A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids

Chromosome and plasmid segregation in bacteria are mostly driven by ParAB S systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites ( parS ). However, the mechanism of how a few parS ‐bound ParB proteins nucleate the formation of highly concent...

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Published inMolecular systems biology Vol. 14; no. 11; pp. e8516 - n/a
Main Authors Debaugny, Roxanne E, Sanchez, Aurore, Rech, Jérôme, Labourdette, Delphine, Dorignac, Jérôme, Geniet, Frédéric, Palmeri, John, Parmeggiani, Andrea, Boudsocq, François, Anton Leberre, Véronique, Walter, Jean‐Charles, Bouet, Jean‐Yves
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.11.2018
EMBO Press
John Wiley and Sons Inc
Springer Nature
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Abstract Chromosome and plasmid segregation in bacteria are mostly driven by ParAB S systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites ( parS ). However, the mechanism of how a few parS ‐bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico‐mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that “Nucleation & caging” is the only coherent model recapitulating in vivo data. We also showed that the stochastic self‐assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the “Nucleation & caging” model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae , indicating that this stochastic self‐assembly mechanism is widely conserved from plasmids to chromosomes. Synopsis High‐resolution ChIP‐seq and physico‐mathematical modeling are used to analyze the in vivo ParB DNA‐binding profiles. The “Nucleation and caging” self‐assembly mechanism is widespread to ensure faithful bacterial DNA segregation by ParAB S systems. ParB S partition complexes are highly dynamic nucleoprotein complexes. The robust ParB DNA binding profiles derived by ChIP‐seq data are well‐described by the “Nucleation and caging” model. The size of the partition complex is invariant to intracellular variation in ParB levels. This self‐assembly mechanism is observed on Escherichia coli and V. cholerae chromosomes and on the F plasmid. Graphical Abstract High‐resolution ChIP‐seq and physico‐mathematical modeling are used to analyze the in vivo ParB DNA‐binding profiles. The “Nucleation and caging” self‐assembly mechanism is widespread to ensure faithful bacterial DNA segregation by ParAB S systems.
AbstractList Chromosome and plasmid segregation in bacteria are mostly driven by ParAB S systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites ( parS ). However, the mechanism of how a few parS ‐bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico‐mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that “Nucleation & caging” is the only coherent model recapitulating in vivo data. We also showed that the stochastic self‐assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the “Nucleation & caging” model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae , indicating that this stochastic self‐assembly mechanism is widely conserved from plasmids to chromosomes. Synopsis High‐resolution ChIP‐seq and physico‐mathematical modeling are used to analyze the in vivo ParB DNA‐binding profiles. The “Nucleation and caging” self‐assembly mechanism is widespread to ensure faithful bacterial DNA segregation by ParAB S systems. ParB S partition complexes are highly dynamic nucleoprotein complexes. The robust ParB DNA binding profiles derived by ChIP‐seq data are well‐described by the “Nucleation and caging” model. The size of the partition complex is invariant to intracellular variation in ParB levels. This self‐assembly mechanism is observed on Escherichia coli and V. cholerae chromosomes and on the F plasmid. Graphical Abstract High‐resolution ChIP‐seq and physico‐mathematical modeling are used to analyze the in vivo ParB DNA‐binding profiles. The “Nucleation and caging” self‐assembly mechanism is widespread to ensure faithful bacterial DNA segregation by ParAB S systems.
Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS‐bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico‐mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that “Nucleation & caging” is the only coherent model recapitulating in vivo data. We also showed that the stochastic self‐assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the “Nucleation & caging” model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae, indicating that this stochastic self‐assembly mechanism is widely conserved from plasmids to chromosomes. Synopsis High‐resolution ChIP‐seq and physico‐mathematical modeling are used to analyze the in vivo ParB DNA‐binding profiles. The “Nucleation and caging” self‐assembly mechanism is widespread to ensure faithful bacterial DNA segregation by ParABS systems. ParBS partition complexes are highly dynamic nucleoprotein complexes. The robust ParB DNA binding profiles derived by ChIP‐seq data are well‐described by the “Nucleation and caging” model. The size of the partition complex is invariant to intracellular variation in ParB levels. This self‐assembly mechanism is observed on Escherichia coli and V. cholerae chromosomes and on the F plasmid. High‐resolution ChIP‐seq and physico‐mathematical modeling are used to analyze the in vivo ParB DNA‐binding profiles. The “Nucleation and caging” self‐assembly mechanism is widespread to ensure faithful bacterial DNA segregation by ParABS systems.
Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS-bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parameters in vivo using the plasmid F partition system. We found that ‘Nucleation & caging’ is the only coherent model recapitulating in vivo data. We also showed that the stochastic self-assembly of partition complexes (i) does not directly involve ParA, (ii) results in a dynamic structure of discrete size independent of ParB concentration, and (iii) is not perturbed by active transcription but is by protein complexes. We refined the ‘Nucleation & Caging’ model and successfully applied it to the chromosomally-encoded Par system of Vibrio cholerae, indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes.
Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS-bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that "Nucleation & caging" is the only coherent model recapitulating in vivo data. We also showed that the stochastic self-assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the "Nucleation & caging" model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae, indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes.
Abstract Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS‐bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico‐mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that “Nucleation & caging” is the only coherent model recapitulating in vivo data. We also showed that the stochastic self‐assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the “Nucleation & caging” model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae, indicating that this stochastic self‐assembly mechanism is widely conserved from plasmids to chromosomes.
Chromosome and plasmid segregation in bacteria are mostly driven by ParAB systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites ( ). However, the mechanism of how a few -bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parameters using the F plasmid partition system. We found that "Nucleation & caging" is the only coherent model recapitulating data. We also showed that the stochastic self-assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the "Nucleation & caging" model and successfully applied it to the chromosomally encoded Par system of , indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes.
Chromosome and plasmid segregation in bacteria are mostly driven by ParAB S systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites ( parS ). However, the mechanism of how a few parS ‐bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico‐mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that “Nucleation & caging” is the only coherent model recapitulating in vivo data. We also showed that the stochastic self‐assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATP ase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the “Nucleation & caging” model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae , indicating that this stochastic self‐assembly mechanism is widely conserved from plasmids to chromosomes.
Author Debaugny, Roxanne E
Dorignac, Jérôme
Labourdette, Delphine
Anton Leberre, Véronique
Rech, Jérôme
Geniet, Frédéric
Parmeggiani, Andrea
Walter, Jean‐Charles
Palmeri, John
Sanchez, Aurore
Boudsocq, François
Bouet, Jean‐Yves
AuthorAffiliation 2 LISBP CNRS INRA INSA Université de Toulouse Toulouse France
4 Dynamique des Interactions Membranaires Normales et Pathologiques CNRS‐Université Montpellier Montpellier France
3 Laboratoire Charles Coulomb CNRS‐Université Montpellier Montpellier France
1 Laboratoire de Microbiologie et Génétique Moléculaires Centre de Biologie Intégrative (CBI) Centre National de la Recherche Scientifique (CNRS) Université de Toulouse, UPS Toulouse France
5 Present address: Institut Curie UMR 3664 CNRS‐IC Paris France
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Issue 11
Keywords DNA segregation
F plasmid
ParABS
plasmid partition
Escherichia coli
Language English
License Attribution
2018 The Authors. Published under the terms of the CC BY 4.0 license.
Attribution: http://creativecommons.org/licenses/by
This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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  doi: 10.1093/nar/gkt018
– ident: e_1_2_9_23_1
  doi: 10.1093/emboj/20.17.4901
– ident: e_1_2_9_19_1
  doi: 10.1016/j.plasmid.2015.03.007
SSID ssj0038182
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Snippet Chromosome and plasmid segregation in bacteria are mostly driven by ParAB S systems. These DNA partitioning machineries rely on large nucleoprotein complexes...
Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes...
Chromosome and plasmid segregation in bacteria are mostly driven by ParAB systems. These DNA partitioning machineries rely on large nucleoprotein complexes...
Chromosome and plasmid segregation in bacteria are mostly driven by ParAB S systems. These DNA partitioning machineries rely on large nucleoprotein complexes...
Abstract Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein...
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StartPage e8516
SubjectTerms Adenosine triphosphatase
Assembly
Bacteria
Bacterial Proteins - metabolism
Bacteriology
Binding
Biochemistry, Molecular Biology
Biological Physics
Chromosome Segregation
Chromosomes
Chromosomes, Bacterial - genetics
Chromosomes, Bacterial - physiology
Coding
Deoxyribonucleic acid
DNA
DNA segregation
E coli
EMBO13
EMBO23
EMBO33
Escherichia coli
F plasmid
Life Sciences
Mathematical models
Microbiology and Parasitology
Models, Theoretical
Nucleation
ParABS
Partitions
Physics
plasmid partition
Plasmids
Plasmids - genetics
Plasmids - physiology
Proteins
Robustness (mathematics)
Stochastic Processes
Stochasticity
Systems Biology - methods
Transcription
Vibrio cholerae - metabolism
Vibrio cholerae - physiology
Waterborne diseases
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Title A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids
URI https://link.springer.com/article/10.15252/msb.20188516
https://onlinelibrary.wiley.com/doi/abs/10.15252%2Fmsb.20188516
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