Peroxisomes are essential subcellular organelles that play crucial roles in the oxidation of fatty-acids and homeostasis of glutathione, as well as reactive oxygen and nitrogen species (ROS and RNS, respectively). They play critical roles in the regulation of intracellular redox states and antiviral signaling, as well as cellular differentiation and metabolism, and their impairment causes many debilitating, and often fatal, human peroxisome biogenesis disorders (PBDs). Their biogenesis is orchestrated by 36 PEX genes, encoding peroxins, involved in the biogenesis of peroxisomal membrane and matrix proteins, as well as in the control of organelle size, number and inheritance. Their biogenesis has been studied in many organisms from yeast to plants and mammals, and more than 15 peroxins and their modes of action are conserved from yeast to man. While much has been learned about the biogenesis of peroxisomal matrix and membrane proteins to pre-existing peroxisomes, far less is known about how this organelle is generated de novo from other endogenous membranes. Such an ability to generate new peroxisomes de novo is obviously relevant under conditions where peroxisome biogenesis is impaired (e.g. human PBDs), or under conditions of stress (e.g. ROS) when peroxisomes are turned over by autophagy (pexophagy). Indeed, any disorders associated with imbalanced peroxisome homeostasis can be corrected, in principle, by manipulating either peroxisome biogenesis or its turnover, as we have shown. Such a global understanding of the mechanisms involved in peroxisome homeostasis is the long-term interest of my lab. Over almost 3 decades, we exploited the yeast, Pichia pastoris, to provide many major insights into our knowledge of peroxisome biogenesis and turnover. This proposal focuses on gleaning a deeper understanding of the proteins involved in the intra-ER sorting and budding of peroxisomal membrane proteins (PMPs) to a pre- peroxisomal exit site on the ER (pER) from where at least two type of pre-peroxisomal vesicles (ppVs) bud to ultimately generate peroxisomes, either by fusion with pre-existing peroxisomes or anew when peroxisomes are absent. Budding of ppVs is conserved between yeast and mammals and several proteins we will study have counterparts involved in human health. There are also reports of ppVs derived from mitochondria contributing to peroxisome biogenesis. Our approach is based on the use of novel genetic and biochemical strategies, including ppV purification and characterization, in vitro budding reactions and the use of innovative techniques to follow what these novel proteins do, where they act, who they interact with and how they function.
The Aims are:
Aim 1 - Isolation and characterization of the ATPase/s and other proteins involved in ppV budding.
Aim 2 ? How do Pex25 and Pex36 act in stimulating intra-ER sorting and budding of Pex2 and other RING- domain peroxins? Aim 3 ? Does ppV budding occur from yeast mitochondria and what is its physiological relevance?!
Peroxisomes are essential and conserved subcellular organelles required for intracellular metabolism and signaling, as well as for human development and health. They arise by growth and division of pre-existing peroxisomes, as well as by synthesis of new peroxisomes from intracellular membranes (de novo biogenesis), such as the endoplasmic reticulum and mitochondria. This proposal seeks to identify and characterize the proteins required for this de novo biogenesis of peroxisomes in a yeast model that is quite likely to be relevant for humans.
| Wang, Wei; Xia, Zhijie; Farré, Jean-Claude et al. (2018) TRIM37 deficiency induces autophagy through deregulating the MTORC1-TFEB axis. Autophagy 14:1574-1585 |
| Zientara-Rytter, Katarzyna; Ozeki, Katharine; Nazarko, Taras Y et al. (2018) Pex3 and Atg37 compete to regulate the interaction between the pexophagy receptor, Atg30, and the Hrr25 kinase. Autophagy 14:368-384 |
| Zientara-Rytter, Katarzyna; Subramani, Suresh (2018) AIM/LIR-based fluorescent sensors-new tools to monitor mAtg8 functions. Autophagy 14:1074-1078 |
| Farré, Jean-Claude; Kramer, Michael; Ideker, Trey et al. (2017) Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy 13:1248-1249 |
| Kramer, Michael H; Farré, Jean-Claude; Mitra, Koyel et al. (2017) Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell 65:761-774.e5 |
| Farré, Jean-Claude; Carolino, Krypton; Stasyk, Oleh V et al. (2017) A New Yeast Peroxin, Pex36, a Functional Homolog of Mammalian PEX16, Functions in the ER-to-Peroxisome Traffic of Peroxisomal Membrane Proteins. J Mol Biol 429:3743-3762 |
| Wang, Wei; Xia, Zhi-Jie; Farré, Jean-Claude et al. (2017) TRIM37, a novel E3 ligase for PEX5-mediated peroxisomal matrix protein import. J Cell Biol 216:2843-2858 |
| Agrawal, Gaurav; Shang, Helen H; Xia, Zhi-Jie et al. (2017) Functional regions of the peroxin Pex19 necessary for peroxisome biogenesis. J Biol Chem 292:11547-11560 |
| Agrawal, Gaurav; Subramani, Suresh (2016) De novo peroxisome biogenesis: Evolving concepts and conundrums. Biochim Biophys Acta 1863:892-901 |
| Zientara-Rytter, Katarzyna; Subramani, Suresh (2016) Autophagic degradation of peroxisomes in mammals. Biochem Soc Trans 44:431-40 |
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