Facebook Pixel Code
About Sickkids
About SickKids

Peter Kijun Kim, PhD

Research Institute
Senior Scientist
Cell Biology

University of Toronto
Department of Biochemistry
Associate Professor


Phone: 416-813-5983
Fax: 416-813-5028
Email: pkim@sickkids.ca

Research Interests

  •  Peroxisome biogenesis
  •  Selective Autophagy of organelles
  •  Membrane protein trafficking
  •  Membrane contact sites
  •  High-resolution light microscopy
  •  Neurodegeneration
  •  Malnutrition Organelle maintenance

Research Activities

The aim of Kim’s research is to understand the mechanisms involved in maintaining the metabolic organelles, peroxisomes and mitochondria and how dysregulation of these mechanisms contributes to various diseases ranging from neurodegenerative disorders to cancer to severe malnutrition.  

Peroxisome Formation and Neurodegenerative Disorders

Peroxisomes are ubiquitous small single membrane bound organelles that are required for the both metabolic and anabolic reaction of lipids and reactive oxygen species. They are formed from two distinct mechanisms: de novo from the endoplasmic reticulum and by growth and division of pre-existing peroxisomes. How these two mechanisms are regulated is not known. Recently, the Kim’s group has identified a number of genes involved in forming membrane contact sites between the ER and peroxisomes. The object of their studies is to determine the molecular and structural events involved in peroxisome biogenesis and examine the role of these contact sites in peroxisome formation and maintenance. With this knowledge, they will be able to understand the regulatory events that govern peroxisomes numbers, and their implications in Neurodegeneration diseases.

Organelle Turnover

Peroxisomes and mitochondria are selectively degraded by the cellular recycling process, called selective autophagy. Although the players differ, growing evidence suggest that both organelles are designation for degradation by tagging of their membrane proteins by a small polypeptide called ubiquitin. Kim’s research examines the molecular events preceding and following the ubiquitination of peroxisomes and mitochondria. As dysfunction in selective autophagy is linked to neurodegenerative diseases and cancer, to severe malnutrition, these studies will provide insight into the relationship between selective autophagy and disease and aid in the future therapeutic treatment of these diseases.

Small Molecule Discover for Selective Autophagy

Genetic mutations in one of 13 peroxisome genes result in the loss of peroxisome number and function. Collectively known as Peroxisome Biogenesis Disorder  (PBD) or Zellweger spectrum disorders, this disorder clinical manifests as multiple organ dysfunction resulting in neurodegenerative, growth delay and development, and can lead to death as early as the first years of life. The most common mutations are found in the three genes composing the peroxisomal AAA ATPase (PEX1, PEX6 and PEX26). Although mutations in the peroxisomal AAA ATPase are largely believed to cause a defect in peroxisome biogenesis, the Kim lab has recently demonstrated that defect in these genes leads to early degradation of peroxisome by pexophagy, the selective autophagic degradation of peroxisomes.  They also found that inhibiting autophagy improves peroxisome number and function in culture cells with mutation in PEX1. The goal of this project is to identity small molecules that specifically inhibit pexophagy and not general autophagy. Development of such drug will aid in treating children with PBD.

External Funding

  • Canadian Foundation for Innovation
  • Canadian Institutes of Health Research
  • Ontario Innovation Trust
  • Natural Sciences and Engineering Research Council

Publications

Law KB., Bronte-Tinkew, D., DiPietro E., Brumell, JH., Braverman, N., Kim, PK. A mechanism of peroxisome degradation in AAA ATPase-deficient peroxisome biogenesis disorder.  Autophagy (2016) in press

van Zutphen T, Ciapaite J, Bloks VW, Ackereley C, Gerding A, Jurdzinski A, de Moraes R, Zhang L, Wolters JC, Bischoff R, Wanders RJ, Houten SM, Bronte-Tinkew D, Shatseva T, Lewis GF, Groen AK, Reijngoud D-J, Bakker BM, Jonder JW, Kim PK,* Bandsma RHJ*. Malnutrition-associated liver steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction and rescued by fibrates. Journal of Hepatology. (2016) 65:1198-1208. *co-corresponding author

Sargent G., van Zutphen, T, Shatseva, T., Zhang, L., Di Giovanni, V., Bandsma, RHJ, and Kim P.K. ¬¬PEX2 is the E3 Ubiquitin Ligase Required for Pexophagy during Starvation. Journal of Cell Biology. (2016) 214:677-90

Klionsky DJ, Abdelmohsen K, Abe A ....Kim PK ...etal (numerous authors) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). (2016) Autophagy 12 (1).

Hua R, Kim PK. Multiple paths to peroxisomes: Mechanism of peroxisome maintenance in mammals. (2016) Biochim. Biophys. Acta. 1863(5): 881-891.

Hua R, Gidda S, Aranovich A, Mullen R, Kim PK. Multiple domains in PEX16 mediate its trafficking and recruitment of peroxisomal proteins to the ER. ( 2015) Traffic 16(8): 832-852.

Wang Y, Serrichhio M, Jauregui M, Shanbhag R, Stoltz T, DiPaolo CT, Kim PK*, McQuibban GA*. Deubiquitinating enzymes regulate PARK2-mediate mitophagy. (2015) Autophagy 11 (4): 595-606. *co-corresponding author

Kim PK, Hettema EH. Multiple pathways for protein transport to peroxisomes. (2015) Journal of Molecular Biology 427: 1176-1190.

Aranovich A, Hua R, Rutenberg AD, Kim PK. PEX16 contributes to peroxisome maintenance by constantly trafficking PEX3 via the ER. (2014) Journal Cell Science 127: 3675-3686.

Brown AI, Kim PK, Rutenberg A. PEX5 and ubiquitin dynamics on mammalian peroxisome membranes. (2014) PLoS Comput. Biol. 10: e1003426.

Jauregui M, Kim PK. Probing peroxisome dynamics and biogenesis by fluorescence imaging. (2013) Current Protocols in Cell Biology 62: 21.9.1-20.

Kim PK, Mullen RT. PEX16: a multifaceted regulator of peroxisome biogenesis. (2013) Frontier in Integrative Physiology 4: 21 (review).

Deosaran E, Larsen KB, Hua R, Sargent G, Wang Y, Kim S, Lamark T, Jauregui M, Law K, Lippincott-Schwartz J, Brech A, Johansen T, Kim PK. NBR1 acts as an autophagy receptor for peroxisomes. (2013) Journal Cell Science 126: 939-952. (Featured in JCS. High-lighted in the journal issue).

Klionsky DJ, et al . Guidelines for the use and interpretation of assays for monitoring autophagy. (2012) Autophagy 8: 455-544.

Wang Y, Nartiss Y, McQuibban GA, Kim PK. ROS-induced mitochondrial depolymerization induces Parkin-dependent mitochondrial degradation by autophagy. (2012). Autophagy 8: 1-15. (Journal cover photo).

Shahnazari S, Namolovan A, Mogridge J, Kim PK, Brumell JH. Bacterial toxins can inhibit host cell autophagy through cAMP generation. (2011) Autophagy 7: 957-965.

Gidda SK, Shockey JM, Falcone M, Kim PK, Rothstein SJ, Andrews DW, Dyer JM, Mullen RT. Hydrophobic-domain-dependent protein-protein interactions mediate the localization of GPAT enzymes to ER subdomains. (2011) Traffic 12(4): 452-472.

Cemma M, Kim PK, Brumell JH. The ubiquitin-binding adaptor proteins p62/SQSTM1 and NDP52 are recruited independently to bacterial-associated microdomains to target Salmonella to the autophagy pathway. (2011) Autophagy 7(3): 22-26.

Huang J, Birmingham CL, Shahnazari S, Shiu J, Zheng YT, Smith AC, Campellone KG, Heo WD, Gruenheid S, Meyer T, Welch MD, Ktistakis NT, Kim PK, Klionsky DJ, Brumell JH. Antibacterial autophagy occurs at PI(3)P-enriched domains of the endoplasmic reticulum and requires Rab1 GTPase. (2011) Autophagy 7(1): 17-26.

Hailey DW, Rambold AS, Satpute-Krishnan P, Mitra K, Sougrat R, Kim, PK, Lippincott-Schwartz J. Mitochondria supply membranes for autophagosome biogenesis during starvation. (2010) Cell, 141(4): 656-67.