Browsing by Author "Rajeev Mishra"

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A novel mutation in FRMD7 causes X-linked idiopathic congenital nystagmus in a North Indian family
(Elsevier Ireland Ltd, 2015) Shashank Gupta; Ekta Pathak; Vidya Nair Chaudhry; Prashaant Chaudhry; Rajeev Mishra; Abhishek Chandra; Ashim Mukherjee; Mousumi Mutsuddi
Idiopathic congenital nystagmus (ICN) is the most common form of oculomotor disorder characterized by involuntary bilateral ocular oscillations. Primarily the disease is an ocular anomaly but the pathophysiology is associated with neuronal cytoskeletal dynamics in the brain. In the current study, a three generation North Indian family affected with X-linked idiopathic congenital nystagmus (XLICN) was recruited. Our aim was to identify the causal mutation for ICN in the family by screening the candidate gene, FERM domain containing-7 (. FRMD7). This gene has been implicated in XLICN as it regulates neuronal cytoskeletal proteins and neurite outgrowth in the developing brain. Therefore, the entire protein coding region, including splice junctions, 5' UTR and 3' UTR of FRMD7 was screened by PCR-Sanger sequencing. Targeted sequencing revealed a novel A to G transition in the exon seven (c.556A.>. G), resulting in a conservative substitution of methionine by valine at codon 186 (p.M186V). A cohort of healthy individuals was also checked for presence of the putative causal variant by allele specific PCR. All the affected males and carriers in the family shared this variant; however, this was absent in the unaffected males as well as 100 unrelated healthy individuals. Further, protein homology modeling revealed that the change p.M186V might destabilize the interaction between the FERM-M and FERM-C domains. The in silico prediction supports pathogenicity of the mutation; nevertheless it needs in vivo validation in the future. This is the first genetic investigation of XLICN in a North Indian family where we report a novel causal mutation c.556A. >. G (p.M186V) in the gene FRMD7. © 2015 Elsevier Ireland Ltd.
An ECF41 family σ factor controls motility and biogenesis of lateral flagella in azospirillum brasilense Sp245
(American Society for Microbiology, 2020) Ashutosh Prakash Dubey; Parul Pandey; Vijay Shankar Singh; Mukti Nath Mishra; Sudhir Singh; Rajeev Mishra; Anil Kumar Tripathi
ECF41 is a large family of bacterial extracytoplasmic function (ECF) σ factors. Their role in bacterial physiology or behavior, however, is not known. One of the 10 ECF σ factors encoded in the genome of Azospirillum brasilense Sp245, RpoE10, exhibits features characteristic of the typical ECF41-type σ factors. Inactivation of rpoE10 in A. brasilense Sp245 led to an increase in motility that could be complemented by the expression of rpoE10. By comparing the number of lateral flagella, transcriptome, and proteome of A. brasilense Sp245 with those of its rpoE10::km mutant, we show here that this ECF41-type σ factor is involved in the negative regulation of swimming motility and biogenesis of lateral flagella of A. brasilense Sp245. The genome of A. brasilense Sp245 also encodes two OmpR-type regulators (LafR1 and LafR2) and three flagellins, including Laf1, the major flagellin of lateral flagella. Elevated levels of laf1 transcripts and Laf1 protein in the rpoE10::km mutant indicated that RpoE10 negatively regulates the expression of Laf1. The elevated level of LafR1 in the rpoE10::km mutant indicated that LafR1 is also negatively regulated by RpoE10. The loss of motility and Laf1 in the lafR1::km mutant, complemented by lafR1 expression, showed that LafR1 is a positive regulator of Laf1 and motility in A. brasilense. In addition, upregulation of laf1:: lacZ and lafR1::lacZ fusions by RpoE10 and downregulation of the laf1::lacZ fusion by LafR1 suggest that RpoE10 negatively regulates swimming motility and the expression of LafR1 and Laf1. However, LafR1 positively regulates the swimming motility and Laf1 expression. IMPORTANCE Among extracytoplasmic function (ECF) σ factors, ECF41-type σ factors are unique due to the presence of a large C-terminal extension in place of a cognate anti-σ factor, which regulates their activity. Despite their wide distribution and abundance in bacterial genomes, their physiological or behavioral roles are not known. We show here an indirect negative role of an ECF41-type of σ factor in the expression of lateral flagellar genes and motility in A. brasilense. This study suggests that the motility of A. brasilense might be controlled by a regulatory cascade involving RpoE10, an unknown repressor, LafR1, and lateral flagellar genes, including that encoding Laf1. Copyright © 2020 American Society for Microbiology. All Rights Reserved.
Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host
(Elsevier Ltd, 2022) Shivangi Agrawal; Ekta Pathak; Rajeev Mishra; Vibha Mishra; Afifa Parveen; Sunil Kumar Mishra; Parameswarappa S. Byadgi; Sushil Kumar Dubey; Ashvanee Kumar Chaudhary; Vishwambhar Singh; Rameshwar Nath Chaurasia; Neelam Atri
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections generate approximately one million virions per day, and the majority of available antivirals are ineffective against it due to the virus's inherent genetic mutability. This necessitates the investigation of concurrent inhibition of multiple SARS-CoV-2 targets. We show that fortunellin (acacetin 7-O-neohesperidoside), a phytochemical, is a promising candidate for preventing and treating coronavirus disease (COVID-19) by targeting multiple key viral target proteins. Fortunellin supports protective immunity while inhibiting pro-inflammatory cytokines and apoptosis pathways and protecting against tissue damage. Fortunellin is a phytochemical found in Gojihwadi kwath, an Indian traditional Ayurvedic formulation with an antiviral activity that is effective in COVID-19 patients. The mechanistic action of its antiviral activity, however, is unknown. The current study comprehensively evaluates the potential therapeutic mechanisms of fortunellin in preventing and treating COVID-19. We have used molecular docking, molecular dynamics simulations, free-energy calculations, host target mining of fortunellin, gene ontology enrichment, pathway analyses, and protein-protein interaction analysis. We discovered that fortunellin reliably binds to key targets that are necessary for viral replication, growth, invasion, and infectivity including Nucleocapsid (N-CTD) (−54.62 kcal/mol), Replicase-monomer at NSP-8 binding site (−34.48 kcal/mol), Replicase-dimer interface (−31.29 kcal/mol), Helicase (−30.02 kcal/mol), Papain-like-protease (−28.12 kcal/mol), 2′-O-methyltransferase (−23.17 kcal/mol), Main-protease (−21.63 kcal/mol), Replicase-monomer at dimer interface (−22.04 kcal/mol), RNA-dependent-RNA-polymerase (−19.98 kcal/mol), Nucleocapsid-NTD (−16.92 kcal/mol), and Endoribonuclease (−16.81 kcal/mol). Furthermore, we identify and evaluate the potential human targets of fortunellin and its effect on the SARS-CoV-2 infected tissues, including normal-human-bronchial-epithelium (NHBE) and lung cells and organoids such as pancreatic, colon, liver, and cornea using a network pharmacology approach. Thus, our findings indicate that fortunellin has a dual role; multi-target antiviral activities against SARS-CoV-2 and immunomodulatory capabilities against the host. © 2022 Elsevier Ltd
Cross-talk between cognate and noncognate rpoe sigma factors and Zn 2+-binding anti-sigma factors regulates photooxidative stress response in azospirillum brasilense
(2014) Namrata Gupta; Ankush Gupta; Santosh Kumar; Rajeev Mishra; Chhaya Singh; Anil Kumar Tripathi
Aims: Azospirillum brasilense harbors two redox-sensitive Zinc-binding anti-sigma (ZAS) factors (ChrR1 and ChrR2), which negatively regulate the activity of their cognate extra-cytoplasmic function (ECF) σ factors (RpoE1 and RpoE2) by occluding their binding to the core enzyme. Both pairs of RpoE-ChrR control responses to photooxidative stress. The aim of this study was to investigate whether the two RpoE-ChrR pairs cross-talk while responding to the stress. Results: In silico analysis showed a high sequence similarity between ChrR1 and ChrR2 proteins, but differences in redox sensitivity. Using in silico and in vitro methods of protein-protein interaction, we have shown that both ChrR1 and ChrR2 proteins physically bind to their noncognate RpoE proteins. Restoration of the phenotypes of chrR1::Tn5 and chrR2::Km mutants related to carotenoid biosynthesis and photooxidative stress tolerance by expressing chrR1 or chrR2 provided in vivo evidence for the cross-talk. In addition, up- or down-regulation of several identical proteins by expressing chrR1 or chrR2 in the chrR1::Tn5 mutant provided another in vivo evidence for the cross-talk. Innovation: Although multiple redox-sensitive ZAS anti-σ factors occur in some Gram-positive bacteria, no cross-talk is reported among them. We report here, for the first time, that the two ZAS anti-σ factors of A. brasilense also interact with their noncognate σ factors and affect gene expression. Conclusion: The two redox-sensitive ZAS anti-σ factors in A. brasilense may interact with their cognate as well as noncognate ECF σ factors to play an important role in redox homeostasis by facilitating recovery from the oxidative stress. Antioxid. Redox Signal. 20, 42-59. © Copyright 2014, Mary Ann Liebert, Inc. 2014.
Deciphering the role of the two conserved motifs of the ECF41 family σ factor in the autoregulation of its own promoter in Azospirillum brasilense Sp245
(John Wiley and Sons Inc, 2022) Ekta Pathak; Ashutosh Prakash Dubey; Vijay Shankar Singh; Rajeev Mishra; Anil Kumar Tripathi
In Azospirillum brasilense, an extra-cytoplasmic function σ factor (RpoE10) shows the characteristic 119 amino acid long C-terminal extension found in ECF41-type σ factors, which possesses three conserved motifs (WLPEP, DGGGR, and NPDKV), one in the linker region between the σ2 and σ4, and the other two in the SnoaL_2 domain of the C-terminal extension. Here, we have described the role of the two conserved motifs in the SnoaL_2 domain of RpoE10 in the inhibition and activation of its activity, respectively. Truncation of the distal part of the C-terminal sequence of the RpoE10 (including NPDKV but excluding the DGGGR motif) results in its promoter's activation suggesting autoregulation. Further truncation of the C-terminal sequence up to its proximal part, including NPDKV and DGGGR motif, abolished promoter activation. Replacement of NPDKV motif with NAAAV in RpoE10 increased its ability to activate its promoter, whereas replacement of DGGGR motif led to reduced promoter activation. We have explored the dynamic modulation of σ2 -σ4 domains and the relevant molecular interactions mediated by the two conserved motifs of the SnoaL2 domain using molecular dynamics simulation. The analysis enabled us to explain that the NPDKV motif located distally in the C-terminus negatively impacts transcriptional activation. In contrast, the DGGGR motif found proximally of the C-terminal extension is required to activate RpoE10. © 2022 Wiley Periodicals LLC.
Effects of herbicide on various life forms with special reference to the paddy fields in the Eastern Belts of India
(Open Science Publishers LLP Inc., 2023) Tripti Kanda; Rupanshee Srivastava; Sadhana Yadav; Nidhi Singh; Rajesh Prajapati; Shivam Yadav; Rajeev Mishra; Neelam Atri
Rice constitutes the most dominant segment of food consumed by the people of India. In modern agriculture practice, it is cultivated by the assistance of agrochemicals called herbicides. The herbicides tend to eradicate the weed infestation in the paddy fields and are known to be the most efficient tool to obtain a high yield of crop. However, their excessive use in the agriculture fields initiates the occurrence of deleterious effects in paddy fields by inhibiting the activity of cyanobacteria, as they consist of several physiological characteristics of vascular plants, which form the site of herbicide action. The agrochemicals influence the activity of enzymes, photosynthetic process, and nitrogen-fixing ability of microbial cell. Percolation of the same to nearby water bodies tends to negatively affect the aquatic ecosystem. These chemicals bring about biochemical, pathological, physiological, and genetic manipulations in humans by accumulating in the food chain. This review attempts to impart an overall understanding on toxic effect of herbicides on various life forms with a noteworthy focus on paddy crops grown in the eastern belts of India. © 2023 Tripti Kanda, et al.
Genome-wide assessment of putative superoxide dismutases in unicellular and filamentous cyanobacteria
(Instituto de Tecnologia do Parana, 2019) Rajesh Prajapati; Shivam Yadav; Sonali Mitra; Priya Rai; Rajeev Mishra; Neelam Atri
Cyanobacteria are photoautotrophic prokaryotes capable to grow in diverse ecological habitats, originated 2.5-3.5 billion years ago and were first to produce oxygen. Since then superoxide dismutases (SOD) acquired great significance due to their ability to catalyze detoxification of byproducts of oxygenic photosynthesis i.e. superoxide radicals. In the present study, we extracted information regarding SODs from species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. 144 putative SOD homologs were identified. Unlike other protein families (ex. serine-threonine kinases) SODs are present in ali cyanobacterial species reflecting their significant role in survival. However, their distribution varies fewer (0.01%-0.09%) found in unicellular marine strains whereas abundant (0.02%-0.07%) in filamentous nitrogen-fixing cyanobacteria. They were classified into three major subfamilies according to their domain structures: Fe/MnSOD, Cu/ZnSOD and NiSOD. Interestingly, they lack additional domains as found in proteins of other families however motifs and invariant amino acids typical in eukaryotic SODs were conserved well in these proteins indicating similar catalytic mechanism as eukaryotic SODs. Phylogenetic relationships correspond well with phylogenies based on 16S rRNA and clustering occurs on the basis of structural characteristics such as domain organization. Gene gain-and-loss is insignificant during SOD evolution as evidenced by the absence of additional domain. This study has not only examined an overall background of sequence-structure-function interactions for the SOD gene family but also revealed variation among SOD distribution based on ecophysiological and morphological characters. © 2018 by the authors.
Identification and characterization of a novel phosphodiesterase from the metagenome of an Indian coalbed
(Public Library of Science, 2015) Durgesh Narain Singh; Ankush Gupta; Vijay Shankar Singh; Rajeev Mishra; Suneel Kateriya; Anil Kumar Tripathi
Phosphoesterases are involved in the degradation of organophosphorus compounds. Although phosphomonoesterases and phosphotriesterases have been studied in detail, studies on phosphodiesterases are rather limited. In our search to find novel phosphodiesterases using metagenomic approach, we cloned a gene encoding a putative phosphodiesterase (PdeM) from the metagenome of the formation water collected from an Indian coal bed. Bioinformatic analysis showed that PdeM sequence possessed the characteristic signature motifs of the class III phosphodiesterases and phylogenetic study of PdeM enabled us to identify three distinct subclasses (A, B, and C) within class III phosphodiesterases, PdeM clustering in new subclass IIIB. Bioinformatic, biochemical and biophysical characterization of PdeM further revealed some of the characteristic features of the phosphodiesterases belonging to newly described subclass IIIB. PdeM is a monomer of 29.3 kDa, which exhibits optimum activity at 25° C and pH 8.5, but low affinity for bis(pNPP) as well as pNPPP. The recombinant PdeM possessed phosphodiesterase, phosphonate-ester hydrolase and nuclease activity. It lacked phosphomonoesterase, phosphotriesterase, and RNAse activities. Overexpression of PdeM in E.coli neither affected catabolite respression nor did the recombinant protein hydrolyzed cAMP in vitro, indicating its inability to hydrolyze cAMP. Although Mn 2+ was required for the activity of PdeM, but addition of metals (Mn2+ or Fe3+) did not induce oligomerization. Further increase in concentration of Mn 2+ upto 3 mM, increased α-helical content as well as the phosphodiesterase activity. Structural comparison of PdeM with its homologs showed that it lacked critical residues required for dimerization, cAMP hydrolysis, and for the high affinity binding of bis(pNPP). PdeM, thus, is a novel representative of new subclass of class III phosphodiesterases. © 2015 Singh et al.
Phycochemistry and bioactivity of cyanobacterial secondary metabolites
(Springer Science and Business Media B.V., 2022) Rupanshee Srivastava; Rajesh Prajapati; Tripti Kanda; Sadhana Yadav; Nidhi Singh; Shivam Yadav; Rajeev Mishra; Neelam Atri
Microbes are a huge contributor to people’s health around the world since they produce a lot of beneficial secondary metabolites. Cyanobacteria are photosynthetic prokaryotic bacteria cosmopolitan in nature. Adaptability of cyanobacteria to wide spectrum of environment can be contributed to the production of various secondary metabolites which are also therapeutic in nature. As a result, they are a good option for the development of medicinal molecules. These metabolites could be interesting COVID-19 therapeutic options because the majority of these compounds have demonstrated substantial pharmacological actions, such as neurotoxicity, cytotoxicity, and antiviral activity against HCMV, HSV-1, HHV-6, and HIV-1. They have been reported to produce a single metabolite active against wide spectrum of microbes like Fischerella ambigua produces ambigols active against bacteria, fungi and protozoa. Similarly, Moorea producens produces malygomides O and P, majusculamide C and somocystinamide which are active against bacteria, fungi and tumour cells, respectively. In addition to the above, Moorea sp. produce apratoxin A and dolastatin 15 possessing anti cancerous activity but unfortunately till date only brentuximab vedotin (trade name Adcetris), a medication derived from marine peptides, for the treatment of Hodgkin lymphoma and anaplastic large cell lymphoma has been approved by FDA. However, several publications have effectively described and categorised cyanobacterial medicines based on their biological action. In present review, an effort is made to categorize cyanobacterial metabolites on the basis of their phycochemistry. The goal of this review is to categorise cyanobacterial metabolites based on their chemical functional group, which has yet to be described. © 2022, The Author(s), under exclusive licence to Springer Nature B.V.
Single-Cell Transcriptome Analysis Reveals the Role of Pancreatic Secretome in COVID-19 Associated Multi-organ Dysfunctions
(Springer Science and Business Media Deutschland GmbH, 2022) Ekta Pathak; Neelam Atri; Rajeev Mishra
The SARS-CoV-2 infection affects the lungs, heart, kidney, intestine, olfactory epithelia, liver, and pancreas and brings forward multi-organ dysfunctions (MODs). However, mechanistic details of SARS-CoV-2-induced MODs are unclear. Here, we have investigated the role of pancreatic secretory proteins to mechanistically link COVID-19 with MODs using single-cell transcriptome analysis. Secretory proteins were identified using the Human Protein Atlas. Gene ontology, pathway, and disease enrichment analyses were used to highlight the role of upregulated pancreatic secretory proteins (secretome). We show that SARS-CoV-2 infection shifts the expression profile of pancreatic endocrine cells to acinar and ductal cell-specific profiles, resulting in increased expression of acinar and ductal cell-specific genes. Among all the secretory proteins, the upregulated expression of IL1B, AGT, ALB, SPP1, CRP, SERPINA1, C3, TFRC, TNFSF10, and MIF was mainly associated with disease of diverse organs. Extensive literature and experimental evidence are used to validate the association of the upregulated pancreatic secretome with the coagulation cascade, complement activation, renin-angiotensinogen system dysregulation, endothelial cell injury and thrombosis, immune system dysregulation, and fibrosis. Our finding suggests the influence of an upregulated secretome on multi-organ systems such as nervous, cardiovascular, immune, digestive, and urogenital systems. Our study provides evidence that an upregulated pancreatic secretome is a possible cause of SARS-CoV-2-induced MODs. This finding may have a significant impact on the clinical setting regarding the prevention of SARS-CoV-2-induced MODs. Graphical abstract: [Figure not available: see fulltext.] © 2022, International Association of Scientists in the Interdisciplinary Areas.
Whole exome sequencing unveils a frameshift mutation in CNGB3 for cone dystrophy
(Lippincott Williams and Wilkins, 2017) Shashank Gupta; Amit Chaurasia; Ekta Pathak; Rajeev Mishra; Vidya Nair Chaudhry; Prashaant Chaudhry; Ashim Mukherjee; Mousumi Mutsuddi
Rationale:Genetic elucidation of cone-dominated retinal dystrophies in Indian subcontinent is much needed to identify and catalog underlying genetic defects. In this context, the present study recruited a consanguineous Indian family affected with autosomal recessive cone dystrophy (CD). Considering the huge genetic heterogeneity and recessive inheritance of the disease, we chose to dissect out causal variant in this family by whole exome sequencing (WES). Patient concerns:In the recruited family, three of the six siblings had complaints of poor visual acuity, photophobia, and disturbed colour vision since early childhood. Fundus examination disclosed vascular attenuation and macular retinal pigment epithelium (RPE) changes in all the affected siblings, signifying degeneration of photoreceptor cells. Diagnosis:Complete clinical investigation and electroretinography studies led to the diagnosis of cone dystrophy in three siblings of the family. Interventions:Detailed ophthalmic examination, including family history, visual function testing, and retinal imaging, was performed. We captured and sequenced exomes of 2 affected siblings and their mother using SureSelect Human All Exon V5 Kit on Illumina HiSeq 2000/2500 platform with 100 bp paired-end sequencing method. Candidates after data analysis were screened by segregation analysis and Sanger sequencing. Considering recessive inheritance and consanguinity in the pedigree, we attempted to map large loci homozygous by descent in the genome of patients using exome sequencing variants. Extensive protein modeling was carried out to assess possible consequences of the identified variant on the 3-dimensional structure of the protein. Outcomes:WES generated more than 65,000 variants for each individual. Assuming recessive inheritance, 13,026 variants were selected. Further filtering on the basis of their position in gene, class, and minor allele frequency constricted the huge list to 12 rare variants. Finally, we ascertained a single base deletion c.1148delC (p.Thr383fs) in the gene CNGB3 as the causal variant. This is a recurrent frameshift mutation resulting in truncated CNGB3 protein. We mapped a large 15-Mb stretch of homozygous markers spanning the causal variant in the proband. The gene CNGB3 encodes modulatory subunit of cyclic nucleotide-gated channels in cone photoreceptors. Protein modeling reveals loss of 2 transmembrane helices and conserved CAP-ED domain in truncated CNGB3, which eventually is predicted to form nonfunctional channels and hamper phototransduction. Lessons:We have identified a recurrent mutation c.1148delC (p.Thr383fs) in CNGB3 for autosomal recessive CD. The present report provides the first description of CNGB3 mutation from India. It is also the foremost investigation of familial CD in Indian patients; therefore, it presents the primary genetic etiology of CD in India. © 2017 the Author(s). Published by Wolters Kluwer Health, Inc.