Biology subjects

Kota, S.

Publications and source records attributed to Kota, S..

5 recordsLinked to original sources

bioRxiv2025

Lysine-specific demethylase 1a is obligatory for gene regulation during kidney development

Histone methyltransferases and demethylases play crucial roles in gene regulation and are vital for proper functioning of multiple tissues. Lysine-specific histone demethylase 1A (Kdm1a), is responsible for the demethylation of specific lysines, namely K4 and K9, on histone H3. In this study, we investigated the functions of Kdm1a during mouse kidney development upon targeted deletion in renal progenitor cells. Loss of Kdm1a in Six2-positive nephron progenitors resulted in significant reduction in renal mass, tissue structural changes and impaired function. To further understand the molecular function of Kdm1a during kidney development, we conducted multi-omics analyses that included transcriptome profiling, Chromatin immunoprecipitation (ChIP) sequencing, and methylome assessments. These omic analyses identified Kdm1a as a critical gene regulator required for sustained expression of several nephron segment marker genes, as well as vast number of solute carrier (Slc) genes and a few imprinted genes. Absence of Kdm1a in kidneys led to an increase in global H3K9 methylation peaks, which correlated with the transcriptional downregulation of numerous genes. Among these were markers of nephron progenitors and presumptive tubular precursors. We also observed that specific gene bodies exhibited altered DNA methylation patterns at intragenic differentially methylated regions (DMRs) upon Kdm1a deletion, while the overall global levels of DNA methylation remained unchanged. Our data point to a key regulatory role for Kdm1a in the renal progenitor epigenome, influencing kidney specific gene expression in the developing nephrons. Together the study highlights an indispensable role for Kdm1a for proper development of mouse kidneys, and its absence leading to significant developmental and functional impairment.

developmental biology↗

bioRxiv2022

FtsK, a DNA motor protein, coordinates the genome segregation and early cell division processes in Deinococcus radiodurans

FtsK/SpoIIIE protein family are DNA translocases known as the fastest DNA motor proteins that use ATP for their movement on DNA. Most of the studies in single chromosome-containing bacteria have established the role of FtsK in chromosome dimer resolution (CDR) connecting the bacterial chromosome segregation process with cell division. But, only limited reports are available on the interdependent regulation of genome segregation and cell division in multipartite genome harbouring (MGH) bacteria. In this study, for the first time, we report the characterization of FtsK from the radioresistant MGH bacterium Deinococcus radiodurans R1 (drFtsK). drFtsK shows the activity characteristics of a typical FtsK/SpoIIIE/Tra family. It stimulates the site-specific recombination catalyzed by Escherichia coli tyrosine recombinases. drFtsK interacts with various cell division and genome segregation proteins of D. radiodurans. Microscopic examination of different domain deletion mutants of this protein reveals alterations in cellular membrane architecture and nucleoid morphology. In-vivo localization studies of drFtsK-RFP show that it forms multiple foci on nucleoid as well as on the membrane with maximum density on the septum. drFtsK coordinates its movement with nucleoid separation. The alignment of its foci shifts from old to new septum indicating its cellular dynamics with the FtsZ ring during the cell division process. Nearly, similar positional dynamicity of FtsK was observed in cells recovering from gamma radiation exposure. These results suggest that FtsK forms a part of chromosome segregation, cell envelope, and cell division machinery in D. radiodurans. ImportanceDeinococcus radiodurans show extraordinary resistance to {gamma}-radiation. It is polyploid and harbours a multipartite genome comprised of two chromosomes and two plasmids, packaged in a doughnut-shaped toroidal nucleoid. Very little is known about how the tightly packed genome is accurately segregated and the next divisional plane is determined. FtsK, a multifunctional protein, helps in pumping the septum-trapped DNA in several bacteria. Here, we characterized FtsK of D. radiodurans R1 (drFtsK) for the first time and showed it to be an active protein. The absence of drFtsK causes many defects in morphology at both cellular and nucleoid levels. The compact packaging of the deinococcal genome and cell membrane formation is hindered in ftsK mutants. In-vivo drFtsK is dynamic, forms foci on both nucleoid and septum, and coordinates with FtsZ for the next cell division. Thus, drFtsK role in maintaining the normal genome phenotype and cell division in Deinococcus radiodurans is suggested.

molecular biology↗

bioRxiv2020

Hippocampal theta oscillations support successful associative memory formation

1.Models of memory formation posit that recollection as compared to familiarity-based memory depends critically on the hippocampus, which binds features of an event to its context. For this reason, the contrast between study items that are later recollected versus those that are recognized on the basis of familiarity should reveal electrophysiological patterns in the hippocampus selectively involved in associative memory encoding. Extensive data from studies in rodents support a model in which theta oscillations fulfill this role, but results in humans results have not been as clear. Here, we employed an associative recognition memory procedure to identify hippocampal correlates of successful associative memory encoding and retrieval in patients undergoing intracranial EEG monitoring. We identified a dissociation between 2- 5 Hz and 5-9 Hz theta oscillations, by which 2-5 Hz oscillations uniquely were linked with successful associative memory in both the anterior and posterior hippocampus. These oscillations exhibited a significant phase reset that also predicted successful associative encoding, distinguished recollected from familiar items at retrieval, and contributed to reinstatement of encoding-related patterns that distinguished these items. Our results provide direct electrophysiological evidence that 2-5 Hz hippocampal theta oscillations support the encoding and retrieval of memories based on recollection but not familiarity. 2. Significance StatementExtensive fMRI evidence suggests that the hippocampus plays a selective role in recollection rather than familiarity, during both encoding and retrieval. However, there is little or no electrophysiological evidence that speaks to whether the hippocampus is selectively involved in recollection. Here, we used intracranial EEG from human participants engaged in an associative recognition paradigm. The findings suggest that oscillatory power and phase reset in the hippocampus are selectively associated with recollection rather than familiarity-based memory judgements. Furthermore, reinstatement of oscillatory patterns in the hippocampus was stronger for successful recollection than familiarity. Collectively, the findings support a role for hippocampal theta oscillations in human episodic memory.

neuroscience↗

bioRxiv2020

DivIVA is essential in Deinococcus radiodurans and its C terminal domain regulates new septum orientation during cell division

FtsZ assembly at mid cell position in rod shaped bacteria is regulated by gradient of MinCDE complex across the poles. In round shaped bacteria, which lack predefined poles and the next plane of cell division is perpendicular to previous plane, the determination of site for FtsZ assembly is intriguing. Deinococcus radiodurans a coccus shaped bacterium, is characterized for its extraordinary resistance to DNA damage. Here we report that DivIVA a putative component of Min system in this bacterium (drDivIVA) interacts with cognate cell division and genome segregation proteins. The deletion of full length drDivIVA was found to be indispensable while its C-terminal deletion ({Delta}divIVAC) was dispensable but produced distinguishable phenotypes like slow growth, altered plane for new septum formation and angular septum. Both wild type and mutant showed FtsZ foci formation and their gamma radiation responses were nearly identical. But unlike in wild type, the FtsZ localization in mutant cells was found to be away from orthogonal axis with respect to plane of previous septum. Notably, DivIVA-RFP localizes to membrane during cell division and then perpendicular to previous plane of cell division. In trans expression of drDivIVA in {Delta}divIVAC background could restore the wild type pattern of septum formation perpendicular to previous septum. These results suggested that DivIVA is an essential protein in D. radiodurans and the C-terminal domain that contributes to its interaction with MinC determines the plane of new septum formation, possibly by controlling MinC oscillation through orthogonal axis in the cells.

microbiology↗

bioRxiv2018

Marker-assisted pyramiding of two major broad-spectrum bacterial blight resistance genes, Xa21 and Xa33 into an elite maintainer line of rice, DRR17B

Bacterial blight (BB) disease reduces the yield of rice varieties and hybrids considerably in many tropical rice growing countries like India. The present study highlights the development of durable BB resistance into the background of an elite maintainer of rice, DRR17B, by incorporating two major dominant genes, Xa21 and Xa33 through marker-assisted backcross breeding (MABB). Through two sets of backcrosses, the two BB resistance genes were transferred separately to DRR17B. In this process, at each stage of backcrossing, foreground selection was carried out for the target resistance genes and for non-fertility restorer alleles concerning the major fertility restorer genes Rf3 and Rf4, using gene-specific PCR-based markers, while background selection was done using a set of 61 and 64 parental polymorphic SSR markers respectively. Backcross derived lines possessing either Xa21 or Xa33 along with maximum genome recovery of DRR17B were identified at BC3F1 generation and selfed to develop BC3F2s. Plants harboring Xa21 or Xa33 in homozygous condition were identified among BC3F2s and were intercrossed with each other to combine both the genes. The intercross F1 plants (ICF1) were selfed and the intercross F2 (ICF2) plants possessing both Xa21 and Xa33 in homozygous condition were identified with the help of markers. They were then advanced further by selfing until ICF4 generation. Selected ICF4 lines were evaluated for their resistance against BB with eight virulent isolates and for key agro-morphological traits. Six promising two-gene pyramiding lines of DRR17B with high level of BB resistance and agro-morphological attributes similar or superior to DRR17B with complete maintenance ability have been identified. These lines with elevated level of durable resistance may be handy tool for BB resistance breeding.

plant biology↗