Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites
Summary: Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are cytosine triphosphate (CTP)-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-12-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004220310580 |
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| author | Jean-Charles Walter Jérôme Rech Nils-Ole Walliser Jérôme Dorignac Frédéric Geniet John Palmeri Andrea Parmeggiani Jean-Yves Bouet |
| author_facet | Jean-Charles Walter Jérôme Rech Nils-Ole Walliser Jérôme Dorignac Frédéric Geniet John Palmeri Andrea Parmeggiani Jean-Yves Bouet |
| author_sort | Jean-Charles Walter |
| collection | DOAJ |
| description | Summary: Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are cytosine triphosphate (CTP)-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been proposed to explain the ParB spreading over large distances from parS centromere sites where ParB is specifically loaded. We modeled such a “clamping and sliding” mechanism as a typical reaction-diffusion system, compared it to the F plasmid ParB DNA binding pattern, and found that it can account neither for the long range of ParB binding to DNA nor for the rapid assembly kinetics observed in vivo after parS duplication. Also, it predicts a strong effect on the F plasmid ParB binding pattern from the presence of a roadblock that is not observed in ChIP-sequencing (ChIP-seq). We conclude that although “clamping and sliding” can occur at short distances from parS, another mechanism must apply for ParB recruitment at larger genomic distances. |
| first_indexed | 2024-12-19T05:50:37Z |
| format | Article |
| id | doaj.art-60f8b707193c430e877ac0d0ff508e17 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-19T05:50:37Z |
| publishDate | 2020-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-60f8b707193c430e877ac0d0ff508e172022-12-21T20:33:38ZengElsevieriScience2589-00422020-12-012312101861Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere SitesJean-Charles Walter0Jérôme Rech1Nils-Ole Walliser2Jérôme Dorignac3Frédéric Geniet4John Palmeri5Andrea Parmeggiani6Jean-Yves Bouet7Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, 34095 Montpellier, France; Corresponding authorLaboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Univ. Toulouse, UPS, 31062 Toulouse, FranceLaboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, 34095 Montpellier, FranceLaboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, 34095 Montpellier, FranceLaboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, 34095 Montpellier, FranceLaboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, 34095 Montpellier, FranceLaboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, 34095 Montpellier, France; Laboratory of Parasite Host Interactions (LPHI), Univ. Montpellier, CNRS, 34095 Montpellier, FranceLaboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Univ. Toulouse, UPS, 31062 Toulouse, France; Corresponding authorSummary: Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are cytosine triphosphate (CTP)-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been proposed to explain the ParB spreading over large distances from parS centromere sites where ParB is specifically loaded. We modeled such a “clamping and sliding” mechanism as a typical reaction-diffusion system, compared it to the F plasmid ParB DNA binding pattern, and found that it can account neither for the long range of ParB binding to DNA nor for the rapid assembly kinetics observed in vivo after parS duplication. Also, it predicts a strong effect on the F plasmid ParB binding pattern from the presence of a roadblock that is not observed in ChIP-sequencing (ChIP-seq). We conclude that although “clamping and sliding” can occur at short distances from parS, another mechanism must apply for ParB recruitment at larger genomic distances.http://www.sciencedirect.com/science/article/pii/S2589004220310580Gene ProcessMicrobial GeneticsSystems Biology |
| spellingShingle | Jean-Charles Walter Jérôme Rech Nils-Ole Walliser Jérôme Dorignac Frédéric Geniet John Palmeri Andrea Parmeggiani Jean-Yves Bouet Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites iScience Gene Process Microbial Genetics Systems Biology |
| title | Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites |
| title_full | Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites |
| title_fullStr | Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites |
| title_full_unstemmed | Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites |
| title_short | Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites |
| title_sort | physical modeling of a sliding clamp mechanism for the spreading of parb at short genomic distance from bacterial centromere sites |
| topic | Gene Process Microbial Genetics Systems Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004220310580 |
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