Biology subjects

Ramesh, N. A.

Publications and source records attributed to Ramesh, N. A..

5 recordsLinked to original sources

bioRxiv2026

Atg8 orchestrates stress-responsive chromatin programs across immunity and metabolism

Organisms must coordinate transcriptional responses to immune and metabolic stress, often within the same tissue. In Drosophila and mammals, adipose tissue integrates these signals by mounting antimicrobial defense during acute infection and remodeling lipid metabolism under chronic nutrient surplus. How one cell-biological system supports both functions, and through what molecular machinery, remains incompletely understood. Atg8/LC3, classically defined by canonical autophagy, has emerging non-canonical roles in nuclear gene regulation, raising the possibility that it contributes to stress-coordinated transcription beyond cargo turnover. Using unbiased CUT&RUN in adult Drosophila nuclei, we find that endogenous Atg8 exhibits broad chromatin occupancy at immune, metabolic, and autophagy loci, and accumulates in nuclei under prolonged high-sugar diet (HSD) and acute Gram-positive infection. We identify two conserved Atg8-interacting motifs (AIMs) within the Rel homology domain of NF-{kappa}B/Dif. Flies carrying CRISPR-engineered AIM-mutant Dif are highly susceptible to both infection and chronic HSD, establishing a physiological requirement for intact Dif AIMs. AIM-mutant Dif shows impaired infection-induced nuclear accumulation, suggesting that Atg8 contributes to both Dif cytoplasmic-to-nuclear shuttling and nuclear function. Unbiased comparison of Atg8 chromatin occupancy across HSD and infection further reveals shared and divergent motif grammar, positioning Atg8 as a stress-responsive chromatin cofactor for immune and metabolic transcription. Together, these findings expand the functional landscape of Atg8/LC3 beyond canonical autophagy and reveal that autophagy machinery contributes to stress-specific transcriptional complex assembly. AIM/LIR-mediated interactions, exemplified by Dif, represent one such interface, while additional mechanisms likely underlie Atg8s broader chromatin engagement at loci enriched for transcription factor motifs whose cognate factors lack known AIM/LIRs. We propose that Atg8/LC3-mediated coordination of immune and metabolic transcription is a general principle by which cells integrate diverse stress signals, with implications for obesity, chronic inflammation, and other disease states in which immune and metabolic dysregulation converge. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/727304v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@15c056dorg.highwire.dtl.DTLVardef@68493dorg.highwire.dtl.DTLVardef@a07c6corg.highwire.dtl.DTLVardef@4896c6_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIStress drives Atg8 into nuclei, where it occupies immune and metabolic chromatin. C_LIO_LITwo conserved AIMs in NF-{kappa}B/Dif bind Atg8 and enable Dif nuclear entry. C_LIO_LIAIM-mutant Dif flies are highly susceptible to infection and chronic high-sugar diet. C_LIO_LIAtg8 occupies stress-related motifs on prolonged HSD and acute infection. C_LI

genomics↗

bioRxiv2025

OCRL regulates lysosomal function and endolysosomal homeostasis in Drosophila nephrocytes

The OCRL gene encodes a lipid phosphatase that dephosphorylates phosphatidylinositol 4,5 bisphosphate [(PI(4,5)P2]. Mutations in OCRL lead to a rare human genetic disorder, Lowe syndrome (LS) that affects the eye, kidney and brain. OCRL is widely expressed in cells and is localized to multiple organelles, including the plasma membrane, endosomes, Golgi and lysosomes. Although multiple defects in the endo-lysosomal system have been reported in OCRL depleted cells, the primary site of action of OCRL is unclear. Here we present a Drosophila nephrocyte model of LS; depletion of Drosophila OCRL (dOCRL) manifests with defects in endocytic uptake, altered endosomal compartments as well as expanded but dysfunctional lysosomes. Reconstitution of dOCRL depleted nephrocytes with a lysosome targeted version of the enzyme rescues not only the lysosomal defects but surprisingly also defects in endosomal structure and function. These findings suggest that the primary defect in LS cells is likely to be altered lysosome structure and function. Therefore, regulation of PI(4,5)P2 homeostasis at the lysosome membrane by OCRL is critical to homeostasis of the endosomal system.

cell biology↗

bioRxiv2025

A window of cell cycle plasticity enables imperfect regeneration of an adult postmitotic organ in Drosophila

The Drosophila ejaculatory duct (ED) is a secretory tissue of the male somatic reproductive system responsible for producing components of the seminal fluid which support fertility, serve antimicrobial functions and influence the physiological changes in the female after mating. The ED is a simple organ made up of secretory epithelial cells that are encased by extracellular matrix and a layer of innervated contractile muscle. The ED secretory epithelial cells are post-mitotic and lack known stem cells or progenitors in the adult, but they are not fully quiescent. They undergo a variant cell cycle called endoreplication immediately post-eclosion to increase organ size and protein synthesis capacity. Polyploid and post-mitotic tissues often face unique challenges in response to cell loss due to their inability to proliferate. Here, we show that the adult ED is capable of significant recovery after cell loss due to a combination of increased nuclear and cellular hypertrophy that partially restores tissue mass and organ function. The early cell cycle plasticity of this adult tissue is critical for this recovery, as older tissues that have few or no endocycles exhibit reduced capacity for recovery after cell loss. Together, our findings establish the Drosophila ED as a model to study post-mitotic polyploid tissue repair and highlight a combination of endocycles and hypertrophy as a key mechanism for functional regeneration in the absence of mitosis.

developmental biology↗

bioRxiv2024

Post-eclosion growth in the Drosophila Ejaculatory Duct is driven by Juvenile Hormone signaling and is essential for male fertility

The Drosophila Ejaculatory duct (ED) is a secretory tissue of the somatic male reproductive system. The ED is involved in the secretion of seminal fluid components and ED-specific antimicrobial peptides that aid in fertility and the female post-mating response. The ED is composed of secretory epithelial cells surrounded by a layer of innervated contractile muscle. The ED grows in young adult males during the first 24h post-eclosion, but the cell cycle status of the ED secretory cells and the role of post-eclosion ED growth have been unexplored. Here, we show that secretory cells of the adult Drosophila ED undergo variant cell cycles lacking mitosis called the endocycle, that lead to an increase in the cell and organ size of the ED post eclosion. The cells largely exit the endocycle by day 3 of adulthood, when the growth of the ED ceases, resulting in a tissue containing cells of ploidies ranging from 8C-32C. The size of the ED directly correlates with the ploidy of the secretory cells, with additional ectopic endocycles increasing organ size. When endoreplication is compromised in ED secretory cells, it leads to reduced organ size, reduced protein synthesis and compromised fertility. We provide evidence that the growth and endocycling in the young adult male ED is dependent on Juvenile hormone (JH) signaling and we suggest that hormone-induced early adult endocycling is required for optimal fertility and function of the ED tissue. We propose to use the ED as a post-mitotic tissue model to study the role of polyploidy in regulating secretory tissue growth and function.

developmental biology↗

bioRxiv2024

A genetic and physiological model of renal dysfunction in Lowe syndrome

Lowe syndrome (LS) is an X-linked recessive genetic disorder characterized by renal dysfunction, neurodevelopmental defects, and cataract. The affected gene, OCRL encodes for a polyphosphoinositide 5-phosphatase. OCRL is localized to multiple sub-cellular locations in the endolysosomal system and defects in these organelles have been described in human cells depleted of OCRL. However, the relationship of the endolysosomal defects in OCRL depleted cells to the altered physiology of kidney cells of LS patients has not been completely determined. Here we model the kidney phenotypes of LS using a Drosophila nephrocyte model. Using this model system, we demonstrate that OCRL plays a cell-autonomous role in nephrocyte function. Deletion of the only OCRL ortholog in Drosophila (dOCRL) leads to cell-autonomous defects in larval nephrocyte structure and function. Null mutants of dOCRL (dOCRLKO) show defects in the endolysosomal system of larval nephrocytes that are associated with physiological defects in nephrocyte function. These defects could be rescued by reconstitution with a human OCRL transgene but not with a phosphatase dead version or a human LS patient derived mutation. Overall, this work provides a model system to understand the mechanisms by which the sub-cellular changes from loss of OCRL leads to defects in kidney function in human patients.

cell biology↗