bims-micpro 2025-06-29 papers

bims-micpro

Biomed News

on Discovery and characterization of microproteins

Issue of 2025–06–29
ten papers selected by
Thomas Farid Martínez, University of California, Irvine

Microproteins in Metabolism.
LncRNA-Encoded Micropeptides: Expression Validation, Translational Mechanisms, and Roles in Cellular Metabolism.
Hiding in plain sight: advances in discovery and functional description of plant sORF encoded peptides.
Translational landscape provides insight into the molecular mechanism of heterosis in inter-subspecific hybrid rice.
LncRNA H19-Encoded Micropeptide altH19 Promotes DNA Replication and Mitosis in Myeloma Cells by Enhancing the Phosphorylation of CDK2 at Threonine 160.
The dual-coding gene SLC35A4 protects against oxidative stress.
Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation.
DWORF expression is reduced in a large animal model of Duchenne muscular dystrophy.
Mitochondrial-Derived Peptides as Therapeutics and Biomarkers for Combating Vascular Aging and Associated Cardiovascular Diseases.
Short peptides from Late Embryogenesis Abundant (LEA) proteins tune liquid-liquid phase separation and prevent aggregation.

Cells. 2025 Jun 07. pii: 859. [Epub ahead of print]14(12):

Microproteins in Metabolism.

Caris A Wadding-Lee, Catherine A Makarewich.

  Metabolism is a complex network of biochemical pathways that break down macromolecules to produce energy essential for cellular function. Disruptions in metabolic homeostasis are closely linked to noncommunicable diseases (NCDs) such as cardiovascular disease, type 2 diabetes, and cancer, which are leading causes of death worldwide. Many NCD-associated conditions, including obesity and insulin resistance, stem from metabolic dysfunction, and current therapies often fall short in preventing disease progression, highlighting the need for novel therapeutic targets. Microproteins, small proteins of ≤100-150 amino acids, have recently emerged as important regulators of metabolism. Encoded by short open reading frames (sORFs), many of these proteins were historically overlooked due to their small size and misclassification as noncoding RNAs. Advances in genomics and proteomics have revealed that these sORFs can encode functional proteins with critical roles in metabolic pathways. In this review, we highlight the microproteins involved in energy metabolism, mitochondrial function, and nutrient signaling. We discuss their emerging roles in the pathogenesis of NCDs and explore their potential as novel therapeutic targets. As microprotein biology continues to evolve, these small but powerful regulators may offer new strategies for treating metabolic dysfunction and reducing the global burden of NCDs.

Keywords:  metabolism; microprotein; mitochondrial function; small open reading frame

DOI:  https://doi.org/10.3390/cells14120859
Int J Mol Sci. 2025 Jun 19. pii: 5913. [Epub ahead of print]26(12):

LncRNA-Encoded Micropeptides: Expression Validation, Translational Mechanisms, and Roles in Cellular Metabolism.

Chul Woong Ho, Ji Won Lee, Chang Hoon Shin, Kyung-Won Min.

  The discovery of functional micropeptides encoded by long noncoding RNAs (lncRNAs) has challenged the traditional view that these transcripts lack coding potential. With the advancement of high-resolution translation profiling combined with enhanced MS-based techniques, numerous lncRNAs have been found to harbor small open reading frames (sORFs) that give rise to bioactive micropeptides. These peptides participate in diverse biological processes, particularly in cellular metabolism, by modulating enzymatic activity and metabolic pathways. However, the identification and functional characterization of these micropeptides remain technically challenging due to their small size, low abundance, and the need for rigorous downstream validation studies. This review encompasses a comprehensive overview of the biogenesis of lncRNA-derived micropeptides, methodologies for detecting and validating their expression, the molecular mechanisms governing their translation, and their emerging roles in metabolic regulation. By integrating current findings and technological advancements, we highlight the potential physiological and pathological implications of these micropeptides and outline future research directions in the field.

Keywords:  long noncoding RNA translation; metabolic regulation; micropeptides

DOI:  https://doi.org/10.3390/ijms26125913
J Exp Bot. 2025 Jun 17. pii: eraf240. [Epub ahead of print]

Hiding in plain sight: advances in discovery and functional description of plant sORF encoded peptides.

Alyssa Kearly, Andrew D L Nelson.

  Short open reading frames (sORFs) and their encoded peptides (SEPs) have confounded functional geneticists, as these genes do not fit historical definitions of protein-coding genes. Evading traditional prediction and detection techniques, plant SEP genes have long been neglected in functional studies, but those that have been identified have proven to play numerous critical biological roles. Recent advances in transcriptomics and proteomics have led to the identification of hundreds of putative sORFs and SEPs in plants, some positioned within genes traditionally thought to be non-coding, highlighting a portion of the proteome that has gone unnoticed thus far. In this review, we examine the historical approaches to answering questions on gene function, how they have impacted and continue to impact sORF and SEP identification, and how they have evolved with technological advancements and developments in the field. Additionally, we emphasize the need for functional validation of putative SEPs in an era of high throughput and -omics based approaches, and discuss potential options for such pursuits. The definition, identification, and characterization of SEPs will ultimately allow for more accurate genomic resources and improved tools with which to develop them, pushing towards a more complete understanding of the functional genome.

Keywords:  Functional genomics; Mass spectrometry; Ribo-seq; long non-coding RNAs; sORF-encoded peptides; short open reading frames

DOI:  https://doi.org/10.1093/jxb/eraf240
Plant J. 2025 Jun;122(6): e70297

Translational landscape provides insight into the molecular mechanism of heterosis in inter-subspecific hybrid rice.

Zengde Xi, Mengyao Wang, Fei Wang, Jianbo Wang.

  Heterosis has been widely applied in crop breeding and has significantly improved grain yield worldwide. Many studies have attempted to elucidate heterosis from various perspectives; however, its genetic basis-especially at the translational level-remains elusive. In this study, we performed RNA-seq and ribosome profiling on the inter-subspecific hybrid rice ZY19 (Oryza sativa L. subsp. indica Kato × O. sativa L. subsp. japonica Kato) and its parental lines to examine genome-wide translational dynamics. Differential gene expression between the hybrid and its parents revealed a strong discordance between transcriptional and translational levels, and translational regulation appeared to buffer the transcriptional differences. Although additive and non-additive gene expression patterns shifted during translation, additive expression remained the predominant pattern at the translational level in the hybrid. Moreover, a high proportion of single-parent expression genes also exhibited additive expression. In the hybrid, allele-specific expression (ASE) was differentially regulated in transcription and translation. Notably, cis and trans-regulation tended to function independently in transcription, whereas they were more likely to act together in translation. Finally, we investigated the effects of various regulatory mechanisms and elements on translation and found that genes with more alternative splicing (AS) events had a lower translational efficiency (TE) than genes with fewer AS events. In addition, translation was repressed by the upstream open reading frames (uORFs), downstream open reading frames (dORFs), N6-methyladenosines (m6As) and microRNAs (miRNAs). Overall, our study provides new insights into the molecular mechanisms of heterosis in inter-subspecific hybrid rice.

Keywords:  Oryza sativa L; additive expression; allele‐specific expression; alternative splicing; dORFs; heterosis; m6As; miRNAs; translational regulation; uORFs

DOI:  https://doi.org/10.1111/tpj.70297
Cell Prolif. 2025 Jun 27. e70089

LncRNA H19-Encoded Micropeptide altH19 Promotes DNA Replication and Mitosis in Myeloma Cells by Enhancing the Phosphorylation of CDK2 at Threonine 160.

Yaxin Zhang, Wenjing Li, Xu Cao, Jiwei Mao, Xiaodan Zhou, Linlin Liu, Ruosi Yao.

  Micropeptides are endogenous peptides translated from alternative open reading frames (alt-ORFs) within coding or non-coding genes. Emerging evidence suggests that some micropeptides play critical roles in both physiological and pathological processes. Multiple myeloma (MM), a haematological malignancy, remains incurable due to frequent relapses and a limited understanding of its underlying mechanisms. In this study, we sought to investigate the function and molecular mechanism of a novel micropeptide in MM pathogenesis. We identified a novel micropeptide, altH19, encoded by the lncRNA H19, which is highly expressed in patients of MM. Functional assays revealed that altH19 promotes myeloma cell proliferation and colony formation significantly. Furthermore, altH19 induces multipolar mitosis by upregulating the expression of Aurora B, Centrin 2 and phosphorylated histone H3. Flow cytometry analyses confirmed that overexpression of altH19 enhances DNA replication and accelerates the transition from early to mid-late stages of the DNA replication process. Conversely, knockout of altH19 reverses these effects. Mechanistically, altH19 directly interacts with phosphorylated CDK2 at threonine 160, thereby enhancing CDK2 T160 phosphorylation and activating the downstream E2F1 target RB phosphorylation. Notably, altH19 was able to restore phosphorylation levels of CDK2 and RB that were otherwise suppressed by the CDK2-selective inhibitor Seliciclib. In summary, we identify altH19 as a novel lncRNA-derived micropeptide with a pivotal role in myeloma progression, highlighting the therapeutic potential of targeting the altH19-CDK2-RB axis in MM treatment.

Keywords:  CDK2; DNA replication; micropeptide; mitosis; multiple myeloma

DOI:  https://doi.org/10.1111/cpr.70089
Protein Sci. 2025 Jul;34(7): e70197

The dual-coding gene SLC35A4 protects against oxidative stress.

Ikram Ajala, Imadeddine Tiaiba, Benoît Grondin, Damien Lipuma, Souleimen Jmii, Hiba Benlyamani, Laurent Cappadocia, Benoît Vanderperre.

  Alternative proteins (AltProts) represent a newly recognized class of biologically active proteins encoded from alternative open reading frames (AltORFs) within already annotated genes. This study focuses on the SLC35A4 gene, which encodes both the reference protein SLC35A4 and the alternative protein AltSLC35A4. Using a combination of microscopy and biochemical analyses, we confirmed the presence of AltSLC35A4 in the inner mitochondrial membrane, resolving previous conflicting reports. Previous studies employing ribosome profiling have revealed that during oxidative stress induced by sodium arsenite, the reference coding sequence of SLC35A4 exhibits the largest increase in translational efficiency among all cellular mRNAs. Our results confirmed this translational upregulation, with the emergence of SLC35A4 protein isoforms during oxidative stress in an upstream ORF-dependent manner. Notably, the expression of AltSLC35A4 remained unchanged during oxidative stress. Knock out of SLC35A4 or AltSLC35A4 enhanced sensitivity to oxidative stress in a rescuable manner, indicating a direct implication for these proteins in stress resistance. In conclusion, our research provides compelling evidence for the functional significance of the dual-coding nature of SLC35A4 for resistance to oxidative stress and highlights the importance of considering AltProts in the functional study of eukaryotic genes.

Keywords:  AltSLC35A4; bicistronic eukaryotic gene; integrated stress response; oxidative stress; translational regulation

DOI:  https://doi.org/10.1002/pro.70197
Mol Cell. 2025 Jun 20. pii: S1097-2765(25)00472-1. [Epub ahead of print]

Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation.

Jiemin Nah, Sreya Mahendran, Baptiste Kerouanton, Liang Cui, Daniella H Hock, Alfredo Cabrera-Orefice, Kyle Dunlap, David Robinson, Desmond W H Tung, Sze Huey Leong, Kiat-Yi Tan, Sonia P Chothani, Jingjing Sun, Agnieszka Dziegowska, Grazyna Leszczynska, Owen J L Rackham, Ilka Wittig, Peter Dedon, Gregory S Ducker, David A Stroud, Lena Ho.

  Mitochondrial small open reading frame (ORF)-encoded microproteins (SEPs) are key regulators and components of the electron transport chain (ETC). Although ETC complex I assembly is tightly coupled to nutrient availability, including serine, the coordinating mechanism remains unknown. A genome-wide CRISPR screen targeting SEPs revealed that deletion of the LINC00493-encoded microprotein SMIM26 sensitizes cells to one-carbon restriction. SMIM26 interacts with mitochondrial serine transporters SFXN1/2 and the mitoribosome, forming a functional triad that facilitates translation of the complex I subunit mt-ND5. SMIM26 loss impairs serine import, reduces folate intermediates, and disrupts key mitochondrial tRNA modifications (τm5U and τm5s²U), resulting in ND5 translation failure and complex I deficiency. SMIM26 deletion is embryonic lethal in mice and impedes tumor growth in a xenograft model of folate-dependent acute myeloid leukemia. These findings define SMIM26 as a critical integrator of one-carbon flux and complex I biogenesis and establish a paradigm for localized mitochondrial translation through transporter-ribosome interactions.

Keywords:  complex I; electron transport chain; micropeptides; mitochondria; mitochondrial translation; one-carbon pathway; oxidative phosphorylation; small ORF-encoded peptides

DOI:  https://doi.org/10.1016/j.molcel.2025.05.033
Dis Model Mech. 2025 Jun 01. pii: dmm052285. [Epub ahead of print]18(6):

DWORF expression is reduced in a large animal model of Duchenne muscular dystrophy.

Aaron M Gibson, Xiufang Pan, Omar Brito-Estrada, James A Teixeira, Lauren K Carl, Yongping Yue, Michael L Kamradt, Matthew J Burke, Caris A Wadding-Lee, Gang Yao, Roland W Herzog, Dongsheng Duan, Catherine A Makarewich.

  Duchenne muscular dystrophy (DMD) is a lethal muscle-wasting disease driven by cytosolic calcium overload, which leads to muscle degeneration. Sarco/endoplasmic reticulum calcium ATPase (SERCA), a key regulator of cytosolic calcium levels, exhibits reduced activity in animal models of DMD and human patients. Dwarf open reading frame (DWORF), a positive SERCA regulator, is downregulated in mdx DMD mice, and adeno-associated virus-mediated DWORF overexpression has been shown to ameliorate DMD cardiomyopathy. The canine DMD model provides a crucial bridge for translating findings from mice to humans. To investigate DWORF expression in this model, we developed a canine-specific anti-DWORF antibody, as the existing murine antibody is ineffective. This antibody detected DWORF in human, pig, cat and rabbit muscle, but not in mouse muscle. DWORF was absent in muscle tissues of neonatal normal dogs but highly expressed in those of adult dogs. In DMD-affected dogs aged 8 months or older, DWORF expression was significantly reduced in both cardiac and skeletal muscle. This study establishes a foundation for evaluating DWORF-based gene therapy in the canine DMD model, advancing the potential for clinical translation.

Keywords:   DMD ; Canine model; DWORF; Duchenne muscular dystrophy; SERCA2a

DOI:  https://doi.org/10.1242/dmm.052285
Curr Cardiol Rev. 2025 Jun 20.

Mitochondrial-Derived Peptides as Therapeutics and Biomarkers for Combating Vascular Aging and Associated Cardiovascular Diseases.

Rooban Sivakumar, K A Arul Senghor, V M Vinodhini, Janardhanan Kumar.

  Vascular aging profoundly affects the onset of cardiovascular diseases in the elderly, mostly as a result of mitochondrial dysfunction. This review examines the protective roles of mitochondrial-derived peptides such as humanin, MOTS-c, and small humanin-like peptides in mitigating vascular aging. These peptides, encoded by mitochondrial DNA, are crucial for regulating apoptosis, inflammation, and oxidative stress, which have a major role in vascular health. MDPs have significant prospects as therapeutic and biomarker possibilities for the early diagnosis and intervention of vascular aging. MDPs influence the functions of endothelial and vascular smooth muscle cells by modulating critical signaling pathways, including AMPK, mTOR, and sirtuins. These pathways are essential for facilitating cellular metabolism, enhancing stress resilience, and prolonging longevity. Moreover, MDPs are essential in mitochondrial bioenergetics and dynamics, vital for mitigating endothelial dysfunction and enhancing vascular resilience. Furthermore, MDPs contribute to immunological modulation and the regulation of inflammatory responses, underscoring their potential therapeutic applications in the treatment of age-related vascular disorders. This review analyzes the various functions of MDPs in vascular health and their therapeutic importance, advocating for more studies to optimize their clinical benefits. By understanding the comprehensive roles and mechanisms of these multifunctional peptides, we can better appreciate their capacity to prevent and treat vascular aging and associated cardiovascular disorders. Future research should aim to further elucidate their therapeutic effects and optimize their clinical applications.

Keywords:  Mitochondrial-derived peptides; cardiovascular diseases.; endothelial function; oxidative stress; vascular aging

DOI:  https://doi.org/10.2174/011573403X375709250616134726
Biochem Biophys Res Commun. 2025 Jun 17. pii: S0006-291X(25)00939-8. [Epub ahead of print]776 152224

Short peptides from Late Embryogenesis Abundant (LEA) proteins tune liquid-liquid phase separation and prevent aggregation.

Yinghan Wu, Yusuke V Morimoto, Shinya Ikeno.

  Short peptides derived from Late Embryogenesis Abundant (LEA) proteins are critically important because they appear to exert their protective functions through liquid-liquid phase separation (LLPS) in vivo. Excitingly, confocal fluorescence microscopy revealed that green fluorescent protein (GFP) exhibited a heterogeneous intracellular distribution in Escherichia coli cells co-expressing LEA peptides. Guided by this observation, we conducted in vitro LLPS assays and found that the LEA-II and LEA-K peptides attenuated segregative LLPS while enhancing solution stability in the associative LLPS mode. These data support our hypothesis that LEA peptides function as molecular shields that suppress protein aggregation, thereby improving heterologous protein expression.

Keywords:  Escherichia coli; Intrinsically disordered peptide; Late Embryogenesis Abundant (LEA) peptide; Liquid–liquid phase separation (LLPS); Molecular shielding; Protein aggregation

DOI:  https://doi.org/10.1016/j.bbrc.2025.152224