Biology and Life Sciences

Abstract: The cap-binding protein eIF4E is a key protein for mRNA metabolism. The eIF4E biological role is defined by the specific protein it interacts with. The best characterized role of eIF4E is in promoting mRNA translation through its interaction with eIF4G. To seek for new interactors in the ascomycete Saccharomyces cerevisiae, we performed a genomic yeast two-hybrid screen using eIF4E as bait. In addition to the already reported p20 and Eap1, we identified Med9, a component of the RNA polymerase II Mediator complex. A physical interaction between eIF4E and Med9 was confirmed using recombinant proteins prepared in E. coli and further isolating the eIF4E―Med9 complex both by size-exclusion chromatography and by m7GTP-Sepharose pull-down experiments. Surprisingly, the eIF4E W75A mutation, which impairs the interaction with eIF4G, p20, and Eap1 only slightly affected the interaction with Med9 in the two-hybrid system. We further performed random mutagenesis to identify the Med9 amino acids involved in eIF4E interaction. Mutants F65A/I66A and F65A/I66A/H68N did not interact with eIF4E. We also demonstrated that the interaction eIF4E―Med9 depended on the carbon source for cell growth and that it might happen within the nucleus. Finally, we found that the eIF4E―Med9 interaction is conserved in the yeast Saccharomyces kudriavzevii.

Abstract: Oleanolic acid (OA) is a pentacyclic triterpenoid with broad biological activity, but its primary molecular points of engagement remain incompletely resolved. Most available studies describe OA through selected pathway markers, particularly within PI3K/AKT/mTOR, AMPK/mTOR, MAPK, NF-κB, and Nrf2 signaling, without clearly distinguishing direct target engagement from downstream adaptive responses. This limits mechanistic interpretation and weakens translational prioritization. This review examines how phosphoproteomics and integrated multi-omics can support OA target deconvolution. We discuss why phosphoproteomics is particularly informative for capturing early signaling events, how it can be combined with proteomics, tran-scriptomics, metabolomics, and chemoproteomic approaches, and why orthogonal tar-get-engagement methods remain essential for stronger causal inference. We also organize the current signaling evidence for OA and its derivatives, highlighting the strongest support for AMPK/mTOR-linked regulation of autophagy and apoptosis while identi-fying major gaps in systems-level validation across other reported pathways. Finally, we propose a stepwise workflow for OA target deconvolution based on time-resolved phosphoproteomics, analysis of informative phosphosite subsets, mul-ti-omics integration, kinase/phosphatase activity inference, and experimental target validation. This framework may help move OA research from descriptive pathway pharmacology toward mechanism-based target prioritization and more rational deriva-tive development.

Abstract: How life originated in the ancient abiotic world is one of the most fundamental questions in modern bioscience. To address this problem, I propose a scientifically credible, fact-based scenario involving a pre life molecular entity that ultimately gave rise to living organisms. This entity consisted of DNA and RNA, in which double stranded linear DNA replicated in a calm environment with the assistance of RNA and served as a stable repository of information essential for evolution and survival. In the same environment, RNA molecules with catalytic activity replicated exclusively in stem–loop forms and gave rise to ribosomal and transfer RNAs. Under such calm, ribonucleotide rich conditions, the information stored in double stranded linear DNA was transcribed into messenger RNA. The seemingly improbable emergence of the extraordinarily complex translational system is hypothesized to have occurred through extended wobble-based recognition of all messenger RNA triplets by only two prebiotic tRNAs, enabling protein synthesis. Finally, independently evolved rRNA and tRNA are proposed to have been abiotically reverse transcribed and integrated into DNA based entities in a calm, deoxynucleotide rich environment. Thus, DNA and RNA are functionally interdependent: DNA stores genetic information encoding essential RNAs and produces self-beneficial protein products, whereas information stable double stranded DNA relies on RNA for its replication and transcription, particularly in calm prebiotic environments. This mutual dependence establishes a self-sustaining molecular system capable of problem solving, thereby enabling the emergence and evolution of life.

Abstract: Bispecific T-cell engager (TCE) development continues to attract substantial industrial investment alongside a translation record that remains uneven across target antigens and disease settings. Multiple independent reports across the field have observed that target antigen density on tumor cells does not predict cytotoxic potency or clinical response, while other reports describe within-target density-potency correlations of widely varying strength. These findings, when read in parallel, appear contradictory and have not been organized by any unifying analytical framework that has gained adoption in the field's standard practice. A mechanistically motivated joint binding-effector framework suggested that this apparent contradiction may reflect a single biological structure being read through analytical conventions that examine target antigen density and effector-side biology in isolation. To investigate this systematically, we assembled a verified dataset of bispecific TCE clinical-stage programs spanning eleven target antigens (CD19, CD20, BCMA, GPRC5D, CD33, CD123, CLL-1, FLT3, EpCAM, PSMA, and DLL3) and read it against the published primary-source record of within-target density-outcome reports. The systematic empirical pattern that emerges is consistent with a joint binding-effector structure in which neither variable alone is sufficient. In the limiting case, target cells lacking the antigen produce no cytotoxicity at any effector-to-target ratio. The published record reflects the two variables asymmetrically by design: target antigen density is reported across cell-line panels, primary samples, and clinical correlative cohorts, while effector-side variation is structurally absent from cell-line panels (which fix effector-to-target ratios at non-biological values with uniform donor T cells) and is observable only in primary-sample and clinical correlative analyses. Across approved drug programs at clinical exposure, target antigen density does not predict outcome (verified in multiple peer-reviewed primary samples and clinical correlative analyses including a registration-trial cohort of n=165); in those same settings, measures of effector-side biology -- effector-to-target ratio, T-cell counts, regulatory T-cell frequency, and exhaustion markers -- are associated with outcome, consistent with the elementary requirement that both antigen-bearing targets and adequate effector cells are needed for TCE activity. Within-program triangulation in a discontinued clinical-development program (CD33/AMG 330) demonstrates the same structural pattern in the failure direction. We propose the joint binding-effector account as a testable explanation that reconciles the systematic empirical record assembled here: it is logically coherent, internally consistent, and consistent with the field's documented findings. The systematic dataset and the verified primary-source documentation are deposited as supplementary material to support independent evaluation.

Abstract: Phase-separated biomolecular condensates in the cytoplasm and nucleus are now recognized to contribute to carcinogenesis through aberrant signaling by assorted transcription factors and fusion oncoproteins. Oral cancer, the sixth most prevalent malignancy worldwide, frequently occurs in a U-shaped “high-risk” zone (floor of mouth, side of tongue, and anterior fauces) reflecting the path of liquid transit through the mouth. We previously reported that environmental stresses of saliva-like hypotonicity and beverage-like temperature changes triggered cycles of disassembly/reassembly of biomolecular condensates of GFP-tagged human myxovirus resistance protein (MxA; alias Mx1) in oral cancer cells. In the present study we identified some of the constituents of GFP-MxA cytoplasmic condensates in oral cells. GFP-MxA condensates were isolated from interferon (IFN)-λ1-treated GFP-MxA expressing OECM1 human oral cancer cells using magnetic bead-based immunoisolation. Unbiased peptide identification confirmed presence of MxA/Mx1 peptides; however, the strongest intensity was for the BACH1 transcription factor family. Immunofluorescence analyses confirmed the association of BACH1 and the family member Nrf2 with cytoplasmic human GFP-MxA condensates. Moreover, GFP-BACH1 and GFP-Nrf2 colocalized with cytoplasmic human HA-MxA condensates in transiently transfected OECM1 cells. Western blot assays confirmed presence of BACH1 and Nrf2 proteins in complexes isolated using anti-MxA pAb. In as much as BACH1 and Nrf2 regulate oxidative stress response genes, it was remarkable that immunofluorescence assays revealed the presence of heme oxygenase 1 (HO1) – a downstream redox regulator - in GFP-MxA condensates. In terms of aberrant function, in live cells, the Nrf2 transcription factor underwent rapid disassembly and reassembly cycles driven by saliva-like hypotonicity. The data highlight the unexpected intersections in oral cells between MxA condensates and BACH1, Nrf2 and HO1 – proteins well known to be involved in pathways regulating cellular responses to environmental and oxidative stresses, antiviral defense, oral epithelial dysplasia, and cancer progression and metastases.

Abstract:

Human immunodeficiency virus type 1 exhibits extensive genetic diversity, which has important implications for transmission dynamics, disease progression, and the effectiveness of antiretroviral therapy. In Mexico, molecular surveillance has largely relied on partial pol gene sequencing, limiting the detection of recombination events and resistance mutations outside canonical regions. In this study, we performed near-full-length whole-genome sequencing of HIV-1 from 40 treatment-naïve adults receiving care at a tertiary-care hospital in Mexico to characterize drug-resistance mutations, viral genetic diversity, and recombinant forms. Viral RNA was extracted from plasma and sequenced on an Illumina platform, followed by bioinformatic processing and interpretation using the DeepChek pipeline for subtype classification, recombinant profiling, and identification of drug-resistance mutations. Drug-resistance mutations were identified in 6/40 (15.0%) participants. NNRTI-associated DRMs were identified in 2/40 patients (5.0%), whereas NRTI- and protease inhibitor-associated DRMs were each identified in 1/40 patient (2.5%). In addition, accessory INSTI-associated substitutions were detected in 2/40 patients (5.0%). No statistically significant differences were observed between patients with and without DRMs with respect to age, sex, or plasma viral load. Furthermore, DRMs were distributed across all recombinant categories, with no significant association between recombinant profile and DRM presence (p = 0.97). Non-B subtypes and recombinant forms predominated (82.5%), while subtype B accounted for 17.5% of cases. Extensive intergenic recombination was observed, with discordant subtype assignments across gag, pol, and env regions, consistent with mosaic viral genomes. Multiple circulating recombinant forms, including CRF03_AB, CRF07_BC, CRF28_BF, and CRF39_BF, were identified, alongside a predominance of BF-related recombinants. In addition, several unique recombinant forms with complex mosaic structures were detected, reflecting ongoing recombination and viral evolution. These findings highlight the high genetic complexity of HIV-1 in this population, characterized by a predominance of recombinant forms and extensive genomic mosaicism. The detection of DRMs across diverse genetic backgrounds supports the value of baseline resistance testing and suggests that broader genomic surveillance may improve HIV-1 molecular epidemiology monitoring in Mexico.

Abstract: Hypoxia is a prevalent pathophysiological condition. Prolonged exposure to hypobaric hypoxia can lead to maladaptation, increasing the risk of chronic hypoxic diseases such as high-altitude polycythemia (HAPC). Dauricine, an alkaloid derived from the root of Menispermum dauricum DC, has been demonstrated to possess anti-hypoxic properties; however, its underlying molecular mechanisms remain elusive. In this study, a multi-target molecular mechanism of dauricine in mitigating hypoxia was systematically investigated using an integrated approach combining network pharmacology, molecular docking, and molecular dynamics simulations. Common targets between dauricine and hypoxia-related genes were identified through network pharmacology screening. A protein-protein interaction (PPI) network was constructed to identify core targets, followed by Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Molecular docking was subsequently employed to evaluate the binding affinities between dauricine and the core targets, while molecular dynamics simulations were performed to validate the stability of the resulting complexes. Additionally, the drug-likeness and safety profiles of dauricine were assessed. The results indicate that dauricine may exert its anti-hypoxic effects by modulating core targets, including ESR1, PIK3CA, and MTOR, and by acting on key signaling pathways such as PI3K-Akt, MAPK, and mTOR. This study provides a theoretical foundation for the development of dauricine as a multi-target candidate for intervention in hypoxia and establishes a bioinformatics basis for subsequent experimental validation.

Abstract: MicroRNAs (miRNAs) have been associated with the initiation, development, and progression of various cancers, including cervical cancer. Their involvement in cervical cancer is extensively documented, as they influence critical biological pathways, including apoptosis, cell cycle progression, immune evasion, and metastasis. In cervical cancer, deregulated miRNA expression contributes to tumor aggressiveness by interfering with key molecular pathways, many of which are also influenced by high-risk human papillomavirus (HPV) oncoproteins. In this review, we highlight key signaling pathways regulated by miRNAs linked to cancer hallmarks, particularly sustained proliferative signaling, which was the most frequently affected pathway across the studies reviewed. Furthermore, the interplay among HPV oncoproteins, dysregulated miRNA expression, and altered signaling pathways drives key oncogenic processes, including uncontrolled proliferation, evasion of apoptosis, and metastasis.

Abstract: The mevalonate pathway (MVA) is a central metabolic route responsible for the biosynthesis of isoprenoids, a vast and diverse class of biomolecules essential for cellular structure, signaling, and physiology. This review provides a comprehensive overview of the MVA pathway, addressing its distribution in different domains of life, evolutionary origins, and overall organization. We describe in detail its biochemical architecture, including enzymatic steps, catalytic mechanisms, structural characteristics, and multilayered regulatory strategies. In parallel, the methylerythritol phosphate pathway is presented as an alternative pathway to isoprenoid biosynthesis. The metabolic outputs of both pathways are explored, emphasizing the remarkable diversity of isoprenoid end products and their roles in membrane dynamics, protein modification, and cellular signaling. Furthermore, we analyze the biological functions and clinical relevance of the MVA pathway, including its involvement in human diseases and its variability in different kingdoms. The review also addresses recent advances in biotechnology, focusing on metabolic engineering and synthetic biology approaches for the microbial production of high-value isoprenoids. Finally, sustainable strategies for optimizing microbial cell factories and production processes are discussed, underscoring the growing importance of isoprenoid biosynthesis in industrial and pharmaceutical applications.

Abstract: Background/Objectives: Plant-based diets are increasingly adopted by families with young children, yet their potential effects on bone development and metabolic regulation during early childhood remain insufficiently understood. This study aimed to evaluate body composition, bone mineral density (BMD), biochemical markers of bone turnover, and adipokine profiles in healthy children aged 5–6 years adhering to lacto-ovo-vegetarian or omnivorous diets. Methods: A cross-sectional analysis was conducted in a well-characterized cohort of 90 healthy normal-weight children consuming either lacto-ovo-vegetarian or omnivorous diets. Body composition and bone mineral density were measured using dual-energy X-ray absorptiometry, and circulating markers of bone formation, resorption, and adipokines were determined using ELISA methods. Correlation analyses were performed to examine the relationships between anthropometric variables, bone parameters, and adipokines. Results: No significant differences were observed between vegetarian and omnivorous diets in anthropometric characteristics, bone mineral content (BMC), or BMD, indicating comparable skeletal status. However, vegetarian children exhibited significantly higher levels of bone turnover markers, including bone alkaline phosphatase (BALP) (p = 0.023) and C-terminal telopeptide of type I collagen (CTX-I) (p = 0.035), and a lower osteocalcin OC/CTX-I ratio (p = 0.027), suggesting increased bone remodeling activity with a relative shift toward resorption. Additionally, higher levels of carboxylated osteocalcin (Gla-OC) (p = 0.022) and an increased carboxylated to undercarboxylated OC (Gla-OC/Glu-OC) ratio (p = 0.005) were noted, potentially reflecting greater vitamin K availability. Among adipokines, vegetarian children showed lower HMW adiponectin levels (p = 0.05) and HMW/total adiponectin ratio (p = 0.012). Correlation analyses revealed distinct metabolic patterns between groups. In vegetarian children, bone parameters were primarily associated with lean mass, indicating the predominant role of mechanical factors in skeletal development. In contrast, omnivorous children demonstrated a more integrated relationship between bone indices and adipokines. Conclusions: In conclusion, while a lacto-ovo-vegetarian balanced diet supports normal bone mass in early childhood, it may be associated with subtle alterations in bone metabolism and its regulatory pathways, including adipokine profile. These findings highlight the importance of adequate dietary planning and underscore the need for longitudinal studies to determine long-term effects on bone status.

Abstract: Cancer cells, like yeast, use fermentation despite the presence of oxygen, a phenomenon called aerobic glycolysis. The advantage is that it maintains most of the C-C bonds of glucose, allowing highly proliferating cells to produce the biomolecules that are necessary for cytokinesis. However, aerobic glycolysis is less energy-efficient than respiration, and it must operate at a higher frequency and produces more toxic by-products like methylglyoxal, which damages DNA. Cancer cells, like yeast cells, developed efficient systems to repair their damaged DNA. This makes cancer cells resistant to radiotherapy, which requires a combination with chemotherapy using drugs that inhibit DNA repair. However, this converts healthy cells to cancer cells, indicating that more research is required regarding the relationship between glycolysis and cancer. Using yeast as a model, we have discovered that the glycolytic enzymes TPI1 and GAPDH interact with the DNA damage-dependent checkpoint Rad9p. Furthermore, we have isolated TPI1 and GAPDH mutant strains that are unable to repair their damaged DNA. The TPI1 mutant strain has lower TPI enzymatic activity, suggesting that it accumulates methylglyoxal, while the GAPDH mutant strains have normal GAPDH enzymatic activity, confirming that GAPDH moonlights in the DNA Damage Response.

Abstract: Methylated flavonoids are abundant phytochemicals in Eucalyptus and are of interest be-cause methylation can alter flavonoid diversity, bioactivity and stability. The enzymes re-sponsible for flavonoid methylation in eucalypts are largely uncharacterised. We used comparative leaf transcriptomics of two species with contrasting flavanone profiles, together with protein-structure-guided candidate selection, to identify prospective O-methyltransferases (OMTs) involved in methylated flavonoid biosynthesis. Five candidate OMTs from E. eugenioides were cloned, heterologously expressed and assayed against a panel of flavonoids and a chalcone precursor. The enzymes showed distinct substrate preferences and regioselectivities. EeOMT1 acted as a broad 7-O-methyltransferase, whereas EeOMT3–EeOMT5 preferentially methylated B and C-ring hydroxyl groups, with differing capacities for sequential methylations at different sites. EeOMT2 was of particu-lar interest because it effectively methylated pinocembrin chalcone to alpinetin chalcone, while only weakly converting pinocembrin to alpinetin. Expression–metabolite analyses across E. eugenioides genotypes supported roles relating to in planta accumulation of 5-O- and 7-O-methylated flavanones, for EeOMT2 and EeOMT1, respectively. These findings support a revised model in which alpinetin biosynthesis proceeds, at least in part, through methylation of a chalcone precursor before flavanone formation. This provides a foundation for elucidating flavonoid methylation pathways and for engineering tailored methylated flavonoids for industrial applications.

Abstract: Monoclonal antibodies (mAbs) have been the subject of extensive study in recent years due to their recognition as highly promising therapeutic molecules offering high specificity and a low risk of side effects. Monitoring the structure of these molecules is crucial for developing new therapeutics, characterizing interactions with antigens or receptors, and explaining potential changes in activity between antibody production batches. However, commonly used biophysical approaches provide only low spatial resolution information, and conventional structural biology techniques such as crystallography and cryo-electron microscopy (cryo-EM) are difficult to apply to these highly dynamic proteins. Solution nuclear magnetic resonance (NMR) spectroscopy is the method of choice for structural studies of flexible proteins at atomic resolution; however, it has traditionally been limited to low-molecular-weight biological systems. In this review, we present recent advances in NMR spectroscopy and advanced isotopic labeling methods that have enabled the atomic-resolution study of both the crystallizable (Fc) and antigen-binding (Fab) fragments of antibodies. We show how NMR is becoming a powerful tool for investigating full-length mAbs at an atomic level, opening up new possibilities for the characterization and in-depth quality control of therapeutic antibodies in solution.

Abstract: Controls are fundamental to ensuring accuracy and reliability in molecular diagnostics, yet their roles are often oversimplified or conflated with broader quality assurance frameworks. As molecular testing expands from centralized laboratories to point-of-care (POC) and over the counter (OTC) settings, the design, implementation, and interpretation of controls must evolve to address diverse operational environments and clinical risks.This review introduces a comprehensive framework for understanding control strategies in molecular diagnostics, integrating internal, external, and orthogonal controls within a tiered, risk-based testing model. We categorize diagnostic systems into three tiers—screening (OTC/POC), confirmatory laboratory testing, and reference-level or adjudication testing—and examine how control requirements scale with analytical complexity, user variability, and clinical impact. Across these tiers, controls serve distinct but complementary roles, including verification of assay functionality, mitigation of contamination, maintenance of cross-platform consistency, and resolution of diagnostic uncertainty. We further analyze common failure modes in molecular diagnostics, including sample-related errors, inhibition, contamination, and interpretation challenges, and map how specific control strategies mitigate these risks. Regulatory perspectives from the U.S. Food and Drug Administration (FDA), Clinical Laboratory Improvement Amendments (CLIA), International Organization for Standardization (ISO), and World Health Organization (WHO) guidelines are discussed, highlighting the shift toward risk-based and context-dependent control design rather than rigid, one-size-fits-all requirements.Importantly, we address the balance between control burden and clinical utility, emphasizing that excessive control implementation may increase system complexity without proportionate gains in diagnostic value particularly in decentralized settings. Emerging trends, including artificial intelligence (AI)-assisted diagnostics and decentralized molecular platforms, are also explored as transformative approaches to enhancing control integration and result validation.We propose that a tier-adaptive, risk-based control framework is essential for next-generation molecular diagnostics, enabling accurate, scalable, and user-centered testing systems. This perspective supports the development of robust diagnostic platforms that maintain analytical integrity while improving accessibility and real-world performance.

Abstract: Caveolae are specialized plasma membrane microdomains whose structure and signaling functions are highly sensitive to nutritional status. They operate as dynamic, metabolically responsive units whose stability depends on membrane cholesterol, sphingolipids, fatty acid composition, and insulin regulated metabolic cues. Dietary lipids, glucose availability, amino acid balance, and micronutrient dependent antioxidant defenses all influence caveolar assembly, membrane curvature, and caveolin expression. Saturated fats, hyperglycemia, and oxidative stress destabilize caveolae by altering lipid packing, promoting caveolin mislocalization, and increasing lipid and protein oxidation. In contrast, unsaturated fatty acids, antioxidant vitamins, polyphenols, and adequate zinc and selenium support membrane fluidity, redox balance, and caveolar integrity. Dietary patterns exert integrated effects: Western style diets impair caveolin 1 expression and endothelial structure, whereas Mediterranean and plant based diets enhance lipid handling and insulin sensitivity, conditions favorable for maintaining functional caveolae. Caveolae also act as nutrient sensing platforms that coordinate insulin receptor signaling, nitric oxide production, and lipid uptake, amplifying the systemic impact of nutritional perturbations. Disruption of caveolae contributes to metabolic disease by impairing adipocyte lipid storage, endothelial nitric oxide signaling, and skeletal muscle glucose uptake. Understanding how nutrition modulates caveolae provides a mechanistic link between diet and metabolic health and highlights membrane targeted nutritional strategies as potential therapeutic approaches.

Abstract: Brain cancer is a highly aggressive disease with limited treatment options, highlighting the need for reliable preclinical models for drug discovery. This study aimed to isolate and characterize Saudi patient–derived primary brain cancer cells and assess the anticancer activity of novel compounds developed in-house. Sixteen tumor samples from Saudi patients were processed to establish primary brain cancer cultures and One Normal Tissue (Control). The cells were successfully isolated and maintained under optimized conditions, with their morphology and growth characteristics monitored. Molecular analysis confirmed the expression of key tumor and neural markers. The anticancer activity of selected compounds KCO69, KCO70, and KCO129 was tested at various concentrations using the MTT and CellTiter-Glo Luminescent Cell Viability Assay. All compounds caused a concentration-dependent reduction in cell viability, with the strongest effects seen at 25 µM. Among them, compound 70 showed the most significant antiproliferative activity, while compounds KCO69 and KCO129 exhibited moderate effects. Variability in treatment response among cultures reflected the inherent heterogeneity of patient-derived tumors. Overall, establishing primary brain cancer cell models from Saudi patients offers a valuable platform for preclinical drug screening and supports further research on these compounds as potential therapies for brain cancer.

Abstract:

Volatile organic compound (VOC)-mediated communication between distinct fungal colonies is a crucial yet poorly understood aspect of interspecies interactions. We investigated the airborne interactions between Trichoderma atroviride (SZMC 24276) and haploid Armillaria ostoyae (SZMC 23085) hyphae using an in vitro face-off system that combined transcriptomic and gas chromatography-mass spectrometry (GC-MS) analyses. Distinct temporal VOC profiles were observed, including the early accumulation of the constitutively produced 6-pentyl-α-pyrone (6-PP) and the later appearance of 2-heptanone from T. atroviride, as well as the production of an interaction-specific cadinane-type sesquiterpene in A. ostoyae. Multi-omics integration revealed a direct coupling between transcriptional regulation and volatile output, with suppression of C8 signaling compounds such as 1-octen-3-ol and non-ribosomal peptide synthetase-associated pathways in T. atroviride under volatile exposure. In contrast, A. ostoyae exhibited extensive transcriptional reprogramming characterized by oxidative stress responses, detoxification pathways, and activation of terpene biosynthetic clusters. These findings indicate that T. atroviride constitutively produces 6-PP as a broad-spectrum volatile irritant and modulates its secondary metabolism in a context-dependent manner, while A. ostoyae responds to volatile cues through stress-associated and defensive mechanisms. Overall, this study demonstrates that VOCs function as active regulators of interactions before physical contact, shaping both metabolic and transcriptional responses, and highlights their potential role in Trichoderma-based biocontrol strategies against Armillaria.

Abstract: Genetic recombination occurs in a wide range of organisms, from simple RNA viruses to mammals and plants with DNA genomes. In sexual reproduction, two parental genomes come together and undergo recombination, producing an offspring genome that has a combination of information from the two parental genomes. Genome recombination occurring during sexual reproduction can involve one of several mechanisms, including copy-choice recombination as well as breakage and exchange. Across widely different organisms, recombination by any mechanism is generally promoted by factors that damage the genetic material. In organisms such as bacteriophage and Paramecium, it was experimentally demonstrated that recombinational repair during sexual reproduction can overcome otherwise deleterious or lethal damages. For many decades it has been recognized that there are larger biological costs of sexual reproduction than for asexual reproduction. Much effort has been invested in theories assuming that genetic variation, due to recombination, is the main adaptive benefit of sexual reproduction. Such a benefit was considered to compensate for the large costs of sexual reproduction. However, it has been difficult to find a strong consistent benefit for variation. Repair of lethal damages, involving recombiantional interactions of two different genomes, now appears to be the major selective factor underlying sexual reproduction in organisms both simple and complex.

Abstract:

Kelch-like ECH-associated protein 1 (Keap1) acts as a repressor of nuclear factor-erythroid 2-related factor 2 (Nrf2), a major transcription factor regulating cellular antioxidant response. Keap1 is the substrate adaptor subunit of the cullin 3-RING E3 ubiquitin ligase complex that specifically facilitates Nrf2 ubiquitination and its proteasomal degradation. Keap1 is rich in cysteine residues and several of them undergo various modifications, such as sulfhydration, nitrosylation and glutathionylation under cellular stress conditions. Some of these modifications alter the conformation of Keap1, preventing Nrf2 from ubiquitination and subsequent proteasome-mediated degradation. As a result, newly synthesised Nrf2 translocates to the nucleus to induce the expression of diverse genes involved in protecting cells against oxidative stress. Protein CoAlation is a reversible redox-dependent post-translational modification (PTM) in which coenzyme A (CoA) forms disulphide bonds with oxidised cysteine residues under oxidative or metabolic stress. In this study, we demonstrate for the first time that disulphide Keap1 dimer undergoes CoAlation in cellular response to oxidative stress induced by various oxidising compounds. Furthermore, glucose deprivation also induces CoAlation of disulphide Keap1 dimer in HEK293/Pank1β cells. We also demonstrate that Keap1^{11 Cys-less} mutant is not CoAlated in response to diamide treatment or glucose deprivation. In summary, this study uncovers a novel PTM of Keap1 by the key metabolic integrator CoA, which provides new insights into the regulation of the Keap1-Nrf2 antioxidant pathway under oxidative and metabolic stress.

Abstract: Background: Recent work has revealed that protein-coding sequences encode regulatory information influencing mRNA stability and translation through a nascent peptide code. However, the evolutionary origin of this regulatory layer remains unclear. This study aims to determine when peptide-mediated translational control emerged during the evolution of the proteome and genetic code. Methods: Dipeptide-specific effects on mRNA stability and translation were integrated with a phylogenetic timeline of dipeptide emergence derived from dipeptide sequences across proteomes. Each of the 400 canonical dipeptides was assigned an evolutionary age, and experimentally derived regulatory effects were mapped onto this timeline, with associations assessed using rank-based correlation and regression analyses. Results: A weak but statistically significant negative association was observed between dipeptide age and mRNA stability, indicating that more recently evolved dipeptides tend to destabilize transcripts. This trend was stronger at the amino acid level, where later-emerging residues showed greater contributions to reduced mRNA levels. Destabilizing effects were associated with physicochemical properties such as positive charge, side-chain bulkiness, and β-strand propensity. Mapping these effects onto codon space revealed a non-random distribution aligned with the evolutionary and structural organization of the genetic code. Destabilizing effects were also enriched within specific codon exchange groups, indicating that regulatory signals are structured within the degeneracy and mutational neighborhoods of the code. Conclusions: These findings indicate that the nascent peptide code is a late evolutionary innovation linked to amino acid expansion and proteomic complexity, with regulation embedded within both peptide sequences and the degeneracy structure of the standard genetic code.