Biology subjects

Chaudhary, V.

Publications and source records attributed to Chaudhary, V..

10 recordsLinked to original sources

bioRxiv2026

Drosophila TRAPPC8-Rab1 module regulates retrograde trafficking of Wingless and Evi/Wntless

Lipid-modified Wnt proteins are secreted from polarized epithelial cells through a multi-step pathway involving membrane delivery, internalization and resecretion. Internalization enables dissociation of Wnt from its cargo receptor Evi/Wntless in endosomes and promotes retromer-mediated recycling of Evi to the Golgi, however, the molecular basis of this retrograde Wnt trafficking remains poorly understood. Here, we identify an essential function of TRAPPC8, the TRAPPIII-specific subunit, in the trafficking of Drosophila Wingless (Wg), the Wnt1 homolog. Loss of TRAPPC8 impaired retrograde trafficking of both Wg and Evi, resulting in their intracellular accumulation in Wg-producing cells. Consistent with the role of TRAPPIII as a Rab1-specific GEF, inhibition of Rab1 phenocopied the trafficking defects caused by TRAPPC8 loss, whereas constitutively active Rab1 rescued these defects. Furthermore depletion of either TRAPPC8 or Rab1 increased the levels of Wg-unbound Evi, indicating that they act downstream of Evi-Wg dissociation. Together, these findings identify the TRAPPIII complex and its effector Rab1 as key regulators of retrograde Wg trafficking required for its efficient secretion.

cell biology↗

bioRxiv2024

Frizzled1 and Frizzled2 are not redundant for competitive survival under low-Wingless levels in the developing Drosophila wing epithelium

In the Drosophila wing epithelium, canonical Wnt signaling is activated by the gradient of secreted Wingless protein (Wnt1 homolog), which interacts redundantly with the Frizzled1 and Frizzled2 receptors. While sharing overlapping functions, these receptors also have distinct non-canonical roles and exhibit differential expression patterns along the Wingless gradient. Moreover, Frizzled2, unlike Frizzled1, is thought to be essential for sustaining low-level Wingless signaling and promoting cell survival in the absence of the ligand. This raises the possibility of the two receptors acting differently along the Wingless gradient. In this study, we investigated the role of these receptors in cell survival across varying Wingless levels. We find that the loss of Frizzled2 in cells at a distance from the Wingless-producing cells--where Wingless levels are low-- leads to competitive elimination of cells. In contrast, Frizzled1 is dispensable for cell survival, regardless of distance from the Wingless source. Our findings show that Frizzled2 is essential for competitive cell survival under low-Wingless conditions and the two receptors are not equally redundant across the Wingless concentration gradient, providing insight into a mechanism for spatial and temporal precision in developmental signaling.

developmental biology↗

bioRxiv2024

IL-10 Targets IRFs to Suppress IFN and Inflammatory Response Genes by Epigenetic Mechanisms

Interleukin-10 (IL-10) is pivotal in suppressing inflammation and innate immune activation, in large part by suppressing induction of genes by potent inflammatory factors such as TLR ligands. Despite decades of research, molecular mechanisms underlying this inhibition have not been resolved. This study utilized an integrated epigenomic analysis of gene transcription, chromatin accessibility, histone modifications and transcription factor binding to investigate IL-10-mediated suppression of LPS and TNF responses in primary human monocytes. Instead of inhibiting core TLR4-activated pathways such as NF-{kappa}B, MAPK-AP-1 and TBK1-IRF3 signaling, IL-10 targeted IRF transcription factor activity and DNA binding, particularly IRF5 and an IRF1-mediated amplification loop that is operative in monocytes. This resulted in suppression of inflammatory NF-{kappa}B target genes, in whose activation IRFs play an amplifying role, and near-complete suppression of interferon-stimulated genes. Mechanisms of TLR4 and TNFR target gene inhibition included downregulation of chromatin accessibility, de novo enhancer formation, and IRF1-associated H3K27ac activating histone marks. These results provide a mechanism by which IL-10 suppresses inflammatory NF-{kappa}B target genes, highlight the role of IRF1 in inflammatory gene expression, and describe an underappreciated suppression of IFN responses by epigenetic mechanisms.

immunology↗

bioRxiv2024

Have AI-Generated Texts from LLM Infiltrated the Realm of Scientific Writing? A Large-Scale Analysis of Preprint Platforms

Since the release of ChatGPT in 2022, AI-generated texts have inevitably permeated various types of writing, sparking debates about the quality and quantity of content produced by such large language models (LLM). This study investigates a critical question: Have AI-generated texts from LLM infiltrated the realm of scientific writing, and if so, to what extent and in what setting? By analyzing a dataset comprised of preprint manuscripts uploaded to arXiv, bioRxiv, and medRxiv over the past two years, we confirmed and quantified the widespread influence of AI-generated texts in scientific publications using the latest LLM-text detection technique, the Binoculars LLM-detector. Further analyses with this tool reveal that: (1) the AI influence correlates with the trend of ChatGPT web searches; (2) it is widespread across many scientific domains but exhibits distinct impacts within them (highest: computer science, engineering sciences); (3) the influence varies with authors who have different language speaking backgrounds and geographic regions according to the location of their affiliations (Italy, China, etc.); (4) AI-generated texts are used in various content types in manuscripts (most significant: hypothesis formulation, conclusion summarization); (5) AI usage has a positive influence on papers impact, measured by its citation numbers. Based on these findings, suggestions about the advantages and regulation of AI-augmented scientific writing are discussed.

scientific communication and education↗

bioRxiv2023

Drosophila Wg and Evi/Wntless dissociation occurs post apical internalization in the late endosomes

Signaling pathways activated by secreted Wnt ligands play an essential role in tissue development and the progression of diseases, like cancer. Secretion of the lipid-modified Wnt proteins is tightly regulated by a repertoire of intracellular factors. For instance, a membrane protein, Evi/Wntless, interacts with the Wnt ligand in the ER, and it is essential for its further trafficking and release in the extracellular space. After dissociating from the Wnt, the Wnt-unbound Evi is recycled back to the ER via Golgi. However, where in this trafficking path Wnt proteins dissociate from Evi remains unclear. Here, we have used the Drosophila wing epithelium to trace the route of the Evi-Wg (Wnt homolog) complex leading up to their separation. In these polarized cells, Wg is first trafficked to the apical surface, however, the secretion of Wg is believed to occur post-internalization via recycling. Our results show that the Evi-Wg complex is internalized from the apical surface. Furthermore, using antibodies that specifically label the Wnt-unbound Evi, we show that Evi and Wg separation occurs post-internalization in the acidic endosomes. These results refine our understanding of the polarized trafficking of Wg and highlight the importance of Wg endocytosis in its secondary secretion.

cell biology↗

bioRxiv2023

Second messenger c-di-AMP regulates multiple antibiotic sensitivity pathways in Mycobacterium smegmatis by discrete mechanisms

One of the debilitating causes of high mortality in the case of tuberculosis and other bacterial infections is the resistance development against standard drugs. There are limited studies so far to describe how a bacterial second messenger molecule can directly participate in distinctive antibiotic tolerance characteristics of a cell in a mechanism-dependent manner. Here we show that intracellular cyclic di-AMP (c-di-AMP) concentration can modulate drug sensitivity of Mycobacterium smegmatis by directly interacting with either a protein effector or with the 5-UTR regions in mRNA of the genes and thus causing transcriptional downregulation of important genes in the pathways. We studied four antibiotics with different mechanisms of action: rifampicin, ciprofloxacin, erythromycin, and tobramycin and subsequently found that the level of drug sensitivity of the bacteria is directly proportional to the c-di-AMP concentration inside the cell. Further, we unraveled the underlying molecular mechanisms to delineate the specific genes and pathways regulated by c-di-AMP and hence result in differential drug sensitivity in M. smegmatis. Thus, our findings of c-di-AMP messenger controlling drug resistance phenotypes of mycobacteria against four different classes of antibiotics is a unique observation that will contribute to scientific advancement in the field. One Sentence SummaryHere we describe how second messenger c-di-AMP modulates the antibiotic sensitivity and resistance profile of M. smegmatis by diverse mechanisms.

microbiology↗

bioRxiv2022

Loss of Rer1 causes proteotoxic stress that drives cell competition and inhibits Myc-driven overgrowth

Cell competition is a developmental phenomenon that allows the selection of healthier cells in a developing tissue. In this process, cells with reduced fitness, conceivably due to harmful mutations, acquire the loser status and are eliminated by the fitter (winner) neighboring cells via juxtacrine cell-cell interactions. How various mutations trigger cell competition is an extensively studied question. However, the mechanism of cell competition remains largely elusive. In this study, we reveal previously unknown functions of an ER and Golgi localized protein Rer1 in the regulation of cell competition in the developing Drosophila wing epithelium. Our data show that loss of Rer1 leads to the proteotoxic stress marked by the increased phosphorylation of eIF2. The increased proteotoxic stress in the rer1 mutant cells led to their elimination via cell competition. Interestingly, we find that Rer1 levels are upregulated upon Myc overexpression, which generates super-competitive cells that overgrow at the expense of the normal neighboring cells. Loss of Rer1 also restricts the growth of Myc-induced super-competitive cells. Moreover, consistent with its known function as a negative regulator of the Notch pathway, our results show that the increased levels of Rer1 in Myc-overexpression led to the downregulation of Notch activity. In summary, these observations provide the first characterization of Rer1 in Drosophila and reveal its role in triggering cell competition via the regulation of proteotoxic stress.

developmental biology↗

bioRxiv2022

Sub-operon promoter arrangement of disA facilitates c-di-AMP homeostasis and selective stress responses in M. smegmatis

Bacterial second messenger signaling often plays an important role in cellular physiology. In this study, we have attempted to understand how c-di-AMP synthesis and degradation are transcriptionally regulated in M. smegmatis. We have discovered that, although c-di-AMP synthesis gene disA exists in a multi-gene operon; a sub-operon promoter arrangement plays a key role under various stress conditions, keeping its dual function property intact. Further, we learned that c-di-AMP plays a role in the autoregulation of the disA promoter to limit intracellular c-di-AMP concentration. We also identified an alternate start codon within the disA gene which can lead to the synthesis of truncated DisA protein at times using an independent stress-inducible promoter. All in all, this study was helpful to understand how c-di-AMP synthesis is regulated under normal and stress conditions linked to its physiological relevance in M. smegmatis.

microbiology↗

bioRxiv2022

Elucidating the role of c-di-AMP in Mycobacterium smegmatis: phenotypic characterization and functional analysis

Cyclic-di-AMP (c-di-AMP) is a newly discovered secondary messenger molecule that plays a critical role in monitoring several important cellular processes, especially in several Gram-positive bacteria signal transduction pathways. In this study, we seek to unravel the physiological significance of the molecule c-di-AMP in Mycobacterium smegmatis under different conditions, using strains with altered c-di-AMP levels: c-di-AMP null mutant ({Delta}disA) and a c-di-AMP over-expression mutant ({Delta}pde). Our thorough analysis of the mutants revealed that the intracellular concentration of c-di-AMP could determine many basic phenotypes such as colony architecture, cell shape, cell size, membrane permeability etc. Additionally, it was shown to play a significant role in multiple stress adaptation pathways in the case of different DNA and membrane stresses. Our study also revealed how the biofilm phenotype of M. smegmatis cells are dependent on intracellular c-di-AMP concentration. Next, we checked how c-di-AMP contributes to antibiotic tolerance characteristics of M. smegmatis, which was followed by a detailed transcriptome profile analysis to reveal key genes and pathways regulated by c-di-AMP in mycobacteria.

microbiology↗

bioRxiv2018

Evidence of functional long-range Wnt/Wg in the developing Drosophila wing epithelium

Wnts are secreted proteins that regulate cell fate specification during development of all metazoans. Wnt proteins were proposed to spread over several cell diameters to activate signalling directly at a distance. In the Drosophila wing epithelium, an extracellular gradient of Wingless (Wg, the homolog of Wnt1) was observed extending over several cells away from producing cells. However, it was also recently shown that a membrane-tethered Neurotactin-Wg fusion protein (NRT-Wg) can rescue the loss-of endogenous Wg, leading to proper patterning of the wing. Therefore, whether Wg spreading is required for correct tissue patterning during development remains controversial and the functional range of wild-type Wg is unclear. Here, by capturing secreted Wg on distally located cells we show that the Wg gradient acts directly up to eleven cell distances. Cells located outside the reach of extracellular Wg depend on the Frizzled2 receptor to maintain target gene expression. We find that NRT-Wg is not restricted to the producing cells and propose that it can rescue signalling defects by perdurance in the receiving cells. These results provide insight into the mechanisms by which Wnt proteins mediate patterning of a rapidly growing tissue.

developmental biology↗