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Membrane protein aggregation and its links with neurodegenerative diseases

Periodic Reporting for period 1 - MPA-ND (Membrane protein aggregation and its links with neurodegenerative diseases)

Reporting period: 2016-03-01 to 2018-02-28

Protein misfolding and aggregation have been linked with many fatal human disorders, including Alzheimer’s and Parkinson’s diseases. These disorders represent the fastest-growing cause of death in developed countries and are putting our healthcare system under severe stress.

The amyloid hypothesis is regarded as one of the most promising causative theories of Alzheimer’s disease and is still being studied extensively. The hypothesis is based on the observation that patient brains contain protein plaques. The structure of these plaques has been studied in much detail; they primarily contain a part of the protein APP, which precursor is originally spanning the cell membrane. Within these plaques, APP has adopted a misfolded beta-sheet structure with fibrillar morphology, referred to as amyloid fibrils. In addition to the specific proteins directly associated with neurodegenerative diseases, widespread aggregation of numerous other proteins into amyloid fibrils has been observed and is likely to contribute to disease progression. In this context, recent studies have highlighted the key roles that membrane protein aggregation may play in misfolding diseases. In follow-up of this work, we set out two projects to increase our insights in the potential role of membrane proteins in neurodegeneration.

* The propensity to misfold and self-assemble into stable aggregates is increasingly being recognized as a common feature of protein molecules. Studies thus far, however, have been almost exclusively focused on cytosolic proteins, resulting in a lack of detailed information about the misfolding and aggregation of membrane proteins. As a consequence, although such proteins make up approximately 30% of the human proteome and have high propensities to aggregate, relatively little is known about the biophysical nature of their assemblies.

To shed light on this issue, a first goal of our study is to elucidate the structures of aggregates formed by model membrane proteins, such as E. coli lactose permease.

* The high aggregation propensity of membrane proteins (Cyriam, Kundra et al 2015 Trends in Pharmacological Sciences) correlates with their downregulation in Alzheimer’s disease (AD), as established for a subset of proteins referred to as the ‘AD metastable subproteome’(Cyriam, Kundra et al 2016 PNAS). This metastable subproteome includes several pathways, most notably the oxidative phosphorylation which is enriched in mitochondrial membrane proteins. Many mitochondrial membrane proteins are encoded in the nucleus and are likely to pose risks to the cell upon their translation and import into the mitochondria. This finding suggests the presence of a specific link between protein aggregation, and mitochondrial dysfunction which has been identified as an early event in several neurodegenerative diseases, including AD.

To investigate in detail the nature of this link, we set out to use different S. cerevisiae models of challenged mitochondrial import to investigate whether mitochondrial membrane proteins indeed aggregate under these conditions, how the cellular homeostasis network responds to such aggregation, and what are the structural features of the formed aggregates.
* We have studied as a model system an archetypical representative of the ubiquitous major facilitator superfamily, the Escherichia coli lactose permease (LacY). By using a combination of established indicators of cross-β structure and morphology, including the amyloid diagnostic dye thioflavin-T, circular dichroism spectroscopy, Fourier transform infrared spectroscopy, X-ray fiber diffraction, and transmission electron microscopy, we have shown that LacY can form amyloid-like fibrils under destabilizing conditions. These results indicate that transmembrane α-helical proteins, similarly to cytosolic proteins, have the ability to adopt this generic state.(Stroobants, Kumita et al 2017 Biochemistry)

This work was presented at ‘STUNNING Structure and function in signaling’, on November 18th 2016, in Brussels, Belgium; ‘Marie Curie Alumni Association (MCAA) conference and general assembly’, on March 24th-25th 2017, in Salamanca, Spain; 9th Building Bridges in Medical Sciences (BBMS) conference, on March 10th 2017, in Cambridge, UK; CSH meeting on Protein Homeostasis In Health & Disease, on April 18th-22nd 2016, in Cold Spring Harbor, US

* We have studied three S. cerevisiae model systems of challenged mitochondrial import; either by overexpression of the import substrates of interest (selected mitochondrial membrane proteins), by chemical disruption of the mitochondrial potential, or temperature sensitive import mutations. In these models, we identified a sarkosyl-resistant aggregate fraction containing presequence-proteins of the oxidative phosphorylation. We found that inhibition of the proteasome leads to an increase in the aggregate load, and we observed a specific aggregate-associated chaperone response in the cytosol.(manuscript in preparation)

This work was presented at Science meets Parliaments, on 28th November 2017, at Brussels, Belgium; Proteostasis in Health and Disease Symposium, on 20th-22nd November 2017, in Wollongong, Australia; 67th Lindau Nobel Laureates Meeting, on 25th-30th June 2017, in Lindau, Germany; EMBO Conference on Protein Quality Control: Success and failure in health and disease, on May 14th-19th 2017, in Girona, Spain
* Our initial work on the structure of LacY aggregates was received with much enthusiasm by the scientific community, and it’s progress beyond the state of the art was described in a Viewpoint by Nicholas Truex and James Nowick: “The work of Stroobants and co-workers is part of a recent shift toward identifying new proteins that can form amyloid. This particular study is important, because transmembrane proteins make up such a large percentage of the human proteome. The study gives a reason to appreciate trans-membrane protein aggregation, rather than to view it as a problem. It also provides a window for many thought- provoking questions: Is amyloid formation of the LacY transmembrane protein the exception or the rule? Is α-helix structure, rather than solubility, the critical component that prevents membrane protein aggregation? Do transmembrane proteins aggregate as part of “normal” processes or “pathological” processes? Do transmembrane proteins promote aggregation of other proteins? Addressing these questions and others will lay the groundwork for understanding the role of transmembrane protein aggregation in biological function.”

* Our follow-up study has a different focus as our main question here relates to biological relevance rather than structural features of membrane protein aggregation. Although this work has not been published yet, early discussions in the field have indicated the potential implications of our findings so far; mitochondrial precursor proteins present a real threat to the cellular homeostasis, and homeostasis collapse could start from mild mitochondrial dysfunction. This hypothesis, if further proven, would have tremendous consequences for the field of neurodegeneration as it has the potential to bring, at least in part, some clarity in the cause versus consequence debate that is ongoing.
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