bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2025–05–18
eight papers selected by
Thomas Farid Martínez, University of California, Irvine
  1. Ribosome association inhibits stress-induced gene mRNA localization to stress granules.
  2. Upstream open reading frames dynamically modulate CLOCK protein translation to regulate circadian rhythms and sleep.
  3. Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery.
  4. Loss of non-canonical translation initiation factors impairs perinatal cardiac function in mice.
  5. Beyond the Transcript: Translating Non-Coding RNAs and Their Impact on Cellular Regulation.
  6. Small protein DDX11-AS1-ORF encoded by lncRNA DDX11-AS1 promotes colorectal cancer progression through VEGFA-activated p38-MAPK pathway.
  7. AEOL-induced NRF2 activation and DWORF overexpression mitigate myocardial I/R injury.
  8. EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53 mediated tumor suppression.
  1. Genes Dev. 2025 May 13.
    Ribosome association inhibits stress-induced gene mRNA localization to stress granules.
    Noah S Helton, Benjamin Dodd, Stephanie L Moon.
      The integrated stress response (ISR) is critical for resilience to stress and is implicated in numerous diseases. During the ISR, translation is repressed, stress-induced genes are expressed, and mRNAs condense into stress granules. The relationship between stress granules and stress-induced gene expression is unclear. We measured endogenous stress-induced gene mRNA localization at the single-molecule level in the presence or absence of small molecule translation inhibitors. Reducing ribosome association increases the localization of stress-induced gene mRNAs to stress granules, whereas increasing ribosome association inhibits their localization to stress granules. The presence of upstream open reading frames (uORFs) in mRNA reporters reduces their localization to stress granules in a ribosome-dependent manner. Furthermore, a single initiating ribosome blocks stress granule formation and inhibits mRNA association with preformed stress granules. Thus, uORF-mediated ribosome association inhibits stress-induced gene mRNA localization to stress granules, suggesting a new role for uORFs in limiting RNA condensation.
    Keywords:  ATF4; GADD34; RNA localization; condensate; integrated stress response; ribosome; stress granules; stress-induced genes; translation; upstream open reading frame
    DOI:  https://doi.org/10.1101/gad.352899.125
  2. PLoS Biol. 2025 May 12. 23(5): e3003173
    Upstream open reading frames dynamically modulate CLOCK protein translation to regulate circadian rhythms and sleep.
    Yuanqiang Sun, Ke Shui, Qinyu Li, Chenlu Liu, Wanting Jin, Jian-Quan Ni, Jian Lu, Luoying Zhang.
      The circadian rhythm is an evolutionarily conserved mechanism with translational regulation increasingly recognized as pivotal in its modulation. In this study, we found that upstream open reading frames (uORFs) are enriched in Drosophila circadian rhythm genes, with particularly conserved uORFs present in core circadian clock genes. We demonstrate evidence that the uORFs of the core clock gene, Clock (Clk), rhythmically and substantially attenuate CLK protein translation in Drosophila, with pronounced suppression occurring during daylight hours. Eliminating Clk uORFs leads to increased CLK protein levels during the day and results in a shortened circadian cycle, along with a broad shift in clock gene expression rhythms. Notably, Clk uORF deletion also augments morning sleep by reducing dopaminergic activity. Beyond daily circadian adjustments, Clk uORFs play a role in modulating sleep patterns in response to seasonal daylight variations. Furthermore, the Clk uORFs act as an important regulator to shape the rhythmic expression of a vast array of genes and influence multifaceted physiological outcomes. Collectively, our research sheds light on the intricate ways uORFs dynamically adjust downstream coding sequences to acclimate to environmental shifts.
    DOI:  https://doi.org/10.1371/journal.pbio.3003173
  3. Nat Protoc. 2025 May 14.
    Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery.
    Fangping Wan, Marcelo D T Torres, Changge Guan, Cesar de la Fuente-Nunez.
      Genomes and proteomes constitute a rich reservoir of molecular diversity. However, they have remained underexplored because of a lack of appropriate tools. In recent years, computational approaches have been developed to mine this unexplored biological information, or dark matter, accelerating the discovery of new antibiotic molecules. Such efforts have yielded a wide range of new molecules. These include peptides released via predicted proteolytic cleavage of larger proteins, termed 'encrypted peptides', which have been found to be widespread in nature. Molecules encoded by and translated from small open reading frames within genomic sequences have also been uncovered, further expanding the landscape of bioactive compounds. Here, we discuss computational approaches, including machine learning and artificial intelligence (AI) tools, which have been used to date to identify antimicrobial compounds, with a special emphasis on peptides. We also propose potential avenues for future exploration in this rapidly evolving field. Moreover, we provide an overview of the experimental methods commonly used to validate these computational predictions. We anticipate that efforts combining cutting-edge AI and experimental approaches for biological sequence mining will reveal new insights into host immunity and continue to accelerate discoveries in the fields of antibiotics and infectious diseases.
    DOI:  https://doi.org/10.1038/s41596-025-01144-w
  4. Exp Anim. 2025 May 10.
    Loss of non-canonical translation initiation factors impairs perinatal cardiac function in mice.
    Takehiro Asai, Ryota Tochinai, Yoshiharu Tsuru, Marie Sekiguchi, Atsushi Minami, Wataru Fujii, Shigeru Kyuwa, Tetsuhiro Ogawa, Shigeru Kakuta.
      Translation regulation is crucial for cellular homeostasis. Recent studies have demonstrated that, in addition to the conventional AUG start codon, eukaryotic mRNA can also possess non-canonical start codons. These non-canonical start codons, including non-AUG codons, can be found both upstream and downstream of the conventional AUG start codon. Translation of these non-canonical open reading frames (ORFs) has been implicated in the development of diseases, such as cardiac diseases, neurodegeneration and cancer development. Non-AUG translation initiation is regulated by eukaryotic initiation factor (eIF) 2A and eIF2D; however, their target non-canonical ORFs, roles in disease development, and the underlying precise mechanisms of translation regulation remain poorly understood. To address these gaps, we generated mice lacking either or both of Eif2a and Eif2d genes on an ICR background and investigated their cardiac function using echocardiography. The results indicated that simultaneous disruption of both Eif2a and Eif2d led to perinatal cardiac impairment, as evidenced by a significant reduction in cardiac contractility as measured by ejection fraction. Furthermore, the absence of phenotypic changes in single knockouts of either Eif2a or Eif2d suggests that eIF2A and eIF2D function redundantly in their molecular roles. These findings underscore the importance of non-AUG translation initiation in maintaining cardiac function and suggest its broader implications in other physiological and pathological processes. We propose the Eif2a and Eif2d double-knockout mice as a novel stress-sensitive animal model to investigate the molecular mechanisms of translation regulation and their contribution to disease pathogenesis.
    Keywords:  echocardiography; eukaryotic initiation factor 2A (eIF2A); eukaryotic initiation factor 2D (eIF2D); non-canonical translation initiation factor; perinatal cardiac function
    DOI:  https://doi.org/10.1538/expanim.25-0021
  5. Cancers (Basel). 2025 May 03. pii: 1555. [Epub ahead of print]17(9):
    Beyond the Transcript: Translating Non-Coding RNAs and Their Impact on Cellular Regulation.
    Ananya Deshpande, Sagar Mahale, Chandrasekhar Kanduri.
      Non-coding RNAs (ncRNAs) constitute the majority of the human transcriptome and play diverse structural, catalytic, and regulatory roles. The ability of ncRNAs to be translated into functional peptides and microproteins expands our understanding of their regulatory potential beyond their established non-coding functions. Our comprehensive search identified 86 translating "non-coding" RNAs. While translating ncRNAs have traditionally been categorized as "peptide-encoding", in this study, we introduce a novel classification based on amino acid length, distinguishing their products as ncRNA encoded peptides (ncRNA-PEPs), which are less than 60 amino acids, or ncRNA encoded microproteins (ncRNA-MPs) ranging from 61 to 200 amino acids. These peptides and microproteins act as co-regulators in cell signaling, transcriptional regulation, and protein complex assembly, playing a role in both health and disease. We outline the molecular pathways by which ncRNA-PEPs and ncRNA-MPs could govern cell cycle progression, highlighting their influence on cell cycle transitions, oncogenic and tumor suppressor pathways, metabolic homeostasis, autophagy, and on key cell cycle regulators like PCNA, Rad18, and CDK-cyclin complexes. Furthermore, we highlight recent advancements in their detection and characterization, exploring their evolutionary origins, species-specific conservation, and potential therapeutic applications. Our findings underscore the emerging significance of ncRNA-PEPs and ncRNA-MPs as integral regulators of cellular processes, highlighting their functional versatility and opening promising avenues for further research and potential therapeutic applications.
    Keywords:  cancer; cell cycle; lncRNA PEPs; lncRNAs; ncRNA-PEPs; oncogenes; peptide ncRNAs; peptide-encoding long non-coding RNAs; tumor suppressor genes
    DOI:  https://doi.org/10.3390/cancers17091555
  6. Am J Cancer Res. 2025 ;15(4): 1662-1672
    Small protein DDX11-AS1-ORF encoded by lncRNA DDX11-AS1 promotes colorectal cancer progression through VEGFA-activated p38-MAPK pathway.
    Yuanfang Cheng, Jiajie Dong, Kai Shang, Lejing Zhang, Yongwei Chen, Rihui Li, Zhaoxi Li, Zheying Zhang, Yajuan Wang.
      This study aims to investigate the expression, function, and mechanism of action of the small protein DDX11 antisense RNA 1 - open reading frame (DDX11-AS1-ORF), encoded by the long non-coding RNA (lncRNA) DDX11 antisense RNA 1 (DDX11-AS1), in the progression of colorectal cancer (CRC). The expression levels of DDX11-AS1 were assessed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis in 10 pairs of colorectal cancer tissues and corresponding non-tumor tissues. Functional evaluations of DDX11-AS1 and DDX11-AS1-ORF were conducted using cell counting kit-8 (CCK8) assays, colony formation assays, Transwell migration assays, and in vitro tube formation assays. The coding potential of DDX11-AS1 was validated by western blot and immunofluorescence. The activation of the p38 mitogen-activated protein kinase (p38-MAPK) pathway by DDX11-AS1-ORF through VEGFA was analyzed using western blot. The results showed that DDX11-AS1 was significantly upregulated in colorectal cancer tissues and cells, promoting cancer cell proliferation, migration, and angiogenesis. DDX11-AS1 translated into a functional small protein, DDX11-AS1-ORF, which independently enhanced the malignant behaviors of tumor cells. DDX11-AS1-ORF promoted colorectal cancer progression by activating the p38-MAPK signaling pathway through Vascular Endothelial Growth Factor A (VEGFA). The critical role of the p38-MAPK pathway in DDX11-AS1-ORF mediated tumor promotion was confirmed using the p38-MAPK pathway inhibitor SB203580. In conclusion, the small protein DDX11-AS1-ORF, encoded by DDX11-AS1, plays a crucial role in the development of colorectal cancer by promoting tumor proliferation, migration, and angiogenesis through the activation of VEGFA and the p38-MAPK signaling pathway. These findings provide a novel potential target for molecular targeted therapy in colorectal cancer.
    Keywords:  Colorectal cancer; VEGFA; lncRNA; p38-MAPK pathway; small protein
    DOI:  https://doi.org/10.62347/VRJE7714
  7. Mol Med. 2025 May 15. 31(1): 189
    AEOL-induced NRF2 activation and DWORF overexpression mitigate myocardial I/R injury.
    Maria Del Carmen Asensio-Lopez, Miriam Ruiz-Ballester, Silvia Pascual-Oliver, Francisco Jose Bastida-Nicolas, Yassine Sassi, Jose Javier Fuster, Domingo Pascual-Figal, Fernando Soler, Antonio Lax.
       BACKGROUND: The causal relationship between the activation of nuclear factor erythroid 2-related factor 2 (NRF2) and the preservation of SERCA2a function in mitigating myocardial ischemia-reperfusion (mI/R) injury, along with the associated regulatory mechanisms, remains incompletely understood. This study aims to unravel how NRF2 directly or indirectly influences SERCA2a function and its regulators, phospholamban (PLN) and Dwarf Open Reading Frame (DWORF), by testing the pharmacological repositioning of AEOL-10150 (AEOL) in the context of mI/R injury.
    METHODS: C57BL6/J, Nrf2 knockout (Nrf2-/-), and wild-type (Nrf2+/+) mice, as well as human induced pluripotent stem cell-derived cardiomyocytes (hiPSCMs) were subjected to I/R injury. Gain/loss of function techniques, RT-qPCR, western blotting, LC/MS/MS, and fluorescence spectroscopy were utilized. Cardiac dimensions and function were assessed by echocardiography.
    RESULTS: In the early stages of mI/R injury, AEOL administration reduced mitochondrial ROS production, decreased myocardial infarct size, and improved cardiac function. These effects were due to NRF2 activation, leading to the overexpression of the micro-peptide DWORF, consequently enhancing SERCA2a activity. The cardioprotective effect induced by AEOL was diminished in Nrf2-/- mice and in Nrf2/Dworf knockdown models in hiPSCMs subjected to simulated I/R injury. Our data show that AEOL-induced NRF2-mediated upregulation of DWORF disrupts the phospholamban-SERCA2a interaction, leading to enhanced SERCA2a activation and improved cardiac function.
    CONCLUSIONS: Taken together, our study reveals that AEOL-induced NRF2-mediated overexpression of DWORF enhances myocardial function through the activation of the SERCA2a offering promising therapeutic avenues for mI/R injury.
    Keywords:  AEOL-10150; Acute myocardial infarction; Cardiac protection; DWORF; NRF2; Reperfusion injury
    DOI:  https://doi.org/10.1186/s10020-025-01242-1
  8. RNA. 2025 May 13. pii: rna.080561.125. [Epub ahead of print]
    EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53 mediated tumor suppression.
    Yu-Hsuan Cheng, Ting-Wen Chen, Wei-Chung Chiang, Jean-Cheng Kuo, Yi-Sheng Ho, Michelle Noble, Chung-Te Chang.
      Processing bodies (P-bodies) are membrane-less organelles in eukaryotic cells that play a central role in mRNA metabolism, including mRNA decay, storage, and translational repression. However, the molecular mechanisms governing their assembly remain incompletely understood. Here, we identify the C-terminal domain of EDC4 as the minimal region required for P-body formation, with residues 1266-1401 driving phase separation and EDC4 condensation. To investigate the functional relevance of P-body integrity, we employed the microprotein Nobody (NBDY) as a selective perturbation tool. Our results revealed that the NBDY 22-41 peptide directly binds the EDC4 C-terminal domain and inhibits its self-association, thereby selectively dissolving P-bodies without affecting the canonical mRNA decay pathway. Using this tool, we further examined the impact of P-body disruption on gene expression. Transcriptome profiling combined with quantitative validation revealed that P-body loss activates the p53 pathway and enhances the stability of associated transcripts. Consistent with these findings, clinical data show that NBDY overexpression is associated with p53 pathway activation in various cancers, and the NBDY 22-41 fragment reduces tumor cell proliferation and invasion, suggesting a potentially complex role of P-body dynamics in cancer biology. Together, our study defines the EDC4 C-terminal domain as a core scaffold for P-body assembly and uncovers a regulatory role of P-body dynamics in p53-mediated gene expression, with potential implications for cancer biology.
    Keywords:  EDC4; NBDY; P-body; mRNA decapping complex; p53 pathway
    DOI:  https://doi.org/10.1261/rna.080561.125
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