Analysis of ParB-centromere interactions by multiplex SPR imaging reveals specific patterns for binding ParB in six centromeres of Burkholderiales chromosomes and plasmids

Pillet, Flavien; Passot, Fanny; Pasta, Franck; Leberre, Véronique Anton; Bouet, Jean‐Yves

doi:10.1371/journal.pone.0177056

Cited by 6 publications

(6 citation statements)

References 38 publications

(72 reference statements)

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“…ParB2 of V. cholerae was shown to bind a non-centromeric site containing a half- parS sequence ( 82 ). Additionally, in the multipartite genome bacterium Burkholderia cenocepacia ParBc1, ParBc3 and ParBpBC displayed enhanced affinity for the corresponding half- parS relative to random-sequence DNA ( 84 ). This data show that the ability of ParB to bind to one arm of parS is not restricted to P. aeruginosa .…”

Section: Discussionmentioning

confidence: 99%

Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif

Kawałek

Bartosik

Glabski

et al. 2018

Nucleic Acids Research

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ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in the separation of ori domains by binding to parS palindromes, mainly localized close to oriC. In Pseudomonas aeruginosa neither ParB deficiency nor modification of all 10 parSs is lethal. However, such mutants show not only defects in chromosome segregation but also growth retardation and motility dysfunctions. Moreover, a lack of parB alters expression of over 1000 genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets. Here, we show that indeed ParB binds specifically to hundreds of sites in the genome. ChIP-seq analysis revealed 420 ParB-associated regions in wild-type strain and around 1000 in a ParB-overproducing strain and in various parS mutants. The vast majority of the ParB-enriched loci contained a heptanucleotide motif corresponding to one arm of the parS palindrome. All previously postulated parSs, except parS5, interacted with ParB in vivo. Whereas the ParB binding to the four parS sites closest to oriC, parS1-4, is involved in chromosome segregation, its genome-wide interactions with hundreds of parS half-sites could affect chromosome topology, compaction and gene expression, thus allowing P. aeruginosa ParB to be classified as a nucleoid-associated protein.

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Section: Discussionmentioning

confidence: 99%

Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif

Kawałek

Bartosik

Glabski

et al. 2018

Nucleic Acids Research

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“…Caulobacter crescentus 5/5/t/cGTTt/cCACGTGAAAca [80,81] essential Indispensable, severe chromosome segregation defects, ParB depletion results in defective Z-ring formation and cell division, formation of long polyploid cells [82] Hyphomonas neptunium 2/2/TGTTTCACGTGAAACA [83] essential anucleate buds [83] parB mutants could not be obtained, depletion of ParA blocks cell division [83] Betaproteobacteria Burkholderia cenocepacia chrI: 2/2/tGTTNCACGTGAAACa chrII: 6/6/gTTTATGCGCATAAAc [84][85][86][87] non-essential 1-14% (depending on mutated system) [85] Reduced growth rate, reduction in cell size, compromised viability, defects in ori positioning [85] Deltaproteobacteria…”

Section: Alphaproteobacteriamentioning

confidence: 99%

Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes

et al. 2020

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The segregation of newly replicated chromosomes in bacterial cells is a highly coordinated spatiotemporal process. In the majority of bacterial species, a tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target(s) parS sequence(s), facilitates the initial steps of chromosome partitioning. ParB nucleates around parS(s) located in the vicinity of newly replicated oriCs to form large nucleoprotein complexes, which are subsequently relocated by ParA to distal cellular compartments. In this review, we describe the role of ParB in various processes within bacterial cells, pointing out interspecies differences. We outline recent progress in understanding the ParB nucleoprotein complex formation and its role in DNA segregation, including ori positioning and anchoring, DNA condensation, and loading of the structural maintenance of chromosome (SMC) proteins. The auxiliary roles of ParBs in the control of chromosome replication initiation and cell division, as well as the regulation of gene expression, are discussed. Moreover, we catalog ParB interacting proteins. Overall, this work highlights how different bacterial species adapt the DNA partitioning ParAB-parS system to meet their specific requirements.

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“…ParB2 of Vibrio cholerae was shown to bind a non centromeric site containing a half- parS sequence (80). Additionally, in multipartite genome bacterium Burkholderia cenocepacia ParBc1, ParBc3 and ParBpBC display enhanced affinity for the corresponding half- parS relative to the background control (83). This data suggests that ParB binding to one arm of parS may not be restricted to P .…”

Section: Discussionmentioning

confidence: 99%

Pseudomonas aeruginosapartitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of aparS-related motif

Kawałek

Bartosik

Glabski

et al. 2018

Preprint

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ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in separation of ori domains by binding to specific parS sites, mainly localized close to oriC. In Pseudomonas aeruginosa neither a lack of parB gene nor modification of ten parSs is lethal.Remarkably, such mutants show not only defects in chromosome segregation but also growth retardation and motility dysfunctions. Moreover, a lack of parB alters expression of over one thousand genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets.Indeed, DNA immunoprecipitation with anti-ParB antibodies followed by deep sequencing (ChIP-seq) revealed 420 enriched regions in WT PAO1161 strain and around 1000 in a ParBoverproducing strain and in various parS mutants. Vast majority of the ParB-enriched loci contained a heptanucleotide motif corresponding to one arm of the parS palindrome. All previously postulated parS sites with the exception of parS5 interacted with ParB in vivo. Whereas the ParB binding to the four parS sites closest to oriC, parS1-4, is involved in chromosome segregation, its genome-wide interactions with hundreds of parS half-sites could affect chromosome topology, compaction and gene expression classifying P. aeruginosa ParB as a Nucleoid Associated Protein (NAP).Bacterial genome segregation is a precise, complex and still only partially understood process. Our knowledge of it originates from studies on low-copy-number plasmids in which partitioning systems have been identified (1, 2). Despite the diversity of these systems, they all contain two protein components: A, a NTPase securing energy supply and B, a DNA binding protein, and the third vital element, a specific DNA motif, designated centromere-like sequence (parC/parS), recognized and bound by B component (2)(3)(4). The discovery of a parA-parB operon located close to oriC and encoding homologs of plasmid partitioning proteins of class IA in the majority of the bacterial chromosomes sequenced, has implicated its potential role in chromosome segregation (5)(6)(7)(8)).Most of the information obtained by studying the segregation of low-copy-number plasmids seems to be relevant to the structure and action of the chromosomal homologs, despite their speciesspecific scope of importance. Deletion of parA-parB genes is lethal in some species, e.g., Caulobacter crescentus or Myxococcus Xanthus (9, 10) whereas in other species par mutants demonstrate defects of chromosome segregation of various severity in the vegetative and/or sporulation phase of growth, e.g., Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, Vibrio cholerae, Streptococcus pneumoniae, Corynebacterium glutamicum, Pseudomonas aeruginosa (11-25). Chromosomal ParAs are Walker-type ATPases lacking the specific DNA binding domain present in the N-terminal part of the plasmid ParAs (26, 27).Chromosomal ParBs, similarly to the plasmidic counterparts, contain an extended HTH motif, a Cterminal dimerization domain and an N-terminal polymeriz...

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Analysis of ParB-centromere interactions by multiplex SPR imaging reveals specific patterns for binding ParB in six centromeres of Burkholderiales chromosomes and plasmids

Cited by 6 publications

References 38 publications

Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif

Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif

Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes

Pseudomonas aeruginosapartitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of aparS-related motif

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