The stochastic dynamical behaviors of the gene regulatory circuit in Bacillus subtilis

ABSTRACTSpoIIQ is an essential component of a channel connecting the developing forespore to the adjacent mother cell duringBacillus subtilissporulation. This channel is generally required for late gene expression in the forespore, including that directed by the late-acting sigma factor σG. Here, we present evidence that SpoIIQ also participates in a previously unknown gene regulatory circuit that specifically represses expression of the gene encoding the anti-sigma factor CsfB, a potent inhibitor of σG. ThecsfBgene is ordinarily transcribed in the forespore only by the early-acting sigma factor σF. However, in a mutant lacking the highly conserved SpoIIQ transmembrane amino acid Tyr-28,csfBwas also aberrantly transcribed later by σG, the very target of CsfB inhibition. This regulation ofcsfBby SpoIIQ Tyr-28 is specific, given that the expression of other σF-dependent genes was unaffected. Moreover, we identified a conserved element within thecsfBpromoter region that is both necessary and sufficient for SpoIIQ Tyr-28-mediated inhibition. These results indicate that SpoIIQ is a bifunctional protein that not only generally promotes σGactivity in the forespore as a channel component but also specifically maximizes σGactivity as part of a gene regulatory circuit that represses σG-dependent expression of its own inhibitor, CsfB. Finally, we demonstrate that SpoIIQ Tyr-28 is required for the proper localization and stability of the SpoIIE phosphatase, raising the possibility that these two multifunctional proteins cooperate to fine-tune developmental gene expression in the forespore at late times.IMPORTANCECellular development is orchestrated by gene regulatory networks that activate or repress developmental genes at the right time and place. Late gene expression in the developingBacillus subtilisspore is directed by the alternative sigma factor σG. The activity of σGrequires a channel apparatus through which the adjacent mother cell provides substrates that generally support gene expression. Here we report that the channel protein SpoIIQ also specifically maximizes σGactivity as part of a previously unknown regulatory circuit that prevents σGfrom activating transcription of the gene encoding its own inhibitor, the anti-sigma factor CsfB. The discovery of this regulatory circuit significantly expands our understanding of the gene regulatory network controlling late gene expression in the developingB. subtilisspore.

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A double-negative gene regulatory circuit underlies the virgin behavioral state

Cell Reports ◽

10.1016/j.celrep.2021.109335 ◽

2021 ◽

Vol 36 (1) ◽

pp. 109335

Author(s):

Daniel L. Garaulet ◽

Albertomaria Moro ◽

Eric C. Lai

Keyword(s):

Double Negative ◽

Behavioral State ◽

Regulatory Circuit ◽

Gene Regulatory ◽

Negative Gene

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A FOXO3–IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses

Nature ◽

10.1038/nature11428 ◽

2012 ◽

Vol 490 (7420) ◽

pp. 421-425 ◽

Cited By ~ 96

Author(s):

Vladimir Litvak ◽

Alexander V. Ratushny ◽

Aaron E. Lampano ◽

Frank Schmitz ◽

Albert C. Huang ◽

...

Keyword(s):

Antiviral Responses ◽

Regulatory Circuit ◽

Gene Regulatory

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Noise effect on persistence of memory in a positive-feedback gene regulatory circuit

Physical Review E ◽

10.1103/physreve.80.011907 ◽

2009 ◽

Vol 80 (1) ◽

Cited By ~ 11

Author(s):

Jun Tang ◽

Xianqing Yang ◽

Jun Ma ◽

Ya Jia

Keyword(s):

Positive Feedback ◽

Noise Effect ◽

Regulatory Circuit ◽

Gene Regulatory

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Point-cycle bistability and stochasticity in a regulatory circuit for Bacillus subtilis competence

Mathematical Biosciences ◽

10.1016/j.mbs.2013.05.002 ◽

2013 ◽

Vol 244 (2) ◽

pp. 135-147 ◽

Cited By ~ 10

Author(s):

Hongguang Xi ◽

Lixia Duan ◽

Marc Turcotte

Keyword(s):

Bacillus Subtilis ◽

Regulatory Circuit

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Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal

Microbiology ◽

10.1099/mic.0.28530-0 ◽

2006 ◽

Vol 152 (3) ◽

pp. 831-853 ◽

Cited By ~ 96

Author(s):

Ina Budde ◽

Leif Steil ◽

Christian Scharf ◽

Uwe Völker ◽

Erhard Bremer

Keyword(s):

Bacillus Subtilis ◽

Low Temperature ◽

Response Regulator ◽

Proteome Analysis ◽

Atp Synthesis ◽

Fine Tuning ◽

Transcriptional Responses ◽

Natural Habitats ◽

Regulatory Circuit ◽

Proteomic Approach

The soil bacterium Bacillus subtilis frequently encounters a reduction in temperature in its natural habitats. Here, a combined transcriptomic and proteomic approach has been used to analyse the adaptational responses of B. subtilis to low temperature. Propagation of B. subtilis in minimal medium at 15 °C triggered the induction of 279 genes and the repression of 301 genes in comparison to cells grown at 37 °C. The analysis thus revealed profound adjustments in the overall gene expression profile in chill-adapted cells. Important transcriptional changes in low-temperature-grown cells comprise the induction of the SigB-controlled general stress regulon, the induction of parts of the early sporulation regulons (SigF, SigE and SigG) and the induction of a regulatory circuit (RapA/PhrA and Opp) that is involved in the fine-tuning of the phosphorylation status of the Spo0A response regulator. The analysis of chill-stress-repressed genes revealed reductions in major catabolic (glycolysis, oxidative phosphorylation, ATP synthesis) and anabolic routes (biosynthesis of purines, pyrimidines, haem and fatty acids) that likely reflect the slower growth rates at low temperature. Low-temperature repression of part of the SigW regulon and of many genes with predicted functions in chemotaxis and motility was also noted. The proteome analysis of chill-adapted cells indicates a major contribution of post-transcriptional regulation phenomena in adaptation to low temperature. Comparative analysis of the previously reported transcriptional responses of cold-shocked B. subtilis cells with this data revealed that cold shock and growth in the cold constitute physiologically distinct phases of the adaptation of B. subtilis to low temperature.

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Vibrio cholerae LexA Coordinates CTX Prophage Gene Expression

Journal of Bacteriology ◽

10.1128/jb.00682-09 ◽

2009 ◽

Vol 191 (22) ◽

pp. 6788-6795 ◽

Cited By ~ 20

Author(s):

Harvey H. Kimsey ◽

Matthew K. Waldor

Keyword(s):

Gene Expression ◽

Cholera Toxin ◽

Vibrio Cholerae ◽

Single Site ◽

Virion Production ◽

Regulatory Circuit ◽

Ctxφ Prophage ◽

Gene Regulatory ◽

Ctx Prophage ◽

Operator Site

ABSTRACT The filamentous bacteriophage CTXΦ transmits the cholera toxin genes by infecting and lysogenizing its host, Vibrio cholerae. CTXΦ genes required for virion production initiate transcription from the strong P A promoter, which is dually repressed in lysogens by the phage-encoded repressor RstR and the host-encoded SOS repressor LexA. Here we identify the neighboring divergent rstR promoter, P R, and show that RstR both positively and negatively autoregulates its own expression from this promoter. LexA is absolutely required for RstR-mediated activation of P R transcription. RstR autoactivation occurs when RstR is bound to an operator site centered 60 bp upstream of the start of transcription, and the coactivator LexA is bound to a 16-bp SOS box centered at position −23.5, within the P R spacer region. Our results indicate that LexA, when bound to its single site in the CTXΦ prophage, both represses transcription from P A and coactivates transcription from the divergent P R. We propose that LexA coordinates P A and P R prophage transcription in a gene regulatory circuit. This circuit is predicted to display transient switch behavior upon induction of CTXΦ lysogens.

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Dynamic modeling ofStreptococcus pneumoniaecompetence provides regulatory mechanistic insights

10.1101/300814 ◽

2018 ◽

Cited By ~ 1

Author(s):

Mathias Weyder ◽

Marc Prudhomme ◽

Mathieu Bergé ◽

Patrice Polard ◽

Gwennaele Fichant

Keyword(s):

Positive Feedback ◽

Feedback Loop ◽

Natural Transformation ◽

Transient State ◽

Ph Change ◽

Positive Feedback Loop ◽

Average Cell ◽

Knowledge Based ◽

Regulatory Circuit ◽

Gene Regulatory

AbstractIn the human pathogenStreptococcus pneumoniae, the gene regulatory circuit leading to the transient state of competence for natural transformation is based on production of an auto-inducer that activates a positive feedback loop. About one hundred genes are activated in two successive waves linked by a central alternative sigma factor ComX. This mechanism appears to be fundamental to the biological fitness ofS. pneumoniae.We have developed a knowledge-based model of the competence cycle that describes average cell behavior. It reveals that the expression rates of the two competence operon,comABandcomCDE, involved in the positive feedback loop must be coordinated to elicit spontaneous competence. Simulations revealed the requirement for an unknown latecomgene product that shuts of competence by impairing ComX activity. Further simulations led to the predictions that the membrane protein ComD bound to CSP reacts directly to pH change of the medium and that blindness to CSP during the post-competence phase is controlled by late DprA protein. Both predictions were confirmed experimentally.

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Genetic signatures of evolution of the pluripotency gene regulating network across mammals

10.1101/2020.04.16.043943 ◽

2020 ◽

Author(s):

Yoshinori Endo ◽

Ken-ichiro Kamei ◽

Miho Inoue-Murayama

Keyword(s):

Gene Regulatory Network ◽

Regulatory Network ◽

Mammalian Species ◽

Rapid Evolution ◽

Network Evolution ◽

Downstream Targets ◽

The Core ◽

Regulatory Circuit ◽

Pluripotency Gene ◽

Gene Regulatory

AbstractMammalian pluripotent stem cells (PSCs) have distinct molecular and biological characteristics, but we lack a comprehensive understanding of regulatory network evolution in mammals. Here, we applied a comparative genetic analysis of 134 genes constituting the pluripotency gene regulatory network across 48 mammalian species covering all the major taxonomic groups. We found evolutionary conservation in JAK-STAT and PI3K-Akt signaling pathways, suggesting equivalent capabilities in self-renewal and proliferation of mammalian PSCs. On the other hand, we discovered rapid evolution of the downstream targets of the core regulatory circuit, providing insights into variations of characteristics. Our data indicate that the variations in the PSCs characteristics may be due to positive selections in the downstream targets of the core regulatory circuit. We further reveal that positively selected genes can be associated with species unique adaptation that is not dedicated to regulation of PSCs. These results provide important insight into the evolution of the pluripotency gene regulatory network underlying variations in characteristics of mammalian PSCs.

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Evolution of Superinfection Immunity in Cluster A Mycobacteriophages

mBio ◽

10.1128/mbio.00971-19 ◽

2019 ◽

Vol 10 (3) ◽

Cited By ~ 14

Author(s):

Travis N. Mavrich ◽

Graham F. Hatfull

Keyword(s):

Gene Expression ◽

Genetic Diversity ◽

Defense Mechanism ◽

Genetic Interactions ◽

Form Complex ◽

Lytic Gene ◽

Regulatory Circuit ◽

Gene Regulatory ◽

Cluster A ◽

Phage Growth

ABSTRACTTemperate phages encode an immunity system to control lytic gene expression during lysogeny. This gene regulatory circuit consists of multiple interacting genetic elements, and although it is essential for controlling phage growth, it is subject to conflicting evolutionary pressures. During superinfection of a lysogen, the prophage’s circuit interacts with the superinfecting phage’s circuit and prevents lytic growth if the two circuits are closely related. The circuitry is advantageous since it provides the prophage with a defense mechanism, but the circuitry is also disadvantageous since it limits the phage’s host range during superinfection. Evolutionarily related phages have divergent, orthogonal immunity systems that no longer interact and are heteroimmune, but we do not understand how immunity systems evolve new specificities. Here, we use a group of Cluster A mycobacteriophages that exhibit a spectrum of genetic diversity to examine how immunity system evolution impacts superinfection immunity. We show that phages with mesotypic (i.e., genetically related but distinct) immunity systems exhibit asymmetric and incomplete superinfection phenotypes. They form complex immunity networks instead of well-defined immunity groups, and mutations conferring escape (i.e., virulence) from homotypic or mesotypic immunity have various escape specificities. Thus, virulence and the evolution of new immune specificities are shaped by interactions with homotypic and mesotypic immunity systems.IMPORTANCEMany aspects regarding superinfection, immunity, virulence, and the evolution of immune specificities are poorly understood due to the lack of large collections of isolated and sequenced phages with a spectrum of genetic diversity. Using a genetically diverse collection of Cluster A phages, we show that the classical and relatively straightforward patterns of homoimmunity, heteroimmunity, and virulence result from interactions between homotypic and heterotypic phages at the extreme edges of an evolutionary continuum of immune specificities. Genetic interactions between mesotypic phages result in more complex mesoimmunity phenotypes and virulence profiles. These results highlight that the evolution of immune specificities can be shaped by homotypic and mesotypic interactions and may be more dynamic than previously considered.

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