bims-micpro 2026-06-28 papers

bims-micpro

Biomed News

on Discovery and characterization of microproteins

Issue of 2026–06–28
nine papers selected by
Thomas Farid Martínez, University of California, Irvine

An immune-associated mitochondrial DNA variant with sex differences reveals a putative novel microprotein called MASL.
Predicted bacterial uRBSs reveal translational coupling and ribosome-mediated RBS occlusion as gene-controlling mechanisms.
A microprotein encoded by FERMT3 modulates endothelial cell protein catabolism and induces cell cycle arrest and senescence.
Hidden in the Pangenome? Machine Learning-Driven Discovery of Antimicrobial Potential in Corynebacterium glutamicum.
Small peptides guard the gate of plant immunity.
In Vivo ORF Overexpression Screening Identifies CCN4 as a Regulator of Glioblastoma Growth Validated Across Multiple Models.
PIGBOS-CLCC1 interaction shapes cellular calcium dynamics and energy metabolism.
Peptides in the Diagnosis and Treatment of Pancreatic Cancer and Other Pancreatic Diseases from Basic Research to Clinical Translation.
Circulating mitochondrial-derived microproteins at rest and in response to an acute bout of endurance exercise in individuals with cerebral palsy.

Immun Ageing. 2026 Jun 23.

An immune-associated mitochondrial DNA variant with sex differences reveals a putative novel microprotein called MASL.

Ana R Silverstein, Thalida E Arpawong, Eileen M Crimmins, Tae Jung Oh, Rong Lu, Melanie Flores, Hiroshi Kumagai, Junxiang Wan, Hemal H Mehta, Kelvin Yen, Brendan Miller, Yeachan Lee, Anna Nogalska, Pinchas Cohen.

  The use of mitochondrial wide association studies (MiWAS) to link mitochondrial DNA variants (mtSNPs) to phenotypes of interest has uncovered important connections between mitochondrial genes and human health. The recent introduction of a re-annotated mitochondrial genome that accounts for small open reading frames (sORFs) with protein coding potential suggests the existence of mitochondrial-derived microproteins, many of which remain uncharacterized. Thus, considering the re-annotated mitochondrial genome when conducting genomic analyses such as MiWAS facilitates the mapping of mtSNPs back to microprotein-encoding sORFs and uncovers interactions between mitochondrial microproteins and biological systems. Here, we employ MiWAS of venous blood samples from the Health and Retirement Study (HRS) and identify a mtSNP associated with sex-specific changes to immune composition. After accounting for re-annotation, we map the identified mtSNP back to a sORF that encodes a novel microprotein, termed MASL (Mitochondrial Associated Small d-Loop peptide). Complementary phenome-wide association studies (PheWAS) in HRS and and UK Biobank confirm interactions between this mtSNP and immune phenotypes of interest, and our targeted RNA-Seq method (mitoSNP-seq) elucidates sex-differences in gene expression and functional pathways potentially altered by this mtSNP that may be relevant to the associated microprotein. Early characterization of the MASL microprotein shows sex-differences in circulating MASL levels in human plasma, and sex-specific interactions when comparing male and female mice treated with synthesized MASL. Together, the results of this study not only contribute to our understanding of mitochondrial dynamics in immunity, but also provide early characterization of a novel mitochondrial-derived microprotein with sex-specific modulatory effects.

Keywords:  Genomics; Immunity; Metabolism; Mitochondria; Mitochondrial microproteins; Sex-dimorphism

DOI:  https://doi.org/10.1186/s12979-026-00576-6
Microlife. 2026 ;7 uqag021

Predicted bacterial uRBSs reveal translational coupling and ribosome-mediated RBS occlusion as gene-controlling mechanisms.

Theresa Dietz, Julian M Hahnfeld, Sophie Neumann, Yonca A Reinsch, Tessa Wenz, Susanne Barth-Weber, Jochen Blom, Alexander Goesmann, Elena Evguenieva-Hackenberg.

  Upstream open reading frames (uORFs) in the 5' leader of bacterial mRNAs can modulate gene expression, yet genome-wide identification remains limited. We combined bioinformatic prediction of ribosome-binding sites (RBSs)-a Shine-Dalgarno sequence and a start codon-with experimental validation to uncover new uORFs in Sinorhizobium meliloti 2011. From totally 1106 predicted upstream RBSs (uRBSs), we first examined 15 candidates using eGFP reporters and integrating existing RNA-seq and Ribo-seq data. Translation was detected at 13 sites, with fluorescence intensity broadly correlating with predicted initiation rates. Two uRBSs correspond to gene start sites, thereby refining gene annotations. In nine cases, uRBS mutations affected downstream gene expression in reporter fusions. Among others, the data suggests that a Type I secretion system operon, the RNA chaperone gene hfq, and metabolic genes are regulated by uORFs. Four uORFs acted through translational coupling. We also identified uRBSs that were ribosome-occupied yet (nearly) silent in eGFP assays, and closely spaced to the downstream main RBS (mRBS). These uRBSs probably mediate ribosomal occlusion downregulating lacR and SM2011_RS36230. A re-screen of the prediction set revealed 335 close uRBS/mRBS pairs. Three of them were analyzed, supporting the proposed ribosomal occlusion mechanism for SM2011_RS03630 and SM2011_RS22110, while for glnK translational coupling to an uORF was suggested. These results indicate that uORFs are more widespread in bacteria than previously recognized and suggest that direct ribosomal occlusion of the mRBS is a novel mechanism for down-regulating protein synthesis.

Keywords:  Sinorhizobium meliloti; alphaproteobacteria; mRNA leader; ribosome binding site occlusion; small open reading frame; translational coupling; upstream Shine–Dalgarno sequence; upstream open reading frame; upstream ribosome binding site

DOI:  https://doi.org/10.1093/femsml/uqag021
Cell Commun Signal. 2026 Jun 25. pii: 372. [Epub ahead of print]24(1):

A microprotein encoded by FERMT3 modulates endothelial cell protein catabolism and induces cell cycle arrest and senescence.

Manav Raheja, Beyza Güven, Witold Szymanski, Stefan Günther, Carsten Kuenne, Vladislav Rakultsev, Marta Segarra, Süleyman Bozkurt, Christian Münch, Manuel Kaulich, Johannes Graumann, Ingrid Fleming, Mauro Siragusa.

   BACKGROUND: Endothelial cells express numerous microproteins (miPs) encoded by small open reading frames (smORFs), yet the biological function of most remains unknown. This study set out to characterize a novel 69 amino acid miP encoded within the FERM domain containing kindlin-3 transcript (miP-FERMT3), which is upregulated under inflammatory conditions.
METHODS: Confocal microscopy was used to determine miP-FERMT3 localization, and its interaction partners were determined by mass spectrometry and immunoblotting. RNA sequencing and quantitative mass spectrometry were performed to assess transcriptional and proteomic alterations. Cell proliferation and cell cycle progression were examined by live cell imaging, EdU incorporation and flow cytometry, while senescence was determined by β-galactosidase staining, live cell imaging and RT-qPCR-based analysis of telomere length.
RESULTS: In endothelial cells, miP-FERMT3 localized mainly to centriole subdistal appendages, where it colocalized with ninein and CEP170 and induced centrosome amplification. The expression of miP-FERMT3 caused cell cycle arrest and DNA damage, evidenced by γ-H2AX foci and nuclear p53 accumulation. Consistent with this, miP-FERMT3-expressing endothelial cells exhibited downregulation of genes required for cell-cycle progression and upregulation of genes involved in cell cycle inhibition and senescence. However, canonical p53 target genes were not induced and cell cycle arrest occurred independently of p53. Mechanistically, miP-FERMT3 interacted with proteins involved in ubiquitin/proteasome-dependent protein catabolism, including PSMD9, CUL2 and TRIM8, and its expression increased protein ubiquitination, centrosomal neddylation and proteasomal activity. Notably, enhanced proteasomal turnover of p21 in miP-FERMT3-expressing endothelial cells resulted in replication stress, as evidenced by increased CHK1 phosphorylation. These alterations culminated in rapid induction of cellular senescence, characterized by enlarged cell size, β-galactosidase activity, telomere shortening and a paracrine pro-inflammatory activation of naïve endothelial cells. Analyses of independent murine and human transcriptomic and proteomic aging datasets further revealed that FERMT3 expression and protein abundance increase with age.
CONCLUSIONS: miP-FERMT3 is a novel regulator of protein catabolism that promotes p21 degradation, replication stress and p53-independent cell cycle arrest and senescence in endothelial cells. Given the aging-associated upregulation of FERMT3 in mouse and human endothelial cells, increased miP-FERMT3 expression may contribute to the onset of vascular senescence as a hallmark of aging.

Keywords:  Endothelial cell; Microprotein; Proteasome; Protein ubiquitination; Senescence; smORF

DOI:  https://doi.org/10.1186/s12964-026-03019-3
Bioinform Biol Insights. 2026 ;20 11779322261461933

Hidden in the Pangenome? Machine Learning-Driven Discovery of Antimicrobial Potential in Corynebacterium glutamicum.

Sk Injamamul Islam, Khandker Shahed, Mst Mahmuda Parvin, Saloa Sanjida.

  Antimicrobial resistance poses an increasing global challenge, driving the urgent need for alternative strategies to identify novel therapeutic agents. Microbial natural products encoded by biosynthetic gene clusters (BGCs) remain among the most promising sources of bioactive compounds. Although Corynebacterium glutamicum is best known as an industrial producer of amino acids, its potential as a producer of secondary metabolites has not been comprehensively assessed, despite the availability of numerous high-quality genome sequences. In this study, we carried out a comparative pangenome analysis of 36 complete C. glutamicum genomes and systematically mined for BGCs to explore the species' biosynthetic repertoire. Our analysis revealed variation in BGC content among strains, with several isolates harboring more hybrid clusters than others, suggesting metabolic diversity across the species. In addition to conserved terpene biosynthetic pathways, we detected polyketide-associated clusters not previously reported in C. glutamicum, expanding its recognized metabolic potential. RiPP-like clusters, including Lactococcin-related variants, were also identified, highlighting an underexplored reservoir of antimicrobials. To prioritize candidates for future validation, Support Vector Machine, Random Forest, and k-Nearest Neighbor models were trained on Composition, Transition, and Distribution (CTD) physicochemical sequence features and applied to genome-mined small open reading frames. The models demonstrated strong predictive performance, with the Support Vector Machine achieving the highest accuracy (84.1%), F1 score (83.8%), and area under the ROC curve (AUC = 0.920). After removing duplicate sequence IDs and applying a high-confidence AMP probability threshold (≥0.95), 18 unique AMP-like candidates were identified as promising. Overall, this study presents C. glutamicum as a promising source of bioactive metabolite candidates and shows how pangenome-scale mining combined with machine learning can support antimicrobial peptide discovery while still requiring experimental validation of the predicted leads.

Keywords:  antimicrobial peptides; bacteria; biosynthetic gene; machine learning; pangenome

DOI:  https://doi.org/10.1177/11779322261461933
Trends Plant Sci. 2026 Jun 23. pii: S1360-1385(26)00181-0. [Epub ahead of print]

Small peptides guard the gate of plant immunity.

Nicole A Freeman, Ujjal J Phukan, Yiqing Wang, Sydney A Greer, M Shahid Mukhtar.

  An upstream open reading frame-encoded peptide mediates rapid systemic stomatal immunity by moving from infected leaves to distal guard cells, where a receptor complex triggers Ca2+-dependent vacuolar remodeling and stomatal closure (Liu et al.). In this article, we discuss this concept, its limitations, and future implications for immune network integration.

Keywords:  metacaspase; receptor kinases; systemic stomatal immunity; uORF

DOI:  https://doi.org/10.1016/j.tplants.2026.05.016
Int J Mol Sci. 2026 Jun 09. pii: 5227. [Epub ahead of print]27(12):

In Vivo ORF Overexpression Screening Identifies CCN4 as a Regulator of Glioblastoma Growth Validated Across Multiple Models.

Pushan Dasgupta.

  Despite current multimodal therapies for glioblastoma (GBM), its prognosis remains grim. Thus, a tremendous need exists to identify new genetic drivers that may serve as potential therapeutic targets in glioblastoma (GBM). We describe an in vivo overexpression screening strategy to identify drivers of glioblastoma where we have leveraged TCGA datasets to conduct a functional genomics screen of prioritized open reading frames (ORFs) that are overexpressed and/or amplified in GBM. To interrogate these potential drivers within a more relevant physiological context, the screening was accomplished in vivo in an orthotopic patient-derived glioma stem-like cell (GSC) model. Among 5 positive "hits" from the screen, Cellular Communication Network factor 4 (CCN4) was prioritized for further evaluation. Our functional analyses demonstrated that CCN4 overexpression drives tumor growth in multiple GBM models. Depletion of CCN4 reduced growth in vitro and in vivo and markedly decreased colony formation with the growth phenotype restored upon ectopic expression of CCN4. Structural functional analysis of CCN4 was also conducted. We believe that this screening strategy can serve as a platform for further identification and validation of drivers of GBM.

Keywords:  CCN4; functional genomics; glioblastoma; glioma; high-grade glioma; in vivo screen; overexpressed driver

DOI:  https://doi.org/10.3390/ijms27125227
Cell Commun Signal. 2026 Jun 25.

PIGBOS-CLCC1 interaction shapes cellular calcium dynamics and energy metabolism.

Seemanti Aditya, Amal Kanti Bera.

  PIGBOS is a recently identified 54-amino acid microprotein localized to the mitochondrial outer membrane and implicated in the endoplasmic reticulum (ER) stress response. Here, we identify a previously unrecognized role for PIGBOS in cellular Ca2+ homeostasis. Manipulation of PIGBOS expression in HEK293T cells revealed that PIGBOS enhances Ca2+ signaling by promoting ER Ca2+ release through inositol 1,4,5-trisphosphate (IP3) receptors and subsequent mitochondrial Ca2+ uptake in response to histamine stimulation. In contrast, siRNA-mediated depletion or genetic ablation of PIGBOS markedly attenuated these responses. PIGBOS influenced Ca2+ transfer from the ER to mitochondria without affecting direct mitochondrial Ca2+ uptake and also promoted store-operated Ca2+ entry. Functional analyses demonstrated that the interaction of PIGBOS with the ER-resident chloride channel CLCC1 via its C-terminal region is required for this activity. Network analysis predicted a direct association between PIGBOS and CLCC1, as well as indirect connections with core Ca2+ signaling components, including IP3 receptors, STIM1, Orai1, and SERCA, whose expression was altered upon modulation of PIGBOS abundance. Loss of PIGBOS impaired mitochondrial respiration, reduced ATP production, and increased reactive oxygen species. Together, these findings establish PIGBOS as a key regulator of ER-mitochondrial Ca2+ signaling that couples Ca2+ dynamics to mitochondrial bioenergetics and cellular stress responses.

Keywords:  CLCC1; Calcium signaling; Microprotein; PIGBOS

DOI:  https://doi.org/10.1186/s12964-026-03027-3
Drug Des Devel Ther. 2026 ;20 610190

Peptides in the Diagnosis and Treatment of Pancreatic Cancer and Other Pancreatic Diseases from Basic Research to Clinical Translation.

Guangshuo Gan, Xiaonan Zhang, Yao Xu, Kunling Bai, Xiangyun Yan, Deshi Dong, Hong Xiang, Xufeng Tao.

  Peptides have emerged as pivotal agents in biomedicine due to their exceptional physicochemical properties, including high binding affinity, minimal immunogenicity, and precise target specificity. This review critically examines recent advancements in peptide-based strategies for pancreatic disorders, encompassing inflammatory conditions (e.g. pancreatitis), metabolic dysfunctions (e.g. diabetes), and notably, pancreatic cancer. We delineate the evolution of peptide therapeutics, emphasizing rational drug design approaches such as backbone cyclization and N-methylation to enhance metabolic stability, complemented by computational methodologies like molecular docking and AI-driven affinity maturation to optimize target engagement. The discussion highlights key innovations, including peptide probes for early diagnostic detection and peptide-drug conjugates for targeted intervention, while evaluating their efficacy in preclinical models and assessing their biosafety profiles. Furthermore, we survey current clinical trials aimed at translating these engineered peptides into clinical applications. Concluding with a perspective on precision medicine, we outline future trajectories necessitating advanced AI-integrated design frameworks and robust clinical validation to accelerate the bench-to-bedside translation of peptide technologies.

Keywords:  clinical translation; diagnosis and therapy; pancreatic diseases; peptides

DOI:  https://doi.org/10.2147/DDDT.S610190
Exp Physiol. 2026 Jun 25.

Circulating mitochondrial-derived microproteins at rest and in response to an acute bout of endurance exercise in individuals with cerebral palsy.

Oscar Horwath, Linnéa Corell, Junxiang Wan, Emma Hjalmarsson, Julia Starck, Stefan M Reitzner, Jessica Norrbom, Rodrigo Fernandez-Gonzalo, Ola Kvist, Pinchas Cohen, Ferdinand von Walden, Sebastian Edman.

  Regular exercise using assistive movement devices, such as running frames, has emerged as a promising strategy to improve cardiorespiratory fitness in individuals with cerebral palsy (CP). However, the molecular pathways underlying these adaptations remain poorly understood. Here, we examined a novel class of signalling molecules, mitochondrial-derived microproteins (MDPs), and assessed whether individuals with CP exhibit altered circulating levels compared with typically developing (TD) individuals at rest and following an acute bout of endurance exercise. Three groups were included: TD adults (31 ± 6 years), TD adolescents (16 ± 1 years) and adults with CP (25 ± 6 years). Individuals with CP were classified as Gross Motor Function Classification System (GMFCS) levels II-IV and had at least 3 months of frame running experience. Habitual physical activity, ultrasound-derived muscle thickness, and peak oxygen uptake were assessed. The exercise session consisted of 45 min of frame running for individuals with CP and conventional running for TD participants. Blood samples were obtained before and 1 h after exercise, and plasma MDP concentrations were measured using in-house enzyme-linked immunosorbent assay. Adults with CP had reduced muscle mass and maximal oxygen uptake compared to TD individuals. Despite this, they exhibited basal circulating levels of MDPs, including humanin, MOTS-c and SHMOOSE, comparable to TD adults and adolescents, with no associations with CP subtype or motor impairment severity. Following exercise, circulating MDPs showed no or only modest changes across groups, with no differences between CP and TD individuals. Overall, these findings suggest preserved mitochondrial-derived signalling via MDPs in individuals with CP.

Keywords:  MOTS‐c; SHMOOSE; cerebral palsy; frame running; humanin; physical exercise

DOI:  https://doi.org/10.1113/EP093298