Research Groups

Neeti Sanan Mishra

Plant RNAi Biology

Group Leader

Research Interests and Description

Group Members

Neeti Sanan-Mishra

International Centre for Genetic Engineering and Biotechnology
Aruna Asaf Ali Marg
110 067 New Delhi, India

E-mail: neetiicgeb.res.in
Tel: +91-11-26741358, ext. 280
Fax: +91-11-26742316

Education

Jawaharlal Nehru University, New Delhi, India, PhD, 1997
Jawaharlal Nehru University, New Delhi, India, MSc, 1992
University of Delhi, India, BSc, 1990

Career History

Since 2016- Group Leader, Plant RNAi Biology,International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
2006-2015, Staff Research Scientist, Plant Molecular Biology, ICGEB, New Delhi, India
2000-2005, Research Associate, ICGEB, New Delhi, India
1998-1999, Research Scientist, University of Delhi, South Campus, New Delhi, India

Teaching Activity

ICGEB PhD Course on "Molecular Biology of Plant Stress"

Scientific Activity

The Group is involved in understanding the RNAi mechanisms operative in plants in response to increasing abiotic stress factors (salt, high temperature, drought) and virus infection. The endeavour is to use this knowledge for crop improvement and protection through employing RNAi based technology. This assumes importance in the era of global climate change, as crop productivity is being affected by rise in temperature, accompanied by increase in soil salinity, decline in fresh water and high incidence of virus infection. Thus new approaches are required to address the emerging challenges for sustainable agriculture.

The microRNAs (miRs) play an important regulatory role in plant development and adaptation towards stresses. Thus, it is proposed to identify the miRs that may play a key role under multiple environmental stresses to deregulate the metabolic circuits related to grain yield. This will not only contribute to basic knowledge but also provide new insights into the mechanisms regulating grain yield. Thus research activities have been directed towards:

i) Genome-wide profiling of the miR expression with the aim to tap the natural variation existent in Indian rice cultivars. The knowledge gained was used to create a miRNA:mRNA database for rice called ARMOUR, that is available as a free web resource. This comprehensive database covers 689 known and 1664 predicted novel miRs along with their predicted target transcripts. The understanding of miR interactome in regulation of functional cellular machinery is supported by the information on the GO annotation and the associated biological pathways.
To decipher the detailed miR-dependent regulatory circuits operative in response to salt stress we performed comparative and integrated data-mining using natural rice varieties and transgenic lines with contrasting behaviors in response to salt-stress (JIB 2017, 14(1), 1613; Curr Genomics 2017, 19(1): 21-35). The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRs, their targets and the associated metabolic pathways. The global profiles clearly indicate a difference in the genetic regulation of salt-susceptible and salt-tolerant rice varieties. By comparing the data within the genetically similar backgrounds using the Gly-transgenics in which salt-tolerance was artificially engineered, the changes in the regulatory networks were apparent. The overall analysis revealed modulation of many biological pathways, which are involved in salt tolerance and play an important role in plant phenotype and physiology.
The study was extended to profile the drought and salt stress deregulated miRs in 11 elite sorghum genotypes (Gene Exp Patterns 2016, 20(2), 88-98). The dynamic expression patterns were indicative of prevailing stress tolerant mechanisms present in these sorghum accessions. This data provides insights into sorghum miRs, which may have potential use in improving drought tolerance in crops. A similar study was performed to comprehend the regulatory miR networks involved in ToLCV infection in tomato. Healthy and infected leaf tissues of two tomato varieties, differing in their susceptibility to ToLCV infection were analyzed.

ii) Functional analysis of specific miRs by generating over-expressing or knockout lines to follow their effect on plant stress responses. The translation of the knowledge genearted is in progress by raising miRNA over-expressing rice plants. This will be useful to gain fundamental knowledge of plant responses to the environment leading to a range of applications for improving plant adaptation and sustaining yields. The amiR approach is also being used in translation studies to engineer plants resistance to virus infection as well as to improve the plant quality for biofuel and fiber production by reducing the lignin content (PMB 2015, 89(4), 511-52; Sci Rep 2017, 7, 39984). Transgenic jute lines with reduced expression of genes involved in lignin biosynthetic pathway were found to have lowered lignin content, altered lignin composition, increase in total cellulose content and improvement, albeit small in enzymatic saccharification. Moreover, none of these alterations led to any growth compensation.
Understanding the role of induction and suppression of miRs in plant viral diseases. To gain an insight into the mechanism of miRNA (dis)-regulation studies are being done using viral suppressors of RNAi. This work involves understanding the role of suppressors in local and systemic silencing of miRNAs and identification of host interacting factors to gain an understanding of the suppressor mediated action. Suppressor overexpressing transgenic lines have been generated to follow the effects on miRNA expression profiles.

Selected publications

Goswami K., Tripathi A., Gautam B., Sanan-Mishra N. 2018. Impact of Next Generation Sequencing in elucidating the role of microRNA related to multiple abiotic stresses, In: Plant Abiotic Stress: Molecular Biology and Biotechnological Advances. Eds A. Roychoudhury and D.K. Tripathi. Wiley. In Press.

Kumar R., Kumar S., Sanan-Mishra N. 2018. miRNAs: the game changer in producing salinity stress tolerant crops. In: Salinity responses and tolerance in plants Vol. II. Eds: V. Kumar, S.H. Wani, P. Suprasanna and L.S. Tran, Springer Cham. PubMed Link

Sanan-Mishra N., Tripathi A., Goswami K., Shukla R.N., Vasudevan M., Goswami H. 2018. ARMOUR - a rice miRNA : mRNA interaction resource. Frontiers Plant Sci. 9, 602. Pubmed Link

Gautam B., Goswami K., Sanan-Mishra N., Wadhwa G., Singh S. 2018. The Role of Bioinformatics in Epigenetics. In: Wadhwa G., Shanmughavel P., Singh A., Bellare J. (eds) Current trends in Bioinformatics: An Insight. Springer, Singapore. Pubmed Link

Sahu A.K., Verma R.K., Gaur R.K., Sanan-Mishra N. 2018. Complexity and recombination analysis of novel begomovirus associated with Spinach yellow vein disease in India. Plant Gene. 13, 42-49. PubMed Link

Singh A.K., Furtado A., Brozynska M., Sanan-Mishra N., Henry R.J. 2018. Phylogeney and molecular evolution of miR820 and miR396 microRNA families in Oryza AA genomes. Tropical Plant Biol. 11, 1-16. PubMed Link

Tripathi A., Goswami K., Tiwari M., Mukherjee S.K., Sanan-Mishra N. 2018. Identification and comparative analysis of novel microRNAs from tomato varieties showing contrasting response to ToLCV infections. Physiol Mol Biol Plants. 24, 185-202. PubMe Link

Das S.S., Yadav S., Singh A., Gautam V., Sarkar A.K., Nandi A.K., Karmakar P., Majee M., Sanan-Mishra N. 2018. Dynamic expression of miRNAs and their targets in seed germination conditions reveals miR390-tasiR-ARF module as regulator of seed germination. Scientific Reports. 8,1233. PubMed Link

Tripathi A., Chacon O., Singla-Pareek S.L., Sopory S.K., Sanan-Mishra N. 2018. Mapping the microRNA expression profiles in glyoxalase over-expressing salinity tolerant rice. Current Genomics. 19, 21-35. PubMed Link

Khan A., Goswami K., Sopory S.K., Sanan-Mishra N. 2017. Mirador on the potential role of miRNAs in synergy of light and heat networks. Indian J Plant Physiol. 22, 587–607. PubMed Link

Hernandez Y., Sanan-Mishra N. 2017. miRNA mediated regulation of NAC Transcription factors in plant development. Plant Gene. 11B, 190-198. PubMed Link

Goswami K., Tripathi A., Sanan-Mishra N. 2017. Comparative miRomics of salt-tolerant and salt-sensitive rice. Journal of Integrative Bioinformatics. 14, 1-18. PubMed Link

Sanan-Mishra N., Chakraborty S., Gupta D., Mukherjee S.K. 2017. RNAi suppressors: Biology and Mechanisms. In Plant Epigenetics, RNA Technologies Eds N Rajewsky, S. Jurga, J. Barciszewski, Springer Nature. 199-230. PubMed Link

Sharma N., Mittal D., Sanan-Mishra N. 2017. Micro-Regulators of Hormones and Stress. In “Mechanism of Plant Hormone Signaling under Stress. Volume 2.” Ed G. K. Pandey, John Wiley & Sons, Inc., Hoboken, NJ, USA pp 319-351. PubMed Link

Sinha V., Anand A., Mukherjee S.K., Sanan-Mishra N. 2017. RNAi based strategies for enhancing plant resistance to virus infection. In: Advances in Biotechnology. Eds: A. Datta, M. Fakruddin, H.M.N. Iqbal and J. Abraham. Open Access eBooks: Chapter 4. PubMed Link

Djami-Tchatchou A.T., Sanan-Mishra N., Ntushelo K., Dubery I.A. 2017. Functional roles of microRNAs in agronomically important plants – potential as targets for crop improvement and protection. Frontiers Plant Sci. 8, 378.  PubMed Link

Shafrin F., Ferdous A.S., Sarkar S.K., Ahmed R., Al-Amin, Zaman A., Hossain K., Sarker M., Rencoret J., Gutiérrez A., del Rio J.C., Sanan-Mishra N., Khan H. 2017. Modification of monolignol biosynthetic pathway in jute: different gene, different consequence. Sci Reports. 7, 39984. PubMed Link

Mathur K., Anand A., Dubey S.K., Sanan-Mishra N., Bhatnagar R., Sunil S. 2016. Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity. Scientific Reports. 6, 38065. PubMed Link

El Sanousi R.S., Hamza N.B., Abdelmula A.A., Mohammed I.A., Seif M.G., Sanan-Mishra N. 2016. Differential expression of miRNAs in Sorghum bicolor under drought and salt stress.  American J Plant Sci. 7, 870-878.PubMed Link

Hamzaa N.B., Sharma N., Tripathi A., Sanan-Mishra N. 2016. MicroRNA expression profiles in response to drought stress in Sorghum bicolor. Gene Expression Patterns. 20, 88-98. PubMed Link

Mittal D., Sharma N., Sharma V., Sopory S.K., Sanan-Mishra N. 2016. Role of microRNAs in rice plant under salt-stress. Annals Applied Biol 168, 2-18. PubMed Link

Saraf S., Sanan-Mishra N., Gursanscky N.R., Carroll B.J., Gupta D., Mukherjee S.K. 2015. 3’ and 5’ microRNA-end post-biogenesis modifications in plant transcriptomes: evidences from small RNA next generation sequencing data analysis. Biochem Biophys Res Commun 467, 892-899. PubMed link

Shafrin F., Das S.S., Sanan-Mishra N., Khan H. 2015. Artificial miRNA- mediated down-regulation of two monolignoid biosynthetic genes (C3H and F5H) cause reduction in lignin content in jute. Plant Mol Biol 89, 511-552. PubMed link

Tripathi A., Goswami K., Sanan-Mishra N. 2015. Role of bioinformatics in establishing miRs as modulators of abiotic stress responses: the new revolution. Front Physiol 6, 286. PubMed link

Das S.S., Karmakar P., Nandi A.K., Sanan-Mishra N. 2015. Small RNA mediated regulation of seed germination. Front Plant Sci 6, 828. PubMed link

Kumar V., Karjee S., Rehman J., Taneja J., Sundaresan G., Sanan-Mishra N., S.K. Mukherjee. 2015. Mungbean yellow mosaic Indian virus encoded AC2 protein suppresses RNA silencing by inhibiting Arabidopsis RDR6 and AGO1 activities. Virology. 486, 158–172. PubMed link

Ngoc T.T., Sanan-Mishra N. (2015) Effect of antibiotics on callus regeneration during transformation of IR 64 rice. Biotechnology Reports. 7, 143-149. PubMed Link

Sharma N., Panchal S., Sanan-Mishra N. (2015) Protocol for artificial microRNA mediated over-expression of miR820 in indica rice. American J Plant Sci. 6, 1951.PubMed Link

Sharma N., Tripathi A., Sanan-Mishra N. (2015) Profiling the expression domains of a rice-specific microRNA under stress. Frontiers Plant Sci. 6, 333.PubMed Link

El Sanousi R.S., Abdelmula A.A., Mohammed I.A., Sanan-Mishra N., Hamza N.B. (2015) Evaluation of Performance and Variability of Six Sorghum Genotypes under Salinity Stress. International J Res Studies Biosci. 3, 23-27. PubMed Link

Das S.S., Sanan-Mishra N. (2015) A direct method for genetically transforming rice seeds with suppressors of RNAi. Plant Cell Tissue and Organ Culture: (J Plant Biotechnol). 120, 277-289. PubMed Link

Rahman J., Sanan-Mishra N., Mukherjee S.K. (2014) RNAi-hairpin mediated gene silencing and suppression of the silencing with Geminivrial MYMIV-AC2 protein. Plant Biotechnol Reports 8, 337-347

Das S.S., Sanan-Mishra N. (2014) Comparative analysis of RNAi Suppression Activity of proteins from two disparate viruses. American J Plant Sci 5, 1789-1798. PubMed Link

Kumar, V., Anand, A., Mukherjee, S.K., Sanan-Mishra, N. 2013. Engineering Viral Suppressors of RNA Silencing: requirement and applications. In “Genetically Engineered Crops in Developing Countries.” Eds A. Kumar, G. Lobenstein and D.V.R. Reddy, Studium Press Texas, USA.

Ngoc, T.T., Ta, H.A., Nang, V.D., Sanan-Mishra, N. 2013. Isolation and molecular analysis of SRBSDV isolates infecting rice in Vietnam. Asian J Agri Food Sci. 1, 5, 258-263. PubMed Link

Anand, A., Mukherjee, S.K., Sanan-Mishra, N. 2013. Tools for pathogenicity: virus encoded RNA silencing suppressors. In “Recent Microbial pathogens and strategies for combating them: science, technology and education” Microbiology Book Series, number 4. Ed A. Mendez-Vilas, Formatex Research Center, Spain 751-763. PubMed Link

Sanan-Mishra, N., Karjee, S., Mukherjee, S.K. 2013. RNAi technology. In “Biotechnology in Medicine and Agriculture: Principles and Practices”, Eds Kumar A., Pareek A., Gupta SM., I.K. International Publishing House, India pp 316-337

ICGEB New Delhi

ICGEB Campus
Aruna Asaf Ali Marg
110 067 New Delhi
INDIA
Tel: +91-11-26741358/1007
Fax: +91-11-26742316
icgebicgeb.res.in

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