bims-micpro 2026-04-19 papers

FEBS Lett. 2026 Apr 15.

Genetically encoded lockdown of SERCA in the endoplasmic reticulum membrane arrests Ca2+ signaling through proximity-covalent crosslinking.

Yiying Li, Kozo Hamada.

Reversible conformational dynamics of membrane proteins are essential for intracellular signaling, but no method enables their irreversible arrest in living cells. Here, we developed a genetically encoded proximity-based lockdown enzyme derived from an engineered transglutaminase catalytic core (TGC) that covalently crosslinks membrane proteins. By fusing TGC to the endoplasmic reticulum (ER)-resident microprotein ALN encoded by a short open reading frame (sORF), we created an organelle-specific module that selectively catalyzes covalent crosslinking within the SERCA Ca2+ pump, strongly suppressing its ATP-dependent pump activity and arresting ER Ca2+ signaling. This engineered lockdown enzyme remodels ER membrane protein architecture and restricts conformational dynamics, providing a versatile platform for long-term covalent control of intracellular signaling and a foundation for future therapeutic cellular applications. Impact statement Our proximity-based lockdown enzyme, engineered from microbial transglutaminase, provides a new strategy to covalently arrest the conformational states of organelle-resident membrane proteins in living cells, enabling long-term control of intracellular signaling and establishing a foundation for next-generation cellular therapeutics.

Keywords: calcium ATPase; calcium homeostasis; calcium signaling; endoplasmic reticulum; microprotein; transglutaminase

DOI: https://doi.org/10.1002/1873-3468.70342

Biology (Basel). 2026 Mar 27. pii: 538. [Epub ahead of print]15(7):

Long Non-Coding RNA-Derived Peptides as a Novel Source of Tumor Neoantigens: Expanding the Immunopeptidome Beyond Canonical Coding Regions.

Ismael López-Calvo, Inés Bao-Camacho, Samuel Martín-Revuelta, Cora Rey-Souto, Anahir Franco-Gacio, José Manuel Pérez-Martínez, Iván Sandino-Somoza, Álvaro Mourenza, Esther Rodríguez-Belmonte, Mónica Lamas-Maceiras, M Esperanza Cerdán, Aida Barreiro-Alonso, Ángel Vizoso-Vázquez.

Cancer immunotherapy has transformed the clinical management of several malignancies; however, its efficacy remains limited in tumors with low mutational burden and restricted availability of classical mutation-derived neoantigens. In this context, increasing evidence indicates that the tumor immunopeptidome extends far beyond canonical protein-coding regions, incorporating peptides derived from non-coding transcripts through non-canonical translation mechanisms. Long non-coding RNAs (lncRNAs), traditionally regarded as transcriptional or post-transcriptional regulators, have recently emerged as an unexpected source of small open reading frame-encoded peptides (lncPEPs). A subset of these peptides is processed and presented by major histocompatibility complex class I molecules, generating tumor-specific neoantigens capable of eliciting CD8+ T cell responses. Owing to the high tissue and context specificity of lncRNA expression, lncRNA-derived neoantigens offer unique advantages over mutation-based targets, including increased tumor selectivity and potential recurrence across patient subsets. In this review, we synthesize current knowledge on the biogenesis, detection, and immunogenic potential of lncRNA-derived peptides, highlighting experimental and computational strategies for their identification within the cancer immunopeptidome. We discuss the challenges associated with their validation and clinical translation, as well as their relevance for the development of vaccines and adoptive T cell-based therapies. Finally, we illustrate these concepts using epithelial ovarian cancer as a representative model of low-mutational-burden tumors, where lncRNA-derived neoantigens may help overcome current limitations of immunotherapy and enable patient stratification for personalized treatment approaches.

Keywords: MHC-I; dark proteome; immunotherapy; lncPEP; precision oncology; proteogenomics; smORFs

DOI: https://doi.org/10.3390/biology15070538

bioRxiv. 2026 Apr 11. pii: 2026.04.10.717766. [Epub ahead of print]

Suppression of upstream ORF translation is not a widespread mechanism of translational stimulation by yeast helicase Ded1.

Rakesh Kumar, Gemma May, Neelam Dabas Sen, Joel McManus, Alan G Hinnebusch.

Ded1 is an essential DEAD-box helicase in yeast that broadly stimulates translation initiation and is critical for mRNAs with structured 5'UTRs. We have evaluated the proposal that Ded1 stimulates translation primarily by preventing initiation at upstream ORFs (uORFs) associated with stable secondary structures. By Ribo-Seq analysis under experimental conditions designed to suppress artifactual 5'UTR translation, we found that reduced translation of the main open-reading-frames (mORFs) in native mRNAs is generally not accompanied by increased 5'UTR translation in ded1 mutant cells, and that the presence of translated uORFs in yeast mRNAs generally does not confer heightened dependence on Ded1 for efficient translation of mORFs. Results from a high-throughput reporter assay examining native 5'UTRs reinforce the importance of Ded1 in initiation from structured 5' UTRs and show that impairing Ded1 has minimal effects on translational repression by uORFs. Our results demonstrate that, in cells growing vegetatively in rich medium, translational stimulation by suppression of inhibitory uORFs is restricted to a minority of Ded1 targets, and that unwinding of 5' UTR secondary structures per se is the principal mechanism for Ded1 stimulation of translation initiation.

DOI: https://doi.org/10.64898/2026.04.10.717766

Genes Dev. 2026 Apr 16.

The microprotein SMIM26 connects metabolite transporters of the outer and inner mitochondrial membranes and is essential for respiratory chain function.

Microproteins represent a class of short polypeptides with very diverse cellular functions. Microproteins frequently escape proteomics-based identification, making the extent and potential functions of small proteins largely elusive. Some microproteins originate from transcripts that are annotated as long noncoding RNAs (lncRNAs). Here, we functionally characterize SMIM26, a microprotein localized to mitochondria. In biochemical and single-molecule tracking studies, we found that SMIM26 interacts with VDAC1/2 in the outer mitochondrial membrane and with SLC25A6 in the inner mitochondrial membrane. It spans the intermembrane space and is phosphorylated at distinct residues. Knockout cells are viable, but respiratory chain activity is strongly reduced. Interestingly, knockout mice are not viable and die at early developmental stages. Zebrafish homozygous smim26 mutants are viable but show reduced fitness and survival compared with their wild-type or heterozygous siblings. Consistent with the mitochondrial phenotype in cell lines, respiration is also reduced in homozygous zebrafish embryos. Our work suggests that SMIM26 coordinates metabolite transport through the inner and outer mitochondrial membranes and is essential for respiratory chain function in vivo.

Keywords: SMIM26; metabolite transport; microprotein; mitochondria; respiratory chain

DOI: https://doi.org/10.1101/gad.353272.125

Invest Ophthalmol Vis Sci. 2026 Apr 01. 67(4): 42

LncRNA DANCR Regulates PARP1-Mediated Oxidative Stress Response in Corneas by Encoding a Novel Micropeptide miPEPDR.

Xiaolu Ma, Jiahui Hao, Halima Ben Hilal, Zina Cheng, Pengfei Feng, Jie Song, Jizhong Yang, Peng Chen, Weiyi Chen, Xiaona Li.

Purpose: Oxidative stress, as a pathogenic factor of multiple corneal diseases, regularly threatens the genome stability in corneal cells. However, the potential significance of long noncoding RNAs (lncRNAs) in this process remains largely unknown. This study aims to elucidate the role and mechanisms of lncRNAs in the oxidative stress response of human corneal epithelial (HCE) cells.
Methods: Published RNA sequencing data of human normal cornea (HNC) and keratoconus (HKC) samples were used to investigate differentially expressed lncRNAs, which were further validated in independent clinical corneal epithelial samples. Hydrogen peroxide (H2O2)-induced oxidative stress was used to evaluate the effect of candidate lncRNAs on the cell viability and genome stability through the cell counting kit-8 (CCK-8), micronucleus formation, and alkaline comet assay. LncRNA-encoded micropeptides were investigated through epitope tagging, frameshift mutagenesis, custom antibody, and mass spectrum-based detection. Comprehensive analyses, including immunofluorescence, immunoblotting, and quantitative real-time PCR were used to assess DNA damage repair, protein, and mRNA expression, respectively.
Results: LncRNA differentiating antagonistic non-protein-coding RNA (DANCR) was found to be downregulated in keratoconus and to confer resistance to oxidative stress in HCE cells. Knockdown of DANCR reduced oxidative stress-induced DNA damage, as evidenced by decreased micronucleus formation rate and DNA strand breaks. Mechanistically, downregulation of DANCR not only inhibits poly(ADP-ribosyl)ation (PARylation) but also promotes the nucleolar-nucleoplasmic shuttling of poly(ADP-ribose) polymerase 1 (PARP1), both of which could be rescued by miPEPDR, a previously unrecognized 56-amino acid micropeptide encoded by DANCR.
Conclusions: LncRNA DANCR functions as a critical regulator of corneal epithelial oxidative stress response through modulating PARP1 activity and nucleolar-nucleoplasmic translocation via its derived micropeptide miPEPDR.

DOI: https://doi.org/10.1167/iovs.67.4.42