bims-micpro 2026-02-15 papers

Dev Cell. 2026 Feb 10. pii: S1534-5807(26)00033-X. [Epub ahead of print]

Noncanonical open reading frames from lncRNAs encode functional micropeptides that help shape agronomic traits in rice.

Yu Cheng, Rui-Rui He, Jie Jiang, Lu Yang, Chao Yuan, Yi-Chao Qin, Wen-Long Zhao, Wan-Ting Mo, Yu-Hong Liao, Zheng-Tong Chen, Jun-Jie Feng, Hui-Yin Pang, Ye -Cheng, Meng-Qi Lei, Yan-Fei Zhou, Jian-Ping Lian, Yu-Chan Zhang, Yue-Qin Chen.

Functional open reading frames (ORFs) originating from long noncoding RNAs (lncRNAs) have historically been overlooked, in part due to the technical challenges associated with their identification and detection in plants. Here, we presented a comprehensive analysis by integrating 119 Ribo-seq (ribosome profiling sequencing) datasets from multiple rice tissues and developmental stages, and examined the biological potential of micropeptides encoded by ORFs translated from lncRNAs (lncORFs). 8,253 lncORFs were identified in the rice (Oryza sativa) genome. We confirmed the existence of 776 lncORF micropeptides by analyzing 1,188 mass spectrometry datasets and experimentally validated a set of lncORF-encoded micropeptides. Evolutionary and variant-association analysis pointed to the contributions of lncORF micropeptides to agronomic traits. Specifically, gain/loss-of-function experiments showed that the micropeptides regulate grain yield by affecting the number of small vascular bundles. Our findings expand the known functional scope of lncRNAs and provide valuable resources for rice improvement.

Keywords: Ribo-seq; agronomic traits; lncRNAs; micropeptides; noncanonical open reading frames; rice improvement; translation

DOI: https://doi.org/10.1016/j.devcel.2026.01.010

FEBS J. 2026 Feb 13.

H2-dependent modulation of tetrahydromethanopterin S-methyltransferase (Mtr complex) activity by the small protein MtrR in Methanosarcina mazei.

Tim Habenicht, Bjarne Hastedt, Liam Cassidy, Claudia Kießling, Andreas Tholey, Jan M Schuller, Ruth A Schmitz.

Small open reading frame (sORF)-encoded proteins, with less than 100 amino acids, have attracted increasing attention over the past decade after being overlooked due to limitations in classical methodologies. For the mesophilic archaeal model system Methanosarcina mazei, a high number of previously unannotated sORFs have recently been identified. However, the physiological role of most of the respective small proteins remains unknown. Here, we report on the functional characterization of the small ORF16-encoded small protein MtrR (49 amino acids). We demonstrate that MtrR forms oligomers localized at the cytoplasmic membrane. There, it interacts with the tetrahydrosarcinapterin S-methyltransferase (Mtr), a key membrane-bound complex of energy metabolism, and impacts its activity. In vitro interaction and in vivo copurification assays showed MtrR interaction with the Mtr complex, which was further validated by microscale thermophoresis analysis demonstrating a specific interaction with the MtrA subunit. Analyzing growth under varying molecular hydrogen (H2) availability demonstrated that the mtrR deletion mutant showed significantly impaired growth in the presence of H2, independent of the carbon source. Further, we observed induction of mtrR transcription in the presence of H2. Consequently, we propose that MtrR fine-tunes the activity of the Mtr complex in response to fluctuating H2 availabilities, allowing adaptation of the energy metabolism to changing environmental H2 conditions.

Keywords: Archaea; energy metabolism; membrane transport; methanogenesis; microbiology; protein regulation

DOI: https://doi.org/10.1111/febs.70457

PLoS Pathog. 2026 Feb;22(2): e1013967

Flexibility and modulation of translation initiation in enterovirus genomes.

Rhian L O'Connor, Georgia M Cook, Jacqueline Hankinson, Ksenia Fominykh, Samantha H Cheng, Daniel A Nash, Aurélie Cenier, Komal M Nayak, Stephen C Graham, Janet E Deane, Matthias Zilbauer, Andrew E Firth, Valeria Lulla.

Enteroviruses comprise a large group of mammalian pathogens that often utilize two open reading frames (ORFs) to encode their proteins: the upstream protein (UP) and the main polyprotein. In some enteroviruses, in addition to the canonical upstream AUG (uAUG), there is another AUG that may represent an alternative upstream initiation site. An analysis of enterovirus sequences containing additional upstream AUGs identified several clusters, including strains of pathogenic Enterovirus alphacoxsackie and E. coxsackiepol. Using ribosome profiling on coxsackievirus CVA13 (E. coxsackiepol), we demonstrate that both upstream AUG codons can be used for translation initiation in infected cells. Moreover, we confirm translation from both upstream AUGs using a reporter system. Mutating the additional upstream AUG in the context of CVA13 did not result in phenotypic changes in immortalized cell lines. However, the wild-type virus outcompeted this mutant in human intestinal organoids and differentiated neuronal systems, representing an advantage in physiologically relevant infection sites. Mutation of the stop codon of the shorter upstream ORF led to dysregulated translation of the other ORFs in the reporter system, suggesting a potential role for the additional uORF in modulating the expression level of the other ORFs. Additionally, we demonstrate regulation of uORF translation in response to stress. These findings reveal the remarkable plasticity of enterovirus IRES-mediated initiation and the competitive advantage of double-upstream-AUG-containing viruses in terminally differentiated intestinal organoids and neuronal systems.

DOI: https://doi.org/10.1371/journal.ppat.1013967

Curr Res Microb Sci. 2026 ;10 100559

The lncRNA GAS5-encoded micropeptide facilitates influenza virus replication through modulation of the Wnt/β-catenin signaling pathway.

Xinni Zhou, Xiaojuan Chi, Benqun Peng, Ming Gao, Ning Li, Lu Liu, Jie Zeng, Yuxin Li, Yuzhang Chen, Song Wang.

Long non-coding RNAs (lncRNAs) have been implicated in various cellular processes, including the regulation of gene expression and cellular response to viral infections. Herein, our RNA-seq analysis revealed a significant increase in the expression of an annotated lncRNA, GAS5, following influenza A virus (IAV) infection. Stimulation of cells with type I interferon, type III interferon or IL-6 can also result in upregulation of GAS5 expression. Additionally, overexpression of GAS5 promoted IAV replication, while knockdown of GAS5 decreased viral titers. Notably, we identified a novel 50-amino acid micropeptide encoded by GAS5, named GAS5-P50, through ribosome profiling and mass spectrometry analysis. It was found that overexpression of GAS5-P50 alone could facilitate the replication of IAV; conversely, frameshift mutation-mediated silencing of GAS5-P50 diminished the capacity of GAS5 to promote IAV replication, implying that GAS5-P50 is essential for GAS5-mediated enhancement of viral replication. Moreover, synthetic GAS5-P50 was demonstrated to boost IAV propagation both in vitro and in vivo. Mechanistically, GAS5-P50 interacted with NOTUM, a negative regulator of Wnt signaling, leading to enhanced Wnt/β-catenin pathway activation, which facilitated viral replication. These findings uncover a previously unrecognized function of GAS5 as a proviral lncRNA that encodes a functional micropeptide, which modulates host Wnt/β-catenin signaling to support IAV infection. Our study not only expands the understanding of lncRNA-encoded micropeptides in viral pathogenesis but also highlights GAS5-P50 as a potential target for antiviral intervention.

Keywords: GAS5; Influenza A virus; Long non-coding RNA; Micropeptide; Wnt/β-catenin signaling pathway

DOI: https://doi.org/10.1016/j.crmicr.2026.100559

FEBS J. 2026 Feb 13.

Structural characterization of endogenous microprotein EMBOW reveals an alternative MRT motif for WDR5-interacting site recognition.

Yang Yang, Yan Pan, Shuting Zhang, Haoran Wang, Xuefang Sun, Tianrong Hang, Li Xu.

WD repeat-containing protein 5 (WDR5) is a conserved chromatin regulator that engages numerous binding partners via a central arginine-binding pocket known as the WDR5-interacting (WIN) site. Endogenous microprotein binder of WDR5 (EMBOW, also known as SCRIB overlapping open reading frame protein), recently identified as an endogenous WDR5 interactor, lacks the canonical [ACR]-R-[TASCK] WIN motif, and its mode of recognition remains unknown. Here, we present the 1.80 Å crystal structure of WDR5 in complex with an EMBOW-derived peptide. Our structural analysis reveals that EMBOW engages the WIN site through a Met1-Arg2-Thr3 (MRT) triad. The bulky Met1 residue occupies the conserved WIN site pocket, and mutation of Thr3 to valine reduces binding affinity, while N-terminal Gly-Ser insertion preserves binding, indicating a degree of structural tolerance. Binding assays and mutational analysis underscore the functional importance of the MRT triad. Furthermore, structural and biochemical studies of MRT-containing peptides from RNA-binding protein 15 (RBM15) and zinc finger and SCAN domain-containing protein 10 (ZSCAN10) suggest that this motif may serve as an alternative WIN site recognition signature. In summary, our findings define the molecular basis of EMBOW-WDR5 interaction and expand the sequence space compatible with WIN site engagement.

Keywords: EMBOW; WDR5; WIN motif; crystal structure; protein–protein interaction

DOI: https://doi.org/10.1111/febs.70450