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Mariappan lab explores the intricate balance between protein synthesis and quality control in cells. We investigate how cells manage protein synthesis and folding within organelles, differentiate misfolded proteins from newly synthesized ones, and determine the pathway for degradation of misfolded proteins. Our multidisciplinary approach combines biochemical reconstitution, proteomics, genetic analysis, structural, and imaging techniques. Our research holds implications for diabetes, aging, and neurodegenerative diseases.

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The GET (Guided Entry of Tail-Anchored Proteins) Pathway

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Membrane proteins are essential for eukaryotic life, but there are challenges to synthesizing and inserting membrane proteins due to their high hydrophobicity. Evolution solved this problem through the co-translational protein targeting and insertion pathway, where protein synthesis and insertion are coupled at the endoplasmic reticulum (ER). However, tail-anchored (TA) membrane proteins are an important class of proteins precluded from the co-translational protein targeting pathway. TA proteins are post-translationally targeted and inserted into the ER, mitochondrial, or peroxisomal membrane. Studies in our lab and other labs have identified many factors that mediate the targeting and insertion of TA proteins into the ER membrane. This pathway is called the GET (guided entry of tail-anchored proteins) pathway. Our lab now focuses on identifying and understanding quality control factors that recognize and eliminate hydrophobic TA proteins that failed reaching membranes in order to prevent their accumulation of damaged or mistargeted proteins in the cytosol.  

The Unfolded Protein Response (UPR) pathway

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One-third of all human proteins, including antibodies and growth factors, are synthesized and matured in the endoplasmic reticulum (ER). The ER's unfolded protein response (UPR) plays a significant role in adjusting the protein folding capacity of the ER to incoming proteins. IRE1 is the conserved UPR sensor that detects misfolded proteins in the ER and activates transcriptional factor XBP1 to alleviate ER stress. If ER stress is not mitigated, IRE1 also can mediate cell death by less understood mechanisms. Studies from our laboratory discovered that IRE1 exists in a direct complex with a Sec61/Sec63 protein translocation channel to which the SRP pathway recruits its substrate XBP1 mRNA. We have recently shown that Sec61/Sec63 recruits luminal chaperone BiP to bind onto IRE1, thus turning off IRE1 signaling during prolonged ER stress conditions. Without the Sec complex, IRE1 is hyperactivated and induces cell death. Our long-term goal is to understand how the Sec61/Sec63 complex helps IRE1 make life or death decisions during ER stress in neuronal and pancreatic beta cells. Second, we want to obtain the structural information of the IRE1/Sec61/Sec63 complex to understand how IRE1 senses the accumulation of unfolded proteins in the ER. 

The ER-associated protein degradation (ERAD) pathway


The ERAD pathway begins with recognizing misfolded proteins by molecular chaperones and targeting them to one of ~25 ER membrane-bound E3 ligases. Subsequently, these proteins are retrotranslocated from the ER membrane to the cytosol for ubiquitination and degradation by the proteasome. Defects in ERAD are associated with many human diseases such as neurodegenerative diseases and cystic fibrosis. Despite its vital physiological roles, it is largely unknown about the endogenous misfolded substrates and their corresponding ER ligases that recognize them. We have recently developed a novel proteomic approach and identified numerous endogenous substrates. We are expanding this technology to identify  and characterize endogenous substrates of all ER-bound E3 ligases. 

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