Biology subjects

Sivadas, A.

Publications and source records attributed to Sivadas, A..

6 recordsLinked to original sources

bioRxiv2026

Restoration of Keratinocyte Homeostasis Drives Resolution of Skin Inflammation

Chronic skin inflammation is sustained by reciprocal interactions between epidermal dysfunction and immune activation, yet whether epithelial state actively governs restoration of tissue homeostasis remains unclear. Using a murine model of inflammatory skin disease, we modulated epidermal lipid metabolism and examined its effects on tissue organization. Transcriptomic profiling revealed coordinated reversal of inflammatory, metabolic, and structural gene programs accompanied by normalization of epidermal architecture. Single-cell RNA sequencing showed that this remodeling was concentrated in differentiated keratinocytes, with suppression of IL-17 and neutrophil-associated responses and restoration of barrier and mitochondrial-lipid programs, while stromal and myeloid compartments displayed secondary adaptation. Cross-species analysis demonstrated that resolution-associated gene networks are inversely regulated in human psoriasis. Integrated proteomic and transcriptomic analyses further identified a conserved epithelial regulatory triad whose concordant regulation in psoriasis and atopic dermatitis, and whose in vivo silencing, establish mechanistic control of disease severity. Together, these findings indicate that inflammatory resolution reflects reorganization of epidermal transcriptional networks and position epithelial state as a determinant of inflammatory persistence.

cell biology↗

bioRxiv2025

CobVar - a comprehensive resource of Vitamin B 12-associated genomic variants

The importance of vitamin B12 (cobalamin) in numerous biological processes, including DNA synthesis and cellular energy production, underscores the need for therapeutic and public health strategies to address B12 insufficiency/deficiency in the population. Genetic variations in pathways influencing cobalamin absorption, transport, and metabolism can affect various direct and indirect measures of vitamin B12 status. To facilitate a structured approach to studying these genetic factors, we aimed to systematically curate and create a user-friendly web database that offers comprehensive data on genetic variants influencing B12 biomarkers. A Pubmed search was performed for 5 B12 traits (total serum/plasma B12, holotranscobalamin (active B12), total transcobalamin, holo haptocorrin, and methylmalonic acid) resulting in 493 research publications, of which 47 relevant publications were reviewed further. The database backend was built using MongoDB and the web interface was coded in PHP, JavaScript, HTML and CSS on an Apache HTTP server. We have manually curated and compiled the Cobalamin Associated Genetic Variant (CobVar) database, comprising a total of 324 genetic variant associations for 5 different vitamin B12 traits involving 222 unique genetic variants and 84 genes identified across several genome-wide association studies (GWAS) and candidate gene studies. About one-third of the total genetic variant associations have been reported in >1 independent studies and 15 variants in >1 ethnic group. FUT2 gene showed the maximum number of associations for total serum/plasma B12 (N=39), followed by MTHFR (N=24) and TCN2 (N=23). The database is accessible online at https://datatools.sjri.res.in/VBG/. CobVar is a vital resource for researchers and nutritionists, offering quick access to the latest developments in B12-related genetic variant research and serves as a valuable tool for advancing personalized treatment. Database URLhttps://datatools.sjri.res.in/VBG/.

genomics↗

bioRxiv2023

Site-Specific Crosslinking Reveals Phosphofructokinase-L Inhibition Drives Self-Assembly and Attenuation of Protein Interactions

Phosphofructokinase is the central enzyme in glycolysis and constitutes a highly regulated step. The liver isoform (PFKL) compartmentalizes during activation and inhibition in vitro and in vivo respectively. Compartmentalized PFKL is hypothesized to modulate metabolic flux consistent with its central role as the rate limiting step in glycolysis. PFKL tetramers self-assemble at two interfaces in the monomer (interface 1 and 2), yet how these interfaces contribute to PFKL compartmentalization and drive protein interactions remains unclear. Here, we used site-specific incorporation of noncanonical photocrosslinking amino acids to identify PFKL interactors at interface 1, 2, and the active site. Tandem mass tag-based quantitative interactomics reveals interface 2 as a hotspot for PFKL interactions, particularly with cytoskeletal, glycolytic, and carbohydrate derivative metabolic proteins. Furthermore, PFKL compartmentalization into puncta was observed in human cells using citrate inhibition. Puncta formation attenuated crosslinked protein-protein interactions with the cytoskeleton at interface 2. This result suggests that PFKL compartmentalization sequesters interface 2, but not interface 1, and may modulate associated protein assemblies with the cytoskeleton.

biochemistry↗

bioRxiv2023

SARS-CoV-2 Nonstructural Proteins 3 and 4 tune the Unfolded Protein Response

Coronaviruses (CoV), including SARS-CoV-2, modulate host proteostasis through activation of stress-responsive signaling pathways such as the Unfolded Protein Response (UPR), which remedies misfolded protein accumulation by attenuating translation and increasing protein folding capacity. While CoV nonstructural proteins (nsps) are essential for infection, little is known about the role of nsps in modulating the UPR. We characterized the impact of SARS-CoV-2 nsp4, a key driver of replication, on the UPR using quantitative proteomics to sensitively detect pathway-wide upregulation of effector proteins. We find nsp4 preferentially activates the ATF6 and PERK branches of the UPR. Previously, we found an N-terminal truncation of nsp3 (nsp3.1) can suppress pharmacological ATF6 activation. To determine how nsp3.1 and nsp4 tune the UPR, their co-expression demonstrated that nsp3.1 suppresses nsp4-mediated PERK, but not ATF6 activation. Re-analysis of SARS-CoV-2 infection proteomics data revealed time-dependent activation of PERK targets early in infection, which subsequently fades. This temporal regulation suggests a role for nsp3 and nsp4 in tuning the PERK pathway to attenuate host translation beneficial for viral replication while avoiding later apoptotic signaling caused by chronic activation. This work furthers our understanding of CoV-host proteostasis interactions and highlights the power of proteomic methods for systems-level analysis of the UPR.

biochemistry↗

bioRxiv2022

Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex.

The S. pombe orthologue of the human PAXT complex, Mtl1-Red1 Core (MTREC), is an eleven-subunit complex which targets cryptic unstable transcripts (CUTs) to the nuclear RNA exosome for degradation. It encompasses the canonical poly(A) polymerase Pla1, responsible for polyadenylation of nascent RNA transcripts as part of the cleavage and polyadenylation factor (CPF/CPSF). In this study we identified and characterised the interaction between Pla1 and the MTREC complex core component Red1 and analysed the functional relevance of this interaction in vivo. Our crystal structure of the Pla1-Red1 complex showed that a 58-residue fragment in Red1 binds to the RNA recognition motif domain of Pla1 and tethers it to the MTREC complex. Structure-based Pla1-Red1 interaction mutations showed that Pla1, as part of MTREC complex, hyper-adenylates CUTs for their efficient degradation. Interestingly, the Red1-Pla1 interaction was also required for the efficient assembly of the fission yeast facultative heterochromatic islands. Together, our data suggest a complex interplay between the RNA surveillance and 3-end processing machineries.

molecular biology↗

bioRxiv2019

A temporal map of gene expression pattern during zebrafish liver regeneration

Background & AimsZebrafish is increasingly being used to study liver injury and regeneration. However, very little is known about molecular players that respond to injury and participate in liver regeneration. Here we aim to generate a temporal map of gene expression changes at injury and during regeneration of the adult zebrafish liver.\n\nMethodsWe use a metronidazole-nitroreductase (MTZ-nfsb) based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Through RNA sequencing of liver samples at multiple time points we generate a comprehensive temporal map of gene expression changes during injury and regeneration.\n\nResultsGene expression reveals that soon after injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole-induced ROS by activating oxido-reductase pathways and apoptosis machinery. Upon injury, liver cells down regulate genes encoding complement proteins, bile acid and lipid biosynthesis pathway in a concerted manner. Midway through regeneration, we discover a spike of cholesterol biosynthesis and protein folding machinery genes suggesting an important role for these pathways in liver regeneration.\n\nConclusionsThe temporal transcriptomic map of liver regeneration would serve as a framework for further studies in understanding, and for screening for compounds that augment liver regeneration.\n\nGeneral significanceUsing a hepatocyte specific ablation of zebrafish liver, we create a model of adult liver regeneration. This model was used to generate a comprehensive transcriptomic map of gene expression trends during liver regeneration. This temporal map lays the groundwork to study important events in liver regeneration.\n\nHighlightsO_LIZebrafish is a valuable model for developing therapeutic strategies to augment liver regeneration\nC_LIO_LILiver regeneration in zebrafish is not well studied and pathways poorly understood\nC_LIO_LIWe develop a hepatocyte ablation model of liver injury and regeneration in adult zebrafish\nC_LIO_LIWe generate a comprehensive transcriptomic map of various stages of liver injury and regeneration\nC_LIO_LIWe discover a novel regulation of cholesterol biosynthesis pathways during liver regeneration\nC_LI\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/677781v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@13a322corg.highwire.dtl.DTLVardef@1b40200org.highwire.dtl.DTLVardef@ef8f80org.highwire.dtl.DTLVardef@1b61e01_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗