156 research outputs found
The Cloning and Expression of Transfer RNA Gene Cluster of Vibrio ekor Phage e4
No full textThe tRNA genes contained in a 3.4-kb Kpnl fragment (S. Chattopadhyay and R. K. Ghosh, 1988, Virology,
162,337-345) have been cloned in pUC 19 at the Kpnl site. Two recombinant plasmids, pSR216 and pSRll2, produced
four of the five tRNA species (arginine, isoleucine, tyrosine, and tryptophan) encoded in the phage genome. The tRNA genes were located on a 1.45-kb-@nl-Hindlll subfragment
Chromatin higher order structure and possible therapeutic target
No full text237-252Canonical form of chromatin structure was unveiled by James Watson and Francis Crick which unravels the better understanding of their structural and functional significance. Experimental observations disclose that non-canonical DNA structures like hairpin, cruciform, Z-DNA, multi-stranded structures such as DNA triplex, G-quadruplex, i-motif forms by depending on specific sequence. Non-canonical structure specifically G-quadruplex stability depends on various factors such as base sequence, ions, super helical stress, and ligands, which ultimately regulates different processes like replication, transcription, translation, and recombination. However, chromatin higher order structure also modifies the gene expression level by modulating nucleosome and also recruited different chromatin remodeler protein to the transcription site to maintain an epigenetic landscape in the genome. Though G-quadruplex regulates multiple cellular processes, but their presence accelerated the mutagenicity and genome instability. The present review is an overview of higher order chromatin structure particularly focussed on G- quadruplex, which is summarized from recent literature, demonstrated the structural form and stability through some specific binding ligand and their role in cellular level. This would provide a mechanistic view to derive the structure-function relation of these non-canonical forms of DNA and their identification as potential therapeutic targets for diverse genetic diseases and cancer
Chemical Decorations of “MARs” Residents in Orchestrating Eukaryotic Gene Regulation
No full textGenome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs
Redox-Responsive Nanocapsules for the Spatiotemporal Release of Miltefosine in Lysosome: Protection against Leishmania
No full textLeishmaniasis, a vector-borne disease, is caused by intracellular parasite Leishmania donovani. Unlike most intracellular pathogens, Leishmania donovani are lodged in parasitophorous vacuoles and replicate within the phagolysosomes in macrophages. Effective vaccines against this disease are still under development, while the efficacy of the available drugs is being questioned owing to the toxicity for nonspecific distribution in human physiology and the reported drug-resistance developed by Leishmania donovani. Thus, a stimuli-responsive nanocarrier that allows specific localization and release of the drug in the lysosome has been highly sought after for addressing two crucial issues, lower drug toxicity and a higher drug efficacy. We report here a unique lysosome targeting polymeric nanocapsules, formed via inverse mini-emulsion technique, for stimuli-responsive release of the drug miltefosine in the lysosome of macrophage RAW 264.7 cell line. A benign polymeric backbone, with a disulfide bonding susceptible to an oxidative cleavage, is utilized for the organelle-specific release of miltefosine. Oxidative rupture of the disulfide bond is induced by intracellular glutathione (GSH) as an endogenous stimulus. Such a stimuli-responsive release of the drug miltefosine in the lysosome of macrophage RAW 264.7 cell line over a few hours helped in achieving an improved drug efficacy by 200 times as compared to pure miltefosine. Such a drug formulation could contribute to a new line of treatment for leishmaniasis.A. Das acknowledges SERB (India) Grants (CRG/2020/000492 and JCB/2017/000004) and DBT Grant (BT/PR22251/NNT/28/1274/2017) for supporting this research. N. Mukherjee acknowledges SERB (India) Grant PDF/2016/001437 and K. Das acknowledges the grant EMR/2015/001674 for supporting this research. Financial support from DST (DST/INSPIRE/03/2017/002477) is acknowledged by R.T. This manuscript bears CSMCRI registration no 7/2021.Pramanik, SK (corresponding author), CSIR Cent Salt & Marine Chem Res Inst, Bhavnagar 364002, Gujarat, India.
Mukherjee, N (corresponding author), CSIR Indian Inst Chem Biol, Canc Biol & Inflammatory Disorder Div, Kolkata 700032, India.
Chattopadhy, S (corresponding author), BITS Pilani, Pilani 403726, Goa, India.
Das, A (corresponding author), Indian Inst Sci Educ & Res Kolkata, Mohanpur 741246, W Bengal, India.
[email protected]; [email protected]; [email protected]
Localization of transfer RNA genes on the physical map of Vibrio eltor phage e<SUB>4</SUB> genome
No full textTransfer RNAs were isolated from uninfected and phage e4-infected Vibrio eltor Mak 757 cells. These tRNAs were then aminoacylated with 3H-labeled amino acids and hybridized to DNA isolated from phage e4. Significant hybridization was observed only with tRNA isolated from phage e4-infected cells. Restriction enzyme digestion of phage e4 DNA followed by Southern blot using [32P]tRNA from infected cells revealed that tRNA genes were contained in a 3.4-kb Kpnl fragment. The tRNA genes were located on the physical map of the phage genome 19 kb from one of the termini
Modulation of chromatin by MARs and MAR binding oncogenic transcription factor SMAR1
No full textThe orchestration of the events in the cell during the progression of the cell cycle is modulated by various phenomenon which are regulated by structural modules of the cell. The nucleus is a major hub for all these regulatory units which harbour the nuclear matrix, matrix proteins and chromatin. The histone modifications etch a complex code on the chromatin and the matrix proteins in consort with the histone code regulate the gene expression. SMAR1 is a matrix attachment region binding protein that interacts with chromatin modulators like HDAC1, Sin3A and causes chromatin condensation. SMAR1 modulates the chromatin at the Vβ locus and plays a prominent role in V(D)J recombination. Such indispensable function of SMAR1 by the modulation of chromatin in the context of malignancy and V(D)J recombination emphasizes that MAR binding proteins regulate the complex events of the cell and perturbed expression causes disease conditions
A nuclear matrix attachment region upstream of the T cell receptor β gene enhancer binds Cux/CDP and SATB1 and modulates enhancer-dependent reporter gene expression but not endogenous gene expression
No full textWe have previously identified a DNase I-hypersensitive site in the T cell receptor β locus, designated HS1, that is located 400 base pairs upstream of the transcriptional enhancer Eβ and is induced during CD4−CD8− to CD4+CD8+thymocyte differentiation. Using electrophoretic mobility shift assays, we show that HS1 induction correlates with increased binding of two nuclear factors, Cux/CDP and SATB1, to a 170-base pair DNA sequence within HS1. Furthermore, we demonstrate that HS1 is a nuclear matrix attachment region, referred to as MARβ. These findings demonstrate that an analogous organization of cis-regulatory elements in which a nuclear matrix attachment region is in close proximity to an enhancer is conserved in the immunoglobulin and T cell receptor loci. In addition, we show that MARβ represses Eβ-dependent reporter gene expression in transient transfection assays. However, the targeted deletion of MARβ from the endogenous locus does not change T cell receptor β gene transcription in developing T cells. These contrasting results suggest a potential pitfall of functional studies of nuclear matrix attachment regions outside of their natural chromosomal context
G-Quadruplex surveillance in BCL-2 gene: a promising therapeutic intervention in cancer treatment
No full textChromatin Remodeling Protein SMAR1 Is a Critical Regulator of T Helper Cell Differentiation and Inflammatory Diseases
No full textT cell differentiation from naïve T cells to specialized effector subsets of mature cells is determined by the iterative action of transcription factors. At each stage of specificT cell lineage differentiation, transcription factor interacts not only with nuclear proteins
such as histone and histone modifiers but also with other factors that are bound to the chromatin and play a critical role in gene expression. In this review, we focus on one
of such nuclear protein known as tumor suppressor and scaffold matrix attachment region-binding protein 1 (SMAR1) in CD4+ T cell differentiation. SMAR1 facilitates Th1
differentiation by negatively regulating T-bet expression via recruiting HDAC1–SMRT complex to its gene promoter. In contrast, regulatory T (Treg) cell functions are dependent
on inhibition of Th17-specific genes mainly IL-17 and STAT3 by SMAR1. Here, we discussed a critical role of chromatin remodeling protein SMAR1 in maintaining a fine-tuned
balance between effector CD4+ T cells and Treg cells by influencing the transcription factors during allergic and autoimmune inflammatory diseases
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