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Bendre AD, Peters PJ, Kumar J. Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM. J Membr Biol 2021; 254:321-341. [PMID: 33954837 PMCID: PMC8099146 DOI: 10.1007/s00232-021-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/23/2021] [Indexed: 12/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target. Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.
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Affiliation(s)
- Ameya D Bendre
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India.
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Anand RS, Ganesan D, Rajasekaran S, Jayavelu T. Astrocytes resolve ER stress through mitochondrial fusion facilitated by biotin availability. Cell Stress Chaperones 2020; 25:945-953. [PMID: 32572785 PMCID: PMC7591659 DOI: 10.1007/s12192-020-01129-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 10/24/2022] Open
Abstract
Structures of cellular organelles are intertwined with their functions that undergo alterations once the organelles are stressed. Since organelle functions are dependent on each other, an organelle-specific stress possibly influences the structure and function of its associated organelles. In this perspective, our study demonstrated that endoplasmic reticulum (ER)-specific stress induced by tunicamycin in primary astroglial culture is associated with altered mitochondrial dynamics and matched with the changes as observed in the aging rat brain. However, the exogenous addition of biotin, a highly lipogenic and mitochondrial vitamin, ameliorates ER stress even though its direct targets are not known within ER. Alternatively, the increased biotinylation of mitochondrial carboxylases preserves its basal respiratory capacity by upregulating mitofusin 2 (Mfn2) and, possibly, its associated role on mitochondrial fusion. Furthermore, the Mfn2 increase by biotin augments physical interaction between ER and functional mitochondria to exchange biomolecules as a part of ER stress resolution. This suggests an increased demand for micronutrient biotin under ER stress resolves the same by undergoing appropriate structural and metabolic contacts between ER and mitochondria. These findings provide a paradigm to resolve stress in one organelle by sustaining the metabolic commitments of another interdependent organelle. The findings also highlight a novel role of biotin in inducing Mfn2 expression and localization under ER stress in addition to its known role as a co-enzyme.
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Panda BB, Sekhar S, Dash SK, Behera L, Shaw BP. Biochemical and molecular characterisation of exogenous cytokinin application on grain filling in rice. BMC Plant Biol 2018; 18:89. [PMID: 29783938 PMCID: PMC5963110 DOI: 10.1186/s12870-018-1279-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 04/03/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Poor filling of grains in the basal spikelets of large size panicles bearing numerous spikelets has been a major limitation in attempts to increase the rice production to feed the world's increasing population. Considering that biotechnological intervention could play important role in overcoming this limitation, the role of cytokinin in grain filling was investigated based on the information on cell proliferating potential of the hormone and reports of its high accumulation in immature seeds. RESULTS A comparative study considering two rice varieties differing in panicle compactness, lax-panicle Upahar and compact-panicle OR-1918, revealed significant difference in grain filling, cytokinin oxidase (CKX) activity and expression, and expression of cell cycle regulators and cytokinin signaling components between the basal and apical spikelets of OR-1918, but not of Upahar. Exogenous application of cytokinin (6-Benzylaminopurine, BAP) to OR-1918 improved grain filling significantly, and this was accompanied by a significant decrease in expression and activity of CKX, particularly in the basal spikelets where the activity of CKX was significantly higher than that in the apical spikelets. Cytokinin application also resulted in significant increase in expression of cell cycle regulators like cyclin dependent kinases and cyclins in the basal spikelets that might be facilitating cell division in the endosperm cells by promoting G1/S phase and G2/M phase transition leading to improvement in grain filling. Expression studies of type-A response regulator (RR) component of cytokinin signaling indicated possible role of OsRR3, OsRR4 and OsRR6 as repressors of CKX expression, much needed for an increased accumulation of CK in cells. Furthermore, the observed effect of BAP might not be solely because of it, but also because of induced synthesis of trans-zeatin (tZ) and N6-(Δ2-isopentenyl)adenine (iP), as reflected from accumulation of tZR (tZ riboside) and iPR (iP riboside), and significantly enhanced expression of an isopentenyl transferase (IPT) isoform. CONCLUSION The results suggested that seed-specific overexpression of OsRR4 and OsRR6, and more importantly of IPT9 could be an effective biotechnological intervention towards improving the CK level of the developing caryopses leading to enhanced grain filling in rice cultivars bearing large panicles with numerous spikelets, and thereby increasing their yield potential.
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Priya P, Yadav A, Chand J, Yadav G. Terzyme: a tool for identification and analysis of the plant terpenome. Plant Methods 2018; 14:4. [PMID: 29339971 PMCID: PMC5761147 DOI: 10.1186/s13007-017-0269-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/19/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data. RESULTS We have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants. CONCLUSIONS Terzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes.
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Affiliation(s)
- Piyush Priya
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Archana Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Jyoti Chand
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA UK
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Sarma S, Lodha M. Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida. BMC Plant Biol 2017; 17:238. [PMID: 29228906 PMCID: PMC5725981 DOI: 10.1186/s12870-017-1177-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND SET is a conserved protein domain with methyltransferase activity. Several genome and transcriptome data in plant lineage (Archaeplastida) are available but status of SET domain proteins in most of the plant lineage is not comprehensively analysed. RESULTS In this study phylogeny and domain organisation of 506 computationally identified SET domain proteins from 16 members of plant lineage (Archaeplastida) are presented. SET domain proteins of rice and Arabidopsis are used as references. This analysis revealed conserved as well as unique features of SET domain proteins in Archaeplastida. SET domain proteins of plant lineage can be categorised into five classes- E(z), Ash, Trx, Su(var) and Orphan. Orphan class of SET proteins contain unique domains predominantly in early Archaeplastida. Contrary to previous study, this study shows first appearance of several domains like SRA on SET domain proteins in chlorophyta instead of bryophyta. CONCLUSION The present study is a framework to experimentally characterize SET domain proteins in plant lineage.
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Affiliation(s)
- Supriya Sarma
- Centre for Cellular and Molecular Biology (CSIR), Uppal Road, Habsiguda, Hyderabad, 500007, India.
| | - Mukesh Lodha
- Centre for Cellular and Molecular Biology (CSIR), Uppal Road, Habsiguda, Hyderabad, 500007, India.
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Rabha M, Sharma S, Acharjee S, Sarmah BK. Isolation and characterization of Bacillus thuringiensis strains native to Assam soil of North East India. 3 Biotech 2017; 7:303. [PMID: 28944151 PMCID: PMC5591175 DOI: 10.1007/s13205-017-0935-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/02/2017] [Indexed: 11/29/2022] Open
Abstract
We have identified both crystalliferous and acrystalliferous Bt isolates from the Assam soil of North East India for the first time. A total of 301 Bacillus type colonies were selected based on their appearance and colony morphology. Out of these colonies, 42 isolates had characteristics similar to Bt isolates on MYP (Mannitol Egg Yolk Polymyxin) agar base medium. The ERIC-PCR and 16S rDNA analyses confirmed that 42 isolates are Bacillus thuringiensis. Phase contrast microscopy showed that 37 isolates produced crystal endospore during the sporulation phase and 5 acrystalliferous isolates were also found. Amplification of cry gene was carried out using general Cry primers along with one cry2 gene specific primer. Out of 42 isolates, 50% of the isolates showed presence of cry2 gene followed by cry9 (40.47) and cry1 (40.47). Moreover, 21.42% of isolates showed the presence of more than one cry genes. We also screened these isolates for the possibility of having new Bt genes using universal primer and found two strains having a new type of Cry1I gene with 82 and 85% similarities with the available Cry1I gene sequences. Thus, these new types of Bt gene could be useful for Bt-based bioformulations and generation of transgenic plants.
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Affiliation(s)
- Mihir Rabha
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Shaswati Sharma
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
- DBT-AAU Centre, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Bidyut Kumar Sarmah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
- DBT-AAU Centre, Assam Agricultural University, Jorhat, Assam 785013 India
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Velmurugan G, Ramprasath T, Swaminathan K, Mithieux G, Rajendhran J, Dhivakar M, Parthasarathy A, Babu DDV, Thumburaj LJ, Freddy AJ, Dinakaran V, Puhari SSM, Rekha B, Christy YJ, Anusha S, Divya G, Suganya K, Meganathan B, Kalyanaraman N, Vasudevan V, Kamaraj R, Karthik M, Jeyakumar B, Abhishek A, Paul E, Pushpanathan M, Rajmohan RK, Velayutham K, Lyon AR, Ramasamy S. Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis. Genome Biol 2017; 18:8. [PMID: 28115022 PMCID: PMC5260025 DOI: 10.1186/s13059-016-1134-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. The diabetogenic nature of organophosphates was recently reported but the underlying molecular mechanism is unclear. We aimed to understand the role of gut microbiota in organophosphate-induced hyperglycemia and to unravel the molecular mechanism behind this process. RESULTS Here we demonstrate a high prevalence of diabetes among people directly exposed to organophosphates in rural India (n = 3080). Correlation and linear regression analysis reveal a strong association between plasma organophosphate residues and HbA1c but no association with acetylcholine esterase was noticed. Chronic treatment of mice with organophosphate for 180 days confirms the induction of glucose intolerance with no significant change in acetylcholine esterase. Further fecal transplantation and culture transplantation experiments confirm the involvement of gut microbiota in organophosphate-induced glucose intolerance. Intestinal metatranscriptomic and host metabolomic analyses reveal that gut microbial organophosphate degradation produces short chain fatty acids like acetic acid, which induces gluconeogenesis and thereby accounts for glucose intolerance. Plasma organophosphate residues are positively correlated with fecal esterase activity and acetate level of human diabetes. CONCLUSION Collectively, our results implicate gluconeogenesis as the key mechanism behind organophosphate-induced hyperglycemia, mediated by the organophosphate-degrading potential of gut microbiota. This study reveals the gut microbiome-mediated diabetogenic nature of organophosphates and hence that the usage of these insecticides should be reconsidered.
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Affiliation(s)
- Ganesan Velmurugan
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India.
| | - Tharmarajan Ramprasath
- Center for Molecular and Translational Medicine, Research Science Center, Georgia State University, Atlanta, GA, 30303, USA
| | - Krishnan Swaminathan
- KMCH Research Foundation, Kovai Medical Centre and Hospital, Coimbatore, Tamil Nadu, 641014, India
| | - Gilles Mithieux
- Institut National de la Santé et de la Recherche Médicale, U1213, Lyon, 69372, France
| | - Jeyaprakash Rajendhran
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Mani Dhivakar
- Department of Immunology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Ayothi Parthasarathy
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - D D Venkatesh Babu
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Leishman John Thumburaj
- Department of Immunology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Allen J Freddy
- Deparment of Zoology, Madras Christian College, Chennai, Tamil Nadu, 600059, India
| | - Vasudevan Dinakaran
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Shanavas Syed Mohamed Puhari
- Department of Biochemistry, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Balakrishnan Rekha
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Yacob Jenifer Christy
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Sivakumar Anusha
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Ganesan Divya
- Department of Biochemistry, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Kannan Suganya
- Department of Microbial Technology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Boominathan Meganathan
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Narayanan Kalyanaraman
- Department of Immunology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Varadaraj Vasudevan
- Department of Biochemistry, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Raju Kamaraj
- Department of Immunology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Maruthan Karthik
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Balakrishnan Jeyakumar
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Albert Abhishek
- Department of Biochemistry, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Eldho Paul
- Department of Biochemistry, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Muthuirulan Pushpanathan
- Laboratory of Gene Regulation and Development, Program in Cellular Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20892, USA
| | - Rajamani Koushick Rajmohan
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Kumaravel Velayutham
- Institute of Diabetes & Endocrinology, Alpha Hospital and Research Centre, Madurai, Tamil Nadu, 625009, India
| | - Alexander R Lyon
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton Hospital and Imperial College, London, UK
| | - Subbiah Ramasamy
- Department of Molecular Biology, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India.
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. Rice (N Y) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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Surendra TV, Roopan SM, Al-Dhabi NA, Arasu MV, Sarkar G, Suthindhiran K. Vegetable Peel Waste for the Production of ZnO Nanoparticles and its Toxicological Efficiency, Antifungal, Hemolytic, and Antibacterial Activities. Nanoscale Res Lett 2016; 11:546. [PMID: 27933594 PMCID: PMC5145819 DOI: 10.1186/s11671-016-1750-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/22/2016] [Indexed: 05/07/2023]
Abstract
Zinc oxide (ZnO) nanoparticles (NPs) are important materials when making different products like sun screens, textiles, and paints. In the current study, the photocatalytic effect of prepared ZnO NPs from Moringa oleifera (M. oleifera) was evaluated on degradation of crystal violet (CV) dye, which is largely released from textile industries and is harmful to the environment. Preliminarily, ZnO NP formation was confirmed using a double beam ultraviolet visible (UV-Vis) spectrophotometer; further, the NP size was estimated using XRD analysis and the functional group analysis was determined using Fourier transform infrared (FT-IR) spectroscopy. The morphology of the synthesized NPs was found to be a hexagonal shape using SEM and TEM analysis and elemental screening was analyzed using EDX. ZnO NPs were shown sized 40-45 nm and spherical in shape. The degradation percentage of ZnO NPs was calculated as 94% at 70 min and the rate of the reaction -k = 0.0282. The synthesized ZnO NPs were determined for effectiveness on biological activities such as antifungal, hemolytic, and antibacterial activity. ZnO NPs showed good antifungal activity against Alternaria saloni and Sclerrotium rolfii strains. Further, we have determined the hemolytic and antibacterial activity of ZnO NPs and we got successive results in antibacterial and hemolytic activities.
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Affiliation(s)
- T V Surendra
- Chemistry of Heterocycles & Natural Product Research Laboratory, Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632 014, Tamilnadu, India
| | - Selvaraj Mohana Roopan
- Chemistry of Heterocycles & Natural Product Research Laboratory, Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632 014, Tamilnadu, India.
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Gargi Sarkar
- Marine Biotechnology and Byproducts Laboratory, Department of Biomedical Sciences, School of Bioscience and Technology, VIT University, Vellore, 632 014, Tamilnadu, India
| | - K Suthindhiran
- Marine Biotechnology and Byproducts Laboratory, Department of Biomedical Sciences, School of Bioscience and Technology, VIT University, Vellore, 632 014, Tamilnadu, India
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Kshetri P, Ningthoujam DS. Keratinolytic activities of alkaliphilic Bacillus sp. MBRL 575 from a novel habitat, limestone deposit site in Manipur, India. Springerplus 2016; 5:595. [PMID: 27247891 PMCID: PMC4864789 DOI: 10.1186/s40064-016-2239-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/27/2016] [Indexed: 12/02/2022]
Abstract
Microbial degradation of keratinous wastes is preferred over physicochemical methods as the latter is costlier and not eco-friendly. Novel habitats are promising for discovery of new microbial strains. Towards discovery of novel keratinolytic bacteria, screening of bacterial strains from a novel limestone habitat in Hundung, Manipur, India was done and a promising isolate, MBRL 575, was found to degrade native chicken feather efficiently. It could grow over a broad pH range (Langeveld et al. in J Infect Dis 188:1782-1789, 2003; Park and Son in Microbiol Res 164:478-485, 2009; Zaghloul et al. in Biodegradation 22:111-128, 2011; Takami et al. in Biosci Biotechnol Biochem 56:1667-1669, 1992; Riffel et al. in J Biotechnol 128:693-703, 2007; Wang et al. in Bioresour Technol 99:5679-5686, 2008) and in presence of 0-15 % NaCl. Based on phenotypic characterization and 16S rRNA gene sequence analysis, the new keratinolytic limestone isolate was identified as Bacillus sp. MBRL 575. It produced 305 ± 12 U/ml keratinase and liberated 120 ± 5.5 mg of soluble peptides and 158 ± 4 mg of amino acids per gram of feather after 48 h of incubation at 30 °C in chicken feather medium. The strain could also degrade feathers of other species besides chicken. The cell-free enzyme was also able to degrade feather. Citrate and soybean meal were found to be the best carbon and nitrogen supplements for enhanced enzyme, soluble peptide and amino acid production. In addition to keratinolytic activity, MBRL 575 also exhibited antagonistic activity against two major rice fungal pathogens, Rhizoctonia oryzae-sativae (65 %) and Rhizoctonia solani (58 %).
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Affiliation(s)
- Pintubala Kshetri
- Microbial Biotechnology Research Laboratory, Department of Biochemistry, Manipur University, Canchipur, 795003 India
| | - Debananda S. Ningthoujam
- Microbial Biotechnology Research Laboratory, Department of Biochemistry, Manipur University, Canchipur, 795003 India
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Mishra RC, Richa, Singh A, Tiwari LD, Grover A. Characterization of 5'UTR of rice ClpB-C/Hsp100 gene: evidence of its involvement in post-transcriptional regulation. Cell Stress Chaperones 2016; 21:271-83. [PMID: 26546418 PMCID: PMC4786525 DOI: 10.1007/s12192-015-0657-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/18/2015] [Accepted: 10/26/2015] [Indexed: 10/22/2022] Open
Abstract
Rice (Oryza sativa) ClpB-C (OsClpB-C) protein is expressed upon heat stress in vegetative tissues and constitutively in seeds. We produced stably transformed Arabidopsis plants carrying β-glucuronidase (Gus) reporter gene downstream to 1-kb OsClpB-C promoter (1kbPro plants). In the 1kbPro plants, expression of Gus transcript and protein followed the expression pattern of OsClpB-C gene in rice plants, i.e., heat induced in vegetative tissues and constitutive in seeds. Next, we produced transgenic Arabidopsis plants containing Gus downstream to 862-bp fragment of OsClpB-C promoter [lacking 138 nucleotides from 3' end of the 5'untranslated region (5'UTR); ∆UTR plants). In ∆UTR plants, Gus transcript was expressed in heat-inducible manner, but strikingly, Gus protein levels were negligible after heat treatment. However, Gus protein was expressed in ∆UTR seedlings at levels comparable to 1kbPro seedlings when recovery treatment of 22 °C/2 h was given post heat stress (38 °C/15 min). This suggests that 5'UTR of OsClpB-C gene is involved in its post-transcriptional regulation and is an obligate requirement for protein expression during persistent heat stress. Furthermore, the Gus transcript levels were higher in the polysomal RNA fraction in heat-stressed seedlings of 1kbPro plants as compared to ∆UTR plants, indicating that 5'UTR aids in assembly of ribosomes onto the Gus transcript during heat stress. Unlike the case of seedlings, Gus protein was formed constitutively in ∆UTR seeds at levels comparable to 1kbPro seeds. Hence, the function of 5'UTR of OsClpB-C is dispensable for expression in seeds.
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Affiliation(s)
- Ratnesh Chandra Mishra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Richa
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Amanjot Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Lalit Dev Tiwari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Gharat SA, Shaw BP. Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants. BMC Plant Biol 2015; 15:301. [PMID: 26714456 PMCID: PMC4696257 DOI: 10.1186/s12870-015-0682-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/13/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Although miRNAs are reportedly involved in the salt stress tolerance of plants, miRNA profiling in plants has largely remained restricted to glycophytes, including certain crop species that do not exhibit any tolerance to salinity. Hence, this manuscript describes the results from the miRNA profiling of the halophyte Suaeda maritima, which is used worldwide to study salt tolerance in plants. RESULTS A total of 134 conserved miRNAs were identified from unique sRNA reads, with 126 identified using miRBase 21.0 and an additional eight identified using the Plant Non-coding RNA Database. The presence of the precursors of seven conserved miRNAs was validated in S. maritima. In addition, 13 novel miRNAs were predicted using the ESTs of two mangrove plants, Rhizophora mangle and Heritiera littoralis, and the precursors of seven miRNAs were found in S. maritima. Most of the miRNAs considered for characterization were responsive to NaCl application, indicating their importance in the regulation of metabolic activities in plants exposed to salinity. An expression study of the novel miRNAs in plants of diverse ecological and taxonomic groups revealed that two of the miRNAs, sma-miR6 and sma-miR7, were also expressed in Oryza sativa, whereas another two, sma-miR2 and sma-miR5, were only expressed in plants growing under the influence of seawater, similar to S. maritima. CONCLUSION The distribution of conserved miRNAs among only 25 families indicated the possibility of identifying a greater number of miRNAs with increase in knowledge of the genomes of more halophytes. The expression of two novel miRNAs, sma-miR2 and sma-miR5, only in plants growing under the influence of seawater suggested their metabolic regulatory roles specific to saline environments, and such behavior might be mediated by alterations in the expression of certain genes, modifications of proteins leading to changes in their activity and production of secondary metabolites as revealed by the miRNA target predictions. Moreover, the auxin responsive factor targeted by sma-miR7 could also be involved in salt tolerance because the target is conserved between species. This study also indicated that the transcriptome of one species can be successfully used to computationally predict the miRNAs in other species, especially those that have similar metabolism, even if they are taxonomically separated.
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Affiliation(s)
- Sachin Ashruba Gharat
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India.
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India.
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