Biology subjects

Singh, D. P.

Publications and source records attributed to Singh, D. P..

7 recordsLinked to original sources

bioRxiv2025

Tomato Omics Research: Mapping Bibliometric Footprints of Global Research Trends, Collaboration Networks, and Impact Trajectories

Tomato is a globally vital crop and model system for fleshy fruit development, with profound agricultural and economic significance. Omics-based tomato research has revolutionized understanding of fruit quality traits, disease resistance mechanisms, and stress tolerance pathways reflecting insights for breeding innovations to address food security challenges. This bibliometric analysis on tomato omics delivered crucial insights into the evolution and impact of tomato omics research over two decades. Examining 1,702 Scopus-indexed publications, we have shown a remarkable acceleration in research output after 2017, signifying the fields growing significance. Our findings revealed that Biochemistry, Genetics and Molecular Biology dominated the landscape with 1,054 publications, establishing the molecular foundation for tomato research. It identified key global research hubs, with the United States (450 publications) leading, followed by China (310) and Italy (171), while mapping eight distinct International collaboration networks that drive innovation. Through citation analysis, we have pinpointed transformative contributions in microRNA research and genome sequencing, with the fields most influential paper garnering 2,570 citations. Co-authorship network visualization exposed 25 research clusters among 8,103 authors, highlighting prolific contributors including Fernie A.R. (39 publications) and Lucini L. (26). The keyword co-occurrence mapping revealed critical research priorities centered on stress responses, fruit quality, and plant immunity, with "Frontiers in Plant Science" emerging as the fields premier publication venue (92 articles). Our analysis provided a roadmap of tomato omics research progression, offering strategic value for prioritization, collaboration development, and funding allocation to address pressing challenges in global food security and crop improvement.

plant biology↗

bioRxiv2025

Mycobacterial MutT1 mediated dephosphorylation of the sensor kinases reveals a new link in the regulation of the two-component signaling in bacteria

Bacterial pathogens such as Mycobacterium tuberculosis majorly rely on two-component signaling (TCS) systems to sense and generate adaptive responses to the dynamic and stressful host environment. TCS comprises a sensor histidine kinase (SK) that perceives the environmental signal, and a response regulator (RR) that modulates the target gene expression. TCS occurs via a phosphotransfer event from SK to RR. However, the mechanisms that regulate phosphotransfer events are not well understood. We explored the role of MutT1, originally characterized to hydrolyze oxidized GTP (8-oxo-GTP) and dGTP (8-oxo-dGTP), in TCS regulation. Unlike other MutT proteins, mycobacterial MutT1 comprises two domains (N-terminal domain, NTD; and C-terminal domain, CTD). Structurally, MutT1 NTD is like MutT proteins in other organisms. However, the MutT1 CTD is similar to E. coli SixA, a histidine phosphatase with an RHG motif. We show that MutT1 CTD dephosphorylates many SKs and impacts expression of their target genes, highlighting the role of MutT1 in regulating TCS. These novel findings are of special significance because they provide us with an extrinsic phosphatase mechanism to reset TCS signaling. The study reveals an intricate interplay between an enzyme that sanitizes the cellular nucleotide pool, and bacterial signaling pathways, offering insights into the adaptation mechanisms.

cell biology↗

bioRxiv2025

Comparative proteomics uncovers distinct biomarkers, protein networks and defense responses in tomato during beneficial and pathogenic microbial interactions

The molecular mechanisms underlying plant responses to beneficial and pathogenic microbial interactions has been uncovered in tomato at the proteomic level. Our study employed LC-MS- based proteomics to investigate differential protein regulation in tomato plants during interactions with beneficial bacteria (Bacillus subtilis BV7) versus pathogenic fungus (Alternaria solani). Comparative analysis revealed distinct protein signatures characterizing each interaction: 232 unique proteins in BV7-treated plants versus 96 in pathogen-infected plants, with 54 proteins shared between treatments. BV7 inoculation enhanced proteins involved in photosynthesis and primary metabolism, with PSI-K emerging as the top biomarker (score 2.53), while pathogen infection triggered focused defense responses with Cytochrome b559 (score 2.38) as the key biomarker. Metabolic pathway analysis demonstrated that BV7 uniquely enhanced vitamin metabolism (thiamine, riboflavin, folate) and energy production pathways, while pathogen infection activated defense-related phenylpropanoid biosynthesis. Analysis of defense enzymes showed pathogen infection induced highest activities of PAL (39.4{+/-}0.46 U h-1 g-1 fw), SOD (29.9{+/-}0.94 U mg-1 protein), POD (3.18{+/-}0.07 g g-1 fw min-1), APx (15.58{+/-}0.23 U mg-1 protein), and GPx (71.51{+/-}0.7 U mg-1 protein), while BV7 maintained moderate enzyme levels, suggesting balanced growth-defense responses. The shared proteins between treatments indicate a common molecular framework potentially contributing to induced systemic resistance. These findings provide novel insights into plant-microbe interactions at the molecular level, identifying specific protein biomarkers and metabolic pathways that could be targeted for enhancing crop productivity and disease resistance. The results have significant implications for developing biological control strategies and improving sustainable agricultural practices.

plant biology↗

bioRxiv2024

An unusual activity of mycobacterial MutT1 Nudix hydrolase domain as a protein phosphatase regulates nucleoside diphosphate kinase (NDK) function

MutT proteins are Nudix hydrolases characterized by the presence of a Nudix box, GX5EX7REUXEEXGU, where U is a bulky hydrophobic residue and X is any residue. Major MutT proteins hydrolyse 8-oxo-(d)GTP (8-oxo-GTP or 8-oxo-dGTP) to the corresponding 8-oxo-(d)GMP, preventing their incorporation into nucleic acids. Mycobacterial MutT1 comprises an N-terminal domain (NTD) harbouring the Nudix box motif, and a C-terminal domain (CTD) harbouring the RHG histidine phosphatase motif. Interestingly, unlike other MutTs, the MutT1 hydrolyses the mutagenic 8-oxo-(d)GTP to corresponding 8-oxo-(d)GDP. Nucleoside diphosphate kinase (NDK), a conserved protein, carries out reversible conversion of (d)NDPs to (d)NTPs through phospho-NDK (NDK-Pi) intermediate. Recently, we showed that NDK-Pi converts 8-oxo-dGDP to 8-oxo-dGTP and escalates A to C mutations in a MutT deficient Escherichia coli. We now show that both Mycobacterium tuberculosis MutT1, and M. smegmatis MutT1, through their NTD (Nudix hydrolase motifs) function as protein phosphatase to regulate the levels of NDK-Pi to NDK and prevent it from catalysing conversion of (d)NDPs to (d)NTPs (including conversion of 8-oxo-dGDP to 8-oxo-dGTP). To corroborate this function, we show that MsmMutT1 decreases A to C mutations in E. coli under the conditions of EcoNDK overexpression. ImportanceMutT proteins, having a Nudix box domain, hydrolyse the mutagenic 8-oxo-dGTP to 8-oxo-dGMP. However, mycobacterial MutT (MutT1) comprises an N-terminal domain (NTD) harboring a Nudix box, and a C-terminal domain (CTD) harboring an RHG histidine phosphatase. Unlike other MutTs, mycobaterial MutT1 hydrolyses 8-oxo-dGTP to 8-oxo-dGDP. Nucleoside diphosphate kinase (NDK), a conserved protein, converts 8-oxo-dGDP to 8-oxo-dGTP through phospho-NDK (NDK-Pi) intermediate, and escalates A to C mutations. Here, we show that the mycobacterial MutT1 is unprecedented in that its NTD (Nudix box), functions as protein phosphatase to regulate NDK-Pi levels and prevents it from converting dNDPs to dNTPs (including 8-oxo-dGDP to 8-oxo-dGTP conversion). In addition, mycobacterial MutT1 decreases A to C mutations in Escherichia coli under the conditions of NDK overexpression.

molecular biology↗

bioRxiv2022

First report of classical knockdown resistance (kdr) mutation, L1014F, in human head louse Pediculus humanus capitis (Phthiraptera: Anoplura)

There are at least three known knockdown resistance (kdr) mutations reported globally in the human head louse Pediculus humanus capitis (Phthiraptera: Anoplura) that are associated with reduced sensitivity to pyrethroids. However, prevalence of kdr mutation is not known in the Indian subcontinent. To identify kdr mutations in the Indian population, the genomic region of the voltage-gated sodium channel gene encompassing IIS1-2 linker to IIS6 segments was PCR-amplified and sequenced from P. humanus capitis samples collected from different geographic localities of India. DNA sequencing revealed the presence of four kdr mutations, i.e., M827I, T929I, L932F and L1014F. The presence of a classical kdr mutation, L1014F, a most widely reported mutation across insect-taxa associated with kdr-trait, is being reported for the first time in P. humanus capitis.

molecular biology↗

bioRxiv2020

Identification of differential gene expression pattern in lens epithelial cells derived from cataractous and non-cataractous lenses of Shumiya cataract rat

The Shumiya cataract rat (SCR) is a model for hereditary cataract. Two-third of these rats develop lens opacity within 10-11-weeks. Onset of cataract is attributed to the synergetic effect of lanosterol synthase (Lss) and farnesyl-diphosphate farnesyltransferase 1 (Fdft1) mutant alleles that lead to cholesterol deficiency in the lenses, which in turn adversely affects lens biology including the growth and differentiation of lens epithelial cells (LECs). Nevertheless, the molecular events and changes in gene expression associated with the onset of lens opacity in SCR is poorly understood. In the present study, a microarray-based approach was employed to analyze comparative gene expression changes in LECs isolated from the pre-cataractous and cataractous stages of lenses of 5-, 8- and 10-week-old SCRs. The changes in gene expression observed in microarray results in the LECs were further validated using real-time PCR and western blot analyses. Lens opacity was not observed in 5-week-old rats. However, histological analysis revealed mild dysplasia in the anterior suture and poorly differentiated fiber cells at the bow region. Expression of approximately 100 genes, including major intrinsic protein of lens fiber (MIP and Aquaporin0), deoxyribonuclease II beta (Dnase2b), heat shock protein B1 (Hspb1), and crystallin {gamma} ({gamma}Cry) B, C, and F were found to be significantly downregulated (0.07-0.5 fold) in rat LECs derived from cataract lenses compared to that in noncataractous lenses (control). Thus, our study aimed to identify the gene expression patterns during cataract formation in SCRs, which may be responsible for cataractogenesis in SCR. We proposed that mutation in lanosterol synthase was responsible for the downregulation of genes associated with lens fiber differentiation, which in turn leads to the formation of cataract in these rats. Our findings may have wider implications in understanding the effect of cholesterol deficiency and the role of cholesterol-lowering therapeutics on cataractogenesis.

cell biology↗

bioRxiv2019

The histidine kinase PdtaS is a cyclic di-GMP binding metabolic sensor that controls mycobacterial adaptation to nutrient deprivation

Cell signalling relies on second messengers to transduce signals from the sensory apparatus to downstream components of the signalling pathway. In bacteria, one of the most important and ubiquitous second messengers is the small molecule cyclic diguanosine monophosphate (c-di-GMP). While the biosynthesis, degradation and regulatory pathways controlled by c-di-GMP are well characterized, the mechanisms through which c-di-GMP controls these processes is not completely understood. Here we present the first report of a c-di-GMP regulated sensor histidine kinase previously named PdtaS (Rv3220c), which binds to c-di-GMP at sub-micromolar concentrations, subsequently perturbing signalling of the PdtaS-PdtaR (Rv1626) two component system. Aided by biochemical analysis, molecular docking and structural modelling, we have characterized the binding site of c-di-GMP in the GAF domain of PdtaS. We show that a pdtaS knockout in M. smegmatis is severely compromised in growth on amino acid deficient media and exhibits global transcriptional dysregulation. Perturbation of the c-di-GMP-PdtaS-PdtaR axis results in a cascade of cellular changes recorded by a multi-parametric systems approach of transcriptomics, unbiased metabolomics and lipid analyses.\n\nOne-sentence summaryThe universal bacterial second messenger cyclic di-GMP controls the mycobacterial nutrient stress response

microbiology↗