JUNQ and IPOD are types of cytosolic protein inclusion bodies in eukaryotes. Neurodegenerative diseases, such as Parkinson's, Alzheimer's, and Huntington's, are associated and correlated with protein aggregation and accumulation of misfolded proteins in inclusion bodies. For many years, protein aggregation was considered a random process by which misfolded proteins stick to each other to form inclusions (imagine a bundle of hairs haphazardly piling up in a corner of a room). Moreover, protein aggregates were thought to be toxic agents and the cause for neuronal dysfunction and death. However, recent studies, using advanced methods (i.e. fluorescence microscopy), show that protein aggregation may actually be a tightly regulated, organized process, by which the cell protects itself from toxic proteins by sequestration to inclusion bodies. In 2008, Daniel Kaganovich working in the Frydman lab showed that eukaryotic cells sort misfolded proteins into two distinct inclusion bodies in a well-managed cellular process:
The JUNQ (JUxta Nuclear Quality control compartment) The IPOD (Insoluble Protein Deposit) JUNQ and IPOD are evolutionarily conserved, and are found in specific and defined cellular sites. Delivery of misfolded, aggregated proteins to JUNQ and IPOD require an intact cytoskeleton and specific cellular quality control components, such as Heat Shock Proteins (HSPs). The partition into the two distinct inclusion bodies is due to the different handling and processing of different kinds of misfolded proteins (e.g. ubiquitinated vs. non-ubiquitinated proteins). Segregation of toxic protein aggregates into JUNQ and IPOD inclusion bodies is a means by which mammalian cells can be rejuvenated through asymmetric division. Thus, the discovery of JUNQ and IPOD provided a new striking perspective of how cells manage misfolded aggregated proteins and gave convincing proof that protein aggregation is a non-random, well regulated and controlled cellular process. Furthermore, the discovery of JUNQ and IPOD suggested that in addition to temporal quality control (i.e. time dependent administration of damaged proteins) cells exploit homeostasis spatially: If degradation is unavailable, protection of the cellular environment from a misfolded protein is accomplished by its sequestration to an aggregate inclusion.
Background To function properly, most proteins must preserve a low-energy, three-dimensional structure known as the native state. The stability of a protein is tightly regulated through all its life stages: from cradle, as it is synthesized at the ribosome, through folding or assembly, till grave – when the protein is degraded and cleared from the cellular environment. Protein homeostasis (proteostasis), results from the coordinated action of the different arms of the cellular quality control system: molecular chaperones, proteases and other regulatory factors. Hence, cellular viability depends on timely and efficient management of misfolded proteins. Such management, by the quality control machinery, includes recognition of the misfolded protein by chaperones and E3 ligases, ubiquitination and degradation. Proteostasis collapse, due to damage, stress, mutations, and aging, has been implicated as a basis for a large number of common human disorders, such as neurodegenerative diseases. Although caused by different kinds of mutated proteins (e.g. in Huntington's disease – the protein Huntingtin) and disruptive to distinct tissues (e.g. in Huntington's disease – the striatum), such diseases share a common feature: accumulation of misfolded proteins in inclusion bodies. Thus, it was thought that the inclusion bodies are the cause of such diseases. However, the nature and characteristics of those intra-cellular inclusion bodies stayed elusive. Different kinds of proteins (e.g. prions, ERAD substrates) were reported to form different kinds of inclusion bodies (e.g. aggresomes, amyloids), yet it remained obscure if those observations combine into one and relate to the same sub-cellular site. Moreover, the pathways leading to inclusion formation and the involvement of the cellular protein quality control machinery were undefined and unknown. Thus, a systematic study providing a comprehensive understanding of protein aggregation and inclusion bodies was required. The discovery of JUNQ and IPOD suggested new insights of how the cell manages different kinds of misfolded proteins and offered a novel framework for putting together the great puzzle of protein aggregation.
Discovery The fate of misfolded proteins and the process leading to the formation of aggregate inclusions, were initially studied using biochemical methods (e.g. western blotting). Deeper insights into the biological process of protein quality control and aggregation was made possible by a novel approach to looking at this problem, termed "Live Cell Imaging". Live cell imaging enables in vivo tracking of proteins in space and time, in their natural endogenous environment. Thus, such a method provides more information about the dynamics and stages of biological events and processes. The method takes advantage of the easily detectable fluorescent proteins fused to a protein of interest, which can then be followed inside a cell using a fluorescence microscope. The cell may then be treated by a perturbation of interest (e.g. a drug, expression of a misfolded protein), and various properties of the fluorescently tagged protein can be assayed using time-lapse microscopy:
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