Biology subjects

Balasubramanian, D.

Publications and source records attributed to Balasubramanian, D..

7 recordsLinked to original sources

bioRxiv2026

COP9 complex maintains neuroblast growth and proliferation by regulating Akt/mTor pathway

The nervous system consists of the brain and associated structures that are replete with highly specialised neurons and glia. Central to the development of the brain are Neural Stem Cells, which self-renew to maintain their number and also give rise to differentiated progeny. To identify genes involved in the maintenance of Drosophila neural stem cells, neuroblasts, we performed a protein expression screen followed by a protein knockdown screen using deGradFP system. Through this, we identified CSN7, a COP9 signalosome (CSN) subunit, which is enriched in neuroblasts and essential for neural development. CSN is a highly conserved multi-protein complex that regulates proteasome-mediated protein degradation via modulation of Cullin-RING E3 ligases. We found that loss of CSN7 and CSN1b lead to a decrease in neuroblast size and a reduced mitotic index. Our results show that CSN7/CSN1b regulates Akt-TOR signalling in the developing larval brain. Furthermore, we found that this regulation is mediated by Cul1. Overall, our work describes a hitherto undescribed role for the components of the CSN complex in neural development.

developmental biology↗

bioRxiv2025

Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity

The spatiotemporal expression of developmental genes is regulated by the interplay of two key regulatory elements: core promoters, generally assumed to support only basal transcription, and enhancers, which enable their tissue- and stage-specific activation. Here, we show that spatiotemporal specificity can also be encoded within the core promoter. Using the Drosophila twist E3 enhancer as a model, we found that E3 is pleiotropic and activates four functionally unrelated genes. Despite receiving the same enhancer input, each target gene displays distinct and non-overlapping expression patterns. We demonstrate that the selective activation of each target gene is encoded within their promoter regions. Core promoters act as "gatekeepers" that restrict enhancer input into precise tissue- and stage-specific transcription, while proximal-promoter elements facilitate enhancer responsiveness. We propose that promoters function as active interpreters rather than passive recipients of enhancer signals, providing a critical but under-appreciated layer of regulatory specificity within complex gene expression programs.

genetics↗

bioRxiv2024

Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae

The sole gain of laterally acquired virulence genes does not fully explain the transition of environmental strains into human pathogens. To date, the specific molecular drivers and fitness trade-offs that enable some strains within a population to undergo this process remain enigmatic. Here, we describe a small RNA (sRNA) with a unique modular structure that shapes the evolution of toxigenic Vibrio cholerae, the agent of cholera. The sRNA comprises of a highly variable 5 module located within the ompU ORF and a conserved 3 one downstream from the gene. This atypical location confers a distinct bimodular structure to the OmpU-encoded sRNA (OueS), generating allelic variants that differentially contribute to the emergence of virulence potential in some strains and associated fitness trade-offs between human infection and environmental survival. Unlike environmental counterparts, the OueS allele from toxigenic strains controls phenotypes essential during host colonization: a) stringently inhibits biofilm formation via a novel sRNA-sRNA interaction by suppressing the iron-responsive sRNA RyhB, and b) confers resistance against intestinal bacteriophages by activating the recently discovered CBASS phage defense system. Toxigenic OueS is also required for successful intestinal colonization and, as the first known example of its kind, acts as a functional surrogate of the master virulence regulator ToxR, controlling over 84% of its regulome. On the other hand, isogenic strains encoding environmental alleles of OueS exhibit higher competitive fitness than those harboring toxigenic ones during colonization of natural reservoirs such as crustaceans and phytoplankton. Our findings provide critical insights into the evolution of toxigenic V. cholerae and reveal specific molecular mechanisms and fitness costs associated with the emergence of pathogenic traits in bacteria.

microbiology↗

bioRxiv2023

Modular small RNA drives pathogen emergence

Pathogen emergence is a poorly understood complex phenomenon. To date, the molecular mechanisms that allow strains within a bacterial population to emerge as human pathogens remain mostly enigmatic. We recently uncovered that toxigenic Vibrio cholerae encode preadaptations to host colonization, what we term virulence adaptive polymorphisms (VAPs), however, the molecular mechanisms driving them are not known. ompU is a VAP-encoding gene that is associated with the production of the major outer membrane porin OmpU. Here, we show that the ompU ORF also encodes a modular small RNA overlapping its 3 terminus that plays a major role in V. cholerae physiology. We determined that the OmpU-encoded sRNA (OueS) strongly suppresses biofilm formation, a phenotype that is essential for host intestinal colonization, via repression of iron uptake. OueS controls over 84% of the genes regulated by ToxR, a major virulence regulator, and plays an integral role during the infection process. We demonstrate that OueS is critical for intestinal colonization and its bimodular nature dictates the virulence potential of V. cholerae. Overall, our study reveals specific molecular mechanisms leading to the emergence of pathogenic traits in bacteria unveiling the hidden genetics associated with this process. We propose a scenario where a limited number of modular genes could explain the emergence of novel phenotypic traits in biological systems.

microbiology↗

bioRxiv2022

Enhancer-promoter interactions form independently of genomic distance and are functional across TAD boundaries

Developmental enhancers are essential regulatory elements that drive precise spatio-temporal gene expression patterns. They do so by interacting with the promoter of their target genes, often across large genomic distances, in a highly specific manner. However, it is unclear how such specificity can be achieved. While several studies have suggested that Topologically Associating Domains (TADs)1-3 facilitate and constrain enhancer-promoter interactions, the role of TAD boundaries in effectively restricting enhancer-promoter interactions is heavily debated. Here we show that enhancers can establish long-range interactions across TAD boundaries and even between different chromosomes. Moreover, some of these interactions are functional in vivo, illustrating their functional importance. Using the twist locus in Drosophila embryos, we systematically relocated one of its enhancers to different regulatory contexts and distances from the twist promoter. We found that the twist promoter can engage in functional enhancer-promoter interactions across a TAD boundary and that distal interactions are sometimes favored over proximal ones. Our results demonstrate that TAD boundaries are not sufficient to constrain enhancer-promoter interactions and that the formation of long-range interactions is not solely driven by distance. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.

genomics↗

bioRxiv2018

Potential application of phage therapy for prophylactic treatment against Pseudomonas aeruginosa biofilm Infections.

The majority of the microbial activity in humans is in the form of biofilms, i.e., an exopolysaccharide-enclosed bacterial mass. Unlike planktonic cells and the cells on the surface of the biofilm, the biofilm-embedded cells are more resistant to the effects of the antibiotics and the host cellular defense mechanisms. A combination of biofilm growth and inherent resistance prevents effective antibiotic treatment of Pseudomonas aeruginosa infections including those in patients with cystic fibrosis. Antibiotic resistance has led to an increasing interest in alternative modalities of treatment. Thus, phages that multiply in situ and in the presence of susceptible hosts can be used as natural, self-limiting, and profoundly penetrating antibacterial agents. The objective of this study is to identify active phages against a collection of P. aeruginosa isolates (PCOR strains) including the prototype PAO1 and the isogenic constitutively alginate-producing PDO300 strains. These PCOR strains were tested against six phages (P105, P134, P140, P168, P175B, and P182). The analysis shows 69 % of the PCOR isolates are sensitive and the rest are resistant to all six phages. These phages were then tested for their ability to inhibit biofilm formation using a modified biofilm assay. The analysis demonstrated that the sensitive strains showed increased resistance, but none of the susceptible strains from the initial screening were resistant. Using the minimum biofilm eradication concentration (MBEC) assay for biofilm formation, the biofilm eradication ability of the phages was tested. The data showed that a higher volume of phage was required to eradicate preformed biofilms than the amount required to prevent colonization of planktonic cells. This data supports the idea of phage therapy more as a prophylactic treatment.

microbiology↗

bioRxiv2017

Gene expression effects of lithium and valproic acid in a serotonergic cell line

Valproic acid (VPA) and lithium are widely used in the treatment of bipolar disorder. However, the underlying mechanism of action of these drugs is not clearly understood. We used RNA-Seq analysis to examine the global profile of gene expression in a rat serotonergic cell line (RN46A) after exposure to these two mood stabilizer drugs. Numerous genes were differentially regulated in response to VPA (log2 fold change [≥] 1.0; i.e. odds ratio of [≥] 2, at FDR <5%), but only two genes (Dynlrb2 and Cdyl2) showed significant differential regulation after exposure of the cells to lithium, with the same analysis criteria. Both of these genes were also regulated by VPA. Many of the differentially expressed genes had functions of potential relevance to mood disorders or their treatment, such as several serpin family genes (including neuroserpin), Nts (neurotensin), Maob (monoamine oxidase B) and Ap2b1, which is important for synaptic vesicle function. Pathway analysis revealed significant enrichment of Gene Ontology terms such as extracellular matrix (ECM) remodelling, cell adhesion and chemotaxis. This study in a cell line derived from the raphe nucleus has identified a range of genes and pathways that provide novel insights into the therapeutic action of the commonly used mood stabilizer drugs.

genomics↗