Biology subjects

Divyanshu, M.

Publications and source records attributed to Divyanshu, M..

5 recordsLinked to original sources

bioRxiv2025

Cycling Molecular Assemblies (CyMA) for Ultrasensitive Golgi Imaging

The Golgi apparatus is central to intracellular trafficking, yet its dynamic visualization remains constrained by probes that require high concentrations and long incubations. Here we present cycling molecular assemblies (CyMA), a design concept that harnesses endogenous dynamic enzymatic futile cycle to drive ultrasensitive imaging. The BODIPY-CyMA probe operates through reversible palmitoylation-depalmitoylation mediated by palmitoyl acyltransferases and thioesterases, establishing a nonequilibrium steady-state that actively concentrates the probe at the Golgi. This enzymatic cycling converts diffusion-limited localization into self-amplifying signal generation, enabling morphology imaging at concentrations as low as 100 pM and real-time tracking of Golgi dynamics within minutes at nanomolar levels. This probe requires minimal incubation time, exhibits negligible cytotoxicity, faithfully reports pharmacological Golgi disassembly, and functions in vivo in Drosophila larvae. BODIPY-CyMA exemplifies how coupling molecular self-assembly to endogenous enzymatic cycles affords a general strategy for constructing dynamic, non-perturbative probes for live cell and in vivo imaging.

biochemistry↗

bioRxiv2025

Knocking out Arl13b completely abolishes primary ciliogenesis

Small G protein ARL13B localizes to the cilium and plays essential roles in cilium biogenesis, organization, trafficking, and signaling. Here, we established multiple ARL13B knockout cell lines using the CRISPR/Cas9 system. Surprisingly, all our cell lines lost their cilia completely, in contrast to the reported short cilium and reduced ciliogenesis phenotype. We found that multiple regions of ARL13B are necessary for a complete rescue. Additionally, we found that ARL13B knockout cells also lost their response to SMO-mediated hedgehog stimulation. Our work demonstrates the critical requirement of ARL13B for ciliogenesis and hedgehog signaling, at least in cultured cells, and suggests that ARL13B plays a more crucial role in ciliary function than previously understood.

cell biology↗

bioRxiv2025

Cycling Molecular Assemblies for Selective Cancer Cell Golgi Disruption

The Golgi apparatus is a critical organelle responsible for intracellular trafficking and signaling, orchestrating essential processes such as protein and lipid sorting1-5. Dysregulation of its function has been implicated in various pathologies, including obesity, diabetes, and cancer, highlighting its importance as a potential therapeutic target. Despite this, the development of tools to selectively target the Golgi in specific cell types remain a significant unmet challenge in imaging and drug discovery. Golgi-specific enzyme activities, such as those mediated by protein acyltransferases and thioesterases6, offer an untapped opportunity to develop subcellularly localized therapeutics. Current approaches predominantly rely on direct protein binding but lack the necessary cell selectivity7, underscoring the unmet need for innovative strategies to selectively disrupt Golgi function in cancer cells. Here, we report the development of cycling molecular assemblies (CyMA), a novel class of small peptide derivatives (e.g., dipeptides), which exploit the unique enzymatic environment of the Golgi to establish futile cycles of reversible S-acylation. These assemblies selectively accumulate in cancer cell Golgi, interfering with protein S-acylation cycles and disrupting organelle homeostasis. CyMA impair key Golgi functions, including protein trafficking, glycosylation, and secretion, while demonstrating selective sparing hepatocytes and immune cells such as M1 macrophages. This selective activity represents a paradigm shift, utilizing an enzyme switch and leveraging intracellular environment rather than direct protein binding. Unlike conventional approaches, CyMA reduce tumor growth, drug resistance, and metastasis by pleiotropically disrupting Golgi related functions. By demonstrating the potential of futile cycles as a therapeutic strategy8, this study introduces a generalizable method for targeting organelle-specific enzyme activities. These findings not only underscore the therapeutic potential of CyMA in cancer but also pave the way for future applications in other Golgi-associated diseases.

biochemistry↗

bioRxiv2024

Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi

How the intra-Golgi secretory transport works remains a mystery. The cisternal progression and the stable compartment models have been proposed and are under debate. Classic cisternal progression model posits that both the intra-Golgi transport and Golgi exit of secretory cargos should occur at a constant velocity dictated by the cisternal progression; furthermore, COPI-mediated intra-Golgi retrograde transport is essential for maintaining the Golgi organization. Leveraging our recently developed Golgi imaging tools in nocodazole-induced Golgi ministacks, we found that the intra-Golgi transport velocity of a secretory cargo decreases during their transition from the cis to the trans-side of the Golgi, and different cargos exhibit distinct velocities even within the same cisternae. We observed a vast variation in the Golgi residence times of different cargos. Remarkably, truncation of the luminal domain causes the Golgi residence time of Tac -- a standard transmembrane secretory cargo without intra-Golgi recycling signals -- to extend from 16 min to a notable 3.4 h. Additionally, when COPI-mediated intra-Golgi retrograde transport was inhibited by brefeldin A, we found that nocodazole-induced Golgi can remain stacked for over 30 - 60 minutes. Therefore, our findings challenge the classical cisternal progression model and suggest the stable compartment nature of the Golgi.

cell biology↗

bioRxiv2018

Amino acids stimulate the endosome-to-Golgi trafficking through Ragulator and small GTPase Arl5

The endosome-to-Golgi or endocytic retrograde trafficking pathway is an important post-Golgi recycling route. We made a novel discovery that the retrograde trafficking of cargos is inhibited and stimulated by the absence and presence, respectively, of amino acids (AAs), especially glutamine. By testing components of the AA-stimulated mTORC1 signaling pathway, we demonstrated that SLC38A9, v-ATPase and Ragulator, but not Rag GTPases and mTORC1, are essential for the AA-stimulated trafficking. Arl5, an ARF-like family small GTPase, interacts with Ragulator in an AA-regulated manner and both Arl5 and its effector, the Golgi-associated retrograde protein complex (GARP), are required for the AA-stimulated trafficking. We have therefore identified a mechanistic connection between the nutrient signaling and the retrograde trafficking pathway, whereby SLC38A9 and v-ATPase sense AA-sufficiency and Ragulator functions as a guanine nucleotide exchange factor to activate Arl5, which, together with GARP, a tethering factor, probably facilitates the endosome-to-Golgi trafficking.

cell biology↗