Biology subjects

Wu, X.-Y.

Publications and source records attributed to Wu, X.-Y..

5 recordsLinked to original sources

bioRxiv2026

m1A58 acts as a conformational checkpoint coupling human initiator tRNA maturation to translation initiation

tRNAs are characterized by extensive chemical modifications that influence tRNA fate. N1-methyladenosine at position 58 (m1A58) is a widespread core tRNA modification linked to physiological and pathological processes. However, how m1A58 coordinate tRNA folding and processing to ensure translational efficiency in mammalian cells remains largely unknown. Using acute dTAG-mediated degradation and CRISPR-Cas9 knockout, we identified initiator methionine tRNA (tRNAiMet) as selectively vulnerable to m1A58 loss, lacking the isodecoder buffering observed for most other tRNA isoacceptors. NMR analysis of the tRNAiMet showed that m1A58 stabilizes D/T-loop interactions, consistent with a maturation-competent conformation. In vitro processing assays further demonstrated that m1A58 promotes RNase P-mediated 5'-leader removal and RNase Z-mediated 3'-trailer cleavage, while La/SSB protects accumulated precursors. Disrupting this checkpoint impaired the assembly of the eIF2-containing 43S pre-initiation complex and global protein synthesis, which was substantially rescued by adding m1A58-modified tRNAiMet. Acute TRMT6 degradation elicited temporally coordinated gene-expression responses involving proteostasis, transport and signaling. Together, these findings establish m1A58 as a conformational checkpoint coupling human initiator-tRNA maturation to translation initiation and stress responses.

molecular biology↗

bioRxiv2026

Ribophorin-1 Governs Spike Abundance of Highly Pathogenic Coronaviruses by ER-associated degradation

The spike protein of highly pathogenic coronaviruses is indispensable for viral entry, pathogenesis, and immune evasion. However, specific host factors governing spike protein degradation and abundance on progeny virions remain largely uncharacterized. Here, we identify Ribophorin-1 (RPN1), a non-catalytic subunit of the oligosaccharyltransferase (OST) complex, as an ER-localized host restriction factor that selectively depletes spike to inhibit coronavirus infection. Conditional knockout of Rpn1 in mouse lung markedly exacerbates SARS-CoV-2 pathogenesis, increasing viral load, immune cell infiltration, and syncytium formation. In cells, RPN1 knockdown enhances susceptibility to diverse variants, whereas its overexpression attenuates infection. Nano-flow cytometry, cryo-EM and LSCM show that RPN1 reduces spike abundance on progeny virions, resulting in reduction in subsequent syncytium formation across SARS-CoV, SARS-CoV-2, and MERS-CoV. Mechanistically, RPN1 promotes VCP/p97-dependent retrotranslocation and AMFR-mediated ubiquitination of spike protein. Heterologous expression of RPN1s functional domain (residues 180-307) confers significant protection against SARS-CoV-2 both in vitro and in vivo. Collectively, our findings define an RPN1-initiated ERAD pathway that selectively targets coronavirus spike for proteasomal destruction, and provide proof-of-concept evidence that targeting this RPN1-dependent pathway represents a promising broad-spectrum antiviral strategy.

microbiology↗

bioRxiv2026

Ultra-sensitive FLORA-seq links cell-type-specific tRNAome dynamics to differentiation trajectories guiding therapeutic suppressor tRNA candidate selection

Mammalian genomes encode hundreds of tRNA genes, but the role of individual tRNAs in development and cell identity remains unclear. Here, we introduce FLORA-seq, a method for simultaneous, low-input profiling of tRNAs, tRNA-derived RNAs (tdRs) and their modifications from as few as 5-20 cells. Applying FLORA-seq to mouse hematopoiesis revealed 50 high-variance isodecoders whose expression profiles recapitulate known hematopoietic cell types and correlate with differentiation trajectories. At the isoacceptor level, tRNA pools are largely stable within hematopoietic stem and progenitor cells (HSPCs), showing only subtle, specific variations, but become both distinct from HSPCs and internally stable within each terminally differentiated lineage. We further detected dynamic changes in tdR ratios and modification patterns, underscoring precise tRNA regulation during differentiation. Crucially, analysis of 54 endogenous tRNA isodecoders and their engineered suppressor counterparts showed that efficient premature termination codon readthrough preferentially arises from highly expressed cognate isodecoders. This correlation provides a rational framework for prioritizing suppressor tRNA candidates and implies non-redundant functions for individual isodecoders.

molecular biology↗

bioRxiv2025

CRlSPR/Cas9 screening revealed BlRC6-AS1/BlRC6 mediates abiraterone resistance via NHEJ pathway-dependent A20 degradation in prostate cancer

Abiraterone acetate serves as the first-line therapeutic agent for prostate cancer (PCa) treatment. However, drug resistance frequently emerges. Employing a genome-wide CRISPR/Cas9 library screening strategy, we identified 523 long non-coding RNAs (lncRNAs) and 2183 protein-coding genes associated with abiraterone resistance. Notably, a pair of sense-antisense genes, BIRC6-AS1/BIRC6, was demonstrated to be a pivotal driver for abiraterone resistance. BIRC6-AS1 depletion led to a reduction in both the mRNA and protein levels of BIRC6. Moreover, depletion of either BIRC6-AS1 or BIRC6 enhanced the chemosensitivity of PCa cells to abiraterone both in vitro and in vivo settings. Further investigation revealed that BIRC6-AS1 stabilized the mRNA of BIRC6 through interaction with ILF2. Diminishing either BIRC6-AS1 or BIRC6 predominantly suppressed non-homologous end joining (NHEJ) repair activity, resulting in the disassembly of 53BP1 foci at DNA damage sites and an increased accumulation of DNA damage in PCa cells induced by abiraterone. Mechanistically, BIRC6 interacted with A20 and facilitated the K48-linked ubiquitination and subsequent degradation of A20 at the K337 residue. Additionally, A20 knockdown effectively reversed the abiraterone sensitivity induced by BIRC6-AS1 depletion. Collectively, we conducted a comprehensive screen to identify lncRNAs and protein-coding genes associated with abiraterone resistance and proposed that targeting BIRC6-AS1/BIRC6 axis represents a promising strategy to overcome abiraterone resistance in prostate cancer.

molecular biology↗

bioRxiv2021

High-throughput tandem-microwell assay for ammonia repositions FDA-Approved drugs to Helicobacter pylori infection

To date, little attempt has been made to develop new treatments for Helicobacter pylori (H. pylori), although the community is aware of the shortage of treatments for H. pylori. In this study, we developed a 192-tandem-microwell-based high-throughput-assay for ammonia that is a known virulence factor of H. pylori and a product of urease. We could identify few drugs, i.e. panobinostat, dacinostat, ebselen, captan and disulfiram, to potently inhibit the activity of ureases from bacterial or plant species. These inhibitors suppress the activity of urease via substrate-competitive or covalent-allosteric mechanism, but all except captan prevent the antibiotic-resistant H. pylori strain from infecting human gastric cells, with a more pronounced effect than acetohydroxamic acid, a well-known urease inhibitor and clinically used drug for the treatment of bacterial infection. This study offers several bases for the development of new treatments for urease-containing pathogens and to study the mechanism responsible for the regulation of urease activity.

biochemistry↗