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Publications

From Plant Signaling Lab

  1. Samrat Banerjee, Puja Agarwal, Swarup Roy Choudhury, Sujit Roy (2024) MYB4, a member of R2R3-subfamily of MYB transcription factor functions as a repressor of key genes involved in flavonoid biosynthesis and repair of UV-B induced DNA double strand breaks in Arabidopsis. Plant Physiology and Biochemistry, DOI: 10.1016/j.plaphy.2024.108698

  2. Maria Daniela Torres-Rodriguez Ж, Soon Goo Lee Ж, Swarup Roy Choudhury Ж, Rabindranath Paul, Balaji Selvam, Diwakar Shukla, Joseph M. Jez, Sona Pandey (2024) Structure-function analysis of plant G-protein regulatory mechanisms identifies key Gα-RGS protein interactions. Journal of Biological Chemistry, doi:10.1016/j.jbc.2024.107252

  3.  Mehali Mitra, Samrat Banerjee, Bhagath Kumar Palaka, Swarup Roy Choudhury, Sujit Roy (2024) A nuclear WD40 repeat protein PRL1 regulates stability of MYB4 transcription factor in Arabidopsis. Current Plant Biology,  doi:10.1016/j.cpb.2024.100341

  4. T N V K V Prasad, M Swethasree, G C Satisha, A R Nirmal Kumar, P Sudhakar, B Ravindra Reddy, M Saritha, N Sabitha, B V Bhaskar Reddy, P Rajasekhar, L Prasanthi, B P Girish, Swarup Roy Choudhury (2023) Nanoparticulate silica internalization and its effect on the growth and yield of groundnut (Arachis hypogaea L.). Environmental  Science and Technology, 57: 5881–5890. doi: 10.1021/acs.est.3c00327

  5. Gokul Babu S, Deependra Singh Gohil, Swarup Roy Choudhury* (2023) Genome-wide identification, evolutionary and expression analysis of the cyclin-dependent kinase gene family in peanut. BMC Plant Biology, 23: 43. doi:10.1186/s12870-023-04045-w

  6. Bhagath Kumar Palaka, Swathi Ghantasala, Raju Kuiry, Akancha Shukla, Swarup Roy Choudhury* (2023) Chapter 16 - Phosphorylation-dependent regulation of receptor-like kinases during root nodule symbiosis (RNS). In: Upadhyay SK, Shumayla, eds. Plant Receptor-Like Kinases: Academic Press, 281-303. doi:10.1016/B978-0-323-90594-7.00020-X

  7. Swathi Ghantasala, Swarup Roy Choudhury* (2022) Nod factor perception: an integrative view of molecular communication during legume symbiosis. Plant Molecular Biology, 110:485-509. doi:10.1007/s11103-022-01307-3

  8. Ana Laura Furlan, Esther M Gonzalez, Swarup Roy Choudhury, Santiago Signorelli (2022) Editorial: Drought stress in legumes. Frontiers in Plant Science, 13:1026157. doi: 10.3389/fpls.2022.1026157

  9. Sona Pandey, Kate Harline, Swarup Roy Choudhury (2022) Modification of G-protein biochemistry and its effect on plant/environment interaction. Methods Enzymology, 676:307-324. doi: 10.1016/bs.mie.2022.06.006

  10. Sayanti De, Jismon Jose, Amita Pal, Swarup Roy Choudhury*, Sujit Roy* (2022) Exposure to low UV-B dose induces DNA double-strand breaks mediated onset of endoreduplication in Vigna radiata (L.) R. Wilczek seedlings. Plant and Cell Physiology, 63:463-483. doi: 10.1093/pcp/pcac012

  11. Bhagath Kumar Palaka, Saravanan Vijayakumar, Swarup Roy Choudhury* (2021) Exploring nod factor receptors activation process in chickpea by bridging modelling, docking and molecular dynamics simulations. International Journal of Biological Macromolecules, 189:965-979. doi: 10.1016/j.ijbiomac.2021.08.152

  12. Abhilasha Abhilasha, Swarup Roy Choudhury* (2021) Molecular and physiological perspectives of abscisic acid mediated drought adjustment strategies. Plants (Basel), 10:2769. doi: 10.3390/plants10122769

  13. Jismon Jose, Swarup Roy Choudhury* (2020) Heterotrimeric G-proteins mediated hormonal responses in plants. Cellular Signalling76:109799. doi: 10.1016/j.cellsig.2020.109799

  14. Jismon Jose, Swathi Ghantasala, Swarup Roy Choudhury(2020) Arabidopsis transmembrane receptor-like kinases (RLKs): A bridge between extracellular signal and intracellular regulatory machinery. International Journal of Molecular Sciences, 21:4000. doi: 10.3390/ijms21114000

* Corresponding Author

Ж Equal contribution

Other Publications by Group Leader

  1. Swarup Roy Choudhury, Sona Pandey (2022) SymRK-dependent phosphorylation of Galpha protein and its role in signaling during soybean (Glycine max) nodulation. The Plant Journal, 110:277-291. doi:10-291.10.1111/tpj.15672.

  2. Sona Pandey, Swarup Roy Choudhury, Chien Van Ha, Boominathan Mohanasundaram, Mao Li, Audrey Dodds  (2022) Evolutionarily conserved and non-conserved roles of heterotrimeric Galpha proteins of plants. Plant and Cell Physiology, 63:817-828. doi: 10.1093/pcp/pcac045

  3. Swarup Roy Choudhury, Mao Li, Raj Nandety, Veronica Lee, Kirankumar Mysore, Sona Pandey (2020) Flexible functional interactions between G-protein subunits contribute to the specificity of plant responses. The Plant Journal, 102:207-221. doi: 10.1111/tpj.14714

  4. Swarup Roy Choudhury, Maria Marlin, Sona Pandey (2019a) The role of Gβ Protein in controlling cell expansion via potential interaction with lipid metabolic pathways. Plant Physiology, 179:1159-1175. doi: 10.1104/pp.18.01312

  5. Swarup Roy Choudhury, Sarah M Johns, Sona Pandey (2019b) A convenient, soil-free method for the production of root nodules in soybean to study the effects of exogenous additives. Plant Direct, 3:e00135. doi: 10.1002/pld3.135

  6. Swarup Roy Choudhury, Sona Pandey (2018) Use of hairy root system to study signaling pathways during nodule formation. In: Srivastava V, Mehrotra S, Mishra S, eds. Hairy Roots: An Effective Tool of Plant Biotechnology. Singapore: Springer Singapore. Hairy Roots, An Effective Tool of Plant Biotechnology, Springer Nature Pte Ltd, Chapter 11:243-274. doi:10.1007/978-981-13-2562-5_11.

  7. Seonghee Lee, Clemencia Rojas, Sunhee Oh, Miyoung Kang, Swarup Roy Choudhury, H. K. Lee, R. D. Allen, Sona Pandey, K. S. Mysore (2018) Nucleolar GTP-binding protein 1-2 (NOG1-2) interacts with jasmonate-ZIM domain protein 9 (JAZ9) to regulate stomatal aperture during plant immunity. International Journal of Molecular Sciences, 19:1922. doi: 10.3390/ijms19071922

  8. Jagdeep Kaur, Swarup Roy Choudhury, A. Vijayakumar, L. Hovis, Z. Rhodes, R. Polzin, D. Blumenthal, Sona Pandey (2018) Arabidopsis type III Gγ protein AGG3 is a positive regulator of yield and stress responses in the model monocot Setaria viridis. Frontiers in Plant Science,  9:109. doi: 10.3389/fpls.2018.00109

  9. D. Hackenberg, M. R. McKain, S. G. Lee, Swarup Roy Choudhury, T. McCann, S. Schreier, A. Harkess, J. C. Pires, G. K. Wong, J. M. Jez, E. A. Kellogg, Sona Pandey (2017) Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. New Phytologist, 216:562-575. doi: 10.1111/nph.14180

  10. Biswa R. Acharya Ж, Swarup Roy Choudhury Ж, Anitha Vijayakumar, Aiden Estelle, Laryssa Hovis and Sona Pandey (2017) Optimization of phenotyping assays for the model monocot Setaria viridis. Frontiers in Plant Science8:2172. doi: 10.3389/fpls.2017.02172                                                                                         

  11. Swarup Roy Choudhury, Sona Pandey (2017a) Phosphatidic acid binding inhibits RGS1 activity to affect specific signaling pathways in Arabidopsis. The Plant Journal, 90:466-477. doi: 10.1111/tpj.13503

  12. Swarup Roy Choudhury, Sona Pandey (2017b) Recently duplicated plant heterotrimeric Gα proteins with subtle biochemical differences influence specific outcomes of signal-response coupling. Journal of Biological Chemistry, 292:16188-16198. doi: 10.1074/jbc.M117.793380

  13. Seonghee Lee, Muthappa Senthil-kumar, Miyoung Kang, Clemencia Rojas, Yuhong Tang, Sunhee Oh, Swarup Roy Choudhury, Hee-Kyung Lee, Yasuhiro Ishiga, Randy Allen, Sona Pandey, Kirankumar Mysore (2017) The small GTPase, nucleolar GTP-binding protein 1 (NOG1), has a novel role in plant innate immunity. Scientific Reports, 7:9260. doi: 10.1038/s41598-017-08932-9

  14. Swarup Roy Choudhury, Sona Pandey (2016a) Heterotrimeric G-protein complex and its role in regulation of nodule development. Endocytobiosis and Cell Research, 27: 29-35. 

  15. Swarup Roy Choudhury, Sona Pandey (2016b) Interaction of heterotrimeric G-protein components with receptor-like kinases in plants: an alternative to the established signaling paradigm? Molecular Plant, 9:1093-1095. doi: 10.1016/j.molp.2016.05.012

  16. Swarup Roy Choudhury, Sona Pandey (2016c) The role of PLDα1 in providing specificity to signal-response coupling by heterotrimeric G-protein components in Arabidopsis. The Plant Journal, 86:50-61. doi: 10.1111/tpj.13151

  17. Rafael A. Romero-CastilloЖ, Swarup Roy ChoudhuryЖ, Josefina León-Félix, Sona Pandey (2015) Characterization of the heterotrimeric G-protein family and its transmembrane regulator from capsicum (Capsicum annuum L.). Plant Science234:97-109. doi: 10.1016/j.plantsci.2015.02.007

  18. Swarup Roy Choudhury, Sona Pandey (2015) Phosphorylation-dependent regulation of G-Protein cycle during nodule formation in soybean. Plant Cell27:3260-76. doi: 10.1105/tpc.15.00517

  19. Sophie AlvarezЖ, Swarup Roy ChoudhuryЖ, Kumaran Sivagnanam, Leslie Hicks, Sona Pandey (2015) Quantitative proteomics analysis of Camelina sativa seeds overexpressing the AGG3 gene to identify the proteomic basis of increased yield and stress tolerance. Journal of Proteome Research, 14:2606-16. doi: 10.1021/acs.jproteome.5b00150

  20. Swarup Roy Choudhury, Yuqi Wang, Sona Pandey (2014a) Soya bean Gα proteins with distinct biochemical properties exhibit differential ability to complement Saccharomyces cerevisiae gpa1 mutant. Biochemical Journal, 461:75-85. doi: 10.1042/BJ20131341

  21. Swarup Roy Choudhury, Adam Riesselman, Sona Pandey (2014b) Constitutive or seed-specific overexpression of Arabidopsis G-protein γ subunit 3 (AGG3) results in increased seed and oil production and improved stress tolerance in Camelina sativa. Plant Biotechnology Journal, 12:49-59. doi: 10.1111/pbi.12115

  22. Sophie AlvarezЖ, Swarup Roy ChoudhuryЖ, Sona Pandey (2014) Comparative quantitative proteomics analysis of the ABA response of roots of drought-sensitive and drought-tolerant wheat varieties identifies proteomic signatures of drought adaptability. Journal of Proteome Research13:1688-701. doi: 10.1021/pr401165b

  23. Sujit Roy, Swarup Roy Choudhury, Kalipada Das (2013a) The interplay of DNA polymerase λ in diverse DNA damage repair pathways in higher plant genome in response to environmental and genotoxic stress factors. Plant Signaling & Behavior, 8:e22715. doi: 10.4161/psb.22715

  24. Sujit Roy, Swarup Roy Choudhury, Dibyendu N. Sengupta, Kali Pada Das (2013b) Involvement of AtPolλ in the repair of high salt- and DNA cross-linking agent-induced double strand breaks in Arabidopsis. Plant Physiology, 162:1195-210. doi: 10.1104/pp.113.219022

  25. Swarup Roy Choudhury Ж, Corey S. Westfall Ж, Dieter Hackenberg Ж, Sona Pandey (2013)  Measurement of GTP-binding and GTPase activity of heterotrimeric Gα proteins. G Protein-Coupled Receptor Signaling in Plants: Methods and Protocols, Methods in Molecular Biology, 1043:13-20. doi: 10.1007/978-1-62703-532-3_2

  26. Swarup Roy Choudhury, Sujit Roy, Dibyendu N. Sengupta (2013) C-terminal phosphorylation is essential for regulation of ethylene synthesizing ACC synthase enzyme. Plant Signaling & Behavior, 8:e23000. doi: 10.4161/psb.23000

  27. Swarup Roy Choudhury, Sona Pandey (2013) Specific subunits of heterotrimeric G proteins play important roles during nodulation in soybean. Plant Physiology, 162:522-33. doi: 10.1104/pp.113.215400

  28. Sophie Alvarez Ж, Swarup Roy Choudhury Ж, Leslie Hicks, Sona Pandey (2013) Quantitative proteomics-based analysis supports a significant role of GTG proteins in regulation of ABA response in Arabidopsis roots. Journal of Proteome Research, 12:1487-501. doi: 10.1021/pr301159u

  29. Sujit Roy, Swarup Roy Choudhury, Sanjay Kumar Singh, Kali Pada Das (2012) Functional analysis of light-regulated promoter region of AtPolλ gene. Planta, 235:411-32. doi: 10.1007/s00425-011-1517-6

  30. Swarup Roy Choudhury, Corey S. Westfall, John P. Laborde, Naveen C. Bisht, Joseph M. Jez, Sona Pandey (2012) Two chimeric regulators of G-protein signaling (RGS) proteins differentially modulate soybean heterotrimeric G-protein cycle. Journal of Biological Chemistry, 287:17870-17881. doi: 10.1074/jbc.M112.353219

  31. Swarup Roy Choudhury*, Sujit Roy, Anish Nag, Sanjay Kumar Singh, Dibyendu N. Sengupta (2012) Characterization of an AGAMOUS-like MADS box protein, a probable constituent of flowering and fruit ripening regulatory system in banana. PLoS One, 7:e44361. doi: 10.1371/journal.pone.0044361

  32. Swarup Roy Choudhury, Corey S Westfall, Sona Pandey (2012) The RGS proteins add to the diversity of soybean heterotrimeric G-protein signaling. Plant Signaling & Behavior, 7:1114-7. doi: 10.4161/psb.21298

  33. Swarup Roy Choudhury, S. Roy, D. N. Sengupta (2012) A Ser/Thr protein kinase phosphorylates MA-ACS1 (Musa acuminata 1-aminocyclopropane-1-carboxylic acid synthase 1) during banana fruit ripening. Planta, 236:491-511. doi: 10.1007/s00425-012-1627-9

  34. Sanjay Kumar Singh, Swarup Roy Choudhury, Sujit Roy, Dibyendu N. Sengupta (2011) Understanding DNA repair and recombination in higher plant genome: information from genome-wide screens in Arabidopsis and rice. Plant Signaling & Behavior, 6:120-2. doi: 10.4161/psb.6.1.14215

  35. Sujit Roy, Swarup Roy Choudhury, Sanjay Kumar Singh, Kalipada Das (2011) AtPolλ, a homolog of mammalian DNA polymerase λ in Arabidopsis thaliana is involved in the repair of UV-B induced DNA damage through the dark repair pathway. Plant and Cell Physiology, 52:448-67. doi: 10.1093/pcp/pcr002

  36. Swarup Roy Choudhury*, Sujit Roy, Sanjay Kumar Singh, Dibyendu N. Sengupta (2011) MA-ACS1: A key operator in ethylene biosynthesis in banana - its role and regulation during fruit ripening): International Society for Horticultural Science (ISHS), Leuven, Belgium, Acta Horticulturae (ISHS), 897:187-194, doi: 10.17660/ActaHortic.2011.897.20.

  37. Swarup Roy Choudhury, Naveen C. Bisht, Rheannon Thompson, Oleg Todorov, Sona Pandey (2011)  Conventional and novel Gγ protein families constitute the heterotrimeric G-protein signaling network in soybean. PLoS One6:e23361. doi: 10.1371/journal.pone.0023361

  38. Swarup Roy Choudhury Ж, Sanjay Kumar Singh Ж, Suit Roy, Dibyendu N. Sengupta (2010) An insight into the sequential, structural and phylogenetic properties of banana 1-aminocyclopropane-1-carboxylate synthase 1 and study of its interaction with pyridoxal-5'-phosphate and aminoethoxyvinylglycine. Journal of Bioscience, 35:281-94. doi: 10.1007/s12038-010-0032-4                                                              

  39. Swarup Roy Choudhury*, Sujit Roy, Sanjay Kumar Singh, Dibyendu N. Sengupta (2010) Understanding the molecular mechanism of transcriptional regulation of banana Sucrose phosphate synthase (SPS) gene during fruit ripening: an insight into the functions of various cis-acting regulatory elements. Plant Signaling & Behavior, 5:553-7. doi: 10.4161/psb.11092

  40. Sanjay Kumar Singh, Sujit Roy, Swarup Roy Choudhury, Dibyendu N. Sengupta (2010) DNA repair and recombination in higher plants: insights from comparative genomics of Arabidopsis and rice. BMC Genomics, 11:443. doi: 10.1186/1471-2164-11-443

  41. Swarup Roy Choudhury*, Sujit Roy, Sanjay Kumar Singh, Dibyendu N. Sengupta (2010) Molecular characterization and differential expression of beta-1,3-glucanase during ripening in banana fruit in response to ethylene, auxin, ABA, wounding, cold and light-dark cycles. Plant Cell Reports, 29:813-28. doi: 10.1007/s00299-010-0866-0

  42. Swarup Roy Choudhury, Sujit Roy, Dibyendu N. Sengupta (2009) A comparative study of cultivar differences in sucrose phosphate synthase gene expression and sucrose formation during banana fruit ripening. Postharvest Biology and Technology, 54:15-24. doi:10.1016/j.postharvbio.2009.05.003

  43. Sujit Roy, Sanjay Kumar Singh, Swarup Roy Choudhury, Dibyendu N. Sengupta (2009) An insight into the biological functions of family X-DNA polymerase in DNA replication and repair of plant genome. Plant Signaling & Behavior, 4:678-81. doi: 10.4161/psb.4.7.9077

  44. Swarup Roy Choudhury* Ж, Sujit Roy Ж, Dibyendu N. Sengupta (2009) Characterization of cultivar differences in beta-1,3 glucanase gene expression, glucanase activity and fruit pulp softening rates during fruit ripening in three naturally occurring banana cultivars. Plant Cell Reports, 28:1641-53. doi: 10.1007/s00299-009-0764-5

  45. Sanjay Kumar Singh, Swarup Roy Choudhury, Sujit Roy, Dibyendu N. Sengupta (2008) Sequential, structural, and phylogenetic study of BRCT module in plants. Journal of Biomolecular Structural Dynamics, 26:235-45. doi: 10.1080/07391102.2008

  46. Sujit Roy, Swarup Roy Choudhury, Dibyendu N. Sengupta (2008) Analysis of processivity of mungbean dideoxynucleotide-sensitive DNA polymerase and detection of the activity and expression of the enzyme in the meristematic and meiotic tissues and following DNA damaging agent. Archives of Biochemistry and Biophysics, 475:55-65. doi: 10.1016/j.abb.2008.04.013

  47. Swarup Roy Choudhury, Sujit Roy, Ranjan Das, Dibyendu N. Sengupta (2008) Differential transcriptional regulation of banana sucrose phosphate synthase gene in response to ethylene, auxin, wounding, low temperature and different photoperiods during fruit ripening and functional analysis of banana SPS gene promoter. Planta229:207-23. doi: 10.1007/s00425-008-0821-2

  48. Swarup Roy Choudhury, Sujit Roy, Dibyendu N. Sengupta (2008) Characterization of transcriptional profiles of MA-ACS1 and MA-ACO1 genes in response to ethylene, auxin, wounding, cold and different photoperiods during ripening in banana fruit. Journal of Plant Physiology, 165:1865-78. doi: 10.1016/j.jplph.2008.04.012

  49. Swarup Roy Choudhury, Sujit Roy, Progya Paramita Saha, Sanjay K. Singh, Dibyendu N. Sengupta (2008) Characterization of differential ripening pattern in association with ethylene biosynthesis in the fruits of five naturally occurring banana cultivars and detection of a GCC-box-specific DNA-binding protein. Plant Cell Reports, 27:1235-49. doi: 10.1007/s00299-008-0547-4

                                                                             

                                                                                                                                                                                    *  Corresponding author                                                                                                                                                                                      Ж Equal contribution

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