RNA under attack: cellular handling of RNA damage

Physiological and transcriptomic analyses provide preliminary insights into the autotoxicity of Lilium brownii

Lilium brownii F. E. Brown ex Miellez var. viridulum Baker (Longya lily) is a variety of Lilium brownii F.E. Br. ex Miellez. We used HS-SPME and GC-MS to screened the tissues of L. brownii roots, stems, bulbs, and leaves and obtained 2,4-DTBP as an autotoxic substance for subsequent analysis. 2,4-DTBP was highly autotoxic in some treatment groups. Based on changes in physiological indicators, we carried out transcriptomic analysis to investigate the mechanisms of autotoxicity of substances on L. brownii and obtained 188,505 Unigenes. GO and KEGG enrichment analyses showed that L. brownii responded differently to different concentrations and treatment times of 2,4-DTBP. We observed significant changes in genes associated with ROS, phytohormones, and MAPK signaling cascades. 2,4-DTBP affects chloroplasts, the integrity of the respiratory electron transport chain, and ribosomes, causing L. brownii autotoxicity. Our findings provide a practical genomic resource for future research on L. brownii autotoxicity and evidence for the mechanism of action of autotoxic substances.

G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets

MicroRNAs (miRNAs) play indispensable roles in post-transcriptional gene regulation. The identification of target mRNAs is essential for dissecting the recognition basis, dynamics, and regulatory mechanism of miRNA-mRNA interactions. However, the lack of an unbiased method for detecting weak miRNA-mRNA interactions remains a long-standing obstacle for miRNA research. Here, we develop and provide proof-of-concept evidence demonstrating a chemical G-clamp-enhanced photo-cross-linking strategy for covalent capture of intracellular miRNA targets in different cell lines. This approach relies on an aryl-diazirine-G-clamp-modified-nucleoside (ARAGON) miRNA probe containing an alkynyl group that improves the thermal stability of miRNA-target mRNA duplex molecules and can rapidly cross-link with the complementary strand upon UV 365 nm activation, enhancing the transient capture of mRNA targets. After validating the accuracy and binding properties of ARAGON-based miRNA probes through the successful enrichment for the known targets of miR-106a, miR-21, and miR-101, we then extend ARAGON's application to screen for previously unknown targets of different miRNAs in various cell lines. Ultimately, results in this study uncover GAB1 as a target of miR-101 in H1299 lung cancer cells and show that miR-101 silencing of GAB1 can promote apoptosis in H1299 cells, suggesting an oncogenic mechanism of GAB1. This study thus provides a powerful and versatile tool for enhanced screening of global miRNA targets in cells to facilitate investigations of miRNA functions in fundamental cellular processes and disease pathogenesis.

Reversible oxidative dimerization of 4-thiouridines in tRNA isolates

The occurrence of non-canonical nucleoside structures in RNA of biological or synthetic origin has encountered several recent boosts in attention, namely in the context of RNA modifications, and with an eye to RNA vaccines. New nucleoside structures introduce added functionality and function into biopolymers that are otherwise rather homogenous in their chemical structure. Here, we report the discovery of a presumed RNA modification that was identified by combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) with stable isotope labelling as a dimer of the known RNA modification 4-thiouridine (s4U). The disulfide-linked structure, which had previously been synthetically introduced into RNA, was here formed spontaneously in isolates of E. coli tRNA. Judicious application of stable isotope labelling suggested that this presumed new RNA modification was rather generated ex vivo by oxidation with ambient oxygen. These findings do not only underscore the need for caution in the discovery of new RNA modifications with respect to artifacts, but also raise awareness of an RNA vulnerability, especially to oxidative damage, during its transport or storage.

A Novel Adductomics Workflow Incorporating FeatureHunter Software: Rapid Detection of Nucleic Acid Modifications for Studying the Exposome

Exposure to the physicochemical agents that interact with nucleic acids (NA) may lead to modification of DNA and RNA (i.e., NA modifications), which have been associated with various diseases, including cancer. The emerging field of NA adductomics aims to identify both known and unknown NA modifications, some of which may also be associated with proteins. One of the main challenges for adductomics is the processing of massive and complex data generated by high-resolution tandem mass spectrometry (HR-MS/MS). To address this, we have developed a software called "FeatureHunter", which provides the automated extraction, annotation, and classification of different types of key NA modifications based on the MS and MS/MS spectra acquired by HR-MS/MS, using a user-defined feature list. The capability and effectiveness of FeatureHunter was demonstrated by analyzing various NA modifications induced by formaldehyde or chlorambucil in mixtures of calf thymus DNA, yeast RNA and proteins, and by analyzing the NA modifications present in the pooled urines of smokers and nonsmokers. The incorporation of FeatureHunter into the NA adductomics workflow offers a powerful tool for the identification and classification of various types of NA modifications induced by reactive chemicals in complex biological samples, providing a valuable resource for studying the exposome.

Homeostasis, injury, and recovery dynamics at multiple scales in a self-organizing mouse intestinal crypt

The maintenance of the functional integrity of the intestinal epithelium requires a tight coordination between cell production, migration, and shedding along the crypt-villus axis. Dysregulation of these processes may result in loss of the intestinal barrier and disease. With the aim of generating a more complete and integrated understanding of how the epithelium maintains homeostasis and recovers after injury, we have built a multi-scale agent-based model (ABM) of the mouse intestinal epithelium. We demonstrate that stable, self-organizing behaviour in the crypt emerges from the dynamic interaction of multiple signalling pathways, such as Wnt, Notch, BMP, ZNRF3/RNF43, and YAP-Hippo pathways, which regulate proliferation and differentiation, respond to environmental mechanical cues, form feedback mechanisms, and modulate the dynamics of the cell cycle protein network. The model recapitulates the crypt phenotype reported after persistent stem cell ablation and after the inhibition of the CDK1 cycle protein. Moreover, we simulated 5-fluorouracil (5-FU)-induced toxicity at multiple scales starting from DNA and RNA damage, which disrupts the cell cycle, cell signalling, proliferation, differentiation, and migration and leads to loss of barrier integrity. During recovery, our in silico crypt regenerates its structure in a self-organizing, dynamic fashion driven by dedifferentiation and enhanced by negative feedback loops. Thus, the model enables the simulation of xenobiotic-, in particular chemotherapy-, induced mechanisms of intestinal toxicity and epithelial recovery. Overall, we present a systems model able to simulate the disruption of molecular events and its impact across multiple levels of epithelial organization and demonstrate its application to epithelial research and drug development.

Chemoproteomic Profiling of 8-Oxoguanosine-Sensitive RNA-Protein Interactions

Cellular nucleic acids are subject to assault by endogenous and exogenous agents that can perturb the flow of genetic information. Oxidative stress leads to the accumulation of 8-oxoguanine (8OG) in DNA and RNA. 8OG lesions on mRNA negatively impact translation, but their effect on global RNA-protein interactions is largely unknown. Here, we apply an RNA chemical proteomics approach to investigate the effect of 8OG on RNA-protein binding. We find proteins that bind preferentially to 8OG-modified RNA, including IGF2BP1-3 and hnRNPD, and proteins that are repelled by 8OG such as RBM4. We characterize these interactions using biochemical and biophysical assays to quantify the effect of 8OG on binding and show that a single 8OG abolishes the binding of RBM4 to its preferred CGG-containing substrate. Taken together, our work establishes the molecular consequences of 8OG on cellular RNA-protein binding and provides a framework for interrogating the role of RNA oxidation in biological systems.

Sublethal consequences of ultraviolet radiation exposure on vertebrates: Synthesis through meta-analysis

Ultraviolet radiation (UVR) from the sun is a natural daytime stressor for vertebrates in both terrestrial and aquatic ecosystems. UVR effects on the physiology of vertebrates manifest at the cellular level, but have bottom-up effects at the tissue level and on whole-animal performance and behaviours. Climate change and habitat loss (i.e. loss of shelter from UVR) could interact with and exacerbate the genotoxic and cytotoxic impacts of UVR on vertebrates. Therefore, it is important to understand the range and magnitude of effects that UVR can have on a diversity of physiological metrics, and how these may be shaped by taxa, life stage or geographical range in the major vertebrate groups. Using a meta-analytical approach, we used 895 observations from 47 different vertebrate species (fish, amphibian, reptile and bird), and 51 physiological metrics (i.e. cellular, tissue and whole-animal metrics), across 73 independent studies, to elucidate the general patterns of UVR effects on vertebrate physiology. We found that while UVR's impacts on vertebrates are generally negative, fish and amphibians were the most susceptible taxa, adult and larvae were the most susceptible life stages, and animals inhabiting temperate and tropical latitudes were the most susceptible to UVR stress. This information is critical to further our understanding of the adaptive capacity of vulnerable taxon to UVR stress, and the wide-spread sublethal physiological effects of UVR on vertebrates, such as DNA damage and cellular stress, which may translate up to impaired growth and locomotor performance. These impairments to individual fitness highlighted by our study may potentially cause disruptions at the ecosystem scale, especially if the effects of this pervasive diurnal stressor are exacerbated by climate change and reduced refuge due to habitat loss and degradation. Therefore, conservation of habitats that provide refuge to UVR stress will be critical to mitigate stress from this pervasive daytime stressor.

UV-driven self-repair of cyclobutane pyrimidine dimers in RNA

Nucleic acids can be damaged by ultraviolet (UV) irradiation, forming structural photolesions such as cyclobutane-pyrimidine-dimers (CPD). In modern organisms, sophisticated enzymes repair CPD lesions in DNA, but to our knowledge, no RNA-specific enzymes exist for CPD repair. Here, we show for the first time that RNA can protect itself from photolesions by an intrinsic UV-induced self-repair mechanism. This mechanism, prior to this study, has exclusively been observed in DNA and is based on charge transfer from CPD-adjacent bases. In a comparative study, we determined the quantum yields of the self-repair of the CPD-containing RNA sequence, GAU = U to GAUU (0.23%), and DNA sequence, d(GAT = T) to d(GATT) (0.44%), upon 285 nm irradiation via UV/Vis spectroscopy and HPLC analysis. After several hours of irradiation, a maximum conversion yield of ∼16% for GAU = U and ∼33% for d(GAT = T) was reached. We examined the dynamics of the intermediate charge transfer (CT) state responsible for the self-repair with ultrafast UV pump - IR probe spectroscopy. In the dinucleotides GA and d(GA), we found comparable quantum yields of the CT state of ∼50% and lifetimes on the order of several hundred picoseconds. Charge transfer in RNA strands might lead to reactions currently not considered in RNA photochemistry and may help understanding RNA damage formation and repair in modern organisms and viruses. On the UV-rich surface of the early Earth, these self-stabilizing mechanisms likely affected the selection of the earliest nucleotide sequences from which the first organisms may have developed.

Targeting RNA oxidation by ISG20-mediated degradation is a potential therapeutic strategy for acute kidney injury

Oxidative stress plays a central role in the pathophysiology of acute kidney injury (AKI). Although RNA is one of the most vulnerable cell components to oxidative damage, it is unclear whether RNA oxidation is involved in the pathogenesis of AKI. In this study, we found that the level of RNA oxidation was significantly enhanced in kidneys of patients with acute tubular necrosis (ATN) and in the renal tubular epithelial cells (TECs) of mice with AKI, and oxidized RNA overload resulted in TEC injury. We further identified interferon-stimulated gene 20 (ISG20) as a novel regulator of RNA oxidation in AKI. Tubule-specific deficiency of ISG20 significantly aggravated renal injury and RNA oxidation in the ischemia/reperfusion-induced AKI mouse model and ISG20 restricted RNA oxidation in an exoribonuclease activity-dependent manner. Importantly, overexpression of ISG20 protected against oxidized RNA overproduction and renal ischemia/reperfusion injury in mice and ameliorated subsequent protein aggresome accumulation, endoplasmic reticulum stress, and unfolded protein response. Thus, our findings provide direct evidence that RNA oxidation contributes to the pathogenesis of AKI and that ISG20 importantly participates in the degradation of oxidized RNA, suggesting that targeting ISG20-handled RNA oxidation may be an innovative therapeutic strategy for AKI.

Pervasive transcriptome interactions of protein-targeted drugs

The off-target toxicity of drugs targeted to proteins imparts substantial health and economic costs. Proteome interaction studies can reveal off-target effects with unintended proteins; however, little attention has been paid to intracellular RNAs as potential off-targets that may contribute to toxicity. To begin to assess this, we developed a reactivity-based RNA profiling methodology and applied it to uncover transcriptome interactions of a set of Food and Drug Administration-approved small-molecule drugs in vivo. We show that these protein-targeted drugs pervasively interact with the human transcriptome and can exert unintended biological effects on RNA functions. In addition, we show that many off-target interactions occur at RNA loci associated with protein binding and structural changes, allowing us to generate hypotheses to infer the biological consequences of RNA off-target binding. The results suggest that rigorous characterization of drugs' transcriptome interactions may help assess target specificity and potentially avoid toxicity and clinical failures.

Virus on surfaces: Chemical mechanism, influence factors, disinfection strategies, and implications for virus repelling surface design

While SARS-CoV-2 is generally under control, the question of variants and infections still persists. Fundamental information on how the virus interacts with inanimate surfaces commonly found in our daily life and when in contact with the skin will be helpful in developing strategies to inhibit the spread of the virus. Here in, a critically important review of current understanding of the interaction between virus and surface is summarized from chemistry point-of-view. The Derjaguin-Landau-Verwey-Overbeek and extended Derjaguin-Landau-Verwey-Overbeek theories to model virus attachments on surfaces are introduced, along with the interaction type and strength, and quantification of each component. The virus survival and transfer are affected by a combination of biological, physical, and chemical parameters, as well as environmental parameters. The surface properties for virus and virus survival on typical surfaces such as metals, plastics, and glass are summarized. Attention is also paid to the transfer of virus to/from surfaces and skin. Typical virus disinfection strategies utilizing heat, light, chemicals, and ozone are discussed together with their disinfection mechanism. In the last section, design principles for virus repelling surface chemistry such as surperhydrophobic or surperhydrophilic surfaces are also introduced, to demonstrate how the integration of surface property control and advanced material fabrication can lead to the development of functional surfaces for mitigating the effect of viral infection upon contact.

Coping with stress: How bacteria fine-tune protein synthesis and protein transport

Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.

Sunlight photolysis of SARS-CoV-2 N1 gene target in the water environment: considerations for the environmental surveillance of wastewater-impacted surface waters

Wastewater surveillance of SARS-CoV-2 has been used around the world to supplement clinical testing data for situational awareness of COVID-19 disease trends. Many regions of the world lack centralized wastewater collection and treatment infrastructure, which presents additional considerations for wastewater surveillance of SARS-CoV-2, including environmental decay of the RT-qPCR gene targets used for quantification of SARS-CoV-2 virions. Given the role of sunlight in the environmental decay of RNA, we evaluated sunlight photolysis kinetics of the N1 gene target in heat-inactivated SARS-CoV-2 with a solar simulator under laboratory conditions. Insignificant photolysis of the N1 target was observed in a photosensitizer-free matrix. Conversely, significant decay of the N1 target was observed in wastewater at a shallow depth (<1 cm). Given that sunlight irradiance is affected by several environmental factors, first-order decay rate models were used to evaluate the effect of water column depth, time of the year, and latitude on decay kinetics. Decay rate constants were found to decrease significantly with greater depth of the well-mixed water column, at high latitudes, and in the winter. Therefore, sunlight-mediated decay of the N1 gene target is likely to be minimal, and is unlikely to confound results from wastewater-based epidemiology programs utilizing wastewater-impacted surface waters.

Host hydrocarbons protect symbiont transmission from a radical host defense

Symbioses with microbes play a pivotal role in the evolutionary success of insects, and can lead to intimate host-symbiont associations. However, how the host maintains a stable symbiosis with its beneficial partners while keeping antagonistic microbes in check remains incompletely understood. Here, we uncover a mechanism by which a host protects its symbiont from the host's own broad-range antimicrobial defense during transmission. Beewolves, a group of solitary digger wasps (Hymenoptera: Crabronidae), provide their brood cells with symbiotic Streptomyces bacteria that are later transferred to the cocoon and protect the offspring from opportunistic pathogens by producing antibiotics. In the brood cell, however, the symbiont-containing secretion is exposed to a toxic burst of nitric oxide (NO) released by the beewolf egg, which effectively kills antagonistic microorganisms. How the symbiont survives this lethal NO burst remained unknown. Here, we report that upon NO exposure in vitro, the symbionts mount a global stress response, but this is insufficient to ensure survival at brood cell-level NO concentrations. Instead, in vivo bioassays demonstrate that the host's antennal gland secretion (AGS) surrounding the symbionts in the brood cell provides an effective diffusion barrier against NO. This physicochemical protection can be reconstituted in vitro by beewolf hydrocarbon extracts and synthetic hydrocarbons, indicating that the host-derived long-chain alkenes and alkanes in the AGS are responsible for shielding the symbionts from NO. Our results reveal how host adaptations can protect a symbiont from host-generated oxidative and nitrosative stress during transmission, thereby efficiently balancing pathogen defense and mutualism maintenance.

A New Bacterial Adenosine-Derived Nucleoside as an Example of RNA Modification Damage

The fields of RNA modification and RNA damage both exhibit a plethora of non-canonical nucleoside structures. While RNA modifications have evolved to improve RNA function, the term RNA damage implies detrimental effects. Based on stable isotope labelling and mass spectrometry, we report the identification and characterisation of 2-methylthio-1,N6-ethenoadenosine (ms² ϵA), which is related to 1,N6-ethenoadenine, a lesion resulting from exposure of nucleic acids to alkylating chemicals in vivo. In contrast, a sophisticated isoprene labelling scheme revealed that ms² ϵA biogenesis involves cleavage of a prenyl moiety in the known transfer RNA (tRNA) modification 2-methylthio-N6-isopentenyladenosine (ms² i⁶ A). The relative abundance of ms² ϵA in tRNAs from translating ribosomes suggests reduced function in comparison to its parent RNA modification, establishing the nature of the new structure in a newly perceived overlap of the two previously separate fields, namely an RNA modification damage.

Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803

Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression. A key endoribonuclease in Gram-negative bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria, such as Escherichia coli, feedback-regulate RNase E expression via the rne 5'-untranslated region (5' UTR) in cis. However, the mechanisms involved in the control of RNase E in other bacteria largely remain unknown. Cyanobacteria rely on solar light as an energy source for photosynthesis, despite the inherent ultraviolet (UV) irradiation. In this study, we first investigated globally the changes in gene expression in the cyanobacterium Synechocystis sp. PCC 6803 after a brief exposure to UV. Among the 407 responding genes 2 h after UV exposure was a prominent upregulation of rne mRNA level. Moreover, the enzymatic activity of RNase E rapidly increased as well, although the protein stability decreased. This unique response was underpinned by the increased accumulation of full-length rne mRNA caused by the stabilization of its 5' UTR and suppression of premature transcriptional termination, but not by an increased transcription rate. Mapping of RNA 3' ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5' UTR, indicating autoregulation. These observations suggest that RNase E in cyanobacteria contributes to reshaping the transcriptome during the UV stress response and that its required activity level is secured at the RNA level despite the enhanced turnover of the protein.

Molecular basis of skin photoaging and therapeutic interventions by plant-derived natural product ingredients: A comprehensive review

Skin areas exposed to ultraviolet radiation (UV) from sunlight are more prone to photoaging than unexposed areas evidenced by several signs which include skin dryness, irregular pigmentation, lentigines, hyperpigmentation, wrinkling, and decreased elasticity. Plant-based natural product ingredients with therapeutic potential against skin photoaging are gaining more attention. This article aims the reviewing the research work done in exploring the cellular and molecular mechanisms involved in UV-induced skin photoaging, followed by summarizing the mechanistic insights involved in its therapeutics by natural product-based ingredients. In the mechanistic section of the convoluted procedure of photoaging, we described the effect of UV radiation (UVR) on different cellular macromolecules (direct damage) and subsequently, the deleterious consequences of UVR-generated reactive oxygen species (indirect damage) and signaling pathways activated or inhibited by UV induced ROS generation in various cellular pathologies of skin photoaging like inflammation, extracellular matrix degradation, apoptosis, mitochondrial dysfunction, and immune suppression. We also discussed the effect of UV radiation on the adipose tissue, and transient receptor potential cation channel V of photoaging skin. In the past few decades, mechanistic studies performed in this area have deciphered various therapeutic targets, opening avenues for different available therapeutic options against this pathological condition. So the remaining portion of the review deals with various natural product-based therapeutic agents available against skin photodamage.

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.

Nucleic acid adductomics - The next generation of adductomics towards assessing environmental health risks

This Discussion article aims to explore the potential for a new generation of assay to emerge from cellular and urinary DNA adductomics which brings together DNA-RNA- and, to some extent, protein adductomics, to better understand the role of the exposome in environmental health. Components of the exposome have been linked to an increased risk of various, major diseases, and to identify the precise nature, and size, of risk, in this complex mixture of exposures, powerful tools are needed. Modification of nucleic acids (NA) is a key consequence of environmental exposures, and a goal of cellular DNA adductomics is to evaluate the totality of DNA modifications in the genome, on the basis that this will be most informative. Consequently, an approach which encompasses modifications of all nucleic acids (NA) would be potentially yet more informative. This article focuses on NA adductomics, which brings together the assessment of both DNA and RNA modifications, including modified (2'-deoxy)ribonucleosides (2'-dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks (DDCL, RRCL, DRCL, DPCL, and RPCL, respectively). We discuss the need for NA adductomics, plus the pros and cons of cellular vs. urinary NA adductomics, and present some evidence for the feasibility of this approach. We propose that NA adductomics provides a more comprehensive approach to the study of nucleic acid modifications, which will facilitate a range of advances, including the identification of novel, unexpected modifications e.g., RNA-RNA, and DNA-RNA crosslinks; key modifications associated with mutagenesis; agent-specific mechanisms; and adductome signatures of key environmental agents, leading to the dissection of the exposome, and its role in human health/disease, across the life course.

Ending a bad start: Triggers and mechanisms of co-translational protein degradation

Proteins are versatile molecular machines that control and execute virtually all cellular processes. They are synthesized in a multilayered process requiring transfer of information from DNA to RNA and finally into polypeptide, with many opportunities for error. In addition, nascent proteins must successfully navigate a complex folding-energy landscape, in which their functional native state represents one of many possible outcomes. Consequently, newly synthesized proteins are at increased risk of misfolding and toxic aggregation. To maintain proteostasis-the state of proteome balance-cells employ a plethora of molecular chaperones that guide proteins along a productive folding pathway and quality control factors that direct misfolded species for degradation. Achieving the correct balance between folding and degradation therefore represents a fundamental task for the proteostasis network. While many chaperones act co-translationally, protein quality control is generally considered to be a post-translational process, as the majority of proteins will only achieve their final native state once translation is completed. Nevertheless, it has been observed that proteins can be ubiquitinated during synthesis. The extent and the relevance of co-translational protein degradation, as well as the underlying molecular mechanisms, remain areas of open investigation. Recent studies made seminal advances in elucidating ribosome-associated quality control processes, and how their loss of function can lead to proteostasis failure and disease. Here, we discuss current understanding of the situations leading to the marking of nascent proteins for degradation before synthesis is completed, and the emerging quality controls pathways engaged in this task in eukaryotic cells. We also highlight the methods used to study co-translational quality control.

222 nm far-UVC efficiently introduces nerve damage in Caenorhabditis elegans

Far-ultraviolet radiation C light (far-UVC; 222 nm wavelength) has received attention as a safer light for killing pathogenic bacteria and viruses, as no or little DNA damage is observed after irradiation in mammalian skin models. Far-UVC does not penetrate deeply into tissues; therefore, it cannot reach the underlying critical basal cells. However, it was unclear whether far-UVC (222-UVC) irradiation could cause more biological damage at shallower depths than the 254 nm UVC irradiation (254-UVC), which penetrates more deeply. This study investigated the biological effects of 222- and 254-UVC on the small and transparent model organism Caenorhabditis elegans. At the same energy level of irradiation, 222-UVC introduced slightly less cyclobutane pyrimidine dimer damage to naked DNA in solution than 254-UVC. The survival of eggs laid during 0-4 h after irradiation showed a marked decrease with 254-UVC but not 222-UVC. In addition, defect of chromosomal condensation was observed in a full-grown oocyte by 254-UVC irradiation. In contrast, 222-UVC had a significant effect on the loss of motility of C. elegans. The sensory nervous system, which includes dopamine CEP and PVD neurons on the body surface, was severely damaged by 222-UVC, but not by the same dose of 254-UVC. Interestingly, increasing 254-UVC irradiation by about 10-fold causes similar damage to CEP neurons. These results suggest that 222-UVC is less penetrating, so energy transfer occurs more effectively in tissues near the surface, causing more severe damage than 254-UVC.

Biological autoluminescence as a perturbance-free method for monitoring oxidation in biosystems

Biological oxidation processes are in the core of life energetics, play an important role in cellular biophysics, physiological cell signaling or cellular pathophysiology. Understanding of biooxidation processes is also crucial for biotechnological applications. Therefore, a plethora of methods has been developed for monitoring oxidation so far, each with distinct advantages and disadvantages. We review here the available methods for monitoring oxidation and their basic characteristics and capabilities. Then we focus on a unique method - the only one that does not require input of additional external energy or chemicals - which employs detection of biological autoluminescence (BAL). We highlight the pros and cons of this method and provide an overview of how BAL can be used to report on various aspects of cellular oxidation processes starting from oxygen consumption to the generation of oxidation products such as carbonyls. This review highlights the application potential of this completely non-invasive and label-free biophotonic diagnostic method.

Preparation of tRNAArg for Arginylation Assay by In Vitro Transcription

This chapter describes the preparation of tRNA^Arg by in vitro transcription. tRNA produced by this method can be efficiently utilized for in vitro arginylation assays, following aminoacylation with Arg-tRNA synthetase, either directly during the arginylation reaction or separately to produce the purified preparation of Arg-tRNA^Arg. tRNA charging is described in other chapters of this book.

Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis

Microbes are by far the dominant biomass in the world's oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic, spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here, we show that extracellular ribosomal RNA (rRNAext) is produced by viral lysis, and that specific lysed populations can be identified by sequencing rRNAext recovered from seawater samples. In ten seawater samples collected at five depths between the surface and 265 m during and following a phytoplankton bloom, lysis was detected in about 15% of 16,946 prokaryotic taxa, identified from amplicon sequence variants (ASVs), with lysis occurring in up to 34% of taxa within a water sample. The ratio of rRNAext to cellular rRNA (rRNAcell) was used as an index of taxon-specific lysis, and revealed that higher relative lysis was most commonly associated with copiotrophic bacteria that were in relatively low abundance, such as those in the genera Escherichia and Shigella spp., as well as members of the Bacteriodetes; whereas, relatively low lysis was more common in taxa that are often relatively abundant, such as members of the Pelagibacterales (i.e., SAR11 clade), cyanobacteria in the genus Synechococcus, and members of the phylum Thaumarchaeota (synonym, Nitrososphaerota) that comprised about 13-15% of the 16 S rRNA gene sequences below 30 m. These results provide an explanation for the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. The ability to estimate taxon-specific cell lysis will help explore the distribution and abundance of microbial populations in nature.

Ultraviolet C Irradiation-Induced Dehybridization of Double-Stranded Oligonucleotides: Mechanism Investigation and Label-Free Measurement of the Photodamage Level

Elucidating the mechanism and estimating the extent of conformation change of double-stranded DNA (dsDNA) upon ultraviolet (UV) exposure are of vital importance for understanding the DNA photodamage process. The existing research was mainly focused on the lesions of single-stranded DNA (ssDNA) and involved off-site measurement of the photodamage level. In this work, short-wavelength UV (UVC) (254 nm) irradiation was demonstrated to induce the dehybridization of dsDNA due to the loss of paring capacity of photodamaged pyrimidine nucleobases. The intrinsic programmability of dsDNA enabled researchers to rationally design the on-demand dehybridization sites. The spatial conformation switch of dsDNA caused by UVC irradiation could be evolved into a label-free sensing platform for the on-site measurement of the DNA photodamage level.

The enigma of ultraviolet radiation stress granules: Research challenges and new perspectives

Stress granules (SGs) are non-membrane bound cytoplasmic condensates that form in response to a variety of different stressors. Canonical SGs are thought to have a cytoprotective role, reallocating cellular resources during stress by activation of the integrated stress response (ISR) to inhibit translation and avoid apoptosis. However, different stresses result in compositionally distinct, non-canonical SG formation that is likely pro-apoptotic, though the exact function(s) of both SGs subtypes remain unclear. A unique non-canonical SG subtype is triggered upon exposure to ultraviolet (UV) radiation. While it is generally agreed that UV SGs are bona fide SGs due to their dependence upon the core SG nucleating protein Ras GTPase-activating protein-binding protein 1 (G3BP1), the localization of other key components of UV SGs are unknown or under debate. Further, the dynamics of UV SGs are not known, though unique properties such as cell cycle dependence have been observed. This Perspective compiles the available information on SG subtypes and on UV SGs in particular in an attempt to understand the formation, dynamics, and function of these mysterious stress-specific complexes. We identify key gaps in knowledge related to UV SGs, and examine the unique aspects of their formation. We propose that more thorough knowledge of the distinct properties of UV SGs will lead to new avenues of understanding of the function of SGs, as well as their roles in disease.

An RNA granule for translation quality control in Saccharomyces cerevisiae

Cytoplasmic RNA granules compartmentalize phases of the translation cycle in eukaryotes. We previously reported the localization of oxidized RNA to cytoplasmic foci called oxidized RNA bodies (ORBs) in human cells. We show here that ORBs are RNA granules in Saccharomyces cerevisiae. Several lines of evidence support a role for ORBs in the compartmentalization of no-go decay and ribosome quality control, the translation quality control pathways that recognize and clear aberrant mRNAs, including those with oxidized bases. Translation is required by these pathways and ORBs. Translation quality control factors localize to ORBs. A substrate of translation quality control, a stalled mRNA-ribosome-nascent-chain complex, localizes to ORBs. Translation quality control mutants have altered ORB numbers, sizes or both. In addition, we identify 68 ORB proteins by immunofluorescence staining directed by proteomics, which further support their role in translation quality control and reveal candidate new factors for these pathways.

Molecular Monitoring of SARS-CoV-2 in Different Sewage Plants in Venice and the Implications for Genetic Surveillance

Wastewater-based epidemiology is now widely used as an indirect tool to monitor the spread of SARS-CoV-2. In this study, five different sample matrices representing diverse phases of the wastewater treatment process were collected during the second wave of SARS-CoV-2 from two wastewater treatment plants (WWTPs) serving the Civil Hospital and Sacca Fisola island in Venice, Italy. Positive SARS-CoV-2 detections occurred at both WWTPs, and data on viral genome detection rate and quantification suggest that the pellet (i.e., the particulate resulting from the influent) is a sensitive matrix that permits reliable assessment of infection prevalence while reducing time to results. On the contrary, analysis of post-treatment matrices provides evidence of the decontamination efficacy of both WWTPs. Finally, direct sequencing of wastewater samples enabled us to identify B.1.177 and B.1.160 as the prevalent SARS-CoV-2 lineages circulating in Venice at the time of sampling. This study confirmed the suitability of wastewater testing for studying SARS-CoV-2 circulation and established a simplified workflow for the prompt detection and characterization of the virus.

Formation and removal of 1,N6-dimethyladenosine in mammalian transfer RNA

RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N⁶-methyladenosine (m⁶A) and 1-methyladenosine (m¹A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosine (m⁶A and m¹A), dual methylation modification occurring in the nucleobase of adenosine, such as N⁶,N⁶-dimethyladenosine (m^6,6A), also has been reported to be present in RNA of mammals. Whether there are other forms of dual methylation modification occurring in the nucleobase of adenosine other than m^6,6A remains elusive. Here, we reported the existence of a novel adenosine dual methylation modification, i.e. 1,N⁶-dimethyladenosine (m^1,6A), in tRNAs of living organisms. We confirmed that m^1,6A is located at position 58 of tRNAs and is prevalent in mammalian cells and tissues. The measured level of m^1,6A ranged from 0.0049% to 0.047% in tRNAs. Furthermore, we demonstrated that TRMT6/61A could catalyze the formation of m^1,6A in tRNAs and m^1,6A could be demethylated by ALKBH3. Collectively, the discovery of m^1,6A expands the diversity of RNA modifications and may elicit a new tRNA modification-mediated gene regulation pathway.

Synthesis of point-modified mRNA

Synthetic mRNA has recently moved into the focus of therapeutic and vaccination efforts. Incorporation of modified nucleotides during in vitro transcription can improve translation and attenuate immunogenicity, but is limited to triphosphate nucleotides which are accepted by RNA polymerases, and their incorporation is either random or complete. In contrast, site-specific modification, herein termed 'point modification' in analogy to point mutations, holds significant technical challenge. We developed fundamental techniques for isolation of long, translatable and internally point-modified mRNAs. Enabling concepts include three-way-one-pot splint ligations, and isolation of mRNA by real-time elution from agarose gels. The use of blue light permitted visualization of mRNA in pre-stained gels without the photochemical damage associated with the use of hard UV-radiation. This allowed visualization of the mRNA through its migration in the agarose gel, which in turn, was a prerequisite for its recovery by electroelution into precast troughs. Co-eluting agarose particles were quantified and found to not be detrimental to mRNA translation in vitro. Translation of EGFP-coding mRNA into functional protein was quantified by incorporation of 35S-labelled methionine and by in-gel EGFP fluorescence. This enabled the functional analysis of point modifications, specifically of ribose methylations in the middle of a 1371 nt long mRNA.

SARS-CoV-2 inactivation by ultraviolet radiation and visible light is dependent on wavelength and sample matrix

Numerous studies have demonstrated that SARS-CoV-2 can be inactivated by ultraviolet (UV) radiation. However, there are few data available on the relative efficacy of different wavelengths of UV radiation and visible light, which complicates assessments of UV decontamination interventions. The present study evaluated the effects of monochromatic radiation at 16 wavelengths from 222 nm through 488 nm on SARS-CoV-2 in liquid aliquots and dried droplets of water and simulated saliva. The data were used to generate a set of action spectra which quantify the susceptibility of SARS-CoV-2 to genome damage and inactivation across the tested wavelengths. UVC wavelengths (≤280 nm) were most effective for inactivating SARS-CoV-2, although inactivation rates were dependent on sample type. Results from this study suggest that UV radiation can effectively inactivate SARS-CoV-2 in liquids and dried droplets, and provide a foundation for understanding the factors which affect the efficacy of different wavelengths in real-world settings.

The absence of PNPase activity in Enterococcus faecalis results in alterations of the bacterial cell-wall but induces high proteolytic and adhesion activities

Enterococci are lactic acid bacteria (LAB) used as starters and probiotics, delineating their positive attributes. Nevertheless, enterococci can be culprit for thousands of infectious diseases, including urinary tract infections, bacteremia and endocarditis. Here, we aim to determine the impact of polynucleotide phosphorylase (PNPase) in the biology of Enterococcus faecalis 14; a human isolate from meconium. Thus, a mutant strain deficient in PNPase synthesis, named ΔpnpA mutant, was genetically obtained. After that, a transcriptomic study revealed a set of 244 genes differentially expressed in the ΔpnpA mutant compared with the wild-type strain, when exploiting RNAs extracted from these strains after 3 and 6 h of growth. Differentially expressed genes include those involved in cell wall synthesis, adhesion, biofilm formation, bacterial competence and conjugation, stress response, transport, DNA repair and many other functions related to the primary and secondary metabolism of the bacteria. Moreover, the ΔpnpA mutant showed an altered cell envelope ultrastructure compared with the WT strain, and is also distinguished by a strong adhesion capacity on eukaryotic cell as well as a high proteolytic activity. This study, which combines genetics, physiology and transcriptomics enabled us to show further biological functions that could be directly or indirectly controlled by the PNPase in E. faecalis 14.

Naked mole-rats resist the accumulation of hypoxia-induced oxidative damage

Naked mole-rats are among the few mammals with the ability to endure severe hypoxia. These unique rodents use metabolic rate depression along with various molecular mechanisms to successfully overcome the challenges of oxygen-limitation, which they experience in their underground borrows. While studies have reported that naked mole-rats exhibit inherently higher levels of oxidative damage across their lifespan as compared to mice, it has yet to be determined whether naked mole-rats are vulnerable to oxidative damage during periods of low oxygen exposure. To investigate this phenomenon, we examined cellular oxidative damage markers of macromolecules: DNA oxidation determined as 8-oxo-2'deoxyguanosine (8-OHdG8) levels, RNA oxidation as 8-hydroxyguanosine (8-OHG), protein carbonylation, and lipid peroxidation in normoxic (control), acute (4 h at 7% O₂), and chronic (24 h at 7% O₂) hypoxia-exposed naked mole-rats. Brain appears to be the most resilient organ to hypoxia-induced oxidative damage, with both brain and heart exhibiting enhanced antioxidant capacity during hypoxia. Levels of DNA and RNA oxidation were minimally changed in all tissues and no changes were observed in protein carbonylation. Most tissues experienced lipid peroxidation, with liver displaying a 9.6-fold increase during hypoxia. Concomitantly, levels of DNA damage repair proteins were dynamically regulated in a tissue-specific manner, with white adipose displaying a significant reduction during hypoxia. Our findings show that naked mole-rats largely avoid hypoxia-induced oxidative damage, possibly due to their high tolerance to redox stress, or to reduced oxidative requirements made possible during their hypometabolic response when oxygen supply is limited.

On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution

UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.

Reduction and discharge of SARS-CoV-2 RNA in Chicago-area water reclamation plants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is commonly excreted in the feces and urine of infected individuals and is, therefore, detected in wastewaters where infection is present in the surrounding population. Water reclamation plants (WRPs) that treat these wastewaters commonly discharge treated effluents into the surrounding environment, yet little is known about the removal or persistence of SARS-CoV-2 RNA through wastewater treatment systems and potential for eventual release into the environment. We collected 361 24-hour composite influent and effluent samples from seven WRPs in the Greater Chicago Area in Illinois. Samples were collected over a period of 21 weeks for three large WRPs (with design max flows of 1.89-2.32 billion gallons per day and serving a combined population of 4.62 million people) and 11 weeks for four smaller WRPs (with design max flows of 96.3-186 million gallons per day and serving a combined population of >0.5 million people). A total of two of the larger WRPs implemented seasonal disinfection (using UV light or chlorination/dechlorination) for 8 weeks of this sampling period. SARS-CoV-2 RNA was quantified in the influent and effluent samples by reverse-transcription quantitative PCR (RT-qPCR) of the N1 and N2 targets of the nucleocapsid (N) gene. Although SARS-CoV-2 RNA was regularly detected in influent and effluent from all WRPs, viral RNA concentrations in the effluent samples were considerably lower, with mean effluent: influent gene copy concentration ratios ranging from 1:160 to 1:2.95 between WRPs. Samples collected while disinfection was active vs. inactive did not show any significant difference in the portion of RNA persisting through the treatment process (P > .05).

Next-generation sequencing: A new avenue to understand viral RNA-protein interactions

The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.

Biology of aging: Oxidative stress and RNA oxidation

The prevalence of aged people has increased rapidly in recent years and brings profound demographic changes worldwide. The multi-level progression of aging occurs at diverse stages of complexity, from cell to organ systems and eventually to the human as a whole. The cellular and molecular damages are usually regulated by the cells; repair or degrade mechanisms. However, these mechanisms are not entirely functional; their effectiveness decreases with age due to influence from endogenous sources like oxidative stress, which all contribute to the aging process. The hunt for novel strategies to increase the man's longevity since ancient times needs better understandings of the biology of aging, oxidative stress, and their roles in RNA oxidation. The critical goal in developing new strategies to increase the man's longevity is to compile the novel developed knowledge on human aging into a single picture, preferably able to understand the biology of aging and the contributing factors. This review discusses the biology of aging, oxidative stress, and their roles in RNA oxidation, leading to aging in humans.

Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress

During the translation surveillance mechanism known as ribosome-associated quality control, the ASC-1 complex (ASCC) disassembles ribosomes stalled on the mRNA. Here, we show that there are two distinct classes of stalled ribosome. Ribosomes stalled by translation elongation inhibitors or methylated mRNA are short lived in human cells because they are split by the ASCC. In contrast, although ultraviolet light and 4-nitroquinoline 1-oxide induce ribosome stalling by damaging mRNA, and the ASCC is recruited to these stalled ribosomes, we found that they are refractory to the ASCC. Consequently, unresolved UV- and 4NQO-stalled ribosomes persist in human cells. We show that ribosome stalling activates cell-cycle arrest, partly through ZAK-p38MAPK signaling, and that this cell-cycle delay is prolonged when the ASCC cannot resolve stalled ribosomes. Thus, we propose that the sensitivity of stalled ribosomes to the ASCC influences the kinetics of stall resolution, which in turn controls the adaptive stress response.

Investigation of mouse hepatitis virus strain A59 inactivation under both ambient and cold environments reveals the mechanisms of infectivity reduction following UVC exposure

The surface contamination of SARS-CoV-2 is becoming a potential source of virus transmission during the pandemic of COVID-19. Under the cold environment, the infection incidents would be more severe with the increase of virus survival time. Thus, the disinfection of contaminated surfaces in both ambient and cold environments is a critical measure to restrain the spread of the virus. In our study, it was demonstrated that the 254 nm ultraviolet-C (UVC) is an efficient method to inactivate a coronavirus, mouse hepatitis virus strain A59 (MHV-A59). The inactivation rate to MHV-A59 coronavirus was up to 99.99% when UVC doses were 2.90 and 14.0 mJ/cm² at room temperature (23 °C) and in cold environment (-20 °C), respectively. Further mechanistic study demonstrated that UVC could induce spike protein damage to partly impede virus attachment and genome penetration processes, which contributes to 12% loss of viral infectivity. Additionally, it can induce genome damage to significantly interrupt genome replication, protein synthesis, virus assembly and release processes, which takes up 88% contribution to viral inactivation. With these mechanistic understandings, it will greatly contribute to the prevention and control of the current SARS-CoV-2 transmissions in cold chains (low temperature-controlled product supply chains), public area such as airport, school, and warehouse.

UV-C Light-Based Surface Disinfection: Analysis of Its Virucidal Efficacy Using a Bacteriophage Model

Background: The reprocessing of medical devices has become more complex due to increasing hygiene requirements. Previous studies showed satisfactory bactericidal disinfection effects of UV-C light in rigid and flexible endoscopes. Especially in the context of the current COVID-19 pandemic, virucidal properties are of high importance. In the present study, the virucidal efficacy of UV-C light surface disinfection was analyzed. Methods: MS-2 bacteriophages were applied to the test samples and irradiated by UV-C light using the UV Smart D25 device; unirradiated test samples were used as controls. A dilution series of the samples was mixed with 1 × 108 Escherichia coli and assayed. Results: 8.6 × 1012 pfu could be harvested from the unprocessed test samples. In the control group without UV-C exposure, a remaining contamination of 1.2 × 1012 pfu was detected, resulting in a procedural baseline reduction rate with a LOG10 reduction factor of 0.72. The LOG10 reduction factor was found to be 3.0 after 25 s of UV-C light exposure. After 50 and 75 s of UV-C radiation LOG10 reduction factors 4.2 and 5.9, respectively, were found, with all reductions being statistically significantly different to baseline. Conclusions: The tested UV system seems to provide a significant virucidal effect after a relatively short irradiation time.

Evaluation of UV-C Radiation Efficiency in the Decontamination of Inanimate Surfaces and Personal Protective Equipment Contaminated with Phage ϕ6

To help halt the global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appropriate disinfection techniques are required. Over the last years, the interest in Ultraviolet-C (UV-C) radiation as a method to disinfect inanimate surfaces and personal protective equipment (PPE) has increased, mainly to efficiently disinfect and prevent SARS-CoV-2 from spreading and allow for the safe reuse of said equipment. The bacteriophage ϕ6 (or simply phage ϕ6) is an RNA virus with a phospholipid envelope and is commonly used in environmental studies as a surrogate for human RNA-enveloped viruses, including SARS-CoV-2. The present study investigated the use of two new UV irradiation systems ((2)2.4W and (8)5.5W)) constituted by conventional mercury UV-C lamps with a strong emission peak at ~254 nm to potentially inactivate phage ϕ6 on different surfaces (glass, plastic, stainless steel, and wood) and personal protective equipment, PPE, (surgical and filtering facepiece 2, FFP2, masks, a clear acetate visor, and disposable protective clothing). The results showed that both UV-C systems were effective in inactivating phage ϕ6, but the UV-C sterilizing chamber (8)5.5W had the best disinfection performance on the tested surfaces. The inactivation effectiveness is material-dependent on all surfaces, reaching the detection limit of the method at different times (between 60 and 240 s of irradiation). The glass surface needed less time to reduce the virus (30 s) when compared with plastic, stainless, and wood surfaces (60 s). The virus inactivation was more effective in the disposable surgical and FFP2 masks (60 and 120 s, respectively) than in the disposable vest and clear acetate visor (240 s). Overall, this study suggests that UV-C lamps with peak emission at ~254 nm could provide rapid, efficient, and sustainable sanitization procedures to different materials and surfaces. However, dosage and irradiation time are important parameters to be considered during their implementation as a tool in the fight against human coronaviruses, namely against SARS-CoV-2.

UV and violet light can Neutralize SARS-CoV-2 Infectivity

We performed an in-depth analysis of the virucidal effect of discrete wavelengths: UV-C (278 nm), UV-B (308 nm), UV-A (366 nm) and violet (405 nm) on SARS-CoV-2. By using a highly infectious titer of SARS-CoV-2 we observed that the violet light-dose resulting in a 2-log viral inactivation is only 10⁴ times less efficient than UV-C light. Moreover, by qPCR (quantitative Polymerase chain reaction) and fluorescence in situ hybridization (FISH) approach we verified that the viral titer typically found in the sputum of COVID-19 patients can be completely inactivated by the long UV-wavelengths corresponding to UV-A and UV-B solar irradiation. The comparison of the UV action spectrum on SARS-CoV-2 to previous results obtained on other pathogens suggests that RNA viruses might be particularly sensitive to long UV wavelengths. Our data extend previous results showing that SARS-CoV-2 is highly susceptible to UV light and offer an explanation to the reduced incidence of SARS-CoV-2 infection seen in the summer season.

Reactivity of Viral Nucleic Acids with Chlorine and the Impact of Virus Encapsidation

Free chlorine disinfection is widely applied to inactivate viruses by reacting with their biomolecules, which include nucleic acids, proteins, and lipids. Knowing the reactivities of viral genomes with free chlorine and the protection that encapsidation provides would ultimately help predict virus susceptibility to the disinfectant. The relative reactivities of different viral genome types and the impact of viral higher order structure with free chlorine are poorly characterized. Here, we studied the reactivity of viral genomes representing four genome types from virus particles with diverse structures, namely, (+)ssRNA (MS2), dsRNA (φ6), ssDNA (φX174), and dsDNA (T3) with free chlorine. We compared the reactivities of these viral nucleic acids when they were suspended in phosphate buffer solutions (naked forms) and when they were in the native virus particles (encapsidated forms). The reactivities of nucleic acids were tracked by polymerase chain reaction (PCR)-based assays. The naked dsDNA of T3 was the least reactive with free chlorine, with an average second order rate constant normalized by the number of bases in the measured regions (in M^-1 s^-1 b^-1) that was 34×, 65×, and 189× lower than those of the dsRNA of φ6, ssRNA of MS2, and ssDNA of φX174, respectively. Moreover, different regions in the ssRNA genome of MS2 and the dsRNA genome of φ6 exhibited statistically different reaction kinetics. The genomes within virus particles reacted slower than the naked genomes overall, but the extent of these differences varied among the four viruses. The results on viral nucleic acid reactivity help explain different susceptibilities of viruses to inactivation by free chlorine and also provide a valuable comparison of the susceptibilities of different nucleic acids to oxidants.

In vivo discovery of RNA proximal proteins via proximity-dependent biotinylation

RNA molecules function as messenger RNAs (mRNAs) that encode proteins and noncoding transcripts that serve as adaptor molecules, structural components, and regulators of genome organization and gene expression. Their function and regulation are largely mediated by RNA binding proteins (RBPs). Here we present RNA proximity labelling (RPL), an RNA-centric method comprising the endonuclease-deficient Type VI CRISPR-Cas protein dCas13b fused to engineered ascorbate peroxidase APEX2. RPL discovers target RNA proximal proteins in vivo via proximity-based biotinylation. RPL applied to U1 identified proteins involved in both U1 canonical and noncanonical functions. Profiling of poly(A) tail proximal proteins uncovered expected categories of RBPs and provided additional evidence for 5'-3' proximity and unexplored subcellular localizations of poly(A)+ RNA. Our results suggest that RPL allows rapid identification of target RNA binding proteins in native cellular contexts, and is expected to pave the way for discovery of novel RNA-protein interactions important for health and disease.

Nanoscopic Imaging of Nucleolar Stress Enabled by Protein-Mimicking Carbon Dots

The nucleolus is a central hub for coordinating cellular stress responses during cancer development and treatment. Accurate identification of nucleolar stress response is crucially desired for nucleolus-based diagnostics and therapeutics but technically challenging due to the need to address the ultrastructural analysis. Here, we report a protein-like CD with the integration of fluorescent blinking domains and RNA-binding motifs, which offers the ability to perform enhanced super-resolution imaging of the nucleolar ultrastructure. This image allows extraction of multidimensional information from the nucleolus for accurate distinguishment of different cells from the same cell types. Furthermore, we demonstrate for the first time this CD-depicted nucleolar ultrastructure as a sensitive hallmark to identify and discriminate subtle responses to various stressors as well as to afford RNA-related information that has been inaccessible by conventional immunofluorescence methods. This protein-mimicking CD could become a broadly useful probe for nucleolar stress studies in cell diagnostics and therapeutics.

Sunlight Inactivation of Human Norovirus and Bacteriophage MS2 Using a Genome-Wide PCR-Based Approach and Enzyme Pretreatment

Human norovirus (hNoV) is an important etiology of gastrointestinal illness and can be transmitted via ingestion of contaminated water. Currently impractical to culture, hNoV detection is reliant on real-time polymerase chain reaction (RT-PCR)-based methods. This approach cannot distinguish between infective and inactivated viruses because intact regions of the RNA genome can amplify even if the damage is present in other regions of the genome or because intact genetic material is not contained within an infectious virion. Herein, we employ a multiple long-amplicon RT-qPCR extrapolation approach to assay genome-wide damage and an enzymatic pretreatment to study the impact of simulated sunlight on the infectivity of hNoV in clear, sensitizer-free water. Using MS2 coliphage as an internal control, the genome-wide damage extrapolation approach, previously successfully applied for UV-254 inactivation, vastly overestimated sunlight inactivation, suggesting key differences in photoinactivation under different spectral conditions. hNoV genomic RNA was more susceptible to simulated sunlight degradation per base compared to MS2 genomic RNA, while enzymatic pretreatment indicated that hNoV experienced more capsid damage than MS2. This work provides practical and mechanistic insight into the endogenous sunlight inactivation of single-stranded RNA bacteriophage MS2, a widely used surrogate, and hNoV GII.4 Sydney, an important health-relevant virus, in clear sensitizer-free water.

Oxidative Damage to RNA is Altered by the Presence of Interacting Proteins or Modified Nucleosides

Oxidative stress triggered by the Fenton reaction (chemical) or UVR exposure (photo) can damage cellular biomolecules including RNA through oxidation of nucleotides. Besides such xenobiotic chemical modifications, RNA also contains several post-transcriptional nucleoside modifications that are installed by enzymes to modulate structure, RNA-protein interactions, and biochemical functions. We examined the extent of oxidative damage to naturally modified RNA which is required for cellular protein synthesis under two different contexts. The extent of oxidative damage is higher when RNA is not associated with proteins, but the degree of damage is lower when the RNA is presented in the form of a ribonucleoprotein complex, such as an intact ribosome. Our studies also indicate that absence of methylations in ribosomal RNA at specific positions could make it more susceptible to photooxidative stress. However, the extent of guanosine oxidation varied with the position at which the modification is deficient, indicating position-dependent structural effects. Further, an E. coli strain deficient in 5-methylaminomethyl-2-thiouridine (mnm⁵s²U) (found in lysine and glutamate tRNA anticodon) is more vulnerable to oxidative RNA damage compared to its wildtype strain suggesting an auxiliary function for the mnm⁵s²U modification. These studies indicate that oxidative damage to RNA is altered by the presence of enzymatic modified nucleosides or protein association inside the cell.

Unexpected Role of Sterol Synthesis in RNA Stability and Translation in Leishmania

Leishmania parasites are trypanosomatid protozoans that cause leishmaniasis affecting millions of people worldwide. Sterols are important components of the plasma and organellar membranes. They also serve as precursors for the synthesis of signaling molecules. Unlike animals, Leishmania does not synthesize cholesterol but makes ergostane-based sterols instead. C-14-demethylase is a key enzyme involved in the biosynthesis of sterols and an important drug target. In Leishmania parasites, the inactivation of C-14-demethylase leads to multiple defects, including increased plasma membrane fluidity, mitochondrion dysfunction, hypersensitivity to stress and reduced virulence. In this study, we revealed a novel role for sterol synthesis in the maintenance of RNA stability and translation. Sterol alteration in C-14-demethylase knockout mutant leads to increased RNA degradation, reduced translation and impaired heat shock response. Thus, sterol biosynthesis in Leishmania plays an unexpected role in global gene regulation.