Biology subjects

Saini, A. K.

Publications and source records attributed to Saini, A. K..

5 recordsLinked to original sources

bioRxiv2026

Global Proteome Remodelling in Rhodococcus jialingiae RS1 to Decipher its Plant Growth-Promoting and Biofertilizer Properties: Gene Identification for Transgenics

1.Abiotic stresses like nitrogen deficiency and soil salinity are major factors contributing to low crop yields. The use of selective biofertilizers alleviates both types of stress. In this study, we investigated the biofertilizer activity and plant growth-promoting properties (PGP) of Rhodococcus jialingiae RS1 through cytosolic proteome remodelling. We cultured RS1 under two conditions, i) without and ii) with 6% NaCl, in nitrogen-deficient defined Burks medium. Under dual stress of nitrogen limitation and salt stress, Orbitrap LC-MS/MS proteomics revealed one-quarter of the proteome remodelling, particularly the upregulation of ribosomal synthesis and protein repair systems. As expected, we found high expression of EctC, an ectoine synthase, a key enzyme in osmolyte biosynthesis. Additionally, ribosomal and translational-associated factors, including RpsL, RpsS, RpsT, RpsR1, RplV, RplL, RplA, and elongation factor Tuf, were highly expressed, suggesting enhanced translational fidelity under dual stress. High levels of DNA protection protein, Dps suggest dual stress may lead to DNA damage. Upregulation of chaperones, environmental sensors (KinE), and redox transcriptional factors like WhiB3, Hsp18, AhpC, and MetE suggests protein misfolding and oxidative stress. Metabolic modulations were evident through high expression of IlvA, NAD-dependent glutamate dehydrogenase, lipid/envelope-remodelling enzymes, cutinase/esterases, lipases, endopeptidases like NlpC/P60 and transport systems. In contrast, proteins involved in urease structural components (urea-G), nitrogen regulators and ammonium transporters (GlnK and Amt) were downregulated. Dual stress may lead to an energy crisis, prompting strategic shifts away from high-ATP-dependent ureolytic nitrogen-scavenging pathways towards lower-energy nitrogen-assimilating routes, such as IlvA-mediated deamination and NAD-dependent glutamate dehydrogenation. Genetic manipulations of the above-mentioned genes or their homologues across the genera of microbes, plants, and crops may enhance resilience to abiotic stresses. Our studies reveal stress-responsive genes and biochemical pathways that could be used to improve transgenic efficacy in nitrogen-limited, saline soil and other (a)biotic stresses. Global Proteome Profiling of Rhodococcus jialingiae RS1 to Develop Transgenics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/724437v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1f29783org.highwire.dtl.DTLVardef@1b953e6org.highwire.dtl.DTLVardef@335951org.highwire.dtl.DTLVardef@12ce661_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

DNA methylation and demethylation driven regulation of sepsis

During dysregulated inflammation and sepsis, there is a sudden surge of cytokines, such as TNF alpha, IL6, and IL10, which disrupts the body homeostasis. This sudden and rapid increase in cytokine gene expression cannot be explained by the conventional central dogma mechanism. DNA methylation is one of the most significant epigenetic modifications. DNA methylation is mostly associated with the suppression of gene activity, and DNA demethylation is associated with the activation of gene activity. There are numerous transcription factors, such as CREB1, c-FOS, AP-1, IRF1, and EGR1, that play pivotal roles in regulating inflammation. Thus, it was hypothesized that changes in the DNA methylation patterns of cytokine promoter regions or in the promoter regions of these specific transcription factors might be the potential reasons for the increase in cytokine levels during sepsis. During endotoxin stimulation, DNA methyltransferases were suppressed, and DNA methylation levels were altered at the global level. Bisulfite sequencing revealed no change in the DNA methylation patterns of the TNF-alpha, IL6 and IL10 cytokine promoters. The CREB1 and c-FOS transcription factor promoters were demethylated after LPS stimulation and in clinical sepsis samples. Overall, this study highlights the importance of the role of DNA methylation in sepsis.

molecular biology↗

bioRxiv2023

Analytical Method Development for Evaluation of Pharmacokinetics and Tissue Distribution of Thiourea-Based Antivirals through nLC/MS-MS

Thiourea-based antivirals are organosulfur chemical compounds. Due to their various medicinal uses, including antiviral, antioxidant, and anticancer properties, they are becoming more popular. In this study, pharmacokinetics, Metabolism, bioavailability, and distribution of thiourea derivatives to organs of rats. Thiourea derivatives, namely DSA-00, DSA-02, and DSA-09, exhibit characteristics similar to those of conventional drugs when evaluated in terms of pharmacokinetics, drug-likeness, and medicinal chemistry through in-silico analysis. Then a simple and sensitive analytical method was developed for quantified DSA-00, DSA-02, and DSA-09, using prednisolone as an internal standard (IS) and nano liquid chromatography tandem mass spectrometry (nLC-MS/MS). The plasma and tissue samples were preprocessing with acetonitrile before chromatographic separation by C18 column with isocratic elution using a mobile phase of water-methanol (30:70, v/v) at a flow rate of 0.6 mL/min. A triplequadrupole tandem mass spectrometer in multiple-reaction monitoring (MRM) scanning via an electrospray ionization (ESI) source functioning in negative and positive mode detection. For DSA-00, DSA-02, DSA-09 and, internal standard the optimized mass transition ion-pairs (m/z) for quantification were 297.2, 311.2, 309.09, and 361.19 respectively. Each analytic run required only 15 minutes between injections. The calibration curve for thiourea derivatives showed good linear regression coefficient (R2 >.99) over a range of 1.00-10000 pg/mL except DSA-09. The lower limit of quantification (LLOQ) was 1.00 ng/mL. The intra- and inter-day precisions were no more than 10.8%, and relative errors (RE) ranged from 0.5 to 5.98%. The validated method was effectively used to explore the pharmacokinetics of orally administrative thiourea derivatives in rats.

pharmacology and toxicology↗

bioRxiv2020

Identification of radiation responsive proteins from Spleen and Intestine tissue of mice using Mass Spectrometry approach.

PurposeExposure to ionizing radiation (IR) can cause tissue damage, which is difficult to diagnose and treat as no biomarker is available for detection. We aimed to identify proteomic signature of radiation exposure (9.5Gry) in mice and to assess the utility of Podophyllotoxin extract (PTOX) in preventing radiation injury. Materials and MethodsSpleen and Small intestinal (SI) tissues were taken from control and lethally irradiated mice at different time intervals with or without pre-treatment with Podophyllotoxin extract. Proteins were identified using Mass Spectrometry and matched with Peptide Mass Fingerprinting. ResultsWe found multiple differentially expressed radiation responsive proteins from Spleen and SI tissues in irradiated mice at 24 hours and 30 days in comparison to healthy controls (p<0.05). Differentially expressed proteins like Chromosome transmission fidelity factor ano thath 18 homolog (CTF18) and Rho GTPase-activating protein from spleen and Acta_Mouse protein from SI were identified. These proteins disappeared at 48 hrs. after IR, but re-appeared after 13 days and fully recovered at 30 days in Podophyllotoxin treated group. ConclusionsSuch proteins may be useful in early detection of radiation exposure. Pre-treatment with Podophyllotoxin leads to recovery of the disappeared proteins and improved survival following exposure to irradiation.

biochemistry↗

bioRxiv2018

Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition

In eukaryotic translation initiation AUG recognition of the mRNA requires accommodation of Met-tRNAi in a \"PIN\" state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a 48S pre-initiation complex (PIC), at an overall resolution of 3.0 [A], featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNAi. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNAi interaction influenced initiation at near-cognate UUG codons in vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.

biophysics↗