Research Description

Mechanisms of Organelle Maintenance

Peroxisomes are one of the latest discovered and the least understood of the classical organelles. First described some 50 years ago, these ubiquitous and pleomorphic organelles remain an enigma in terms of their biogenesis, maintenance and degradation. A comprehensive understanding of these mechanisms is critical to understanding the role of these essential organelles in maintaining cellular homeostasis and viability, and ultimately, its role in various human diseases.

Peroxisomes are essential organelles that are required for the cellular metabolism of fatty acids, amino acids, and cellular toxins such as hydrogen peroxides. They also play a crucial role in the biosynthesis of bile salts (salts necessary for lipid digestion), and plasmalogen (essential lipids for the brain, heart and muscles). The importance of peroxisomes for proper cellular function is seen in the numerous inheritable genetic disorders resulting from a mutation in a single enzyme in peroxisomes, or mutation in proteins involved in the assembly of peroxisomes. Although the effects of these mutations in peroxisomal functions/assembly can be seen in various organs, such as, the liver, kidneys, blood and the heart; all peroxisomal disorders affect the development and function of the brain, thus, suggesting the importance of peroxisomes in brain development.

The primary objective of our group is to understand the basic mechanisms involved in the maintenance of peroxisomes in the mammalian cell, particularly in brain development. To achieve this goal, we are focusing on understanding the

1) biogenesis and 2) degradation of peroxisomes using cutting-edge live-cell microscopy techniques on state of the art microscopes in combination with biochemical approaches.

Peroxisome Biogenesis

The long-standing view has been that peroxisomes are autonomous organelles, like mitochondria and chloroplasts that multiply strictly by growth and division. This position is supported by evidence showing that most peroxisomal proteins are synthesized on free ribosomes and are imported directly into peroxisomes from the cytoplasm. However, unlike mitochondria, peroxisomes can disappear from a cell and then be regenerated de novo . This regenerative capacity has led to an alternative view in which other organelles, such as, ER-, participates in the formation and maintenance of peroxisomal membranes.

Our work with peroxisomes addresses whether the ER plays a role in peroxisomal biogenesis in mammalian cells, and if so, how this is regulated. Towards this end, we have employed diverse live cell fluorescent labeling strategies, including photoactivation, to pulse-label peroxisomal components (including the early event peroxin, PEX16) and to follow their targeting to peroxisomes. Evidence favouring an ER origin of peroxisomal membranes came from our finding that when the ER pool of PEX16-PAGFP was photoactivated and followed over time, the photoactivated molecules redistributed to peroxisomes. This result has helped solidify the view that peroxisomes are derived from the ER and have provided insight into peroxisomes proliferation and maintenance within mammalian cells. Ongoing work in the lab is aimed at using the new live-cell imaging and super-resolution light microscopy strategies to investigate the mechanism of peroxisome formation from the ER.

Peroxisome Degradation

Dysfunctional peroxisomes or excess peroxisomes are recycled through a process called Pexophagy. Pexophagy is the substrate-specific degradation by the autophagy pathways. This process involves the sequestration of peroxisomes by a double membrane structure and delivers peroxisomes to lysosomes for degradation. We believe that either an inhibition of pexophagy or an over-activation of pexophagy can lead to neurodegeneration. To test this hypothesis, a better understanding of pexophagy is required.

To this end, we have used both biochemical and imaging techniques to identify the molecular signal to designate a peroxisome for degradation. Using these various methods, we have shown that the modification of peroxisomal membrane protein with ubiquitin (ubiquitination) is the signal to target peroxisomes to nascent autophagosomes. We are now using advance siRNA gene knockdown techniques in combination with high-throughput screening and fluorescent microscopy to identify all the factors involved in the ubiquitination and targeting of peroxisomes for degradation.

Ultimately, these advances will aid in the future understanding of organelle maintenance and cellular homeostasis, which are essential in understanding all cellular functions and processes. The research into peroxisome biology will not only advance our knowledge of these vital yet understudied organelles, but will also provide a deeper understanding of the role of peroxisomes in the development of the brain and in neurodegenerative diseases.

Publications

View all publications on PubMed

Multiple paths to peroxisomes: Mechanism of peroxisome maintenance in mammals.
Hua R, Kim PK.
Biochim Biophys Acta. 2016 May;1863(5):881-91  Read

Multiple Domains in PEX16 Mediate Its Trafficking and Recruitment of Peroxisomal Proteins to the ER.
Hua R, Gidda SK, Aranovich A, Mullen RT, Kim PK
Traffic. 2015 Aug;16(8):832-52.  Read

Deubiquitinating enzymes regulate PARK2-mediated mitophagy.
Wang Y, Serricchio M, Jauregui M, Shanbhag R, Stoltz T, Di Paolo CT, Kim PK, McQuibban GA
Autophagy. 2015 Apr 3;11(4):595-606  Read

PEX16 Contribues to peroxisome maintenance by constantly trafficking PEX3 via the ER.
Aranovich A, Hua R, Rutneberg AD, Kim PK.
J Cell Sci. 2014; 127:3675-3686  Read

Probing peroxisome dynamics and biogenesis by fluorescence imaging.
Jauregui, M and Kim PK.
Current Protocols in Cell Biology. 2014; 62:Unit 21.9.1-20.  Read

PEX5 and Ubiquitin dynamics on mammalian peroxisome membranes. PLoS Computational Biology.
Brown AL, Kim PK, Rutenberg AD.
PLoS Comput Biol. 2014; 10(1):e1003426  Read

NBR1 acts as an autophagy receptor for peroxisomes.
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 and Kim PK.
J Cell Sci. 2013; 126(4):939-52.  Read

PEX16: a multifaceted regulator of peroxisome biogenesis.
Kim, PK, and Mullen, RT
Front Physiol. 2013; 4:241  Read

ROS-induced mitochondrial depolymerization induces Parkin-dependent mitochondrial degradation by autophagy.
Wang Y, Nartiss Y, Steipe B, McQuibban GA, Kim PK.
Autophagy. 2012; 8:1-15.  Read

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

Bacterial toxins can inhibit host cell autophagy through cAMP generation.
Shahnazari S, Namolovan A, Mogridge J, Kim PK, Brumell JH.
Autophagy. 2011; 7:957-65.  Read

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

Kim PK, Hailey DW, Mullen RT, Lippincott-Schwartz J.
Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes.
PNAS. 2008; 105:20567-74.  Read

The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER.
Kim PK, Mullen RT, Schumann U, Lippincott-Schwartz J.
J Cell Biol. 2006; 173:521-32.  Read