Biology subjects

Gupta, B. P.

Publications and source records attributed to Gupta, B. P..

10 recordsLinked to original sources

bioRxiv2025

Comparative analysis of hsp16 and hsp70 heat shock protein families in Caenorhabditis nematodes

The heat shock response (HSR), driven by molecular chaperons, is a key defense mechanism against proteotoxic stress. In nematodes, the hsp16 family and hsp70 family play central roles in the HSR, but their evolutionary conservation and expression patterns remain poorly understood. Here, we performed phylogenetic, genomic, and transcriptomic analyses of hsp16 and hsp70 genes in Caenorhabditis elegans and C. briggsae, and other related nematodes. Our findings show that hsp16 genes are rapidly evolving and often organized in clusters of closely spaced and oppositely oriented pairs. These genes show dynamic temporal expression in C. elegans and C. briggsae under basal, unstressed conditions. In contrast, hsp70 genes are more conserved across species and display stable expression. We also found that C. briggsae contains more orthologous HSP genes than C. elegans, and exhibits a higher proportion of constitutive expression, consistent with its greater thermal tolerance. These findings highlight the evolutionary diversification and functional organization of heat shock proteins in nematodes, offering insights into how genomic architecture and gene expression contribute to species-specific thermal adaptation.

evolutionary biology↗

bioRxiv2025

Heavy Metal Exposure Disrupts Electrotactic Behavior in Caenorhabditis elegans

Environmental toxicants such as heavy metals can profoundly impact organismal physiology, yet sensitive and rapid behavioral assays to quantify such effects are limited. Here, we employed a microfluidic-based electrotaxis assay to systematically evaluate the impact of chronic exposure to metal salts on the electrotactic swimming behavior of the nematode Caenorhabditis elegans. We report that exposure to Ag, Hg, MeHg, Cu, Mn, and Pb significantly alters electrotaxis speed. Notably, Cu required higher concentrations to induce phenotypes, whereas Ag and Hg disrupted behavior at lower doses. Three other metals (Ni, Fe, and Cd) did not elicit marked electrotaxis defects. Bioaccumulation analysis of Cu, Ag, Hg, and MeHg via ICP-MS revealed that MeHg was present in highest amount in worms. Consistent with this, MeHg showed the highest toxicity. We also found dopaminergic neurodegeneration in most metal-exposed animals, correlating with behavioral impairments. Although heat shock factor-1 (HSF-1) and its downstream target hsp-16.2 were induced by some metals, their expression did not consistently correlate with electrotaxis defects. Moreover, metal-induced impairments persisted even after recovery on toxin-free media, indicating possible irreversible damage. Our findings establish electrotaxis in C. elegans as a robust, non-invasive assay to assess neurobehavioral toxicity and demonstrate its utility for detecting sub-lethal impacts of environmental metals.

animal behavior and cognition↗

bioRxiv2024

Genome-wide temporal gene expression reveals a post-reproductive shift in the nematode C. briggsae

C. briggsae offers a robust system for comparative investigations of genetic pathways that affect physiological processes. One key process, reproduction, significantly impacts longevity due to its high energetic cost, which limits resources for somatic maintenance. Long-lived mutants often exhibit reproductive impairments, and studies in C. elegans have demonstrated that germline mutations and complete germline removal can promote longevity, underscoring the link between reproduction and aging. We are interested in identifying genes and biological processes affected during the reproductive and post-reproductive periods in C. briggsae. To achieve this, we conducted whole-genome transcriptome profiling on animals at various adult stages. analysis of differentially expressed (DE) genes revealed that the majority were downregulated during the reproductive period. Interestingly, this trend reversed post-reproduction, with three-quarters of the genes upregulated--a phenomenon we termed the reproductive shift. A similar analysis in C. elegans also showed a downregulation bias during the reproductive period, but the reproductive shift was absent. Further examination of C. briggsae DE genes showed enrichment in processes related to the matrisome, muscle development and function during the reproductive period. Post-reproductive downregulated genes were enriched in DNA damage repair, stress response, and immune response. Additionally, terms related to fatty acid metabolism, catabolism, and transcriptional regulation exhibited complex patterns, with different biological processes being up or downregulated between the reproductive and post-reproductive stages. Overall, our transcriptomic data provides a valuable resource for cross-sectional comparative studies of reproductive and post-reproductive changes in nematodes. Additionally, the findings prompt similar studies in other animal models thereby advancing our understanding of genetic pathways affecting reproduction and aging.

genomics↗

bioRxiv2023

Comparative study of thermal tolerance and other physiological characteristics in C. briggsae and C. elegans

The nematode Caenorhabditis briggsae (C. briggsae) is routinely used in genetic and evolutionary studies involving its well-known cousin, C. elegans. The two species are morphologically almost identical but exhibit significant developmental, genetic, and genomic differences. The AF16 isolate of C. briggsae is an established reference strain. We used additional wild isolates from tropical and temperate regions to perform a comparative study of phenotypic characters. The analysis revealed both intra (between C. briggsae isolates) and inter (compared to C. elegans N2) species variability in dimensions and opacity. Our data also showed that C. briggsae isolates prefer higher temperatures for growth, reproduction, and survival than C. elegans N2. The preference for higher temperatures further translated into a higher tolerance for heat stress, as evidenced by its survival at temperatures lethal to N2. Interestingly, we found that while C. briggsae is more resistant to heat and shows greater sensitivity to other forms of stress, namely oxidative and osmotic, compared to C. elegans. The heat resistance of C. briggsae was correlated with efficient upregulation of the cytosolic chaperon hsp-16.2. Overall, this work has revealed significant differences in stress sensitivities between the two nematodes and forms the basis to investigate changes in underlying mechanisms that affect their stress responses.

evolutionary biology↗

bioRxiv2023

The neurotrophic factor MANF regulates autophagic flux and lysosome function to promote proteostasis in C. elegans

The conserved mesencephalic astrocyte-derived neurotrophic factor (MANF) protects dopaminergic neurons but also functions in several other tissues. Previously, we showed that Caenorhabditis elegans manf-1 null mutants have increased ER stress, dopaminergic neurodegeneration, protein aggregation, slower growth, and a reduced lifespan. The multiple requirements of MANF in different systems suggest its essential role in regulating cellular processes. However, how intracellular and extracellular MANF regulates broader cellular function remains unknown. Here, we report a novel mechanism of action for manf-1 that involves the autophagy transcription factor HLH-30/TFEB-mediated signaling to regulate lysosomal function and aging. We generated multiple transgenic strains overexpressing MANF-1 and found that animals had extended lifespan, reduced protein aggregation, and improved neuronal health. Using a fluorescently tagged MANF-1, we observed different tissue localization of MANF-1 depending on the ER retention signal. Further subcellular analysis showed that MANF-1 localizes within cells to the lysosomes. These findings were consistent with our transcriptomic studies and, together with analysis of autophagy regulators, demonstrate that MANF-1 regulates protein homeostasis through increased autophagy and lysosomal activity. Collectively, our findings establish MANF as a critical regulator of the stress response, proteostasis, and aging.

genetics↗

bioRxiv2021

picd-1, a gene that encodes CABIN1 domain-containing protein, interacts with pry-1/Axin to regulate multiple processes in Caenorhabditis elegans

AXIN family members control diverse biological processes in eukaryotes. As a scaffolding protein, AXIN facilitates interactions between cellular components and provides specificity to signaling pathways. Despite its crucial roles in metazoans and discovery of a large number of family members, the mechanism of AXIN function is not very well understood. The C. elegans AXIN homolog PRY-1 provides a powerful tool to identify interacting genes and downstream effectors that function in a conserved manner to regulate AXIN-mediated signaling. Previous work demonstrated pry-1s essential role in developmental processes such as reproductive system, seam cells, and a P lineage cell P11.p. More recently, our lab carried out a transcriptome profiling of pry-1 mutant and uncovered the essential role of the gene in lipid metabolism, stress response, and aging. In this study, we have extended the work on pry-1 by reporting a novel interacting gene picd-1 (pry-1-interacting CABIN1 domain containing). Our findings have revealed that picd-1 plays an essential role in C. elegans and is involved in several pry-1-mediated processes including regulation of stress response and lifespan maintenance. In support of this, picd-1 expression overlaps with pry-1 in multiple tissues throughout the lifespan of animals. Further experiments showed that picd-1 inhibits CREB-regulated transcriptional coactivator homolog CRTC-1 function, which promotes longevity in a calcineurin-dependent manner. These data provide evidence for an essential role of the CABIN1 domain protein PICD-1 in mediating PRY-1 signaling in C. elegans.

genetics↗

bioRxiv2021

Gene identification and genome annotation in Caenorhabditis briggsae by high throughput 5' RNA end determination

The nematode Caenorhabditis briggsae is routinely used in comparative and evolutionary studies involving its well-known cousin C. elegans. The C. briggsae genome sequence has accelerated research by facilitating the generation of new resources, tools, and functional studies of genes. While substantial progress has been made in predicting genes and start sites, experimental evidence is still lacking in many cases. Here, we report an improved annotation of the C. briggsae genome using the Trans-spliced Exon Coupled RNA End Determination (TEC-RED) technique. In addition to identifying the 5 ends of expressed genes, we have discovered operons and paralogs. In summary, our analysis yielded 10,243 unique 5 end sequence tags with matches in the C. briggsae genome. Of these, 6,395 were found to represent 4,252 unique genes along with 362 paralogs and 52 previously unknown exons. These genes included 14 that are exclusively trans-spliced in C. briggsae when compared with C. elegans orthologs. A major contribution of this study is the identification of 493 operons, of which two-thirds are fully supported by tags. In addition, two SL1-type operons were discovered. Interestingly, comparisons with C. elegans showed that only 40% of operons are conserved. Of the remaining operons, 73 are novel, including 12 that entirely lack orthologs in C. elegans. Further analysis revealed that four of the 12 novel operons are conserved in C. nigoni. Altogether, the work described here has significantly advanced our understanding of the C. briggsae system and serves as a rich resource to aid biological studies involving this species.

evolutionary biology↗

bioRxiv2021

Genetic analysis of Caenorhabditis elegans pry-1/Axin suppressors identifies genes involved in reproductive structure development, stress response, and aging

The Axin family of scaffolding proteins regulates a wide array of developmental and post-developmental processes in eukaryotes. Studies in the nematode, Caenorhabditis elegans, have shown that the Axin homolog, PRY-1, plays essential roles in multiple tissues. To understand the genetic network of pry-1, we focused on a set of genes that are differentially expressed in the pry-1-mutant transcriptome and are linked to reproductive structure development. Eight of the genes (ard-1, rpn-7, cpz-1, his-7, cdk-1, rnr-1, clsp-1, and spp-1), when knocked down by RNA interference, efficiently suppressed the plate-level multivulva phenotype of pry-1 mutants. In every case, other than clsp-1 and spp-1, the ectopic vulval precursor cell (VPC) induction was also inhibited. The suppressor genes are members of known gene families in eukaryotes and perform essential functions. Our genetic interaction experiments revealed that except for clsp-1, the genes participate in one or more pry-1-mediated biological events. While four of them (cpz-1, his-7, cdk-1, and rnr-1) function in VPC induction, stress response, and aging, the other three (spp-1, ard-1, and rpn-7) are specific to one or more of these processes. Further analysis of the genes involved in aging showed that his-7, cdk-1, and rnr-1 also interacted with daf-16/FOXO. The results of genetic epistasis experiments suggested that his-7 functions upstream of daf-16, whereas cdk-1 and rnr-1 act downstream of the pry-1-daf-16 pathway. Altogether, these findings demonstrate the important role of pry-1 suppressors in C. elegans. Given that all of the genes described in this study are conserved, future investigations of their interactions with Axin and their functional specificity promises to uncover the genetic network of Axin under normal and disease states.

genetics↗

bioRxiv2020

Axin-mediated regulation of lifespan and muscle health in C. elegans involves AMPK-FOXO signaling

Aging is a significant risk factor for several diseases. Studies have uncovered multiple signaling pathways that modulate the process of aging including the Insulin/IGF-1 signaling (IIS). In C. elegans the key regulator of IIS is DAF-16/FOXO whose activity is regulated by phosphorylation. A major kinase involved in DAF-16-mediated lifespan extension is the AMPK catalytic subunit homolog, AAK-2. In this study, we demonstrate a novel role of PRY-1/Axin in AAK-2 activation to regulate DAF-16 function. The pry-1 transcriptome contains many genes associated with aging and muscle function. Consistent with this, pry-1 is strongly expressed in muscles and muscle-specific overexpression of pry-1 extends the lifespan, delays muscle aging, and improves mitochondrial morphology in DAF-16-dependent manner. Furthermore, PRY-1 is necessary for AAK-2 phosphorylation. Together, our data demonstrate a crucial role of PRY-1 in maintaining the lifespan and muscle health. Since muscle health declines with age, our study offers new possibilities to manipulate Axin function to delay muscle aging and improve lifespan.

cell biology↗

bioRxiv2018

PRY-1/AXIN signaling regulates lipid metabolism in Caenorhabditis elegans

The nematode Caenorhabditis elegans is a leading animal model to study how signaling pathway components function in conserved biological processes. Here, we describe the role of an Axin family member, pry-1, in lipid metabolism. As a central component of the canonical Wnt signaling pathway, pry-1 acts as a scaffold to multiprotein destruction complex that negatively regulates the expression of Wnt target genes. A genome-wide transcriptome profiling of pry-1 mutant revealed genes associated with aging and lipid metabolism such as vitellogenins (yolk lipoproteins), fatty acid desaturases, lipases, and fatty acid transporters. Consistent with this we found that pry-1 is crucial for the normal adult lifespan and maintenance of lipid levels. Knock-downs of vit genes in pry-1 mutant background restored lipid levels, suggesting that Vitellogenins contribute to PRY-1 function in lipid metabolic processes. Additionally, lowered expression of desaturases and lipidomics analysis provided evidence that the fatty acid synthesis is reduced in pry-1 mutants. In agreement with this an exogenous supply of oleic acid restored depleted lipids in somatic tissues of worms. Overall, our findings demonstrate that PRY-1/Axin signaling is essential for lipid metabolism and involves regulation of yolk proteins.

physiology↗