Renu Tuteja - Academia.edu (original) (raw)

Papers by Renu Tuteja

Nova Science eBooks, 2011

Preface Repetitive DNA sequences in Phyllostachys pubescens genome Transcriptional networks: dyna... more Preface Repetitive DNA sequences in Phyllostachys pubescens genome Transcriptional networks: dynamics information fluxes A new method for the identification of leucine-rich repeats by incorporating protein secondary structure prediction MicroRNA profiling involved in human tumorigenesis using Bioinformatics tools Biobanking: the bioethical dimensions Application of next-generation DNA sequencing in medical discovery Phylogenomics Transposons: the alchemists in 'junk' disguise.

Protoplasma, Jan 4, 2017

RuvB, a member of AAA+ (ATPases Associated with diverse cellular Activities) superfamily of prote... more RuvB, a member of AAA+ (ATPases Associated with diverse cellular Activities) superfamily of proteins, is essential, highly conserved and multifunctional in nature as it is involved in DNA damage repair, mitotic assembly, switching of histone variants and assembly of telomerase core complex. RuvB family is widely studied in various systems such as Escherichia coli, yeast, human, Drosophila, Plasmodium falciparum and mouse, but not well studied in plants. We have studied the transcript level of rice homologue of RuvB gene (OsRuvBL1a) under various abiotic stress conditions, and the results suggest that it is upregulated under salinity, cold and heat stress. Therefore, the OsRuvBL1a protein was characterized using in silico and biochemical approaches. In silico study confirmed the presence of all the four characteristic motifs of AAA+ superfamily-Walker A, Walker B, Sensor I and Sensor II. Structurally, OsRuvBL1a is similar to RuvB1 from Chaetomium thermophilum. The purified recombinan...

Communicative & Integrative Biology, May 1, 2011

Antioxidants

Helicases function as key enzymes in salinity stress tolerance, and the role and function of PDH4... more Helicases function as key enzymes in salinity stress tolerance, and the role and function of PDH45 (pea DNA helicase 45) in stress tolerance have been reported in different crops with selectable markers, raising public and regulatory concerns. In the present study, we developed five lines of marker-free PDH45-overexpressing transgenic lines of rice (Oryza sativa L. cv. IR64). The overexpression of PDH45 driven by CaMV35S promoter in transgenic rice conferred high salinity (200 mM NaCl) tolerance in the T1 generation. Molecular attributes such as PCR, RT-PCR, and Southern and Western blot analyses confirmed stable integration and expression of the PDH45 gene in the PDH45-overexpressing lines. We observed higher endogenous levels of sugars (glucose and fructose) and hormones (GA, zeatin, and IAA) in the transgenic lines in comparison to control plants (empty vector (VC) and wild type (WT)) under salt treatments. Furthermore, photosynthetic characteristics such as net photosynthetic ra...

Journal of Biological Chemistry, Nov 1, 1986

Advancements in Genetic Engineering, Oct 30, 2013

Immunology, May 1, 1999

In the present study, the genetic mechanisms responsible for generation of antibodies recognizing... more In the present study, the genetic mechanisms responsible for generation of antibodies recognizing the dominant epitope within a synthetic peptide PS1CT3 were examined. PS1CT3 is a peptide model antigen containing residues 28–42 of the large protein of the surface antigen of hepatitis B virus as B epitope (designated PS1), and the known T-helper-cell epitope derived from the circumsporozoite protein of the malaria parasite Plasmodium falciparum (designated CT3). To characterize the repertoire generated, the immunoglobulin heavy chain variable regions from IgM and IgG monoclonal antibodies against PS1CT3 were sequenced. Although all IgG monoclonal antibodies were directed against the immunodominant epitope, the genetic elements used were diverse. Comparison of the sequence of germ line precursor IgM to a mature IgG revealed that during maturation of the primary IgM response only the heavy chain fragment of the antibody molecule underwent somatic mutation.

Parasitology International, Dec 1, 2016

The cellular response to various stresses is a universal phenomenon and involves a common set of ... more The cellular response to various stresses is a universal phenomenon and involves a common set of stress responses that are largely independent of the type of stress. The response to stress is complex and cells can activate multiple signaling pathways that act in concert to influence cell fate and results in a specific cellular outcome, including reduction in macromolecular synthesis by shared pathways, cell cycle arrest, DNA repair, senescence and/or apoptosis. Whether cells mount a protective response or die depends to a great degree on the nature and duration of the stress and the particular cell type. Helicases play essential roles in DNA replication, repair, recombination, transcription and translation, and also participate in RNA metabolic processes including pre-mRNA processing, ribosome biogenesis, RNA turnover, export, translation, surveillance, storage and decay. In order to survive in the human host, the malaria parasite Plasmodium falciparum has to handle variety of stresses, which it encounters during the erythrocytic stages of its life cycle. In recent past the role of helicases in imparting various stress responses has emerged. Therefore in the present review an attempt has been made to highlight the emerging importance of helicases in stress responses in malaria parasite and their comparison with human host is also presented. It is noteworthy that PfDHX33 and PfDDX60 are larger in size and different in sequence as compared to the HsDHX33 and HsDDX60. The study suggests that helicases are multifunctional and play major role in helping the cells to combat various stresses.

Journal of Proteomics

There are important challenges when investigating individual post-translational modifications (PT... more There are important challenges when investigating individual post-translational modifications (PTMs) or protein interaction network and delineating if PTMs or their changes and cross-talks are involved during infection, disease initiation or as a result of disease progression. Proteomics and in silico approaches now offer the possibility to complement each other to further understand the regulatory involvement of these modifications in parasites and infection biology. Accordingly, the current review highlights key expressed or altered proteins and PTMs are invisible switches that turn on and off the function of most of the proteins. PTMs include phosphorylation, glycosylation, ubiquitylation, palmitoylation, myristoylation, prenylation, acetylation, methylation, and epigenetic PTMs in P. falciparum which have been recently identified. But also other low-abundant or overlooked PTMs that might be important for the parasite's survival, infectivity, antigenicity, immunomodulation and pathogenesis. We here emphasize the PTMs as regulatory pathways playing major roles in the biology, pathogenicity, metabolic pathways, survival, host-parasite interactions and the life cycle of P. falciparum. Further validations and functional characterizations of such proteins might confirm the discovery of therapeutic targets and might most likely provide valuable data for the treatment of P. falciparum, the main cause of severe malaria in human.

The influence of imposing various conformational constraints on immune responses to a model epito... more The influence of imposing various conformational constraints on immune responses to a model epitope within a synthetic peptide immunogen was examined in mice. Although overall immunogenicity was affected, the model epitope (sequence DPAF) remained the predominant recognition site regardless of the conformation in which it was presented. A comparison of anti-DPAF mAbs obtained in response to two analogue peptides, PS1CT3 and CysCT3, in which the DPAF segment was either unconstrained or held within a cyclic loop, respectively, revealed a significant homology in the paratope composition. At one level a subset of anti-PS1CT3 and anti-CysCT3 mAbs was found to share a common heavy chain variable region. In addition, nucleotide sequence homology comparisons of both heavy and light chain variable regions identified the presence of anti-PS1CT3 and anti-CysCT3 mAbs that collectively appeared to derive from a common progenitor, but with nonidentical somatic mutations. Interestingly, however, no bias toward homologous Ag could be discerned on measurement of relative affinities of the mAbs for the two peptides. In contrast, mAb binding on-rates clearly discriminated between peptides representing the homologous vs the heterologous confomer of the DPAF epitope. Thus, it would appear that the kinetics of Ag recognition dominate over equilibrium binding criteria both in epitope-driven repertoire selection and Ab maturation in a humoral response.

Methods and Applications, 2002

Abstract Leishmania is one of the most important protozoan parasites that causes infections in hu... more Abstract Leishmania is one of the most important protozoan parasites that causes infections in humans and is responsible for three main forms of leishmaniases—visceral (also known as kala-azar and the most serious form of the disease), cutaneous (the most common), and mucocutaneous. The availability of whole genome sequence has facilitated the genome wide analysis of genes including helicases. Helicases are ubiquitously characterized by the presence of seven to nine conserved motifs and catalyze the unwinding of nucleic acid duplexes and are involved in nucleic acid metabolism. The control of leishmaniasis is becoming increasingly challenging due to the spread of resistance with antileishmanial drugs. Helicases have been targeted to control various pathogens including viruses and for cancer control also. Whole genome of Leishmania donovani is completely sequenced, but annotation of various important genes is still in progress. A bioinformatics-based approach was used to identify the homologues in L. donovani for several human helicase families such as DEAD-box, DEAH-box, DNA repair helicases, MCM, RecQ, and RuvB families. Interestingly, we also identified an UvrD helicase in L. donovani while it was absent in the human host. This detailed genome wide in silico studies of helicases identified various important helicases, which could be used as a potential target to control the replication and transmission of the Leishmania parasite.

Protoplasma, Mar 3, 2020

Malaria is one of the major causes of mortality as well as morbidity in many tropical and subtrop... more Malaria is one of the major causes of mortality as well as morbidity in many tropical and subtropical countries around the world. Although artemisinin combination therapies (ACTs) are contributing to substantial decline in the worldwide malaria burden, it is becoming vulnerable by the emergence of artemisinin resistance in Plasmodium falciparum leading to clinical failure of ACTs in Southeast Asia. Helicases play important role in nucleic acid metabolic processes and have been also identified as therapeutic drug target for different diseases. Previously, it has been reported that P. falciparum contains a group of DEAD-box family of helicases which are homologous to Has1 family of yeast. Here, we present the characterization of a member of Has1 family (PlasmoDB number PF3D7_1419100) named as PfDDX55. The biochemical characterization of PfDDX55C revealed that it contains both DNA-and RNA-dependent ATPase activity. PfDDX55C unwinds partially duplex DNA in 3′ to 5′ direction and utilizes mainly ATP or dATP for its activity. The immunofluorescence assay and q-RT PCR analysis show that PfDDX55 is a nucleocytoplasmic protein expressed in all the intraerythrocytic development of P. falciparum 3D7 strain with maximum expression level in trophozoite stage. The LC-MS/MS experiment results and STRING analysis show that PfDDX55 interacts with AAA-ATPase which has been shown to be involved in ribosomal biogenesis.

Human Genetics, Sep 1, 1994

FEBS Open Bio, Sep 30, 2019

Malaria, a disease caused by infection with parasites of the genus Plasmodium, causes millions of... more Malaria, a disease caused by infection with parasites of the genus Plasmodium, causes millions of deaths worldwide annually. Of the five Plasmodium species that can infect humans, Plasmodium falciparum causes the most serious parasitic infection. The emergence of drug resistance and the ineffectiveness of old therapeutic regimes against malaria mean there is an urgent need to better understand the basic biology of the malaria parasite. Previously, we have reported the presence of parasite-specific helicases identified through genome-wide analysis of the P. falciparum (3D7) strain. Helicases are involved in various biological pathways in addition to nucleic acid metabolism, making them an important target of study. Here, we report the detailed biochemical characterization of P. falciparum parasitespecific helicase 1 (PfPSH1) and the effect of phosphorylation on its biochemical activities. The C-terminal of PfPSH1 (PfPSH1C) containing all conserved domains was used for biochemical characterization. PfPSH1C exhibits DNA-or ribonucleic acid (RNA)-stimulated ATPase activity, and it can unwind DNA and RNA duplex substrates. It shows bipolar directionality because it can translocate in both (3 0-5 0 and 5 0-3 0) directions. PfPSH1 is mainly localized to the cytoplasm during early stages (including ring and trophozoite stages of intraerythrocytic development), but at late stages, it is partially located in the cytoplasm. The biochemical activities of PfPSH1 are upregulated after phosphorylation with PKC. The detailed biochemical characterization of PfPSH1 will help us understand its functional role in the parasite and pave the way for future studies.

Communicative & Integrative Biology, Nov 9, 2013

Scientific Reports, Feb 6, 2019

Human malaria infection is a major challenge across the globe and is responsible for millions of ... more Human malaria infection is a major challenge across the globe and is responsible for millions of deaths annually. Rapidly emerging drug resistant strains against the new class of anti-malarial drugs are major threat to control the disease burden worldwide. Helicases are present in every organism and have important role in various nucleic acid metabolic processes. Previously we have reported the presence of three parasite specific helicases (PSH) in Plasmodium falciparum 3D7 strain. Here we present the detailed biochemical characterization of PfPSH2. PfPSH2 is DNA and RNA stimulated ATPase and is able to unwind partially duplex DNA and RNA substrates. It can translocate in both 3′ to 5′ and 5′ to 3′ directions. PfPSH2 is expressed in all the stages of intraerythrocytic development and it is localized in cytoplasm in P. falciparum 3D7 strain. The dsRNA mediated inhibition study suggests that PfPSH2 is important for the growth and survival of the parasite. This study presents the detailed characterization of PfPSH2 and lays the foundation for future development of PfPSH2 as drug target.