Subramani Lab

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UC San Diego Division of Biological Sciences
Section of Cell and Developmental Biology

Research

Our research examines how peroxisomes are formed, maintained, remodeled, and removed, with emphasis on mechanisms that connect organelle homeostasis to cellular stress and disease.

Proteotoxic stress and peroxisome proliferation

Recent work shows that protein-misfolding stress in the endoplasmic reticulum (ER) or cytosol can increase peroxisome abundance, primarily by stimulating de novo biogenesis and, to a lesser extent, growth and division. In yeast, this response can be triggered by loss of Kar2 function, tunicamycin, or DTT. The response does not require the classical UPR regulators Ire1, Hac1, or Gcn4, and instead involves activation of heat-shock signaling and inhibition of TOR signaling. The response is conserved from yeast to human cells, and peroxisome biogenesis contributes to survival during proteotoxic stress.

De novo peroxisome biogenesis from the ER

The lab studies how new peroxisomes arise from the ER using genetics, in vitro biochemistry, and high-throughput microscopy. Mutants that affect de novo peroxisome biogenesis are being used to define the proteins and membrane-trafficking steps required for this pathway.

Interorganelle communication

A complementary line of work examines communication between mitochondria and peroxisomes, including how mitochondrial energy production feeds back on peroxisome proliferation and how other cellular compartments influence peroxisome homeostasis.

Protein targeting, import, and quality control

Earlier work from the lab helped establish the principles of peroxisomal matrix-protein targeting, characterized targeting-signal receptors and membrane-protein targeting pathways, demonstrated import of folded proteins, and defined PTS receptor-recycling and quality-control mechanisms.

Pexophagy and selective autophagy

The lab has defined morphological, receptor, adaptor, signaling, and network-level mechanisms that control pexophagy, the selective autophagic turnover of peroxisomes, as well as selective autophagy of cytosolic pools of peroxisomal proteins.

Publications

Google Scholar profile: Suresh Subramani on Google Scholar

ResearchGate profile: Suresh Subramani on ResearchGate

Our past accomplishments are captured in the following publications:

Identification and Conservation of the First Peroxisomal Targeting Signals (PTSs)

  • Keller, G., Gould, S., DeLuca, M., Subramani, S. Firefly luciferase is targeted to peroxisomes in mammalian cells. PNAS 84: 3264-3268 (1987).
  • Gould, S.J., Keller, G.-A., Subramani, S. Identification of a peroxisomal targeting signal at the carboxy-terminus of firefly luciferase. JCB, 105: 2923-2931 (1987).
  • Gould, S.J., Keller, G.-A., Subramani, S. Identification of peroxisomal targeting signals located at the carboxy terminus of four peroxisomal proteins. JCB, 107: 897-905 (1988).
  • Gould, S.J., Keller, G.-A., Hosken, N., Wilkinson, J., Subramani, S. A conserved tripeptide sorts proteins to peroxisomes. JCB, 108:1657-1664 (1989).
  • Gould, S.J., Keller, G.-A., Schneider, M., Howell, S.H., Garrard, L.J., Goodman, J.M., Distel, B., Tabak, H., Subramani, S. Peroxisomal protein import is conserved between yeast, plants, insects and mammals. EMBO J, 9: 85-90 (1990).
  • Gould, S.J., Krisans, S. Keller, G., Subramani, S. Antibodies directed against the peroxisomal targeting signal of firefly luciferase recognize multiple mammalian peroxisomal proteins. JCB, 110: 27-34 (1990).
  • Keller, G.-A., Krisans, S.K., Gould, S.J., Sommer, J., Wang, C.C., Schliebs, W., Kunau, W., Brody, S., Subramani, S. Evolutionary conservation of a signal that targets proteins to peroxisomes, glyoxysomes and glycosomes. JCB, 114: 893-904 (1991).
  • Swinkels, B.W., Gould, S.J., Subramani, S. Targeting efficiencies of various permutations of the consensus C-terminal tripeptide peroxisomal targeting signal. FEBS Lett, 305: 133-136 (1992).
  • Blattner, J., Swinkels, B., Dörsam, M., Prospero, T., Subramani, S. and Clayton, C. Glycosome assembly in trypanosomes: variations in the acceptable degeneracy of a C-terminal microbody targeting signal. JCB, 119: 1129-1136 (1992).
  • Swinkels, B.W., Gould, S.J., Bodnar, A.G., Rachubinski, R.A., Subramani, S. A novel cleavable peroxisomal targeting signal at the amino terminus of the rat 3-ketoacyl-CoA thiolase. EMBO J, 10: 3255-3261 (1991).
  • Glover, J. R., Andrews, D. W., Subramani, S., Rachubinski, R. A. Mutagenesis of the amino-targeting signal of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase reveals conserved amino acids required for import into peroxisomes in vivo. JBC, 269: 7558-7563 (1994).

PTS and mPTS/PMP Receptors

  • McCollum, D. M., Monosov, E. and Subramani, S. The pas8 mutant of Pichia pastoris exhibits the peroxisomal protein import deficiencies of Zellweger Syndrome cells – The PAS8 protein binds the COOH-terminal tripeptide peroxisomal targeting signal and is a member of the TPR protein family. JCB, 121: 761-774 (1993).
  • Terlecky, S.R., Nuttley, W. M., McCollum, D., Sock, E., Subramani, S. The Pichia pastoris peroxisomal protein, PAS8p, is the receptor for the carboxy-terminal, tripeptide peroxisomal targeting signal. EMBO J,14: 3627-3634 (1995).
  • Wiemer, E. A. C., Nuttley, W. M., Bertolaet, B. L., Li, X., Francke, U., Wheelock, M. J., Anne, U. K., Johnson, K. R., Subramani, S. The human PTS1 receptor restores peroxisomal protein import in cells from patients with fatal peroxisomal disorders. JCB, 130: 51-65 (1995).
  • Wiemer, E. A. C., Terlecky, S. R., Nuttley, W. M., Subramani, S. Characterization of the yeast and human receptors for the carboxy-terminal, tripeptide peroxisomal targeting signal. Cold Spring Harbor Symp. Quant. Biol. Vol LX, 637-648 (1995).
  • 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).
  • 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. MBC, 10: 1745-1761 (1999).
  • Snyder, W.B., Koller, A., Choy, A.J., Subramani, S. The peroxin Pex19p interacts with multiple, integral membrane proteins at the peroxisomal membrane. JCB, 149: 1171-1177 (2000).
  • Agrawal, G., Shang, H.H., Xia, Z.-J., Subramani, S. Functional regions of the peroxin Pex19 necessary for peroxisome biogenesis. JBC, 292: 11547-11560 (2017).
  • Zientara-Rytter. K.M., Mahalingam, S.S., Farré, J.C., Carolino, K., Subramani, S. Recognition and chaperoning by Pex19, followed by trafficking and membrane insertion of the peroxisome proliferation protein, Pex11. Cells, 11: 157 (2022).

PTS Receptor/Co-receptor Dynamics Including Quality Control by RADAR and Autophagy

  • Dammai, V., 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).
  • Wang, W., Subramani, S. Role of PEX5 ubiquitination in maintaining peroxisome dynamics and homeostasis. Cell Cycle, 16: 2037-2045 (2017).
  • 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. JCB, 140: 807-820 (1998).
  • 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. JCB, 172: 67-78 (2006).
  • Léon, S., Subramani, S. A conserved cysteine residue of Pichia pastoris Pex20p is essential for its recycling from the peroxisome to the cytosol. JBC, 282: 7424-30 (2007).
  • Liu, X., Subramani, S. Unique requirements for mono- and poly-ubiquitination of the peroxisomal targeting signal co-receptor, Pex20. JBC, 288: 7230-7240 (2013).
  • Hagstrom D, Ma C, Guha-Polley S, Subramani S. The unique degradation pathway of the PTS2 receptor, Pex7, is dependent on the PTS receptor/coreceptor, Pex5 and Pex20. MBC, 25: 2634-43 (2014).
  • Wang, X., Wang, P., Zhang, Z., Farré, J.C., Li, X., Wang, R., Xia, Z., Subramani, S., Ma, C. The autophagic degradation of cytosolic pools of peroxisomal proteins by a new selective pathway. Autophagy, 16(1): 154-166 (2020). doi:10.1080/15548627.2019.1603546.

Involvement of Hsp70 and Other Chaperones in Peroxisomal Protein Import

Matrix Protein Import

  • Walton, P. A., Wendland, M., Subramani, S., Rachubinski, R. A., Welch, W. J. Involvement of 70-kD heat-shock proteins in peroxisomal import. JCB, 125: 1037-46 (1994).
  • 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).

PMP Import

  • Snyder, W.B., Koller, A., Choy, A.J., Subramani, S. The peroxin Pex19p interacts with multiple, integral membrane proteins at the peroxisomal membrane. JCB, 149: 1171-1177 (2000).
  • Zientara-Rytter. K.M., Mahalingam, S.S., Farré, J.C., Carolino, K., Subramani, S. Recognition and chaperoning by Pex19, followed by trafficking and membrane insertion of the peroxisome proliferation protein, Pex11. Cells, 11: 157 (2022).

Import of Folded and Oligomeric Proteins into the Peroxisome Matrix

  • Walton, P. A., Hill, P. E., Subramani, S. Import of stably folded proteins into peroxisomes. MBC, 6: 675-83 (1995).

ER Involvement in Peroxisome Biogenesis

  • 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 peroxisome assembly in S. cerevisiae, causes proliferation of the endoplasmic reticulum membrane. EMBO J, 16: 7326-41 (1997).
  • 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. MBC, 19: 885-98 (2008).
  • Agrawal, G., Joshi, S.S., Subramani, S. Cell-free sorting of peroxisomal membrane proteins from the endoplasmic reticulum. PNAS, 108: 9113-8 (2011).
  • Agrawal, G., Fassas, S. N., Xia, Z., Subramani, S. Distinct requirements for intra-ER sorting and budding of peroxisomal membrane proteins from the endoplasmic reticulum. JCB, 212: 335-48 (2016).
  • Farre, J.-C., et al. A new yeast peroxin, Pex36, a functional homologue of mammalian PEX16, functions in the ER-to-peroxisome traffic of peroxisomal membrane proteins. JMB, 429: 3743-3762 (2017).
  • Shukla, N., Neal, M.L., Farré, J.-C., Mast, F.D., Sarkar, R., Truong, L., Simon, T., Miller, L.R., Aitchison, J.D., Subramani, S. TOR and heat shock response pathways regulate peroxisome biogenesis during proteotoxic stress. Nature Communications, 16:10743 (2025). doi:10.1038/s41467-025-65776-y.

Influence of Other Subcellular Compartments on Peroxisome Homeostasis

Membrane Contact Sites

  • Farré, J.-C., Mahalingam, S.S., Proietto, M., Subramani, S. Peroxisome biogenesis, membrane contact sites, and quality control. EMBO Rep, doi: 10.15252/embr.201846864 (2018).

Mitochondrial, Nuclear and Cytosolic Influence

  • Farré, J.C., Carolino, K., Devanneaux, L., Subramani, S. OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway. ELife, doi: 10.7554/eLife.75143 (2022).

ER, Cytosol and Nucleus

  • Shukla, N., Neal, M.L., Farré, J.-C., Mast, F.D., Sarkar, R., Truong, L., Simon, T., Miller, L.R., Aitchison, J.D., Subramani, S. TOR and heat shock response pathways regulate peroxisome biogenesis during proteotoxic stress. Nature Communications, 16:10743 (2025). doi:10.1038/s41467-025-65776-y.

Vacuolar Role

  • Farré, J.C., Manjithaya, R., Mathewson, R.D., Subramani, S. PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev. Cell, 14: 365-76 (2008).
  • 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, 6: 86-99 (2010).

Control of Peroxisome Size and Number by Peroxins, Mitochondria and Stress

  • 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. MBC, 19: 885-98 (2008).
  • Farré, J.C., Carolino, K., Devanneaux, L., Subramani, S. OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway. ELife, doi: 10.7554/eLife.75143. (2022).
  • Shukla, N., Neal, M.L., Farré, J.-C., Mast, F.D., Sarkar, R., Truong, L., Simon, T., Miller, L.R., Aitchison, J.D., Subramani, S. TOR and heat shock response pathways regulate peroxisome biogenesis during proteotoxic stress. Nature Communications, 16:10743 (2025). doi:10.1038/s41467-025-65776-y.

Development of in vitro Systems for Matrix Protein Import and Peroxisome Biogenesis

PTS1 Protein Import

  • Wendland, M., Subramani, S. Cytosol-dependent peroxisomal protein import in a permeabilized cell system. JCB, 120: 675-85 (1993).
  • Walton, P. A., Gould, S. J., Rachubinski, R. A., Subramani, S., Feramisco, J.R. Transport of microinjected alcohol oxidase from Pichia pastoris into vesicles in mammalian cells: involvement of the peroxisomal targeting signal. JCB, 118: 499-508 (1992).
  • Walton, P. A., Gould, S. J., Feramisco, J. R., Subramani, S. Transport of microinjected proteins into peroxisomes of mammalian cells: inability of Zellweger cell lines to import proteins with the SKL tripeptide peroxisomal targeting signal. MCB, 12: 531-41 (1992).
  • Walton, P. A., Hill, P. E., Subramani, S. Import of stably folded proteins into peroxisomes. MBC, 6: 675-83 (1995).
  • 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).

de novo Biogenesis

  • Agrawal, G., Joshi, S.S., Subramani, S. Cell-free sorting of peroxisomal membrane proteins from the endoplasmic reticulum. PNAS, 108: 9113-8 (2011).
  • Agrawal, G., Fassas, S. N., Xia, Z., Subramani, S. Distinct requirements for intra-ER sorting and budding of peroxisomal membrane proteins from the endoplasmic reticulum. J. Cell Biol., 212: 335-48 (2016).

Pexophagy, Pexophagy Receptor, Adaptors and Mechanisms

Morphological Steps in Macropexophagy and Micropexophagy

  • 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. JCB, 141: 625-636 (1998).

Pexophagy Receptor (first organelle-specific receptor for selective autophagy)

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

Pexophagy Adaptor

  • Farré, J.-C., Burkenroad, A., Burnett, S.F., Subramani, S. Phosphorylation of mitophagy and pexophagy receptors coordinates their interaction with Atg8 and Atg11. EMBO Rep, 14: 441-449 (2013).
  • Zientara-Rytter, K., Subramani, S. Mechanistic insights into the role of Atg11 in selective autophagy, JMB, 432: 104-122 (2020).

Other Pexophagy Proteins

  • 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, 6: 86-99 (2010).
  • 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).
  • Nazarko, V.Y., Nazarko, T.Y., Farré, J.-C., Stasyk, O.V., Warnecke, D., Ulazewski, S., Cregg, J. M., Sibirny, A.A., Subramani, S. Atg35, a micropexophagy-specific protein that regulates micropexophagic apparatus formation in Pichia pastoris, Autophagy, 7: 375-85 (2011).
  • Nazarko, T. Y., Ozeki, K., Till, A., Ramakrishnan, G., Lotfi, P., Yan, M., Subramani, S. Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy. JCB, 204: 541-57 (2014).

Pexophagy Mechanisms, Significance & Networks and Proteome Remodeling

Pexophagy Activation and Mechanism

  • Manjithaya, R.R., Jain, S. Farré, J. -C., Subramani, S. A yeast MAPK cascade regulates pexophagy but not other autophagy pathways. JCB, 189: 303-10 (2010).
  • Farré, J.-C., Burkenroad, A., Burnett, S.F., Subramani, S. Phosphorylation of mitophagy and pexophagy receptors coordinates their interaction with Atg8 and Atg11. EMBO Rep, 14: 441-449 (2013).
  • Lakhani, R., Till, A., Vogel, K., Gibson, M.A., Subramani, S. Defects in GABA metabolism affect selective autophagy pathways and are alleviated by mTOR inhibition. EMBO Mol Med, 6: 551-66 (2014).
  • Burnett, S.F., Farré, J.-C., Nazarko, T. Y., Subramani, S. Peroxisomal Pex3 activates selective autophagy of peroxisomes via interaction with pexophagy receptor, Atg30. JBC, 290: 8623-8631 (2015).
  • Zientara-Rytter, K., Ozeki, K., Nazarko, T.Y., Subramani, S. Pex3 and Atg37 compete to regulate the interaction between the pexophagy receptor, Atg30, and the Hrr25 kinase. Autophagy, 14: 368-384 (2017).

Selective Autophagy of Cytosolic Pools of Peroxisomal Proteins and Fungal Proteome Remodeling

  • Wang, X., Wang, P., Zhang, Z., Farré, J.C., Li, X., Wang, R., Xia, Z., Subramani, S., Ma, C. The autophagic degradation of cytosolic pools of peroxisomal proteins by a new selective pathway. Autophagy, 16(1): 154-166 (2020).
  • Telusma, B., Farré, J.-C., Cui, D.S., Subramani, S., Davis, J.H. Bulk and selective autophagy cooperate to remodel a fungal proteome in response to changing nutrient availability. Cell Rep, 44:116585 (2025). doi: 10.1016/j.celrep.2025.116585.

Autophagy Networks

  • Kramer, M.H., Farré, J.C., Mitra, K., Yu, M.K., Ono, K., Demchak, B., Licon, K., Flagg, M., Balakrishnan, R., Cherry, J.M., Subramani, S., Ideker, T. Active Interaction Mapping reveals the hierarchical organization of autophagy. Mol Cell, 65: 761-774 (2017).