Biology subjects

Som, S.

Publications and source records attributed to Som, S..

10 recordsLinked to original sources

bioRxiv2026

Translation of a four-codon ORF in the 3'UTR of MAP3K10 regulates its expression

Several eukaryotic mRNAs are polycistronic because of translatable open reading frames (ORFs) embedded in their untranslated regions (UTRs), in addition to the primary ORF (i.e., the coding sequence). While 5'UTR upstream ORFs (uORFs) are mechanistically and functionally well studied, 3'UTR downstream ORFs (dORFs) remain poorly understood. Here, we identify and characterize a short, translatable dORF in the 3'UTR of MAP3K10, which encodes a serine/threonine kinase involved in JNK signalling. A stringent computational screen predicted a conserved RNA G-quadruplex (rG4) within the 3'UTR of MAP3K10. Biophysical assays provided more evidence for rG4 formation, which drives translation of a conserved four-codon dORF. Disruption of the rG4 by point mutations or by an rG4-binding ligand reduced dORF translation. Reporter assays using constructs with strategically placed hairpin structures show that translation of the dORF is independent of both the 5 cap and the translation of the canonical ORF. Notably, deletion of the rG4-dORF module, either in exogenous constructs or in CRISPR-edited cells, led to reduced MAP3K10 expression. Together, these results provide evidence for the regulation of MAP3K10 expression by rG4-driven translation of a dORF. Thus, our study contributes to the growing body of evidence suggesting that dORF translation can regulate gene 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↗

bioRxiv2025

A mechanistic model of early centrosome separation during prophase

Initial centrosome separation during prophase is crucial for faithfully completing the mammalian mitosis. Though kinesin-5 pushes the two centrosomes apart in prometaphase by sliding the inter-centrosomal anti-parallel microtubules, it is still under debate that whether kinesin-5 plays any role in the prophase centrosome separation. It is also controversial that whether dyneins separate the centrosomes by pulling the centrosomal microtubules from two opposite directions. Therefore, the active drivers involved in the early centrosome separation are still elusive. Interactions of the centrosomal microtubules with cellular objects (e.g. cortex, cell wall and nucleus) generate forces on the centrosome, thereby promotes centrosomal movements. Using an in-silico model, we show that a concerted interplay of centrosomal microtubules with cortex, cell wall and nucleus can promote centrosome separation during prophase.

biophysics↗

bioRxiv2024

IVISc-L: A quick and simple in vivo assay to study the regulation of gene expression

Several methods are available to study the regulation of gene expression at cellular and molecular levels. Adaptation of these methods in vivo is cumbersome and often requires animal sacrifice. Here, we report an assay (IVISc-L, In Vivo Imaging of Subcutaneous Luminescence) to study gene regulation in vivo. This assay involves subcutaneous injection of a plasmid DNA encoding firefly luciferase, whose expression is under the regulatory mechanism to be investigated. We could infer its regulated expression by detecting the subcutaneous luminescence using an in vivo imaging system. Using this assay, we have demonstrated the regulation of gene expression mediated by a promoter, micro-RNAs, stop codon readthrough, and rare codons. This minimally invasive assay does not require animal sacrifice or any tissue extraction. The entire assay can be completed within 24 hours. Therefore, this assay will be useful in investigating the mechanisms of gene expression regulation, and screening molecules that can alter gene expression in vivo.

molecular biology↗

bioRxiv2024

Multiple clustered centrosomes in antigen-presenting cells foster T cell activation without MTOC polarization

Cellular polarization plays a pivotal role in regulating immunological processes and is often associated with centrosome reorientation. During immune synapse (IS) formation centrosome repositioning in lymphocytes assists in T cell activation. While a single centrosome, consisting of two centrioles, is present in T cells, antigen-presenting cells (APCs) such as dendritic cells (DCs) amplify centrioles during maturation leading to increased centrosome numbers upon immune activation. How centrosome amplification in DCs affects IS formation and T cell activation is unclear. In this study, we combine experimental data with mathematical and computational modelling to provide evidence that centrosome amplification in DCs enhances antigen-specific T cell activation. Extra centrioles in DCs form active centrosomes, which cluster during DC-T cell interactions and unlike in T cells, localize close to the cell center. Perturbing either centriole numbers or centrosome configuration in DCs results in impaired T cell activation. Collectively, our results highlight a crucial role for centrosome amplification and optimal centrosome positioning in APCs for controlling T cell responses.

cell biology↗

bioRxiv2023

Concurrent measurement of O2 and isoprene production during photosynthesis: pros, cons, and metabolic implications

During oxygenic photosynthesis, oxygen (O2) is generated from water photolysis, which provides reducing power to sustain CO2 assimilation. To date, traditional leaf gas-exchange experiments have been focused on net CO2 exchange (Anet), with limited observations of net oxygen production (NOP). Here, we present the first gas-exchange/fluorescence system, coupling CO2/H2O analysis (photosynthesis and transpiration) with NOP and isoprene emission measurements. This configuration allowed us to calculate the assimilatory quotient (AQ = Anet/NOP) and thus obtain a more complete picture of the photosynthetic redox budget via photosynthetic production of O2, electron transport rate (ETR), and isoprene biosynthesis. We used cottonwood leaves (Populus trichocarpa) and carried out response curves to light, CO2 and temperature along with 18O-labelling with 18O-enriched water. We found that Anet and NOP were linearly correlated across environmental variables with AQ of 1.27 +/- 0.12 regardless of light, CO2, and temperature. Anet and NOP had optimal temperatures (Topt) of 31{degrees}C, while ETR (35{degrees}C) and isoprene emissions (39{degrees}C) had distinctly higher Topt. Leaves labelled with H218O produced labeled (18O16O) oxygen with the same Topt as ETR (35{degrees}C). The results confirm a tight connection between water oxidation and ETR and are consistent with a suppression of Anet and NOP at high temperature driven by an acceleration of (photo)respiration. The findings support the view of isoprene biosynthesis primarily driven by excess photosynthetic ATP/NADPH not consumed by the Calvin cycle during photorespiratory conditions as an important thermotolerance mechanism linked with high rates of CO2 and O2 recycling. KeywordsPhotosynthesis, net oxygen production, gross oxygen production, H218O labeling One sentence summaryA leaf gas-exchange system is presented enabling a more complete picture of the photosynthetic redox budget and calculation of the assimilatory quotient.

plant biology↗

bioRxiv2023

A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria

Bacteriophages, the viruses of bacteria, are proposed to drive bacterial population dynamics, yet direct evidence of their impact on natural populations is limited. Here we identified viral sequences in a metapopulation of wild plant-associated Pseudomonas spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin - a phage-derived element that bacteria use to kill competitors for interbacterial warfare. Each pathogenic Pseudomonas sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the last 170 years revealed that the same tailocin and receptor variants have persisted in the Pseudomonas populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control. One-Sentence SummaryBacterial pathogens in a host-associated metapopulation use a repurposed prophage to kill their competitors.

microbiology↗

bioRxiv2023

A mechanistic model for nuclear migration in hyphae during mitosis

S. Cerevisiae and C. Albicans, the two well-known human pathogens, can be found in all three morphologies, i.e., yeast, pseudo-hyphae and true-hyphae. The cylindrical daughter-bud (germ tube) grows very long for true-hyphae, and the cell cycle is delayed compared to the other two morphologies. The place of the nuclear division is specific for true-hyphae determined by the position of the septin ring. However, the septin ring can localize anywhere inside the germ tube, unlike the mother-bud junction in budding yeast. Since the nucleus often migrates a long path in the hyphae, the underlying mechanism must be robust for executing mitosis in a timely manner. We explore the mechanism of nuclear migration through hyphae in light of mechanical interactions between astral microtubules and the cell cortex. We report that proper migration through constricted hyphae requires a large dynein pull applied on the astral microtubules from the hyphal cortex. This is achieved when the microtubules frequently slide along the hyphal cortex so that a large population of dyneins actively participate, pulling on them. Simulation shows timely migration when the dyneins from the mother cortex do not participate in pulling on the microtubules. These findings are robust for long migration and positioning of the nucleus in the germ tube at the septin ring.

biophysics↗

bioRxiv2019

A negative feedback loop between Insulin-like Growth Factor signaling and the lncRNA SNHG7 tightly regulates transcript levels and proliferation

Evidence suggests Insulin-like growth factor 1 (IGF1) signaling is involved in the initiation and progression of a subset of breast cancers by inducing cell proliferation and survival(1, 2). Although the signaling cascade following IGF1 receptor activation is well-studied(3, 4), the key elements of the transcriptional response governing IGF1s actions are not well understood. Recent studies reveal that the majority of the genome is transcribed and that there are more long non-coding RNAs (lncRNAs) than protein coding genes(5), several of which are dysegulated in human cancer(6, 7). However, studies on the regulation and mechanism of action of these lncRNAs are in their infancy. Here we show that IGF1 alters the expression levels of a subset of lncRNAs. SNHG7, a member of the small nucleolar host gene family, is a highly-expressed lncRNA that is consistently and significantly down-regulated by IGF1 signaling by a post-transcriptional mechanism through the MAPK pathway. SNHG7 regulates proliferation of breast cancer cell lines in a dose-dependent manner, and silencing SNHG7 expression causes cell cycle arrest in G0/G1. Intriguingly, SNHG7 alters the expression of many IGF1 signaling intermediates and IGF1-regulated genes suggesting a feedback mechanism to tightly regulate the IGF1 response. Finally, we show with TCGA data that SNHG7 is overexpressed in tumors of a subset of breast cancer patients and that these patients have lower disease-free survival than patients without elevated SNHG7 expression. We propose that SNHG7 is a lncRNA oncogene that is controlled by growth factor signaling in a feedback mechanism to prevent hyperproliferation, and that this regulation can be lost in the development or progression of breast cancer.\n\nSIGNIFICANCE STATEMENTIGF1 signaling drives proliferation and survival and is important for the initiation and development of a subset of breast cancers. IGF1 is known to control the expression of thousands of protein coding genes, but it is unknown if it alters the expression of other gene types, such as long noncoding RNAs. Here we demonstrate that IGF regulates lncRNAs including the mostly unstudied SNHG7. We further show that SNHG7 is necessary for proliferation and modulates IGF1 signaling through a novel feedback mechanism that is required for fine-tuning of the transcriptional response to growth factor signaling and proliferation of breast cancer cells. SNHG7 is highly expressed in a subset of breast cancer patients with poor prognosis giving further credence that it is a novel oncogene.

cancer biology↗

bioRxiv2019

MTOC clustering and nuclear division through proper spindle positioning in yeast: a microtubule grow-and-catch model

The dynamic process of mitotic spindle assembly depends on multitudes of inter-dependent interactions involving kinetochores (KTs), microtubules (MTs), spindle pole bodies (SPBs), and molecular motors. Before forming the mitotic spindle, multiple visible microtubule organizing centers (MTOCs) coalesce into a single focus to serve as a SPB in the pathogenic budding yeast, Cryptococcus neoformans. To explain this unusual phenomenon in the fungal kingdom, we propose a search and capture model, in which cytoplasmic MTs (cMTs) nucleated by MTOCs grow and capture each other to promote MTOC clustering. Our quantitative modeling identifies multiple redundant mechanisms mediated by a combination of cMT-cell cortex interactions and inter-cMT coupling to facilitate MTOC clustering within the physiological time limit as determined by time-lapse live-cell microscopy. Besides, we screen various possible mechanisms by computational modeling and propose optimal conditions that favor proper spindle positioning - a critical determinant for timely chromosome segregation. These analyses also reveal that a combined effect of MT buckling, dynein pull, and cortical push maintains spatiotemporal spindle localization.

biophysics↗