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Microorganisms
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Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution
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Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (31 October 2019) | Viewed by 37112

Special Issue Editor

Prof. Dr. Remus T. Dame

E-Mail Website
Guest Editor
Leiden Institute of Chemistry, Leiden, The Netherlands
Interests: gene regulation; genome organisation; transcription; bacteria; archaea

Special Issue Information

Dear Colleagues,

Bacterial genomes are organized and compacted into a structure called the ‘nucleoid’ by a multitude of factors that include architectural proteins, DNA topology and macromolecular crowding. Due to interplay between genome organization and DNA transactions, these factors play specific and generic roles in processes such as transcription, replication, repair and chromosome segregation. Environmental signals that alter genome organization thus drive adaptive responses to changes in the environment. It has become clear that the genomic incorporation and maintenance of foreign DNA is facilitated by factors involved in silencing the expression of foreign DNA (xenogeneic silencing) until relieved by specific signals. In this light, the spatio-temporal organization of the genome is currently a topic of great interest, explored at both the cellular and molecular levels. At the same time, over the last years there has been increasing interest in genome organization in non-canonical model organisms, providing comparative perspectives, demonstrating unanticipated activities of proteins involved in shaping the nucleoid of these organisms and revealing novel architectural proteins. In this Special Issue of Microorganisms, we invite contributions concerning any aspect of bacterial genome organization, with a particular emphasis on the interplay between genome organization and DNA transactions, xenogeneic silencing and environmental sensing in model and non-model bacterial species.

Dr. Remus Dame
Guest Editor

Manuscript Submission Information

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Published Papers (8 papers)

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Editorial

Jump to: Research, Review

4 pages, 210 KiB  
Editorial
Special Issue: Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution
by Remus T. Dame
Microorganisms 2021, 9(11), 2406; https://doi.org/10.3390/microorganisms9112406 - 22 Nov 2021
Viewed by 1439
Abstract
A typical bacterial cell is micron-sized and contains a genome several million base pairs in length [...] Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)

Research

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16 pages, 1637 KiB  
Article
Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli
by Virali J. Parekh, Brittany A. Niccum, Rachna Shah, Marisa A. Rivera, Mark J. Novak, Frederic Geinguenaud, Frank Wien, Véronique Arluison and Richard R. Sinden
Microorganisms 2020, 8(1), 28; https://doi.org/10.3390/microorganisms8010028 - 22 Dec 2019
Cited by 11 | Viewed by 4273
Abstract
Certain G-rich DNA repeats can form quadruplex in bacterial chromatin that can present blocks to DNA replication and, if not properly resolved, may lead to mutations. To understand the participation of quadruplex DNA in genomic instability in Escherichia coli (E. coli), [...] Read more.
Certain G-rich DNA repeats can form quadruplex in bacterial chromatin that can present blocks to DNA replication and, if not properly resolved, may lead to mutations. To understand the participation of quadruplex DNA in genomic instability in Escherichia coli (E. coli), mutation rates were measured for quadruplex-forming DNA repeats, including (G3T)4, (G3T)8, and a RET oncogene sequence, cloned as the template or nontemplate strand. We evidence that these alternative structures strongly influence mutagenesis rates. Precisely, our results suggest that G-quadruplexes form in E. coli cells, especially during transcription when the G-rich strand can be displaced by R-loop formation. Structure formation may then facilitate replication misalignment, presumably associated with replication fork blockage, promoting genomic instability. Furthermore, our results also evidence that the nucleoid-associated protein Hfq is involved in the genetic instability associated with these sequences. Hfq binds and stabilizes G-quadruplex structure in vitro and likely in cells. Collectively, our results thus implicate quadruplexes structures and Hfq nucleoid protein in the potential for genetic change that may drive evolution or alterations of bacterial gene expression. Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)
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Graphical abstract

12 pages, 2490 KiB  
Article
The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment
by Frank Wien, Denis Martinez, Etienne Le Brun, Nykola C. Jones, Søren Vrønning Hoffmann, Jehan Waeytens, Melanie Berbon, Birgit Habenstein and Véronique Arluison
Microorganisms 2019, 7(12), 639; https://doi.org/10.3390/microorganisms7120639 - 3 Dec 2019
Cited by 20 | Viewed by 3997
Abstract
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is [...] Read more.
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment. Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)
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20 pages, 3747 KiB  
Article
Preferential Localization of the Bacterial Nucleoid
by Marc Joyeux
Microorganisms 2019, 7(7), 204; https://doi.org/10.3390/microorganisms7070204 - 19 Jul 2019
Cited by 14 | Viewed by 5706
Abstract
Prokaryotes do not make use of a nucleus membrane to segregate their genetic material from the cytoplasm, so that their nucleoid is potentially free to explore the whole volume of the cell. Nonetheless, high resolution images of bacteria with very compact nucleoids show [...] Read more.
Prokaryotes do not make use of a nucleus membrane to segregate their genetic material from the cytoplasm, so that their nucleoid is potentially free to explore the whole volume of the cell. Nonetheless, high resolution images of bacteria with very compact nucleoids show that such spherical nucleoids are invariably positioned at the center of mononucleoid cells. The present work aims to determine whether such preferential localization results from generic (entropic) interactions between the nucleoid and the cell membrane or instead requires some specific mechanism, like the tethering of DNA at mid-cell or periodic fluctuations of the concentration gradient of given chemical species. To this end, we performed numerical simulations using a coarse-grained model based on the assumption that the formation of the nucleoid results from a segregative phase separation mechanism driven by the de-mixing of the DNA and non-binding globular macromolecules. These simulations show that the abrupt compaction of the DNA coil, which takes place at large crowder density, close to the jamming threshold, is accompanied by the re-localization of the DNA coil close to the regions of the bounding wall with the largest curvature, like the hemispherical caps of rod-like cells, as if the DNA coil were suddenly acquiring the localization properties of a solid sphere. This work therefore supports the hypothesis that the localization of compact nucleoids at regular cell positions involves either some anchoring of the DNA to the cell membrane or some dynamical localization mechanism. Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)
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Review

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30 pages, 2933 KiB  
Review
Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes
by Adam Kawalek, Pawel Wawrzyniak, Aneta Agnieszka Bartosik and Grazyna Jagura-Burdzy
Microorganisms 2020, 8(1), 105; https://doi.org/10.3390/microorganisms8010105 - 11 Jan 2020
Cited by 26 | Viewed by 7025
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)
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11 pages, 411 KiB  
Review
Mutation and Recombination Rates Vary Across Bacterial Chromosome
by Maia Kivisaar
Microorganisms 2020, 8(1), 25; https://doi.org/10.3390/microorganisms8010025 - 21 Dec 2019
Cited by 16 | Viewed by 6313
Abstract
Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure [...] Read more.
Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure which is established by binding of the nucleoid-associated proteins (NAPs) and other proteins. This review gives an overview of recent findings indicating that the mutagenic and recombination processes in bacteria vary at different chromosomal positions. Involvement of NAPs and other possible mechanisms in these regional differences are discussed. Variations in mutation and recombination rates across the bacterial chromosome may have implications in the evolution of bacteria. Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)
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13 pages, 5149 KiB  
Review
Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation
by Georgi Muskhelishvili, Raphaël Forquet, Sylvie Reverchon, Sam Meyer and William Nasser
Microorganisms 2019, 7(12), 694; https://doi.org/10.3390/microorganisms7120694 - 13 Dec 2019
Cited by 12 | Viewed by 3283
Abstract
Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. In this [...] Read more.
Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. In this article, we explore the relationship between genomic sequence organization and transcription in the commensal bacterium Escherichia coli and the plant pathogen Dickeya. We argue that, while in E. coli the gradient of DNA thermodynamic stability and gene order along the origin-to-terminus axis represent major organizational features orchestrating temporal gene expression, the genomic sequence organization of Dickeya is more complex, demonstrating extended chromosomal domains of thermodynamically distinct DNA sequences eliciting specific transcriptional responses to various kinds of stress encountered during pathogenic growth. This feature of the Dickeya genome is likely an adaptation to the pathogenic lifestyle utilizing differences in genomic sequence organization for the selective expression of virulence traits. We propose that the coupling of DNA thermodynamic stability and genetic function provides a common organizational principle for the coordinated expression of genes during both normal and pathogenic bacterial growth. Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)
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17 pages, 3313 KiB  
Review
What Happens in the Staphylococcal Nucleoid under Oxidative Stress?
by Kazuya Morikawa, Yuri Ushijima, Ryosuke L. Ohniwa, Masatoshi Miyakoshi and Kunio Takeyasu
Microorganisms 2019, 7(12), 631; https://doi.org/10.3390/microorganisms7120631 - 29 Nov 2019
Cited by 7 | Viewed by 4202
Abstract
The evolutionary success of Staphylococcus aureus as an opportunistic human pathogen is largely attributed to its prominent abilities to cope with a variety of stresses and host bactericidal factors. Reactive oxygen species are important weapons in the host arsenal that inactivate phagocytosed pathogens, [...] Read more.
The evolutionary success of Staphylococcus aureus as an opportunistic human pathogen is largely attributed to its prominent abilities to cope with a variety of stresses and host bactericidal factors. Reactive oxygen species are important weapons in the host arsenal that inactivate phagocytosed pathogens, but S. aureus can survive in phagosomes and escape from phagocytic cells to establish infections. Molecular genetic analyses combined with atomic force microscopy have revealed that the MrgA protein (part of the Dps family of proteins) is induced specifically in response to oxidative stress and converts the nucleoid from the fibrous to the clogged state. This review collates a series of evidences on the staphylococcal nucleoid dynamics under oxidative stress, which is functionally and physically distinct from compacted Escherichia coli nucleoid under stationary phase. In addition, potential new roles of nucleoid clogging in the staphylococcal life cycle will be proposed. Full article
(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)
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