Biology subjects

Eswarappa, S. M.

Publications and source records attributed to Eswarappa, S. M..

4 recordsLinked to original sources

bioRxiv2026

Tardigrades survive reversible dormancy during spaceflight: In-orbit revival, post-flight recovery, and transcriptomic responses

Long-duration space missions face substantial challenges, including limited resources and prolonged exposure to microgravity and radiation. Transporting organisms in a dormant state and reviving them at their destination could help overcome some of these limitations. However, the feasibility of this strategy has not been experimentally demonstrated in multicellular animals beyond Earth. Here, we investigated this possibility using tardigrades, microscopic invertebrates capable of entering a reversible state of dormancy. We demonstrate that dormant tardigrades can withstand near-absolute-zero temperatures (~12 mK), near-vacuum conditions (10-9 mbar), high doses of ionizing radiation (3000 Gy), and complete desiccation. We transported dormant tardigrades to the International Space Station (ISS). They were revived aboard the ISS, subsequently returned to a dormant state, and successfully revived again following their return to Earth. Approximately 45% of the space-flown tardigrades survived the 64-day experimental period. This included two dormancy-revival cycles, 18 days aboard the ISS, and prolonged periods without food or water. Importantly, surviving tardigrades retained their reproductive capacity. Transcriptomic analysis of ISS-exposed tardigrades revealed upregulation of genes associated with protein folding and stress responses, accompanied by downregulation of genes involved in energy metabolism and protein synthesis, providing insights into their molecular responses to the spaceflight environment. Together, these findings demonstrate the successful revival and re-induction of dormancy in a multicellular animal beyond Earth and establish an experimental foundation for exploring dormancy-based strategies for future long-duration space missions.

zoology↗

bioRxiv2026

Leaky scanning translates a conserved ORF in the 3'UTR of RPL36A and regulates the expression of ribosomal protein L36a.

The 3'UTRs of eukaryotic mRNAs are major hubs of post-transcriptional regulation that govern the spatial and temporal regulation of gene expression. Although 3'UTRs were long considered non-coding, recent studies have revealed translation within downstream open reading frames (dORFs) located in 3'UTRs. In contrast to upstream ORFs (uORFs) in 5'UTRs, the mechanisms governing dORF translation and their functional significance remain poorly understood. Here, we identify and characterize a dORF within the 3'UTR of RPL36A, which encodes ribosomal protein L36a. Analysis of ribosome profiling datasets revealed ribosome footprints aligned with the dORF reading frame across multiple human tissues and cell lines. Conservation analysis together with luciferase- and GFP-based reporter assays further supported active translation of the dORF. Using strategically placed RNA hairpin structures and mutational analyses, we show that dORF translation is consistent with ribosomal leaky scanning. Disruption of dORF translation, either by mutating its start codon in exogenous constructs or by CRISPR-mediated deletion of the endogenous dORF-containing region, reduced RPL36A mRNA and protein levels and resulted in impaired global translation. We further identified a miR-5701-binding site within the dORF region and provide evidence that dORF translation antagonizes miR-5701-mediated repression of RPL36A. Finally, we identify a similar dORF-associated regulatory mechanism in RPS3, which encodes ribosomal protein S3. Together, our findings uncover dORF translation as a regulatory mechanism controlling ribosomal protein expression.

molecular biology↗

bioRxiv2026

A compact, portable degron tool derived from the 3'UTR of MTCH2 for tunable degradation of proteins

Targeted protein degradation relies on short sequence elements, termed degrons, that direct proteins to the cellular degradation machinery. Here, we report a nine-amino-acid degron (FYTVWRAFL) derived from the 3' untranslated region (UTR) of human MTCH2 and demonstrate its utility as a tuneable protein-degradation tool. When appended to the C-terminus of proteins, FYTVWRAFL induces rapid and robust degradation by the ubiquitin-proteasome system. Using pharmacological inhibition and genetic perturbation, we show that degradation mediated by this degron is dependent on the E3 ubiquitin ligase MDM2. Structural modeling revealed that FYTVWRAFL interacts with the hydrophobic cleft of MDM2 in a manner similar to the p53 degron. Three hydrophobic residues form the core interaction interface. By systematic mutagenesis of these residues, we generated a panel of degron variants that confer graded levels of protein stability. We demonstrate the versatility of this system by achieving tunable expression of the endogenous protein Elm1 in Saccharomyces cerevisiae. Collectively, our study establishes a compact, transportable, and tunable degron system as a robust toolkit for quantitative control of protein abundance across eukaryotic systems.

molecular biology↗

bioRxiv2021

Identification of mRNAs that undergo stop codon readthrough in Arabidopsis thaliana

A stop codon ensures termination of translation at a specific position on an mRNA. Sometimes, termination fails as translation machinery recognizes a stop codon as a sense codon. This leads to stop codon readthrough (SCR) resulting in the continuation of translation beyond the stop codon, generating protein isoforms with C-terminal extension. SCR has been observed in viruses, fungi, and multicellular organisms including mammals. However, SCR is largely unexplored in plants. In this study, we have analyzed ribosome profiling datasets to identify mRNAs that undergo SCR in Arabidopsis thaliana. Analyses of the ribosome density, ribosome coverage and three-nucleotide periodicity of the ribosome profiling reads, in the mRNA region downstream of the stop codon, provided strong evidence for SCR in mRNAs of 144 genes. This process generates putative peroxisomal targeting signal, nuclear localization signal, prenylation signal, transmembrane helix and intrinsically disordered regions in the C-terminal extension of several of these proteins. Gene ontology (GO) functional enrichment analysis revealed that these 144 genes belong to three major functional groups - translation, photosynthesis and abiotic stress tolerance. Finally, using a luminescence-based assay, we experimentally demonstrate SCR in representative mRNAs belonging to these functional classes. Based on these observations, we propose that SCR plays an important role in plant physiology by regulating the protein localization and function. AUTHOR SUMMARYProtein synthesis executed by macromolecular complexes, termed ribosomes, starts and stops at specific locations on a messenger RNA (mRNA). This fidelity is critical for the normal functioning of cells. However, sometimes ribosomes dont stop translation at the stop signal (termed stop codon) on an mRNA resulting in longer proteins with properties different from those of the canonical shorter protein. This process called stop codon readthrough (SCR) has been observed in viruses, fungi, and multicellular organisms including mammals. However, it remains largely unexplored in plants. In this study, we report evidence of SCR in 144 genes of Arabidopsis thaliana, a small flowering weed widely used as a model system to study plant biology. These genes are involved in protein synthesis, photosynthesis and stress tolerance in plants. We have also experimentally demonstrated SCR in a few genes that represent these functional classes. Our analysis shows that SCR can change the localization and functional properties of these proteins. We propose that SCR plays an important role in plant physiology.

plant biology↗