Nuclear protein quality control
Proteomics

One of the major problems the cell must contend with is the production and accumulation of aberrant proteins. Aberrant proteins are a normal consequence of life and can arise through DNA mutations, errors during transcription or translation, mistakes during protein folding or packaging, mislocalization, or damage by metabolic byproducts, or physical or chemical stresses. It is especially important that the cell appropriately handle aberrant proteins that arise because, in many cases, the abnormality of the protein can have dire consequences for the cell. For example, aberrant proteins may lose crucial regulatory controls and gain rampant activity, they may form inactive complexes that compete with functional complexes, they may assemble into aggregates that eliminate protein function or cause toxicity, or they may introduce harmful activities to cellular compartments if mislocalized. In humans, accumulation of aberrant proteins appears to underlie the pathology of diseases such as Alzheimer's, Huntington's, Parkinson's, and prion pathologies like Creutzfeld-Jakob's.

There are a number of general ways the cell can deal with aberrant proteins and those include repair of misfolded or unfolded proteins by protein chaperones, prevention of aggregation or disaggregation by heat shock proteins, and removal by autophagy or proteosome-mediated degradation. The latter, degradation, is one of the more critical protein quality control mechanisms because it is the only one that completely removes aberrant proteins from the cell. In this way, quality control degradation can be thought of as the cell's last line of defence against aberrant protein accumulation.

Prior to our studies, protein quality control degradation pathways had been characterized in virtually every major cellular compartment including the cytoplasm, the secretory pathway, and the mitochondria, which all happen to be primary sites of protein synthesis. Protein quality control systems are expected in these compartments because they're required to handle the natural load of proteins that are synthesized incorrectly. Interestingly, no protein quality control degradation pathways had been identified in the nucleus. One idea is that perhaps they wouldn't exist in a compartment where there is little or no protein synthesis since there'd be little burden of incorrectly synthesized proteins. However, while cytoplasmic protein quality control may deal with aberrant nuclear proteins resulting from synthesis defects before they enter the nucleus, they would fail to recognize proteins that were damaged either en route to the nucleus or after nuclear localization where the nuclear membrane now serves as a barrier. Cytoplasmic protein quality control would also fail to detect proteins that did not assemble appropriately once they arrived in the nucleus, or whose defects were realized only after exposure to the nuclear environment. Of course, dedicated nuclear protein quality control systems wouldn't be necessary during mitosis because the nuclear envelope breaks down and the nuclear contents are exposed to the cytoplasm. However, in non-dividing somatic cells, such as neurons and muscle cells, or in organisms with a closed mitosis in which the nuclear envelope doesn't break down, such as in S. cerevisiae, a distinct, nuclear-localized protein quality control machinery would be required to handle aberrant proteins that arise in the nucleus.

Accumulation of aberrant proteins in the nucleus is known to have deleterious effects on cell viability, and may be the underlying cause of a number of polyglutamine-expansion diseases, such as Huntington's, and polyalanine-expansion diseases, such as oculapharyngeal muscular dystrophy. In trying to understand the mechanisms for toxicity in these disease cases it would be useful to know if there are no protein quality control systems in the nucleus at all and that's why these aberrant proteins are toxic, or if they somehow elude protein quality control systems in the nucleus and become toxic. The latter is especially intriguing because these diseases are all late age onset, indicating that, early in life, the nucleus can deal with these aberrant proteins, whereas, later in life, something happens so that they can no longer be tolerated. Perhaps the loss of functional nuclear protein quality control systems through overburden or damage is the key. To address this, however, we need to know what the nuclear protein quality control systems are.

Despite the importance of this process, relatively little is known about how protein quality is managed in the nucleus, and no nucleus-specific protein quality control pathways had been identified. Therefore, we initiated studies in yeast to see if we could dissect the protein quality control systems that operate in the nucleus in a tractable genetic organism. From our studies, we've recently discovered a protein quality control degradation pathway that operates exclusively in the nucleus. The pathway is defined by San1, a ubiquitin-protein ligase that targets a variety of mutant nuclear proteins for ubiquitination and subsequent destruction by the proteasome. As expected for a dedicated nuclear protein quality control pathway, San1 function requires its nuclear localization. Furthermore, we've also found a number of aberrant proteins that are toxic to the cell in the absence of San1, underscoring the idea that San1 does indeed serve as a last line of defense against toxic aberrant proteins. Interestingly, in the absence of San1, the cell undergoes a transcriptional stress response that includes the increased expression of a number of protein chaperones and heat shock proteins, indicating that the cell can detect the accumulation of aberrant proteins in the nucleus when San1 function is lost and mount a compensating response. This is very reminiscent of what happens in the ER with the unfolded protein response. Furthermore, there appears to be at least one other quality control degradation pathway in the nucleus that appears to recognize a different type of aberrancy than San1. Altogether, our results indicate that the nucleus possesses a robust system for sensing aberrant protein accumulation and dealing with the aberrant proteins both through the action of protein chaperones and nuclear-localized degradation systems.

Future studies in the lab include understanding what the San1 pathway recognizes as aberrant, how the nucleus detects aberrant proteins and coordinates global nuclear protein quality control, and what exactly causes one aberrant protein to be toxic but not another. We'll be developing studies of nuclear protein quality control in metazoans as well as trying to understand how lesions in nuclear protein quality control might affect the progression of nuclear quality control diseases like Huntington's.

The other projects
Intro text Chromatin text Proteomics text
Introduction Chromatin UbProteomics
There are a variety of projects going on in the lab from devising global ubiquitin proteomic strategies that will allow us to elucidate the functions of ubiquitin-protein ligases and ubiquitin proteases, to understanding the roles ubiquitination and deubiquitination play in gene transcription and silencing, to uncovering the ways in which the cell destroys aberrant proteins in the nucleus for the purposes of protein quality control. Move mouse over pictures to learn more...