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Bacterial DNA Organization and Segregation
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Bacterial DNA Organization and Segregation

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (25 April 2022) | Viewed by 10799

Special Issue Editor

Dr. Jean-Yves Bouet

E-Mail Website
Guest Editor
Center for Integrative Biology, Centre National de la Recherche Scientifique (CNRS), Université Toulouse, Toulouse, France
Interests: DNA segregation; plasmids; chromosomes; bacteria; bacterial genetics; molecular biology; fluorescence microscopy

Special Issue Information

Dear colleagues,

Bacterial genomes are highly dynamic and diverse. They are composed of a primary chromosome and a variable number of other replicons, including secondary chromosomes and plasmids. All these replicons are folded to compact DNA. At the same time, they manage all the processes involved in DNA metabolism. How these different DNA molecules are organized in a unique cellular compartment to faithfully segregate these varieties of replicons is still under intense investigation. Numerous controlled mechanisms are at play and are interconnected to achieve their transmission and maintenance over generations.

This Special Issue of Genes on “Bacterial DNA Organization and Segregation” will address the mechanisms by which bacteria organize their genomes and manage the segregation and maintenance of all the replicons, providing an overview of recent developments in specialized research topics and of critical perspectives on upcoming challenges. We welcome original research articles and reviews.

We look forward to receiving your contributions.

Dr. Jean-Yves Bouet 
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bacterial replicons
  • DNA organization
  • DNA segregation
  • partition
  • chromosomes
  • plasmids maintenance
  • plasmid copy-number
  • dimer resolution
  • decatenation
  • addiction

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Published Papers (3 papers)

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Research

14 pages, 1801 KiB  
Article
Vibrio cholerae Chromosome Partitioning without Polar Anchoring by HubP
by Christophe Possoz, Yoshiharu Yamaichi, Elisa Galli, Jean-Luc Ferat and Francois-Xavier Barre
Genes 2022, 13(5), 877; https://doi.org/10.3390/genes13050877 - 13 May 2022
Cited by 4 | Viewed by 2521
Abstract
Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part [...] Read more.
Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part because they serve to properly position sister copies of oriC. A fourth element, located at cell poles, is also involved in some cases, such as HubP for the ParABS1 system of Vibrio cholerae chromosome 1 (ch1). The polar anchoring of oriC of ch1 (oriC1) is lost when HubP or ParABS1 are inactivated. Here, we report that in the absence of HubP, ParABS1 actively maintains oriC1 at mid-cell, leading to the subcellular separation of the two ch1 replication arms. We further show that parS1 sites ectopically inserted in chromosome 2 (ch2) stabilize the inheritance of this replicon in the absence of its endogenous partition system, even without HubP. We also observe the positioning interference between oriC1 and oriC of ch2 regions when their positionings are both driven by ParABS1. Altogether, these data indicate that ParABS1 remains functional in the absence of HubP, which raises questions about the role of the polar anchoring of oriC1 in the cell cycle. Full article
(This article belongs to the Special Issue Bacterial DNA Organization and Segregation)
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23 pages, 6185 KiB  
Article
Subcellular Dynamics of a Conserved Bacterial Polar Scaffold Protein
by Giacomo Giacomelli, Helge Feddersen, Feng Peng, Gustavo Benevides Martins, Manuela Grafemeyer, Fabian Meyer, Benjamin Mayer, Peter L. Graumann and Marc Bramkamp
Genes 2022, 13(2), 278; https://doi.org/10.3390/genes13020278 - 30 Jan 2022
Cited by 10 | Viewed by 4880
Abstract
In order to survive, bacterial cells rely on precise spatiotemporal organization and coordination of essential processes such as cell growth, chromosome segregation, and cell division. Given the general lack of organelles, most bacteria are forced to depend on alternative localization mechanisms, such as, [...] Read more.
In order to survive, bacterial cells rely on precise spatiotemporal organization and coordination of essential processes such as cell growth, chromosome segregation, and cell division. Given the general lack of organelles, most bacteria are forced to depend on alternative localization mechanisms, such as, for example, geometrical cues. DivIVA proteins are widely distributed in mainly Gram-positive bacteria and were shown to bind the membrane, typically in regions of strong negative curvature, such as the cell poles and division septa. Here, they have been shown to be involved in a multitude of processes: from apical cell growth and chromosome segregation in actinobacteria to sporulation and inhibition of division re-initiation in firmicutes. Structural analyses revealed that DivIVA proteins can form oligomeric assemblies that constitute a scaffold for recruitment of other proteins. However, it remained unclear whether interaction with partner proteins influences DivIVA dynamics. Using structured illumination microscopy (SIM), single-particle tracking (SPT) microscopy, and fluorescent recovery after photobleaching (FRAP) experiments, we show that DivIVA from Corynebacterium glutamicum is mobilized by its binding partner ParB. In contrast, we show that the interaction between Bacillus subtilis DivIVA and its partner protein MinJ reduces DivIVA mobility. Furthermore, we show that the loss of the rod-shape leads to an increase in DivIVA dynamics in both organisms. Taken together, our study reveals the modulation of the polar scaffold protein by protein interactors and cell morphology. We reason that this leads to a very simple, yet robust way for actinobacteria to maintain polar growth and their rod-shape. In B. subtilis, however, the DivIVA protein is tailored towards a more dynamic function that allows quick relocalization from poles to septa upon division. Full article
(This article belongs to the Special Issue Bacterial DNA Organization and Segregation)
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19 pages, 2455 KiB  
Article
Three ParA Dimers Cooperatively Assemble on Type Ia Partition Promoters
by François Boudsocq, Maya Salhi, Sophie Barbe and Jean-Yves Bouet
Genes 2021, 12(9), 1345; https://doi.org/10.3390/genes12091345 - 28 Aug 2021
Cited by 3 | Viewed by 2376
Abstract
Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by partition systems composed of two proteins, ParA and ParB, and a centromere site. Auto-regulation of Par operon expression is important for efficient partitioning and [...] Read more.
Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by partition systems composed of two proteins, ParA and ParB, and a centromere site. Auto-regulation of Par operon expression is important for efficient partitioning and is primarily mediated by ParA for type Ia plasmid partition systems. For the F-plasmid, four ParAF monomers were proposed to bind to four repeated sequences in the promoter region. By contrast, using quantitative surface-plasmon-resonance, we showed that three ParAF dimers bind to this region. We uncovered that one perfect inverted repeat (IR) motif, consisting of two hexamer sequences spaced by 28-bp, constitutes the primary ParAF DNA binding site. A similar but degenerated motif overlaps the former. ParAF binding to these motifs is well supported by biochemical and modeling analyses. Molecular dynamics simulations predict that the winged-HTH domain displays high flexibility, which may favor the cooperative ParA binding to the promoter. We propose that three ParAF dimers bind cooperatively to overlapping motifs, thus covering the promoter region. A similar organization is found on closely related and distant plasmid partition systems, suggesting that such promoter organization for auto-regulated Par operons is widespread and may have evolved from a common ancestor. Full article
(This article belongs to the Special Issue Bacterial DNA Organization and Segregation)
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