Scientist Profile

Jomon Joseph, Ph.D.

Email

josephj@nccs.res.in

Research Areas

Cell Organization and Function, Regulatory RNAs and Gene Expression

Education

Post-doctoral Fellow, 2000-2005, National Institutes of Health, Bethesda, USA

Ph.D. (Biochemistry), 2000, Indian Institute of Science, Bangalore, India

M.Sc. (Agriculture), 1993, University of Agricultural Sciences, Bangalore, India

 

Experience

Scientist G, 2022-present, National Centre for Cell Science, Pune, India

Scientist F, 2016-2021, National Centre for Cell Science, Pune, India

Scientist E, 2010-2016, National Centre for Cell Science, Pune, India

Scientist D, 2005-2010, National Centre for Cell Science, Pune, India

Fogarty International Research Fellow, 2000-2005, NICHD, NIH, USA

Research Interests

Cell biology of Annulate Lamellae, ER-mitochondrial contact sites, Intercellular communication, Extracellular vesicles

 

Cell Biology of Annulate Lamellae

Our laboratory is interested non-traditional roles of nucleoporins. Nucleoporins (Nups) are thought to have an important role in the regulation of nucleo-cytoplasmic transport of macromolecules across the nuclear envelope. However, recent studies suggest that this group of proteins could be involved in a broad range of other processes such as chromatin remodelling, transcription regulation, DNA repair, cell migration, cell polarity, etc.

We primarily work on the nucleoporin Nup358, which is located on the cytoplasmic face of the nuclear pore complex (NPC). In addition to the localization to the NPC, Nup358, along with a subset of other nucleoporins, also is present in a less known cytoplasmic organelle called annulate lamellae (AL). This organelle has been extensively studied at the ultrastructural level using electron microscopy and is characterized as stacked endoplasmic reticulum (ER), containing pore-like structures. So far, it is thought to be the storehouse of nucleoporins, with some recent evidence supporting such a notion. Our lab is exploring the function of AL in general, and Nup358 as a component of AL in particular. Our studies suggest an interesting role for this organelle as the cytoplasmic platforms, where regulation of mRNAs could be achieved. Recent findings also unravel a role for Nup358 in ER-mitochondrial contact site remodelling and regulation of growth factor signalling and autophagy. We are constantly in pursuit of understanding the new functions of this underexplored cytoplasmic organelle.

 

Ran GTPase & inter-cellular communication

We serendipitously found that the GTPase Ran, a critical regulator of nucleo-cytoplasmic transport, also possesses the ability to move from cell to cell in a GTP- and CRM1-dependent manner. We are addressing the possible role of Ran in inter-cellular communication. Ran is overexpressed in many cancers and the inter-cellular transport function we recently uncovered could contribute to tumorigenesis.

 

Publications


Pubmed Article Listing

Selected Publications    All Publications

Selected Publications

Sahoo MR, Gaikwad S, Khuperkar D, Ashok M, Helen M, Yadav SK, Singh A, Magre I, Deshmukh P, Dhanvijay S, Sahoo PK, Ramtirtha Y, Madhusudhan MS, Gayathri P, Seshadri V, Joseph J*. Nup358 binds to AGO proteins through its SUMO-interacting motifs and promotes the association of target mRNA with miRISC. EMBO Rep. 2017, 18(2):241-263. PMID: 28039207.
Banerjee P, Markande S, Kalarikkal M, Joseph J*. SUMOylation modulates the function of DDX19 in mRNA export. J Cell Sci. 2022, 135(4):jcs259449. PMID: 35080244. (Selected for First Author interview).
Magre I, Fandade V, Damle I, Banerjee P, Yadav SK, Sonawane M*, Joseph J*. Nup358 regulates microridge length by controlling SUMOylation-dependent activity of aPKC in zebrafish epidermis. J Cell Sci. 2019, 132(12):jcs224501. PMID: 31164446. (Cover page article) (Also selected for First Author interview).
Chavan S, Khuperkar D, Lonare A, Panigrahi S, Bellare J, Rapole S, Seshadri V, Joseph J*. RanGTPase links nucleo-cytoplasmic transport to the recruitment of cargoes into small extracellular vesicles. Cell Mol. Life Sci. volume 79, Article number: 392 (2022).
Murawala P, Tripathi MM, Vyas P, Salunke A, Joseph J*. Nup358 interacts with APC and plays a role in cell polarization. J Cell Sci. 2009, 122(Pt 17):3113-22. PMID: 19654215.

 

 

All Publications

Chavan S, Khuperkar D, Lonare A, Panigrahi S, Bellare J, Rapole S, Seshadri V, Joseph J*. RanGTPase links nucleo-cytoplasmic transport to the recruitment of cargoes into small extracellular vesicles. Cell Mol. Life Sci. volume 79, Article number: 392 (2022).

Palazzo AF, Joseph J, Lim M, Thakur KT. Workshop on RanBP2/Nup358 and acute necrotizing encephalopathy. Nucleus. 2022, 13(1):154-169. PMID: 35485383.

Banerjee P, Markande S, Kalarikkal M, Joseph J*. SUMOylation modulates the function of DDX19 in mRNA export. J Cell Sci. 2022, 135(4):jcs259449. PMID: 35080244. (Selected for First Author interview).

Saikia R, Joseph J*. AMPK: a key regulator of energy stress and calcium-induced autophagy. J Mol Med (Berl). 2021, 99(11):1539-1551. PMID: 34398293.

Deshmukh P, Singh A, Khuperkar D, Joseph J*. Acute necrotizing encephalopathy-linked mutations in Nup358 impair interaction of Nup358 with TNRC6/GW182 and miRNA function. Biochem Biophys Res Commun. 2021, 559:230-237. PMID: 33962210.

Deshmukh P, Markande S, Fandade V, Ramtirtha Y, Madhusudhan MS, Joseph J*. The miRISC component AGO2 has multiple binding sites for Nup358 SUMO-interacting motif. Biochem Biophys Res Commun. 2021, 556:45-52. PMID: 33838501.

Dandewad V, Vindu A, Joseph J, Seshadri V. Import of human miRNA-RISC complex into Plasmodium falciparum and regulation of the parasite gene expression. J Biosci. 2019, 44(2):50. PMID: 31180063.

Magre I, Fandade V, Damle I, Banerjee P, Yadav SK, Sonawane M*, Joseph J*. Nup358 regulates microridge length by controlling SUMOylation-dependent activity of aPKC in zebrafish epidermis. J Cell Sci. 2019, 132(12):jcs224501. PMID: 31164446. (Cover page article) (Also selected for First Author interview).

Khuperkar D, Kamble A, Singh A, Ghate A, Nawadkar R, Sahu A*, Joseph J*. Selective recruitment of nucleoporins on vaccinia virus factories and the role of Nup358 in viral infection. Virology. 2017, 512:151-160. PMID: 28963881.

Sahoo MR, Gaikwad S, Khuperkar D, Ashok M, Helen M, Yadav SK, Singh A, Magre I, Deshmukh P, Dhanvijay S, Sahoo PK, Ramtirtha Y, Madhusudhan MS, Gayathri P, Seshadri V, Joseph J*. Nup358 binds to AGO proteins through its SUMO-interacting motifs and promotes the association of target mRNA with miRISC. EMBO Rep. 2017, 18(2):241-263. PMID: 28039207.

Yadav SK, Magre I, Singh A, Khuperkar D, Joseph J*. Regulation of aPKC activity by Nup358 dependent SUMO modification. Sci Rep. 2016, 6:34100. PMID: 27682244.

Chouhan S, Singh S, Athavale D, Ramteke P, Pandey V, Joseph J, Mohan R, Shetty PK, Bhat MK. Glucose induced activation of canonical Wnt signaling pathway in hepatocellular carcinoma is regulated by DKK4. Sci Rep. 2016, 6:27558. PMID: 27272409.

Khuperkar D, Helen M, Magre I, Joseph J*. Inter-cellular transport of ran GTPase. PLoS One. 2015, 10(4):e0125506. PMID: 25894517.

Panda AC, Sahu I, Kulkarni SD, Martindale JL, Abdelmohsen K, Vindu A, Joseph J, Gorospe M, Seshadri V. miR-196b-mediated translation regulation of mouse insulin2 via the 5'UTR. PLoS One. 2014, 9(7):e101084. PMID: 25003985.

Zaim M, Ali A, Joseph J, Khan F. Serological and molecular studies of a novel virus isolate causing yellow mosaic of Patchouli [Pogostemon cablin (Blanco) Benth]. PLoS One. 2013, 8(12):e83790. PMID: 24386278.

Vyas P, Singh A, Murawala P, Joseph J*. Nup358 interacts with Dishevelled and aPKC to regulate neuronal polarity. Biol Open. 2013, 2(11):1270-8. PMID: 24244865.

Sahoo PK, Murawala P, Sawale PT, Sahoo MR, Tripathi MM, Gaikwad SR, Seshadri V, Joseph J*. Wnt signalling antagonizes stress granule assembly through a Dishevelled-dependent mechanism. Biol Open. 2012, 1(2):109-19. PMID: 23213403.

Hamada M, Haeger A, Jeganathan KB, van Ree JH, Malureanu L, Wälde S, Joseph J, Kehlenbach RH, van Deursen JM. Ran-dependent docking of importin-beta to RanBP2/Nup358 filaments is essential for protein import and cell viability. J Cell Biol. 2011, 194(4):597-612. PMID: 21859863.

Notani D, Gottimukkala KP, Jayani RS, Limaye AS, Damle MV, Mehta S, Purbey PK, Joseph J, Galande S. Global regulator SATB1 recruits beta-catenin and regulates T(H)2 differentiation in Wnt-dependent manner. PLoS Biol. 2010, 8(1):e1000296. PMID: 20126258.

Murawala P, Tripathi MM, Vyas P, Salunke A, Joseph J*. Nup358 interacts with APC and plays a role in cell polarization. J Cell Sci. 2009, 122(Pt 17):3113-22. PMID: 19654215.

Atre AN, Surve SV, Shouche YS, Joseph J, Patole MS, Deopurkar RL. Association of small Rho GTPases and actin ring formation in epithelial cells during the invasion by Candida albicans. FEMS Immunol Med Microbiol. 2009, 55(1):74-84. PMID: 19077030.

Joseph J*, Dasso M*. The nucleoporin Nup358 associates with and regulates interphase microtubules. FEBS Lett. 2008, 582(2):190-6. PMID: 18070602. (Cover page article).

Rundle NT, Nelson J, Flory MR, Joseph J, Th'ng J, Aebersold R, Dasso M, Andersen RJ, Roberge M. An ent-kaurene that inhibits mitotic chromosome movement and binds the kinetochore protein ran-binding protein 2. ACS Chem Biol. 2006, 1(7):443-50. PMID: 17168522.

Joseph J*. Ran at a glance. J Cell Sci. 2006, 119(Pt 17):3481-4. PMID: 16931595.

Prunuske AJ, Liu J, Elgort S, Joseph J, Dasso M, Ullman KS. Nuclear envelope breakdown is coordinated by both Nup358/RanBP2 and Nup153, two nucleoporins with zinc finger modules. Mol Biol Cell. 2006, 17(2):760-9. PMID: 16314393.

Arnaoutov A, Azuma Y, Ribbeck K, Joseph J, Boyarchuk Y, Karpova T, McNally J, Dasso M. Crm1 is a mitotic effector of Ran-GTP in somatic cells. Nat Cell Biol. 2005, 7(6):626-32. PMID: 15908946.

Jeong SY, Rose A, Joseph J, Dasso M, Meier I. Plant-specific mitotic targeting of RanGAP requires a functional WPP domain. Plant J. 2005, 42(2):270-82. PMID: 15807788.

Joseph J, Liu ST, Jablonski SA, Yen TJ, Dasso M. The RanGAP1-RanBP2 complex is essential for microtubule-kinetochore interactions in vivo. Curr Biol. 2004, 14(7):611-7. PMID: 15062103.

Anindya R, Joseph J, Gowri TDS, Savithri HS. Complete genomic sequence of Pepper vein banding virus (PVBV): a distinct member of the genus Potyvirus. Archives of virology. 2004, 149 (3), 625-632.

Joseph J, Dasso M. Cellular roles of the RanGTPase. Handbook of Cell Signaling. 2003, 695-699.

Joseph J, Tan SH, Karpova TS, McNally JG, Dasso M. SUMO-1 targets RanGAP1 to kinetochores and mitotic spindles. J Cell Biol. 2002, 156(4):595-602. PMID: 11854305. [Significance of this paper has been highlighted in the Editor’s Choice section of Science 295(5561): 1795 (2002)].

Joseph J, Savithri HS. Mutational analysis of the NIa protease from pepper vein banding potyvirus. Archives of virology. 2000, 145 (12), 2493-2502.

Joseph J, Savithri HS. Determination of 3′-terminal nucleotide sequence of pepper\break vein banding virus RNA and expression of its coat protein in Escherichia coli. Archives of virology. 1999, 144 (9), 1679-1687.

Cherian S, Joseph J, Muniyappa V, Savithri HS. Characterization of tobacco mosaic virus isolated from tomato in India. Current Science 1999, 1384-1388.

Hema M, Joseph J, Gopinath K, Sreenivasulu P, Savithri HS. Molecular characterization and interviral relationships of a flexuous filamentous virus causing mosaic disease of sugarcane (Saccharum officinarum L.) in India. Archives of Virology. 1999 144 (3), 479-490.

Ravi S, Joseph J, Nagaraju N, Prasad SK, Reddy HR, Savithri HS. Characterization of a pepper vein banding virus from chili pepper in India. Plant disease. 1997, 81 (6), 673-676.

* Corresponding author

Affiliations and Awards

 

  • Elected Member, Guha Research Conference, 2019
  • Elected Member, Molecular Immunology Forum, 2019
  • Life Member, Indian Society for Cell Biology (2008 onwards)
  • Life Member, Society of Biological Chemists, India (2014 onwards)
  • Life Member, Indian Society for Developmental Biologists (2017 onwards)
  • International Travel Award from EMBO for attending EMBO Conference on ‘Ubiquitin and SUMO: From molecular mechanisms to system-wide responses’ (2017)
  • International Travel Award from organizers of ‘WNT meeting’ (2010)
  • John E. Fogarty International Visiting Fellowship (Postdoctoral, 2000-2005)
  • Council of Scientific and Industrial Research-Senior Research Fellowship (1996-1999)
  • Council of Scientific and Industrial Research-Junior Research Fellowship (1993-1996)
  • Indian Council of Agricultural Research-Junior Research Fellowship (1991-1993)
  • National Merit Scholarship (1984-1990)


 

Current/Past Lab Members

 

Phd Students :  Current 2022 

 

 

 

Phd Students :  Years 2015-2018

 

Phd Students :  Years 2008-2011

 

Current Lab Members

  • Sakalya Chavan, Ph.D. Student, M.Sc. (Biotechnology), S.P. Pune University, Maharashtra
  • Misha, K.R., Ph.D. Student, M.Sc. (Biotechnology), Amrita Vishwa Vidhyapeetham, Kerala
  • Rimpi Saikia, Ph.D. Student, Int. M.Sc. (Biosciences & Bioinformatics), Tezpur University, Assam
  • Nikhil More, Ph.D. Student, M.Sc. (Biotechnology), North Maharashtra University, Maharashtra
  • Akshay Lonare, Ph.D. student, M.Sc. (Biotechnology), Sant Gadge Baba Amravati University, Maharashtra.
  • Lizanne Oliveira, Ph.D. Student, M.Sc. (Life Sciences), Mumbai University, Maharashtra
  • Swagathika Panigrahi, Project JRF, M.Sc. (Zoology), Utkal University, Odisha
  • Yashashree Borkar, Project Assistant, M.Sc. (Biotechnology), S.P. Pune University, Maharashtra
  • Aparna S. Salunke, Technical Officer 'A'

Lab Alumni -Ph.D. Students

  • Prayag Murawala, Principal Investigator, Mount Desert Island Biological Laboratory, Maine, USA
  • Mukesh Mani Tripathi, Scientific Officer; Yashraj Biotechnology GmbH, Berlin, Germany
  • Pankhuri Vyas, Clinical Trials Site Regulatory Specialist, Quantum Leap Healthcare Collaborative, San Francisco, California, USA
  • Pabitra Kumar Sahoo, Post-doctoral fellow; University of South Carolina, USA
  • Manas R. Sahoo, Manager, Application & Technical Services, Promega
  • Santosh K. Yadav, Post-doctoral fellow, Thomas Jefferson University, USA
  • Swati R. Gaikwad, Post-doctoral fellow, NICHD, NIH, USA
  • Deepak R. Khuperkar, Post-doctoral fellow, King’s College, London, UK
  • Aditi Singh
  • Indrasen A. Magre, Post-doctoral fellow, Duke University Medical Centre, USA
  • Prachi R. Deshmukh
  • Poulomi Banerjee

 

DBT-RA

Dr. Pallavi Varshney

 

Project personnel

  • Pravin Sawale
  • Mary Helen
  • Maitreyi Ashok
  • Supriya Dhanvijay
  • Shubha Markande

 

Project Trainees

  • Ganesh Babu
  • Fatema Kothari
  • Prajakta Kulkarni
  • Raina Priyadarshini
  • Salik Borbora
  • Parijat Kundu
  • Hina Jhelum
  • Alagu Lakshmi
  • Pradip Yadav
  • Anushree Shinde
  • Geetanjali Gaurav
  • Neema Bisht
  • Zimpi Hazarika
  • Surbhi Gupta
  • Trupti Murkute
  • Vaishnavi More
  • Aparna Panicker

 


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