bims-micpro 2025-04-20 papers

bims-micpro

Biomed News

on Discovery and characterization of microproteins

Issue of 2025–04–20
seven papers selected by
Thomas Farid Martínez, University of California, Irvine

Eukaryotic Microproteins.
Emerging roles for microproteins as critical regulators of endoplasmic reticulum function and cellular homeostasis.
RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling.
lncRNA-Encoded Small Peptide Promotes Viral Infection.
Expression of De Novo Open Reading Frames in Natural Populations of Drosophila melanogaster.
Analysis of RNA translation with a deep learning architecture provides new insight into translation control.
A microprotein encoded by LINC00263 promotes breast cancer osteolytic bone metastasis by inducing osteoclastogenesis and inhibiting osteoclast ferroptosis.

Annu Rev Biochem. 2025 Apr 17.

Eukaryotic Microproteins.

Nadiya Jaunbocus, Valerie Ebenki, Haomiao Su, Sarah A Slavoff.

Microproteins are polypeptides of 100-150 amino acids or fewer that have not been annotated by genome annotation consortia, given their small size and other noncanonical properties. Translated microproteins are now known to number in the thousands in the human genome, to function in critical cellular and physiological processes, and to be dysregulated or mutated in diseases including neurodegeneration and cancer. Knowledge about microproteins has rapidly accumulated since the advent of ribosome profiling enabled their global discovery 15 years ago. In this review, we summarize what is known about eukaryotic microprotein discovery, the sequences and expression mechanisms of small open reading frames, and microprotein functions from yeast to human.

DOI: https://doi.org/10.1146/annurev-biochem-080124-012840
Semin Cell Dev Biol. 2025 Apr 16. pii: S1084-9521(25)00018-7. [Epub ahead of print]170 103608

Emerging roles for microproteins as critical regulators of endoplasmic reticulum function and cellular homeostasis.

Taylor M Coughlin, Catherine A Makarewich.

  The endoplasmic reticulum (ER) is a multifunctional organelle essential for key cellular processes including protein synthesis, calcium homeostasis, and the cellular stress response. It is composed of distinct domains, such as the rough and smooth ER, as well as membrane regions that facilitate direct communication with other organelles, enabling its diverse functions. While many well-characterized ER proteins contribute to these processes, recent studies have revealed a previously underappreciated class of small proteins that play critical regulatory roles. Microproteins, typically under 100 amino acids in length, were historically overlooked due to size-based biases in genome annotation and often misannotated as noncoding RNAs. Advances in ribosome profiling, mass spectrometry, and computational approaches have now enabled the discovery of numerous previously unrecognized microproteins, significantly expanding our understanding of the proteome. While some ER-associated microproteins, such as phospholamban and sarcolipin, were identified decades ago, newly discovered microproteins share similar fundamental characteristics, underscoring the need to refine our understanding of the coding potential of the genome. Molecular studies have demonstrated that ER microproteins play essential roles in calcium regulation, ER stress response, organelle communication, and protein translocation. Moreover, growing evidence suggests that ER microproteins contribute to cellular homeostasis and are implicated in disease processes, including cardiovascular disease and cancer. This review examines the shared and unique functions of ER microproteins, their implications for health and disease, and their potential as therapeutic targets for conditions associated with ER dysfunction.

Keywords:  Calcium; Cellular stress response; Endoplasmic reticulum; Micropeptide; Microprotein; sORF

DOI:  https://doi.org/10.1016/j.semcdb.2025.103608
Brief Bioinform. 2025 Mar 04. pii: bbaf164. [Epub ahead of print]26(2):

RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling.

Chun Shen Lim, Alexandra K Gibbon, Anh Thu Tran Nguyen, Gabrielle S W Chieng, Chris M Brown.

  Ribosome profiling is a high-throughput sequencing technique that captures the positions of translating ribosomes on RNAs. Recent advancements in ribosome profiling include achieving highly phased ribosome footprints for plant translatomes and more recently for bacterial translatomes. This substantially increases the specificity of detecting open reading frames (ORFs) that can be translated, such as small ORFs located upstream and downstream of the annotated ORFs. However, most genomes (e.g. bacterial genomes) lack the annotations for the transcription start and termination sites. This hinders the systematic discovery of novel ORFs in the 'untranslated' regions in ribosome profiling data. Here, we develop a new computational pipeline called RIBOSS to discover noncanonical ORFs and assess their translational potential against annotated ORFs. The RIBOSS Python modules are versatile, and we use them to analyse both prokaryotic and eukaryotic data. We present a resulting list of noncanonical ORFs with high translational potential in Homo sapiens, Arabidopsis thaliana, and Salmonella enterica. We further illustrate RIBOSS utility when studying organisms with incomplete transcriptome annotations. We leverage long-read and short-read data for reference-guided transcriptome assembly and highly phased ribosome profiling data for detecting novel translational events in the assembled transcriptome for S. enterica. In sum, RIBOSS is the first integrated computational pipeline for noncanonical ORF detection and translational potential assessment that incorporates long- and short-read sequencing technologies to investigate translation. RIBOSS is freely available at https://github.com/lcscs12345/riboss.

Keywords:  Nanopore long-read direct RNA sequencing; gene annotation; protein synthesis; ribosome profiling analysis method; transcriptome assembly

DOI:  https://doi.org/10.1093/bib/bbaf164
Mol Plant Pathol. 2025 Apr;26(4): e70084

lncRNA-Encoded Small Peptide Promotes Viral Infection.

Yaoyao Li, Juan Zhang, Chunyan Qi, Qitao Mo, Kaili Zhong, Jiaqian Liu, Hailin Cai, Jianyong Li, Jianping Chen, Jian Yang, Peng Liu.

  The small open reading frames (ORFs) embedded in lncRNA have been identified to encode biologically functional peptides in many species. However, the function of lncRNA-encoded small peptides in the plant antiviral response remains unclear. In this study, an lncRNA Talnc54748 was identified, which encodes the small peptide ORF4. Transgenic Nicotiana benthamiana overexpressing ORF4 could enhance wheat yellow mosaic virus (WYMV) infection. RNA-sequencing analysis revealed that many genes in plant hormone signalling and MAPK signalling pathways were reduced in ORF4-overexpressing lines. The function of SAUR21 and MKK2, involved in plant hormone signalling and MAPK signalling pathways, respectively, was investigated by virus-induced gene silencing assay. Silencing SAUR21 or MKK2 in wheat and N. benthamiana enhanced WYMV infection. Transgenic overexpression of ORF4 not only enhanced the accumulation of tobacco mosaic virus (TMV) and tomato mosaic virus (ToMV), but also promoted Phytophthora capsici or Pseudomonas syringae pv. tomato DC3000 infection. Our results demonstrated that an lncRNA-encoded small peptide plays an important role in plant immunity and provides new insights into the roles of this lncRNA-encoded small peptide in the plant antiviral response.

Keywords:  lncRNA; plant immunity; small peptide; virus; wheat

DOI:  https://doi.org/10.1111/mpp.70084
J Exp Zool B Mol Dev Evol. 2025 Apr 15.

Expression of De Novo Open Reading Frames in Natural Populations of Drosophila melanogaster.

Amanda Glaser-Schmitt, Marie Lebherz, Ezgi Saydam, Erich Bornberg-Bauer, John Parsch.

  De novo genes, which originate from noncoding DNA, are known to have a high rate of turnover over short evolutionary timescales, such as within a species. Thus, their expression is often lineage- or genetic background-specific. However, little is known about their levels and breadth of expression as populations of a species diverge. In this study, we utilized publicly available RNA-seq data to examine the expression of newly evolved open reading frames (neORFs) in comparison to non- and protein-coding genes in Drosophila melanogaster populations from the derived species range in Europe and the ancestral range in sub-Saharan Africa. Our datasets included two adult tissue types as well as whole bodies at two temperatures for both sexes and three larval/prepupal developmental stages in a single tissue and sex, which allowed us to examine neORF expression and divergence across multiple sample types as well as sex and population. We detected a relatively large proportion (approximately 50%) of annotated neORFs as expressed in the population samples, with neORFs often showing greater expression divergence between populations than non- or protein-coding genes. However, differential expression of neORFs between populations tended to occur in a sample type-specific manner. On the other hand, neORFs displayed less sex-biased expression than the other two gene classes, with the majority of sex-biased neORFs detected in whole bodies, which may be attributable to the presence of the gonads. We also found that neORFs shared among multiple lines in the original set of inbred lines in which they were first detected were more likely to be both expressed and differentially expressed in the new population samples, suggesting that neORFs at a higher frequency (i.e. present in more individuals) within a species are more likely to be functional.

Keywords:  de novo genes; gene expression; genome evolution; innovations; novelty; population genetics

DOI:  https://doi.org/10.1002/jez.b.23297
Nucleic Acids Res. 2025 Apr 10. pii: gkaf277. [Epub ahead of print]53(7):

Analysis of RNA translation with a deep learning architecture provides new insight into translation control.

Xiaojuan Fan, Tiangen Chang, Chuyun Chen, Markus Hafner, Zefeng Wang.

Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human transcripts, our model learned hidden rules of translation control and achieved a near perfect prediction of canonical translation sites across entire human transcriptome. Surprisingly, this model revealed a new role of codon usage in regulating translation termination, which was experimentally validated. We also identified thousands of new open reading frames in mRNAs or lncRNAs, some of which were confirmed experimentally. The model trained with human mRNAs achieved high prediction accuracy of canonical translation sites in all eukaryotes and good prediction in polycistronic transcripts from prokaryotes or RNA viruses, suggesting a high degree of conservation in translation control. Collectively, we present TranslationAI (https://www.biosino.org/TranslationAI/), a general and efficient deep learning model for RNA translation that generates new insights into the complexity of translation regulation.

DOI: https://doi.org/10.1093/nar/gkaf277
Oncogene. 2025 Apr 12.

A microprotein encoded by LINC00263 promotes breast cancer osteolytic bone metastasis by inducing osteoclastogenesis and inhibiting osteoclast ferroptosis.

Suwen Chen, Miaoling Tang, Xuexin Yu, Wanying Qian, Yingru Xu, Jun Li, Geyan Wu, Shuxia Zhang.

Currently, there are no effective prevention or therapeutic methods for breast cancer bone metastasis (BC-BM), which leading to severe skeletal complications and increased mortality. Understanding the mechanisms underlying BC-BM could provide potential strategies for its prevention and treatment. In this study, we identified a new microprotein encoded by lncRNA LINC00263, which we named LINC00263-encoded protein (LINC00263-P), was significantly upregulated in bone metastatic breast cancer tissues and correlated with BC-BM. Overexpression of LINC00263 significantly promoted BC-BM, while treatment with the neutralizing anti-LINC00263-P antibody effectively inhibited BC-BM. Mechanically, the LINC00263-P binds to integrin αvβ3 for activating Src/Syk/Vav-3 axis and yes-associated protein 1 (YAP1) pathway, which enhanced osteoclastogenesis and diminishes ferroptosis in osteoclasts, thereby creating an osteolytic bone metastasis niche that fosters BC-BM. Importantly, treatment with angoroside C, an active component from the traditional Chinese medicine Scrophulariae Radix extract, effectively blocked the binding of LINC00263-P to αvβ3, thereby inhibiting abnormal osteoclastogenesis and preventing BC-BM. These findings highlight the crucial role of microprotein LINC00263-P in disrupting bone homeostasis and propose a potential molecular mechanism of BC-BM.

DOI: https://doi.org/10.1038/s41388-025-03400-5