bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2025–05–11
six papers selected by
Thomas Farid Martínez, University of California, Irvine



  1. Int J Mol Sci. 2025 Apr 12. pii: 3651. [Epub ahead of print]26(8):
      Micropeptides (miPEPs), encoded by short open reading frames (sORFs) within various genomic regions, have recently emerged as critical regulators of multiple biological processes. In particular, these small molecules are now increasingly being recognized for their role in modulating viral replication, pathogenesis, and host immune responses. Both host miPEPs and virus-derived miPEPs have been noted for their ability to regulate virus-host interactions through diversified mechanisms such as altering protein stability and modulating protein-protein interactions. Although thousands of sORFs have been annotated as having the potential to encode miPEPs, only a small number have been experimentally validated so far, with some directly linked to virus-host interactions and a small subset associated with immune modulation, indicating that the investigation of miPEPs is still in its infancy. The systematic identification, translational status assessment, in-depth characterization, and functional analysis of a substantial fraction of sORFs encoding miPEPs remain largely underexplored. Further studies are anticipated to uncover the intricate mechanisms underlying virus-host interactions, host immune modulation, and the broader biological functions of miPEPs. This article will review the emerging roles of miPEPs in virus-host interactions and host immunity, and discuss the challenges and future perspectives of miPEP studies.
    Keywords:  innate immunity; micropeptides; sORFs; virus–host interactions
    DOI:  https://doi.org/10.3390/ijms26083651
  2. bioRxiv. 2025 Apr 19. pii: 2025.04.18.649583. [Epub ahead of print]
      Enhancer RNAs (eRNAs) are transcribed by RNA polymerase II during enhancer activation but are typically rapidly degraded in the nucleus. During states of reduced RNA surveillance, however, eRNAs and other similar "noncoding" RNAs, including for example upstream antisense RNAs, are stabilized, and some are exported to the cytoplasm and can even be found on polysomes. Here, we report unexpectedly that ∼12% of human intergenic eRNAs contain long open reading frames (>300 nts), many of which can be actively translated, as determined by ribosome profiling, and produce proteins that accumulate in cells, as shown by mass spectrometry (MS) data. Focusing on the largest of the encoded proteins, which we designate as eORFs, and which can be up to ∼45 KDa, we found remarkably that most are highly basic, with pIs >11.5. This unusual chemistry reflects a striking overabundance of arginine residues, and occurs despite a relative paucity of lysines. Exogenous expression of the ten largest eORFs revealed that they accumulate stably in cells as full-length proteins, and most localize to the nucleus and associate with chromatin. Identification of interacting proteins by MS suggested possible roles for these proteins in several nuclear processes. The eORFs studied are well-conserved among primates, although they are largely absent from other mammals. Notably, several contain human-specific C-terminal extensions and display properties suggestive of de novo gene birth. In summary, we have discovered that a fraction of human eRNAs can function as mRNAs, revealing a new and unexpected role for these transcripts.
    DOI:  https://doi.org/10.1101/2025.04.18.649583
  3. Biotechnol Biofuels Bioprod. 2025 May 08. 18(1): 51
      ABRE BINDING FACTOR 4 (ABF4) is a pivotal regulatory gene in the abscisic acid (ABA) signaling pathway, and changes in its expression levels can modulate the plant's stress resistance. To further explore the specific regulatory mechanisms of alternative splicing (AS) in the ABA signaling pathway and to identify new breakthroughs for breeding high stress-resistant varieties of Brassica napus, we identified 17 homologous genes of ABF4 in the genome. Utilizing bioinformatics techniques, we analyzed their motifs, conserved domains, and cis-acting elements of their promoters. Through transcriptome data from the stress-tolerant dwarf strain ndf2 and its parental line 3529, we uncovered a significantly differentially expressed ABF4 gene, which we named BnABF4L. Subsequently, we analyzed the AS events of BnABF4L under normal growth conditions and different abiotic stresses, as well as the impact of different transcript variants' 5' untranslated region (5'UTR) on gene translation. BnABF4L undergoes alternative 3' splice site (A3SS) selection to produce three transcripts (V1-V3) with divergent 5'UTRs. While V1 translation is suppressed by upstream ORFs (uORFs), V2/V3 exhibit enhanced translational efficiency. Under stress, ndf2 shifts splicing toward V3, circumventing uORF-mediated repression to upregulate stress-adapted isoforms. We validated the inhibitory effect of upstream open reading frames (uORFs) on protein-coding open reading frame (pORFs) and, based on the collective experimental results, proposed the flexible regulatory mechanism of AS events of BnABF4L in response to stress. Our findings provide new insights for future studies on stress resistance in rapeseed as well as for research on the regulation of alternative splicing mechanisms in the ABA signaling pathway.
    Keywords:  ABA signaling pathway; Abiotic stress; Alternative splicing; UORF
    DOI:  https://doi.org/10.1186/s13068-025-02645-2
  4. Cancer Res. 2025 May 06.
      The integrated stress response (ISR) is an adaptive pathway hijacked by cancer cells to survive cellular stresses in the tumor microenvironment. ISR activation potently induces PD-L1, leading to suppression of anti-tumor immunity. Here, we sought to uncover additional immune checkpoint proteins regulated by the ISR to elucidate mechanisms of tumor immune escape. ISR coordinately induced CD155 and PD-L1, enhancing translation of both immune checkpoint proteins through bypass of inhibitory upstream open reading frames in their 5' UTRs. Analysis of primary human lung tumors identified a significant correlation between expression of PD-L1 and CD155. ISR activation accelerated tumorigenesis and inhibited T cell function, which could be overcome by combining PD-1 and TIGIT blockade with the ISR inhibitor ISRIB. This study uncovers a mechanism by which two immune checkpoint proteins are coordinately regulated and suggests a therapeutic strategy for lung cancer patients.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-3844
  5. Nucleic Acids Res. 2025 Apr 22. pii: gkaf292. [Epub ahead of print]53(8):
      Translational regulation at the stage of initiation can impact the number of ribosomes translating each mRNA molecule. However, the translational activity of single 80S ribosomes (monosomes) on mRNA is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in vivo. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues in Drosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5'-UTRs, short ORFs and are enriched for the presence of uORFs. Overall, these findings highlight that regulation of translation initiation and protein synthesis is mostly performed by monosomes in head and embryo, while polysomes are the main source of protein production in testis and ovary.
    DOI:  https://doi.org/10.1093/nar/gkaf292
  6. Adv Sci (Weinh). 2025 May 08. e2413473
      Macrophages play vital roles in innate and adaptive immunity, and their essential functions are mediated by phagocytosis and antigen presentation. Long non-coding ribonucleic acid nuclear enriched abundant transcript 1 (LincNEAT1) is specifically translated during phagocytosis. Great efforts have been made to explore the potential mechanisms of action of these phagocytic checkpoints. However, the use of a systematic checkpoint scanning strategy has been far from satisfactory, and intrinsic phagocytic activators have not been fully elucidated. Therefore, in vitro phagocytosis assays are performed using primary healthy donor macrophages and breast cancer cells. An equal number of cells are subjected to ribosome profiling, and immune system-specific phagocytic activators are identified. LincNEAT1 and encoded micro peptide NEAT1-31, are considerably upregulated in phagocytic macrophages. Moreover, purified NEAT1-31 promoted the phagocytosis of multiple cancer cell-types. Phosphoproteomic analysis reveals that NEAT1-31 directly promoted Aurora-A activity and activated phosphatidylinositol 3-kinase/protein kinase B signaling. NEAT1-31 enhanced the efficacy of anti-CD47 in vivo and in vitro. Thus, the study identified a novel protein drug that can directly enhance the phagocytic function, thereby providing a new option for immunotherapy.
    Keywords:  Aurora‐A; LincNEAT1; macrophages; phagocytosis; protein kinase B
    DOI:  https://doi.org/10.1002/advs.202413473