Direct, Rapid, and Simple Evaluation of the Expression and Conformation of Beta-Amyloid in Bacterial Cells by FTIR Spectroscopy.

The expression and conformation of bacterial proteins and peptides can be monitored in situ by Fourier transform infrared spectroscopy (FTIR), provided that the concentration of the protein of interest is sufficient. Here, we describe a simple protocol to analyze the conformation adopted by a specific amyloid protein in Escherichia coli cells, the pleiotropic regulator Hfq.E. coli cells expressing Hfq under an inducible promoter are analyzed. The change in protein conformation is analyzed by comparing the different populations versus controls (i.e., Δhfq cells, totally devoid of the Hfq protein) by difference spectroscopy, second derivation, curve-fitting, and principal component analysis. All the analyses were performed in the free, open-source software Quasar. We describe the detailed protocol for analyzing the data in Quasar. We show that the specific absorption of the ß-amyloid conformation can be easily detected in the WT-Hfq, with bands at 1624 cm-1 and 1693 cm-1 indicating the presence of both parallel and antiparallel ß-sheets. Furthermore, we show that FTIR spectroscopy is sensitive enough to probe the conformation of an amyloid protein backbone in vivo and to analyze its conformation in situ, directly in bacterial cells, without the need for protein purification.

Apomorphine Targets the Pleiotropic Bacterial Regulator Hfq.

Hfq is a bacterial regulator with key roles in gene expression. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, thanks to its binding to small regulatory noncoding RNAs. This property is of primary importance for bacterial adaptation and survival in hosts. Small RNAs and Hfq are, for instance, involved in the response to antibiotics. Previous work has shown that the E. coli Hfq C-terminal region (Hfq-CTR) self-assembles into an amyloid structure. It was also demonstrated that the green tea compound EpiGallo Catechin Gallate (EGCG) binds to Hfq-CTR amyloid fibrils and remodels them into nonamyloid structures. Thus, compounds that target the amyloid region of Hfq may be used as antibacterial agents. Here, we show that another compound that inhibits amyloid formation, apomorphine, may also serve as a new antibacterial. Our results provide an alternative in order to repurpose apomorphine, commonly used in the treatment of Parkinson's disease, as an antibiotic to block bacterial adaptation to treat infections.

Identification and characterization of the Hfq bacterial amyloid region DNA interactions.

Nucleic acid amyloid proteins interactions have been observed in the past few years. These interactions often promote protein aggregation. Nevertheless, molecular basis and physiological consequences of these interactions are still poorly understood. Additionally, it is unknown whether the nucleic acid promotes the formation of self-assembly due to direct interactions or indirectly via sequences surrounding the amyloid region. Here we focus our attention on a bacterial amyloid, Hfq. This protein is a pleiotropic bacterial regulator that mediates many aspects of nucleic acids metabolism. The protein notably mediates mRNA stability and translation efficiency by using stress-related small non coding regulatory RNA. In addition, Hfq, thanks to its amyloid C-terminal region, binds and compacts DNA. A combination of experimental methodologies, including synchrotron radiation circular dichroism (SRCD), gel shift assay and infrared (FTIR) spectroscopy have been used to probe the interaction of Hfq C-terminal region with DNA. We clearly identify important amino acids in this region involved in DNA binding and polymerization properties. This allows to understand better how this bacterial amyloid interacts with DNA. Possible functional consequence to answer to stresses are discussed.

Direct Synthesis of Mesoporous Organosilica and Proof-of-Concept Applications in Lysozyme Adsorption and Supported Catalysis.

Mesoporous materials represent a useful alternative for exploiting the effects of confinement on molecular trapping and catalysis. Their efficiency often depends on the interactions between the surface and the targeted molecules. One way to enhance these interactions is to adjust the hydrophobic/hydrophilic balance of the surface. In the case of mesoporous silica, the incorporation of organic groups is an efficient solution to adapt the material for specific applications. In this work, we have used the co-condensation method to control the hydrophobicity of mesoporous organosilica. The obtained materials are methyl- or phenyl-containing silica with a pore size between 3 and 5 nm. The surface chemistry control has shown the enhanced performance of the materials in two proof-of-concept (PoC) applications: lysozyme adsorption and supported catalysis. The lysozyme adsorption is observed to be over 3 times more efficient with the phenyl-functionalized material than MCM-41, due to π-π interactions. For the catalysis, copper(II) was immobilized on the organosilica surface. In this case, the presence of methyl groups significantly enhanced the product yield for the catalyzed synthesis of a triazole derivative; this was attributed to the enhanced hydrophobic surface-reactant interactions. It was also found that the materials have a higher water adsorption capacity and an improved resistance to hydrolysis. The modulation of water properties in confinement with hydrophobic surfaces, consistently with the water as tuneable solvent (WaTuSo) concept, is a crucial aspect in the efficiency of mesoporous materials for dedicated applications.

In Situ Characterization of Hfq Bacterial Amyloid: A Fourier-Transform Infrared Spectroscopy Study.

Hfq is a bacterial protein that regulates gene expression at the post-transcriptional level in Gram-negative bacteria. We have previously shown that Escherichia coli Hfq protein, and more precisely its C-terminal region (CTR), self-assembles into an amyloid-like structure in vitro. In the present work, we present evidence that Hfq unambiguously forms amyloid structures also in vivo. Taking into account the role of this protein in bacterial adaptation and virulence, our work opens possibilities to target Hfq amyloid self-assembly and cell location, with important potential to block bacterial adaptation and treat infections.

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

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.

Epigallocatechin Gallate Remodelling of Hfq Amyloid-Like Region Affects Escherichia coli Survival.

Hfq is a pleiotropic regulator that has key roles in the control of genetic expression. The protein noticeably regulates translation efficiency and RNA decay in Gram-negative bacteria, due to the Hfq-mediated interaction between small regulatory noncoding RNA and mRNA. This property is of primary importance for bacterial adaptation and virulence. We have previously shown that the Hfq E. coli protein, and more precisely its C-terminal region (CTR), self-assembles into an amyloid-like structure. In the present work, we demonstrate that epigallocatechin gallate (EGCG), a major green tea polyphenol compound, targets the Hfq amyloid region and can be used as a potential antibacterial agent. We analysed the effect of this compound on Hfq amyloid fibril stability and show that EGCG both disrupts Hfq-CTR fibrils and inhibits their formation. We show that, even if EGCG affects other bacterial amyloids, it also specifically targets Hfq-CTR in vivo. Our results provide an alternative approach for the utilisation of EGCG that may be used synergistically with conventional antibiotics to block bacterial adaptation and treat infections.

Revised role for Hfq bacterial regulator on DNA topology.

Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNA. Besides these RNA-related functions, Hfq has also been described as one of the nucleoid associated proteins shaping the bacterial chromosome. Therefore, Hfq appears as a versatile nucleic acid-binding protein, which functions are probably even more numerous than those initially suggested. For instance, E. coli Hfq, and more precisely its C-terminal region (CTR), has been shown to induce DNA compaction into a condensed form. In this paper, we establish that DNA induces Hfq-CTR amyloidogenesis, resulting in a change of DNA local conformation. Furthermore, we clarify the effect of Hfq on DNA topology. Our results evidence that, even if the protein has a strong propensity to compact DNA thanks to its amyloid region, it does not affect overall DNA topology. We confirm however that hfq gene disruption influences plasmid supercoiling in vivo, indicating that the effect on DNA topology in former reports was indirect. Most likely, this effect is related to small regulatory sRNA-Hfq-based regulation of another protein that influences DNA supercoiling, possibly a nucleoid associated protein such as H-NS or Dps. Finally, we hypothesise that this indirect effect on DNA topology explains, at least partially, the previously reported effect of Hfq on plasmid replication efficiency.

Techniques to Analyze sRNA Protein Cofactor Self-Assembly In Vitro.

Post-transcriptional control of gene expression by small regulatory noncoding RNA (sRNA) needs protein accomplices to occur. Past research mainly focused on the RNA chaperone Hfq as cofactor. Nevertheless, recent studies indicated that other proteins might be involved in sRNA-based regulations. As some of these proteins have been shown to self-assemble, we describe in this chapter protocols to analyze the nano-assemblies formed. Precisely, we focus our analysis on Escherichia coli Hfq as a model, but the protocols presented here can be applied to analyze any polymer of proteins. This chapter thus provides a guideline to develop commonly used approaches to detect prokaryotic protein self-assembly, with a special focus on the detection of amyloidogenic polymers.

Maghemite-human serum albumin hybrid nanoparticles: towards a theranostic system with high MRI r2* relaxivity.

Human Serum Albumin (HSA) is the most abundant plasma protein in human blood, and therefore, it is the material of choice for the development of particulate formulations due to its biodegradable and biocompatible nature. Over the last decade, HSA nanoparticles (NPs) have been prepared mostly using desolvation techniques and evaluated as promising drug carriers. In addition, controlling the particle size has become a primary concern while formulating such nanoparticulate systems. Since many of these HSA-based carrier systems have often demonstrated batch-to-batch fabrication variability, significant efforts have been made to develop and characterize HSA-based NPs featuring a robust and controllable particle size, by using a desolvation/cross-linking-type Divinyl Sulfone (DVS)-mediated nanofabrication method. For this purpose and for global multi-parameter fabrication process optimization, a statistically significant Design of Experiment (DoE, MINITAB® 17 DoE software) methodology has been successfully implemented. It aimed to disclose an optimal set of HSA NP fabrication conditions in order to afford highly reproducible and stable 23.05 ± 5.3 nm-sized DoE-globally optimized core HSA NPs. Due to the use of bifunctional DVS as a cross-linker for the preparation of such DoE-optimized HSA NPs, their surface contains a variety of free functional groups which are available for further second step functional modifications. Moreover, related hybrid organic/inorganic nanosystems consisting of DoE-optimized HSA NPs that encapsulated hydrophilic (NH4)2Ce(IV)(NO3)6 (Ceric Ammonium Nitrate - CAN) modified γ-Fe2O3 NPs (CAN-maghemite or CAN-γ-Fe2O3 NPs), which enable medical imaging using magnetic resonance imaging (MRI), have also been fabricated and characterized. The resulting hybrid magnetic NPs are a quite powerful T2* contrast agent (r2* of 482 mM-1 s-1), which may be used as a powerful dual phase platform for both therapeutic (drug delivery) and diagnostic imaging (MRI) applications.