How do cells cope with RNA damage and its consequences?

Current advances in microalgae-based fucoxanthin production and downstream processes

Fucoxanthin, a marine carotenoid primarily found in brown algae and microalgae, offers significant health benefits, including antioxidant, anti-obesity, and anti-cancer effects. While brown algae remain the dominant commercial source, microalgae such as Phaeodactylum tricornutum are emerging as promising candidates for large-scale, sustainable fucoxanthin production. This review explores advancements in fucoxanthin biosynthesis, focusing on cultivation methods, extraction techniques, and genetic engineering strategies. Different cultivation systems - including autotrophic, heterotrophic, and mixotrophic approaches - have been assessed for their biomass yield, cost-effectiveness, and scalability, together with a quantitative meta-analysis to highlight specific trends or correlations in fucoxanthin production. The efficiency and environmental impact of extraction methods, such as supercritical fluid extraction, ultrasound-assisted extraction, and microwave-assisted extraction, have also been evaluated. In addition, synthetic biology and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based genetic modifications show potential for enhancing fucoxanthin biosynthesis. However, challenges remain in terms of cost, scalability, and regulatory constraints. This review highlights the need for integrated biotechnological solutions to enhance commercial viability, combining metabolic engineering, efficient extraction techniques, and optimized cultivation strategies. As demand continues to grow in the nutraceutical, pharmaceutical, and cosmetic industries, ongoing advancements in microalgae-based fucoxanthin production will be critical for ensuring sustainable and cost-effective manufacturing.

Development of an Optimized Two-Step Solid-Phase Extraction Method for Urinary Nucleic Acid Adductomics

The exposome represents the totality of endogenous and exogenous exposures across the lifespan. These exposures may result in DNA and RNA damage, in the form of adducts, which is a key factor in the etiology of a variety of human diseases, including cancer. It is understood that, following their repair, nucleic acid adducts are excreted into the urine, making urine an ideal, non-invasive matrix in which to study the whole-body nucleic acid adductome (the totality of nucleic acid adducts). However, the measurement of these adducts in urine presents challenges due to matrix interference and the variety of the chemical nature across the spectrum of nucleic adducts making their "one-size-fits-all" extraction by solid-phase extraction (SPE) challenging. Here, different types of SPE sorbents, and their combination, were evaluated for maximal recovery of nucleic acid adducts from urine. The SPE column combination of ENV+ coupled with PHE provided the best retention of a cocktail of 20 nucleic acid adduct standards. An untargeted high resolution mass spectrometry approach incorporating FeatureHunter 1.3 software was used to demonstrate the ability of this SPE method to successfully recover endogenous urinary nucleic acid adducts in addition to those represented by the cocktail of isotopically labeled standards. Using our approach, FeatureHunter 1.3 recognized approximately 500 adducts in both mouse and human urine samples. Isotopically labeled standards were used to identify a selection of the endogenous adducts and begin the characterization of the urinary nucleic acid adductome of mice and humans.

Purine Chemistry in the Early RNA World at the Origins of Life: From RNA and Nucleobases Lesions to Current Key Metabolic Routes

In early life, RNA probably played the central role and, in the corresponding RNA world, the main produced amino acids and small peptides had to react continuously with RNA, ribonucleos(t)ides and nucleobases, especially with purines. A RNA-peptide world and key metabolic pathways have emerged from the corresponding chemical modifications such as the translation process performed by the ribosome. Some interesting reactions of the purine bicycle and of the corresponding ribonucleos(t)ides are performed under plausible prebiotic conditions and described RNA chemical lesions are reviewed with the prospect to highlight their connection with some major steps of the purine and histidine biosynthetic pathways that are, in an intriguingly way, related through two key metabolites, adenosine 5'-triphosphate and the imidazole ribonucleotide 5-aminoimidazole-4-carboxamide ribonucleotide. Ring-opening reactions of purines stand out as efficient accesses to imidazole ribonucleotides and to formamidopyrimidine (Fapy) ribonucleotides suggesting that biosynthetic pathway' first steps have emerged from RNA and ribonucleos(t)ide damages. Also, are summarized the works on the formation and catalytic properties, under plausible prebiotic conditions, of N6-derivatives of the purine base adenine as potential surrogates of histidine in catalysis accordingly to their structural relationship.

Effects of oxidative stress on viral infections: an overview

Viral infections can trigger increased reactive oxygen species (ROS) production and a reduced antioxidant response in the host, leading to redox stress, inflammation, apoptosis, and ultimately, cell and tissue damage, which contribute to disease development. A better understanding of how ROS contributes to viral pathogenesis is critical for the development of novel therapeutic interventions. In this review, we discuss the current knowledge on ROS production and its effects across various viral infections, including severe acute respiratory syndrome-coronavirus-2, influenza A virus, dengue virus, Zika virus, hepatitis B virus, hepatitis C virus, and human immunodeficiency virus infections, to improve future therapeutic and preventive strategies for these infections.

Active biomonitoring of stream ecosystems: untargeted metabolomic and proteomic responses and free radical scavenging activities in mussels

Many contaminants from scattered sources constantly endanger streams that flow through heavily inhabited areas, commercial districts, and industrial hubs. The responses of transplanted mussels in streams in active biomonitoring programs will reflect the dynamics of environmental stream conditions. This study evaluated the untargeted metabolomic and proteomic responses and free radical scavenging activities of transplanted mussels Sinanodonta woodiana in the Winongo Stream at three stations (S1, S2, S3) representing different pollution levels: low (S1), high (S2), and moderate (S3). The investigation examined untargeted metabolomic and proteomic responses in the gills and 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) activities in the gills, mantle, and digestive glands. Metabolomic analysis revealed a clear separation between mussel responses from the three stations after 28 days of exposure, with specific metabolites responding to different pollution levels. Proteomic analysis identified β-Actin protein in all stations. The β-Actin protein sequence of unexposed mussels had coverage of 17%, and increased to 23% at S1 on day 28 and 34% at S2 and S3 on day 28. All tissues showed increased DPPH and ABTS activities from day 3 to day 28, mainly in stations S2 and S3. These findings underscore the impact of pollution levels on the metabolomic and proteomic responses of S. woodiana and the importance of these discoveries as early indicators (biomarkers) of long-term aquatic environmental problems. In the face of current environmental challenges, this research raises concerns about the health of water bodies. It underscores the importance of developing robust, standardized, and dependable analytical techniques for monitoring the health of aquatic environments.

YTHDC1 cooperates with the THO complex to prevent RNA-damage-induced DNA breaks

Certain environmental toxins and chemotherapeutics are nucleic acid-damaging agents, causing adducts in DNA and RNA. While most of these adducts occur in RNA, the consequences of RNA damage are largely unexplored. Here, we demonstrate that nuclear RNA damage can result in loss of genome integrity in human cells. Specifically, we show that YTHDC1 regulates alkylation damage responses with the THO complex (THOC). In addition to its established binding to N6-methyladenosine (m6A), YTHDC1 binds to chemically induced N1-methyladenosine (m1A). Without YTHDC1, cells have greater alkylation damage sensitivity and increased DNA breaks, which are rescued by an RNA-specific dealkylase. These RNA-damage-induced DNA breaks (RDIBs) depend on R-loop formation, which is converted to DNA breaks by the XPG nuclease. Strikingly, in the absence of YTHDC1 or THOC, a nuclear RNA m1A methyltransferase is sufficient to induce DNA breaks. Our results provide mechanistic insight into how damaged RNAs can impact genomic integrity.

Chemical Strategies to Modulate and Manipulate RNA Epigenetic Modifications

ConspectusRNA epigenetics has rapidly emerged as a key frontier in chemical biology, revealing that modifications to RNA bases and riboses can fine-tune essential cellular processes such as gene expression, translation, and metabolic homeostasis. Traditionally, researchers have relied on manipulating the "writers," "erasers," and "readers" of RNA modifications─i.e., protein cofactors─to alter and study these marks. Those enzyme-centric strategies, including small molecule inhibitors and CRISPR/Cas-based genetic perturbations, have been highly effective and are advancing in clinical applications. However, purely chemical approaches for installing, removing, or transforming RNA modifications without enzyme disturbance have offered distinct advantages, such as temporal control, reversibility, and bypassing compensatory biological feedback mechanisms that often arise with genetic or enzymatic inhibition. Every chemist should be concerned about RNA modifications, because they represent a striking intersection of molecular recognition, organic transformation, and cellular function. The ability to direct chemical reactivity at specific nucleosides in RNA can illuminate how individual modifications impact the overall gene regulation. Further, since improper RNA modification and damage patterns are implicated in cancer, metabolic disorders, and neurodegeneration, these chemical repair tools have potential as diagnostic and therapeutic interventions. Beyond medicine, agriculture also stands to benefit from chemical control of nucleoside-based plant hormones, possibly leading to improved crop productivity and resilience.In this Account, we outline several innovative chemical strategies tailored to different classes of RNA modifications. Flavin-based bioorthogonal chemistry has enabled demethylation of N6-methyladenosine (m6A) independent of endogenous demethylases, while oxidative bioorthogonal reactions can convert 5-methylcytidine (m5C) into distinct formyl derivatives for labeling and sequencing. Nitrogen-oxide and photochemical routes provided access for the selective removal of the side chain of N6-isopentenyladenosine (i6A), offering insights for both cell biology and plant hormone research. We also showcase how rationally designed small molecules can rewire complex RNA damage repair pathways, facilitating selective correction of vinyl-adduct lesions otherwise resistant to enzymatic repair. These purely chemical methods bypass the constraints of enzyme dependence, affording temporal precision (e.g., via light activation) and site-selective modification or labeling of RNA. By strategically engineering reactivity, we have uncovered new epitranscriptomic phenomena, such as in situ generation of non-native RNA modification, that offer fresh capabilities for cell imaging or targeted manipulation of plant callus development. Together, these discoveries signal a paradigm shift: chemical tools can complement or even surpass conventional enzyme-based methods for investigating, editing, and repairing RNA modifications. The ramifications are broad. Chemists can leverage these new reactivities to dissect the molecular underpinnings of diseases linked to epitranscriptomic dysregulation and to engineer next-generation therapeutic, diagnostic, and sequencing platforms. Plant biologists can apply the same chemical strategies to hone agronomic traits, from seed vigor to stress resilience. Ultimately, as we have deepened the mechanistic insights and refined reaction design for increased biocompatibility, purely chemical control of the RNA epigenome is poised to become one of the mainstream approaches across fields spanning chemistry, biology, and medicine─fostering deeper understanding of RNA's role in health and disease and opening new avenues for precise interventions.

RNA damage and its implications in genome stability

Endogenous and environmental stressors can damage DNA and RNA to compromise genome and transcriptome stability and integrity in cells, leading to genetic instability and diseases. Recent studies have demonstrated that RNA damage can also modulate genome stability via RNA-templated DNA synthesis, suggesting that it is essential to maintain RNA integrity for the sustainment of genome stability. However, little is known about RNA damage and repair and their roles in modulating genome stability. Current efforts have mainly focused on revealing RNA surveillance pathways that detect and degrade damaged RNA, while the critical role of RNA repair is often overlooked. Due to their abundance and susceptibility to nucleobase damaging agents, it is essential for cells to evolve robust RNA repair mechanisms that can remove RNA damage, maintaining RNA integrity during gene transcription. This is supported by the discovery of the alkylated RNA nucleobase repair enzyme human AlkB homolog 3 that can directly remove the methyl group on damaged RNA nucleobases, predominantly in the nucleus of human cells, thereby restoring the integrity of the damaged RNA nucleobases. This is further supported by the fact that several DNA repair enzymes can also process RNA damage. In this review, we discuss RNA damage and its effects on cellular function, DNA repair, genome instability, and potential RNA damage repair mechanisms. Our review underscores the necessity for future research on RNA damage and repair and their essential roles in modulating genome stability.

TGT Damages its Substrate tRNAs by the Formation of Abasic Sites in the Anticodon Loop

RNA modification is a well-recognized way for gene expression regulation in a living cell. Natural enzymatic RNA modifications have been characterized for decades. Recently, additional mechanisms, more related to RNA damage, have emerged, which do not involve targeted enzymatic activity but nonetheless alter the chemical structure of nucleosides. Aberrantly modified RNA may also appear due to incomplete or erroneous enzymatic reactions. We demonstrate that tRNA-guanine transglycosylase (TGT) in bacteria and eukaryotes accidentally leaves RNA abasic sites (rAP) in the anticodon loop of substrate tRNAs. The formation of an rAP site is a part of the TGT catalytic mechanism, involving the cleavage of the N-glycosidic bond, and the formation of a covalent enzyme-tRNA adduct. The phenomenon of rAP site formation is readily detectable for tRNATyr(GUA) in bacteria and tRNAAsp(GUC) in eukaryotes and is amplified when the supply for preQ1 in bacteria is compromised. The TGT-mediated accumulation of rAP sites in tRNAs is strongly induced upon stress, and most prominent upon oxidative stress in bacteria. Polysome profiling in bacteria points out the partial exclusion of rAP-containing tRNAs from the translating ribosome fraction, prompting a consideration of these tRNA species as "damaged" and most likely non-functional. The exploratory analysis of rAP tRNA(GUN) sites in mice demonstrates a substantial variability among different tissues, with the highest accumulation of damaged tRNA observed in the brain, the lung and the spleen. Altogether, these results uncover a unique molecular mechanism of RNA modification that, via a presumably erroneous reaction, diminishes RNA function rather than enhancing it.

Cellular responses to RNA damage

RNA plays a central role in protein biosynthesis and performs diverse regulatory and catalytic functions, making it essential for all processes of life. Like DNA, RNA is constantly subjected to damage from endogenous and environmental sources. However, while the DNA damage response has been extensively studied, it was long assumed that RNA lesions are relatively inconsequential due to the transient nature of most RNA molecules. Here, we review recent studies that challenge this view by revealing complex RNA damage responses that determine survival when cells are exposed to nucleic acid-damaging agents and promote the resolution of RNA lesions.

Potent inhibitors of the human RNA ligase Rlig1 highlights its role in RNA integrity maintenance under oxidative cellular stress

Human RNA ligase 1 (Rlig1) catalyzes the ligation of 5'-phosphate to 3'-hydroxyl ends via a conserved three-step mechanism. Rlig1-deficient HEK293 cells exhibit reduced cell viability and RNA integrity under oxidative stress, suggesting Rlig1's role in RNA repair maintenance. Reactive oxygen species (ROS) are linked to various diseases, including neurodegenerative disorders and cancer, where RNA damage has significant effects. This study identifies and characterizes Rlig1 inhibitors to elucidate its role in RNA metabolism. We developed a fluorescence resonance energy transfer (FRET)-based assay to monitor RNA ligation and screened a library of 13 026 bioactive small molecules. SGI-1027 emerged as a promising lead compound, and structure-activity relationship (SAR) studies revealed that the terminal residues play a key role in its inhibitory effect. In total 22 SGI-1027 derivatives were synthesized and tested, providing insights into the structural requirements for effective Rlig1 inhibition. Three derivatives showed low micromolar IC50 values and minimal cytotoxicity in HEK293 cells under physiological conditions. The combination of Rlig1 inhibition and oxidative stress led to reduced cell viability and compromised RNA integrity, reinforcing Rlig1's role in RNA maintenance. These findings provide a foundation for developing novel therapeutics aimed at targeting RNA maintenance pathways in conditions of dysregulated ROS levels.

The ribosome as a platform to coordinate mRNA decay

Messenger RNA (mRNA) homeostasis is a critical aspect of cellular function, involving the dynamic interplay between transcription and decay processes. Recent advances have revealed that the ribosome plays a central role in coordinating mRNA decay, challenging the traditional view that free mRNA is the primary substrate for degradation. This review examines the mechanisms whereby ribosomes facilitate both the licensing and execution of mRNA decay. This involves factors such as the Ccr4-Not complex, small MutS-related domain endonucleases, and various quality control pathways. We discuss how translational fidelity, as well as the presence of nonoptimal codons and ribosome collisions, can trigger decay pathways such as nonstop decay and no-go decay. Furthermore, we highlight the direct association of canonical exonucleases, such as Xrn1 and the Ski-exosome system, with the ribosome, underscoring the ribosome's multifaceted role as a platform for regulatory processes governing mRNA stability. By integrating recent findings, this review offers a comprehensive overview of the structural basis of how ribosomes not only facilitate translation but also serve as critical hubs for mRNA decay coordination.

Evolution of pollutant biodegradation

Pollutant-derived risks to human and environmental health are exacerbated by slow natural attenuation rates, often driven by pollutant toxicity to microorganisms that can degrade them or limitations to the ability of microorganisms to metabolise them. This review explores mechanisms employed by bacteria to protect themselves from pollutant toxicity in the context of the evolution of pollutant-degrading abilities. The role of promiscuous enzymes in pollutant transformation is subsequently reviewed, highlighting the emergence of novel metabolic pathways and their transcriptional regulation in response to pollutant exposure, followed by the gene transcription regulation to optimise the cellular component synthesis for adaptation on the novel substrate. Additionally, we discuss epistatic interactions among mutations vital for this process both at macromolecular and at cellular levels. Finally, evolutionary constraints towards enhanced fitness in the context of pollutant degradation are considered, the constraints imposed by the epistasis from mutations on both enzyme level and cellular level, concluding with challenges and emerging opportunities to develop sustainable contaminated site remediation technologies. KEY POINTS: •Pollutants can exert toxicity on cellular membrane, enzyme and gene transcription. •Bacteria can patch promiscuous enzymes into novel pathway to degrade pollutants. •The evolution trajectory is constrained by epistasis from mutations on enzyme and cellular level.

Exploring the protective role of caffeine against Taraxacum-Induced ribotoxic stress mediated through autophagy and mitochondrial depolarization

The ribotoxic stress response is a pathway that gets activated when ribosomes get impaired, leading to disruptions in protein synthesis, increased inflammatory signaling, and cell death if left unresolved. Taraxacum can induce apoptosis-associated ribosomal RNA (rRNA) cleavage, however, the exact working mechanism of Taraxacum-induced rRNA cleavage remains unclear. In this study, we used the RNA integrity (RIN) value and 28S/18S ratio to confirm the integrity of experiments. Our RNA sequencing data showed that Taraxacum formosanum (T. formosanum) upregulated 893 genes and downregulated 509 genes and triggered hallmark genes of spliceosomes, TNF-α signaling via NF-κB, inflammatory response, and IL6-JAK-STAT3 signaling. Additionally, T. formosanum imbalanced the levels of ribosomal proteins of the large and small subunits. We found that caffeine was the only screening agent that could rescue the cleavage of 28S and 18S rRNA induced by T. formosanum. However, caffeine failed to rescue T. formosanum-targeted mRNAs when the RIN values were relatively lower. T. formosanum induced the N-terminal clipping of histone H3, which was observed not only in human HeLa cervical cancer cells but also in human Huh6 and HepG2 liver cancer cells. Our study revealed that caffeine could reverse the effects of T. formosanum on the reduction of autophagy and the disruption of mitochondrial membrane potential. However, caffeine could only change the populations of necrotic and apoptotic cells but not T. formosanum-induced cell death. By providing detailed information on Taraxacum-induced rRNA cleavage and N-truncated histone H3's mechanisms of gene regulation, we hope to understand their respective cellular death and survival stresses.

A Direct Chemical Repair of Etheno-Type RNA Damages

Etheno damages in RNA represent a unique class of structural alterations that arise from exposure to various environmental stressors or endogenous processes. They significantly distort the RNA structure and affect crucial biological functions, including RNA-protein interactions, ribosome function, and translation fidelity. However, repair mechanisms for those etheno damages in RNA are still being elucidated. Here, a synthetic flavin derivative PS9 has been identified as the first example of chemical repair approach for this type of RNA damages. It efficiently managed the removal of etheno-type ϵA and ϵC damages in nucleosides, oligonucleotides in vitro, and in E. coli RNA in vivo under blue light irradiation. The capacity of the chemical approach relies on a unique cycloaddition activation of the etheno-bridge with singlet oxygen, which is distinct from traditional epoxidation of the C=C double bonds by proteins from the AlkB family. The understanding and effective manipulation of etheno damages in RNA with chemical tools hold implications for deciphering their role in mutagenesis and RNA biology, potentially opening avenues for targeted therapeutic interventions and biomarker development.

Production, Isolation, and Characterization of Stable Isotope-Labeled Standards for Mass Spectrometric Measurements of Oxidatively-Damaged Nucleosides in RNA

RNA undergoes oxidatively induced damage in living organisms analogous to DNA. RNA is even more vulnerable to damage than DNA due to its greater abundance, single-strandedness, lack of repair and chromatin proteins shield, and instability, among other effects. RNA damage can adversely affect gene expression, leading to protein synthesis alterations, cell death, and other detrimental biological consequences. Growing indications suggest the involvement of oxidatively induced RNA damage in the pathogenesis of various human diseases, aging, and age-related diseases. Oxidatively induced damage can cause modifications to all four heterocyclic bases in RNA. Precise measurement of such modifications in RNA is essential for understanding the biological effects of oxidatively induced RNA damage. In the past, mass spectrometry has been used for this purpose. In mass spectrometric measurements, the use of stable isotope-labeled analogues of analytes as internal standards is essential for accurate quantifications. Past work utilized a stable isotope-labeled analogue of 8-hydroxyguanosine only as an internal standard. Thus, far, no stable isotope-labeled analogues of other oxidatively modified RNA nucleosides were available. In the present work, we report on the preparation, isolation, and characterization of the 13C- and 15N-labeled analogues of a variety of modified pyrimidine- and purine-derived RNA nucleosides. We also show the application of these internal standards for the measurement of oxidatively induced RNA damage in several commercially available RNA samples and in DNA along with DNA damage.

Ruthenium(II) Complex with 1-Hydroxy-9,10-Anthraquinone Inhibits Cell Cycle Progression at G0/G1 and Induces Apoptosis in Melanoma Cells

BACKGROUND

Melanoma is the most aggressive and lethal skin cancer that affects thousands of people worldwide. Ruthenium complexes have shown promising results as cancer chemotherapeutics, offering several advantages over platinum drugs, such as potent efficacy, low toxicity, and less drug resistance. Additionally, anthraquinone derivatives have broad therapeutic applications, including melanoma.

OBJECTIVES

Thus, two new ruthenium complexes with 1-hydroxy-9,10-anthraquinone were obtained: trans-[Ru(HQ)(PPh3)2(bipy)]PF6 (1) and cis-[RuCl2(HQ)(dppb)] (2), where HQ = 1-hydroxy-9,10-anthraquinone, PPh3 = triphenylphospine, bipy = 2,2'-bipyridine, PF6 = hexafluorophosphate, and dppb = 1,4-bis(diphenylphosphine)butane.

METHODS

The complexes were characterized by infrared (IR), UV-vis, 1H, 13C{1H}, and 31P{1H} NMR spectroscopies, molar conductivity, cyclic voltammetry, and elemental analysis. Furthermore, density functional theory (DFT) calculations were performed.

RESULTS

Compound (2) was determined by single-crystal X-ray diffraction, which confirms the bidentate coordination mode of HQ through the carbonyl and phenolate oxygens. Additionally, DNA-binding experiments yielded constants of 105 M-1 (Kb = 6.93 × 105 for (1) and 1.60 × 105 for (2)) and demonstrate that both complexes can interact with DNA through intercalation, electrostatic attraction, or hydrogen bonding.

CONCLUSIONS

The cytotoxicity profiles of the compounds were evaluated in human melanoma cell lines (SK-MEL-147, CHL-1, and WM1366), revealing greater cytotoxic activity for (1) on the CHL-1 cell line with an IC50 of 14.50 ± 1.09 µM. Subsequent studies showed that (1) inhibits the proliferation of CHL-1 cells and induces apoptosis, associated at least in part with the pro-oxidant effect and cell cycle arrest at the G1/S transition.

RNA Damage Responses in Cellular Homeostasis, Genome Stability, and Disease

All cells are exposed to chemicals that can damage their nucleic acids. Cells must protect these polymers because they code for key factors or complexes essential for life. Much of the work on nucleic acid damage has naturally focused on DNA, partly due to the connection between mutagenesis and human disease, especially cancer. Recent work has shed light on the importance of RNA damage, which triggers a host of conserved RNA quality control mechanisms. Because many RNA species are transient, and because of their ability to be retranscribed, RNA damage has largely been ignored. Yet, because of the connection between damaged RNA and DNA during transcription, and the association between essential complexes that process or decode RNAs, notably spliceosomes and ribosomes, the appropriate handling of damaged RNAs is critical for maintaining cellular homeostasis. This notion is bolstered by disease states, including neurodevelopmental and neurodegenerative diseases, that may arise upon loss or misregulation of RNA quality control mechanisms.

Insights into the transcriptomic responses of silver-lipped pearl oysters Pinctada maxima exposed to a simulated large-scale seismic survey

BACKGROUND

The wild stocks of Pinctada maxima pearl oysters found off the coast of northern Australia are of critical importance for the sustainability of Australia's pearling industry. Locations inhabited by pearl oysters often have oil and gas reserves in the seafloor below and are therefore potentially subjected to seismic exploration surveys. The present study assessed the impact of a simulated commercial seismic survey on the transcriptome of pearl oysters. Animals were placed at seven distances (-1000, 0, 300, 500, 1000, 2000, and 6000 m) from the first of six operational seismic source sail lines. Vessel control groups were collected before the seismic survey started and exposed groups were collected after completion of six operational seismic sail lines (operated at varying distances over a four-day period). Samples from these groups were taken immediately and at 1, 3, and 6 months post-exposure. RNA-seq was used to identify candidate genes and pathways impacted by the seismic noise in pearl oyster mantle tissues. The quantified transcripts were compared using DESeq2 and pathway enrichment analysis was conducted using KEGG pathway, identifying differentially expressed genes and pathways associated with the seismic activity.

RESULTS

The study revealed the highest gene expression and pathway dysregulation after four days of exposure and a month post-exposure. However, this dysregulation diminished after three months, with only oysters at -1000 and 0 m displaying differential gene expression and pathway disruption six months post-exposure. Stress-induced responses were evident and impacted energy production, transcription, translation, and protein synthesis.

CONCLUSION

Seismic activity impacted the gene expression and pathways of pearl oysters at distances up to 2000 m from the source after four days of exposure, and at distances up to 1000 m from the source one-month post-exposure. At three- and six-months post-exposure, gene and pathway dysregulations were mostly observed in oysters located closest to the seismic source at 0 and - 1000 m. Overall, our results suggest that oysters successfully activated stress responses to mitigate damage and maintain cellular homeostasis and growth in response to seismic noise exposure.

Apurinic/Apyrimidinic Endodeoxyribonuclease 1 modulates RNA G-quadruplex folding of miR-92b and controls its expression in cancer cells

In the last decade, several novel functions of the mammalian Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) have been discovered, going far beyond its canonical function as DNA repair enzyme and unveiling its potential roles in cancer development. Indeed, it was shown to be involved in DNA G-quadruplex biology and RNA metabolism, most importantly in the miRNA maturation pathway and the decay of oxidized or abasic miRNAs during oxidative stress conditions. In recent years, several noncanonical pathways of miRNA biogenesis have emerged, with a specific focus on guanosine-rich precursors that can form RNA G-quadruplex (rG4) structures. Here, we show that several miRNA precursors, dysregulated upon APE1 depletion, contain an rG4 motif and that their corresponding target genes are up-regulated after APE1 depletion. We also demonstrate, both by in vitro assays and by using different cancer cell lines, that APE1 can modulate the folding of an rG4 structure contained in pre-miR-92b, with a mechanism strictly dependent on lysine residues present in its N-terminal disordered region. Furthermore, APE1 cellular depletion alters the maturation process of miR-92b, mainly affecting the shuttling between the nucleus and cytosol. Bioinformatic analysis of APE1-regulated rG4-containing miRNAs supports the relevance of our findings in cancer biology. Specifically, these miRNAs exhibit high prognostic significance in lung, cervical, and liver tumors, as suggested by their involvement in several cancer-related pathways.

Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil

Ribosome quality control (RQC) resolves collided ribosomes, thus preventing their cytotoxic effects. The chemotherapeutic agent 5-Fluorouracil (5FU) is best known for its misincorporation into DNA and inhibition of thymidylate synthase. However, while a major determinant of 5FU's anticancer activity is its misincorporation into RNAs, the mechanisms by which cancer cells overcome the RNA-dependent 5FU toxicity remain ill-defined. Here, we report a role for RQC in mitigating the cytotoxic effects of 5FU. We show that 5FU treatment results in rapid induction of the mTOR signalling pathway, enhanced rate of mRNA translation initiation, and increased ribosome collisions. Consistently, a defective RQC exacerbates the 5FU-induced cell death, which is mitigated by blocking mTOR pathway or mRNA translation initiation. Furthermore, 5FU treatment enhances the expression of the key RQC factors ZNF598 and GIGYF2 via an mTOR-dependent post-translational mechanism. This adaptation likely mitigates the cytotoxic consequences of increased ribosome collisions upon 5FU treatment.

Chronic stress antagonizes formation of Stress Granules

Chronic stress mediates cellular changes that can contribute to human disease. However, fluctuations in RNA metabolism caused by chronic stress have been largely neglected in the field. Stress granules (SGs) are cytoplasmic ribonucleoprotein condensates formed in response to stress-induced inhibition of mRNA translation and polysome disassembly. Despite the broad interest in SG assembly and disassembly in response to acute stress, SG assembly in response to chronic stress has not been extensively investigated. In this study, we show that cells pre-conditioned with low dose chronic (24-hour exposure) stresses such as oxidative stress, endoplasmic reticulum stress, mitochondrial stress, and starvation, fail to assemble SGs in response to acute stress. While translation is drastically decreased by acute stress in pre-conditioned cells, polysome profiling analysis reveals the partial preservation of polysomes resistant to puromycin-induced disassembly. We showed that chronic stress slows down the rate of mRNA translation at the elongation phase and triggers phosphorylation of translation elongation factor eEF2. Polysome profiling followed by RNase treatment confirmed that chronic stress induces ribosome stalling. Chronic stress-induced ribosome stalling is distinct from ribosome collisions that are known to trigger a specific stress response pathway. In summary, chronic stress triggers ribosome stalling, which blocks polysome disassembly and SG formation by subsequent acute stress.

Significant statements

Stress granules (SGs) are dynamic cytoplasmic biocondensates assembled in response to stress-induced inhibition of mRNA translation and polysome disassembly. SGs have been proposed to contribute to the survival of cells exposed to toxic conditions. Although the mechanisms of SG assembly and disassembly in the acute stress response are well understood, the role of SGs in modulating the response to chronic stress is unclear. Here, we show that human cells pre-conditioned with chronic stress fail to assemble SGs in response to acute stress despite inhibition of mRNA translation. Mechanistically, chronic stress induces ribosome stalling, which prevents polysome disassembly and subsequent SG formation. This finding suggests that chronically stressed or diseased human cells may have a dysfunctional SG response that could inhibit cell survival and promote disease.

Ribosome Assembly and Repair

Ribosomes synthesize protein in all cells. Maintaining both the correct number and composition of ribosomes is critical for protein homeostasis. To address this challenge, cells have evolved intricate quality control mechanisms during assembly to ensure that only correctly matured ribosomes are released into the translating pool. However, these assembly-associated quality control mechanisms do not deal with damage that arises during the ribosomes' exceptionally long lifetimes and might equally compromise their function or lead to reduced ribosome numbers. Recent research has revealed that ribosomes with damaged ribosomal proteins can be repaired by the release of the damaged protein, thereby ensuring ribosome integrity at a fraction of the energetic cost of producing new ribosomes, appropriate for stress conditions. In this article, we cover the types of ribosome damage known so far, and then we review the known repair mechanisms before surveying the literature for possible additional instances of repair.

Redox system and ROS-related disorders in peroxisomes

Peroxisomes are essential organelles that help mitigate the oxidative damage caused by reactive oxygen species (ROS) through their antioxidant systems. They perform functions such as α-oxidation, β-oxidation, and the synthesis of cholesterol and ether phospholipids. During the breakdown of specific metabolites, peroxisomes generate ROS as byproducts, which can either be neutralized or contribute to oxidative stress. The relationship between peroxisomal metabolism and ROS-related disorders, including neurodegenerative diseases and cancers, has been studied for decades; however, the exact mechanisms remain unclear. Our review will provide recent insights into the peroxisomal redox system and its association with oxidative stress-related diseases.

Dealkylation of Macromolecules by Eukaryotic α-Ketoglutarate-Dependent Dioxygenases from the AlkB-like Family

Alkylating modifications induced by either exogenous chemical agents or endogenous metabolites are some of the main types of damage to DNA, RNA, and proteins in the cell. Although research in recent decades has been almost entirely devoted to the repair of alkyl and in particular methyl DNA damage, more and more data lately suggest that the methylation of RNA bases plays an equally important role in normal functioning and in the development of diseases. Among the most prominent participants in the repair of methylation-induced DNA and RNA damage are human homologs of Escherichia coli AlkB, nonheme Fe(II)/α-ketoglutarate-dependent dioxygenases ABH1-8, and FTO. Moreover, some of these enzymes have been found to act on several protein targets. In this review, we present up-to-date data on specific features of protein structure, substrate specificity, known roles in the organism, and consequences of disfunction of each of the nine human homologs of AlkB. Special attention is given to reports about the effects of natural single-nucleotide polymorphisms on the activity of these enzymes and to potential consequences for carriers of such natural variants.

The DNA damage response and RNA Polymerase II regulator Def1 has posttranscriptional functions in the cytoplasm

Yeast Def1 mediates RNA polymerase II degradation and transcription elongation during stress. Def1 is predominantly cytoplasmic, and DNA damage signals cause its proteolytic processing, liberating its N-terminus to enter the nucleus. Cytoplasmic functions for this abundant protein have not been identified. Proximity-labeling (BioID) experiments indicate that Def1 binds to an array of proteins involved in posttranscriptional control and translation of mRNAs. Deleting DEF1 reduces both mRNA synthesis and decay rates, indicating transcript buffering in the mutant. Directly tethering Def1 to a reporter mRNA suppressed expression, suggesting that Def1 directly regulates mRNAs. Surprisingly, we found that Def1 interacts with polyribosomes, which requires its ubiquitin-binding domain located in its N-terminus. The binding of Def1 to ribosomes requires the ubiquitylation of eS7a (Rsp7A) in the small subunit by the Not4 protein in the Ccr4-Not complex. Not4 ubiquitylation of the ribosome regulates translation quality control and co-translational mRNA decay. The polyglutamine-rich unstructured C-terminus of Def1 is required for its interaction with decay and translation factors, suggesting that Def1 acts as a ubiquitin-dependent scaffold to link translation status to mRNA decay. Thus, we have identified a novel function for this transcription and DNA damage response factor in posttranscriptional regulation in the cytoplasm and establish Def1 as a master regulator of gene expression, functioning during transcription, mRNA decay, and translation.

OTUD6 deubiquitination of RPS7/eS7 on the free 40 S ribosome regulates global protein translation and stress

Ribosomes are regulated by evolutionarily conserved ubiquitination/deubiquitination events. We uncover the role of the deubiquitinase OTUD6 in regulating global protein translation through deubiquitination of the RPS7/eS7 subunit on the free 40 S ribosome in vivo in Drosophila. Coimmunoprecipitation and enrichment of monoubiquitinated proteins from catalytically inactive OTUD6 flies reveal RPS7 as the ribosomal substrate. The 40 S protein RACK1 and E3 ligases CNOT4 and RNF10 function upstream of OTUD6 to regulate alkylation stress. OTUD6 interacts with RPS7 specifically on the free 40 S, and not on 43 S/48 S initiation complexes or the translating ribosome. Global protein translation levels are bidirectionally regulated by OTUD6 protein abundance. OTUD6 protein abundance is physiologically regulated in aging and in response to translational and alkylation stress. Thus, OTUD6 may promote translation initiation, the rate limiting step in protein translation, by titering the amount of 40 S ribosome that recycles.

The ribotoxic stress response drives UV-mediated cell death

While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.

Accurate identification of 8-oxoguanine in RNA with single-nucleotide resolution using ligase-dependent qPCR

8-oxoguanine (o8G), a prevalent oxidative modification in RNA induced by reactive oxygen species (ROS), plays a pivotal role in regulating RNA functions. Accurate detection and quantification of o8G modifications is critical to understanding their biological significance and potential as disease biomarkers, but effective detection methods remain limited. Here, we have developed a highly specific T3 DNA ligase-dependent qPCR assay that exploits the enzyme's ability to discriminate o8G from guanine (G) with single-nucleotide resolution. This method can detect o8G in RNA at levels as low as 500 fM, with an up to 18-fold higher selectivity for discriminating o8G from G. By simulating oxidative stress conditions in SH-SY5Y and HS683 cell lines treated with rotenone, we successfully identified site-specific o8G modifications in key miRNAs associated with neuroprotective responses, including miR-124, let-7a and miR-29a. The developed assay holds significant promise for the practical identification of o8G, facilitating its potential for detailed studies of o8G dynamics in various biological contexts and diseases.

The role of DNA and RNA guanosine oxidation in cardiovascular diseases

Cardiovascular diseases (CVD) persist as a prominent cause of mortality worldwide, with oxidative stress constituting a pivotal contributory element. The oxidative modification of guanosine, specifically 8-oxoguanine, has emerged as a crucial biomarker for oxidative stress, providing novel insights into the molecular underpinnings of CVD. 8-Oxoguanine can be directly generated at the DNA (8-oxo-dG) and RNA (8-oxo-G) levels, as well as at the free nucleotide level (8-oxo-dGTP or 8-oxo-GTP), which are produced and can be integrated through DNA replication or RNA transcription. When exposed to oxidative stress, guanine is more readily produced in RNA than in DNA. A burgeoning body of research surrounds 8-oxoguanine, exhibits its accumulation playing a pivotal role in the development of CVD. Therapeutic approaches targeting oxidative 8-Oxoguanine damage to DNA and RNA, encompassing the modulation of repair enzymes and the development of small molecule inhibitors, are anticipated to enhance CVD management. In conclusion, we explore the noteworthy elevation of 8-oxoguanine levels in patients with various cardiac conditions and deliberate upon the formation and regulation of 8-oxo-dG and 8-oxo-G under oxidative stress, as well as their function in CVD.

Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging

Rules of biology typically involve conservation of resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, and scaling laws involve conservation of energy. Here a relationship with the opposite theme is discussed, which is the selectively advantageous instability (SAI) of one or more components of a replicating system, such as the cell. By increasing the complexity of the system, SAI can have benefits in addition to the generation of energy or the mobilization of building blocks. SAI involves a potential cost to the replicating system for the materials and/or energy required to create the unstable component, and in some cases, the energy required for its active degradation. SAI is well-studied in cells. Short-lived transcription and signaling factors enable a rapid response to a changing environment, and turnover is critical for replacement of damaged macromolecules. The minimal gene set for a viable cell includes proteases and a nuclease, suggesting SAI is essential for life. SAI promotes genetic diversity in several ways. Toxin/antitoxin systems promote maintenance of genes, and SAI of mitochondria facilitates uniparental transmission. By creating two distinct states, subject to different selective pressures, SAI can maintain genetic diversity. SAI of components of synthetic replicators favors replicator cycling, promoting emergence of replicators with increased complexity. Both classical and recent computer modeling of replicators reveals SAI. SAI may be involved at additional levels of biological organization. In summary, SAI promotes replicator genetic diversity and reproductive fitness, and may promote aging through loss of resources and maintenance of deleterious alleles.

The Structural and Molecular Mechanisms of Mycobacterium tuberculosis Translational Elongation Factor Proteins

Targeting translation factor proteins holds promise for developing innovative anti-tuberculosis drugs. During protein translation, many factors cause ribosomes to stall at messenger RNA (mRNA). To maintain protein homeostasis, bacteria have evolved various ribosome rescue mechanisms, including the predominant trans-translation process, to release stalled ribosomes and remove aberrant mRNAs. The rescue systems require the participation of translation elongation factor proteins (EFs) and are essential for bacterial physiology and reproduction. However, they disappear during eukaryotic evolution, which makes the essential proteins and translation elongation factors promising antimicrobial drug targets. Here, we review the structural and molecular mechanisms of the translation elongation factors EF-Tu, EF-Ts, and EF-G, which play essential roles in the normal translation and ribosome rescue mechanisms of Mycobacterium tuberculosis (Mtb). We also briefly describe the structure-based, computer-assisted study of anti-tuberculosis drugs.

A Journey of Challenges and Victories: A Bibliometric Worldview of Nanomedicine since the 21st Century

Nanotechnology profoundly affects the advancement of medicine. Limitations in diagnosing and treating cancer and chronic diseases promote the growth of nanomedicine. However, there are very few analytical and descriptive studies regarding the trajectory of nanomedicine, key research powers, present research landscape, focal investigative points, and future outlooks. Herein, articles and reviews published in the Science Citation Index Expanded of Web of Science Core Collection from first January 2000 to 18th July 2023 are analyzed. Herein, a bibliometric visualization of publication trends, countries/regions, institutions, journals, research categories, themes, references, and keywords is produced and elaborated. Nanomedicine-related academic output is increasing since the COVID-19 pandemic, solidifying the uneven global distribution of research performance. While China leads in terms of publication quantity and has numerous highly productive institutions, the USA has advantages in academic impact, commercialization, and industrial value. Nanomedicine integrates with other disciplines, establishing interdisciplinary platforms, in which drug delivery and nanoparticles remain focal points. Current research focuses on integrating nanomedicine and cell ferroptosis induction in cancer immunotherapy. The keyword "burst testing" identifies promising research directions, including immunogenic cell death, chemodynamic therapy, tumor microenvironment, immunotherapy, and extracellular vesicles. The prospects, major challenges, and barriers to addressing these directions are discussed.

YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks

Certain environmental toxins are nucleic acid damaging agents, as are many chemotherapeutics used for cancer therapy. These agents induce various adducts in DNA as well as RNA. Indeed, most of the nucleic acid adducts (>90%) formed due to these chemicals, such as alkylating agents, occur in RNA 1 . However, compared to the well-studied mechanisms for DNA alkylation repair, the biological consequences of RNA damage are largely unexplored. Here, we demonstrate that RNA damage can directly result in loss of genome integrity. Specifically, we show that a human YTH domain-containing protein, YTHDC1, regulates alkylation damage responses in association with the THO complex (THOC) 2 . In addition to its established binding to N 6-methyladenosine (m6A)-containing RNAs, YTHDC1 binds to N 1-methyladenosine (m1A)-containing RNAs upon alkylation. In the absence of YTHDC1, alkylation damage results in increased alkylation damage sensitivity and DNA breaks. Such phenotypes are fully attributable to RNA damage, since an RNA-specific dealkylase can rescue these phenotypes. These R NA d amage-induced DNA b reaks (RDIBs) depend on R-loop formation, which in turn are processed by factors involved in transcription-coupled nucleotide excision repair. Strikingly, in the absence of YTHDC1 or THOC, an RNA m1A methyltransferase targeted to the nucleus is sufficient to induce DNA breaks. Our results uncover a unique role for YTHDC1-THOC in base damage responses by preventing RDIBs, providing definitive evidence for how damaged RNAs can impact genomic integrity.

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.

General Principles and Limitations for Detection of RNA Modifications by Sequencing

Among the many analytical methods applied to RNA modifications, a particularly pronounced surge has occurred in the past decade in the field of modification mapping. The occurrence of modifications such as m6A in mRNA, albeit known since the 1980s, became amenable to transcriptome-wide analyses through the advent of next-generation sequencing techniques in a rather sudden manner. The term "mapping" here refers to detection of RNA modifications in a sequence context, which has a dramatic impact on the interpretation of biological functions. As a consequence, an impressive number of mapping techniques were published, most in the perspective of what now has become known as "epitranscriptomics". While more and more different modifications were reported to occur in mRNA, conflicting reports and controversial results pointed to a number of technical and theoretical problems rooted in analytics, statistics, and reagents. Rather than finding the proverbial needle in a haystack, the tasks were to determine how many needles of what color in what size of a haystack one was looking at.As the authors of this Account, we think it important to outline the limitations of different mapping methods since many life scientists freshly entering the field confuse the accuracy and precision of modification mapping with that of normal sequencing, which already features numerous caveats by itself. Indeed, we propose here to qualify a specific mapping method by the size of the transcriptome that can be meaningfully analyzed with it.We here focus on high throughput sequencing by Illumina technology, referred to as RNA-Seq. We noted with interest the development of methods for modification detection by other high throughput sequencing platforms that act directly on RNA, e.g., PacBio SMRT and nanopore sequencing, but those are not considered here.In contrast to approaches relying on direct RNA sequencing, current Illumina RNA-Seq protocols require prior conversion of RNA into DNA. This conversion relies on reverse transcription (RT) to create cDNA; thereafter, the cDNA undergoes a sequencing-by-synthesis type of analysis. Thus, a particular behavior of RNA modified nucleotides during the RT-step is a prerequisite for their detection (and quantification) by deep sequencing, and RT properties have great influence on the detection efficiency and reliability. Moreover, the RT-step requires annealing of a synthetic primer, a prerequisite with a crucial impact on library preparation. Thus, all RNA-Seq protocols must feature steps for the introduction of primers, primer landing sites, or adapters on both the RNA 3'- and 5'-ends.

B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage

Stalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. In E. coli, these pathways are triggered by ribosome collisions through the recruitment of SmrB, a nuclease that cleaves the mRNA. In B. subtilis, the related protein MutS2 was recently implicated in ribosome rescue. Here we show that MutS2 is recruited to collisions by its SMR and KOW domains, and we reveal the interaction of these domains with collided ribosomes by cryo-EM. Using a combination of in vivo and in vitro approaches, we show that MutS2 uses its ABC ATPase activity to split ribosomes, targeting the nascent peptide for degradation through the ribosome quality control pathway. However, unlike SmrB, which cleaves mRNA in E. coli, we see no evidence that MutS2 mediates mRNA cleavage or promotes ribosome rescue by tmRNA. These findings clarify the biochemical and cellular roles of MutS2 in ribosome rescue in B. subtilis and raise questions about how these pathways function differently in diverse bacteria.

Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance

YPEL2 is a member of the evolutionarily conserved YPEL family involved in cellular proliferation, mobility, differentiation, senescence, and death. However, the mechanism by which YPEL2, or YPEL proteins, mediates its effects is largely unknown. Proteins perform their functions in a network of proteins whose identities, amounts, and compositions change spatiotemporally in a lineage-specific manner in response to internal and external stimuli. Here, we explored interaction partners of YPEL2 by using dynamic TurboID-coupled mass spectrometry analyses to infer a function for the protein. Our results using inducible transgene expressions in COS7 cells indicate that proximity interaction partners of YPEL2 are mainly involved in RNA and mRNA metabolic processes, ribonucleoprotein complex biogenesis, regulation of gene silencing by miRNA, and cellular responses to stress. We showed that YPEL2 interacts with the RNA-binding protein ELAVL1 and the selective autophagy receptor SQSTM1. We also found that YPEL2 localizes stress granules in response to sodium arsenite, an oxidative stress inducer, which suggests that YPEL2 participates in stress granule-related processes. Establishing a point of departure in the delineation of structural/functional features of YPEL2, our results suggest that YPEL2 may be involved in stress surveillance mechanisms.

The Versatile Attributes of MGMT: Its Repair Mechanism, Crosstalk with Other DNA Repair Pathways, and Its Role in Cancer

O6-methylguanine-DNA methyltransferase (MGMT or AGT) is a DNA repair protein with the capability to remove alkyl groups from O6-AlkylG adducts. Moreover, MGMT plays a crucial role in repairing DNA damage induced by methylating agents like temozolomide and chloroethylating agents such as carmustine, and thereby contributes to chemotherapeutic resistance when these agents are used. This review delves into the structural roles and repair mechanisms of MGMT, with emphasis on the potential structural and functional roles of the N-terminal domain of MGMT. It also explores the development of cancer therapeutic strategies that target MGMT. Finally, it discusses the intriguing crosstalk between MGMT and other DNA repair pathways.

Epitranscriptomic modifications in mesenchymal stem cell differentiation: advances, mechanistic insights, and beyond

RNA modifications, known as the "epitranscriptome", represent a key layer of regulation that influences a wide array of biological processes in mesenchymal stem cells (MSCs). These modifications, catalyzed by specific enzymes, often termed "writers", "readers", and "erasers", can dynamically alter the MSCs' transcriptomic landscape, thereby modulating cell differentiation, proliferation, and responses to environmental cues. These enzymes include members of the classes METTL, IGF2BP, WTAP, YTHD, FTO, NAT, and others. Many of these RNA-modifying agents are active during MSC lineage differentiation. This review provides a comprehensive overview of the current understanding of different RNA modifications in MSCs, their roles in regulating stem cell behavior, and their implications in MSC-based therapies. It delves into how RNA modifications impact MSC biology, the functional significance of individual modifications, and the complex interplay among these modifications. We further discuss how these intricate regulatory mechanisms contribute to the functional diversity of MSCs, and how they might be harnessed for therapeutic applications. The review also highlights current challenges and potential future directions in the study of RNA modifications in MSCs, emphasizing the need for innovative tools to precisely map these modifications and decipher their context-specific effects. Collectively, this work paves the way for a deeper understanding of the role of the epitranscriptome in MSC biology, potentially advancing therapeutic strategies in regenerative medicine and MSC-based therapies.

RNF14-dependent atypical ubiquitylation promotes translation-coupled resolution of RNA-protein crosslinks

Reactive aldehydes are abundant endogenous metabolites that challenge homeostasis by crosslinking cellular macromolecules. Aldehyde-induced DNA damage requires repair to prevent cancer and premature aging, but it is unknown whether cells also possess mechanisms that resolve aldehyde-induced RNA lesions. Here, we establish photoactivatable ribonucleoside-enhanced crosslinking (PAR-CL) as a model system to study RNA crosslinking damage in the absence of confounding DNA damage in human cells. We find that such RNA damage causes translation stress by stalling elongating ribosomes, which leads to collisions with trailing ribosomes and activation of multiple stress response pathways. Moreover, we discovered a translation-coupled quality control mechanism that resolves covalent RNA-protein crosslinks. Collisions between translating ribosomes and crosslinked mRNA-binding proteins trigger their modification with atypical K6- and K48-linked ubiquitin chains. Ubiquitylation requires the E3 ligase RNF14 and leads to proteasomal degradation of the protein adduct. Our findings identify RNA lesion-induced translational stress as a central component of crosslinking damage.

The Role of mRNA Quality Control in the Aging of Caenorhabditis elegans

The proper maintenance of mRNA quality that is regulated by diverse surveillance pathways is essential for cellular homeostasis and is highly conserved among eukaryotes. Here, we review findings regarding the role of mRNA quality control in the aging and longevity of Caenorhabditis elegans, an outstanding model for aging research. We discuss the recently discovered functions of the proper regulation of nonsense-mediated mRNA decay, ribosome-associated quality control, and mRNA splicing in the aging of C. elegans. We describe how mRNA quality control contributes to longevity conferred by various regimens, including inhibition of insulin/insulin-like growth factor 1 (IGF-1) signaling, dietary restriction, and reduced mechanistic target of rapamycin signaling. This review provides valuable information regarding the relationship between the mRNA quality control and aging in C. elegans, which may lead to insights into healthy longevity in complex organisms, including humans.

Is there a localized role for translational quality control?

It is known that mRNAs and the machinery that translates them are not uniformly distributed throughout the cytoplasm. As a result, the expression of some genes is localized to particular parts of the cell and this makes it possible to carry out important activities, such as growth and signaling, in three-dimensional space. However, the functions of localized gene expression are not fully understood, and the underlying mechanisms that enable localized expression have not been determined in many cases. One consideration that could help in addressing these challenges is the role of quality control (QC) mechanisms that monitor translating ribosomes. On a global level, QC pathways are critical for detecting aberrant translation events, such as a ribosome that stalls while translating, and responding by activating stress pathways and resolving problematic ribosomes and mRNAs at the molecular level. However, it is unclear how these pathways, even when uniformly active throughout the cell, affect local translation. Importantly, some QC pathways have themselves been reported to be enriched in the proximity of particular organelles, but the extent of such localized activity remains largely unknown. Here, we describe the major QC pathways and review studies that have begun to explore their roles in localized translation. Given the limited data in this area, we also pose broad questions about the possibilities and limitations for how QC pathways could facilitate localized gene expression in the cell with the goal of offering ideas for future experimentation.

A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells

Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.

Impact of Polyphenols on Inflammatory and Oxidative Stress Factors in Diabetes Mellitus: Nutritional Antioxidants and Their Application in Improving Antidiabetic Therapy

Diabetes mellitus is a chronic metabolic disorder characterized by hyperglycaemia and oxidative stress. Oxidative stress plays a crucial role in the development and progression of diabetes and its complications. Nutritional antioxidants derived from dietary sources have gained significant attention due to their potential to improve antidiabetic therapy. This review will delve into the world of polyphenols, investigating their origins in plants, metabolism in the human body, and relevance to the antioxidant mechanism in the context of improving antidiabetic therapy by attenuating oxidative stress, improving insulin sensitivity, and preserving β-cell function. The potential mechanisms of, clinical evidence for, and future perspectives on nutritional antioxidants as adjuvant therapy in diabetes management are discussed.

An integrated approach to evaluate acetamiprid-induced oxidative damage to tRNA in human cells based on oxidized nucleotide and tRNA profiling

Acetamiprid is poisonous to mammals due to severe acetamiprid-induced oxidative stress that could cause mitochondrial dysfunctions, lipid and protein oxidation, inflammation, apoptosis, and DNA damage. Evidence has accumulated for the role of oxidative stress in changing structures and functions of transfer RNAs (tRNAs) by inducing tRNA cleavage, reprogramming tRNA modifications and impairing aminoacyl-tRNA synthetase editing sites. However, the impact of acetamiprid-induced oxidative stress on tRNA is still unknown. Here, we investigated the effects of acetamiprid on cell viability, reactive oxygen species (ROS) levels, DNA damage, cellular oxidized nucleotide concentrations, and oxidative damage to tRNA in HepG2 cells and LO2 cells. Acetamiprid can cause the significant increment of ROS and DNA oxidative damage. In this study, an integrated approach was established to simultaneously study the network of oxidized nucleotides and explore the tRNA oxidative damage after acetamiprid exposure. A simple and high-throughput liquid chromatography with tandem mass spectrometry (LC-MS/MS) method coupled with (trimethylsilyl)diazomethane (TMSD) derivatization was successfully developed to quantify 12 cellular oxidized nucleotides that cannot be detected using traditional detection methods because of the huge interferences from naturally abundant nucleotides. Meanwhile, the accumulation rate and the locating sites of 8-oxo-2, 7-dihydro-guanine (8-oxo-G) in tRNA were inspected using the established N-(tert-Butyldimethylsilyl)-N-methyl-trifluoroacetamide (MTBSTFA) labeling-based tRNA profiling method. After acetamiprid treatment, the increment of oxidized nucleoside triphosphates is smaller than that of their corresponding mono- and diphosphates, as well as the dephosphorylated nucleosides, on account of the existence of sanitization enzymes. Several tRNA fragments, CUC[m1A]Gp, CACGp, [Cm]C[m2G]p, and DDGp, are significantly downregulated in acetamiprid-treated HepG2 cells, while only [Cm]C[m2G]p in acetamiprid-treated LO2 cells. According to the profiling results, the significantly changed fragment CUC[m1A]Gp might be caused by the oxidation of guanine (G) to form 8-oxo-G at position 15 in human tRNAphe([Gm]AA), providing more information about the effect of oxidized nucleobases on tRNA's functions.

DNA Glycosylases Define the Outcome of Endogenous Base Modifications

Chemically modified nucleic acid bases are sources of genomic instability and mutations but may also regulate gene expression as epigenetic or epitranscriptomic modifications. Depending on the cellular context, they can have vastly diverse impacts on cells, from mutagenesis or cytotoxicity to changing cell fate by regulating chromatin organisation and gene expression. Identical chemical modifications exerting different functions pose a challenge for the cell's DNA repair machinery, as it needs to accurately distinguish between epigenetic marks and DNA damage to ensure proper repair and maintenance of (epi)genomic integrity. The specificity and selectivity of the recognition of these modified bases relies on DNA glycosylases, which acts as DNA damage, or more correctly, as modified bases sensors for the base excision repair (BER) pathway. Here, we will illustrate this duality by summarizing the role of uracil-DNA glycosylases, with particular attention to SMUG1, in the regulation of the epigenetic landscape as active regulators of gene expression and chromatin remodelling. We will also describe how epigenetic marks, with a special focus on 5-hydroxymethyluracil, can affect the damage susceptibility of nucleic acids and conversely how DNA damage can induce changes in the epigenetic landscape by altering the pattern of DNA methylation and chromatin structure.

RNAs as Sensors of Oxidative Stress in Bacteria

Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.

Effects of Two- and Twelve-Weeks Sodium-Glucose Cotransporter 2 Inhibition on DNA and RNA Oxidation: Two Randomized, Placebo-Controlled Trials

Animal studies have shown that SGLT2 inhibition decreases oxidative stress, which may explain the cardiovascular protective effects observed following SGLT2 inhibition treatment. Thus, we investigated the effects of two and twelve weeks SGLT2 inhibition on DNA and RNA oxidation. Individuals with type 2 diabetes (n = 31) were randomized to two weeks of treatment with the SGLT2 inhibitor empagliflozin treatment (25 mg once daily) or placebo. The primary outcome was changes in DNA and RNA oxidation measured as urinary excretion of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-oxo-7,8-dihydroguanosine (8-oxoGuo), respectively. In another trial, individuals with type 2 diabetes (n = 35) were randomized to twelve weeks of dapagliflozin treatment (10 mg once daily) or placebo in a crossover study. Changes in urinary excretion of 8-oxodG and 8-oxoGuo were investigated as a post-hoc analysis. Compared with placebo treatment, two weeks of empagliflozin treatment did not change urinary excretion of 8-oxodG (between-group difference: 0.3 nmol/24-hour (95% CI: -4.2 to 4.8)) or 8-oxoGuo (1.3 nmol/24-hour (95% CI: -4.7 to 7.3)). From a mean baseline 8-oxodG/creatinine urinary excretion of 1.34 nmol/mmol, dapagliflozin-treated individuals changed 8-oxodG/creatinine by -0.17 nmol/mmol (95% CI: -0.29 to -0.04) following twelve weeks of treatment, whereas placebo-treated individuals did not change 8-oxodG/creatinine (within-group effect: 0.10 nmol/mmol (95% CI: -0.02 to 0.22)) resulting in a significant between-group difference (P = 0.01). Urinary excretion of 8-oxoGuo was unaffected by dapagliflozin treatment. In conclusion, two weeks of empagliflozin treatment did not change DNA or RNA oxidation. However, a post-hoc analysis revealed that longer term dapagliflozin treatment decreased DNA oxidation. Clinicaltrials.gov: NCT02890745 and NCT02914691.HighlightsPlasma ferritin correlated with DNA and RNA oxidation in individuals with T2DTwelve weeks dapagliflozin treatment decreased DNA oxidationDapagliflozin and empagliflozin treatment did not change RNA oxidationLipid peroxidation was unaffected by two weeks empagliflozin treatment.

Methylated guanosine and uridine modifications in S. cerevisiae mRNAs modulate translation elongation

Chemical modifications to protein encoding messenger RNAs (mRNAs) influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. We have overcome these challenges by improving the mRNA purification and LC-MS/MS pipelines. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples, quantify 50 ribonucleosides in a single analysis, and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and reveal the presence of four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2, respectively), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells. To evaluate this possibility, we used a reconstituted translation system to investigate the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context.