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Umate P.,Plant Molecular Biology Group | Tuteja R.,Plant Molecular Biology Group | Tuteja N.,Plant Molecular Biology Group
Plant Molecular Biology | Year: 2010

Helicases are motor proteins which can catalyze the unwinding of stable RNA or DNA duplex utilizing mainly ATP as source of energy. In this study we have identified complete sets of helicases from rice and Arabidopsis. The helicase gene family in rice and Arabidopsis contains 115 and 113 genes respectively. These helicases were validated based on their annotations and supported with organization of conserved helicase signature motifs. We have also identified homologs of 64 rice RNA and DNA helicases in Arabidopsis, yeast and human. We explored Arabidopsis oligonucleotide array data to gain functional insights into the transcriptome of helicase family members under ten different stress conditions. Our results revealed that expression of helicase genes is profoundly regulated under various stress conditions. The helicases identified in this study lay a foundation for the in depth characterization of each helicase type. © 2010 Springer Science+Business Media B.V.


Gill S.S.,Plant Molecular Biology Group | Tuteja N.,Plant Molecular Biology Group
Plant Physiology and Biochemistry | Year: 2010

Various abiotic stresses lead to the overproduction of reactive oxygen species (ROS) in plants which are highly reactive and toxic and cause damage to proteins, lipids, carbohydrates and DNA which ultimately results in oxidative stress. The ROS comprises both free radical (O2 -, superoxide radicals; OH, hydroxyl radical; HO2, perhydroxy radical and RO, alkoxy radicals) and non-radical (molecular) forms (H2O2, hydrogen peroxide and 1O2, singlet oxygen). In chloroplasts, photosystem I and II (PSI and PSII) are the major sites for the production of 1O2 and O2 -. In mitochondria, complex I, ubiquinone and complex III of electron transport chain (ETC) are the major sites for the generation of O2 -. The antioxidant defense machinery protects plants against oxidative stress damages. Plants possess very efficient enzymatic (superoxide dismutase, SOD; catalase, CAT; ascorbate peroxidase, APX; glutathione reductase, GR; monodehydroascorbate reductase, MDHAR; dehydroascorbate reductase, DHAR; glutathione peroxidase, GPX; guaicol peroxidase, GOPX and glutathione-S- transferase, GST) and non-enzymatic (ascorbic acid, ASH; glutathione, GSH; phenolic compounds, alkaloids, non-protein amino acids and α-tocopherols) antioxidant defense systems which work in concert to control the cascades of uncontrolled oxidation and protect plant cells from oxidative damage by scavenging of ROS. ROS also influence the expression of a number of genes and therefore control the many processes like growth, cell cycle, programmed cell death (PCD), abiotic stress responses, pathogen defense, systemic signaling and development. In this review, we describe the biochemistry of ROS and their production sites, and ROS scavenging antioxidant defense machinery. © 2010 Elsevier Masson SAS.


Macovei A.,Plant Molecular Biology Group | Tuteja N.,Plant Molecular Biology Group
BMC Plant Biology | Year: 2012

Background: Rice (Oryza sativa L.), one of the most important food crop in the world, is considered to be a salt-sensitive crop. Excess levels of salt adversely affect all the major metabolic activities, including cell wall damage, cytoplasmic lysis and genomic stability. In order to cope with salt stress, plants have evolved high degrees of developmental plasticity, including adaptation via cascades of molecular networks and changes in gene expression profiles. Posttranscriptional regulation, through the activity of microRNAs, also plays an important role in the plant response to salinity conditions. MicroRNAs are small endogenous RNAs that modulate gene expression and are involved in the most essential physiological processes, including plant development and adaptation to environmental changes.Results: In the present study, we investigated the expression profiles of osa-MIR414, osa-MIR408 and osa-MIR164e along with their targeted genes, under salinity stress conditions in wild type and transgenic rice plants ectopically expressing the PDH45 (Pea DNA Helicase) gene. The present miRNAs were predicted to target the OsABP (ATP-Binding Protein), OsDSHCT (DOB1/SK12/helY-like DEAD-box Helicase) and OsDBH (DEAD-Box Helicase) genes, included in the DEAD-box helicase family. An in silico characterization of the proteins was performed and the miRNAs predicted targets were validated by RLM-5′RACE. The qRT-PCR analysis showed that the OsABP, OsDBH and OsDSHCT genes were up-regulated in response to 100 and 200 mM NaCl treatments. The present study also highlighted an increased accumulation of the gene transcripts in wild type plants, with the exception of the OsABP mRNA which showed the highest level (15.1-fold change compared to control) in the transgenic plants treated with 200 mM NaCl. Salinity treatments also affected the expression of osa-MIR414, osa-MIR164e and osa-MIR408, found to be significantly down-regulated, although the changes in miRNA expression were limited.Conclusions: Osa-MIR414, osa-MIR164e and osa-MIR408 were experimentally validated for the first time in plants as targeting the OsABP, OsDBH and OsDSHCT genes. Our data showed that that the genes were up-regulated and the miRNAs were down-regulated in relation to salt stress. The negative correlation between the miRNAs and their targets was proven. © 2012 Macovei and Tuteja; licensee BioMed Central Ltd.


Gill S.S.,Plant Molecular Biology Group | Tuteja N.,Plant Molecular Biology Group
Plant Signaling and Behavior | Year: 2010

Environmental stresses including climate change, especially global warming, are severely affecting plant growth and productivity worldwide. It has been estimated that two-thirds of the yield potential of major crops are routinely lost due to the unfavorable environmental factors. On the other hand, the world population is estimated to reach about 10 billion by 2050, which will witness serious food shortages. Therefore, crops with enhanced vigour and high tolerance to various environmental factors should be developed to feed the increasing world population. Maintaining crop yields under adverse environmental stresses is probably the major challenge facing modern agriculture where polyamines can play important role. Polyamines (PAs)(putrescine, spermidine and spermine) are group of phytohormone-like aliphatic amine natural compounds with aliphatic nitrogen structure and present in almost all living organisms including plants. Evidences showed that polyamines are involved in many physiological processes, such as cell growth and development and respond to stress tolerance to various environmental factors. in many cases the relationship of plant stress tolerance was noted with the production of conjugated and bound polyamines as well as stimulation of polyamine oxidation. Therefore, genetic manipulation of crop plants with genes encoding enzymes of polyamine biosynthetic pathways may provide better stress tolerance to crop plants. Furthermore, the exogenous application of PAs is also another option for increasing the stress tolerance potential in plants. Here, we have described the synthesis and role of various polyamines in abiotic stress tolerance in plants. © 2010 Landes Bioscience.


Macovei A.,Plant Molecular Biology Group
Plant signaling & behavior | Year: 2012

Rice (Oryza sativa) represents one of the most important food crops in the world, since it feeds more than two billion people. The increased rice production can play significant roles in upgrading the economic status of countries like India and China. A great deal of research has been carried out in the recent past on the molecular biology, genomics and biotechnology of rice. By employing recombinant DNA technology, remarkable progress had been made towards production of rice plants with increase yield, improved nutritional quality and resistance to various diseases. Under these circumstances, the study of microRNAs can contribute to new discoveries in this field. The miRNAs are assign to modulate gene expression at the post-transcriptional level. They are small, non-coding, single stranded RNAs that are abundantly found in prokaryotic and eukaryotic cells and can trigger translational repression or gene silencing by binding to complementary sequences on target mRNA transcripts. In the recent years, miRNAs have been reported to control a variety of biological processes, such as plant development, differentiation, signal transduction or stress responses. The present review provides an up-date on microRNAs and their involvement in the stress response in rice. A section is specifically dedicated to the genetic engineering perspectives regarding the miRNAs applications in rice tolerance to stress conditions.


Vu T.V.,Plant Molecular Biology Group | Roy Choudhury N.,Plant Molecular Biology Group | Mukherjee S.K.,Plant Molecular Biology Group
Virus Research | Year: 2013

Designing artificial microRNAs (amiRs) targeting the genes responsible for viral replication, transmission and symptom development after viral infection offers a promising strategy to contain the multiplication and spread of geminiviruses in host plants. Here, we report the design of two amiRs targeting the middle region of the AV1 (coat protein) transcript (amiR-AV1-3) and the overlapping region of the AV1 and AV2 (pre-coat protein) transcripts (amiR-AV1-1) of a model geminivirus, Tomato leaf curl virus (ToLCV). Our analyses demonstrate that transgenic tomato plants expressing amiR-AV1-1, propagated until the T2 generation and were highly tolerant to Tomato leaf curl New Delhi virus (ToLCNDV), whereas those harboring amiR-AV1-3 exhibited only moderate tolerance. Biochemical analyses revealed that in these cases, the amiRs acted through the slicing mechanism, cleaving their respective targets. Although ToLCVs are generally difficult targets for manipulations related to virus resistance, our data reveal that an amiR strategy could be employed to protect plants in an effective manner. © 2012 Elsevier B.V.


Vaid N.,Plant Molecular Biology Group | Macovei A.,Plant Molecular Biology Group | Tuteja N.,Plant Molecular Biology Group
Molecular Plant | Year: 2013

The Receptor-Like Kinase (RLK) is a vast protein family with over 600 genes in Arabidopsis and 1100 in rice. The Lectin RLK (LecRLK) family is believed to play crucial roles in saccharide signaling as well as stress perception. All the LecRLKs possess three domains: an N-terminal lectin domain, an intermediate transmembrane domain, and a C-terminal kinase domain. On the basis of lectin domain variability, LecRLKs have been subgrouped into three subclasses: L-, G-, and C-type LecRLKs. While the previous studies on LecRLKs were dedicated to classification, comparative structural analysis and expression analysis by promoter-based studies, most of the recent studies on LecRLKs have laid special emphasis on the potential of this gene family in regulating biotic/abiotic stress and developmental pathways in plants, thus making the prospects of studying the LecRLK-mediated regulatory mechanism exceptionally promising. In this review, we have described in detail the LecRLK gene family with respect to a historical, evolutionary, and structural point of view. Furthermore, we have laid emphasis on the LecRLKs roles in development, stress conditions, and hormonal response. We have also discussed the exciting research prospects offered by the current knowledge on the LecRLK gene family. The multitude of the LecRLK gene family members and their functional diversity mark these genes as both interesting and worthy candidates for further analysis, especially in the field of crop improvement. © 2013 © The Author 2013. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS.


Trivedi D.K.,Plant Molecular Biology Group
Plant signaling & behavior | Year: 2012

Cyclophilin proteins are the members of immunophillin group of proteins, known for their property of binding to the immune-suppressant drug cyclosporin A, hence named as cyclophilins. These proteins are characterized by the presence of peptidyl prolyl isomerase (PPIase) domain which catalyzes the cis-trans isomerisation process of proline residues. In the present study, an in-silico based approach was followed to identify and characterize the cyclophilin family from rice, Arabidopsis and yeast. We were able to identify 28 rice, 35 Arabidopsis and 8 yeast cyclophilin genes from their respective genomes on the basis of their annotation as well as the presence of highly conserved PPIase domain. The evolutionary relationship of the cyclophilin genes from the three genomes was analyzed using the phylogenetic tree. We have also classified the rice cyclophilin genes on the basis of localization of the protein in cell. The structural similarity of the cyclophilins was also analyzed on the basis of their homology model. The expression analysis performed using Genevestigator revealed a very strong stress responsive behavior of the gene family which was more prominent in later stages of stress. The study indicates the importance of the gene family in stress response as well as several developmental stages thus opening up many avenues for future study on the cyclophilin proteins.


Tuteja N.,Plant Molecular Biology Group | Umate P.,Plant Molecular Biology Group | van Bel A.J.E.,Justus Liebig University
Trends in Biotechnology | Year: 2010

Sieve tubes in legumes contain forisomes, which are spindle-like bodies that are composed of ATP-independent, mechanically active proteins. Upon injury, forisomes occlude sieve tubes by dispersion and thus, help to prevent loss of nutrient-rich transport sap. Forisome enlargement by dispersion is brought about by Ca2+-induced conformational changes that confer radial expansion and longitudinal contraction. Forisomes recontract upon Ca2+ removal. In vitro, forisomes reversibly disperse and contract in the presence or absence of Ca2+, respectively, and at distinct pHs. Recently, forisomes have received renewed attention because of their unique capacity to convert chemical into mechanical energy independent of high-energy organic compounds. Forisome-based 'smart' materials can be used to produce self-powered monitoring and diagnostic systems. Here, we focus on physiological, chemical and physical aspects of forisomes and discuss their potential as biomimetic devices. © 2009 Elsevier Ltd. All rights reserved.


Tuteja N.,Plant Molecular Biology Group
Methods in Molecular Biology | Year: 2010

High salinity stress adversely affects plant growth and limits agricultural production worldwide. To minimize these losses it is essential to develop stress-tolerant plants. Several genes, including the genes encoding for helicases, are induced in response to salinity stress. Helicases are ubiquitous motor enzymes that catalyze the unwinding of energetically stable duplex DNA (DNA helicases) or duplex RNA secondary structures (RNA helicases) in an ATP-dependent manner. Helicase members of DEAD-box protein family play essential roles in cellular processes that regulate plant growth and development. Overexpression of one helicase in plant by using Agrobacterium tumefaciens-mediated transformation system confers salinity stress tolerance. To develop the salinity stress tolerant transgenic plants several sequential steps are required including cloning the helicase gene into plant transformation vector, transformation of the gene into Agrobacterium followed by Agrobacterium-mediated transformation of the gene into plant, selection and regeneration of the transgenic plants, confirmation of transgenic plants by PCR or GUS assay, and finally analysis of transgenic plants (T 0 and T 1 generations) for salinity stress tolerance. © 2009 Humana Press, a part of Springer Science+Business Media, LLC.

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