Novel regulatory mechanism of establishment genes of conjugative plasmids

Val-Calvo, Jorge; Luque‐Ortega, Juan Román; Miguel-Arribas, Andrés; Abia, David; Sánchez-Hevia, Dione L.; Serrano, Ester; Gago-Córdoba, César; Ares, Saúl; Alfonso, Carlos; Rojo, Fernando; Wu, Ling Juan; Boer, Roeland; Meijer, Wilfried J. J.

doi:10.1093/nar/gky996

Cited by 7 publications

(15 citation statements)

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“…10). Analogous consequences are found in other areas, in which the search of simple and compact models leads the dimensionality reduction that precludes non-monotonic temporal profiles as the ones described in this article (Fernandez-Lopez, del Campo, Revilla, Cuevas, & de la Cruz, 2014; Val-Calvo et al, 2018).…”

Section: Discussionsupporting

confidence: 75%

Frequency preference response in covalent modification cycles under substrate sequestration conditions

Szemere

Rotstein

Ventura

2021

Preprint

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Covalent modification cycles (CMCs) are basic units of signaling systems and their properties are well understood. However, the behavior of such systems has been mostly characterized in situations where the substrate is in excess over the modifying enzymes. Experimental data on protein abundance suggest that the enzymes and their target proteins are present in comparable concentrations, leading to a different scenario in which the substrate is mostly sequestered by the enzymes. In this enzyme-in-excess regime, CMCs have been shown to exhibit signal termination, the ability of the product to return to a stationary value lower than the its peak in response to constant stimulation, while this stimulation is still active, with possible implications for the ability of systems to adapt to environmental inputs. We characterize the conditions leading to signal termination in CMCs in the enzyme-in-excess regime. We also demonstrate that this behavior leads to a preferred frequency response (band-pass filters) when the cycle is subjected to periodic stimulation, while the literature reports that CMCs investigated so far behave as low pass filters. We characterize the relationship between signal termination and the preferred frequency response to periodic inputs and we explore the dynamic mechanism underlying these phenomena. Finally, we describe how the behavior of CMCs is reflected in similar types of responses in the cascades of which they are part. Evidence of protein abundance in vivo shows that enzymes and substrates are present in comparable concentrations, thus suggesting that signal termination and frequency preference response to periodic inputs are also important dynamic features of cell signaling systems, which have been overlooked.

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Section: Discussionsupporting

confidence: 75%

Frequency preference response in covalent modification cycles under substrate sequestration conditions

Szemere

Rotstein

Ventura

2021

Preprint

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“…10 ). Analogous consequences are found in other areas, in which the search of simple and compact models leads to dimensionality reduction that precludes non-monotonic temporal profiles such as the ones described in this article 59 , 60 .…”

Section: Discussionsupporting

confidence: 64%

Frequency-preference response in covalent modification cycles under substrate sequestration conditions

2021

View full text Add to dashboard Cite

Covalent modification cycles (CMCs) are basic units of signaling systems and their properties are well understood. However, their behavior has been mostly characterized in situations where the substrate is in excess over the modifying enzymes. Experimental data on protein abundance suggest that the enzymes and their target proteins are present in comparable concentrations, leading to substrate sequestration by the enzymes. In this enzyme-in-excess regime, CMCs have been shown to exhibit signal termination, the ability of the product to return to a stationary value lower than its peak in response to constant stimulation, while this stimulation is still active, with possible implications for the ability of systems to adapt to environmental inputs. We characterize the conditions leading to signal termination in CMCs in the enzyme-in-excess regime. We also demonstrate that this behavior leads to a preferred frequency response (band-pass filters) when the cycle is subjected to periodic stimulation, whereas the literature reports that CMCs investigated so far behave as low-pass filters. We characterize the relationship between signal termination and the preferred frequency response to periodic inputs and we explore the dynamic mechanism underlying these phenomena. Finally, we describe how the behavior of CMCs is reflected in similar types of responses in the cascades of which they are part. Evidence of protein abundance in vivo shows that enzymes and substrates are present in comparable concentrations, thus suggesting that signal termination and frequency-preference response to periodic inputs are also important dynamic features of cell signaling systems, which have been overlooked.

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“…To confirm these data by an independent approach, we took advantage of the stoichiometry determination of DNA-protein complexes by multi-signal sedimentation velocity (MSSV) ( 44 ). Thus, SV experiments were performed using samples containing the 219 bp DNA fragment FIII (encompassing Rco pLS20 operator O II ) alone or with increasing Rco pLS20 concentrations.…”

Section: Resultsmentioning

confidence: 99%

Reversible regulation of conjugation of Bacillus subtilis plasmid pLS20 by the quorum sensing peptide responsive anti-repressor RappLS20

Singh

Serrano

Ramachandran

et al. 2020

Nucleic Acids Research

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Quorum sensing plays crucial roles in bacterial communication including in the process of conjugation, which has large economical and health-related impacts by spreading antibiotic resistance. The conjugative Bacillus subtilis plasmid pLS20 uses quorum sensing to determine when to activate the conjugation genes. The main conjugation promoter, Pc, is by default repressed by a regulator RcopLS20 involving DNA looping. A plasmid-encoded signalling peptide, Phr*pLS20, inactivates the anti-repressor of RcopLS20, named RappLS20, which belongs to the large group of RRNPP family of regulatory proteins. Here we show that DNA looping occurs through interactions between two RcopLS20 tetramers, each bound to an operator site. We determined the relative promoter strengths for all the promoters involved in synthesizing the regulatory proteins of the conjugation genes, and constructed an in vivo system uncoupling these regulatory genes to show that RappLS20 is sufficient for activating conjugation in vivo. We also show that RappLS20 actively detaches RcopLS20 from DNA by preferentially acting on the RcopLS20 molecules involved in DNA looping, resulting in sequestration but not inactivation of RcopLS20. Finally, results presented here in combination with our previous results show that activation of conjugation inhibits competence and competence development inhibits conjugation, indicating that both processes are mutually exclusive.

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Novel regulatory mechanism of establishment genes of conjugative plasmids

Cited by 7 publications

References 50 publications

Frequency preference response in covalent modification cycles under substrate sequestration conditions

Frequency preference response in covalent modification cycles under substrate sequestration conditions

Frequency-preference response in covalent modification cycles under substrate sequestration conditions

Reversible regulation of conjugation of Bacillus subtilis plasmid pLS20 by the quorum sensing peptide responsive anti-repressor RappLS20

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