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Davis Ng Associate Professor/Senior Principal Investigator (TLL) Contact Information:  Department of Biological Sciences, 14 Science Dr 4 National University of Singapore Singapore 117543. Email: dbsdntw@nus.edu.sg

Academic qualification :

PhD Northwestern University 1991
BSc University of California, Berkeley 1984

Research Interests

• Quality control of protein folding in the secretory pathway
• Regulation of organelle homeostasis
• Stress tolerance mechanisms

Research Projects

The long-term interest of my laboratory is to understand the mechanisms governing the biosynthesis of secretory proteins. The current areas of research include the quality control of protein folding, stress-tolerance mechanisms, and how homeostasis is maintained in the endoplasmic reticulum (ER).

Genetic analysis of the unfolded protein response uncovers novel genes required for secretory protein biogenesis and quality control

The biogenesis of secreted proteins is a complex process that begins with their translation from cytosolic ribosomes. Nascent polypeptides entering the secretory pathway translocate across the endoplasmic reticulum (ER) membrane entirely unfolded. Consequently, protein folding and maturation occur in the lumen as subsequent steps. Also localized in the ER are chaperones, modifying enzymes, and cofactors required for the process. Once folded, the new molecules are packaged into membrane vesicles and transported to their sites of function. The sequence of events is strictly regulated, as unfettered transport of unfolded proteins, which are inherently toxic, would be disastrous. Averting this scenario are quality control mechanisms that monitor folded states and permits only fully assembled proteins to exit. Proteins that are irreversibly misfolded are neutralized and targeted for degradation. Underscoring the importance of these pathways are the numerous human diseases caused by aberrantly folded proteins or the corruption of quality control mechanisms. A few include cystic fibrosis, infantile diabetes, Alzheimer's, Huntington's, Parkinson's, and prion diseases.

Our experimental foothold for unraveling protein folding and quality control mechanisms developed rather serendipitously. A genetic strategy devised to reveal the physiology of the unfolded protein response (UPR; an ER-to-nucleus stress signaling pathway) in Saccharomyces cerevisiae, generated a panel of mutant strains that collectively affect virtually every aspect of secretory protein biosynthesis and quality control. These functions included protein folding, glycosylation, GPI-anchor addition, ER quality control, ER-associated protein degradation (ERAD), protein trafficking, and ER ion homeostasis. We exploited this discovery with an expanded screen to identify novel genes for each of these processes. Although tackling just a small fraction of the panel, our efforts have already revealed novel mechanistic insights. Furthermore, our collaborations expanding into other important areas have also borne fruit. We identified the gene for the long sought dolichyl oligosaccharyl flippase - an essential function of N-linked glycosylation. The mutant pool (termed per, for protein processing in the ER) was remarkably free of 'junk'. Every strain examined was defective in some aspect of ER function. As a unique resource, the outcome of the screen provides a strong foundation for current and future studies.

Quality control of secretory protein folding
A major effort of my group focuses on the quality control mechanisms of protein folding. To this end, we employ a multi-faceted approach that combines genetic and biochemical approaches. One emphasis is to identify the genes required for the sorting and degradation of misfolded proteins. The UPR synthetic lethal screen described above has proven to be a powerful means for this purpose and remains an ongoing effort. Another involves detailed analysis of substrates. The characteristics or signals used to differentiate misfolded proteins from folded proteins are unknown. It is essential understand these determinants if we wish make sense of the sorting machinery. For this, we assembled a panel of model proteins that includes established and newly constructed substrates. From their analysis, we discovered that protein quality control consists of a series of sequential checkpoints, each comprising distinct pathways. The first checkpoint monitors the cytosolic domains of membrane proteins and the second checkpoint monitors lumenal domains and soluble proteins. Proteins detected by either checkpoint are degraded by ERAD. Under conditions of severe stress, proteins are transported to the Golgi where a third checkpoint sorts misfolded proteins for degradation in the vacuole. Recently, we identified a novel context-specific carbohydrate that signals its entry into the ERAD pathway. This result indicated that recognition and retention functions are distinct from targeting and degradation. We recently identified a novel receptor for this signal that is required for the degradation of misfolded glycoproteins. Our current efforts are directed to understanding the molecular dynamics of this signal/receptor mechanism. In the future, we plan to focus more on the cytosolic checkpoint where little is known. Already, we have identified the Doa10p E3 ubiquitin ligase as a key component of the pathway.

Stress tolerance of misfolded proteins
Using a direct approach, we showed that the UPR is essential for the stress tolerance of misfolded proteins. To analyze the contribution of regulating individual genes, we created strains compromised for inducibility of specific UPR targets. For one major target, BiP, we showed that induction is required for stress tolerance while the rest of the UPR pathway is functional. Using this system, we are assessing the specific roles of BiP and other UPR targets in maintaining misfolded protein stress tolerance. In addition, we have identified several novel genes that provide stress tolerance against misfolded secretory proteins.

We are comparing the toxicity of two classes of aberrant proteins: soluble misfolded and amyloid. For the latter, we have introduced a prion protein into the secretory pathway of yeast. Although past studies using yeast prions have provided remarkable insight into biogenesis and transmission, they were cytosolic so the results are less relevant to the disease-causing prion, PrP, which is a GPI-anchored secretory protein. We will perform in vivo studies on factors that promote conversion to the amyloid state, the mechanism of transmission, and the cellular mechanisms providing stress tolerance to the prion.

Selected recent publications :

• Vashist, S., W. Kim, W. Belden, E. D. Spear, C. Barlowe, and D. T. W. Ng. 2001. Distinct retrieval and retention mechanisms are required for the quality control of endoplasmic reticulum protein folding. J. Cell Biol. 155:355-367.

• Helenius, J., D. T.W. Ng, C. L. Marolda, P. Walter, M. A. Valvano and M. Aebi. 2002. The RFT1 protein is required for the translocation of lipid-linked oligosaccharides across the membrane of the endoplasmic reticulum. Nature. 415:447-450.

• Vashist, S., C. G. Frank, C. A. Jakob, and D.T.W. Ng. 2002. Two Distinctly Localized P-Type ATPases Collaborate to Maintain Organelle Homeostasis Required for Glycoprotein Processing and Quality Control. Mol. Biol. Cell. 13:3955-3966.

• Spear, E. D. and D. T. W. Ng. 2003. Stress tolerance of misfolded carboxypeptidase Y requires maintenance of protein trafficking and degradation pathways. Mol. Biol. Cell. 14:2756-2767.

• Vashist and D. T. W. Ng. 2004. Misfolded proteins are sorted by a sequential checkpoint mechanism of ER quality control. J. Cell Biol. 165:41-42.

• Ng, D. T. W. 2004. Heat/Stress Responses. In Encyclopedia of Biological Chemistry. 2:343-347. Elsevier Inc., San Diego, CA.

• Ng, D. T. W. 2005. Screening for mutants defective in secretory protein maturation and ER quality control. Methods. 35:366-372.

• Spear, E. D. and D. T. W. Ng. 2005. Single, context-specific glycans can target misfolded glycoproteins for ER-associated degradation. J. Cell Biol. 169:73-82.

• Kim, W., E. D. Spear, and D. T. W. Ng. 2005. Yos9p detects and targets misfolded glycoproteins for ER-associated degradation. Mol. Cell. 19:753-764.

• Ismail, N. and D. T. W. Ng. 2006. Have you HRD? Understanding ERAD Is DOAble! Cell. 126:237-239.

Updated: April 2007