Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

Advances in chaperone-assisted RNA crystallography using synthetic antibodies

RNA molecules play essential roles in many biological functions, from gene expression regulation, cellular growth, and metabolism to catalysis. They frequently fold into three-dimensional structures to perform their functions. Therefore, determining RNA structure represents a key step for understanding the structure-function relationships and developing RNA-targeted therapeutics. X-ray crystallography remains a method of choice for determining high-resolution RNA structures, but it has been challenging due to difficulties associated with RNA crystallization and phasing. Several natural and synthetic RNA binding proteins have been used to facilitate RNA crystallography. Having unique properties to help crystal packing and phasing, synthetic antibody fragments, specifically the Fabs, have emerged as promising RNA crystallization chaperones, and so far, over a dozen of RNA structures have been solved using this strategy. Nevertheless, multiple steps in this approach need to be improved, including the recombinant expression of these anti-RNA Fabs, to warrant the full potential of these synthetic Fabs as RNA crystallization chaperones. This review highlights the nuts and bolts and recent advances in the chaperone-assisted RNA crystallography approach, specifically emphasizing the Fab antibody fragments as RNA crystallization chaperones.

The bacterial protein Hfq: Stable modifications and growth phase-dependent changes in SPAM profiles

In bacteria transcription is coupled to translation, and while it is broadly accepted that transcription-translation complexes (TTCs) are formed in growing bacterial cells, the exact spatial organization of these macromolecular assemblies is not known with certainty. Recent studies indicated the formation of orderly cytosolic superstructures in growing E. coli cells. The bacterial nucleic acid (NA)-binding protein Hfq has been shown to function at the interface of RNA synthesis-degradation machinery; multiple, independent studies link Hfq to orderly cytosolic assemblies. In this work, using fast cell lysis/2D-PAGE and in vitro reconstitution analyses we studied the Hfq modifications and small protein-associated molecules (SPAM). We demonstrate that native Hfq carries stable modifications and simulate 2D patterns of native Hfq-SPAM complexes in reconstitution experiments with purified Hfq and synthetic NA probes. We also demonstrate that genetically engineered Hfq lacking the conserved arginine residues positioned near the rim of the disc formed by the subunits' N-terminal domains binds DNA with a reduced affinity in comparison with wild-type Hfq. These results are consistent with the proposed Hfq-mediated DNA remodeling and point to the involvement of this patch of conserved arginines in interactions with DNA.

The Amyloid Region of Hfq Riboregulator Promotes DsrA:rpoS RNAs Annealing

Hfq is a bacterial RNA chaperone which promotes the pairing of small noncoding RNAs to target mRNAs, allowing post-transcriptional regulation. This RNA annealing activity has been attributed for years to the N-terminal region of the protein that forms a toroidal structure with a typical Sm-fold. Nevertheless, many Hfqs, including that of Escherichia coli, have a C-terminal region with unclear functions. Here we use a biophysical approach, Synchrotron Radiation Circular Dichroism (SRCD), to probe the interaction of the E. coli Hfq C-terminal amyloid region with RNA and its effect on RNA annealing. This C-terminal region of Hfq, which has been described to be dispensable for sRNA:mRNA annealing, has an unexpected and significant effect on this activity. The functional consequences of this novel property of the amyloid region of Hfq in relation to physiological stress are discussed.

The role of RNA-binding proteins in mediating adaptive responses in Gram-positive bacteria

Bacteria are constantly subjected to stressful conditions, such as antibiotic exposure, nutrient limitation and oxidative stress. For pathogenic bacteria, adapting to the host environment, escaping defence mechanisms and coping with antibiotic stress are crucial for their survival and the establishment of a successful infection. Stress adaptation relies heavily on the rate at which the organism can remodel its gene expression programme to counteract the stress. RNA-binding proteins mediating co- and post-transcriptional regulation have recently emerged as important players in regulating gene expression during adaptive responses. Most of the research on these layers of gene expression regulation has been done in Gram-negative model organisms where, thanks to a wide variety of global studies, large post-transcriptional regulatory networks have been uncovered. Unfortunately, our understanding of post-transcriptional regulation in Gram-positive bacteria is lagging behind. One possible explanation for this is that many proteins employed by Gram-negative bacteria are not well conserved in Gram-positives. And even if they are conserved, they do not always play similar roles as in Gram-negative bacteria. This raises the important question whether Gram-positive bacteria regulate gene expression in a significantly different way. The goal of this review was to discuss this in more detail by reviewing the role of well-known RNA-binding proteins in Gram-positive bacteria and by highlighting their different behaviours with respect to some of their Gram-negative counterparts. Finally, the second part of this review introduces several unusual RNA-binding proteins of Gram-positive species that we believe could also play an important role in adaptive responses.

Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode

Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.

The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment

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.

Normal Mode Analysis as a Routine Part of a Structural Investigation

Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.

Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly

Hfq is a bacterial RNA-binding protein that plays key roles in the post-transcriptional regulation of gene expression. Like other Sm proteins, Hfq assembles into toroidal discs that bind RNAs with varying affinities and degrees of sequence specificity. By simultaneously binding to a regulatory small RNA (sRNA) and an mRNA target, Hfq hexamers facilitate productive RNA∙∙∙RNA interactions; the generic nature of this chaperone-like functionality makes Hfq a hub in many sRNA-based regulatory networks. That Hfq is crucial in diverse cellular pathways-including stress response, quorum sensing, and biofilm formation-has motivated genetic and "RNAomic" studies of its function and physiology (in vivo), as well as biochemical and structural analyses of Hfq∙∙∙RNA interactions (in vitro). Indeed, crystallographic and biophysical studies first established Hfq as a member of the phylogenetically conserved Sm superfamily. Crystallography and other biophysical methodologies enable the RNA-binding properties of Hfq to be elucidated in atomic detail, but such approaches have stringent sample requirements, viz.: reconstituting and characterizing an Hfq·RNA complex requires ample quantities of well-behaved (sufficient purity, homogeneity) specimens of Hfq and RNA (sRNA, mRNA fragments, short oligoribonucleotides, or even single nucleotides). The production of such materials is covered in this chapter, with a particular focus on recombinant Hfq proteins for crystallization experiments.

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.

The Small β-Barrel Domain: A Survey-Based Structural Analysis

The small β-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an "urfold." To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure ↔ function versatility of the SBB.

Structural biology meets data science: does anything change?

Data science has emerged from the proliferation of digital data, coupled with advances in algorithms, software and hardware (e.g., GPU computing). Innovations in structural biology have been driven by similar factors, spurring us to ask: can these two fields impact one another in deep and hitherto unforeseen ways? We posit that the answer is yes. New biological knowledge lies in the relationships between sequence, structure, function and disease, all of which play out on the stage of evolution, and data science enables us to elucidate these relationships at scale. Here, we consider the above question from the five key pillars of data science: acquisition, engineering, analytics, visualization and policy, with an emphasis on machine learning as the premier analytics approach.

Hfq chaperone brings speed dating to bacterial sRNA

Hfq is a ubiquitous, Sm-like RNA binding protein found in most bacteria and some archaea. Hfq binds small regulatory RNAs (sRNAs), facilitates base pairing between sRNAs and their mRNA targets, and directly binds and regulates translation of certain mRNAs. Because sRNAs regulate many stress response pathways in bacteria, Hfq is essential for adaptation to different environments and growth conditions. The chaperone activities of Hfq arise from multipronged RNA binding by three different surfaces of the Hfq hexamer. The manner in which the structured Sm core of Hfq binds RNA has been well studied, but recent work shows that the intrinsically disordered C-terminal domain of Hfq modulates sRNA binding, creating a kinetic hierarchy of RNA competition for Hfq and ensuring the release of double-stranded sRNA-mRNA complexes. A combination of structural, biophysical, and genetic experiments reveals how Hfq recognizes its RNA substrates and plays matchmaker for sRNAs and mRNAs in the cell. The interplay between structured and disordered domains of Hfq optimizes sRNA-mediated post-transcriptional regulation, and is a common theme in RNA chaperones. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry.

Membrane association of the bacterial riboregulator Hfq and functional perspectives

Hfq is a bacterial RNA binding protein that carries out several roles in genetic expression regulation, mainly at the post-transcriptional level. Previous studies have shown its importance in growth and virulence of bacteria. Here, we provide the direct observation of its ability to interact with membranes. This was established by co-sedimentation assay, cryo-transmission electron (cryo-TEM) and atomic force (AFM) microscopies. Furthermore, our results suggest a role for its C-terminus amyloidogenic domain in membrane disruption. Precisely, AFM images of lipid bilayers in contact with Hfq C-terminus fibrils show the emergence of holes with a size dependent on the time of interaction. Cryo-TEM observations also show that liposomes are in contact with clusters of fibrils, with occasional deformation of the vesicles and afterward the apparition of a multitude of tiny vesicles in the proximity of the fibrils, suggesting peptide-induced breakage of the liposomes. Finally, circular dichroism spectroscopy demonstrated a change in the secondary structure of Hfq C-terminus upon interaction with liposomes. Altogether, these results show an unexpected property of Hfq and suggest a possible new role for the protein, exporting sRNA outside of the bacterial cell.