Functional genomics and crop improvement for stress adaptation

My research focuses on understanding the basis of plant adaptation to drought to improve the productivity of our crops. Under natural environmental conditions, many stresses in combinations such as drought and pathogen or heat affect growth and productivity.

Under stress conditions, the acquired tolerant traits play a crucial role as a measure of cellular level tolerance (CLT). However, many complex process and mechanisms are involved in the regulation of CLT such as maintenance of redox homeostasis, regulation of gene expression, protein turnover, DNA/protein repair mechanisms, etc. The cumulative effect of all these processes results in survival, recovery, and productivity of plants under stress conditions. From this context, the emphasis of our research is on DNA repair and protein turnover mechanisms. The focus is to identify genes and genetic networks associated with protein turnover mechanisms and functional characterization of relevant genes using genome editing tools and chemical genomic approaches.

To maintain the genome integrity under stress DNA repair mechanisms are crucial which can control the epigenetic modifications, genome stability, and longevity, which can also be used to create genetic variability. Genome editing tools will be used to create genetic variability in rice, by targeting DNA mismatch repair genes. The whole genome Indels and drought tolerance in the variants will be assessed.

Emphasis is on Ribosomal proteins and E3 ligases involved in protein degradation mechanisms to improve protein turnover. The extra-ribosomal function of ribosomal proteins in abiotic stress will be studied. Plant E3 ligase targets will be identified and modulate their function using genome editing tools. The role of these genes in combined drought and bacterial blight causing Xanthomonas infection in rice will be studied to understand pathogenicity and improve plant health.
Another emphasis is to develop high throughput (HTP) chemical genomic platform to discover novel small molecules against bacterial pathogens and regulate plant processes under drought to improve crop yields.

• Innovative Young Biotechnologist Award- (IYBA), 2016- 2020, DBT India
• Ramanujan Fellow - DST, SERB -2017-22
• CSIR-senior research Associate (Scientist pool) -December 2016 to April 2017
• Fulbright-Nehru Postdoctoral Fellow- Sept 2014 to June 2016

• Patent file No. 154/CHE/2012, “Selectable marker system”, Ramu S.V, Babitha K.C, Nataraja N Karaba, Udayakumar M,. Indian patent
• Patent file No. 2646/CHE/2014, “An expression construct and its use for increasing abiotic stress tolerance in a plant cell”, Ramu S.V, Babitha K.C, Sheela. H.S, Prasad, T.G, Tuteja N, Udayakumar M,. Indian patent
• Patent file No. 4195/CHE/2014, Herbicide tolerant multigene construct, Ramu S.V, Amaranatha, Reddy V, Udayakumar.M,. Indian Patent

• Garima Pal
  PhD Scholar
  

• Shobhna Yadav
  PhD Scholar
  

• Libin Thomas
  PhD Scholar
  

• Subham Agarwal
  Project JRF
  

• Akashata Dawane
  PhD Scholar
  

Alumni

• Dr Chanchal Kumari (DBT RA)
• Mukund Mendirata (Project assistant)
• Labeena Usmani (Trainee)
• Sai Chandeeramaulee (Trainee)
• Mohammad Ahmar Rashid Khan (Trainee)
• Kishore Ingole (Project JRF)
• Chethan Chauhan (Project fellows)
• Pooja (Project fellows)
• Ocean Khajuria (Trainees )
• Shristi sharma (Project JRF)

• Lekshmy V. S, Preethi V, Karthik N, Arpitha G D, Chaitanya P M, Sathishraj R, Dhananjay Shindhe, Vemanna R S, Xinyou Yin, Paul C. Struik, Sheshshayee Sreeman (2023). Phenotyping and metabolome analysis reveal the role of AdoMetDC and Di19 genes in determining acquired tolerance to drought in rice.Physiologia plantarum. 175, 5:e13992
• Sujitha D, Jalendra Kumar H. G, Thapliayal G, Pal G, Vanitha P. A, Uttarkar A, Patil M, Rajashekar Reddy B. H, Niranjan V, Rayalcheruvu U, Geetha G, Udayakumar M, Vemanna RS. Transcription factors controlling the expression of oxidative stress associated genes in rice (Oryza sativa L.).Plant Biotechnology Reports. 2023. https://doi.org/10.1007/s11816-023-00819-8.
• Saini V, Mehta D, Gupta S, Kumar S, Rani P, Rana K, Rajput K, Jain D, Pal G, Aggarwal B, Pal S, Gupta SK, Kumar Y, Ramu VS, Bajaj A. Targeting Vancomycin-Resistant Enterococci (VRE) Infections and Van Operon-Mediated Drug Resistance Using Dimeric Cholic Acid-Peptide Conjugates.J Med Chem. 2022 Nov 4. doi: 10.1021/acs.jmedchem.2c01293.PMID: 36331380
• Vennapusa AR, Agarwal S, Rao Hm H, Aarthy T, Babitha KC, Thulasiram HV, Kulkarni MJ, Melmaiee K, Sudhakar C, Udayakumar M, Vemanna RS.Stacking herbicide detoxification and resistant genes improves glyphosate tolerance and reduces phytotoxicity in tobacco (Nicotiana tabacum L.) and rice (Oryza sativa L.) Plant Physiol Biochem. 2022.15;189:126-138. doi: 10.1016/j.plaphy.2022.08.025. Epub 2022 Sep 3. PMID: 36084528.
• Garima T, Bhandari MS., Vemanna RS., Pandey S, Meena RK, Barthwal S. (2022).Engineering traits through CRISPR/cas genome editing in woody species to improve forest diversity and yield. Critical Reviews in Biotechnology, DOI: 10.1080/07388551.2022.2092714
• Pal G, Bakade R, Deshpande S, Sureshkumar V, Patil SS, Dawane A, Agarwal S, Niranjan V, PrasannaKumar MK, Vemanna RS. (2022). Transcriptomic responses under combined bacterial blight and drought stress in rice reveal potential genes to improve multi-stress tolerance.BMC Plant Biol 22, 349. https://doi.org/10.1186/s12870-022-03725-3
• Lee S, Vemanna RS, Oh S, Rojas CM, Oh Y, Kaundal A, Kwon T, Lee HK, Senthil-Kumar M, Mysore KS. (2022). Functional role of formate dehydrogenase 1 (FDH1) for host and nonhost disease resistance against bacterial pathogens. PLoS ONE 17(5): e0264917.

• Vanitha PA, Vijayaraghavareddy P, Uttarkar A, Dawane A, Sujitha D, Ashwin V, Babitha KC, Niranjan V, Sheshshayee MS, Anuradha CV, Makarla U, Vemanna RS. (2022) Novel small molecules targeting bZIP23 TF improve stomatal conductance and photosynthesis under mild drought stress by regulating ABA. FEBS J, doi: 10.1111/febs.16461

• Vanitha A, Preethi V, Ashwin V, Sujitha D, Akshay U, Vidya N, Anuradha C V, Sheshshayee M. S, Ramu V. (2022) A Simple and Rapid Oxidative Stress Screening Method of Small Molecules for Functional Studies of Transcription Factor. Rice Science. 2022, 29

• Roy A, Ghosh D, Kasera M, Girish TR, Nori S, Vemanna RS, Mohapatra S, Surya Narayan S, Bhattacharjee S*. (2022) Kappaphycus alvarezii-derived formulations enhance salicylic acid-mediated anti-bacterial defenses in Arabidopsis thaliana and rice. J. Appl. Phycol. https://doi.org/10.1007/s10811-021-02658-y

• Vemanna RS*, Garima P, Sunhee O, and Mysore KS (2021). Proteasomal degradation of JAZ9 by SALT- AND DROUGHT-INDUCED RING FINGER1 during pathogen infection. Molecular Plant-Microbe Interactions, doi.org/10.1094/MPMI-07-21-0192-SC

• Pal G, Mehta D, Singh S, Magal K, Gupta S, Jha G, Bajaj A and Ramu VS (2021). Foliar Application or Seed Priming of Cholic Acid-Glycine Conjugates can Mitigate/Prevent the Rice Bacterial Leaf Blight Disease via Activating Plant Defense Genes. Front. Plant Sci. 12:746912. doi: 10.3389/fpls.2021.746912

• Bakade R, Ingole KD, Deshpande S, Pal G, Patil SS, Bhattacharjee S, Prasannakumar MK, Ramu VS. (2021) Comparative Transcriptome Analysis of Rice Resistant and Susceptible Genotypes to Xanthomonas oryzae pv. oryzae Identifies Novel Genes to Control Bacterial Leaf Blight. Mol Biotechnol, Online ahead of print.

• Karthika V, Babitha K. Chandrashekar, Kiranmai K, Shankar AG, Udayakumar Makarla, and Vemanna S. Ramu, (2021) Disruption in the DNA Mismatch Repair Gene MSH2 by CRISPR-Cas9 in Indica Rice Can Create Genetic Variability. J. Agric. Food Chem. 2021, /doi.org/10.1021/acs.jafc.1c00328

• PreethiV, Nagashree N. Vemanna RS, Raviswamy GH, Dhananjay DS, XinyouYin, Paul C.Struik, Udayakumar M, Sheshshayee MS. (2021) Metabolome profiling reveals impact of water limitation on grain filling in contrasting rice genotypes. Plant Physiology and Biochemistry, 162, 690-698.

• Lekshmy VS, Vijayaraghavareddy P, Nagashree AN, Vemanna RS, Ramegowda V, Makarla U and Sreeman S (2021) Induction of Acquired Tolerance Through Gradual Progression of Drought Is the Key for Maintenance of Spikelet Fertility and Yield in Rice Under Semi-irrigated Aerobic Conditions. Front. Plant Sci. 11:632919

• Vidya N, Akshay Ur, Sujitha D, Akashata D, Ashwin V, Udayakumar M, Vemanna RS (2021) Stress-Induced Detoxification Enzymes in Rice Have Broad Substrate Affinity. ACS Omega, 3399–3410

• Prasannakumar MK, Parivallal BP, Manjunatha C, Pramesh D, Narayan KS, Venkatesh G, Banakar SN, Mahesh HB, Vemanna RS, Rangaswamy KT (2021) Rapid genotyping of bacterial leaf blight resistant genes of rice using loop-mediated isothermal amplification assay. Mol Biol Rep, 48:467

• Vemanna RS, Oh S, Lee HK, Nandety RS, Oh Y, Lee S, Nakashima J, Tang Y, Senthil-Kumar M, Mysore KS. (2020) A novel role of salt and drought induced RING 1 protein in modulating plant defense against hemibiotrophic and necrotrophic pathogens. Mol Plant Microbe Interact, doi: 10.1094/MPMI-09-20-0257-R

• Vemanna RS, Akashata D, Lee S, Oh S, Lee HK, Sun L, Senthil-Kumar M, and Mysore KS (2020) Ribosomal protein QM/RPL10 positively regulates defense and protein translation mechanisms during nonhost disease resistance. Molecular Plant Pathology, https://doi.org/10.1111/mpp.12991

• Kaundal A, Vemanna RS, Mysore KS (2020) The ATPase Activity of Escherichia coli Expressed AAA+-ATPase Protein. BIO-PROTOCOL. 10:15

• Ahmed F, Senthil-Kumar M, Dai X, Vemanna RS, Lee S, Mysore KS, Zhao PX. (2020) pssRNAit-a web server for designing effective and specific plant siRNAs with genome-wide off-target assessment. Plant Physiology. DOI: https://doi.org/10.1104/pp.20.00293

• Preethi V, Vemanna RS, Xinyou Y, Paul CS, Udayakumar M, and Sheshshayee S. (2020) Acquired Traits Contribute More to Drought Tolerance in Wheat Than in Rice. Plant Phenomics, DOI: 10.34133/2020/5905371

• Vemanna R.S*, Preethi V, Nisarga KN, Srivatsava K R , Sheshshayee MS, KS Mysore and Kumar U (2020) Carbonyl cytotoxicity affects plant cellular processes and detoxifying enzymes scavenge these compounds to improve stress tolerance. Journal of Agricultural and Food Chemistry, doi.org/10.1021/acs.jafc.0c02005

• Karthika V, Babitha K.C, Kiranmai K, Shankar A.G, Vemanna R.S* and Udayakumar M (2020) Involvement of DNA mismatch repair systems to create genetic diversity in plants for speed breeding programs. Plant Physiol. Rep. doi.org/10.1007/s40502-020-00521-9

• Thapliyal, G., Vemanna, R.S., Pawar, P.M, Barthwal, S, Meena K.R, Pandey, S, Bhandari M.S. (2020) First record of off-season flowering in Populus deltoides from India: paradigm of climate change indicator. International Journal of Biometeorology. https://doi.org/10.1007/s00484-020-01915-y

• Kumar A.N, Subbarao S, Vennapusa A.R, Ashwin V, Banarjee R, Kulkarni M.J, Ramu V.S, Kumar M.U (2020) Enzymatic and Non‑enzymatic Detoxifcation of Reactive Carbonyl Compounds Improves the Oxidative Stress Tolerance in Cucumber, Tobacco and Rice Seedlings. Journal of Plant Growth Regulation . doi.org/10.1007/s00344-020-10072-w

• Vemanna RS, Bakade R, Bharti P, Kumar MKP, Sreeman SM, Senthil-Kumar M and Makarla U (2019) Cross-Talk Signaling in Rice During Combined Drought and Bacterial Blight Stress Front. Plant Sci. 10:193. doi: 10.3389/fpls.2019.00193 (Review article)

• G Keshavareddy, ARV Kumar, VS Ramu, Methods of Plant Transformation-A Review, Int. J. Curr. Microbiol.App. Sci, (2018) 7 (7), 2656-2668

• G. KeshavareddyG. KeshavareddyA.R.V. KumarA. Makarla Udayakumar, Synthetic cry1AcF Gene Imparts Resistance to Spodoptera litura (F.) and Amsacta albistriga Walker in Peanut (Arachis hypogaea L.) cv. VRI-2 Aug 2018, Int. J. Curr. Microbiol. App. Sci. (2018) 7(8): 2567-2583

• Raksha Singh, Seonghee Lee, Sunhee Oh, Vemanna S Ramu. Hee-Kyung Lee, Muthappa Senthil-Kumar, Wendy Daniela Fernandez-Bohorquez, Clemencia M Rojas, Kirankumar S Mysore, The Nonhost resistance protein 2B that functions in cell wall strengthening during plant immunity is a target for bacterial pathogens. (2018) MPMI-04-18-0094-R

• Amita Kaundal*, Vemanna S Ramu*, Sunhee Oh, Seonghee Lee, Clemencia M. Rojas, Muthappa Senthil-Kumar, Kirankumar S Mysore. Degradation of GCN4 interacting RIN4 and 14-3-3 proteins reduce plasma membrane H+-ATPases activity and regulate stomatal opening and closing during pathogen attack. 2017. Plant cell, 29 (9), 2233-2248, DOI: * Equal contribution as first author

• Preethi V, Vanitha P, Ramu S Vemanna, Sheshshayee MS, Udayakumar M Quantification of Membrane Damage/Cell Death Using Evan’s Blue Staining Technique. Bio-Protocol;. 7, 16, 2017

• Nisarga KN*, Ramu S Vemanna*, Babitha KC, Mohan Raju BM, Udayakumar M. Aldo-ketoreductase 1 (AKR1) improves seed longevity in tobacco and rice by detoxifying reactive cytotoxic compounds generated during ageing. 2017. Rice Journal 10 (1), 11 * Equal contribution as first author

• Ramu S Vemanna*, Babitha, KC, Jayant K Solanki, Amarnatha Reddy V, Sarangi S.K, Udayakumar M. Aldo-keto reductase-1 (AKR1) protect cellular enzymes from salt stress by detoxifying reactive cytotoxic compounds. Plant Physiology and Biochemistry, 2017. 113, 177-186

• Vemanna S. Ramu, Amarnatha Reddy V, Murugesh Easwaran, Babitha K.C., Hanumantha Rao, Kirankumar Ghanti, Kirankumar S. Mysore, Udayakumar M. Aldo-keto reductase enzymes detoxify glyphosate and improve herbicide resistance in plants. 2017, Plant Biotechnology, 15 (7), 794-804

• Vemanna S Ramu, Anjugam Paramanantham, Venkategowda Ramegowda, Basavaiah Mohan-Raju, Makarla Udayakumar and Muthappa Senthil-Kumar. Transcriptome analysis of sunflower genotypes with contrasting oxidative stress tolerance reveals individual- and combined- biotic and abiotic stress tolerance mechanisms. PlosOne 2016, 11 (6), e0157522

• Satish Nagaraj, Muthappa Senthil-Kumar, Vemanna S. Ramu, Keri Wang, Kirankumar S. Mysore. Plant ribosomal proteins, RPL12 and RPL19, play a role in nonhost disease resistance against bacterial pathogens. 2016, Frontiers in Plant Science, 6: 1192. doi: 10.3389/fpls.2015.01192.

• S.V Ramu, Swetha, T.N, H.S.Sheela, K.C. Babitha, P.Chandrashekar reddy, T.G. Prasad, M. Udayakumar. Simultaneous expression of regulatory genes associated with specific drought-adaptive traits improves drought adaptation in peanut. 2015, Plant Biotechnology Journal, doi: 10.1111/pbi.12461.

• K.C. Babitha*, S.V. Ramu*, Karaba N. Nataraja, M. Udayakumar. Overexpression of EcbHLH57 transcription factor from Eleusine coracana L. in tobacco confers tolerance to salt, oxidative and drought stress, 2015, PLOS ONE, 10(9):e0137098. (*Equal contribution as first author)

• K.C. Babitha*, S.V. Ramu*, Karaba N. Nataraja, Sheshshayee, M.S, M. Udayakumar. EcbZIP60, a basic leucine zipper transcription factor from Eleusine coracana L. improves abiotic stress tolerance in tobacco by activating unfolded protein response pathway, 2015, Molecular Breeding, 35:181. (*Equal contribution as first author)

• Amaranatha Reddy Vennapusa, Ramu S. Vemanna, Rajashekar Reddy B. H., K. C. Babitha, K. Kiranmai, A. Nareshkumar, Chinta Sudhakar. An efficient callus induction and regeneration protocol for a drought tolerant rice Indica genotype AC39020. 2015, Journal of Plant Sciences, 3(5): 248-254

• Hema Ramanna, Ramu S. Vemanna, Shivakumar Sreeramulu, Chandrasekhara P. Reddy, Muthappa Senthil-Kumar and Makarla Udayakumar. 2014. Stable expression of mtlD gene imparted multiple stress tolerance in finger millet. 2014, PLOS ONE, 9(6):e99110.

• Ramu S. Vemanna, Babitha K. Chandrashekar, H. M. Hanumantha Rao, Shailesh K. Sathyanarayanagupta, K. S. Sarangi, Karaba N. Nataraja, M. Udayakumar. A modified multisite gateway cloning strategy for consolidation of genes in plants. 2013, Molecular Biotechnology, 53:129–138

• Babitha K. Chandrashekar, Ramu S. Vemanna, Pruthvi V, Patil Mahesh, Karaba N. Nataraja, Makarla Udayakumar. Co-expression of AtbHLH17 and AtWRKY28 Confers Resistance to Several Abiotic Stresses in Arabidopsis. 2013, Transgenic research, 22(2):327-41

• Mahesh Patil, S V Ramu, P Jathish, Rohini Sreevathsa, P Chandrashekar Reddy, T.G Prasad. Overexpression of AtNAC2 in Groundnut (Arachis hypogaea L.) improves abiotic stress tolerance. 2013, Plant Biotechnology Reports, 8(2): 161-169

• Keshavareddy G, Rohini S, S. V. Ramu, Sundaresha S, A. R. V. Kumar, P. Ananda Kumar, Udayakumar Makarla. Transgenics in groundnut (Arachis hypogaea L.) expressing cry1AcF gene for resistance to Spodoptera litura (F.). 2013, Physiology and Molecular Biology of Plants. 19(3):343-52

• S. V. Ramu, S. Rohini, G. Keshavareddy, M. Gowri Neelima, N. B. Shanmugam, A. R. V. Kumar,S. K. Sarangi, P. Ananda Kumar & M. Udayakumar. Expression of a synthetic cry1AcF gene in transgenic Pigeon pea confers resistance to Helicoverpa armigera. 2012, J of Applied Entomology. 136(9): 675–687

• S.V. Ramu, K.C. Babitha, K.S. Shailesh, Karaba N Nataraja and M. Udayakumar. Modification of alkaline lysis method for rapid plasmid DNA isolation. 2011, Current biotica. Vol 4 Issue 3, ISSN 0973-4031

• M.Gowri neelima, S.V. Ramu, Rohini Sreevthsa, B.M. Asha Rani, A.R.V. Kumar, M.C. Gayathri. Inplanta transformation strategy to generate transgenic plants in chick pea: proof of concept with a cry gene. 2008, Indian Journal of Plant Biology, Vol 35, No 3, 201-206

• 23. Mahesh salimat and Ramu.S.V. Fate of nutrients in Food. 2009, AGROBIOS Newsletter. Vol VIII, Issue No.3, p62-63 agrbiosindia.

Book chapters

• Udayakumar M, Ramu S Vemanna, D Prathibha, Gowsiya Shaik, S Mahesh, GJ Pavithra, MS Sheshshayee. Adaptation of Crops to Climate Change: Relevant Mechanisms and their Genetic Enhancement. Agriculture under Climate Change: Threats, Strategies and Policies. Allied Publishers. 2017, 1: 126

• Ramu S Vemanna, Babitha K C, Kirankumar S Mysore. RNAi and microRNA technologies to combat plant insect pests. Chandrakanth Emani (Ed). The biology of plant-insect interactions: a compendium for plant biotechnologists. Science Publishers/CRC Press, Taylor & Francis Group: ISBN 9781498709736. 150-177

• Ramu SV, Rohini Sreevathsa, Sarangi S.K, Udayakumar M. Plant protection through RNAi: Alternative for pesticides and chemical approaches to pest control. In book Genetically Engineered Crops: Biotechnology, Biosafety and Benefits. Lindsay M. Grover(Ed) Nova publications. 2010, (ISBN: 978-1-61122-526-6)