The Subramani Lab, University of California, San Diego, Division of Biological Sciences Publications from 2006-1987 See what our current research projects right now
Meet the members of the Subramani Lab Contact Dr. Subramani and his Lab Link to other UCSD Labs and More.
Publications 2006-2000
Publications 2014-1996


Lakhani R., Vogel K  R, Till A, Liu J, Burnett S F, Gibson K M, Subramani S: Defects in GABA metabolism affect selective autophagy pathways and are alleviated by mTOR inhibition. EMBO Mol Med ,2014 6: 551–566 PDF

Nazarko T., Ozeki K, Till A, Ramakirshnan G, Lotfi P, Yan M, Subranami S: Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy, J. Cell Biol. Vol. 204 No. 4 541–557 2014 PDF

Gaurav A, Subramani S: Redox-regulated Cargo Binding and Release by the Peroxisomal Targeting Signal Receptor, Pex5Frontiers in Physiology, Vol 4, 2013 PDF

Ma C, Hagstrom D, Polley S G, Subrmanai S:  The Journal of Biological Chemistry, Vol. 288, No. 38, pp. 27220–27231, September 2013 PDF

Till A, Lipinski S, Ellinghaus D, Mayr G, Subrmanai S, Rosenstiel P, Franke A: Autophagy receptor CALCOCO2/NDP52 takes center stage in Crohn disease, Autophagy 9:8, 1256–1257; August 2013 PDF

Farre J.C., Burkenroad A, Burnett S, Subramani S: Phosphorylation ofmitophagy and pexophagy receptors
coordinates their interaction with Atg8 and Atg11, EMBO reports Vol 14, No 5, 2013 PDF

Liu X, Subramani S: Unique Requirements for Mono- and Polyubiquitination of the Peroxisomal Targeting Signal Co-receptor, Pex20, Volume 288•Number 10•March 8, 2013PDF

Subramani S, Malhotra V: Non-autophagic roles of autophagy-related proteins, EMBO reports Vol 14, N0 2, 2013 PDF

Liu X, Ma C, Subramani S: Recent advances in peroxisomal matrix protein import, Current Opinion in Cell Biology 2012, 24:484–489 PDF

Till A., R. Lakhani, S.F. Burnett, and S. Subramani, Pexophagy: The Selective Degradation of Peroxisomes. Int J Cell Biol 2012 (2012) 18.


Joshi S., G. Agrawal, and S. Subramani, Phosphorylation-dependent Pex11p and Fis1p interaction regulates peroxisome division. Mol Biol Cell (2012).


Nazarko V.Y., T.Y. Nazarko, J.C. Farre, O.V. Stasyk, D. Warnecke, S. Ulaszewski, J.M. Cregg, A.A. Sibirny, and S. Subramani, Atg35, a micropexophagy-specific protein that regulates micropexophagic apparatus formation in Pichia pastoris. Autophagy 7 (2011) 375-85.


Manjithaya R., and S. Subramani, Autophagy: a broad role in unconventional protein secretion? Trends Cell Biol 21 (2011) 67-73.


Ma C., G. Agrawal, and S. Subramani, Peroxisome assembly: matrix and membrane protein biogenesis. J Cell Biol 193 (2011) 7-16.


Farre J.C., and S. Subramani, Rallying the exocyst as an autophagy scaffold. Cell 144 (2011) 172-4.


Agrawal G., S. Joshi, and S. Subramani, Cell-free sorting of peroxisomal membrane proteins from the endoplasmic reticulum. Proc Natl Acad Sci U S A 108 (2011) 9113-8.


Till A., and S. Subramani, A balancing act for autophagin. J Clin Invest 120 (2010) 2273-6.


Manjithaya R., and S. Subramani, Role of autophagy in unconventional protein secretion. Autophagy 6 (2010).


Manjithaya R., T.Y. Nazarko, J.C. Farre, and S. Subramani, Molecular mechanism and physiological role of pexophagy. FEBS Lett 584 (2010) 1367-73.


Manjithaya R., S. Jain, J.C. Farre, and S. Subramani, A yeast MAPK cascade regulates pexophagy but not other autophagy pathways. J Cell Biol 189 (2010) 303-10.


Manjithaya R., C. Anjard, W.F. Loomis, and S. Subramani, Unconventional secretion of Pichia pastoris Acb1 is dependent on GRASP protein, peroxisomal functions, and autophagosome formation. J Cell Biol 188 (2010) 537-46.


Farré, J. -C., Mathewson, R. D., Manjithaya, R., Subramani, S. Roles of Pichia pastoris Uvrag in vacuolar protein sorting and the phosphatidylinositol 3-kinase complex in phagophore elongation in autophagy pathways. Autophagy, in press (2010).

Ma, C., Schumann, U., Rayapuram, N., Subramani, S. The peroxisomal matrix import of Pex8p requires only PTS receptors and Pex14p. Mol. Biol. Cell, Aug;20(16):3680-9. Epub 2009 Jul 1, (2009).PDF

Nazarko, T.Y., Farré, J.-C., Subramani, S. Peroxisome size provides insights into the function of autophagy-related proteins. Mol. Biol. Cell, Sep;20(17):3828-39. Epub 2009 Jul 15, (2009).PDF

Farré, J.-C., Krick, R., Subramani, S., Thumm, M. Turnover of organelles by autophagy in yeast. Curr. Opin Cell Biol., Aug;21(4):522-30. Epub 2009 Jun 8, (2009).

Ma, C. and Subramani, S. Peroxisome matrix and membrane protein biogenesis. IUBMB Life, Jul;61(7):713-22 (2009).PDF

Schumann, U., Subramani, S. Special delivery from mitochondria to peroxisomes. Trends Cell Biol., Jun;18(6):253-6. Epub 2008 May 28 (2008).PDF

Baker, M.E., Subramani, S. A structural balancing act: activity versus peroxisomal targeting of carbonyl reductase. Structure, 16(3):331-332 March 11  (2008).PDF

Farré, J.C., Manjithaya, R., Mathewson, R.D., Subramani, S. PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev. Cell, 14: 365-76 (2008).PDF

Yan, M., Rachubinski, D. A., Joshi, S., Rachubinski, R.A., Subramani, S. Dysferlin domain-containing proteins, Pex30p and Pex31p, localized to two compartments, control the number and size of oleate-induced peroxisomes in Pichia pastoris. Mol. Biol. Cell, Dec 19; [Epub ahead of print] (2007).PDF

Subramani, S., Farré, J.-C. A  ubiquitin-like protein involved in membrane fusion. Cell 130: 7-9 (2007).PDF

Léon, S., Suriapranata, I., Yan, M., Rayapuram, N., Patel, A., Subramani, S. Characterization of protein-protein interactions: Application to the understanding of peroxisome biogenesis, in Pichia Protocols, (Cregg, J. M. ed.), 2nd edition, Humana Press, Totowa, NJ, Ch 16, pp 219-37 (2007).PDF

Léon, S., Subramani, S. The role of shuttling targeting signal receptors and heat-shock proteins in peroxisomal matrix protein import. The Enzymes, Vol XXV, Chapter 20, 513-528 (2007).PDF

Farré, J.C., Shirahama-Noda, K., Zhang, L., Booher, K., Subramani, S. Localization of proteins and organelles using fluorescence microscopy, in Pichia Protocol, (Cregg, J. M. ed.), 2nd edition, Humana Press, Totowa, NJ, Ch. 17, pp239-49  (2007).PDF

Rayapuram, N., Subramani, S.  Peroxisomes, organization and transport in neurons. Encyclopedia Neurosci., Elsevier, in press (2007).PDF

Farré, J.C., Vidal, J., Subramani, S. A cytoplasm to vacuole targeting pathway in P. pastoris. Autophagy, , 3(3):230-4 (2007). (2007).PDF

Nazarko, T.Y., Farré, J.-C., Polupanov, A.S., Sibirny, A.A., Subramani, S. Autophagy-related pathways and specific role of sterol glucoside in yeasts. Autophagy, 3(3):263-5 (2007).PDF

Nazarko, T.Y., Polupanov, A.S., Manjithaya, R.R., Subramani, S., Sibirny, A.A. The requirement of sterol glucoside for pexophagy in yeasts is dependent on the species and nature of peroxisome inducers. Mol. Biol. Cell 18: 106-118 (2007).PDF

Léon, S., Subramani, S. A conserved cysteine residue of Pichia pastoris Pex20p is essential for its recycling from the peroxisome to the cytosol. J. Biol. Chem. Jan 5, 282(10):7424-30 (2007).PDF

Stasyk, O. V,  Stasyk, O. G., Mathewson, R. D., Farré, J. –C.,  Nazarko, V. Y.,  Krasovska, O. S.,  Subramani, S.,  Cregg, J. M.,  Sbirny, A. Atg28, a novel coiled-coil protein involved in autophagic degradation of peroxisomes in the methylotrophic yeast Pichia pastoris. Autophagy, 2:30-38 (2006).PDF

Lin-Cereghino, G. P., Godfrey, L., De la Cruz, B. J., Johnson, S., Khuongsathiene, S., Tolstorukov, I., Yan, M., Lin-Cereghino, J., Veenhuis, M., Subramani, S., Cregg, J. M. Mxr1p: a key regulator of the methanol-utilization pathway and peroxisomal genes in Pichia pastoris. Mol. Cell. Biol., 26: 883-897 (2006).PDF

Rayapuram, N., Subramani, S. The importomer – a peroxisomal membrane complex involved in protein translocation into the peroxisome matrix. Biochim. Biophys. Acta, 1763: 1613-9 (2006).PDF

Léon, S., Goodman, J.M., Subramani, S. Uniqueness of the mechanism of protein import into the peroxisome matrix: transport of folded, co-factor-bound and oligomeric proteins by shuttling receptors. Biochim. Biophys. Acta, 1763: 1552-1564 (2006).PDF

Léon, S., Zhang, L., McDonald, H., Yates III, J., Cregg, J. M., Subramani, S. Dynamics of the peroxisomal import cycle of PpPex20p: ubiquitin-dependent localization and regulation. J. Cell Biol., 172: 67-78 (2006).PDF

Zhang, L., Léon, S., Subramani, S. Two independent pathways traffic the intraperoxisomal peroxin Pex8p into peroxisomes: mechanism and evolutionary implications. Mol. Biol. Cell, 17:690-699 (2006).PDF

Yan, M., Rayapuram, N. and Subramani, S. The control of peroxisome number and size during division and proliferation, Curr. Opin. Cell Biol., 14: 376-383 (2005).PDF

Farré, J.-C. Subramani, S. Peroxisome turnover by micropexophagy – an autophagy-related process. Trends Cell Biol., 14: 515-523 (2004).PDF

Subramani, S. Peroxisomes, in Encyclopedia of Biological Chemistry (eds. W.J. Lennarz and M.D. Lane, eds), Elsevier, Oxford, 3: 246-250 (2004).PDF

Klionsky, D. J., Cregg, J. M., Dunn, W. A. Jr., Emr, S. D., Sakai, Y., Sandoval, I. V., Sbirny, A., Subramani, S., Thumm, M., Veenhuis, M. Ohsumi, Y.  Unified nomenclature for yeast autophagy-related genes. Dev. Cell 5: 539-545 (2003).PDF

Hazra, P., Suriapranata, I., Snyder, W. and Subramani, S. Peroxisome remnants in pex3D cells and the requirement of Pex3p for interactions between the peroxisomal docking and translocation subcomplexes. Traffic, 3: 560-574 (2002).PDF

Subramani, S., Dammai, V., Hazra, P., Suriapranata, I. and Lee, S. Import of proteins into peroxisomes. In Protein targeting, transport and translocation, (eds. Dalbey, R.E. and von Heijne, G.), Ch. 12, pp. 268-292, Academic Press (2002).

Subramani, S. Hitchhiking fads en route to peroxisomes. J. Cell Biol.,  156: 415-417 (2002).PDF 

Luers, G., Otte, D.M., Subramani, S. and Franz, T. Genomic organization, chromosomal localization and tissue specific expression of the murine Pxmp2 gene encoding the 22 kDa peroxisomal membrane protein (Pmp22). Gene, 272: 45-50 (2001).PDF

Subramani, S. Self destruction in the line of duty. Dev. Cell, 1: 6-8 (2001).PDF

Dammai, V. and Subramani, S. The human peroxisomal targeting signal receptor, Pex5p, is translocated into the peroxisome matrix and recycled to the cytosol. Cell, 105: 187-196  (2001).PDF

Amery, L., Mannaerts, G.P., Subramani, S., Van Veldhoven, P. P., Fransen, M. Identification of a novel human peroxisomal  2,4-dienoyl-CoA reductase related protein using the M13 phage protein VI phage display technology. Combinatorial Chem. and High Throughput Screening, 4: 545-552  (2001).PDF

Johnson, M.A., Snyder, W.B., Cereghino, J.L., Veenhuis, M., Subramani, S., Cregg, J.M.  Pichia pastoris Pex14p, a phosphorylated  peroxisomal membrane protein, is part of a PTS-receptor docking complex and interacts with many peroxins. Yeast, 18: 621-641 (2001).PDF

Terlecky,  S.R., Legakis, J.E.,  Hueni,  S.E., Subramani, S. Quantitative analysis of peroxisomal protein import in vitro. Exper. Cell Res. 263:98-106  (2001).PDF

Sakai, Y., Subramani, S. Environmental response of yeast peroxisomes: aspects of organelle assembly and degradation. Cell Biochemistry and Biophysics, 32: 51-61 (2000).PDF

Snyder, W.B., Koller, A., Choy, A.J., Subramani, S. The peroxin Pex19p interacts with multiple, integral membrane proteins at the peroxisomal membrane. J. Cell Biol., 149: 1171-1177 (2000).PDF

Koller, A., Velasco, J., Subramani, S. The CUP1 promoter of Saccharomyces cerevisiae is inducible by copper in Pichia pastoris. Yeast, 16: 651-656 (2000).PDF

Subramani, S., Koller, A., Snyder, W.B.  Import of peroxisomal matrix and membrane proteins. Annu. Rev. Biochem. 69: 399-418 (2000).PDF

Snyder, W.B., Koller, A., Choy, A.J., Johnson, M., Cregg, J.M., Rangell, L., Keller, G.A., Subramani, S. Pex17p is required for import of both peroxisome membrane and lumenal proteins and interacts with Pex19p and the PTS-receptor docking complex in Pichia pastoris. Mol. Biol. Cell, 10: 4005-4019 (1999).PDF

Yamashita, H., Avraham, S., Jiang, S., London, R., Van Veldhoven, P.P., Subramani, S, Rogers, R.A., Avraham, H. Characterization of the human and murine PMP20 peroxisomal membrane proteins that exhibit antioxidant activity in vitro.  J. Biol. Chem., 274: 29897-29904 (1999).PDF

Koller, A., Snyder, W.B., Faber, K.N., Wenzel, T.J., Rangell, L., Keller, G.A., Subramani, S. Pex22p of Pichia pastoris, essential for peroxisomal matrix protein import, anchors the ubiquitin-conjugating enzyme, Pex4p, on the peroxisomal membrane. J. Cell Biol., 146: 99-112  (1999).PDF

Lenormand, J.L., Dellinger, R.W., Knudsen, K.E., Subramani, S., Donoghue, D.J. Speedy: a novel cell cycle regulator of the G2/M transition. EMBO J., 18: 1869-1877 (1999).PDF

Koller, A., Spong, A.P., Lüers, G.H., Subramani, S. Analysis of the peroxisomal Acyl-CoA oxidase gene product from Pichia pastoris and determination of its targeting signal. Yeast, 15:1035-1044 (1999).PDF

Snyder, W.B., Faber, K.N., Wenzel, T.J., Koller, A., Lüers, G.H., Rangell, L., Keller, G.A., Subramani, S. Pex19p interacts with Pex3p and Pex10p and is essential for peroxisome biogenesis in Pichia pastoris. Mol. Biol. Cell, 10:1745-1761  (1999).PDF

Fransen, M., Van Veldhoven, P.P., Subramani, S. Identification of peroxisomal proteins using pVI-phage display: Molecular evidence that mammalian peroxisomes contain a 2,4-dienoyl-CoA  reductase.  Biochem. J., 340: 561-568  (1999).PDF

Subramani, S. Biogenesis of peroxisomes, in Lipid  and Protein Traffic, Pathways and Molecular Mechanisms, (ed. J. A. F. Op den Kamp), NATO ASI Series, Vol. H 106, pp65-76, Springer-Verlag (1998).

Fransen, M.F., Terlecky, S.R., Subramani, S.  Identification of a  human PTS1 receptor docking protein directly required  for peroxisomal protein import. Proc. Natl. Acad. Sci. USA, 95: 8087-8092 (1998).PDF

Kostrub, C. F.,  Knudsen, K., Subramani, S., Enoch, T. Hus1p, a conserved fission yeast checkpoint protein, interacts with Rad1p and is phosphorylated in response to DNA damage.  EMBO J.,  17: 2055-2066  (1998).PDF

Sakai, Y., Koller, A., Rangell, L.K., Keller, G.A., Subramani, S. Peroxisome degradation by microautophagy in Pichia pastoris: identification of specific steps and morphological intermediates.  J. Cell Biol., 141: 625-636 (1998).PDF

Lüers, G.H., Advani, R., Wenzel, T., Subramani, S. The P. pastoris dihydroxyacetone kinase is a PTS1-containing, but cytosolic, protein that is essential for growth on methanol. Yeast, 14: 759-771  (1998).PDF

Elgersma, Y., Elgersma-Hooisma, M., Wenzel, T., McCaffery, J.M., Farquhar, M.G., Subramani, S. A mobile PTS2-receptor for peroxisomal protein import in Pichia pastoris. J. Cell Biol., 140: 807-820 (1998).PDF

Faber, K. N., Heyman, J.A., Subramani, S. The AAA-family peroxins, PpPex1p and PpPex6p, interact with each other in an ATP-dependent  manner and are associated with different subcellular membranous structures distinct from peroxisomes. Mol. Cell. Biol. 18: 936-943(1998).PDF

Subramani, S. Components involved in peroxisome import, biogenesis, proliferation, turnover and movement. Physiol. Rev. 78: 171-188 (1998).PDF

Osman, F., Subramani, S. Double-strand break-induced recombination in eukaryotes. Prog.  Nucl. Acids Res. and Mol. Biol. 58: 263-299 (1998).PDF

Faber, K. N., Elgersma, Y., Heyman, J. A., Koller, A., Lüers, G. H., Nuttley, W. M., Terlecky, S. R., Wenzel, T. J., Subramani, S. Use of Pichia pastoris as a model eukaryotic system: Peroxisome biogenesis, in Methods in Molecular Biology: Pichia protocols (ed. D. R. Higgins),  Humana Press, Totowa, NJ, USA, Ch. 10, pp 121-147 (1998).

Sakai, Y., Subramani, S.  Green fluorescent protein (GFP) fluorescence through the rhodamine channel after excitation using the FITC filter set.  Tech. Tips Online ( ), T01319 (1997).

Elgersma, Y., Kwast, L., van den Berg, M., Snyder, W.B., Distel, B., Subramani, S., Tabak, H.F. Overexpression of Pex15p, a phosphorylated peroxisomal integral membrane protein required for peroxisomal assembly  in S. cerevisiae, causes proliferation of the endoplasmic reticulum membrane. EMBO J.,  16: 7326-7341  (1997).PDF

Subramani, S. PEX genes on the rise. Nature Genetics, 15: 331-333 (1997).PDF

Wiemer, E. A.C.,  Wenzel, T., Deerinck, T. J.,  Ellisman, M. H. , Subramani, S.  Visualization of the peroxisomal  compartment in living mammalian cells: dynamic behavior and association with microtubules. J. Cell Biol. 136: 71-80 (1997).

Distel, B., Erdmann, R., Gould, S.J., Blobel, G., Crane, D.I., Cregg, J.M., Dodt, G., Fujiki, Y., Goodman, J.M., Just, W.W., Kiel, J.A.K.W., Kunau, W.H., Lazarow, P.B., Mannaerts, G.P., Moser, H., Osumi, T., Rachubinski, R.A., Roscher, A., Subramani, S., Tabak, H.F., Valle, D., van der Klei, I., van Veldhoven, P.P., Veenhuis, M. A unified nomenclature for peroxisome biogenesis. J. Cell Biol. 135: 1-3 (1996).

Terlecky, S. R., Nuttley, W. M.,  Subramani, S. The requisite cytosolic and membrane components of peroxisomal protein  import.  Experientia  52: 1050-1054 (1996).

Subramani, S. Protein translocation into peroxisomes. J. Biol. Chem. 271: 32483-32486  (1996).

Wiemer, E.A.C.,  Lüers, G., Faber, K. N., Wenzel, T., Veenhuis, M., Subramani, S. Isolation and characterization of Pas2p, a peroxisomal membrane protein essential for peroxisome biogenesis in the methylotrophic yeast Pichia pastoris. J. Biol. Chem. 271: 18973-18980 (1996).

Knudsen, K. E., Knudsen, E. S., Wang, J. Y. J., Subramani, S. p34cdc2  kinase activity is maintained upon activation of the replication checkpoint in Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA93: 8278-8283 (1996).

Subramani, S. Converging models of peroxisome biogenesis. Curr. Opin. Cell Biol. 8: 513-518  (1996).

Fortunato, E. A., Osman, F., Subramani, S. Analysis of spontaneous and double-strand break-induced recombination in rad mutants of S. pombe. Mutation Res. 364: 147-160 (1996).

Monosov, E., Wenzel, T. J., Lüers, G. H., Heyman, J. A., Subramani, S. Labeling of peroxisomes with green fluorescent protein in living P. pastoris cells.  J. Histochem. Cytochem. 44: 581-589 (1996).

Terlecky, S. R., Wiemer, E. A. C., Nuttley, W. M. , Walton, P. A., Subramani, S.  Signals, receptors and cytosolic factors involved in peroxisomal protein import,  in Peroxisomes: Biology and Role in Toxicology and Disease.  (eds. J. K. Reddy, T. Suga, G.P. Mannaerts, P.B. Lazarow and S. Subramani) Annals New York Acad. Sci. 804: 11-20 (1996).


UCSD Division of Biological Sciences
home | lab members | research | publications | links | contact