SuhB is an integral part of the ribosomal antitermination complex and interacts with NusA

Major-groove sequence-specific RNA recognition by LoaP, a paralog of transcription elongation factor NusG

LoaP is a member of the universal NusG protein family. Previously, we reported that unlike other characterized homologs, LoaP binds RNA sequence-specifically, recognizing a stem-loop in the 5'-untranslated region of operons it regulates. To elucidate how this NusG homolog acquired this ability, we now determined the co-crystal structure of Thermoanaerobacter pseudethanolicus LoaP bound to its cognate 26-nucleotide dfn RNA element. Our structure reveals that the LoaP C-terminal KOW domain recognizes the helical portion of the RNA by docking into a broadened major groove, while a protruding β-hairpin of the N-terminal NusG-like domain binds the UNCG tetraloop capping the stem-loop. Major-groove RNA recognition is unusual and is made possible by conserved features of the dfn hairpin. Superposition with structures of other NusG proteins implies that LoaP can bind concurrently to the dfn RNA and the transcription elongation complex, suggesting a new level of co-transcriptional regulation by proteins of this conserved family.

A comprehensive examination of ACE2 receptor and prediction of spike glycoprotein and ACE2 interaction based on in silico analysis of ACE2 receptor

The ACE2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in various other diseases, including cardiovascular diseases and ARDS. While studies have explored the interactions between ACE2 and SARS-CoV proteins, comprehensive research utilizing bioinformatic tools on the ACE2 protein has been lacking. The one aim of present study was to extensively analyze the regions of the ACE2 protein. After utilizing all bioinformatics tools especially G104 and L108 regions on ACE2 were come forward. The results of our analysis revealed that possible mutations or deletions in the G104 and L108 regions play a critical role in both the biological functioning and the determination of the chemical-physical properties of ACE2. Additionally, these regions were found to be more susceptible to mutations or deletions compared to other regions of the ACE2 protein. Notably, the randomly selected peptide, LQQNGSSVLS (100-109), which includes G104 and L108, exhibited a crucial role in binding the RBD of the spike protein, as supported by docking scores. Furthermore, both MDs and iMODs results provided evidence that G104 and L108 influence the dynamics of ACE2-spike complexes. This study is expected to offer a new perspective on the ACE2-SARS-CoV interaction and other research areas where ACE2 plays a significant role, such as biotechnology (protein engineering, enzyme optimization), medicine (RAS, pulmonary and cardiac diseases), and basic research (structural motifs, stabilizing protein folds, or facilitating important inter molecular contacts, protein's proper structure and function).Communicated by Ramaswamy H. Sarma.

Bacterial RNase III: Targets and physiology

Bacteria can rapidly adapt to changes in their environment thanks to the innate flexibility of their genetic expression. The high turnover rate of RNAs, in particular messenger and regulatory RNAs, provides an important contribution to this dynamic adjustment. Recycling of RNAs is ensured by ribonucleases, among which RNase III is the focus of this review. RNase III enzymes are highly conserved from prokaryotes to eukaryotes and have the specific ability to cleave double-stranded RNAs. The role of RNase III in bacterial physiology has remained poorly explored for a long time. However, transcriptomic approaches recently uncovered a large impact of RNase III in gene expression in a wide range of bacteria, generating renewed interest in the physiological role of RNase III. In this review, we first describe the RNase III targets identified from global approaches in 8 bacterial species within 4 Phyla. We then present the conserved and unique functions of bacterial RNase III focusing on growth, resistance to stress, biofilm formation, motility and virulence. Altogether, this review highlights the underestimated impact of RNase III in bacterial adaptation.

Transcription complexes as RNA chaperones

To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.

Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity

The B.1.1.7 SARS-CoV-2 strain that has emerged in the UK in early December presents seven mutations and three deletions on S-protein structure that could lead to a more infective strain. The P681H mutation in the “PRRAR” furin cleavage site might affect the binding affinity to furin enzyme and hence its infectivity.

Therefore, in this study, various structural bioinformatics approaches were used to model the S-protein structure with the B.1.1.7 variant amino acid substitutions and deletions. In addition to modelling the binding of furin to the cleavage site of the wild-type and the B.1.1.7 variant.

Conclusively the B.1.1.7 variant resulted in dynamic stability, conformational changes and variations in binding energies in the S-protein structure, resulting in a more favourable binding of furin enzyme to the SARS-CoV-2 S-protein.

Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors

The coordination of bacterial genomic transcription involves an intricate network of interdependent genes encoding nucleoid-associated proteins (NAPs), DNA topoisomerases, RNA polymerase subunits and modulators of transcription machinery. The central element of this homeostatic regulatory system, integrating the information on cellular physiological state and producing a corresponding transcriptional response, is the multi-subunit RNA polymerase (RNAP) holoenzyme. In this review article, we argue that recent observations revealing DNA topoisomerases and metabolic enzymes associated with RNAP supramolecular complex support the notion of structural coupling between transcription machinery, DNA topology and cellular metabolism as a fundamental device coordinating the spatiotemporal genomic transcription. We analyse the impacts of various combinations of RNAP holoenzymes and global transcriptional regulators such as abundant NAPs, on genomic transcription from this viewpoint, monitoring the spatiotemporal patterns of couplons—overlapping subsets of the regulons of NAPs and RNAP sigma factors. We show that the temporal expression of regulons is by and large, correlated with that of cognate regulatory genes, whereas both the spatial organization and temporal expression of couplons is distinctly impacted by the regulons of NAPs and sigma factors. We propose that the coordination of the growth phase-dependent concentration gradients of global regulators with chromosome configurational dynamics determines the spatiotemporal patterns of genomic expression.

A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity

Bacterial NusG associates with RNA polymerase (RNAP) through its N-terminal domain, while the C-terminal domain (CTD) forms dynamic interactions with Rho, S10, NusB and NusA to affect transcription elongation. While virtually all bacteria encode for a core NusG, many also synthesize paralogs that transiently bind RNAP to alter expression of targeted genes. Yet, despite the importance of the genes they regulate, most of the subfamilies of NusG paralogs (e.g., UpxY, TaA, ActX and LoaP) have not been investigated in depth. Herein, we discover that LoaP requires a small RNA hairpin located within the 5' leader region of its targeted operons. LoaP binds the RNA element with nanomolar affinity and high specificity, in contrast to other NusG proteins, which have not been shown to exhibit RNA-binding activity. These data reveal a sequence feature that can be used to identify LoaP-regulated operons. This discovery also expands the repertoire of macromolecular interactions exhibited by the NusG CTD during transcription elongation to include an RNA ligand.

Transcription termination and antitermination of bacterial CRISPR arrays

A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequences in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.

Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity

Objective

The coronavirus disease 2019 (COVID-19) pandemic has caused an exponential rise in death rates and hospitalizations. The aim of this study was to characterize the D614G substitution in the severe acute respiratory syndome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S protein), which may affect viral infectivity.

Methods

The effect of D614G substitution on the structure and thermodynamic stability of the S protein was analyzed with use of DynaMut and SCooP. HDOCK and PRODIGY were used to model furin protease binding to the S protein RRAR cleavage site and calculate binding affinities. Molecular dynamics simulations were used to predict the S protein apo structure, the S protein–furin complex structure, and the free binding energy of the complex.

Results

The D614G substitution in the G clade of SARS-CoV-2 strains introduced structural mobility and decreased the thermal stability of the S protein (ΔΔG = −0.086 kcal mol⁻¹). The substitution resulted in stronger binding affinity (K_d = 1.6 × 10⁻⁸) for furin, which may enhance S protein cleavage. The results were corroborated by molecular dynamics simulations demonstrating higher binding energy of furin and the S protein D614G mutant (−61.9 kcal mol⁻¹ compared with −56.78 kcal mol⁻¹ for wild-type S protein).

Conclusions

The D614G substitution in the G clade induced flexibility of the S protein, resulting in increased furin binding, which may enhance S protein cleavage and infiltration of host cells. Therefore, the SARS-CoV-2 D614G substitution may result in a more virulent strain.

Escherichia coli NusG Links the Lead Ribosome with the Transcription Elongation Complex

It has been known for more than 50 years that transcription and translation are physically coupled in bacteria, but whether or not this coupling may be mediated by the two-domain protein N-utilization substance (Nus) G in Escherichia coli is still heavily debated. Here, we combine integrative structural biology and functional analyses to provide conclusive evidence that NusG can physically link transcription with translation by contacting both RNA polymerase and the ribosome. We present a cryo-electron microscopy structure of a NusG:70S ribosome complex and nuclear magnetic resonance spectroscopy data revealing simultaneous binding of NusG to RNAP and the intact 70S ribosome, providing the first direct structural evidence for NusG-mediated coupling. Furthermore, in vivo reporter assays show that recruitment of NusG occurs late in transcription and strongly depends on translation. Thus, our data suggest that coupling occurs initially via direct RNAP:ribosome contacts and is then mediated by NusG.

Nusbiarylins Inhibit Transcription and Target Virulence Factors in Bacterial Pathogen Staphylococcus aureus

The emergence of multidrug resistance in the clinically significant pathogen Staphylococcus aureus is a global health burden, compounded by a diminishing drug development pipeline, and a lack of approved novel antimicrobials. Our previously reported first-in-class bacterial transcription inhibitors “nusbiarylins” presented a promising prospect towards the discovery of novel antimicrobial agents with a novel mechanism. Here we investigated and characterised the lead nusbiarylin compound, MC4, and several of its chemical derivatives in both methicillin-resistant S. aureus (MRSA) and the S. aureus type strains, demonstrating their capacity for the arrest of growth and cellular respiration, impairment of RNA and intracellular protein levels at subinhibitory concentrations. In some instances, derivatives of MC4 were also shown to attenuate the production of staphylococcal virulence factors in vitro, such as the exoproteins α-toxin and Panton–Valentine Leukocidin (PVL). Trends observed from quantitative PCR assays suggested that nusbiarylins elicited these effects possibly by acting via but not limited to the modulation of global regulatory pathways, such as the agr regulon, which coordinates the expression of S. aureus genes associated with virulence. Our findings encourage the continued development of more potent compounds within this novel family of bacterial transcription inhibitors.

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation

Bacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid–liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid–liquid phase separation is a common mechanism for intracellular organization in both eukaryotic and prokaryotic cells.

Once described as mere “bags of enzymes,” bacterial cells are in fact highly organized, with many macromolecules exhibiting nonuniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid–liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in Escherichia coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and demonstrates that this process can serve as a mechanism for intracellular organization in prokaryotes and eukaryotes alike.

NusA directly interacts with antitermination factor Q from phage λ

Antitermination (AT) is a ubiquitous principle in the regulation of bacterial transcription to suppress termination signals. In phage λ antiterminator protein Q controls the expression of the phage’s late genes with loading of λQ onto the transcription elongation complex halted at a σ-dependent pause requiring a specific DNA element. The molecular basis of λQ-dependent AT and its dependence on N-utilization substance (Nus) A is so far only poorly understood. Here we used solution-state nuclear magnetic resonance spectroscopy to show that the solution structure of λQ is in agreement with the crystal structure of an N-terminally truncated variant and that the 60 residues at the N-terminus are unstructured. We also provide evidence that multidomain protein NusA interacts directly with λQ via its N-terminal domain (NTD) and the acidic repeat (AR) 2 domain, with the λQ:NusA-AR2 interaction being able to release NusA autoinhibition. The binding sites for NusA-NTD and NusA-AR2 on λQ overlap and the interactions are mutually exclusive with similar affinities, suggesting distinct roles during λQ-dependent AT, e.g. the λQ:NusA-NTD interaction might position NusA-NTD in a way to suppress termination, making NusA-NTD repositioning a general scheme in AT mechanisms.