bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2025–12–14
eight papers selected by
Thomas Farid Martínez, University of California, Irvine
  1. Methodological Toolbox for Identifying and Studying Micropeptides: From Genome to Function.
  2. The degradation of extended protein isoforms points to a misfiring translation initiation process.
  3. De novo origin of numerous microproteins in enterobacteria.
  4. Circulating Mitochondrial Open Reading Frame of the 12S Ribosomal RNA Type-c Is Higher in Acute Coronary Syndrome and Is a Prognostic Biomarker for Major Cardiac Events in Patients With Acute Myocardial Infarction: A Case-Control Study.
  5. The long non-coding RNA UGDH-AS1 encodes an NK-cell-inhibiting micropeptide in triple-negative breast cancers.
  6. MCARE enhances SERCA1 activity in fast-twitch muscle to maintain calcium handling and muscle integrity.
  7. Long non-coding RNAs in cancer glycolysis and metabolism: mechanisms and translational opportunities.
  8. LncRNA HAND2OT encoding micropeptide regulates the estradiol secretion, proliferation and apoptosis of ovarian follicular theca cells in chickens.
  1. Biochemistry (Mosc). 2025 Nov;90(11): 1521-1535
    Methodological Toolbox for Identifying and Studying Micropeptides: From Genome to Function.
    Aleksandr I Lavrov, Nikita M Shepelev, Olga A Dontsova, Maria P Rubtsova.
      Micropeptides encoded by small open reading frames (sORFs) represent a novel, actively studied class of functional molecules regulating key cellular processes. Studying micropeptides is complicated by methodological challenges, in particular, their small size, low cellular abundance, and difficulty in generating specific antibodies. The review systematizes modern approaches to the identification and functional characterization of micropeptides. The main strategies for their discovery include the use of bioinformatic algorithms, global translation analysis via ribosome profiling, direct detection using mass spectrometry-based proteomics, and phenotypic screenings. The methods for confirming the functions of micropeptides and elucidating molecular mechanisms of their action genetic knockouts, affinity tagging for visualization, and investigation of protein-protein interactions. The review discusses key challenges and future prospects in the field, emphasizing the importance of an integrated multi-omics approach for the comprehensive micropeptidome mapping.
    Keywords:  Ribo-Seq; affinity labeling; co-immunoprecipitation; long non-coding RNAs; mass spectrometry; micropeptides; small open reading frames
    DOI:  https://doi.org/10.1134/S0006297925602242
  2. Mol Genet Genomics. 2025 Dec 12. 301(1): 3
    The degradation of extended protein isoforms points to a misfiring translation initiation process.
    Michael L Tress.
      There is ever increasing evidence for significant amounts of translation upstream of known AUG start codons in protein coding genes. Some of this translation is from upstream open reading frames (ORFs) that are unconnected to the main coding exons, but upstream initiation codons that are in-frame with coding exons can produce N-terminally extended protein isoforms. N-terminal extensions have much more proteomics support than the shorter proteins predicted to be produced from upstream ORFs. The upstream regions that produce N-terminal extensions have certain characteristics in common. They are highly GC-rich, most of the predicted start codons are non-AUG, and most do not conserve their reading frames beyond simians. The extended isoforms themselves are found significantly more frequently in dysregulated cells than in normal tissues. Approximately one in seven of these N-terminal extensions are upstream of signal peptides and would almost certainly block their recognition by the signal recognition particle. As a result, N-terminally extended isoforms containing exposed, hydrophobic signal peptides would be expected to accumulate in the cytoplasm. However, this analysis finds that those N-terminal extensions that would block signal recognition are practically not detected at the protein level even though the transcripts that would produce these extensions are found as expected in ribosome profiling experiments. This is a clear indication that these mislocated proteins are degraded after translation. Theprobable degradation of these extended proteins strongly suggests that their translation is a side effect of inefficient translation initiation.
    Keywords:  Protein degradation; Proteomics; Ribosome profiling; Signal peptides; Translation initiation; Upstream translation
    DOI:  https://doi.org/10.1007/s00438-025-02324-9
  3. Nucleic Acids Res. 2025 Nov 26. pii: gkaf1319. [Epub ahead of print]53(22):
    De novo origin of numerous microproteins in enterobacteria.
    Igor Fesenko, Svetlana A Shabalina, Gisela Storz, Eugene V Koonin.
      Bacterial genomes encompass numerous small open reading frames (smORFs), some of which encode functional microproteins or perform noncoding regulatory roles. The evolution of microproteins remains poorly understood, largely due to challenges in homology detection for these short sequences. To address this challenge, we constructed 36 957 orthologous groups of microproteins (microOGs) across 5668 Enterobacteriaceae genomes. Our pipeline identified dozens of novel, widely distributed microprotein families and refined conservation patterns for known ones. However, 86% of the microOGs are genus-specific and functionally uncharacterized, suggesting that enterobacteria harbor a pool of evolutionarily young, de novo-originated small genes. Nevertheless, the microprotein-encoding smORFs in the microOGs are preferentially adjacent to membrane transporter genes suggesting a role in regulating transport processes. MicroOGs formed closed pangenomes, indicative of a limited contribution to the noncore genome of enterobacteria, likely due to the limitations on the size of intergenic regions where microproteins could arise de novo and frequent loss of microprotein-encoding smORFs during bacterial evolution. Overall, we identified 4838 microOGs with clear signatures of de novo origin from noncoding sequences. Many of the microprotein-encoding smORFs overlap transcriptional regulatory signals or repetitive elements suggesting that the origin of microproteins is tied to selection for maintenance of regulatory sequences.
    DOI:  https://doi.org/10.1093/nar/gkaf1319
  4. J Am Heart Assoc. 2025 Dec 10. e041905
    Circulating Mitochondrial Open Reading Frame of the 12S Ribosomal RNA Type-c Is Higher in Acute Coronary Syndrome and Is a Prognostic Biomarker for Major Cardiac Events in Patients With Acute Myocardial Infarction: A Case-Control Study.
    Pengyu Cao, Bojian Wang, Ningning Zhang, Jinting Yang, Qian Tong, Zhenwei Gong.
       BACKGROUND: To date, the role of MOTS-c (mitochondrial open reading frame of the 12S ribosomal RNA type-c) in acute coronary syndrome remains largely unknown. We measured circulating MOTS-c levels, markers of oxidative stress, and blood biochemical parameters in patients with acute coronary syndrome and examined their relationship with major adverse cardiac events (MACE).
    METHODS: A total of 400 subjects were recruited and divided into 3 groups: normal controls, unstable angina, and acute myocardial infarction, based on the clinical data and angiography results. Serum MOTS-c and thiobarbituric acid reactive substances were measured upon initial admission. Hospitalization data, major adverse cardiac events, and a follow-up duration of 18 months were recorded.
    RESULTS: The serum levels of MOTS-c and thiobarbituric acid reactive substances were higher in patients with acute coronary syndrome and there was a positive correlation between MOTS-c and thiobarbituric acid reactive substances. In addition, MOTS-c levels showed a high sensitivity of 0.890 (cutoff value, 326.65 [95% CI, 253.41-631.84]; area under the curve, 0.739 [95% CI, 0.647-0.832], P<0.001) in predicting the occurrence of unstable angina and acute myocardial infarction in the general population. Our data also showed that MOTS-c/thiobarbituric acid reactive substances levels could be used to predict major adverse cardiac events in the group with acute myocardial infarction, with a sensitivity of 0.800 and specificity of 0.667 (cutoff value, 48.26 ng/umol [95% CI, 45.43-90.16 ng/umol]; area under the curve, 0.718 [95% CI, 0.598-0.839], P=0.003). In vitro studies demonstrated that oxidative stress induces MOTS-c levels and MOTS-c treatment reduces hypoxia-induced oxidative stress through activating antioxidants.
    CONCLUSIONS: The circulating MOTS-c is associated with an increased risk of acute coronary syndrome and the imbalance between oxidative stress and circulating MOTS-c may play a role in predicting major adverse cardiac events in patients with acute myocardial infarction.
    Keywords:  MOTS‐c; acute myocardial infarction; diagnosis; oxidative stress; prognosis
    DOI:  https://doi.org/10.1161/JAHA.125.041905
  5. Nat Commun. 2025 Dec 12.
    The long non-coding RNA UGDH-AS1 encodes an NK-cell-inhibiting micropeptide in triple-negative breast cancers.
    Zheng Zhang, Fanrong Li, Xiaoxiao Dai, Jieqiong Deng, Binbin Guo, Yirong Wang, Wei Liu, Yacheng Pan, Tong Zhao, Shuang Wang, Wanqiu Li, Congnan Jin, Hebin Zhang, Shenghua Zhang, Yifeng Zhou.
      NK cells are important for the anti-tumour immune response for their potential to kill MHC class I-deficient tumor cells, but they often become dysfunctional in the immune-hostile tumour microenvironment. Here, using single-cell RNA sequencing, we identify an NK cell subpopulation that is specific to triple-negative breast cancers (TNBC) subtype, characterised by the expression of the long non-coding RNA UGDH-AS1. In these NK cells, UGDH-AS1 encodes the micropeptide, NKSM, which renders these NK cells dysfunctional due to the loss of their activation program, which leads to cancer progression. Conditional NKSM knock-in into NK cells of mice results in NK cell deactivation and increased growth of transplanted tumours. Targeted NKSM therapy effectively reduces tumor growth in TNBC mouse models. We find that UGDH-AS1+ NK cells are shaped by the tumor microenvironment (TME). Following upregulation by the TGF-β signaling pathway, NKSM binds to Myc, inhibiting its ERK1/2-mediated phosphorylation at Serine 62 and thus reducing its stability. Decreased Myc activity results in deregulation of T-bet, a key protein involved in NK cell function, which leads to NK cell deactivation. Our study thus provides mechanistic insight int NK cell dysfunctionality in TNBC and lays down the proof of principle for an NK-cell-targeting TNBC immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-025-66266-x
  6. Nat Commun. 2025 Dec 10.
    MCARE enhances SERCA1 activity in fast-twitch muscle to maintain calcium handling and muscle integrity.
    Takashi Sasaki, Hayataka Takase, Michinori Koebis, Atsu Aiba, Yu Takahashi, Yoshio Yamauchi, Ryuichiro Sato.
      The release of Ca2+ from the sarcoplasmic reticulum into the cytoplasm, followed by its reuptake by sarco/endoplasmic reticulum Ca2+ ATPase (SERCA), is critical for the muscle contraction-relaxation cycle. In this study, we identify a small transmembrane protein, predominantly expressed in fast-twitch muscles, which regulates SERCA1 activity. This protein, termed muscle-enriched Ca2+ regulator (MCARE), enhances SERCA1 function by competitively inhibiting myoregulin, a muscle-specific micropeptide that otherwise suppresses SERCA1 activity. By facilitating more efficient Ca2+ clearance from the cytoplasm, MCARE accelerates muscle relaxation. Mcare-deficient mice exhibit symptoms resembling muscular dystrophy, including progressive muscle wasting in fast-twitch muscles, reduced muscle strength, and increased susceptibility to exercise-induced muscle damage. Notably, these mice also present with distinctive rippling muscle contractions. Our findings establish MCARE as a key regulator of SERCA1 activity, essential for maintaining Ca2+ homeostasis and the functional integrity of fast-twitch muscle fibers.
    DOI:  https://doi.org/10.1038/s41467-025-67358-4
  7. Cell Death Dis. 2025 Dec 08.
    Long non-coding RNAs in cancer glycolysis and metabolism: mechanisms and translational opportunities.
    Yaru Ren, Ziyu Zhang, Xudong Lei, Lei Shi.
      Long non-coding RNAs (lncRNAs) have emerged as critical regulators of cancer metabolism, particularly in the reprogramming of glycolysis that supports tumor growth and survival. Once considered non-functional genomic "noise", lncRNAs influence metabolic adaptation by modulating glycolytic enzymes, transcription factors, and signaling pathways, while also shaping the tumor microenvironment through immune and stromal interactions. In addition, lncRNA-encoded micropeptides provide an extra layer of metabolic control, underscoring their functional diversity. These features indicate lncRNAs as promising diagnostic biomarkers and therapeutic targets, particularly in the context of personalized cancer treatments. RNA-based therapies demonstrate preclinical efficacy in targeting glycolytic lncRNA and reversing drug resistances. Nonetheless, challenges remain, including delivery specificity, off-target effects, and limited clinical validation. Advances in single-cell multi-omics, spatial transcriptomics, and artificial intelligence may offer new avenues to overcome these challenges. Collectively, lncRNAs represent both mechanistic drivers of glycolysis and promising targets for innovative diagnostic and therapeutic strategies in cancer.
    DOI:  https://doi.org/10.1038/s41419-025-08289-2
  8. Poult Sci. 2025 Dec 05. pii: S0032-5791(25)01446-4. [Epub ahead of print]105(1): 106206
    LncRNA HAND2OT encoding micropeptide regulates the estradiol secretion, proliferation and apoptosis of ovarian follicular theca cells in chickens.
    Xinmei Shu, Qingqing Wei, Li Kang, Yi Sun, Yunliang Jiang.
      Long non-coding RNAs (lncRNAs) are critical regulators of ovarian follicular development. In chicken ovarian follicles, theca cells are primarily responsible for androgen and estradiol biosynthesis and play an important role in chicken follicular development, however, the function of lncRNAs in chicken theca cells remains unknown. This study characterized a novel lncRNA HAND2OT (heart and neural crest derivatives expressed 2 overlapping transcript) and elucidated its role in chicken theca cells. With a full length of 950 nt, HAND2OT was localized predominantly in the cytoplasm. The expression of HAND2OT was highest in large white follicles (LW), increased progressively from F6 to F1 follicles, declined in granulosa cells but increased in theca cells following follicle selection. HAND2OT expression was upregulated by estradiol, while downregulated by progesterone and follicle-stimulating hormone (FSH). Functionally, HAND2OT suppressed estradiol secretion, inhibited theca cell proliferation by inducing cell cycle arrest at the G0/G1 phase and promoted apoptosis. The open reading frame 2(ORF2) of HAND2OT encoded a 66-amino-acid peptide (HAND2OT-66aa) exerting no effect on HAND2OT expression. Both the lncRNA HAND2OT lacking the HAND2OT-66aa and HAND2OT-66aa itself exhibited weaker effects on the cell proliferation and apoptosis of theca cells, compared with the full length HAND2OT, suggesting that HAND2OT regulates the survival and function of chicken theca cells via its RNA moiety and the HAND2OT-66aa micropeptide it encodes.
    Keywords:  Chicken; HAND2OT; LncRNA; Ovarian follicle; Theca cell
    DOI:  https://doi.org/10.1016/j.psj.2025.106206
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