Academy of Scientific & Innovative Research

Saussurea costus (Falc.) is an endangered medicinal plant possessing diverse phytochemical compounds with clinical significance and used to treat numerous human ailments. Despite the source of enriched phytochemicals, molecular insights into spatialized metabolism are poorly understood in S. costus. This study investigated the dynamics of organ-specific secondary metabolite biosynthesis using deep transcriptome sequencing and high-throughput UHPLC-QTOF based untargeted metabolomic profiling. A de novo assembly from quality reads fetched 59,725 transcripts with structural (53.02%) and functional (66.13%) annotations of non-redundant transcripts. Of the 7,683 predicted gene families, 3,211 were categorized as 'single gene families'. Interestingly, out of the 4,664 core gene families within the Asterids, 4,560 families were captured in S. costus. Organ-specific differential gene expression analysis revealed significant variations between leaves vs. stems (23,102 transcripts), leaves vs. roots (30,590 transcripts), and roots vs. stems (21,759 transcripts). Like-wise, putative metabolites (PMs) were recorded with significant differences in leaves vs. roots (250 PMs), leaves vs. stem (350 PMs), and roots vs. stem (107 PMs). The integrative transcriptomic and metabolomic analysis identified organ-specific differences in the accumulation of important metabolites, including secologanin, menthofuran, taraxerol, lupeol, acetyleugenol, scopoletin, costunolide, and dehydrocostus lactone. Furthermore, a global gene co-expression network (GCN) identified putative regulators controlling the expression of key target genes of secondary metabolite pathways including terpenoid, phenylpropanoid, and flavonoid. The comprehensive functionally relevant genomic resource created here provides beneficial insights for upscaling targeted metabolite biosynthesis through genetic engineering, and for expediting association mapping efforts to elucidate the casual genetic elements controlling specific bioactive metabolites.

Endoplasmic reticulum plays a central role in protein folding and cellular detoxification. NEDD4, a HECT E3 ubiquitin ligase, has been implicated in endoplasmic reticulum stress in humans. In this study, we have explored the role of S. pombe Bsd1, an ortholog of mammalian Ndfip1 (NEDD4 interacting protein 1) in tunicamycin-induced stress response pathway.

Bsd1, an ortholog of mammalian NEDD4 interacting protein 1 (Ndfip1) plays a protective role against tunicamycin-induced ER stress. The confocal microscopy using GFP tagged Bsd1 revealed its localization to the membrane, with a more pronounced signal in the presence of tunicamycin. Additionally, the expression analysis showed a two-fold increase in the expression of Bsd1 after 4 h exposure to tunicamycin. Furthermore, acridine orange/ ethidium bromide staining and MTT assay revealed an increase in apoptotic cell death in bsd1Δ as compared to wild type cells after treatment with ER stressors. Compared to the wild type, we observed punctate FM4-64 staining in bsd1Δ cells in the presence of tunicamycin suggesting a significant loss of vacuolar structures. In a genetic interaction analysis, we observed enhanced sensitivity of tunicamycin in bsd1Δ ire1Δ double mutant as compared to each single mutant, suggesting the role of Bsd1 in the tunicamycin-induced ER stress response might be independent of the Ire1 pathway.

Our study has implicated the role of fission yeast Bsd1 in ER stress response in an Ire1 independent pathway. Further, we have shown its role in apoptotic cell death and the maintenance of vacuolar structures.

CRP is a biomarker of acute inflammation linked to metabolic complications. Given the rising prevalence of these conditions in India, we investigated the genetic basis of CRP levels in Indian adolescents, an underrepresented group in genetic studies, to identify early markers of metabolic risk. We performed a two-phased genome-wide association study (GWAS; N = 5052) and an independent Exome-wide association study (ExWAS; N = 4547), to identify both common and rare genetic variants associated with CRP levels. The study identified intergenic variants near CRP and CRPP1 genes, and APOC1 gene as the key regulators of CRP levels establishing the universality of these associations. The GWAS identified the variant rs4247360 (PITPNC1) to be associated at a suggestive significance. The ExWAS single variant association identified novel associations in genes FGL1 (rs35431851), C19orf45 (rs608144, rs475923, rs484870), TRAPPC12 (rs11686212) and KIAA0087 (rs17153822). The SKATO analysis of the rare variants highlighted the role of loss of function and missense variants in genes EPS15, CCDC15, ZNF286A, ELF1, B3GNT8, ZNF850, MAP2, and PSG2. The GWAS and ExWAS in the present study validated the association of 56 variants previously reported for CRP levels. The meta-analysis with the CRP GWAS earlier reported in Indian adults revealed the shared genetic architecture of CRP levels across age groups. The gene-set enrichment analysis highlighted the role of CRP-associated genes in inflammatory and cardiometabolic pathways. The study enhances understanding of genetic predispositions to inflammation and metabolic disorders confirming known associations, identifying novel loci, and validating shared genetic architecture across age-groups, guiding targeted prevention for at-risk youth.