Biology subjects

Kumari, J.

Publications and source records attributed to Kumari, J..

13 recordsLinked to original sources

bioRxiv2025

MicroRNA166-HD-ZIP III module impacts tuber shape, color and productivity in potato

Tuber shape and size are important traits in potato. Although several factors governing tuberization have been well studied, the molecular mechanisms regulating the tuber shape and size are still elusive. Here, we demonstrate that suppression of miR166, which targets class III HD-ZIP transcription factors, alters tuber morphology and productivity in potato. Target mimicry of miR166 (MIM166) in Solanum tuberosum ssp. Andigena resulted in elongated, pigmented tubers with reduced yield under short-day conditions. Transcriptome profiling of the tuberizing stolons - swollen head vs. stalk revealed differential expression of auxin-, cytokinin-, and gibberellin-associated genes, consistent with altered hormone levels. The coloured tubers from MIM166 line exhibited differential accumulation of cyanidin 3-glucoside, pelargonidin 3-glucoside, and delphinidin 3-glucoside. Tuber productivity in these lines was reduced possibly due to the decreased expression of SWEET11b and distorted vascular structures. Further, the miR166 target-StREVOLUTA exhibited dynamic expression during stolon-to-tuber transition, and could modulate StYUCCA7 expression, an auxin biosynthesis gene. Increased pigmentation and auxin accumulation in MIM166, reduced expression of auxin biosynthesis genes in REVOLUTA antisense, and low tuber yield collectively suggest miR166-REV as a regulatory module of auxin homeostasis in differentiating stolons that influences tuber morphology. These results reveal a previously unrecognized miRNA-mediated pathway governing storage organ shape, and extends the functional scope of the miR166-HD-ZIP III module beyond organ polarity. Significance statementLimited studies describe the molecular mechanisms regulating tuber shape in storage organ development. Here, we show that the miR166-REVOLUTA-auxin network has significant regulatory roles in potato development, influencing tuber shape, pigmentation, and productivity. These findings provide insights into molecular control of tuber morphology, uncover hitherto unknown functions of the miR166-REVOLUTA module in tuber crops, and broadens our understanding of miR166-mediated developmental regulation in plants.

plant biology↗

bioRxiv2025

Nim1-related kinases regulate septin organization and cytokinesis by modulating Hof1 at the cell division site

The septin scaffold recruits and organizes actomyosin ring (AMR) components, thus, ensuring faithful cytokinesis. The septin-associated kinases - Elm1, Gin4, Hsl1, and Kcc4 are thought to stabilize and regulate the septin architecture at the bud neck, but the underlying mechanisms remain largely unknown. Here, we present a comprehensive, quantitative analysis of these four septin-associated kinases and reveal major roles for Elm1 and Gin4 in septin stability and architectural transitions during the cell cycle. We find that Elm1 and Gin4 play a previously overlooked role in AMR organization and constriction during cytokinesis. We report that the Gin4 kinase interacts directly with the AMR component and F-BAR protein Hof1 via its C-terminal membrane-binding kinase associated-1 (KA1) domain, and is likely involved in the proper organization and anchoring of Hof1 at the bud neck, representing an unappreciated mode of regulation during cytokinesis. We further show that Gin4 controls septin organization and AMR constriction in a kinase-independent manner, similar to Elm1. Using an extensive GFP-GBP-based tethering assay in elm1{Delta} and gin4{Delta} cells, we identify an important role for Hsl1 in maintaining septin organization and cell shape in coordination with Elm1, Gin4, and Kcc4, independent of its role in the morphogenetic checkpoint. Furthermore, our data indicate that Hsl1 acts downstream of Elm1, with its membrane-binding KA1 domain being critical for its function. Together, these findings reveal new insights into the modes by which the kinases Gin4 and Elm1 regulate cytokinesis, highlight a redundant role for Hsl1 in controlling septin organization and cytokinesis, and uncover the inherent redundancy and adaptability of the septin kinase network in Saccharomyces cerevisiae.

cell biology↗

bioRxiv2025

Distinct filament morphology and membrane tethering features of the dual FtsZs in Odinarchaeota

The deep-branching Asgard archaea have emerged as a model to study Eukaryogenesis as they harbor homologs of many of the major eukaryotic protein families. In this study, we use Candidatus Odinarchaeota FtsZs as representatives to understand the probable origin, evolution, and assembly of the FtsZ-Tubulin protein superfamily in Asgard archaea. We have performed a comparative analysis of the biochemical properties and cytoskeletal assembly of FtsZ1 and FtsZ2, the two FtsZ isoforms in the Odinarchaeota metagenome. Our electron microscopy analysis reveals that OdinFtsZ1 assembles into curved single protofilaments, while OdinFtsZ2 forms stacked spiral ring-like structures. Upon sequence analysis, we identified an N-terminal amphipathic helix in OdinFtsZ1, which mediates direct membrane tethering. In contrast, OdinFtsZ2 is recruited to the membrane by the membrane-anchor OdinSepF via OdinFtsZ2s C-terminal tail. Overall, we report the presence of two distant evolutionary paralogs of FtsZ in Odinarchaeota, with distinct filament assemblies and differing modes of membrane targeting mechanisms, namely direct vs SepF-mediated membrane binding. Our findings highlight the diversity of FtsZ proteins in the transitional archaeal phylum Odinarchaeota, providing valuable insights into the evolution and differentiation of tubulin family proteins.

biochemistry↗

bioRxiv2024

Functional redundancy and formin-independent localization of tropomyosin isoforms in Saccharomyces cerevisiae

Tropomyosin is an actin binding protein which protects actin filaments from cofilin-mediated disassembly. Distinct tropomyosin isoforms have long been hypothesized to differentially sort to subcellular actin networks and impart distinct functionalities. Nevertheless, a mechanistic understanding of the interplay between Tpm isoforms and their functional contributions to actin dynamics has been lacking. In this study, we present and charcaterize mNeonGreen-Tpm fusion proteins that exhibit good functionality in cells as a sole copy, surpassing limitations of existing probes and enabling real-time dynamic tracking of Tpm-actin filaments in vivo. Using these functional Tpm fusion proteins, we find that S. cerevisiae Tpm isoforms, Tpm1 and Tpm2, colocalize on actin cables and indiscriminately bind to actin filaments nucleated by either formin isoform-Bnr1 and Bni1 in vivo, in contrast to the long-held paradigm of Tpm-formin pairing. We show that cellular Tpm levels regulate endocytosis by affecting balance between linear and branched actin networks in yeast cells. Finally, we discover that Tpm2 can protect and organize functional actin cables in absence of Tpm1. Overall, our work supports a concentration-dependent and formin isoform independent model of Tpm isoform binding to F-actin and demonstrates for the first time, the functional redundancy of the paralog Tpm2 in actin cable maintenance in S. cerevisiae.

cell biology↗

bioRxiv2023

Hippo effector, Yorkie, is a Tumor Suppressor in Select Drosophila Squamous Epithelia

Out-of-context gain of nuclear signaling of mammalian YAP/TAZ or Drosophila Yki--the transcription cofactors of the highly conserved Hippo tumor suppressor pathway--is oncogenic. By contrast, in mechanically strained squamous epithelia (SE), YAP/TAZ/Yki displays developmentally programmed nuclear translocation, leading to its constitutive signaling. How organ homeostasis is maintained in constitutively YAP/TAZ/Yki signaling SE is unclear. Here, we show that Yki signaling negatively regulates the cell growth-promoting PI3K/Akt/TOR signaling in the SEs in the tubular organs of Drosophila. Thus, in the adult male accessory gland (MAG), knockdown of Yki signaling upregulates PI3K/Akt/TOR signaling in its SE-lined lumen, inducing cell hypertrophy, culminating in squamous cell carcinoma (SCC). MAG SCC-bearing adults display early mortality due to cancer cachexia, which is reversed by simultaneous knockdown of a secreted factor, ImpL2--a Drosophila homolog of mammalian IGFBP7--without arresting tumor progression per se. By contrast, a knockdown of PI3K/Akt/TOR signaling suppresses MAG SCC, reversing adult mortality. In the SE-lined lumens in other tubular organs, like the dorsal trunk of larval tracheal airways or adult Malpighian tubules, too, knockdown of Yki signaling triggers PI3K/Akt/TOR-induced cell hypertrophy and loss of epithelial homeostasis, culminating in their tumor-like transformation. Thus, Yki signaling turns tumor suppressive in the SEs of tubular organs in Drosophila by arresting runaway PI3K/Akt/TOR signaling.

cancer biology↗

bioRxiv2023

In-Silico analysis of Human Insulin Gene for Mirror repeat sequences

The genetic material contains all the instructions necessary for the development, functioning & regulation of biological processes. This is also considering as a regulatory molecule. The structure constitute by its unique pattern of bases make it unique for every living being consider from bacteria to human. The varied pattern of bases in genomes or genes represents different types of repeats. These repeats types constitute the major fraction of the genomes. Among varied types Mirror repeats (MRs) play crucial roles in the genome especially in formation of H-DNA structure by Non Watson pairing. Some studies suggest that mirror sequences responsible for neurological diseases also. Now days in modern era of technology in silico techniques were develop to extract any type of repeat sequences from any gene or genome. The major focus of current work is on identification of mirror repeats (MRs) from human insulin gene sequence using an in silico approach. The approach is refer to as FPCB (FASTA Parallel Complement Analysis) were utilized to extract MR sequences. From the current study a total no of 210 MR sequenced were identified in Human insulin gene. The identified repeats vary in their length and majority of them are imperfect in nature. The maximum no of MR were reported in the region 3 & minimum is in the region 8 (8). In the remaining regions the no of MR sequences were lies in between maximum & minimum values. These sequences may be helpful in many molecular level studies.

bioinformatics↗

bioRxiv2023

Identification of Mirror Repeats in Viral Genomes using FPCB Analysis

The majority of living domains consist of DNA as genetic material with the minor exception of viruses. The unique nature of every species determines by its unique pattern of genome or gene products. The genomic features become an evident example of evolutionary study also. Different types of repeat patterns are observed in genomes of living domains including human beings whose two third portion of the genome is repetitive. Among the varied type of repeat sequences Mirror Repeats (MR) play crucial roles at the genetic level in every species. The major focus of our research is on identification & to check the distribution of mirror repeat. For this, we employed a bioinformatics-based approach refer as FASTA PARALLEL COMPLEMENT BLAST (FPCB) to identify unique mirror repeat (MR) sequences in some selected viral genomes from three different categories (Animal, Plant & Human). The identified repeats vary in their length as well as found to be distributed throughout the selected viral genomes. The maximum no of MR were reported in the case of Dengue virus (229) & minimum is in the case of TMV (97). In the remaining selected viruses - HCV, HPV, HTLV-1, PVY, Rabies virus 178, 156, 175, 203 & 204 MR sequences were reported. These sequences can be utilized in many ways like in molecular diagnosis, drug delivery target as well as evolutionary study, etc. The present research also helps in the development of novel tools of bioinformatics to study mirror repeats and their functional perspective in the context of their occurrence in all domains.

bioinformatics↗

bioRxiv2022

Targeted editing of GTR1 and GTR2 homologs directs the development of ideal low-seed and high-leaf glucosinolate oilseed mustard

Glucosinolate content in the Brassica oilseed crops has been reduced to the globally accepted Canola quality levels, making the seed meal useful as a protein-rich animal feed. However, the overall lower glucosinolate content in such plants renders them vulnerable to pests. We report CRISPR/Cas9-based editing of glucosinolate transporter (GTR) family genes to develop ideal oilseed mustard lines with the desired low levels of seed glucosinolates while maintaining high glucosinolate levels in leaves and pod walls, without affecting the seed yield and seed quality traits. The low-seed and high-leaf glucosinolate mustard lines with improved nutritional and defense traits will raise its international trade potential both as oilseed and feed crop.

plant biology↗

bioRxiv2022

Chaperonin activity of Plasmodium prefoldin complex is essential to guard proteotoxic stress response and presents a new target for drug discovery

The intraerythrocytic growth of malaria parasite is challenged by the presence of proteotoxic stress and intrinsically unstructured proteins in the cytoplasm due to formation of toxic heme during haemoglobin digestion. To overcome the unavoidable stress and maintain the cellular protein homeostasis, parasite encodes for a number of chaperones and co-chaperones. Here, we functionally characterize the Plasmodium falciparum prefoldins (PfPFD1-6), a hexameric co-chaperone complex, for their role in protein homeostasis. We demonstrate that PfPFD1-6 localise to cytosol of the parasite and the subunits perform an orchestrated interaction (-PFD3-PFD2-PFD1-PFD5-PFD6-PFD4-) to form an active jelly-fish like complex. Biperiden, an N-propylpiperidine analogue identified by chemotype search from FDA, strongly binds and restricts the formation of prefoldin complex and inhibited its interaction with the substrates, PfMSP-1 and -tubulin-I. Biperiden treatment potently inhibited the in vitro (IC50: 1M) and in vivo growth of malaria parasite. Thus, this study provides novel virtues towards understanding the role of PfPFDs in regulating protein homeostasis and opens new avenues for drug discovery against malaria.

molecular biology↗

bioRxiv2022

'Erythritol, a safe natural sweetener exhibits multi-stage anti-malarial activity by blocking Plasmodium falciparum membrane transporter 'aquaporin

The increased resistance of human malaria parasite Plasmodium falciparum to currently used drugs necessities the development of novel anti-malarials. In the present study, we examine the potential of erythritol, a sugar substitute, for therapeutic intervention that target a multifunctional transporter protein Plasmodium aquaglyceroporin (PfAQP) responsible for maintaining hydro-homeostasis. We show that erythritol effectively inhibited growth and progression of asexual blood stage malaria parasite by suppressing invasion and egress processes. It inhibited the liver stage (sporozoites) and transmission stage parasite (gametocytes) development that suggest its multi-stage, transmission-blocking potential. Interestingly, erythritol inhibited in vivo growth of malaria parasite in mouse experimental model. It was more effective in inhibiting parasite growth both in vivo and in vitro when tested together with a known anti-malarial artesunate. No Evans blue staining in treated mice indicated erythritol mediated protection of blood-brain barrier integrity in mice infected with P. berghei. Additionally, erythritol showed cytokine-modulating effect which suggest its direct effect on the host immune system. Our results of cellular thermal shift assay and ammonia detection assay demonstrate that erythritol binds with PfAQP and reduce the amount of ammonia release across the parasite respectively. We performed functional complementation assays which suggest that PfAQP expression in yeast mutant restores its growth in hyperosmotic conditions but showed reduced growth in the presence of erythritol, suggesting erythritol as an inhibitor of PfAQP. Overall, our data bestow erythritol as a promising new lead compound with an attractive antimalarial profile and could possibly be combined with known drugs without losing its efficacy.

molecular biology↗

bioRxiv2021

Drosophila Male Accessory Gland Displays Developmental Ground Plan of a Primitive Prostate

Conservation of developmental genetic toolkits of functionally comparable organs from disparate phyla reveals their deep homology, which may help overcome the challenges of their confounding categorization as either homologous or analogous organs. A male accessory sexual organ in mammals, prostate, for instance, is anatomically disparate from its phylogenetically distant counterpart--the male accessory gland (MAG)--in insects like Drosophila. By examining a select set of toolkit gene expression patterns, here we show that Drosophila MAG displays deep homology with the mammalian prostate. Like mammalian prostate, MAG morphogenesis is marked by recruitment of fibroblast growth factor receptor, FGFR, a tubulogenesis toolkit signaling pathway, starting early during its adepithelial genesis. Specialization of the individual domains of the developing MAG tube on the other hand is marked by expression of a posterior Hox gene transcription factor, Abd-B, while Hh-Dpp signaling marks its growth. Drosophila MAG thus reveals developmental design of unitary bud-derived tube--a ground plan that appears to have been reiteratively co-opted during evolutionary diversification of male accessory sexual organs across distant phylogeny.

developmental biology↗

bioRxiv2021

Targeting the artemisinin resistant malaria by repositioning of the anti-Hepatitis C Virus drug Alisporivir

The rapid emergence of P. falciparum-resistant strains raises an urgent need to find new antimalarial drug candidates. This study reports the rational repositioning of the anti-Hepatitis C Virus drug, Alisporivir, a non-immunosuppressive analog of cyclosporin A (CsA) against multiple, drug-resistant strains of P. falciparum. Alisporivir being non-hemolytic has been proven to be a better drug than CsA. Indeed, our study also demonstrated the same. Alisporivir inhibited chloroquine-sensitive parasite growth with an IC50 of 196.6nM. Alisporivir also inhibited the growth of chloroquine-resistant parasites with an IC50 of 422.1nM. Alisporivir exhibited, anti-malarial activity in in vivo. Further, we exploited the Cyclophilins targeting potential of Alisporivir against artemisinin-resistant malaria parasite owing to the fact that PfCyP-19B is one of the genes that is overexpressed in artemisinin-resistant parasite revealed by a population transcriptomic study. Our semiquantitative real-time transcript and immunofluorescence analysis confirmed the overexpression of PfCyP-19B in Artemisinin-resistant P. falciparum (PfKelch13R539T). Artemisinin resistance is attributed to slow clearance of ring stage parasites. Ring survival assay (RSA) is designed to access the potency of compounds on these dormant slow clearing parasites leading to drug resistance. Thus, the potency of Alisporivir against PfKelch13R539T was evaluated by RSA. A 2.5-fold decrease in parasite survival was detected with Alisporivir. Further, combination of Alisporivir with DHA found to potentiate the efficacy of DHA by 4.55-fold. These results support the hypothesis that targeting of resistance mechanism is a potential approach to deal with resistant parasite. Overall, this study demonstrates the rational reposition of Alisporivir against resistant malaria resistance.

microbiology↗

bioRxiv2019

Structural Insights into GluK3-kainate Receptor Desensitization and Recovery

GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play key role in regulation of synaptic transmission. For better understanding of structural changes that underlie receptor recovery from desensitized state, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. We show that receptor recovery from desensitization requires major rearrangements of the ligand binding domains (LBD) while the amino terminal (ATD) and transmembrane domains remain virtually unaltered. While, the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a partially \"recovered\" state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using these structures as guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. Mutational analysis also identifies putative N-glycan interacting residues. These results provide a molecular framework for understanding gating properties unique to GluK3 and identify role of N-linked glycosylation in their modulation.

biochemistry↗