Biology subjects

Leidel, S. A.

Publications and source records attributed to Leidel, S. A..

6 recordsLinked to original sources

bioRxiv2026

The small ORF (smORF)-encoded polypeptide MIRINE promotes neuronal differentiation in vertebrate brain development

The vertebrate brain expresses an extensive repertoire of long-noncoding RNAs (lncRNAs), an emerging source of small open reading frame (smORF)-encoded polypeptides (SEPs) whose functions remain largely unknown. Using ribosome profiling and proteomics of zebrafish and mouse brain, we identified hundreds of translated smORFs. We characterized MIRINE, a SEP of 83 amino acids conserved across 205 vertebrate species. MIRINE contains a transmembrane domain that targets it to the plasma membrane and intracellular vesicles, and is enriched in cortical and hippocampal neurons, with expression rising during neurogenesis. Downregulation of Mirine increased cell proliferation and impaired neuronal maturation in neuroblastoma cells, in mouse primary cortical neurons and cortex, and in the zebrafish forebrain, identifying MIRINE as a regulator of the balance between neuronal proliferation and differentiation. Mechanistically, MIRINE associates with the synaptic-vesicle protein Synaptogyrin-3 and related membrane proteins. Our findings define a conserved, membrane-associated SEP controlling neuronal maturation and illustrate the functional potential of brain SEPs.

biochemistry↗

bioRxiv2025

A dietary pan-amino acid dropout screen in vivo reveals a critical role for histidine in T-ALL

Dietary interventions show therapeutic potential in cancer, but systematic comparisons are lacking. We performed a dietary pan-amino acid dropout screen in an orthotopic model of NOTCH1-driven T-cell acute lymphoblastic leukemia and identified histidine depletion as uniquely antileukemic. Histidine-restricted diets extended survival of leukemic mice in a dose-dependent manner, while remaining well-tolerated. Mechanistically, multiomic profiling revealed that histidine deprivation-induced ribosome stalling activates GCN2 to suppress cholesterol biosynthesis pathways critical for leukemic proliferation. Dietary cholesterol supplementation partially reverted the antileukemic effects of histidine restriction in vivo. These findings couple histidine levels and translational control to cholesterol metabolism, which can be therapeutically exploited for cancer treatment. Our results suggest that defined dietary amino acid restrictions may expose broader therapeutic opportunities in diseases beyond cancer.

cancer biology↗

bioRxiv2025

tRNA thiolation defects disrupt cellular proteostasis and tissue homeostasis in mammals

Sulfur modification of tRNA wobble uridines is an evolutionarily conserved mechanism that ensures efficient protein synthesis. In humans, loss of this anticodon modification due to mutations in CTU2 (cytosolic thiouridylase 2) causes DREAM-PL syndrome, a severe congenital disorder often leading to early postnatal death. However, the mechanisms by which loss of tRNA thiolation drives pathology remain unclear. Here, we show that loss of CTU2 triggers significant cellular proteostasis defects in patient cells and model cell lines. Structural and biochemical analyses reveal that the pathogenic CTU2L63P mutation destabilizes the CTU1/CTU2 complex and abolishes tRNA binding and thiolation. Acute loss of CTU2 caused codon-specific ribosome pausing at A-ending codons decoded by thiolated tRNAs, and decreased ribosome occupancy of A-rich transcripts in a dosage-dependent manner. Codon-biased mRNAs transcribed from genes critical for ciliogenesis are predicted to be most affected, linking their reduced translation to DREAM-PL etiology in humans. Surprisingly, Ctu2L63P mice display severe thiolation defects, but develop normally, are viable and fertile. Our findings highlight the importance of functional tRNA thiolation for organismal health in humans and identify species-specific vulnerabilities during embryonic development in mammals.

cell biology↗

bioRxiv2024

Codon Pair-Specific Translation Defects Trigger Ribosome-Associated Quality Control to Avoid Proteotoxic Stress

tRNA modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding, but how codon optimality defects trigger cellular phenotypes remains unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs, triggering ribosome collisions and inducing a coordinated and hierarchical response of cellular quality control pathways. Ribosome profiling reveals an unexpected functional diversity for wobble-uridine (U34) modifications during decoding. The same modification can have different effects at the A and P sites. Furthermore, modification-dependent stalling codon pairs induce ribosome collisions, triggering ribosome-associated quality control (RQC) to prevent protein aggregation by degrading aberrant nascent peptides and mRNAs. RQC inactivation stimulates the expression of molecular chaperones to remove protein aggregates. Our results show that loss of tRNA modifications primarily disrupts translation rates of suboptimal codon pairs and reveal the coordinated regulation and adaptability of cellular surveillance systems to ensure efficient and accurate protein synthesis and maintain protein homeostasis.

biochemistry↗

bioRxiv2019

The translation inhibitor cycloheximide affects ribosome profiling data in a species-specific manner

Ribosome profiling provides genome-wide snapshots of translation dynamics by determining ribosomal positions at sub-codon resolution. To maintain this positional information, the translation inhibitor cycloheximide (CHX) has been widely used to arrest translating ribosomes prior to library preparation. Several studies have reported CHX-induced biases in yeast data casting uncertainty about its continued use and questioning the accuracy of many ribosome profiling studies. However, the presence of these biases has not been investigated comprehensively in organisms other than Saccharomyces cerevisiae. Here, we use a highly standardized and optimized protocol to compare different CHX-treatment conditions in yeast and human cells. Our data suggest that unlike in S. cerevisiae, translating ribosomes in human cells are not susceptible to conformational restrictions by CHX. Furthermore, CHX-induced codon-specific effects on ribosome occupancy are not detectable in human cells nor in other model organisms including Schizosaccharomyces pombe and Candida albicans. In fact, we find that even in S. cerevisiae most biases can be avoided by omitting CHX pre-treatment, indicating that other parameters of library generation contribute to differences between ribosome profiling experiments. Together our findings provide a framework for researchers who plan their own ribosome profiling experiments or who analyze published datasets to draw judicious conclusions.

molecular biology↗

bioRxiv2018

Estrogen receptor alpha controls gene expression via translational offsetting

Estrogen receptor alpha (ER) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ER on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ER coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ER largely manifest as \"translational offsetting\" of the transcriptome, whereby amounts of translated mRNA and protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome-association, are reduced following ER depletion lack features which limit translational efficiency including structured 5UTRs and miRNA target sites. In contrast, mRNAs induced upon ER depletion whose polysome-association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ER regulates levels of U34-modification enzymes, whereas altered expression of U34-modification enzymes disrupts ER dependent translational offsetting. Altogether, we unravel a hitherto unprecedented mechanism of ER-dependent orchestration of transcriptional and translational programs, and highlight that translational offsetting may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers.

systems biology↗