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Research Interests

Our main research focus areas come under physiological and molecular aspects of how vegetative developmental events are regulated in plants. We use rice, Arabidopsis and the mangrove tree Avicennia officinalis for our experiments. Our research projects span physiological and molecular aspects of plant development.

We work on plant hormone signaling (with special focus on gibberellins and abscisic acid) and shoot development representing the genetic pathway of gibberellin signaling (e.g., RGL2-DOF6 protein complex inducing the expression of GATA12 gene) that affects primary seed dormancy. Additionally, we study selected gibberellin signal transduction intermediates in the regulation of primary seed dormancy.

We also aim to improve leafy vegetable species such as kailan (Brassica oleracea var alboglabra) by gene editing efforts to improve their phytonutrient contents (glucosinolates), vegetative growth and plant architecture.

Another key research interest in our lab is to understand the salt secretion and salt ultrafiltration mechanisms in the mangrove tree Avicennia officinalis. We focused on aquaporins and ion transporters from the mangrove. Based on this knowledge, we designed synthetic pores that can be used for biomimetic membrane preparation. We are also attempting to apply the molecular mechanisms discovered to crop plants such as rice with a view of enhancing their salinity tolerance.

Besides helping to gain a better understanding of plant development, we hope that our work can contribute towards crop improvement in the long-term.

Research Accomplishments

We showed that the GA signaling intermediate protein RGL2 (a DELLA protein) has positive influence on transcription of downstream target genes. Also, we identified DOF6 transcription factor as the novel partner of RGL2  (DELLA) to activate GATA12 gene in the process of regulating seed germination. This study has helped to describe a novel molecular mechanism of regulation of seed germination by GA.

We are studying selected genes for improvement of rice crop with special interest on salt tolerance mechanism and plant architecture. Another aspect of study is to understand salt exclusion and secretion mechanisms in the mangrove plant Avicennia. The broader objectives of the study with mangroves include understanding the salinity tolerance mechanism in plants. Related to this, we identified a novel molecular mechanism downstream of ABA signaling that confers salt tolerance in rice mediated by trehalose-6-phosphate synthase (OsTPS8) and the rice SnRK gene SAPK9. Overexpressing SAPK9 gene alone could confer salt tolerance, suggesting that this is a key intermediate in the process. This tolerance was associated with increased suberin deposition in the endodermis and exodermis cells of the rice roots, which is a physical mode of action to exclude salt uptake by the roots. The link to suberin deposition in the root endodermis layer was also a common mechanistic change associated with enhanced salt tolerance with the involvement of several differentially expressed CYP genes in the mangrove and Arabidopsis systems.

We uncovered a novel mechanism of plant adaptation to salt stress involving the NaCl-induced translocation of a specific chloride channel protein, AtCLCf. This work revealed that AtCLCf protein is made and stored in the endomembrane system (the Golgi apparatus) under normal growth conditions. When the root cells are treated with salt, AtCLCf gets translocated to the plasma membrane with the help of a small GTPase named AtRABA1b or BEX5. Thus, in the root cells the chloride channel helps to secrete excess chloride ions. This study also helped to identify a transcription factor, AtWRKY9, which directly regulates the expression of the AtCLCf gene under salt stress. This represents a novel mechanism to increase plant’s salinity tolerance, and this information will be useful for crop improvement.

The long-term goal of our research program is to better understand the physiological and molecular genetic mechanisms of vegetative shoot development. Additionally, some of the findings may be applicable for biotechnological improvement of crop species. Our attempts to improve leafy vegetable crops (e.g., kailan) by selected gene editing efforts to enhance their nutritional (glucosinolate content) or agronomic traits (increased biomass by modifying branching pattern) help to address these objectives. Such efforts are also envisaged to improve vegetable varieties for indoor farming application.

Current Projects

Our current research projects come under the following themes:

1. Cloning genes that regulate primary seed dormancy and plant development.

2. Phytohormone (gibberellin & abscisic acid) signaling intermediates and plant development.

3. Transgenic plants for functional analysis of selected cDNA.

4. Mechanism of salt secretion in the mangrove Avicennia officinalis.

5. Synthesis of pores for water and ion transport on biomimetic membranes.

Research Accomplishments

Full List of Publications

Membership on Editorial Boards

1. Editor – Plant Cell Reports (Springer) – Jan 1999-onwards.

2. Associate Editor – Plant Biotechnology Reports (Springer), – Nov 2009-onwards.

3. Editorial Board Member – BMC Plant Biology –Feb 2015-May 2024.

4. Editorial Board Member – Frontiers in Plant Science –Oct 2014-Oct 2016.

5. Editor – Plant Biotechnology Reports (Springer), April 2007-Nov2009.

6. Reviews Editor – Plant Cell Reports (Springer), additional responsibility April 2002-Nov 2008.

7. Editor – Plant Cell Tissue and Organ Culture (Springer), Jan 1999 to Feb 2006.

 

Selected Publications

1. Rajappa S, Krishnamurthy P, Huang H, Yu D, Friml J, Xu J, Kumar PP. The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. Nature Communications (2024) 15:3978 – doi.org/10.1038/s41467-024-48234-z

2. Vishal B, Krishnamurthy P, Kumar PP. Arabidopsis class II TPS controls root development and confers salt stress tolerance through enhanced hydrophobic barrier deposition. Plant Cell Reports (2024) 43:115 doi.org/10.1007/s00299-024-03215-w

3. Yang Y, He T, Ravindran P, Wen F, Krishnamurthy P, Wang L, Zhang Z, Kumar PP, Chae E, Lee C. All-organic transparent plant e-skin for non-invasive phenotyping. Science Advances (2024) 10, eadk7488, doi.org/10.1126/sciadv.adk7488

4. Dutta C, Krishnamurthy P, Su D, Yoo SH, Collie GW, Pasco M, Marzinek JK, Bond PJ, Verma C, Grélard A, Loquet A, Li J, Luo M, Barboiu M, Guichard G, Kini RM, Kumar PP. 2023. Nature-inspired synthetic oligourea foldamer channels allow water transport with high salt rejection. Chem (Cell Press) (2023) 9:2237-2254.

5. Verma V, Vishal B, Kohli A, Kumar PP. Systems-based rice improvement approaches for sustainable food and nutritional security. Plant Cell Reports (2021) 40:2021–2036.

6. Krishnamurthy P, Vishal B, Ho WJ, Lok CJF, Lee F, Kumar PP. Regulation of CYP94B1 by WRKY33 controls root apoplastic barrier formation leading to salt tolerance. Plant Physiology (2020) 184:2199-2215.

7. Ravindran P, Kumar PP. Regulation of seed germination: The involvement of multiple forces exerted via gibberellic acid signalling. Mol Plant (2019) 12: 24-26.

8. Vishal B, Krishnamurthy P, Ramamoorthy R, Kumar PP. OsTPS8 controls yield-related traits and confers salt stress tolerance in rice by enhancing suberin deposition. New Phytologist 221: 1369–1386 (doi: 10.1111/nph.15464).

9. Ravindran P, Verma V, Stamm P, Kumar PP. A novel RGL2-DOF6 complex contributes to primary seed dormancy in Arabidopsis thaliana by regulating a GATA transcription factor. Molecular Plant (2017) http://dx.doi.org/10.1016/j.molp.2017.09.004.

10. Verma V, Sivaraman J, Srivastava AK, Sadanandom A, Kumar PP. Destabilization of interaction between cytokinin signaling intermediates AHP1 and ARR4 modulates Arabidopsis development. New Phytologist (2015) 206: 726–737 doi: 10.1111/nph.13297

11. Krishnamurthy P, Jyothi-Prakash PA, Lin Qin, He J, Lin Q, Loh CS, Kumar PP. Role of root hydrophobic barriers in salt exclusion of a mangrove plant Avicennia officinalis. Plant, Cell & Environment(2014) 37:1656–1671.

12. Kohli A, Sreenivasulu N, Lakshmanan P, Kumar PP. The phytohormone crosstalk paradigm takes center stage in understanding how plants respond to abiotic stresses. Plant Cell Reports (2013) 32:945-957 DOI: 10.1007/s00299-013-1461-y

13. Tan W-K, Lin Q, Lim TM, Kumar PP, Loh CS. Dynamic secretion changes in the salt glands of the mangrove tree species Avicennia officinalis in response to a changing saline environment. Plant, Cell & Environment (2013) 36:1410-1422. DOI: 10.1111/pce.12068

14. Stamm P, Ravindran P, Mohanty B, Tan EL, Yu H, Kumar PP. Insights into the molecular mechanism of RGL2-mediated inhibition of seed germination in Arabidopsis thaliana. BMC Plant Biology (2012) 12:179 doi:10.1186/1471-2229-12-179 (http://www.biomedcentral.com/1471-2229/12/179).

15. Stamm P, Kumar PP. The phytohormone signal network regulating elongation growth during shade avoidance. Journal of Experimental Botany (2010) 61: 2889-2903.

16. Xu Y, Teo LL, Zhou J, Kumar PP, Yu H. Floral organ identity genes in the orchid Dendrobium crumenatum. Plant Journal (2006) 46: 54-68.

17. Yu H, Ito T, Zhao Y, Peng J, Kumar PP, Meyerowitz EM. Floral homeotic genes are targets of gibberellin signaling in flower development. Proc. Natl. Acad. Sci., USA (2004) 101:7827-7832.

18. Zhang P, Pwee KH, Tan HT, Kumar PP. Conservation of class C function of floral organ development during 300 million years of evolution from gymnosperms to angiosperms. Plant Journal (2004) 37: 566-577.

19. Yu H, Xu Y, Tan EL, Kumar PP. 2002. AGAMOUS-LIKE 24, a dosage-dependent mediator of the flowering signals. Proc. Natl. Acad. Sci., USA. 99:16336-16341.

20. Prakash AP, Kumar PP. 2002. PkMADS1 is a novel MADS-box gene regulating adventitious shoot induction and vegetative shoot development in Paulownia kawakamii. Plant Journal 29:141-151.