bims-mirnam 2025-11-02 papers

bims-mirnam

Biomed News

on Mitochondrial RNA metabolism

Issue of 2025–11–02
sixteen papers selected by
Hana Antonicka, McGill University

YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly.
Substrate recognition by the human mitochondrial processing peptidase and its processing of PINK1.
Mixed Messages: Dynamic and Compositional Heterogeneity of Nuclear Messenger Ribonucleoprotein (mRNP) Complexes.
BioLLMNet: enhancing RNA-interaction prediction with a specialized cross-LLM transformation network.
Cytosine methylase and hydroxymethylase activity in mammalian mitochondria.
RNA Granules at the Crossroads of Synaptic Dysfunction and Neurodegeneration.
TERT translocation to mitochondria: Exploring its role in mitochondrial homeostasis.
Transcriptome Analysis Reveals Gemykibivirus Infection Induces Mitochondrial DNA Release in HEK293T Cells.
Coronaviruses remodel the mature human tRNAome to modulate infection.
Protein-Centric Mapping of RNA-DNA Interactions with RedChIP.
Heterogenous mitochondrial ultrastructure and metabolism of human glioblastoma cells: differences between stem-like and differentiated cancer cells in response to chemotherapy.
RNA Degradation in Pluripotent Stem Cells: Mechanisms, Crosstalk, and Fate Regulation.
mRNA Stability: An Unresolved Challenge for Broad Therapeutic Applications.
Mitochondrial Translation Inhibition Triggers an Rst2-Controlled Transcriptional Reprogramming of Carbon Metabolism in Stationary-Phase Cells of Fission Yeast.
Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases.
Expanding the Clinical and Molecular Spectrum of Primary Autosomal Recessive Microcephaly: Novel CDK5RAP2 Gene Variants and Functional Insights on the Intronic Variants.

Nucleic Acids Res. 2025 Oct 28. pii: gkaf1071. [Epub ahead of print]53(20):

YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly.

Amal Seffouh, Dominic Arpin, Kaustuv Basu, Joaquin Ortega.

The maturation of the functional core of the 50S ribosomal subunit in Bacillus subtilis is assisted by assembly factors that enhance the efficiency of the process. Two essential assembly factors, the GTPases RbgA and YphC, bind at or near the functional sites of the 50S subunit to promote the folding of ribosomal RNA helices that play key functional roles. YsxC is another GTPase involved in the maturation of the 50S subunit, whose function remains unknown. We demonstrate that YsxC aids 50S assembly through a drastically different mechanism. YsxC binds in the body of the 44.5S large ribosome assembly intermediate, occupying the site where uL2 binds and controls the timing in the folding of rRNA helices forming the binding site for uL2. It creates a "primordial" binding site that includes six out of the eleven rRNA helices forming the uL2 mature binding site. Once YsxC is released, uL2 binds to this "primordial" binding site, and the remaining helices that stabilize uL2 fold, and the entire region adopts the mature conformation. This role of YsxC functioning as a placeholder factor for ribosomal protein uL2 provides the first example of such a factor's involvement in the ribosome assembly process in bacteria.

DOI: https://doi.org/10.1093/nar/gkaf1071
J Biol Chem. 2025 Oct 27. pii: S0021-9258(25)02712-7. [Epub ahead of print] 110860

Substrate recognition by the human mitochondrial processing peptidase and its processing of PINK1.

Andrew N Bayne, Danielle M Simons, Naoto Soya, Karl Grenier, Gergely L Lukacs, Edward A Fon, Jean-François Trempe.

  Nuclear-encoded mitochondrial proteins rely on N-terminal targeting sequences (N-MTS) for their import. Most N-MTSs are cleaved in the matrix by the mitochondrial processing peptidase (MPP), a heterodimeric metalloprotease composed of (α) and catalytic (β) subunits, essential for the maturation of imported proteins. Import and processing of PINK1, a kinase implicated in Parkinson's disease, govern its ability to sense mitochondrial damage. The current paradigm suggests PINK1 undergoes two sequential processing steps: first, MPP removes the PINK1 N-MTS in the matrix; second, the inner mitochondrial membrane protease PARL cleaves the PINK1 transmembrane domain, leading to PINK1 degradation. Upon depolarization, PINK1 escapes proteolysis and accumulates on mitochondria to initiate mitophagy. However, the MPP cleavage site on PINK1, the role of MPP in PINK1 signalling, and the mechanisms of substrate recognition by human MPP remain unclear. Here, we define the MPP cleavage site on PINK1 between Ala28-Tyr29 and show it is inefficiently processed compared to canonical N-MTSs. In cells, MPP cleavage is dispensable for both PARL processing and PINK1 function, decoupling PINK1 import and damage sensing from its N-MTS removal. However, in vitro, the PINK1 N-MTS binds potently to MPP, inhibits the cleavage of other substrates, and traps MPP in a slowly processing complex. Exploiting PINK1 as a mechanistic probe, we use hydrogen-deuterium exchange mass spectrometry to map the PINK1 binding site on MPPα. We identify a two-step mechanism involving MPPα lid rearrangement followed by active site engagement, providing key insight into PINK1's unique import pathway and fundamental MPP processing mechanisms.

Keywords:  PTEN-induced putative kinase 1 (PINK1); Parkinson disease; hydrogen-deuterium exchange; mitochondria; mitochondrial processing peptidase (MPP); protein import; protein processing

DOI:  https://doi.org/10.1016/j.jbc.2025.110860
Wiley Interdiscip Rev RNA. 2025 Nov-Dec;16(6):16(6): e70032

Mixed Messages: Dynamic and Compositional Heterogeneity of Nuclear Messenger Ribonucleoprotein (mRNP) Complexes.

Theresa Wechsler, Ryuta Asada, Ben Montpetit.

  Messenger ribonucleoprotein (mRNP) complexes assemble co-transcriptionally in the nucleus as RNA-binding proteins (RBPs) engage nascent transcripts. Ongoing RNA processing and RBP dynamics generate a diverse set of mRNPs, often producing a mature mRNA-capped, spliced, and polyadenylated-within a compact mRNP particle poised for nuclear export. The processing, packaging, and export of nuclear mRNPs are tightly regulated to ensure the fidelity of gene expression and to reprogram cellular function under changing organismal and environmental conditions. Understanding the compositional and organizational dynamics of nuclear mRNP assembly and maturation is essential, as dysregulation is linked to viral infections and a range of human diseases, including neurological disorders and cancer. Recent structural, biochemical, and in-cell studies have revealed key roles for the evolutionarily conserved Yra1/ALYREF proteins and the TRanscription-EXport (TREX) complex in mRNP packaging and export, highlighting broadly conserved functions across eukaryotes. While many questions remain, these advances have deepened our understanding of nuclear mRNA metabolism and offer new opportunities to investigate how disruptions in mRNA biogenesis and export factors, and their associated processes, contribute to disease. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Export and Localization > Nuclear Export/Import.

Keywords:   Saccharomyces cerevisiae ; ALYREF; RBP; RNA‐binding protein; THO; TREX; Yra1; gene expression; mRNA; mRNP

DOI:  https://doi.org/10.1002/wrna.70032
Brief Bioinform. 2025 Aug 31. pii: bbaf549. [Epub ahead of print]26(5):

BioLLMNet: enhancing RNA-interaction prediction with a specialized cross-LLM transformation network.

Abrar Rahman Abir, Md Toki Tahmid, Md Shamsuzzoha Bayzid.

  Ribonucleic acids (RNAs) play a central role in cellular processes by interacting with proteins, small molecules, and other RNAs. Accurate prediction of these interactions is critical for understanding post-transcriptional regulation and advancing RNA-targeted therapeutics. However, existing computational methods are limited by their reliance on hand-crafted features, modality-specific architectures, and often require structural or physicochemical data, which are experimentally challenging to obtain and unavailable for many RNA molecules. These constraints hinder generalizability and fail to capture the complex, context-dependent semantics of RNA interactions. We present BioLLMNet, a unified sequence-only framework that leverages pretrained biological language models to encode rich, contextualized representations for both RNA molecules and their interacting partners, including proteins, small molecules, and other RNAs. Our key innovation is the introduction of a novel learnable gating mechanism, which dynamically computes feature-wise weights to adaptively integrate multimodal embeddings based on input context. This mechanism, proposed here for the first time in RNA interaction modeling, enables the model to emphasize the most informative features from each partner and achieves seamless fusion of heterogeneous modalities. As a result, BioLLMNet represents a unified framework and can flexibly and consistently model all three types of interaction (RNA-protein, RNA-small molecule, and RNA-RNA) within a shared architecture, eliminating the need for modality-specific designs. Comprehensive evaluations on benchmark data sets demonstrate that BioLLMNet achieves state-of-the-art performance across all three types of interaction. Our results underscore the power of language model-based representations combined with dynamic feature fusion for generalizable, modality-aware RNA interaction prediction.

Keywords:  RNA interaction prediction; biological language models; multimodal representation learning

DOI:  https://doi.org/10.1093/bib/bbaf549
Front Cell Dev Biol. 2025 ;13 1677402

Cytosine methylase and hydroxymethylase activity in mammalian mitochondria.

Lisa S Shock, Prashant V Thakkar, Jason M Robinson, Shirley M Taylor.

   Introduction: Mitochondria are integral components of eukaryotic cells, functioning as energy powerhouses and key mediators of diverse metabolic and signaling cascades. As endosymbiotic remnants, these unique organelles retain and express their own DNA. Mitochondrial DNA (mtDNA) is packaged into DNA-protein complexes called nucleoids, and is also subject to epigenetic modification. We identified a mitochondrial isoform of DNA methyltransferase 1 (mtDNMT1) that binds to mtDNA in critical control regions; however, its enzymatic activity remained unexplored.
Results: Here, we show that endogenously-tagged mtDNMT1 purified from mitochondria exhibits time- and concentration-dependent CpG-specific DNA methyltransferase activity, but it is not working alone: DNMT3b cooperates with mtDNMT1 to methylate mtDNA and regulate mitochondrial transcription. In addition, we detect ten-eleven translocase (TET)-like hydroxymethylase activity in mitochondria, demonstrating that mechanisms for both writing and erasing 5-methylcytosine marks are functional in this organelle. CRISPR/Cas9-mediated inactivation of mtDNMT1 and/or DNMT3b activity resulted in a stepwise decrease in mitochondrial methylation across the heavy and light strand promoters of mtDNA, with a significant reduction in transcription of several mtDNA-encoded OXPHOS genes. Interestingly, the effects of mtDNA methylation on mitochondrial transcription are diametrically opposed to the role of promoter methylation in the nucleus, suggesting a novel mode of gene regulation in mitochondria. Cells lacking mtDNMT1 and/or DNMT3b also exhibited a modest reduction in mtDNA content, suggesting that methylation impacts both mtDNA transcription and replication.
Discussion: These observations implicate mtDNA methylation in the fine-tuning of mitochondrial function and suggest a role for aberrant mitochondrial methylase activity in disease.

Keywords:  DNA demethylation; DNA methylation; DNA methyltransferase; DNA replication; epigenetics; mitochondrial DNA (mtDNA); transcription

DOI:  https://doi.org/10.3389/fcell.2025.1677402
J Neurochem. 2025 Nov;169(11): e70269

RNA Granules at the Crossroads of Synaptic Dysfunction and Neurodegeneration.

Rita Nóbrega-Martins, Beatriz Barros-Santos, Georgia Papadimitriou, Ioannis Sotiropoulos, Benjamin Wolozin, Joana Margarida Silva.

  RNA granules are dynamic, membraneless organelles essential for the spatial and temporal regulation of mRNA metabolism, particularly in neurons, where local protein synthesis supports synaptic plasticity and function. This review explores the diverse types of RNA granules (e.g., transport granules, stress granules, and processing bodies), their formation mechanisms, molecular composition, and relevance to synaptic physiology. We focus on the central role of RNA-binding proteins (RBPs) in orchestrating granule dynamics and their fine-tuning of synaptic responses under both physiological and stress conditions. Mounting evidence implicates the dysfunction of RNA granules in neurodegenerative diseases. Altered phase separation, RBP aggregation, and persistent stress granules contribute to the formation of pathological RNA granules that interfere with local translation and synaptic maintenance. Key RBPs, including TDP-43, FUS, and TIA-1, are frequently misregulated in disease contexts. Furthermore, Tau is a multifunctional protein traditionally associated with microtubule stabilization but is increasingly recognized for its role in the translational stress response, which includes RBP mislocalization and RNA granule disruption. We examine how chronic stress can exacerbate these mechanisms, acting as an environmental trigger of synaptic vulnerability associated with neurodegeneration. In summary, we explore a conceptual framework connecting RNA granule dysregulation, Tau pathology, and local translation disruption, three processes that converge on synaptic impairment, a central feature of many neurodegenerative diseases characterized by abnormal Tau. Investigating this triad presents a promising avenue for understanding disease mechanisms and identifying novel therapeutic targets that aim to restore RNA metabolism, prevent toxic Tau interactions, and preserve synaptic health.

Keywords:  RNA‐binding proteins; neurodegeneration; stress granules; synaptic dysfunction; tau pathology

DOI:  https://doi.org/10.1111/jnc.70269
PLoS Genet. 2025 Oct 27. 21(10): e1011923

TERT translocation to mitochondria: Exploring its role in mitochondrial homeostasis.

Jessica Marinaccio, Erica Rossi, Emanuela Micheli, Ion Udroiu, Nicolò Baranzini, Gaia Marcolli, Antonella Sgura.

Telomerase Reverse Transcriptase (TERT), in addition to its well-known role in telomere lengthening, also has non-canonical functions, including gene regulation and protection against apoptosis. Beyond its nuclear functions, it is now recognized for its presence inside mitochondria. However, the biological role of TERT in mitochondrial physiological activity, with its specific mechanism of action, still needs to be clarified. This work clearly demonstrates the presence of TERT inside the mitochondrion under physiological conditions, in different cellular contexts, both with endogenous and ectopic TERT expression, and regardless of the presence of telomerase RNA counterpart TERC. TERT was shown to bind mitochondrial DNA, influencing mitochondrial replication and transcription. Furthermore, electron microscopy analysis of morphology revealed TERT-induced fragmentation of the mitochondrial network. Collectively, our findings suggest that TERT may play a role in regulating mitochondrial biogenesis and dynamics, and influencing processes such as fission and mitophagy, essential for maintaining mitochondrial homeostasis and closely connected to cellular states.

DOI: https://doi.org/10.1371/journal.pgen.1011923
Viruses. 2025 Sep 30. pii: 1331. [Epub ahead of print]17(10):

Transcriptome Analysis Reveals Gemykibivirus Infection Induces Mitochondrial DNA Release in HEK293T Cells.

Runbo Yang, Hao Yan, Yifan Wang, Wenqing Yang, Jianru Qin.

  Gemykibivirus, an emerging single-stranded DNA (ssDNA) virus of the recently established genus in the family of Genomoviridae, had been discovered in human blood and cerebrospinal fluid and a variety of other body fluids. However, the molecular mechanisms of gemykibivirus entrance into the host cells and its pathogenicity remain poorly understood. To investigate the host response of gemykibivirus, we used an infectious clone of gemykibivirus previously established through molecular biology techniques to rescue virus in HEK293T cells and analyzed the changes in the host transcriptome during the infection period by RNA-Seq. Our findings indicate that gemykibivirus can both express viral proteins and accomplish replication, and high-throughput transcriptome analysis identified a total 1732 significantly different genes. Functional enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for differentially expressed genes (DEGs) showed gemykibivirus involving several important pathways, including MAPK signaling pathway, Chemical carcinogenesis-reactive oxygen species and Oxidative phosphorylation. Interestingly, mitochondrial DNA-encoded mRNAs exhibited varying levels of upregulation, suggesting that gemykibivirus may be involved in mitochondrial fission and the regulation of mitochondrial function. Subsequently, a series of experiments proved that gemykibivirus can lead an increase in mitochondrial DNA copy number, promote the release of mtDNA into the cytoplasm, enhance reactive oxygen species production and trigger other cellular antiviral responses. Overall, we lay a foundation for revealing the relationship between Gemykibivirus and human diseases through mitochondrial functional alterations.

Keywords:  Genomoviridae; RNA sequencing; emerging viruses; gemykibivirus; mitochondrial dysfunction

DOI:  https://doi.org/10.3390/v17101331
Virulence. 2025 Dec;16(1): 2580129

Coronaviruses remodel the mature human tRNAome to modulate infection.

Yining Wang, Xin Wang, Amine Avan, Pengfei Li, Xumin Ou, Qiuwei Pan.

  Current research on virus-host interactions primarily focuses on the transcription and translation of viral and host genes. However, there is a major knowledge gap between transcription and translation, known as translational decoding mediated by mature transfer RNAs (tRNAs) charged with amino acids. Codon usage analysis of seven human coronaviruses indicates that they are highly dissimilar from the human host. Quantification of the human tRNAome, consisting of 57 species, demonstrated that infections with these coronaviruses robustly upregulate the global tRNAome landscapes in host cells. Deprivation of individual amino acids or knockdown of TRNT1, the enzyme adding 3'-ACC terminal for tRNA aminoacylation, inhibited coronavirus infection. Integrative analysis of codon usage and the tRNAome landscape identified a prominent role of tRNA-Asn-AUU in translational decoding of different human coronaviruses. Deprivation of asparagine (Asn) or knockdown of Asparaginyl-tRNA Synthetase 1, an enzyme that charges the Asn amino acid onto tRNA-Asn acceptors, including tRNA-Asn-AUU, profoundly inhibited coronavirus 229E infection, but to a much lesser extent for NL63 and SARS-CoV-2. Collectively, we demonstrated that human coronaviruses are capable of remodeling the host mature tRNAome to facilitate infection. However, the regulatory patterns and sensitivities to interference, particularly at the single amino acid or tRNA levels, vary among different coronavirus species. These findings provide a new perspective for understanding virus-host interactions.

Keywords:  Coronaviruses; amino acid; infection; tRNA

DOI:  https://doi.org/10.1080/21505594.2025.2580129
Methods Mol Biol. 2026 ;2949 3-30

Protein-Centric Mapping of RNA-DNA Interactions with RedChIP.

Alexey A Gavrilov, Sergey V Razin.

  Noncoding RNAs (ncRNAs) are involved in a variety of processes in the cell nucleus, including transcriptional control, shaping 3D genome, and assembly/maintenance of functional nuclear compartments. However, the specific functions of most of the currently identified ncRNAs remain unclear. To gain further insight into the role of ncRNA in the eukaryotic genome functioning, it is important to determine genome-wide association patterns of various ncRNAs with chromatin. To address this question, a panel of RNA-DNA proximity ligation-based approaches have been developed, which have allowed deciphering RNA-chromatin interactions at the genome-wide level. An important drawback of all these techniques, however, is that they do not reveal the proteins involved in RNA-DNA interactions. In this chapter, we describe RedChIP, a method combining RNA-DNA ligation with chromatin immunoprecipitation to identify RNA-chromatin interactions mediated by a particular protein. We present a detailed protocol for RedChIP, focusing on the technical nuances and subtleties of the experimental procedure, and discuss algorithms for processing and analyzing the sequencing data. RedChIP can be used to identify RNAs associated with genomic regions occupied by any protein of interest, enabling disclosure of ncRNAs involved in recruiting various protein complexes to chromatin.

Keywords:  Cell nucleus; Chromatin; Immunoprecipitation; Noncoding RNA; RNA–DNA interactome

DOI:  https://doi.org/10.1007/978-1-0716-4670-0_1
Radiol Oncol. 2025 Oct 27.

Heterogenous mitochondrial ultrastructure and metabolism of human glioblastoma cells: differences between stem-like and differentiated cancer cells in response to chemotherapy.

Urban Bogataj, Metka Novak, Simona Katrin Galun, Klementina Fon Tacer, Milos Vittori, Cornelis J F Van Noorden, Barbara Breznik.

   BACKGROUND: Glioblastoma stem-like cells (GSCs) contribute to the resistance of glioblastoma (GBM) tumors to standard therapies. The background of the resistance of GSCs to the chemotherapeutic agent temozolomide is not yet fully understood in the context of cellular metabolism and the role of mitochondria. The aim of this study was to perform a detailed ultrastructural characterization of the mitochondria of GSCs prior and post temozolomide exposure and to compare it to differentiated GBM cells.
MATERIALS AND METHODS: Patient-derived and established GBM cell lines were used for the study. The ultrastructure of the mitochondria of the examined cell lines was assessed by transmission electron microscopy. The microscopic analysis was complemented and compared by an analysis of cell metabolism using Seahorse extracellular flux analysis.
RESULTS: We found that the metabolic profile of GSCs is quiescent and aerobic. Their elongated mitochondria with highly organized cristae are indicating increased biogenesis and mitochondrial fusion and corresponds to a more oxidative phosphorylation (OXPHOS)-dependent metabolism. The metabolism of GSCs is dependent on OXPHOS and there are no changes in defective mitochondria fraction after the treatment with temozolomide. In contrast, differentiated GBM cells with fragmented mitochondria, which have less organized cristae, are more energetic and glycolytic. Temozolomide treatment induced ultrastructural mitochondrial damage in differentiated GBM cells.
CONCLUSIONS: We demonstrated differences in mitochondrial ultrastructure and cellular metabolism between GSCs and differentiated GBM cells in response to temozolomide, suggesting that mitochondria play an important role in the resistance of GSCs to temozolomide. This study provides a basis for further studies addressing GSC chemotherapy resistance in the context of mitochondrial structure and function.

Keywords:  chemotherapy resistance; glioblastoma; metabolism; mitochondria ultrastructure; stem cells

DOI:  https://doi.org/10.2478/raon-2025-0056
Cells. 2025 Oct 20. pii: 1634. [Epub ahead of print]14(20):

RNA Degradation in Pluripotent Stem Cells: Mechanisms, Crosstalk, and Fate Regulation.

Seunghwa Jeong, Myunggeun Oh, Jaeil Han, Seung-Kyoon Kim.

  Pluripotent stem cells (PSCs) exhibit remarkable self-renewal capacity and differentiation potential, necessitating tight regulation of gene expression at both transcriptional and post-transcriptional levels. Among post-transcriptional mechanisms, RNA turnover and degradation together play pivotal roles in maintaining transcriptome homeostasis and controlling RNA stability. RNA degradation plays a pivotal role in determining transcript stability for both messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), thereby influencing cell identity and fate transitions. The core RNA decay machinery, which includes exonucleases, decapping complexes, RNA helicases, and the RNA exosome, ensures timely and selective decay of transcripts. In addition, RNA modifications such as 5' capping and N6-methyladenosine (m6A) further modulate RNA stability, contributing to the fine-tuning of gene regulatory networks essential for maintaining PSC states. Recent single-cell and multi-omics studies have revealed that RNA degradation exhibits heterogeneous and dynamic kinetics during cell fate transitions, highlighting its role in preserving transcriptome homeostasis. Conversely, disruption of RNA decay pathways has been implicated in developmental defects and disease, underscoring their potential as therapeutic targets. Collectively, RNA degradation emerges as a central regulator of PSC biology, integrating the decay of both mRNAs and ncRNAs to orchestrate pluripotency maintenance, lineage commitment, and disease susceptibility.

Keywords:  RNA degradation; RNA modifications; degradome dynamics; pluripotency stem cell; post-transcriptional regulation

DOI:  https://doi.org/10.3390/cells14201634
Biotechnol J. 2025 Oct;20(10): e70146

mRNA Stability: An Unresolved Challenge for Broad Therapeutic Applications.

Yiming Wang, Xiaoxue Wang, Yuan Lu.

  From infectious diseases and cancers to various rare diseases, mRNAs have demonstrated considerable therapeutic potential for a wide range of diseases. However, due to their single-stranded structure, mRNA molecules are vulnerable to enzyme-mediated degradation. Therefore, the inherent instability of mRNA poses a significant challenge. In this review, we explore strategies to slow down the degradation rate, such as removing degradative enzymes, adding protective substances, and optimizing storage and transport conditions to enhance mRNA stability. Furthermore, optimizing the sequence and structure of mRNAs is crucial for improving stability, which can be significantly aided by fine-tuning the sequences of the 5' untranslated region, open reading frame, and 3' untranslated region, along with introducing various RNA modifications. The design of novel mRNA structures, including circular mRNA and self-amplifying RNA, also offers novel approaches for enhancing mRNA stability. Additionally, we briefly introduce the use of mRNA delivery materials for improving stability and discuss current challenges and future directions in mRNA development. With ongoing technological advancements and the gradual maturation of the market, mRNA is set to play an increasingly significant role in versatile biotechnology fields.

Keywords:  mRNA delivery; mRNA design; mRNA modification; mRNA stability; mRNA structure

DOI:  https://doi.org/10.1002/biot.70146
Biomolecules. 2025 Sep 24. pii: 1354. [Epub ahead of print]15(10):

Mitochondrial Translation Inhibition Triggers an Rst2-Controlled Transcriptional Reprogramming of Carbon Metabolism in Stationary-Phase Cells of Fission Yeast.

Ying Luo, Shaimaa Hassan, Saniya Raut, Jürg Bähler.

  Mitochondria possess their own genome, which encodes subunits of the electron transport chain, rendering mitochondrial protein translation essential for cellular energy metabolism. Mitochondrial dysfunction affects nuclear transcription through the retrograde response. We applied RNA-seq to investigate whether and how the inhibition of mitochondrial translation by chloramphenicol (CAP) affects transcriptome regulation in proliferating or stationary-phase cells of Schizosaccharomyces pombe growing in fermentative or respiratory media. Stationary-phase cells in glucose medium exhibited the strongest transcriptome response to CAP, characterized by expression signatures similar to those observed under other stresses, including the retrograde response. The induced genes were also significantly enriched in cytoplasmic carbon metabolism pathways, reflecting a transcriptional reprogramming from respiration to fermentation. The transcription factors Scr1 and Rst2, regulators of carbon catabolite repression (CCR), controlled a common set of carbon metabolism genes in CAP-treated stationary-phase cells, and they showed opposing effects on the lifespan of these cells. Rst2 was required for the induction of carbon metabolism genes and maintained nuclear localization in CAP-treated stationary-phase cells. A systematic genetic interaction screen revealed functional relationships of Rst2 with processes related to stress and starvation responses. These findings uncover a complex transcriptional program in stationary-phase cells that adapt to inhibited mitochondrial translation, including stress- and retrograde-like responses, contributions of the CCR factors Scr1 and Rst2, and adjustment of carbon metabolism to deal with mitochondrial dysfunction.

Keywords:  RNA-seq; S. pombe; Scr1; carbon catabolite repression; genetic interactions; mitochondrial metabolism; retrograde response; stress response; transcription factor; transcriptome

DOI:  https://doi.org/10.3390/biom15101354
Virus Evol. 2025 ;11(1): veaf074

Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases.

Katherine Brown, Andrew Edwin Firth.

  Public databases of protein sequences, such as the National Center for Biotechnology Information (NCBI) Protein repository and UniProt, contain millions of proteins identified in samples from specific species but named as uncharacterized or hypothetical due to a lack of information about their function. Many such sequences are actually derived from RNA viruses, either due to viral infection of the original sample, contamination, or endogenous viral elements (EVEs) integrated into the genome of the sample species. Many proteins from RNA virus discovery research are also deposited into these repositories but are labelled as uncharacterized and only classified taxonomically at a superkingdom or realm level. Sequences from protein repositories not labelled specifically as being derived from the RNA-viral RNA-dependent RNA polymerase (RdRp) protein are often used as negative controls when looking to identify viral RdRp sequences, so the presence of unlabelled viruses amongst these datasets is problematic. These sequences also represent a source of information about novel viruses and EVEs. In this study, we screened uncharacterized proteins from two large public protein repositories-NCBI Protein and UniProt-to identify sequences likely to be derived from RNA viral RdRp and to perform detailed characterization of sequences of interest. We identified 3560 such sequences, many derived from EVEs. Many are previously unknown EVEs, which led to characterization of additional, related sequences. For example, a group of orbi-like viruses infecting nematodes was uncovered that appears to have both ancient endogenous and circulating exogenous members. Many integrations of mito-like viruses into plant genomes were also found. In several host taxonomic groups, the first example of an EVE, and in some cases the first example of any RNA virus, was uncovered. The large number of EVEs uncovered by this relatively small-scale search suggests that only a fraction of the true diversity of EVEs is currently known. We also provide provisional taxonomic annotations for RdRps, currently only listed as members of the Riboviria realm. A number of sequences are identified that are indistinguishable from viruses but are labelled as bacteria, seemingly as a result of mislabelling or contamination. Non-RdRp sequences that share near-significant similarity with RdRp are also characterized. Finally, recommendations are made for generating useful negative controls and sets of negative control sequences are provided.

Keywords:  RNA virus; RdRp; endogenous viral elements; metatranscriptomics; paleovirology; virus discovery

DOI:  https://doi.org/10.1093/ve/veaf074
Genes (Basel). 2025 Sep 23. pii: 1120. [Epub ahead of print]16(10):

Expanding the Clinical and Molecular Spectrum of Primary Autosomal Recessive Microcephaly: Novel CDK5RAP2 Gene Variants and Functional Insights on the Intronic Variants.

Burcu Yeter, Yasemin Kendir Demirkol, Esra Usluer, İpek Görüşen Kavak, Sena Gjota Ergin, Nursel H Elçioğlu.

  Background/Objectives: Autosomal recessive primary microcephaly is a rare and genetically heterogeneous disorder characterized by congenital non-syndromic microcephaly, with at least 28 causative genes identified to date. Biallelic variants in the CDK5RAP2 gene, an ultra-rare cause of autosomal recessive primary microcephaly, lead to Primary Autosomal Recessive Microcephaly 3 (MCPH3). Methods: We present seven patients from six families diagnosed with MCPH3 in light of clinical and molecular findings using whole-exome sequencing (WES). Furthermore, we investigated the effects of the identified intronic variants on splicing through RNA analysis. Results: Almost all patients had severe microcephaly, mild to moderate intellectual disability, speech delay, and cutaneous pigmentary abnormalities. Four patients presented with postnatal short stature, and two showed weight deficiency. Dysmorphic evaluation revealed that the most prominent features included brachycephaly, hypertelorism, epicanthus, high-arched eyebrows, prominent nasal bridge, and micrognathia. We identified five distinct homozygous CDK5RAP2 variants in our patients, including four novel variants. Segregation analysis verified that the parents were carriers. Two of these variants were intronic (c.3148+5G>C and c.383+4dupA), two were frameshift (c.3168del), and one was a nonsense variant (c.1591C>T). Both intronic variants disrupted splicing, generating a premature stop codon and resulting in a truncated protein. Conclusions: This study broadens the mutational landscape of CDK5RAP2. We also sought to demonstrate the functional consequences of the CDK5RAP2 intronic variants on gene function using RNA analysis. The identification of four novel variants underscores the importance of molecular diagnostics in patients with primary microcephaly and provides valuable data for genetic counseling and future functional studies.

Keywords:  CDK5RAP2; MCPH3; autosomal recessive primary microcephaly 3; primary microcephaly; rare disease; whole-exome sequencing

DOI:  https://doi.org/10.3390/genes16101120