Biology subjects

Kundu, T. K.

Publications and source records attributed to Kundu, T. K..

15 recordsLinked to original sources

bioRxiv2025

T13F2.2 of C. elegans is Critical for Chromatin Organization, Autophagy, and Longevity

Intricately modulated by a spectrum of proteins, Chromatin structure governs gene expression and cellular homeostasis. In Caenorhabditis elegans, critical components like the TATA-binding protein tbp-1 play pivotal roles in orchestrating chromatin dynamics. While the function of many of the interacting partners of tbp-1 is well-understood, our study brings into focus a lesser-known entity, T13F2.2, an unexplored tbp-1 interacting protein and a putative RNA polymerase II transcriptional coactivator. Employing reverse genetics, we found that RNAi-induced depletion of T13F2.2 resulted in pronounced disruptions to nuclear architecture, evidenced by nuclear staining and transmission electron microscopy. Accompanying these structural anomalies, we observed increased autophagy, pointing to cellular stress and a hyperacetylation of the core histones, suggesting potential chromatin decompaction. Notably, multifaceted functional alterations, upon the partial knockdown of the T13F2.2, culminated in a substantial reduction in the worms lifespan. Intriguingly, interventions such as administering ROS scavengers and autophagy modulators offered a reprieve from this life-shortening effect. Transcriptomic analysis upon T13F2.2 knockdown revealed upregulation of genes related to autophagy and chromatin remodelling, alongside downregulation of genes involved in longevity pathways and oxidative stress response. This study, thus, not only puts forward the functional implication of an uncharacterized gene in C. elegans biology, but also further emphasizes the role of chromatin organization in aging at the organismal level.

genetics↗

bioRxiv2025

Promoter evolution in HIV-1C establishes latent reservoirs highly resistant to reversal

Latent viral reservoirs remain a major barrier to curing HIV-1, with the long-terminal repeat (LTR) and Tat playing crucial roles in regulating viral transcription. Subtype-specific transcription factor binding site (TFBS) variations within the LTR significantly influence latency and reservoir stability. In earlier work, we identified HIV-1C LTR variants with duplicated TFBS motifs, including NF-{kappa}B, AP1, RBEIII, and TCF-1/LEF-1. Using five cell models, including Jurkat and primary CD4 T cells, we compared canonical R-LTR and variant R2-LTR strains. Across sub-genomic reporters, single-round infections, and full-length viral vectors, we found that the balance between RBEIII and NF-{kappa}B motifs governs stability of latency. The two-viruses-one-cell system that normalized confounding environmental factors further revealed that latency is primarily controlled by intrinsic transcriptional circuits rather than external stimuli. In longitudinal studies of HIV-1 individuals from acute and chronic infection phases, we observed dominant R strains during early infection and the spontaneous emergence of R2 strains in nearly half of chronic-phase subjects, a process accelerated by ART. Upon CD4 T cell activation, R strains preferentially rebounded, while R2 strains showed strong resistance to reversal, even in subjects harbouring a co-infection. Together, these findings establish the clinical significance of LTR variation in latency regulation and identify the R2 phenotype as a critical determinant of reservoir persistence. These results underscore the importance of addressing reservoir heterogeneity in cure strategies, particularly in HIV-1C-prevalent regions.

microbiology↗

bioRxiv2024

Epigenetic Modulation to perturb the SYNGAP1 Intellectual Disability (ID) that ameliorates synaptic and behavioural deficits

Sporadic heterozygous mutations in SYNGAP1 affects social and emotional behaviour that are often observed in intellectual disability (ID) and autism spectrum disorder (ASD). Although neurophysiological deficits have been extensively studied, the epigenetic landscape of SYNGAP1 mutation-mediated intellectual disability is unexplored. Here, we have surprisingly found that the p300/CBP specific acetylation marks of histones are significantly repressed in the adolescent hippocampus of Syngap1+/- mouse. To establish the causal relationship of Syngap1+/- phenotype and the altered histone acetylation signature we have treated 2-4 months old Syngap1+/- mouse with glucose-derived carbon nanosphere (CSP) conjugated potent small molecule activator (TTK21) of p300/CBP lysine acetyltransferase (CSP-TTK21). The enhancement of the p300/CBP specific acetylation marks of histones by CSP-TTK21 restored deficits in spine density, synaptic function, and social preferences of Syngap1+/- mouse that is very closely comparable to wild type littermates. The hippocampal RNA-Seq analysis of the treated mice revealed that the expression of many critical genes related to the ID/ASD reversed due to the treatment of the specific small molecule activator. This study could be the first demonstration of the reversal of autistic behaviour and neural wiring upon the modulation of altered epigenetic modification (s).

neuroscience↗

bioRxiv2023

Oral administration of a specific p300/CBP Lysine acetyltransferase activator induces synaptic plasticity and repairing spinal cord injury

TTK21 is a small molecule activator of p300/CBP acetyltransferase activity, which upon conjugation with glucose-derived carbon nanosphere (CSP) can efficiently cross the blood-brain barrier and activate histone acetylation in the brain. Its role in adult neurogenesis and retention of long-term spatial memory upon intraperitoneal (IP) administration is well established. In this study, we have successfully demonstrated that CSP-TTK21 can be effectively administered via oral gavage. Using a combination of molecular biology, microscopy, and electrophysiological techniques, we systematically investigated the comparative efficacy of oral administration of CSP and CSP-TTK21 in wild-type mice, evaluating their functional effects in comparison to intraperitoneal (IP) administration. Our findings indicate that CSP-TTK21, when administered orally, induces long-term potentiation in the hippocampus without significantly altering basal synaptic transmission, a response comparable to that achieved through IP injection. Remarkably, in a spinal cord injury model, oral administration of CSP-TTK21 exhibits equivalent efficacy to IP administration. Furthermore, our research demonstrates that oral delivery of CSP-TTK21 leads to improvements in motor functions, histone acetylation dynamics, and increased expression of regeneration associated genes (RAGs) in a spinal injury rat model, mirroring the effectiveness of IP administration. Collectively, these results underscore the potential utility of CSP as an oral drug delivery system, particularly for targeting the neural system.

neuroscience↗

bioRxiv2023

Reversal of drug resistance by disruption of a Gain-of-Function mutant p53 and transcriptional co-activator PC4 interaction

The positive coactivator 4 or PC4 is a chromatin-associated protein whose role in gene regulation by wild-type p53 is now well-known. During tumorigenesis, p53 is often mutated resulting in its loss of function. A sub-class of these mutants gain new pro-proliferation properties which occur largely due to the upregulation of many pro-proliferation genes. Little is known about the roles of PC4 in tumor cells bearing mutant p53 genes. In this article, we show that PC4 associates with one of the tumor-associated gain-of-function p53 mutants, R273H. This association drives its recruitment to two promoters, UBE2C, and MDR1, known to be responsible for imparting aggressive growth and resistance to many drugs. A previously reported peptide that disrupts PC4-wild-type p53 interaction also disrupts the PC4-R273Hp53 protein-protein interaction. The introduction of this peptide to tumor cells bearing the R273HTP53 gene resulted in a lowering of MDR1 expression and abrogation of drug resistance. Interestingly, cells bearing another gain-of-function mutant R248W do not show the same type of response, suggesting that the action of PC4 on mutant p53s may differ for different GOF mutants. The results presented here suggest that PC4-R273H interaction may be a promising target for reducing proliferation and tumor drug resistance.

molecular biology↗

bioRxiv2021

EP300 (p300) mediated histone butyrylation is critical for adipogenesis

ObjectiveThe master epigenetic enzyme EP300 (p300) besides having lysine acetyltransferase activity can also catalyse other acylation modifications (propionylation, butyrylation, crotonylation etc.), the physiological implications of which are yet to be established fully. We hypothesized that p300 catalysed histone butyrylation may have a causal relationship with adipogenesis and the consequent obesity. MethodsHistone butyrylation pattern was investigated in 3T3L1 cells upon adipogenesis by immunoblotting and chromatin immunoprecipitation experiments. A small molecule modulator that could specifically inhibit p300 catalysed butyrylation without affecting its canonical acetyltransferase activity was screened from a series of compounds and then administered in differentiating 3T3L1 adipocytes as well as high fat diet-induced and genetically obese mice to validate the importance of butyrylation in adipogenesis. ResultsHistone butyrylation was increased upon adipogenesis both globally and locally in the promoters of pro-adipogenic genes along with an upregulation in the expression of acyl CoA generating enzyme Acss2, knockdown of which led to reduced butyrylation. Treatment of differentiating 3T3L1 cells with the p300 specific butyrylation inhibitor LTK-14A led to abrogation of adipogenesis with reduced expression of pro-adipogenic genes and inhibition of H4K5 butyrylation. LTK-14A administration could also attenuate weight gain in both mice models of obesity by preventing adipocyte hypertrophy via H4K5 butyrylation inhibition. ConclusionOur results indicate that p300 catalysed histone butyrylation may have a causal relationship with the process of adipogenesis. Site specific inhibition of butyrylation could lead to adipogenesis repression and hence this epigenetic modification could be targeted for obesity treatment. HighlightsO_LIHistone butyrylation has been established as a new epigenetic signature in the context of adipogenesis. C_LIO_LITo the best of our knowledge, this is the first report of a selective inhibitor of p300 catalysed histone acylation (butyrylation) without affecting its canonical acetyltransferase activity. C_LIO_LISpecific inhibition of H4K5 butyrylation could be a possible mechanism for inhibiting adipogenesis and hepatic steatosis leading to better control of obesity. C_LIO_LILTK-14A class of molecule could be developed as anti-obesity therapeutics. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/454641v3_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1f29b35org.highwire.dtl.DTLVardef@abc5fcorg.highwire.dtl.DTLVardef@1534388org.highwire.dtl.DTLVardef@176d706_HPS_FORMAT_FIGEXP M_FIG Proposed model for the role of p300-mediated histone butyrylation in adipogenesis: In pre-adipocytes, there exists a basal level of histone acetylation while butyrylation is present to a much lesser extent owing to low stoichiometric levels of butyryl CoA. Induction of adipogenesis causes a simultaneous upregulation of histone acetylation and butyrylation marks leading to increased rate of adipogenesis and concomitant transcriptional activation of pro-adipogeneic genes. Onset of obesity in mice, either due to excess energy intake through high fat diet consumption or increased de novo synthesis of fatty acids due to leptin receptor gene mutation leading to hyperphagic behavior, is accompanied by adipocyte hyperplasia and hypertrophy. Both the organs of adipose tissue and liver were found to have enhanced levels of H4K5 butyrylation during obesity. LTK-14A, a butyrylation specific inhibitor could efficiently prevent the processes of adipogenesis and adipocyte hypertrophy due to inhibition of H4K5 butyrylation in these organs. Thus the compound could attenuate weight gain by selective inhibition of butyrylation without affecting acetylation, thereby highlighting the importance of histone butyrylation in adipogenesis and obesity. C_FIG

molecular biology↗

bioRxiv2021

Severe Acute Respiratory Syndrome Coronavirus-2 genome sequence variations relate to morbidity and mortality in Coronavirus Disease-19

Outcome of infection with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) may depend on the host, virus or the host-virus interaction-related factors. Complete SARS-CoV-2 genome was sequenced using Illumina and Nanopore platforms from naso-/oro-pharyngeal ribonucleic acid (RNA) specimens from COVID-19 patients of varying severity and outcomes, including patients with mild upper respiratory symptoms (n=35), severe disease ad-mitted to intensive care with respiratory and gastrointestinal symptoms (n=21), fatal COVID-19 outcome (n=17) and asymptomatic (n=42). Of a number of genome variants observed, p.16L>L (Nsp1), p.39C>C (Nsp3), p.57Q>H (ORF3a), p.71Y>Y (Membrane glycoprotein), p.194S>L (Nucleocapsid protein) were observed in similar frequencies in different patient subgroups. However, seventeen other variants were observed only in symptomatic patients with severe and fatal COVID-19. Out of the latter, one was in the 5UTR (g.241C>T), eight were synonymous (p.14V>V and p.92L>L in Nsp1 protein, p.226D>D, p.253V>V, and p.305N>N in Nsp3, p.34G>G and p.79C>C in Nsp10 protein, p.789Y>Y in Spike protein), and eight were non-synonymous (p.106P>S, p.157V>F and p.159A>V in Nsp2, p.1197S>R and p.1198T>K in Nsp3, p.97A>V in RdRp, p.614D>G in Spike protein, p.13P>L in nucleocapsid). These were completely absent in the asymptomatic group. SARS-CoV-2 genome variations have a significant impact on COVID-19 presentation, severity and outcome.

genomics↗

bioRxiv2019

14-3-3γ prevents centrosome duplication by inhibiting NPM1 function.

14-3-3 proteins bind to ligands via phospho-Serine containing consensus motifs. However, the molecular mechanisms underlying complex formation and dissociation between 14-3-3 proteins and their ligands remain unclear. We identified two conserved acidic residues in the 14-3-3 peptide-binding pocket (D129 and E136) that potentially regulate complex formation and dissociation. Altering these residues to Alanine led to opposing effects on centrosome duplication. D129A inhibited centrosome duplication while E136A stimulated centrosome amplification. These results were due to the differing abilities of these mutant proteins to form a complex with NPM1. Inhibiting complex formation between NPM1 and 14-3-3{gamma} led to an increase in centrosome duplication and overrode the ability of D129A to inhibit centrosome duplication. We identify a novel role of 14-3-3 in regulating centrosome licensing and a novel mechanism underlying the formation and dissociation of 14-3-3 ligand complexes dictated by conserved residues in the 14-3-3 family.

cell biology↗

bioRxiv2019

Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis.

Nucleophosmin (NPM1) is a multifunctional histone chaperone that can activate RNA Polymerase II-driven chromatin transcription. Acetylation of NPM1 by acetyltransferase p300 has been shown to further enhance its transcription activation potential. Moreover, its total and acetylated pools are increased in oral squamous cell carcinoma. However, the role of NPM1 or its acetylated form (AcNPM1) in transcriptional regulation in cells is not fully elucidated. Using ChIP-seq analyses, we show that AcNPM1 co-occupies marks of active transcription at promoters and DNase I hypersensitive sites at enhancers. Moreover, NPM1 interacts with proteins involved in transcription, including RNA Pol II, general transcription factors, mediator subunits, histone acetyltransferase complexes, and chromatin remodelers. Moreover, its histone chaperone also contributes to transcriptional activation. We further show that AcNPM1 regulates key genes required for proliferation, migration and invasion potential of oral cancer cells and knockdown of NPM1 mitigates these processes in cells as well as orthotopic tumors in mice. Collectively, these results establish that AcNPM1 functions as a coactivator and regulates the expression of key genes involved in oral tumorigenesis.

biochemistry↗

bioRxiv2019

The haploinsufficient tumor suppressor Tip60 negatively regulates the oncogenic Aurora B kinase

The Aurora kinases represent a group of serine/threonine kinases which are crucial regulators of mitosis. Dysregulated Aurora kinase B (AurkB) expression, stemming from genomic amplification, increased gene transcription or overexpression of its allosteric activators, is capable of initiating and sustaining malignant phenotypes. Although AurkB level in cells is well-orchestrated, studies that relate to its stability or activity, independent of mitosis, are lacking. We report that AurkB undergoes acetylation in vitro by lysine acetyltransferases (KATs) belonging to different families, namely by p300 and Tip60. The haploinsufficient tumor suppressor Tip60 acetylates two highly conserved lysine residues within the kinase domain of AurkB which not only impinges the protein stability but also its kinase activity. These results signify a probable outcome on the increase in \"overall activity\" of AurkB upon Tip60 downregulation, as observed under cancerous conditions. The present work, therefore, uncovers an important functional interplay between AurkB and Tip60, frailty of which may be an initial event in carcinogenesis.

biochemistry↗

bioRxiv2019

Aurora kinase A mediated phosphorylation of mPOU is critical for skeletal muscle differentiation

Aurora kinases are Ser/Thr-directed protein kinases which play pivotal roles in mitosis. Recent evidences highlight the importance of these kinases in non-mitotic biological events like skeletal myogenesis. Our earlier study identified POU6F1 (or mPOU) as a novel Aurora kinase A (AurkA) substrate. Here, we report that AurkA phosphorylates POU6F1 at Ser197 and inhibits its DNA binding ability. Delving into POU6F1 physiology, we find that the phospho-mimic (S197D) POU6F1 mutant exhibits enhancement, while wild type (WT) or phospho-deficient (S197A) mutant shows retardation in C2C12 myoblast differentiation. Interestingly, POU6F1 depletion phenocopies S197D-POU6F1 overexpression in the differentiation context. Collectively, our results signify mPOU as a negative regulator of skeletal muscle differentiation and strengthens the importance of AurkA in skeletal myogenesis.

cell biology↗

bioRxiv2019

The Largest Subunit of Human TFIIIC Complex, TFIIIC220, a Lysine Acetyltransferase Targets Histone H3K18

TFIIIC is a multisubunit complex that recognizes promoter elements and recruits TFIIIB and RNA polymerase III. Human TFIIIC complex possess lysine acetyltransferase activity which is critical in relieving chromatin mediated repression for RNA polymerase III-mediated transcription; two subunits of the TFIIIC complex, TFIIIC110 and TFIIIC90, were shown to acetylate H3 in vitro. Here we show that the largest and DNA binding subunit of TFIIIC complex, TFIIIC220, possesses intrinsic lysine acetyltransferase activity and acetylates histone H3K18 residue. By employing homology search we have identified the potential catalytic domain of TFIIIC220 which efficiently acetylate core histones in vitro. Point mutations at the critical residues of the identified acetyltransferase domain drastically reduces the acetyltransferase activity. Significantly, knockdown of TFIIIC220 in HepG2 cell line dramatically reduces global H3K18 acetylation level suggesting that TFIIIC220 is a crucial KAT to maintain acetylation homeostasis in the cell.

molecular biology↗

bioRxiv2018

Deacetylation of catalytic lysine in CDK1 is essential for Cyclin-B binding and cell cycle

Cyclin-dependent-kinases (CDKs) are essential for cell cycle progression. While dependence of CDK activity on Cyclin levels is established, molecular mechanisms that regulate their binding are less studied. Here, we show that CDKl:Cyclin-B interactions are regulated by acetylation, which was hitherto unknown. We demonstrate that cell cycle dependent acetylation of the evolutionarily conserved catalytic lysine in CDK1 or eliminating its charge state abrogates Cyclin-B binding. Opposing activities of SIRT1 and P300 regulate acetylation, which marks a reserved pool of CDK1. Our high resolution structural analyses into the formation of kinase competent CDK1: Cyclin-B complex have unveiled long-range effects of catalytic lysine in configuring the CDK1 interface for Cyclin-B binding. Cells expressing acetylation mimic mutant of Cdc2 in yeast are arrested in G2 and fail to divide. Thus, by illustrating cell cycle dependent deacetylation as a determinant of CDK1:Cyclin-B interaction, our results redefine the current model of CDK1 activation and cell cycle progression.

cell biology↗

bioRxiv2018

Non-histone human chromatin protein, PC4 is critical for genomic integrity and negatively regulates autophagy

Multifunctional human transcriptional positive co-activator 4 (PC4) is a bonafide non-histone component of the chromatin and plays a pivotal role in the process of chromatin compaction and functional genome organization. Knockdown of PC4 expression leads to a drastic open conformation of the chromatin and thereby altered nuclear architecture, defects in chromosome segregation and changed epigenetic landscape. Interestingly, these defects do not induce cellular death but result in enhanced cellular proliferation possibly through enhanced autophagic activity. PC4 depletion confers significant resistance to gamma irradiation. Exposure to gamma irradiation further induced autophagy in these cells. Inhibition of autophagy by small molecule inhibitors as well as by silencing of a critical autophagy gene drastically reduces the survivability PC4 knockdown cells. On the contrary, complementation with wild type PC4 could reverse this phenomenon, confirming the process of autophagy as the key mechanism for radiation resistance in absence of PC4. These data connect the unexplored role of chromatin architecture in regulating autophagy during a stress condition such as radiation.

molecular biology↗

bioRxiv2017

Allosteric Activation of p300 Autoacetylation by the Tumor Suppressor p53

The transcriptional coactivator p300 is essential for p53 transactivation, although its precise mechanism remains unclear. We report that, p53 allosterically activates the acetyltransferase activity of p300 through the enhancement of p300 autoacetylation. Cryo-electron microscopy revealed that the domain organization of p300 is substantially altered upon binding of p53, suggesting that a structural switch may underpin the activation. Acetylated p300 accumulates near the transcription start sites accompanied by a similar enrichment of activating histone marks near those sites. Disruption of p53-p300 interaction by a site-directed peptide inhibitor abolished autoacetylated p300-mediated enhanced histone acetylation, suggesting a crucial role played by the allosteric activation in p53-mediated gene regulation. Gain-of-function mutant p53, known to impart aggressive proliferative properties in tumor cells, also activate p300 autoacetylation. The same peptide abolished many of the gain-of-functions of mutant p53 as well. We conclude that allosteric activation of p300 by p53 underpins gene regulation by p53. Reversal of gain-of-function properties of mutant p53 suggests that molecules targeting the p53-p300 interface may be good candidates for anti-tumor drugs.

molecular biology↗