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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 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. 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 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 (http://www.elsevier.com/locate/tto ), 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
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). |