Biology subjects

Shiber, A.

Publications and source records attributed to Shiber, A..

3 recordsLinked to original sources

bioRxiv2026

A Ubiquitin network safeguards cell identity by continuously degrading stem-cell related translational machinery

How cell identity is maintained is a fundamental question, and loss of cell identity is a hallmark of aging that is associated with multiple age-related diseases. In the adult Drosophila midgut, we identified a post-transcriptional regulatory layer that supervises enterocyte (EC) identity and fails upon aging. Combining single-cell RNA-seq with lineage tracing in aging ECs and classical genetics we found that aging ECs express genes that unlock the differentiated state. Upon aging, the protein Rogue (CG13928), a translational repressor, orchestrates reactivation of a stem-cell-related translational repression machinery involving p-body-associated RNA-binding proteins that cancels the differentiated state. In young ECs, this machinery is continuously suppressed by the deubiquitinase Non-stop (dUSP22) and the ubiquitin E2 dUbcH8/Kdo and the E3 enzyme CTLH, together suppress the stem-cell related RNA binding proteins safeguarding EC identity. Upon aging, the levels of dUSP22 decline, dUbcH8/Kdo and the E3 CTLH complex are cleared via Rogue, and the stem cell-related p-bodies are reactivated, self-destroying EC identity.

cell biology↗

bioRxiv2025

Distinct cis-acting elements mediate co-localization of mRNAs encoding for co-translational interactors in cytoplasmic clusters

Many newly synthesized proteins assemble co-translationally, providing a vital mechanism to prevent subunit misfolding in the crowded cytoplasm. Initial evidence indicates that the spatial organization of mRNAs aids this assembly, but it is unclear how these mRNAs are organized and how common this mechanism is. We used single-molecule Fluorescence in situ Hybridization in Saccharomyces cerevisiae to examine the spatial organization of mRNAs encoding subunits of various cytosolic complexes involved in critical cellular functions, such as fatty acid synthesis, glycolysis, translation and various amino acid biosynthesis. We found that mRNAs of the same protein complex often co-localize in specific cytoplasmic clusters. Additionally, we observed that the mRNAs encoding enzymes of biosynthetic pathways are organized in cytosolic clusters. Focusing on mRNAs encoding fatty acid synthase complex subunits, we discovered that non-coding cis elements significantly influence mRNA localization in an additive manner. Specifically, 5 and 3 UTRs, together with further upstream and downstream regions, facilitate co-localization. Inhibiting mRNA co-localization impaired growth when complex activity was essential, highlighting the importance of mRNA spatial organization for cellular survival. Transiently disrupting mRNA translation also affected clustering, indicating that both the nascent chains and mRNA sequence targeting cues are combinatorically contributing to spatial organization. Proteomics analysis demonstrates the impact of cis-elements on the abundance of the encoded subunits, as well as the entire pathway. In summary, we provide evidence that mRNA co-localization in cytoplasmic foci is coordinated by complementary mechanisms crucial for co-translational assembly, allowing efficient regulation of protein complex formation and entire pathways.

cell biology↗

bioRxiv2024

Structural determinants of co-translational protein complex assembly

The assembly of proteins into functional complexes is critical to lifes processes. While textbooks depict complex assembly as occurring between fully synthesized proteins, we know today that thousands of proteins in the human proteome assemble co-translationally during their synthesis. Why this process takes place, however, remains unknown. We show that co-translational assembly is governed by biophysical and structural characteristics of the protein complex, and involves mutually stabilized, intertwined subunits. Consequently, these subunits are also co-regulated across the central dogma, from transcription to protein degradation. Leveraging structural signatures with AlphaFold2-based predictions enables us to accurately predict co-translational assembly on a proteome-wide scale, which we validated by ribosome profiling, genetic perturbations, and smFISH experiments. Notably, the latter showed that co-translationally assembling subunits exhibit co-localized mRNAs. This work unveils a fundamental connection between protein structure and the translation process, highlighting the overarching impact of three-dimensional structure on gene expression, mRNA localization, and proteostasis. One Sentence SummaryProtein complexes with topologically intertwined subunits require co-translational assembly and synchronized proteostasis of subunits, with implications in protein stability, mRNA localization, and evolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/576408v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@712a2org.highwire.dtl.DTLVardef@58894borg.highwire.dtl.DTLVardef@9db5c6org.highwire.dtl.DTLVardef@8eae4_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗