Publications

Publications for Padinjat Raghu

Corresponding author*

Primary Research Papers

Preprints

  • Mishra S,  Manohar V, Chandel S,  Manoj T,  Bhattacharya S, Hegde N,  Nath VR,  Wendling C,  Di Mattia T,  Martinet A,  Chimata P,  Alpy A, Raghu P*. A genetic screen to uncover molecular mechanisms underlying lipid transfer protein function at membrane contact sites and neurodegeneration. bioRxiv 2023.07.28.550979v1. https://www.biorxiv.org/content/10.1101/2023.07.28.550979v1
  • Saha S, Krishnan H, Raghu P. IMPA1 dependent regulation of plasma membrane phosphatidylinositol 4,5-bisphosphate turnover and calcium signalling by lithium. bioRxiv 2022.10.14.512101; doi: https://doi.org/10.1101/2022.10.14.512101
  • Pallikonda HA, Singh P,  Thakur RS, Aastha Kumari,  Krishnan H,  Philip RG ,  Vasudevan A,  Raghu P. Genomic sequencing of Lowe syndrome trios reveal a mechanism for the heterogeneity of neurodevelopmental phenotypes. bioRxiv 2021.06.22.449382; doi: https://doi.org/10.1101/2021.06.22.449382 
  • Gupta K, Janardan V, Banerjee S, Chakrabarti S, Swarna Srinivas, Mahishi D, Raghu P, Visweswariah SV. An evolutionarily conserved metallophosphodiesterase is a determinant of lifespan in Drosophila. bioRxiv doi: https://doi.org/10.1101/2020.05.08.084137

2021-Till date 

  • Ghosh A, Venugopal A, Shinde D, Sharma S, Krishnan M, Mathre S, Krishnan H, Saha S, Raghu P*. PI3P-dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase. Life Sci Alliance. 2023 Jun 14;6(9):e202301920. doi: 10.26508/lsa.202301920. PMID: 3731629
  • Ansil BR,  George CE,  Chandrasingh S,  Viswanathan A, Thattai M,  Raghu P,  Devadiga S,  Harikumar   AG,  Harsha PK,  Nair I,  Ramakrishnan U,  Mayor S. Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2. In .J. Med. Micrbiol. 2023. Volume 45, September–October 2023, 100384. https://doi.org/10.1016/j.ijmmb.2023.100384
  • Bhattacharyya T ,  Ghosh A , Verma S,  Raghu P,  Sowdhamini R. Structural rationale to understand the effect of disease-associated mutations on Myotubularin. Curr. Res. Struc. Biol.  2023: 5: 100100 https://doi.org/10.1016/j.crstbi.2023.100100 
  • Krishnan H, Basak B, Nath VR, Mishra S, Raghu P*. Structural organization of RDGB (retinal degeneration B), a multi-domain lipid transfer protein: a molecular modelling and simulation-based approach. J Biomol Struct Dyn. 2023 Feb 20:1-15. doi: 10.1080/07391102.2023.2179545.  Online ahead of print. PMID: 36803287
  • Akhtar BM, Bhatia P, Acharya S, Sharma S, Sharma Y, Aswathy BS, Ganapathy K, Vasudevan A & Raghu P*. A human stem cell resource to decipher the biochemical and cellular basis of neurodevelopmental defects in Lowe Syndrome. Biology Open 2022 15;11(1):bio059066. doi:10.1242/bio.059066  
  • Kumari A, Ghosh A, Kolay S and Raghu P*. Septins tune lipid kinase activity and PI(4,5)P 2 turnover during G-protein-coupled PLC signalling in vivo. Life Sci Alliance. 2022 Mar 11;5(6):e202101293.  doi: 10.26508/lsa.202101293. 
  • Panda A, Thakur R, Kumari A and Raghu P*. Analysis of Lipid Signaling in Drosophila Photoreceptors using Mass Spectrometry. J Vis Exp. 2022 Mar 7;(181). doi: 10.3791/63516.
  • Basak B, Krishnan H, Raghu P*. Interdomain interactions regulate the localization of a lipid transfer protein at ER-PM contact sites. Biology Open. 2021. Feb 17;bio.057422. doi: 10.1242/bio.057422.

2015-2020

  • Basak B,Krishnan H,Raghu P*. Interdomain interactions regulate the localization of a lipid transfer protein at ER-PM contact sites.Biol Open. 2021. 10 (3): bio058657.

  • Trivedi D,Vinitha CM,Bisht K,Janardan V,Pandit A, Basak B,Shwetha H,Ramesh R, & Raghu P*.. A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signaling. eLife. 2020 Dec 15;9:e55793. https://doi.org/10.7554/eLife.55793

  • Nath VR, Basak B, Mishra S, Trivedi D and Raghu P*. Extended synaptotagmin regulates membrane contact site structure and lipid transfer function in vivo. 2020. EMBO Reports. 27 July. e50264. https://doi.org/10.15252/embr.202050264

  • Basu U, Balakrishnan S, Janardan V and Raghu P*. A PI4KIIIprotein complex is required for cell viability during Drosophila wing development. 2020. Dev.Biol. 2020 Jun 15;462(2):208-222. doi: 10.1016/j.ydbio.2020.03.008

  • JanardanV,Sharma S,Basu U,Raghu P*. A Genetic Screen inDrosophilaTo Identify Novel Regulation of Cell Growth by Phosphoinositide Signaling. G3 (Bethesda).2020 Jan 7;10(1):57-67. doi: 10.1534/g3.119.400851.

  • SharmaY, Saha S, Joseph A, Krishnan H,RaghuP*. In vitrohuman stem cell derived cultures to monitor calcium signaling in neuronal development and function. Wellcome Open Res. 2020 Feb 3;5:16. doi: 10.12688/wellcomeopenres.15626.1. eCollection 2020. PMID: 32195361

  • Ghosh A, Sharma S, Shinde D, Ramya V, Raghu P*.A novel mass assay to measure phosphatidylinositol-5-phosphate from cells and tissues. Biosci. Rep. 2019 Oct 30;39(10). pii: BSR20192502. doi: 10.1042/BSR20192502.

  • Sharma S, Mathre S, Ramya V, Shinde S, Raghu P*. Phosphatidylinositol 5 Phosphate 4-Kinase Regulates Plasma-Membrane PIP3 Turnover and Insulin Signaling. Cell Rep. 2019 May 14;27(7):1991-2001.e5. doi: 10.1016/j.celrep.2019.04.070

  • MathreS,Reddy B,Ramya V,KrishnanH,Ghosh A,RaghuP*. Functional analysis of the biochemical activity of mammalian phosphatidylinositol 5 phosphate 4-kinase enzymes. Biosci Rep.2019 Feb 4. pii: BSR20182210. doi: 10.1042/BSR20182210. [Epub ahead of print]

  • PandaA,Thakur R,Krishnan H,Naik A,Shinde D,RaghuP*. Functional analysis of mammalian phospholipase D enzymes. Biosci Rep.2018Oct 28. pii: BSR20181690. doi: 10.1042/BSR20181690. [Epub ahead of print]

  • BalakrishnanSS,Basu U,Shinde D,Thakur R,Jaiswal M,RaghuP*. Regulation of PI4P levels by PI4KIIIα during G-protein coupled PLC signaling inDrosophila photoreceptors. J Cell Sci.2018Jul 6. pii: jcs.217257. doi: 10.1242/jcs.217257.

  • Suratekar R, Panda A, Raghu P & Krishna S. Evidence of sinks and sources in the phospholipase C‐activated PIP2cycle. FEBS. Lett. 2018. https://doi.org/10.1002/1873-3468.12998

  • Ashe S, Malhotra V and Raghu, P*. Protein kinase D regulates metabolism and growth by controlling secretion of insulin like peptide. Dev.Biol, 2017. doi.org/10.1016/j.ydbio.2017.12.008

  • Yadav S, Thakur R, Georgiev P, Deivasigamani S, Ratnaparkhi G and Raghu P*. FFAT/VAP interaction imposes intramolecular regulation on lipid transfer function at membrane contact sites. J. Cell. Sci, 2017:jcs.207985doi:10.1242/jcs.207985

  • Kamalesh K, Trivedi D, Toscano S, Kolay, S, Sharma, S and ­­­Raghu P*. Phosphatidylinositol 5-phosphate 4-kinase regulates clathrin mediated endocytosis in developing Drosophila photoreceptors J. Cell. Sci, 2017; 130:2119-2133;doi:10.1242/jcs.202259.

  • Thakur RS, Panda A, Coessens E, Raj N, Yadav S, Balakrishnan S, Zhang Q, Georgiev P, Basak B, Pasricha R, Wakelam MJO, Ktistakis N and Raghu P*. Phospholipase D activity couples plasma membrane endocytosis with retromer dependent recycling. eLife. 2016 5:e18515. DOI: 10.7554/eLife.18515.

  • Choudhury SD, Mushtaq Z, Reddy-Alla S, Balakrishnan SS, Thakur RS, Krishnan KS,Raghu P, Ramaswami M, Kumar V. σ2-adaptin Facilitates Basal Synaptic Transmission and Is required for Regenerating Endo-Exo Cycling Pool under High Frequency Nerve Stimulation in Drosophila.Genetics. 2016;203(1):369-85. doi: 10.1534/genetics.115.183863.

  • Yadav, S., Garner, K., Georgiev, P., Li, M., Gomez Espinosa, E., Panda, A., Mathre, M., Cockcroft, S and Raghu, P*. RDGBα, a PtdIns-PtdOH transfer protein, regulates G-protein-coupled PtdIns(4,5)P2signalling duringDrosophilaphototransduction. J.Cell.Sci. 2015; 128:3330-3344

  • Chakrabarti, P., Kolay, S., Yadav, S, Kamalesh Kumari, K., Nair, A., Trivedi, D and Raghu, P*. A dPIP5K dependent pool of phosphatidylinositol 4,5 bisphosphate (PIP2) is required for G-protein coupled signal transduction in Drosophila photoreceptors. PLOS Genetics. 2015; 11(1):e1004948. doi: 10.1371/journal.pgen.1004948. eCollection 201

2010-2014

  • Lowe, N, Rees, J and the UK Drosophila Protein Trap Screening Consortium@. Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library. Development 2014 141, 3994-4005. @Raghu P member of Consortium.

  • Gupta, A, Sarah Toscano, S, Trivedi, D, Jones DJ, Mathre S, Clarke J, Georgiev P, Divecha N and Raghu P*. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) regulates TOR signalling and cell growth during Drosophila development. Proc. Natl. Acad. Sci. USA 2013;110 (15):5963-8

  • Chu B,Liu CH,Sengupta S,Gupta A,RaghuP,HardieRC.  Common mechanisms regulating dark noise and quantum bump amplification in Drosophila photoreceptors. J NeuroPhysiol. 2013; 109(8):2044-55

  • BadshaF, Kain P, Prabhakar S, Sundaram S, Raghu P, Rodrigues V,HasanG. Mutants in Drosophila TRPC Channels Reduce Olfactory Sensitivity to Carbon Dioxide. PLoS One. 2012; 7(11): e49848.

  • Garner K, Hunt AN, Koster G, Somerharju P, Groves E, Li M, Raghu P, Holic R, Cockcroft S.  Phosphatidylinositol transfer protein, cytoplasmic 1 (PITPNC1) binds and transfers Phosphatidic Acid. J.Biol.Chem. 2012; 287(38): 32263-7.

  • Georgiev P, Toscano S, Nair A, Hardie R,Raghu P*. Identification of a suppressor of retinal degeneration in Drosophila photoreceptors. J. Neurogenet. 2012 (3-4): 338-47.

  • Georgiev, P., Okkenhaug, H, Drews, A, Wright, D., Flick, M, Lambert, S, Oberwinkler, J and Raghu, P*. TRPM channels mediate zinc homeostasis and cellular growth during Drosophila larval development. Cell Metabolism. 2010; 12, 386–397

          2005-2009

  • Raghu, P*, Coessens E, Manifava M, Georgiev P, Pettitt T, Wood E, Garcia-Murillas I, Okkenhaug H, Trivedi D, Zhang Q, Razzaq A, Zaid O, Wakelam MJO, O'Kane CJ, Ktistakis NT Rhabdomere biogenesis in Drosophila photoreceptors is acutely sensitive to phosphatidic acid levels. J. Cell.Biol. 2009; 185 129-145.

  • Garcia-Murillas I, Pettit T, Macdonald E, Okkenhaug H, Georgiev P, Trivedi D, Hassan B, Wakelam M and Raghu, P*. lazaro encodes a lipid phosphate phosphohydrolase that regulates phosphatidylinositol turnover during Drosophila phototransduction. Neuron. 2006. 29:4, 533-546.

  • Georgiev, P, Garcia-Murillas, I, Ulahannan, D Hardie, R.C and Raghu, P*. Functional INAD complexes are required to mediate degeneration in photoreceptors of the Drosophila rdgA mutant.” J.Cell.Sci. 2005. 118:1373-1384

2000-2004

  • Hardie, R.C, Gu, Y., Martin, M., Sweeney, S.T and Raghu, P. In Vivo light-induced and basal phospholipase C activity in Drosophila photoreceptors measured with genetically targeted phosphatidylinositol 4,5-bisphosphate-sensitive ion channels (Kir2.1) J. Biol. Chem. 2002 279: 47773 – 47782

  • Hardie, RC, Martin F, Chyb S and Raghu, P. Rescue of light responses in the Drosophila "null” phospholipase C mutant, norpAP24 by diacylglycerol kinase mutant, rdgA and by metabolic inhibition. J. Biol. Chem. 2003; 278: 18851 – 18858

  • Hardie, R.C., Martin, F., Cochrane, G.R., Jussola, M.G, Georgiev, P & Raghu, P. Molecular basis of amplification in Drosophila phototransduction: roles for G-protein, phospholipase C and diacylglycerol kinase. Neuron. 2002 36: 689-701.

  • Hardie, R.C, Raghu, P, Moore, S, Juusola M,Baines RA,Sweeney ST, Calcium influx via TRP channels is required to maintain PIP2 levels in Drosophila photoreceptors. Neuron. 2001; 30: 1-20.

  • Raghu, P, Usher, K.R, Jonas S,Chyb S,Polyanovsky A,HardieRC.et.al, Constitutive activity of the light sensitive channels, TRP and TRPL, in the Drosophila diacylglycerol kinase mutant, retinal degeneration A (rdgA) . Neuron. 2000. 26: 169-179.

  • Raghu, P, Colley,N.J, Webel, R,James T,Hasan G,Danin M,Selinger Z,HardieRC. Normal phototransduction in Drosophila photoreceptors lacking an InsP3 receptor. Mol. Cell. Neurosci. 2000; 15: 429-445.

Prior to 2000

  • Chyb, S, Raghu, P & Hardie, R.C. Polyunsaturated fatty acids activate the Drosophila light-sensitive channels TRP and TRPL. Nature. 1999. 397: 255-259

  • Hardie, R.C. & Raghu, P. Activation of heterologously expressed Drosophila TRPL channels: Ca2+ is not required and InsP3 is not sufficient. Cell Calcium. 1998; 24(2): 153-163.

  • Raghu, P., Habib, S., Hasnain, E. & Hasan, G. Development of a functional assay for Ca2+ release activity of IP3R and expression of an IP3R gene fragment in the baculovirus-insect cell system. Gene. 1996; 190:151-156.

  • Raghu, P. & Hasan G. The inositol 1, 4, 5 trisphosphate receptor expression in Drosophila suggests a role for IP3 signalling in muscle development and adult chemosensory function. Dev.Biol. 1995; 171:564-577.

      Consortia papers (ADBS consortium- P. Raghu is a member and leader of the ADBS consortium)

  • Ganesh S, Ahmed P H, Nadella RK, More RP, Seshadri M, Viswanath B, Rao M, Jain S;ADBSConsortium, Mukherjee O Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes. Psychiatry Clin Neurosci. 2019 Jan;73(1):11-19. doi: 10.1111/pcn.12788. Epub 2018 Dec 12.

  • Ahmed P H, V V, More RP, Viswanath B, Jain S, Rao MS, Mukherjee O;ADBSConsortium. INDEX-db: The Indian Exome Reference Database (Phase I). J Comput Biol. 2019 Mar;26(3):225-234. doi: 10.1089/cmb.2018.0199. Epub 2019 Jan 7.

  • Paul P, Iyer S, Nadella RK, Nayak R, Chellappa AS, Ambardar S, Sud R, Sukumaran SK, Purushottam M, Jain S, Viswanath B and ADBS Consortium. Lithium response in bipolar disorder correlates with improved cell viability of patient derived cell lines. Sci Rep. 2020 May 4;10(1):7428. doi: 10.1038/s41598-020-64202-1

  • Someshwar A, Holla B, Pansari Agarwal P, Thomas A, Jose A, Joseph B, Raju B, Karle H, Muthukumaran M, Kodancha PG, Kumar P, Reddy PV, Kumar Nadella R, Naik ST, Mitra S, Mallappagiri S, Sreeraj VS, Balachander S, Ganesh S, Murthy P, Benegal V, Reddy JY, Jain S, Mahadevan J, Viswanath B; ADBS Consortium. Adverse childhood experiences in families with multiple members diagnosed to have psychiatric illnesses. Aust N Z J Psychiatry. 2020 Jun 15:4867420931157. doi: 10.1177/0004867420931157.

  • Vanteemar S Sreeraj, Bharath Holla, Dhruva Ithal, Ravi Kumar Nadella, Jayant Mahadevan, Srinivas Balachander, Furkhan Ali, Sweta Sheth, Janardhanan C Narayanaswamy, Ganesan Venkatasubramanian, John P John, Mathew Varghese, Vivek Benegal, Sanjeev Jain, YC Janardhan Reddy, ADBS Consortium, Biju Viswanath. Psychiatric symptoms and syndromes transcending diagnostic boundaries in Indian multiplex families: The cohort of ADBS study. Psychiatry Research. 2021 Jan. https://doi.org/10.1016/j.psychres.2020.113647

      Reviews

  • Raghu P*. Emerging cell-biological functions of phosphatidylinositol 5 phosphate 4 kinase. Curr Opin Cell Biol.2021 (in press)

  • Raghu P*. Functional Diversity in a lipidome. Proc. Natl. Acad. Sci. USA. 2020. 117(21)11191-11193; https://doi.org/10.1073/pnas.2004764117

  • Raghu P*, Joseph A, Krishnan H, Singh P and Saha S. Phosphoinositides; regulators of nervous system function in health and disease. Fron. Mol. Neurosci. 2019 Aug 29; https://doi.org/10.3389/fnmol.2019.00208

  • Thakur R, Naik A, Panda A and Raghu P*. Regulation of membrane turnover by phosphatidic acid: cellular functions and disease implications. Fron. Cell Devl. Biol 2019 Jun 4;7:83. doi: 10.3389/fcell.2019.00083. eCollection

  • CockcroftS,Raghu P. Phospholipid transport protein function at organelle contact sites. Curr Opin Cell Biol.2018Aug; 53:52-60. doi: 10.1016/j.ceb.2018.04.011. Epub2018May 30.

  • Topological organisation of the phosphatidylinositol 4,5-bisphosphate-phospholipase C resynthesis cycle: PITPs bridge the ER–PM gap. Cockcroft S and Raghu P*. Biochemical Journal (2016) Dec 1;473(23):4289-4310

  • RdgBα reciprocally transfers PA and PI at ER-PM contact sites to maintain PI(4,5)P2 homoeostasis during phospholipase C signalling in Drosophila photoreceptorsCockcroftS, Garner K,YadavS, Gomez-Espinoza E, Raghu P*. Biochem Soc Trans. (2016) Feb 15;44(1):286-92. doi: 10.1042/BST20150228.

  • The Drosophila photoreceptor as a model system for studying signalling at membrane contact sites. YadavS, CockcroftS and Raghu P*. Biochem Soc Trans. (2016) Apr 15;44(2):447-51. doi: 10.1042/BST20150256

  • Control of diverse sub-cellular processes by a single multi-functional lipid phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2]. Kolay, S., Basu, U and Raghu, P*. Biochemical Journal. (2016) Jun 15;473(12):1681-92. doi: 10.1042/BCJ20160069.

  • BalakrishnanSS,BasuU,RaghuP*. Phosphoinositide signalling in Drosophila. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids; Phosphoinositide Signalling (2014) Oct 30. pii: S1388-1981(14)00219-4

  • Raghu, P*, Yadav, S and Mallampati, N. Lipid signalling in Drosophila photoreceptors. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids. Vesicular Transport. 2012; 1821(8):1154-65.

  • Raghu P, Hardie RC. Regulation of Drosophila TRPC channels by lipid messengers. Cell Calcium. 2009; 45(6): 566-73.

  • Raghu, P, Manifava M, Coadwell WJ, Ktistakis NT. Emerging findings from studies of phospholipase D in model organisms (and a short update on phosphatidic acid effectors). Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids 2009; 1791(9):889-97

  • Trivedi D and Raghu P*. RdgB proteins; functions in lipid homeostasis and signal transduction. BBA; Molecular and Cell Biology of Lipids. 2007. 1771:692-699.

  • Raghu, P*. Regulation of Drosophila TRPC channels by protein and lipid interactions. Semin Cell Dev Biol 2006. 17(6):646-653

  • Raghu, P and Andrews, S (TRP channels at a glance. J.Cell.Sci. 2004. 117:5707-5709

  • Raghu, P. LPP2. AfCS-Nature Molecule Pages (2005). doi: 10.1038/mp.a003072.0

  • Hardie, R.C. & Raghu, P. Visual transduction in Drosophila. Nature. 2001; 413:186-193.

         Book Chapters

  • Dolph, P, Nair, A and Raghu, P*. Analysis of visual physiology in the adult Drosophila eye. 2010; Chapter 14. 225-235. In Drosophila Neurobiology Methods: A Laboratory Manual. Cold Spring Harbor Laboratory Press.

  • Ghosh A and Raghu P*. Label free quantification of phosphoinositides in Drosophila by mass spectrometry. 2020; Chapter 2. P19-37. In Phosphoinositides: Methods and Protocols, Methods in Molecular Biology, vol. 2251, https://doi.org/10.1007/978-1-0716-1142-5_2

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