽  
The Family ◽  
Molecular Bases

Abstract The study of the molecular bases of thrombophilia in a large family with 4 symptomatic members is reported. Three thrombophilic genetic components (FV R506Q, FV H1299R, and PT 20210G/A), all affecting the activity of the prothrombinase complex, were detected alone and in combination in various family members. In addition, a newly identified missense mutation (factor V [FV] Y1702C), causing FV deficiency, was also present in the family and appeared to enhance activated protein C (APC) resistance in carriers of FV R506Q or FV H1299R by abolishing the expression of the counterpart FV allele. The relationships between complex genotypes, coagulation laboratory findings, and clinical phenotypes were analyzed in the family. All symptomatic family members were carriers of combined defects and showed APC resistance and elevated F1 + 2 values. Evidence for the causative role of the FV Y1702C mutation, which affects a residue absolutely conserved in all 3 A domains of FV, factor VIII, and ceruloplasmin, relies on (1) the absolute cosegregation between the mutation and FV deficiency, both in the family and in the general population; (2) FV antigen and immunoblot studies indicating the absence of Y1702C FV molecules in plasma of carriers of the mutation, despite normal levels of the FV Y1702C messenger RNA; and (3) molecular modeling data that support a crucial role of the mutated residue in the A domain structure. These findings help to interpret the variable penetrance of thrombosis in thrombophilic families and to define the molecular bases of FV deficiency.

scholarly journals A four-step regulatory cascade controls bistable transfer competence development of the integrative and conjugative element ICEclc in Pseudomonas

2019 ◽  
Author(s):  
Nicolas Carraro ◽  
Xavier Richard ◽  
Sandra Sulser ◽  
François Delavat ◽  
Christian Mazza ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Stationary Phase ◽  
Network Architecture ◽  
Recipient Cell ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Bistable Switch ◽  
Integrative And Conjugative Elements ◽  
Regulatory Cascade ◽  
Integrative And Conjugative Element

AbstractGenetic bistability controls different phenotypic programs in defined subpopulations of genetically identical bacteria. Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, but this state arises only in 3-5% of individual cells. The mechanisms controlling and underlying the bistable switch between non-active and transfer competence cells have long remained enigmatic. Using a variety of genetic tools combined with stochastic modeling, we characterize here the factors and overall network architecture controlling bistable ICEclc activation of transfer competence. Two new key regulators (BisR and BisDC) were uncovered, that link the hierarchical cascade of ICEclc transfer competence activation to in total four regulatory nodes. The final activator complex named BisDC drives a positive feedback on its own transcription, and directly controls the “late” ICE promoters for excision and transfer. Stochastic mathematical modeling conceptually explained the arisal and maintenance of bistability by the feedback loop, and demonstrated its importance to guarantee consistent prolonged downstream output in activated cells. A minimized gene set allowing controllable bistable output in a Pseudomonas putida in absence of the ICEclc largely confirmed model predictions. Phylogenetic analyses further showed that the two new ICEclc regulatory factors are widespread among putative ICEs found in Gamma- and Beta- proteobacteria, highlighting the conceptual importance of our findings for the behaviour of this wide family of conjugative elements.Author summaryIntegrative and conjugative elements (ICEs) are mobile genetic elements present in virtually every bacterial species, which can confer adaptive functions to their host, such as antibiotic resistance or xenometabolic pathways. Integrated ICEs maintain by replication along with the genome of their bacterial host, but in order to transfer, the ICE excises and conjugates into a new recipient cell. Single-cell studies on a unique but widely representative ICE model from Pseudomonas (ICEclc) showed that transfer only occurs from a small dedicated subpopulation of cells that arises during stationary phase conditions. This bistable subpopulation differentiation is highly significant for ICE behaviour and fitness, but how it is regulated has remained largely unknown. The present work unveiled the architecture of the ICEclc transfer competence regulation, and showed its widespread occurrence among ICEs of the same family. Stochastic mathematical modeling explained how bistability is generated and maintained, prolonging the capacity of stationary phase cells to complete all stages of ICE activation.

scholarly journals Combinations of 4 mutations (FV R506Q, FV H1299R, FV Y1702C, PT 20210G/A) affecting the prothrombinase complex in a thrombophilic family

Blood ◽  
2000 ◽  
Vol 96 (4) ◽  
pp. 1443-1448 ◽  
Author(s):  
Elisabetta Castoldi ◽  
Paolo Simioni ◽  
Michael Kalafatis ◽  
Barbara Lunghi ◽  
Daniela Tormene ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Family Members ◽  
Causative Role ◽  
Laboratory Findings ◽  
Prothrombinase Complex ◽  
Apc Resistance ◽  
Genetic Components ◽  
The Family ◽  
Molecular Bases

The study of the molecular bases of thrombophilia in a large family with 4 symptomatic members is reported. Three thrombophilic genetic components (FV R506Q, FV H1299R, and PT 20210G/A), all affecting the activity of the prothrombinase complex, were detected alone and in combination in various family members. In addition, a newly identified missense mutation (factor V [FV] Y1702C), causing FV deficiency, was also present in the family and appeared to enhance activated protein C (APC) resistance in carriers of FV R506Q or FV H1299R by abolishing the expression of the counterpart FV allele. The relationships between complex genotypes, coagulation laboratory findings, and clinical phenotypes were analyzed in the family. All symptomatic family members were carriers of combined defects and showed APC resistance and elevated F1 + 2 values. Evidence for the causative role of the FV Y1702C mutation, which affects a residue absolutely conserved in all 3 A domains of FV, factor VIII, and ceruloplasmin, relies on (1) the absolute cosegregation between the mutation and FV deficiency, both in the family and in the general population; (2) FV antigen and immunoblot studies indicating the absence of Y1702C FV molecules in plasma of carriers of the mutation, despite normal levels of the FV Y1702C messenger RNA; and (3) molecular modeling data that support a crucial role of the mutated residue in the A domain structure. These findings help to interpret the variable penetrance of thrombosis in thrombophilic families and to define the molecular bases of FV deficiency.

scholarly journals BAX and SMAC Regulate Bistable Properties of the Apoptotic Caspase System

2019 ◽  
Author(s):  
Stephanie McKenna ◽  
Lucía García-Gutiérrez ◽  
David Matallanas ◽  
Dirk Fey
Keyword(s):  
Cell Line ◽  
Cellular Response ◽  
Current Knowledge ◽  
Cellular Biology ◽  
Caspase Activation ◽  
Activation Threshold ◽  
Bistable Switch ◽  
Bax Protein ◽  
Cell Line Panel ◽  
Biochemical Mechanisms

AbstractThe initiation of apoptosis is a core mechanism in cellular biology by which organisms control the removal of damaged or unnecessary cells. The irreversible activation of caspases is essential for apoptosis, and mathematical models have demonstrated that the process is tightly regulated by positive feedback and a bistable switch. BAX and SMAC are often dysregulated in diseases such as cancer or neurodegeneration and are two key regulators that interact with the caspase system generating the apoptotic switch. Here we present a mathematical model of how BAX and SMAC control the apoptotic switch. Formulated as a system of ordinary differential equations, the model summarises experimental and computational evidence form the literature and incorporates the biochemical mechanisms of how BAX and SMAC interact with the components of the caspase system. Using simulations and bifurcation analysis, we find that both BAX and SMAC regulate the time-delay and activation threshold of the apoptotic switch. Interestingly, the model predicted that BAX (not SMAC) controls the amplitude of the apoptotic switch. Cell culture experiments using siRNA mediated BAX and SMAC knockdowns this model prediction. We further validated the model on data of the NCI-60 cell line panel using BAX protein expression as cell-line specific parameter and show that model simulations correlated with the cellular response to DNA damaging drugs and established a defined threshold for caspase activation that could distinguish between sensitive and resistant melanoma cells. In summary, we present an experimentally validated dynamic model that summarises our current knowledge of how BAX and SMAC regulate the bistable properties of irreversible caspase activation during apoptosis.

Morphological Characterization of Mycobacteriophage R1

1974 ◽  
Vol 32 ◽  
pp. 254-255
Author(s):  
B. L. Soloff ◽  
T. A. Rado
Keyword(s):  
Carbon Source ◽  
Stationary Phase ◽  
Growth Phase ◽  
Minimal Medium ◽  
Morphological Characterization ◽  
Logarithmic Growth Phase ◽  
Complete Lysis ◽  
Lysogenic Culture ◽  
Logarithmic Growth

Mycobacteriophage R1 was originally isolated from a lysogenic culture of M. butyricum. The virus was propagated on a leucine-requiring derivative of M. smegmatis, 607 leu−, isolated by nitrosoguanidine mutagenesis of typestrain ATCC 607. Growth was accomplished in a minimal medium containing glycerol and glucose as carbon source and enriched by the addition of 80 μg/ ml L-leucine. Bacteria in early logarithmic growth phase were infected with virus at a multiplicity of 5, and incubated with aeration for 8 hours. The partially lysed suspension was diluted 1:10 in growth medium and incubated for a further 8 hours. This permitted stationary phase cells to re-enter logarithmic growth and resulted in complete lysis of the culture.

Molecular Bases of Protective Immune Responses against BotuIInum Neurotoxin A—How Antitoxin Antibodies Block Its Action

2007 ◽  
Vol 27 (4) ◽  
pp. 319-341 ◽  
Author(s):  
M. Zouhair Atassi ◽  
Behzod Z. Dolimbek ◽  
Lance E. Steward ◽  
K. Roger Aoki
Keyword(s):  
Immune Responses ◽  
Molecular Bases

The Determination of Shortwave Asymptotics of Scattered Fields by the Stationary-Phase Method

2000 ◽  
Vol 54 (7) ◽  
pp. 14-22 ◽  
Author(s):  
Il'ya Vladimirovich Sukharevskii ◽  
Oleg ll'ich Sukharevsky
Keyword(s):  
Stationary Phase ◽  
Phase Method ◽  
Stationary Phase Method ◽  
Scattered Fields

Chiral drugs separation by a new antibiotics-based chiral stationary phase

2014 ◽  
Author(s):  
Chunye Liu ◽  
Yanqing Miao ◽  
Yihui Guo ◽  
Yinjuan An ◽  
Yunfang Li ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Chiral Stationary Phase ◽  
Chiral Drugs ◽  
New Antibiotics
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