Membrane association of the bacterial riboregulator Hfq and functional perspectives

Malabirade, Antoine; Morgado-Brajones, Javier; Trépout, Sylvain; Wien, Frank; Márquez, Ileana; Seguin, Jérôme; Marco, Sergio; Vélez, Marisela; Arluison, Véronique

doi:10.1038/s41598-017-11157-5

Cited by 43 publications

(50 citation statements)

References 61 publications

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“…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). Different from all the fixed-cell experiment, single-molecule tracking of fluorescent protein-tagged Hfq in live-cell reveals that Hfq is essentially freely diffusing inside the cell, with the diffusion rate slowed down when Hfq binds to the newly transcribed RNA attached to the nucleoid (116).…”

Section: Localization Of Small Rnasmentioning

confidence: 71%

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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Section: Localization Of Small Rnasmentioning

confidence: 71%

RNA Localization in Bacteria

Fei

Sharma

2018

Microbiol Spectr

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“…The peptide corresponding to the CTR region of Hfq (residues 64-102, referred to as Hfq-CTR throughout the manuscript) was synthetized by Proteogenix SA (Schitilgheim, France). The sequence of the peptide is SRPVSHHSNNAGGGTSSNYHHGSSAQNTSAQQDSEETE (the amyloid region is underlined, [42]). Single strand dA 59 and dT 59 oligonucleotides solutions (Eurogentec, Seraing, Belgium) were mixed together and heated at 90 • C for 2 min to form the (dA:dT) 59 duplex.…”

Section: Preparation Of the Complexes For Srcd Srld And Afmmentioning

confidence: 99%

The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment

et al. 2019

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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.

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“…Hfq forms amyloidogenic structures and is known to be a nucleic acid binding protein (Cech et al ., ; Malabirade et al ., ). Hfq self‐assembles into amyloid fibres due to the presence of a 38 amino acid residue sequence in its CTR (Arluison et al ., ; Fortas et al ., ; Malabirade et al ., ). Only a patch of 11 amino acids over 38 are necessary for Hfq to self‐assemble, but not to interact with nucleic acid (NA).…”

Section: Introductionmentioning

confidence: 98%

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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Membrane association of the bacterial riboregulator Hfq and functional perspectives

Cited by 43 publications

References 61 publications

RNA Localization in Bacteria

RNA Localization in Bacteria

The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment

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

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