bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–05–17
forty-four papers selected by
Cédric Chaveroux, CNRS



  1. Virology. 2026 May 08. pii: S0042-6822(26)00162-5. [Epub ahead of print]621 110947
      Translation initiation in eukaryotic cells is usually driven by recognition of a 5' cap and a 3' poly(A) tail, which cooperate through interactions with eukaryotic initiation factors (eIFs) and poly(A)-binding protein (PABP) to promote mRNA circularization and efficient ribosome recruitment. However, many viral RNAs lack one or both of these canonical features and must use alternative strategies to access the host translational machinery. Diverse mechanisms are used to bypass cap dependence, including internal ribosome entry sites that recruit ribosomal subunits with variable requirements for canonical initiation factors as well as viral protein genome-linked strategies that functionally substitute for the cap by engaging components of the eIF4F complex. For viral mRNAs lacking poly(A) tails, translation can be supported by long-range RNA-RNA interactions that mediate 5'-3' communication and viral or host proteins that replace PABP to facilitate closed-loop formation. Emerging examples, including host protein ATXN2L during reovirus infection, illustrate how viruses use or mimic cellular factors to promote selective translation. Collectively, these strategies reveal fundamental principles of mRNA circularization and translational control, highlighting the dynamic interplay between viral and host machinery in regulating protein synthesis.
    Keywords:  ATXN2L; Cap-independent translation; Internal ribosome entry site (IRES); Nonpolyadenylated mRNA; Translation initiation; Viral protein genome-linked (VPg); mRNA circularization
    DOI:  https://doi.org/10.1016/j.virol.2026.110947
  2. Int J Mol Sci. 2026 Apr 29. pii: 3955. [Epub ahead of print]27(9):
      Programmed cell death 4 (PDCD4) protein is a tumour suppressor protein that inhibits mRNA translation by inhibiting RNA helicase, eukaryotic initiation factor 4A (eIF4A). We have previously reported that PDCD4 interacts with the internal ribosome entry site (IRES) element of B-cell lymphoma extra-large (Bcl-xL) mRNA and inhibits its IRES-mediated translation initiation. S6 kinase (S6K)-mediated phosphorylation of PDCD4 activates its degradation and derepresses IRES-mediated translation initiation of Bcl-xL mRNA. eIF3F (one of the subunits of eIF3 complex) was reported to recruit S6K to phosphorylate eIF3G. Therefore, we investigated the possibility of co-regulation of PDCD4 and eIF3F by S6K and the regulation of IRES-mediated translation initiation by PDCD4-eIF3F. Here, we demonstrated that PDCD4 interacts with several subunits of eIF3. Specifically, eIF3F directly interacts with PDCD4 in an RNA-independent manner. Depletion of PDCD4 in glioblastoma (GBM) cells resulted in decreased levels of certain eIF3 subunits, including eIF3F. Additionally, depletion of eIF3F from GBM cells decreased the levels of PDCD4 protein. We also showed that PDCD4 and eIF3F directly interact with Bcl-xL RNA independently of each other. By performing IRES reporter, polysome profiling assays and EMSA we have demonstrated that eIF3F regulates IRES-mediated translation of Bcl-xL mRNA, likely via its interaction with PDCD4.
    Keywords:  Bcl-xL; IRES-mediated translation; ITAFs; PDCD4; eIF3; mRNA translation
    DOI:  https://doi.org/10.3390/ijms27093955
  3. Mitochondrion. 2026 May 14. pii: S1567-7249(26)00056-5. [Epub ahead of print] 102166
      Mitochondrial dysfunction is a common pathology of neurodegenerative diseases, which contributes to neuronal vulnerability via excessive oxidative stress, impaired bioenergetics, and dysregulated apoptosis. Emerging studies highlighted the critical role of epitranscriptomic RNA modifications, particularly N6-methyladenosine (m6A), in mitochondrial gene expression regulation and cellular stress responses. m6A modifications are installed by methyltransferases ("writers," METTL3/METTL14), recognized by readers proteins (YTH domain family proteins, IGF2BPs), and removed by demethylases ("erasers," FTO, ALKBH5), collectively orchestrating mRNA splicing, localization, stability, and translation. Recent evidence demonstrates that m6A modifications modulate both nuclear-encoded and mitochondrially encoded transcripts and regulate key mitochondrial processes, including fission/fusion dynamics, oxidative phosphorylation, mitophagy, and apoptosis. Dysregulation of m6A machinery disrupts mitochondrial homeostasis, exacerbates oxidative stress and neuroinflammation, and promotes neuronal loss. Importantly, pharmacological or genetic modulation of m6A regulators can restore mitochondrial function, inhibit caspase activation, and dampen pro-inflammatory signaling, underscoring their therapeutic potential. This review consolidates current insights into mitochondrial epitranscriptomics, emphasizing how m6A modifications act as central regulators of mitochondrial stress responses and neurodegeneration.
    Keywords:  Epitranscriptomics; Mitochondrial dysfunction; Neurodegeneration; m(6)A RNA modification
    DOI:  https://doi.org/10.1016/j.mito.2026.102166
  4. bioRxiv. 2026 Feb 26. pii: 2026.02.25.708058. [Epub ahead of print]
      Medulloblastoma is the most common pediatric brain cancer, but current treatments are largely non-specific, often causing developmental side effects. Genomic sequencing identified the RNA helicase DDX3X as one of the most frequently mutated genes in this cancer and a potential treatment target, yet its role in tumor progression remains elusive. Prior studies have indicated that the mutations cause specific defects in translation; however, both DDX3X and its yeast ortholog Ded1 have also been associated with cellular stress responses, suggesting that the contribution of the DDX3X mutations to medulloblastoma might result from defects in the translational response to stress. Building on our prior study that replicated the DDX3X mutations in yeast DED1 ( ded1-mam ), we examined the mutants' effects following TOR pathway inactivation. First, we demonstrated that ded1-mam displayed substantial rapamycin-resistant growth compared to wild-type cells. In addition, similar to other ded1 mutants, the ded1-mam had decreased degradation of Ded1 and the translation factor eIF4G1 under TOR inactivation. Notably, these differences did not result in increased bulk translation following rapamycin; rather, the growth phenotypes appeared to be driven by translation of specific mRNAs. Reporter assays demonstrated enhanced translation of mRNAs with unstructured 5' UTRs in ded1-mam following TOR inhibition and a decrease in structured reporters. Furthermore, known Ded1 target genes with relatively unstructured 5' UTRs showed upregulated protein levels in rapamycin. We thus hypothesize that mutant DDX3X selectively upregulates translation of unstructured, pro-growth transcripts while downregulating other structured transcripts, allowing tumor cells to bypass stress-induced growth controls and promoting medulloblastoma progression.
    DOI:  https://doi.org/10.64898/2026.02.25.708058
  5. Bioessays. 2026 May;48(5): e70146
      Mitochondria are vital not only for energy production but also for regulating signaling pathways that influence aging. While mitochondrial dysfunction contributes to age-related decline, emerging evidence shows that mild, regulated mitochondrial stress can paradoxically promote longevity. This review highlights recent advances in mitochondrial biology and aging across species. We explore the dual role of reactive oxygen species (ROS) as both damaging agents and signaling molecules that activate adaptive stress responses. Key pathways such as the mitochondrial unfolded protein response (UPRMT) and integrated stress response (ISR) are discussed, including their tissue-specific as well as non-cell-autonomous effects on aging. Additionally, we examine the impact of mitochondrial protein import/export, dynamics (fission, fusion, mitophagy, biogenesis), and quality control in aging. Finally, we address challenges in understanding context-dependent mitochondrial responses and mitonuclear communication. Together, these insights position mitochondria as central regulators of aging and highlight their potential as therapeutic targets to enhance health span and longevity.
    Keywords:  aging; integrated stress response; mitochondria ROS; mitochondrial dynamics; mitochondrial unfolded protein response
    DOI:  https://doi.org/10.1002/bies.70146
  6. Nat Cell Biol. 2026 May 12.
      Major advances over the past few decades have highlighted the complex regulation of RNA from transcription to nuclear export and from translation to decay. Despite the emerging cellular landscape of malleable and multifunctional RNA molecules, the role of RNA dysregulation in ageing, one of the most fundamental processes of human biology, is underappreciated. Here we focus on ageing-linked dysregulation of the mRNA life cycle. We summarize how RNA metabolism steadily deviates throughout ageing and senescence: in transcription, aged cells bias shorter genes at the expense of complex transcripts; in splicing, ageing-linked alternative exon usage is common; in translation, ribosomal collisions on mRNAs decouple transcriptional output from protein production; and in decay, aberrant RNAs accumulate due to poor degradation activity. We close by discussing how ageing-linked dysregulation of RNA biology can drive cellular stress and thus serve as a therapeutic target to reverse disease.
    DOI:  https://doi.org/10.1038/s41556-026-01946-4
  7. Microbiol Res. 2026 May 07. pii: S0944-5013(26)00108-4. [Epub ahead of print]310 128544
      Post-transcriptional regulation by small RNAs (sRNAs) allows bacteria to fine-tune gene expression and rapidly adapt to fluctuating environmental conditions. In the environmental alphaproteobacterium Sphingopyxis granuli TFA, SuhB is the only sRNA characterized to date and was previously shown to control the degradation of the organic solvent tetralin under carbon catabolite repression. Here, we reveal additional regulatory roles of SuhB beyond carbon metabolism that position this sRNA as a global post-transcriptional regulator influencing metabolic adaptation and stress response. Deletion of suhB increases sensitivity to multiple abiotic stresses, including osmotic, oxidative, desiccation, and copper stress. Label-free quantitative proteomic analysis further reveals widespread alterations in the proteome in the absence of SuhB, affecting metabolic pathways and membrane-associated proteins with a notable impact on TonB-dependent receptors. Combining these results with bioinformatic analysis and translational reporter assays, we identified new SuhB targets, including genes involved in polyhydroxybutyrate biosynthesis. In addition, we identify a LysR-type transcriptional regulator that directly binds to the suhB promoter and activates its expression.
    Keywords:  Gene expression regulation; Small RNA; Stress response; Targets
    DOI:  https://doi.org/10.1016/j.micres.2026.128544
  8. Int J Oncol. 2026 Jul;pii: 80. [Epub ahead of print]69(1):
      Small nucleolar RNAs (snoRNAs) are a conserved class of non‑coding RNAs that guide 2'‑O‑methylation and pseudouridylation of ribosomal RNA. First identified over five decades ago, snoRNAs have emerged as critical regulators of cellular function, with high‑throughput sequencing revealing their dysregulation in numerous human diseases, particularly cancer. In the present review, the biogenesis, classification, and modification mechanisms of snoRNAs and snoRNA‑derived fragments (sdRNAs) are comprehensively summarized. Recent advances in understanding their non‑canonical functions are highlighted, which extend beyond ribosomal RNA modification to include regulation of mRNA splicing, stability, and protein interactions. These diverse mechanisms enable snoRNAs to influence key cancer‑related processes such as proliferation, metastasis, metabolic reprogramming, and therapy resistance. A comprehensive overview of snoRNA dysregulation across major cancer types is provided, including colorectal, hepatocellular, gastric, lung, breast, and ovarian cancers, with a detailed discussion of underlying molecular pathways. Furthermore, their emerging potential as diagnostic and prognostic biomarkers detectable in liquid biopsies is examined, as well as their promise as therapeutic targets amenable to antisense oligonucleotide and small molecule intervention. The present review integrates current knowledge of snoRNA/sdRNA biology and highlights critical gaps and future directions, providing a foundation for translating these regulatory RNAs into clinical oncology applications.
    Keywords:  cancer biomarker; small nucleolar RNAs; small nucleolar RNA‑derived fragments; therapeutic target; tumor microenvironment
    DOI:  https://doi.org/10.3892/ijo.2026.5893
  9. Int J Mol Sci. 2026 Apr 24. pii: 3784. [Epub ahead of print]27(9):
      Activating transcription factor 4 (ATF4) is a master transcription factor of integrated stress response (ISR), an evolutionarily conserved intracellular signaling network that helps the cell, tissue, and organism to adapt to various unpredictable environmental fluctuations, mitigate the challenges, and maintain health. Stress-induced ATF4 expression regulates a wild variety of gene expression programs to enable stress management and repair for cell homeostasis and integrity. However, chronic ATF4 activation contributes to pathologies including cancer, inflammation, and neurodegeneration. Extensive studies have revealed that ATF4 regulates many cellular processes including autophagy, apoptosis, metabolism, and inflammation. Emerging evidence has uncovered new signaling pathways in regulation of ATF4 expression and activation, including at transcriptional, translational, and post-translational levels, and new functions of ATF4 in the progression of various metabolic and stress-related diseases, including inflammation, cancer, and cardiovascular disease. The diversity of ATF4 functions is increasingly appreciated. This review summarizes the recent findings of the complex regulatory network of ATF4 activity and its roles in integrating stress responses, metabolic reprogramming, unfolded protein responses, autophagy, inflammation, and immunity.
    Keywords:  ATF4; endoplasmic reticulum; integrative stress response; unfolded protein response
    DOI:  https://doi.org/10.3390/ijms27093784
  10. Mol Reprod Dev. 2026 05;93(5): e70106
      Male infertility is a global health concern, with sperm dysfunction being a major contributing factor. Phospholipase C zeta (PLCζ), a key sperm-specific factor essential for oocyte activation, is closely linked to fertilization failure. This study investigated the role of METTL3-mediated N6-methyladenosine (m6A) modification in regulating PLCζ expression and sperm function. The mRNA and protein expression levels of PLCζ, METTL3, METTL14, and WTAP in sperm were measured using qRT-PCR and western blotting, respectively. The morphology of the sperm was evaluated by Giemsa staining. The zinc ion content of the semen was measured using the 5-Br-PAPS colorimetric method, and the citrate concentration and the total m6A level were measured using commercial kits. The m6A modification level of PLCζ mRNA in mouse sperm and the binding interaction between METTL3 and PLCζ mRNA were analyzed by RNA immunoprecipitation (RIP). Finally, the stability of PLCζ mRNA was examined using an actinomycin d-mediated transcription inhibition assay. The results showed that PLCζ expression was downregulated in the semen of patients with low fertilization rates (LFR), and its level correlated positively with reduced zinc/citrate content. These patients also exhibited a marked decrease in global m6A modification levels. Inhibition of METTL3 downregulated PLCζ expression in mouse sperm and was accompanied by impaired prostate secretory function. Mechanistically, METTL3 inhibition reduced the stability of PLCζ mRNA by decreasing its m6A modification. In conclusion, METTL3 enhances the stability of PLCζ mRNA through m6A methylation, thereby maintaining its normal expression level in sperm and ultimately supporting fertilization capacity and secretory homeostasis of the prostate.
    Keywords:  METTL3; PLCζ; infertility; m6A modification
    DOI:  https://doi.org/10.1002/mrd.70106
  11. J Cell Biol. 2026 Jun 01. pii: e202511091. [Epub ahead of print]225(6):
      Ribosome specialization, whereby ribosomes of distinct composition translate different sets of mRNAs, is a concept that has garnered both wide-spread excitement and skepticism from the translation field. The controversy is rooted in experimental challenges, which make rigorous controls difficult and not obvious to the nonexpert. In addition, considerations of translation mechanisms and ribosome homeostasis also suggest heterogeneity to be limited, fueling doubt. Lastly, the mechanisms by which heterogeneity can lead to specialization are often challenging to imagine and not spelled out. In this perspective, we define ribosome heterogeneity and specialization, use examples to examine both the technical challenges and potential solutions. We then consider the mechanism-based challenges with the goal of proposing biologically relevant circumstances where ribosome specialization might exist and how it might affect translation in an mRNA-specific manner. It is hoped that this article will help resolve the controversy around the subject, in addition to providing a guide for scientists entering the field, so they can concentrate their efforts fruitfully and rigorously.
    DOI:  https://doi.org/10.1083/jcb.202511091
  12. Am J Physiol Cell Physiol. 2026 May 13.
      Protein homeostasis is critical for mitochondrial function and is maintained by proteases and chaperones that respond to stress and mediate adaptive changes such as the mitochondrial unfolded protein response (UPRmt), the integrated stress response (ISR) and antioxidant signaling. However, the mechanisms by which stressors regulate these retrograde responses remains uncharacterized in muscle. Thus, we examined the effect of mitochondrial stressors on the activation of these pathways in myoblasts and differentiated myotubes. Cells were exposed to either 1) CDDO, a LonP1 protease inhibitor, 2) GTPP, an HSP90 chaperone inhibitor, 3) CCCP, an energetic uncoupler, or 4) MB-10, an inhibitor of protein import, and responses were compared to those induced by acute contractile activity (ACA). LonP1 inhibition activated ATF4 and Nrf2 signaling, increased mitochondrial chaperones, and resulted in protein aggregation without elevating reactive oxygen species (ROS). In contrast, blocking HSP90 led to increases in mitochondrial ROS and activation of CHOP, indicating protein homeostasis-related stress with limited antioxidant signaling. ACA elicited responses similar to the inhibition of LonP1, including the activation of ATF4 and Nrf2, increased UPRmt markers, and a redox balance. Although CCCP and MB-10 both impaired protein import, they activated distinct downstream responses. CCCP resulted in ISR activation, while MB-10 induced Nrf2-mediated antioxidant responses. Together, these findings show that the type of mitochondrial stress determines the direction of the retrograde signaling pathways between protein homeostasis and redox signaling in muscle cells, and they provide insights on how muscle coordinates signaling pathways as part of mitochondrial adaptations to contractile activity.
    Keywords:  integrated stress response; mitochondrial biogenesis; mitochondrial proteostasis; mitochondrial unfolded protein response; muscle contractile activity
    DOI:  https://doi.org/10.1152/ajpcell.00167.2026
  13. Int J Mol Sci. 2026 Apr 29. pii: 3978. [Epub ahead of print]27(9):
      Amyloid-β (Aβ) protein, a cleavage product of the amyloid precursor protein (APP), is the main component of neuritic plaques in Alzheimer's disease (AD), and its accumulation has been considered as the molecular driver of Alzheimer's pathogenesis. Aβ has been a primary target for therapy since the amyloid cascade theory was put forth, with methods designed to prevent the generation of Aβ. The APP 5'-untranslated region (UTR) mRNA encodes a functional structured iron-responsive element (IRE) that represents a potential target for small molecule inhibitors as an anti-amyloid therapy for AD. Here, we offer a comprehensive strategy that uses RNA-targeted binding to inhibit APP translation. The IRE family is among the few 3-D mRNA regulatory elements with a known 3-D structure. Accordingly, we exploit these structural and functional characteristics as our strategy to target APP IRE structured mRNA to identify anti-amyloid drugs. The mRNA encoding proteins involved in iron metabolism are regulated by this family of similar nucleotide sequences. Post-transcriptional control of cytoplasmic mRNA is a rapidly developing area of biomedicine. Across animals, evolutionarily conserved IRE mRNAs serve as a model system for 3-D mRNAs. IRE mRNAs have shown great promise for chemical manipulation of mRNA and protein expression in biological systems by yielding "proof of principle" data for small molecules targeting mRNA structures. A novel approach to identifying RNA-directed therapeutics to regulate APP expression and Aβ-peptide generation for AD treatments is exemplified by APP 5'-UTR-directed small molecule inhibitors.
    Keywords:  Alzheimer’s disease; amyloid precursor protein; protein synthesis; small molecule inhibitors; structured mRNA
    DOI:  https://doi.org/10.3390/ijms27093978
  14. Trends Cell Biol. 2026 May 11. pii: S0962-8924(26)00063-2. [Epub ahead of print]
      Errors in transcription and RNA processing generate aberrant transcripts that can produce truncated, nonfunctional, or dominant-negative proteins. RNA surveillance pathways, centered on the RNA exosome, recognize diverse processing defects and initiate targeted RNA degradation. These mechanisms also regulate the short half-life of chromatin-associated noncoding RNAs through co- and/or post-transcriptional degradation. This review examines how the RNA exosome achieves substrate specificity, focusing on its interactions with the helicase cofactors mRNA transport 4 (MTR4) and superkiller 2 (SKIV2L) and the modulatory role of RNA modifications such as N6-methyladenosine. The broad spectrum of RNA exosome targets underscores its central functions in transcription, translation, genome integrity, and cell fate determination.
    Keywords:  MTR4; RNA exosome; RNA surveillance; SKI complex; ribosomes; transcriptional stalling
    DOI:  https://doi.org/10.1016/j.tcb.2026.04.005
  15. J Phys Chem B. 2026 May 14.
      RNA-binding motif protein 45 (RBM45) is an RNA-binding protein crucial for brain development and plays a key role in RNA metabolism and disease. Its RNA recognition motif (RRM) domains can recognize GAC-containing motifs, with or without N6-methyladenosine (m6A) modification. While its RRM domains individually do not preferentially recognize m6A, RBM45 preferentially recognizes m6A motifs over unmodified motifs. In this study, we used molecular dynamics (MD) simulations to investigate the binding of a series of RNAs in complex with different RRM domains individually and in complex with RRM3 in the context of the full-length protein. Our study complies with previous experiments and provides in-depth biophysical insights into the binding of unmodified and m6A-modified GACG, GACU, and GACA RNA motifs in complex with all RRMs individually. While GACA and GACU bind unfavorably to the individual RRM3 domain, we suggest that they bind favorably to RRM3 in the context of the full-length protein. Importantly, in the context of the entire protein, we present for the first time how RRM3, in combination with additional residues in different RRM domains and linker domains, can synergistically cooperate for m6A preferential binding over adenine in the context of GACA and GACU motifs, uncovering the preferential binding of full-length RBM45 for m6A observed in previous experiments. The presence of the m6A methyl group provides further stability to the RNA, as well as strengthens the particular interactions between RNA and protein, while contributing to additional stabilization of the C-terminal domain with the linker domain between RRM2 and homo-oligomer assembly (HOA). Our simulations highlight the role of various other domains beyond RRMs (i.e., the C-terminal, HOA, and linkers between different RRMs) in the interaction of RBM45 with RNA, particularly m6A-modified RNA. Overall, our study elucidated how an RRM class of proteins can preferentially bind m6A in the context of its common motif written by methyltransferases. We consider that our study presents the first mechanistic insights into how an RRM domain binds directly and preferentially recognizes m6A over adenine in synergy with other domains, which include intrinsically disordered regions.
    DOI:  https://doi.org/10.1021/acs.jpcb.6c01856
  16. Sci Adv. 2026 May 15. 12(20): eaed7122
      TP53-mutated acute myeloid leukemia (AML) represents a particularly aggressive and therapeutically refractory subtype of the disease. While recurrent chromosomal abnormalities such as -5/del(5q), -7/del(7q), and del(17p) are well studied in this context, additional co-occurring events remain less well defined. Using the multidimensional Leucegene dataset (~700 primary AML specimens), we identified and comprehensively characterized a distinct subset of TP53-altered AML marked by recurrent deletions on the short arm of chromosome 3 [del(3p), >20% TP53-mutated cases]. These deletions frequently co-occur with del(5q) and encompass several ribosomal protein genes (RPGs), leading to a global down-regulation of the ribosomal network and reduced protein synthesis. We show that this ribosomopathy-like phenotype is most pronounced in TP53-mutated cases with combined RPG deletions on chromosomes 3p and 5q, suggesting a cooperative oncogenic mechanism. Chemical screening identified HSP90 inhibition as a selective vulnerability in AML with low RPG expression. These findings highlight a previously unappreciated TP53-altered AML subset characterized by converging genomic and translational defects and suggest that ribosomal stress may serve as a therapeutic entry point for targeted intervention of this patient subgroup.
    DOI:  https://doi.org/10.1126/sciadv.aed7122
  17. Mycologia. 2026 May 12. 1-14
      The edible fungus Aspergillus oryzae is well known for its powerful ability to secrete numerous proteolytic enzymes, such as lipases, proteases, and amylases. However, the mechanisms that regulate the translation of these enzymes in A. oryzae remain poorly understood. In this study, we investigated the biological function of the translation initiation factor eIF3j in A. oryzae. Our findings revealed that deletion of the eIF3j gene significantly inhibited mycelial growth and conidiation compared with the control strain. Furthermore, the eIF3j mutant showed increased sensitivity to various stressors relative to the control strain. Interestingly, the eIF3j-deleted strain exhibited enhanced production of amylase and kojic acid when compared with the control strain. Additional quantitative proteomic analysis suggested that eIF3j was involved in RNA processing, ribosome biogenesis, and amino acid metabolism. Taken together, these findings underscore the multifaceted role of eIF3j in A. oryzae and its potential as a target for improving traits relevant to industrial applications.
    Keywords:  Amylase; Aspergillus oryzae; kojic acid; proteome; translation initiation factor eIF3j
    DOI:  https://doi.org/10.1080/00275514.2026.2657612
  18. Nucleic Acids Res. 2026 May 05. pii: gkag452. [Epub ahead of print]54(9):
      A significant body of research has been devoted to pinpointing and cataloguing the binding sites of RNA-binding proteins (RBPs) on target transcripts. The most common techniques involve crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing. In this review, we provide a comprehensive summary of the major advancements in CLIP-based techniques and state-of-the-art data analysis methods designed for identifying and analysing the binding sites of RBPs. We also brief on methods used to determine the functional relevance of these binding sites and, in addition, delve into the major hurdles faced in the detection and elucidation of the binding sites of RBPs. Finally, we explore reproducibility concerns in the CLIP field, and conclude by suggesting potential avenues for future improvements.
    DOI:  https://doi.org/10.1093/nar/gkag452
  19. Biochem Soc Trans. 2026 May 27. 54(5): 561-569
      Haem-regulated inhibitor (HRI) is emerging as a potential therapeutic target in several disease areas, including cancers such as multiple myeloma and neurodegenerative disease. As one of four related mammalian kinases that phosphorylate the mRNA translation machinery substrate eIF2α, it has a central role in sensing several disparate proteotoxic stresses and preventing subsequent rounds of protein production. In this review, we will examine the latest research on the structural and molecular basis of HRI inhibition and activation, examining both regulatory biological interactions with proteins and cofactors. What emerges is that despite almost 75 years since the first identification of HRI, we still know remarkably little about how this kinase functions and is regulated.
    Keywords:  DELE1-CTD; HRI; ISR; eIF2alpha; haem; kinases
    DOI:  https://doi.org/10.1042/BST20250541
  20. Comput Struct Biotechnol J. 2026 ;35(1): 0090
      Background: Linezolid is a key component of treatment regimens for multidrug-resistant and extensively drug-resistant tuberculosis, which is caused by the pathogen Mycobacterium tuberculosis (MTB). Resistance to linezolid in MTB has traditionally been attributed to mutations in the 23S ribosomal RNA (rrl) and ribosomal protein L3 (rplC), but only a fraction of clinically observed linezolid resistance is explained by mutations in these 2 genes. Results: We report that an analysis of strains with paired whole-genome sequencing and linezolid minimum inhibitory concentration phenotyping from the Bacterial and Viral Bioinformatics Resource Center reveals that a relatively common frameshift mutation in MTB methyltransferase rlmN (5.3% of assessed isolates, encompassing all isolates known to be in the globally distributed MTB lineage 4.10) is significantly associated with increased linezolid minimum inhibitory concentration. In addition to statistical associations, we provide evolutionary evidence of homology to an established linezolid resistance mechanism in Staphylococcus aureus and structural evidence that the frameshift mutation likely ablates rlmN methyltransferase functionality. Conclusions: We find a novel gene associated with increased linezolid resistance in MTB, with potential implications for resistance diagnostics and therapeutic strategies.
    DOI:  https://doi.org/10.34133/csbj.0090
  21. J Mol Biol. 2026 May 08. pii: S0022-2836(26)00220-2. [Epub ahead of print] 169847
      RNA-binding proteins (RBP) interact with mRNA untranslated regions containing cis-regulatory elements to govern mRNA localization, stability, and translational efficiency. Among these trans-regulatory factors, RNA helicase UPF1 is a central factor which play a role in multiple mRNA decay pathways, including nonsense-mediated mRNA decay (NMD). NMD is triggered when an exon-junction complex (EJC) is located downstream of a premature termination codon. However, in some cases, NMD can be activated in an EJC-independent manner through mechanisms involving the 3'UTR. In the present study, we focused on the GABARAPL1 3'UTR, as previous studies had shown that this region plays a key role in NMD targeting, although the underlying molecular mechanism had not yet been elucidated. Unlike canonical NMD targets such as SC35, we found that the chemical inhibition of eIF4AIII helicase activity did not affect GABARAPL1 transcript levels, indicating that this transcript is regulated through its 3'UTR via an EJC-independent mechanism. We therefore investigated the potential presence of cis-regulatory element within the 3'UTR of GABARAPL1 which can regulate mRNA and protein levels in a UPF1-dependent manner. Furthermore, we identified a conserved RNA region spanning nucleotides 364-421 involved in GABARAPL1 targeting and used biochemical analysis to demonstrate the direct binding of UPF1 and eIF4AIII to this RNA region, to analyse its secondary structure in solution, and to map the protein-binding sites. By complementing these approaches with molecular modelling, we showed that this stem-loop adopts a stable global fold but a local flexibility and dynamic behaviour properties. Together, our results support the role of UPF1 and eIF4AIII as specific regulators of GABARAPL1 transcript and reveal a novel RNA regulatory element within its 3'UTR, which provides a completely unexpected binding site for these factors.
    Keywords:  3′UTR; GABARAPL1; UPF1; eIF4AIII; stem-loop
    DOI:  https://doi.org/10.1016/j.jmb.2026.169847
  22. Nucleic Acids Res. 2026 May 05. pii: gkag481. [Epub ahead of print]54(9):
      RNA-mediated control of virulence gene expression plays a crucial role in many pathogenic bacteria. However, our understanding of these processes in Streptococcus pneumoniae, a major human pathogen, remains limited. Here we discover a novel regulatory element located in the 3'-untranslated region (3' UTR) of the mRNA encoding a major pneumococcal virulence factor, pneumococcal surface protein A (PspA). Quantitative proteomics and western blot analysis reveal that this 3' UTR acts as a trans-acting riboregulatory element, modulating the expression of the protein chaperone, Caseinolytic protease L (ClpL), in a temperature-dependent manner. We show that it is the full-length pspA mRNA, and not the pspA-3'-located processed F5 RNA, which is involved in the regulation of ClpL expression, with the sRNA-interacting exoribonuclease Cbf1 playing an important role. Furthermore, complement deposition assays show that the regulatory pspA-3' UTR contributes to inhibition of complement C3 deposition in a PspA-independent and temperature-dependent manner. This discovery adds a new dimension to our understanding of PspA's role in bacterial virulence, highlighting an intricate layer of RNA-mediated regulation that contributes to the pathogenicity of S. pneumoniae.
    DOI:  https://doi.org/10.1093/nar/gkag481
  23. Front Cell Dev Biol. 2026 ;14 1802689
      N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in eukaryotes and serves as a key post-transcriptional regulator in insect development. This review synthesizes current knowledge on m6A in insect sexual development, beginning with its well-established role in Drosophila melanogaster, where it ensures female fate by promoting the female-specific splicing of the master switch gene Sex-lethal (Sxl). Notably, classical female-lethal genes such as Fl(2)d and Virilizer are now recognized as essential regulatory subunits of the m6A methyltransferase complex, linking classic genetics to epitranscriptomics. In insects lacking an Sxl-centric pathway, such as Coleoptera, Hymenoptera, and Lepidoptera, m6A depletion does not disrupt core sex differentiation but instead plays essential roles in related processes, including metamorphosis in Tribolium, caste differentiation in honey bees, and gametogenesis across multiple orders.These findings underscore that m6A functions extend beyond the initial sex determination switch to regulate a broad spectrum of sex-related developmental processes across insect taxa, providing insights into the evolution of epigenetic regulation.
    Keywords:  N6-methylAdenosine (m6A); alternative splicing; development; insect; sex determination
    DOI:  https://doi.org/10.3389/fcell.2026.1802689
  24. Biochim Biophys Acta Gene Regul Mech. 2026 May 07. pii: S1874-9399(26)00020-9. [Epub ahead of print] 195154
      In recent years, circular RNAs (circRNAs), a class of RNA molecules characterized by a covalently closed circular structure, have emerged as a complex family of eukaryotic transcripts with distinctive biological features. Beyond their unusual structure, which generally enhances stability by eliminating free ends, circRNAs have attracted attention because their expression is often cell- and tissue-specific and many are conserved across species. These characteristics support diverse molecular functions, including regulation through interactions with microRNAs and RNA-binding proteins (RBP), and in selected contexts, protein translation. The recognition of circRNAs has therefore added an additional layer of post-transcriptional regulation and expanded our understanding of how gene expression programs are organized across cellular states. Notably, an increasing number of studies links circRNA dynamics to differentiation and development, implicating circRNAs in the regulatory logic that governs stemness maintenance and lineage commitment. In this Review, we summarize current knowledge of circRNA biogenesis and function, highlight emerging connections between circRNAs and cell fate decisions, and discuss how these insights can inform the rational development of bioengineered circRNAs as stable yet programmable platforms to steer differentiation toward targeted cell types and support future RNA-based therapeutic strategies.
    Keywords:  Back-splicing; Circular RNA (circRNA); Differentiation; Non-coding RNAs; Stem cells
    DOI:  https://doi.org/10.1016/j.bbagrm.2026.195154
  25. bioRxiv. 2025 Jul 22. pii: 2025.07.22.666192. [Epub ahead of print]
      Microbes live in environments that fluctuate faster than they can adjust their cellular machinery. To survive these fluctuations, they must dynamically regulate protein synthesis-a resource-intensive process that is often slower than environmental changes. Here, we develop a mechanistic model coupling antibiotic kinetics with dynamic proteome allocation to understand how limitations in translational capacity shape acclimation strategies. Using translation-inhibiting antibiotics and resistance proteins, we show that the temporal mismatch between environmental perturbations (seconds) and protein synthesis responses (hours) creates a growth advantage for anticipatory strategies where cells pre-synthesize resistance proteins before antibiotic exposure. Further, we find that the largest benefits of anticipation and the largest protein fractions reserved for anticipation are realized in environments with multiple antibiotics, suggesting that anticipation is most important in complex environments. This work establishes a framework for quantifying the costs and benefits of various acclimation strategies in dynamical environments based on the fundamental constraints of protein synthesis, with implications for microbial ecology, antibiotic resistance, and biotechnology applications.
    DOI:  https://doi.org/10.1101/2025.07.22.666192
  26. FASEB J. 2026 May 31. 40(10): e71812
      The Integrated Stress Response (ISR) is a vital cellular mechanism that regulates cell survival during various stress conditions, including hypoxia. Activating transcription factor 4 (ATF4) is recognized as a key regulator of ISR, however, its role in hypoxic stress responses remain underexplored. In the present study, we generated an Atf4a-deficient zebrafish model to investigate the role of Atf4a in hypoxia tolerance, mitochondrial homeostasis, and cellular stress adaptation. The results showed that atf4a knockout led to significant growth impairment, endoplasmic reticulum and mitochondrial dysfunction, and disrupted energy metabolism, particularly under hypoxic conditions. We observed an increase in mitochondrial DNA and impaired mitochondrial morphology in Atf4a-deficient zebrafish. Metabolomic analysis revealed significant alterations in the pentose phosphate pathway and TCA cycle following atf4a knockout. Additionally, we observed increased mitochondrial oxidative stress and reduced antioxidant capacity in atf4a mutants. Atf4a-deficiency also led to decreased expression of the mitophagy-related gene p62 and parkin. Atf4a transcriptionally regulates the expression of parkin, suggesting that Atf4a regulates mitochondrial homeostasis through parkin-mediated mitophagy in zebrafish. These results underscore the critical role of Atf4a in maintaining cellular homeostasis, mitochondrial integrity, and metabolic adaptation during hypoxic stress, highlighting its potential as a therapeutic target for stress-related diseases.
    Keywords:  ATF4; ISR; hypoxia; mitophagy; parkin
    DOI:  https://doi.org/10.1096/fj.202502855R
  27. Cells. 2026 May 06. pii: 847. [Epub ahead of print]15(9):
      Chemical modifications of RNA add a dynamic regulatory layer to gene expression beyond the genome and epigenome. Among these modifications, 5-methylcytidine (m5C) has emerged as a key epitranscriptomic modification that influences RNA stability, translation, localization, and stress responses across diverse biological systems. Recent advances in high-resolution mapping and functional interrogation of m5C have revealed its involvement in development, metabolism, immune regulation, and disease pathogenesis. Notably, many of these processes are highly relevant to women's health, which is shaped by hormone-responsive tissues, reproductive transitions, and pregnancy-associated physiological adaptations. In this review, we provide a comprehensive and integrative overview of m5C RNA modification with a focus on its roles in female biology and disease. We summarize the molecular machinery responsible for m5C deposition, recognition, and regulation, as well as current detection technologies. We further highlight emerging evidence linking m5C dysregulation to early embryonic development, women-specific cancers, gynecologic and reproductive disorders, pregnancy complications, and metabolic and cardiovascular diseases. In addition, we discuss the interplay between m5C and sex hormone signaling, as well as the potential of m5C as a biomarker and therapeutic target. Finally, we identify key knowledge gaps, including the need for tissue-specific, longitudinal, single-cell, and spatial epitranscriptomic studies in women. By integrating epitranscriptomics into women's health research, this review underscores m5C as a previously underappreciated regulatory layer with significant implications for precision medicine and clinical translation.
    Keywords:  5-methylcytidine (m5C); RNA modification; biomarkers and therapeutics; cardiac remodeling; epitranscriptomics; gynecologic diseases; hormone-responsive tissues; metabolic homeostasis; placenta and pregnancy; reproductive biology; vascular disease; women’s health
    DOI:  https://doi.org/10.3390/cells15090847
  28. ACS Pharmacol Transl Sci. 2026 May 08. 9(5): 1055-1067
      Alzheimer's disease (AD) is a neurodegenerative disorder associated with cognitive decline. Pathologically, AD is characterized by the accumulation of amyloid β (Aβ) monomers that may generate oligomers or fibrils in the extracellular space and inside the neurons. With time, the oligomers and fibrils aggregate into insoluble plaques, which may trigger a cascade of molecular events. These include altering gene expression at a broader level, implicating cross-talk with the nuclear machinery, including transcription. There is now emerging evidence implicating the role of RNAs and other nuclear proteins in AD pathogenesis, especially those associated with RNA splicing and ribonucleoproteins, which, along with post-transcriptional modifications, give rise to multiple functional proteoforms. Notably, RBPs themselves exist as multiple proteoforms, adding complexity to the proteome involved in AD. Therefore, in this review, we limit the discussion to the canonical protein forms of RBPs already established to have some role in AD pathophysiology. Recently, our proteomic study identified three such RBPs (SRSF2, hnRNPH1, and hnRNPA2B1) copurifying with amyloid, suggesting a possible interaction with Aβ and contribution to AD pathology. SRSF2 is a splicing factor involved in tau exon splicing, while hnRNPH1 and hnRNPA2B1 are both heterogeneous nuclear RBPs (hnRNPs) involved in mRNA processing. Some of the other hnRNPs have previously been implicated in AD and tau pathology. This review focuses on some of the recent evidence that suggests a possible involvement of RNA-associated nuclear proteins in dysregulation of widespread RNA processing affecting the AD pathogenesis pathways. We discuss how their dysfunction could modulate Aβ and tau-associated changes with an emphasis on understanding the linkage between nuclear RNA machinery and AD pathophysiology. Understanding this crosstalk may offer new insights into our understanding of AD and could provide RNA-centric therapeutic avenues.
    Keywords:  Alzheimer’s disease; RNA-binding proteins (RBPs); SRSF2; TDP43; U1-70K; heterogeneous nuclear ribonucleoproteins (hnRNPs)
    DOI:  https://doi.org/10.1021/acsptsci.6c00028
  29. Cell Signal. 2026 May 09. pii: S0898-6568(26)00236-6. [Epub ahead of print]145 112583
      Kidney disorders, including acute kidney injury (AKI), chronic kidney disease (CKD), diabetic nephropathy (DN), and clear cell renal cell carcinoma (ccRCC), represent major causes of morbidity and mortality worldwide and remain significant challenges in clinical management because of their complex pathogenesis and limited therapeutic options. Recent advances in epitranscriptomics have highlighted RNA methylation as an important post-transcriptional regulatory mechanism involved in renal physiology and disease development. Diverse RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), and 3-methylcytidine (m3C), dynamically regulate RNA metabolism by affecting transcript stability, translation, splicing, and degradation. Increasing evidence demonstrates that RNA methylation regulators, including methyltransferases such as METTL3 and METTL14, demethylases such as FTO and ALKBH5, and reader proteins such as YTH domain-containing family members, participate in multiple pathogenic processes, including inflammation, fibrosis, oxidative stress, metabolic dysregulation, and tumor progression in renal disorders. Aberrant expression of these regulators has been closely associated with disease severity and progression. In this review, we summarize current knowledge regarding major RNA methylation modifications and their regulatory machinery in a spectrum of kidney diseases, with particular emphasis on the molecular mechanisms through which RNA methylation influences renal injury and repair. We further discuss the emerging value of RNA methylation-related molecules as potential biomarkers and therapeutic targets, aiming to provide new insights into epitranscriptomic regulation in kidney disease and its translational potential.
    Keywords:  Clinical significance; Epitranscriptomic regulation; Kidney diseases; Molecular mechanisms; RNA methylation
    DOI:  https://doi.org/10.1016/j.cellsig.2026.112583
  30. bioRxiv. 2026 Feb 23. pii: 2026.02.21.707190. [Epub ahead of print]
      Aggressive subtypes of acute myeloid leukemia (AML) are characterized by increased migratory behavior and poor prognosis prioritizing the need for uncovering relevant mechanisms. While attributed to transcriptional changes, these AMLs manifest dysregulated eIF4E implicating disrupted mRNA metabolism. Here, we observed in AML mouse models, patient specimens, and cell lines that eIF4E drives motility, colonization, engraftment and AML progression. AML cells migrate utilizing Ezrin-positive pseudopods. Unexpectedly, we discovered that eIF4E interacts with Ezrin, that these physically associated factors are required and cooperated to drive an on-demand translation program in pseudopods for motility. Indeed, pseudopods were sites of eIF4E- and Ezrin-dependent translation by implementing the first method to directly mark active ribosomes in situ ( Vis ualizing T ranslation A ctivity using R iboLace, VISTA-R). Biochemically, Ezrin bound eIF4E, ribosomal components, and mRNAs consistent with our observed Ezrin-dependent modulation of protein production. This unprecedented physical coupling of motility and translation provisions migratory sites to sustain AML progression.
    Highlights: eIF4E reduction impairs AML cell motility and disease progressioneIF4E-dependent motility requires EzrinEzrin binds eIF4E, transcripts encoding motility factors and active ribosomesVISTA-R enabled visualization of active ribosomes and translationally active pseudopods (T-PODs)T-PODs provide novel on-demand localized translation to sustain mobility at migratory sites.
    DOI:  https://doi.org/10.64898/2026.02.21.707190
  31. Brain Circ. 2026 Apr-Jun;12(2):12(2): 133-143
       BACKGROUND: Heme-regulated inhibitor (HRI/EIF2AK1) is a protein kinase that initiates the integrated stress response (ISR) following mitochondrial damage and/or oxidative stress. Dependent on a context, ISR may promote death or recovery of cells under stress. This study was initiated to determine HRI contributions to brain damage after experimental intracerebral hemorrhage (ICH) where oxidative toxicity of hemoglobin is a major trigger of neural cell loss.
    MATERIALS AND METHODS: Publicly available transcriptomic data from a mouse model of ICH were analyzed using standard bioinformatic tools. Hri-/- and wild-type control mice were subjected to unilateral collagenase-induced ICH followed by evaluation of forelimb functional deficits (adhesive tape removal), brain histology (Fluoro-Jade B staining of degenerating neurons and immunofluorescence for GFAP and CD36), and extravasated brain hemoglobin assays. Tail bleeding time and platelet number were determined to assess hemostasis.
    RESULTS: ISR transcripts were robustly overrepresented in the transcriptome of the peri-hematoma region of wild-type mice at 1-day post-ICH induction, suggesting acute ISR activation. After ICH, Hri-/- mice showed greater impairment of forelimb function and exacerbated brain damage as indicated by increases of (1) GFAP-negative lesion area, (2) number of degenerating neurons, and (3) signal area of the activated macrophage marker CD36. These effects correlated with acute increases of hemoglobin extravasation, lower platelet counts, and prolonged tail bleeding.
    CONCLUSIONS: While ISR is activated by ICH and may play a role in secondary injury, impaired hemostasis is a likely driver of enhanced ICH severity in Hri-/- mice.
    Keywords:  Hemostasis; integrated stress response; intracerebral hemorrhage; neuroprotection; secondary injury
    DOI:  https://doi.org/10.4103/bc.bc_163_24
  32. Dev Dyn. 2026 May 10.
       BACKGROUND: Elp1, a subunit of the Elongator complex, is essential for tRNA modification and neuronal development. Mutations in ELP1 underlie familial dysautonomia (FD), a disorder marked by sensory and autonomic neuropathy. While loss of Elp1 disrupts trigeminal ganglion formation and survival, the downstream molecular consequences remain poorly defined.
    RESULTS: We performed quantitative proteomic profiling of trigeminal ganglia from Elp1 conditional knockout (CKO) and control embryos at E13.5. Across 5650 detected proteins, 25 were significantly up-regulated and 26 down-regulated in Elp1 CKO embryos. EnrichR analysis revealed enrichment of up-regulated proteins in amino acid transport and tRNA aminoacylation pathways, with links to neuromuscular and neuropathic diseases. Down-regulated proteins were associated with RNA modification, cholesterol biosynthesis, and synaptic organization. Validation by immunohistochemistry confirmed decreased expression of the neurotrophic receptor Gfra3 and the neuropeptide Galanin, and increased levels of the chromatin regulator Chd1, in Elp1 CKO embryos relative to controls.
    CONCLUSIONS: These findings demonstrate that Elp1 loss disrupts metabolic, RNA modification, and neurotrophic signaling pathways in the developing trigeminal ganglion. Proteomic analysis thus provides new insight into the molecular consequences of Elp1 deficiency and highlights candidate mechanisms contributing to sensory neuron vulnerability in FD.
    Keywords:  Elp1; elongator; familial dysautonomia; proteomics; trigeminal ganglion
    DOI:  https://doi.org/10.1002/dvdy.70145
  33. PLoS Pathog. 2026 May 13. 22(5): e1014007
      Inhibiting the activation of hepatic stellate cells (HSCs) represents a key therapeutic strategy for alleviating liver fibrosis induced by schistosomiasis. Diverse cell populations secrete pro-inflammatory cytokines and chemokines, which induce HSC activation and thereby promote hepatic fibrosis progression. Tristetraprolin (TTP) exerts a pivotal role in the post-transcriptional regulation of pro-inflammatory cytokines by either accelerating mRNA degradation or suppressing translation, a regulatory mechanism closely associated with the pathogenesis of various hepatic disorders. However, the pathological roles of TTP in Schistosoma japonicum-induced liver fibrosis remain largely elusive. Here, we report that TTP is upregulated in the liver during S. japonicum-induced liver fibrosis, and its overexpression markedly ameliorates this fibrotic pathology in vivo. We further identify that TTP negatively regulates TGF-β1 mRNA stability by promoting N6-methyladenosine (m6A) RNA methylation, thereby inhibiting HSC activation. Mechanistically, TTP enhances transcription of the WT1-associated protein (WTAP) gene through its interaction with SMAD2/3. Furthermore, treatment with an m6A RNA methylation inhibitor confirms that TTP-mediated protection against S. japonicum-induced liver fibrosis, an effect associated with increased m⁶A RNA methylation in vivo. Thus, our findings uncover a novel and critical role of TTP in exerting its anti-fibrotic function via the WTAP/m6A epitranscriptomic machinery in the pathogenesis of S. japonicum-induced liver fibrosis. This finding provides a rationale for the therapeutic targeting of TTP-mediated m6A RNA methylation in S. japonicum-induced liver fibrosis.
    DOI:  https://doi.org/10.1371/journal.ppat.1014007
  34. Cells. 2026 Apr 23. pii: 755. [Epub ahead of print]15(9):
      CARP-1, a perinuclear phospho-protein, is a biphasic regulator of cell survival and apoptosis signaling. We previously found that UV cross-linking of proteins from HeLa cervical cancer cells resulted in STAT3 interacting with the CARP-1 (614-638) peptide. Mutagenesis and co-IP-WB experiments revealed that CARP-1 interacts with a 40-amino-acid epitope from positions 441-480 (CE Epitope) located in the STAT3 DNA-binding domain. Overexpression of mutant STAT3 with in-frame deletion of the CE epitope (Gst-STAT3 (ΔCE) mutant), but not Gst-STAT3 (WT), failed to translocate to the nucleus in IL-6-treated cells. The small GTPase p21Rac1 interacts with and regulates STAT3 activation and nuclear translocation. Here we report the interaction of p21Rac1 with the CE epitope of STAT3 and the CARP-1 (600-650) region, suggesting that CARP-1 is part of a dynamic STAT3-p21Rac1 complex that functions in STAT3 activation and nuclear translocation. Expression of a STAT3 (ΔCE) mutant abolished STAT3 Y705 phosphorylation in cells that were treated with EGF or IL-6. Fine mapping revealed that scrambling the CE epitope peptide or a small peptide from positions 456-465 within the CE epitope resulted in abrogation of STAT3 Y705 phosphorylation by IL-6. Moreover, STAT3 phosphorylation by EGF or IL-6 was diminished in multiple CARP-1 null cancer cells. Importantly, incubation of a TAT-tagged STAT3 (454-467) peptide but not its scrambled version resulted in a reduction in STAT3 Y705 phosphorylation by IL-6/EGF. Taken together, our data demonstrates that the STAT3 CE epitope interacts with CARP-1 and p21Rac1, harbors novel sequences that activate STAT3 and promotes its nuclear translocation by IL-6/EGF.
    Keywords:  CARP-1/CCAR1; EGF; IL-6; STAT3; p21Rac1
    DOI:  https://doi.org/10.3390/cells15090755
  35. Anim Biosci. 2026 May 07.
      Improving nitrogen (N) efficiency in dairy production systems is important due to environmental concerns and the economic cost of dietary protein. A substantial proportion of dietary N consumed by lactating dairy cows is not converted into milk protein and is instead excreted in urine and consequently manure. Advances in protein nutrition have shifted feeding strategies from CP-based approaches toward metabolizable protein and, more recently, amino acid (AA)-based systems designed to better match absorbed AA supply with animal needs. This review synthesizes current knowledge on AA nutrition in lactating dairy cows, with emphasis on the biological regulation of milk protein synthesis, identification of limiting AA, and opportunities to improve N utilization efficiency through more precise diet formulation. Absorbed AA originate primarily from microbial protein synthesized in the rumen and rumen-undegraded feed protein digested postruminally, and the relative contribution of these sources influences both the quantity and profile of AA available for metabolism. Milk protein synthesis is regulated not only by AA supply but also by energy availability, endocrine signaling, and tissue nutrient partitioning. Among individual AA, methionine, lysine, and histidine are most consistently associated with limitations to milk protein synthesis in dairy cows under common feeding conditions. Evidence indicates that balancing diets for these AA can increase milk protein yield, improve feed N conversion into milk N, and allows reductions in dietary crude protein without compromising production. However, practical implementation of AA-based feeding strategies remains constrained by limitations in predicting microbial protein synthesis and postruminal AA supply. Nutritional models provide useful tools for evaluating AA adequacy, but prediction errors and biological variability require that model outputs be interpreted alongside production responses and metabolic context. Overall, improved alignment of AA supply with metabolic demand represents a key strategy for enhancing productivity while reducing environmental N losses in dairy production systems.
    Keywords:  Amino acids; Dairy cattle; Histidine; Lysine; Methionine; Nitrogen utilization
    DOI:  https://doi.org/10.5713/ab.260271
  36. Front Mol Biosci. 2026 ;13 1844239
      
    Keywords:  RNA; homeostasis; post-transcriptional control; stress response; transcriptional regulation
    DOI:  https://doi.org/10.3389/fmolb.2026.1844239
  37. Int J Mol Sci. 2026 Apr 27. pii: 3871. [Epub ahead of print]27(9):
      Mitochondria are increasingly recognized as multifunctional organelles that integrate metabolic, redox, immune, and cell fate signaling, thereby maintaining cellular and tissue homeostasis under physiological conditions. Beyond their classical role in ATP production, mitochondria act as central regulatory hubs coordinating adaptive responses to metabolic demands and environmental stress. These functions are sustained through tightly regulated quality control mechanisms, including mitochondrial biogenesis, dynamic fusion-fission remodeling, redox signaling, and selective removal of damaged organelles via mitophagy. Disruption of these processes compromises cellular resilience and contributes to disease initiation and progression. This review summarizes and critically evaluates current evidence on mitochondrial function in health and its dysregulation in pathological conditions, with a particular focus on rheumatoid arthritis (RA), ischemic stroke (IS), and autism spectrum disorder (ASD). Despite their distinct clinical manifestations, these disorders share convergent mitochondrial abnormalities, including metabolic reprogramming toward glycolysis, excessive or persistent reactive oxygen species production, impaired mitophagy, mitochondrial DNA-driven innate immune activation, and hypoxia-related stress. In RA, mitochondrial dysfunction sustains chronic inflammation and joint destruction; in IS, acute mitochondrial failure and reperfusion-associated oxidative stress drive neuronal injury; and in ASD, mitochondrial metabolic inflexibility and defective quality control contribute to chronic low-grade inflammation and neurodevelopmental vulnerability. A variety of methods for the assessment of mitochondrial function are available to study these pathological conditions. Collectively, these findings position mitochondrial dysfunction as a unifying pathogenic mechanism linking inflammatory, neurodegenerative, and neurodevelopmental processes. Targeting mitochondrial metabolism, redox balance, and quality control pathways therefore represents a promising cross-disease therapeutic strategy.
    Keywords:  autism spectrum disorder; ischemic stroke; mitochondrial function; rheumatoid arthritis
    DOI:  https://doi.org/10.3390/ijms27093871
  38. Mol Biol Rep. 2026 May 12. pii: 745. [Epub ahead of print]53(1):
      Drosophila melanogaster provides a genetically tractable and evolutionarily conserved platform for interrogating mechanisms of human neurodegeneration. This revised review critically evaluates how transgenic and genome-edited fly models expressing amyloid-beta, tau, alpha-synuclein, mutant huntingtin, and patient-relevant variants reproduce selective aspects of Alzheimer's disease, Parkinson's disease, and polyglutamine disorders, while also highlighting the boundaries of translational inference. We emphasize conserved pathogenic modules, including oxidative stress, mitochondrial dysfunction, impaired proteostasis, and stress signaling through Nrf2, JNK, and PINK1/Parkin, and distinguish robust mechanistic insights from findings that are primarily descriptive or overexpression-driven. We further discuss the specific contribution of Drosophila genetic tools such as GAL4/UAS, RNA interference, CRISPR-Cas9, and FLP/FRT-based mosaic analysis for dissecting cell-autonomous and non-cell-autonomous neurotoxicity. To improve usability, the manuscript now summarizes major disease models and natural compounds in dedicated tables, expands therapeutic discussion to include HDAC inhibitors and mitochondria/redox-directed small molecules, and outlines how fly studies can function within translational pipelines for variant interpretation, target prioritization, and preclinical triage before mammalian validation and human trials. Finally, we address key limitations of Drosophila relative to humans, including differences in metabolism, blood-brain barrier properties, immune complexity, and disease timescale, to provide a more balanced framework for using fly neurodegeneration models in precision medicine.
    Keywords:   Drosophila melanogaster ; Alzheimer’s disease; Antioxidants; Genetic modeling; Neurodegeneration; Oxidative stress; Parkinson’s disease; Precision medicine
    DOI:  https://doi.org/10.1007/s11033-026-11844-5
  39. Curr Med Chem. 2026 May 08.
      Lysine succinylation is a dynamic post-translational modification that alters protein structure and function by adding a succinyl group to lysine residues. This review first presents current evidence on the discovery of lysine succinylation and its regulatory enzymes, and then focuses on its roles in diabetes and its complications. We summarize that succinylation is potentially governed by writers (HAT1), erasers (SIRT5), and readers (GAS41), linking metabolic state to signaling and epigenetic regulation. Dysregulation of succinylation is associated with mitochondrial dysfunction, oxidative stress, and insulin resistance in key metabolic tissues, including the pancreas, liver, kidney, and heart. However, most studies remain correlative, and mechanistic insights into site-specific modifications are limited. The identities of bona fide succinyltransferases and dedicated reader domains are still uncertain, and tissue-specific regulatory networks in diabetes require further exploration. By synthesizing these findings, this review aims to inspire scientists to explore the succinylome to deepen our understanding of diabetic pathophysiology and identify novel therapeutic strategies.
    Keywords:  Post-translational modification; SIRT5; acylation; complications; diabetes; review.; succinylation
    DOI:  https://doi.org/10.2174/0109298673447130260302035115
  40. J Physiol Biochem. 2026 May 11. pii: 50. [Epub ahead of print]82(1):
      Muscle wasting, prevalent in various pathological conditions including cancer, cardiac dysfunction, and neurodegeneration, is typified by sustained protein depletion in muscle and a compromised ability of the tissue to repair and regenerate effectively. Triggered by disruptions in protein folding in the endoplasmic reticulum (ER), the unfolded protein response (UPR) represents a key regulatory system that sustains intracellular proteostasis under conditions of stress. While the UPR is crucial for cellular survival, prolonged activation or dysfunction of the pathway can contribute to muscle atrophy and the progression of muscle wasting diseases. Recent evidence suggests that exercise, through its impact on cellular stress responses, can modulate the UPR in muscle cells, promoting a protective response that enhances protein folding capacity, reduces ER stress, and stimulates muscle regeneration. This review explores how exercise influences the UPR in muscle cells, focusing on the activation of key UPR sensors, including IRE1, PERK, and ATF6, and their downstream effects on protein quality control, autophagy, and muscle fiber maintenance. We also examine the role of exercise in promoting adaptive responses in muscle cells, including increased mitochondrial function, autophagy, and the activation of stress resistance pathways, all of which can counteract muscle wasting. The review also emphasizes exercise as an effective strategy to influence ER stress pathways and attenuate muscle atrophy associated with pathological conditions, offering critical insights into the molecular benefits of physical activity for muscle preservation.
    Keywords:  Autophagy; Endoplasmic reticulum stress; Exercise; Muscle wasting; Unfolded protein response
    DOI:  https://doi.org/10.1007/s13105-026-01190-2
  41. Environ Sci Pollut Res Int. 2026 May 11.
      Climate change and environmental pollution are two primary challenges facing biodiversity and ecosystem stability. Earthworms are key contributors to soil structure and nutrient cycling, and their molecular stress responses can provide an early indication of soil health impairment. Heat shock proteins are central to the stress response, and small heat shock proteins (sHSPs) are ATP-independent chaperones that limit stress-induced protein aggregation. Because their expression is stress-sensitive, sHSPs are promising molecular markers for soil stress and contributors to thermotolerance. Eisenia fetida, a widely used ecotoxicology model, relies on molecular chaperones like small heat shock proteins (sHSPs) for stress tolerance. We previously characterized sHSPs containing a single α-crystallin domain (ACD) in E. fetida. Here, we report the first identification of sHSPs containing two α-crystallin domains (ACDs) in annelid species. These genes were identified from an E. fetida transcriptome, their domain architecture was defined, and their transcriptional responses were quantified under heat stress, desiccation, and exposure to two pollutants (bisphenol A and endosulfan), including combined exposure with elevated temperature. Double-ACD sHSPs showed stimulus- and time-dependent transcriptional patterns. Moderate heat and desiccation primarily induced late (24 h) upregulation of several sHSP genes, whereas bisphenol A at optimal temperature did not result in significant transcriptional change and endosulfan produced only limited changes under single-stressor exposure. In contrast, combined exposure to endosulfan and elevated temperature triggered a significant upregulation of multiple sHSP genes, consistent with an additive stress effect. These results expand this protein family diversity in annelids and support a staged sHSP response in which structurally distinct sHSPs may contribute to resilience under prolonged or combined environmental stress.
    Keywords:  Adaptation; Climate change; Earthworms; Environmental stress; Heat shock response; Stress biomarkers
    DOI:  https://doi.org/10.1007/s11356-026-37811-y
  42. Planta. 2026 May 11. pii: 151. [Epub ahead of print]263(6):
       MAIN CONCLUSION: Great progress has been made in understanding the mechanisms of floral induction based on physiology and molecular genetics, whereas recent research suggests that future developments will come from protein biochemistry, genomics, imaging, and mathematical modeling. During the twentieth century, plant physiologists showed how the developmental transition from vegetative growth to flowering is controlled by environmental cues, such as day length and temperature. They defined a number of interesting questions such as the identity of the signal induced in response to day length in leaves that is translocated to the shoot meristem to induce flowering, and the mechanism by which plants sense and remember exposure to winter temperatures. Application of molecular-genetics approaches from the 1990s identified regulatory proteins and small RNAs that control these responses, first in Arabidopsis and later in several crops. These advances identified a series of new questions. In this Perspective article, I highlight some of these issues and select some recent papers that show how protein biochemistry, genomics, imaging, and mathematical modeling address these questions, and will in turn improve our understanding of the mechanisms of floral induction.
    Keywords:  Florigen; Flowering regulators; Quantitative models; Transcription factors; Vernalization
    DOI:  https://doi.org/10.1007/s00425-026-05018-7
  43. Life Sci. 2026 May 09. pii: S0024-3205(26)00260-2. [Epub ahead of print]398 124451
      Acute kidney injury (AKI) is the most frequent renal complication, characterized by a rapid and severe loss of kidney function. Given its high incidence and strong propensity to progress into chronic kidney disease (CKD), a deeper insight into its molecular pathology is critical for the development of more effective therapies. In this review, we offer a novel conceptual framework illustrating how diverse AKI triggers induce oxidative stress-driven protein damage, which can exceed the capacity of endogenous protein quality control systems, ultimately promoting proteotoxic stress and renal tubular epithelial cells (RTECs) demise. Importantly, we emphasize the central role of proteotoxicity in shaping the core features of unresolved AKI such as tubular cast formation, impaired proliferation and differentiation of surviving RTECs, mitochondrial and metabolic dysfunction in RTECs. Through this discussion on the relevance of proteotoxicity to the major molecular mechanisms underlying AKI, we highlight its central role in regulating renal tubular epithelial cell fate-balancing survival and death under AKI conditions-and propose that sustained proteotoxic stress may serve as a critical link driving the transition from AKI to CKD. We further outline experimental approaches to identify RTEC proteins susceptible to aggregation during AKI and discussed emerging therapeutic strategies aimed at enhancing their clearance. By delineating key mechanisms linking RTEC proteotoxic stress to cell survival and repair, we aim to spotlight this underexplored dimension of AKI biology, inspiring future research and therapeutic innovation to alleviate AKI burden and hinder AKI-to-CKD progression.
    Keywords:  Acute kidney injury; Autophagy; Chronic kidney disease; Protein quality control; Proteotoxicity; Renal tubular epithelial cells
    DOI:  https://doi.org/10.1016/j.lfs.2026.124451