Compaction and condensation of DNA mediated by the C-terminal domain of Hfq

Malabirade, Antoine; Jiang, Kai; Kubiak, K.; Diaz-Mendoza, Alvaro; Liu, Fan; Kan, J.A. van; Berret, Jean‐François; Arluison, Véronique; Maarel, Johan R. C. van der

doi:10.1093/nar/gkx431

Cited by 49 publications

(77 citation statements)

References 48 publications

(67 reference statements)

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“…Mutations in Hfq can alter DNA topology and have pleiotropic effects in cells [35,39,41,43,78]. Hfq binds to sRNA and can alter mRNA translation or message stability [79] that can alter expression levels of many genes.…”

Section: A Mutation In Hfq Increases Stability Of G-quadruplex Repeatsmentioning

confidence: 99%

“…In E. coli, in addition to proteins and enzymes involved in genome maintenance, proteins involved in chromosome organization and compaction (nucleoid-associated proteins, NAP), which can often bind in a sequence nonspecific fashion, may also have the capacity to interact with alternative DNA conformations. The role of these proteins in DNA organization and packaging in chromosomes and large DNAs has been studied [35,36]. However, investigations into how proteins involved in chromosome organization may influence the equilibrium between canonical B-form DNA and alternative helical structures are lacking.…”

Section: Introductionmentioning

confidence: 99%

“…Hfq notably mediates translation efficiency by using stress-related small regulatory RNA (sRNA) and modulates the cellular levels of RNAs, either by changing their stability or through an unsolved transcriptional mechanism [37]. More recent analyses focused attention on the action of Hfq on nucleoid structure [35,[38][39][40][41][42]. These analyses evidenced that Hfq cooperatively binds to DNA through a DNA:protein:DNA bridging mechanism, that it can form filaments on DNA, changing the mechanical properties of the double helix, with important implications for bacterial transcription and replication [35,36].…”

Section: Introductionmentioning

confidence: 99%

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Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli

et al. 2019

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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 (G 3 T) 4 , (G 3 T) 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. variable with strands arranged in a parallel, antiparallel, or mixed orientations associated with various glycosidic configurations of guanines [1,[3][4][5]. A single repeat motif can often form multiple structures depending on ionic conditions, as shown for repeats at human telomeres and oncogene promoters [4][5][6][7]. When G-quadruplex structures form in duplex DNA, the C-rich DNA strand complementary to G-quadruplex-forming sequences can form a four stranded i-motif at low pH [8], in which two tracts of cytosines form interdigitated C•C + base pairs [7,9,10] (Figure 1C).Microorganisms 2019, 7, x 2 of 16 quartets are stabilized by monovalent cations. The topology of quadruplex structures is highly variable with strands arranged in a parallel, antiparallel, or mixed orientations associated with various glycosidic configurations of guanines [1,[3][4][5]. A single repeat motif can often form multiple structures depending on ionic conditions, as shown for repeats at human telomeres and oncogene promoters [4][5][6][7]. When G-quadruplex structures form in duplex DNA, the C-rich DNA strand complementary to G-quadruplex-forming sequences can form a four stranded i-motif at low pH [8], in which two tracts of cytosines form interdigitated C•C + base pairs [7,9,10] (Figure 1C).

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Section: A Mutation In Hfq Increases Stability Of G-quadruplex Repeatsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli

et al. 2019

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“…However, results from various studies using different labeling and imaging approaches to study Hfq localization are conflicting, and therefore its localization in the cell remains controversial. Hfq has been observed to adopt a diffuse cytoplasmic localization outside of the nucleoid region by immunofluorescence staining (79), as well as preferential membrane localization by electron microscopy (113), which was recently recapitulated in an in vitro system using artificial vesicles (113, 114). A helical organization of Hfq along the longitudinal direction of the cell has also been observed by immunofluorescence staining (99, 113, 115).…”

Section: Localization Of Small Rnasmentioning

confidence: 99%

RNA Localization in Bacteria

Fei

Sharma

2018

Microbiol Spectr

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Diverse mechanisms and functions of post-transcriptional regulation by small regulatory RNAs (sRNAs) and RNA binding proteins (RBPs) have been described in bacteria. In contrast, little is known about the spatial organization of RNAs in bacterial cells. In eukaryotes, subcellular localization and transport of RNAs play important roles in diverse physiological processes, such as embryonic patterning, asymmetric cell division, epithelial polarity, and neuronal plasticity. It is now clear that bacterial RNAs also can accumulate at distinct sites in the cell. However, due the small size of bacterial cells, localized RNA and translation are more challenging to study in bacterial cells, and the underlying molecular mechanisms of transcript localization are less understood. Here we review the emerging examples of RNAs localized to specific subcellular locations in bacteria, with indications that subcellular localization of transcripts might be important for regulatory processes. Diverse mechanisms for bacterial RNA localization have been suggested, including close association to their genomic site of transcription, or to the localizations of their protein products in translation-dependent or independent processes. We also provide an overview of the state-of-the-art of technologies to visualize and track bacterial RNAs, ranging from hybridization-based approaches in fixed cells to in vivo imaging approaches using fluorescent protein reporters and/or RNA aptamers in single living bacterial cells. We conclude with a discussion of open questions in the field and ongoing technological developments regarding RNA imaging in eukaryotic systems that might likewise provide novel insights into RNA localization in bacteria.

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“…Only a patch of 11 amino acids over 38 are necessary for Hfq to self‐assemble, but not to interact with nucleic acid (NA). As this analysis could open perspectives in the future to correlatively image nucleoprotein complexes (Malabirade et al ., ; Malabirade et al ., ), the synthetic 38 amino acid long sequence (referred as CTR 38 through the manuscript) rather than the shorter peptide with 11 amino acids was chosen for this work. With this sequence, in the absence of NA, about 20% of the peptide may show an intermolecular β‐sheet secondary structure characteristic of the amyloid moiety.…”

Section: Introductionmentioning

confidence: 99%

Correlative infrared nanospectroscopy and transmission electron microscopy to investigate nanometric amyloid fibrils: prospects and challenges

Partouche

Mathurin

Malabirade

et al. 2019

Journal of Microscopy

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Summary Propagation of structural information through conformational changes in host‐encoded amyloid proteins is at the root of many neurodegenerative disorders. Although important breakthroughs have been made in the field, fundamental issues like the 3D‐structures of the fibrils involved in some of those disorders are still to be elucidated. To better characterise those nanometric fibrils, a broad range of techniques is currently available. Nevertheless none of them is able to perform direct chemical characterisation of single protein fibrils. In this work, we propose to investigate the structure of the C‐terminal region of a bacterial protein called Hfq as a model amyloidogenic protein, using a correlative approach. The complementary techniques used are transmission electron microscopy and a newly developed infrared nanospectroscopy technique called AFM‐IR. We introduce and discuss the strategy that we have implemented as well as the protocol, challenges and difficulties encountered during this study to characterise amyloid assemblies at the nearly single‐molecule level. Lay Description Propagation of structural information through conformational changes in amyloid proteins is at the root of many neurodegenerative disorders. Amyloids are nanostructures originating from the aggregation of multiple copies of peptide or protein monomers that eventually form fibrils. Often described as being the cause for the development of various diseases, amyloid fibrils are of major significance in the public health domain. While important breakthroughs have been made in the field, fundamental issues like the 3D‐structures of the fibrils implied in some of those disorders are still to be elucidated. To better characterise these fibrils, a broad range of techniques is currently available for the detection and visualisation of amyloid nanostructures. Nevertheless none of them is able to perform direct chemical characterisation of single protein fibrils. In this work, we propose to investigate the structure of model amyloidogenic fibrils using a correlative approach. The complementary techniques used are transmission electron microscopy and a newly developed infrared nanospectroscopy technique called AFM‐IR that allows chemical characterisation at the nanometric scale. The strategy, protocol, challenges and difficulties encountered in this approach are introduced and discussed herein.

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Compaction and condensation of DNA mediated by the C-terminal domain of Hfq

Cited by 49 publications

References 48 publications

Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli

Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli

RNA Localization in Bacteria

Correlative infrared nanospectroscopy and transmission electron microscopy to investigate nanometric amyloid fibrils: prospects and challenges

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