Dr. Daniel Nickerson
Assistant Professor of Biology
Office: CS-112 (ph. 909.537.3671)
Lab: CS-125 (ph. 909-537.3324)
B.S. in Biology, Kenyon College
Ph.D. in Molecular Cellular and Developmental Biology, Univ of Colorado, Boulder
Postdoctoral studies in Biochemistry, University of Washington, Seattle
CURRENTLY RECRUITING GRADUATE STUDENTS
BIOL 300 – Cell Physiology (Winter)
BIOL 400 – Molecular Biology (Spring)
BIOL 591 – Biology Seminar
BIOL 691 – Biology Journal Club
BIOL 396 – Directed Study
Molecular Signaling at Intracellular Membranes.
Eukaryotic cells use membranes to divide up their interior space into compartments (organelles) that provide appropriate microenvironments for specific biochemical functions.
Many textbooks and reviews describe membrane compartments in cells as 'discrete,' but that word also implies isolation or disconnection. In fact, 'discrete' organelles are gregarious, consistently bumping into one another, forming stable or transient docking sites to exchange materials and interrogate one another. When membranes possess compatible fusion factors (SNAREs, SM proteins and Rab GTPases), the steep energetic barrier preventing membrane fusion can be overcome and the compartments merge. Several layers of quality control govern when and whether docked membranes fuse.
I seek to understand how separate membranes in cells can meet, communicate, swap components, and how the identities of compartments are either maintained or adjusted as circumstances demand. Rab GTPases perform a central role in mediating compartmental interactions and membrane transport, and the yeast Saccahromyces cerevisiae is the ideal system, both genetically and biochemically, for exploring novel cellular functions and regulatory mechanisms for Rabs. I also use yeast as a platform for developing new cellular probes and diagnostics, such as the quantitative endocytic transport assay, LUCID (Luciferase assay of Intraluminal Deposition). Importantly, my research interests and experimental system are immediately accessible to early stage trainees, with opportunities for undergraduate and masters students interested in molecular and cell biology, biochemistry, microbiology and biotechnology, as well as classical and modern genetic analyses.
Lipid-anchored Rab GTPases are 'master switches' regulating membrane docking and fusion decisions, and the presence of a particular Rab at a membrane is a key molecular marker of compartmental identity, distinguishing ER from Golgi membranes or early endosomes from late endosomes and lysosomes. When bound to GTP, Rabs bind and mobilize membrane tethers and fusion machinery. Initiation and termination of Rab signals are mediated by accessory proteins called GEFs (guanine nucleotide exchange factors) and GAPs (GTPase accelerating proteins) that promote nucleotide exchange and GTP hydrolysis, respectively. Rabs typically undergo complete GTP-GDP cycles in properly guiding membrane events and compartment fates. Misregulated Rabs and Rab GAPs are increasingly recognized for their roles in numerous human diseases, including microbial pathogenesis, lipid homeostasis, cancers and neurodegenerative disorders (to name just a few), but regulation of Rab signals at most cellular membranes is understood only in rough outline at best.
Available projects include:
- Rab GTPase regulation of lipid metabolism
- Identification of GAPs that regulate Rab GTPases in the endocytic and secretory pathways
- Regulation of organelle inheritance
- Development of novel transport probes (endolysosomal fusion, peroxisomes)
- Chemical library screening using LUCID probes to find potential therapeutics
Nickerson, D.P. and A.J. Merz. 2015. LUCID: a quantitative assay of ESCRT-mediated cargo sorting into multivesicular bodies. Traffic, 16:1318-1329.
Shideler, T. D.P. Nickerson, A.J. Merz, and G. Odorizzi. 2015. Ubiquitin binding by the CUE domain promotes endosomal localization of the Rab5 GEF Vps9. Mol. Biol. Cell., 26:1345-1356.
Lobingier, B.T., D.P. Nickerson, S.-Y. Lo, and A.J. Merz. 2014. SM proteins Sly1 and Vps33 co-assemble with Sec17 and SNARE complexes to oppose SNARE disassembly by Sec18. eLife, e02272.
Paulsel, A.L., A.J. Merz, and D.P. Nickerson. 2013. Vps9 family protein Muk1 is the second Rab5 guanosine nucleotide exchange factor in budding yeast. J. Biol. Chem., 288:18162-71.
Russell, M.R.G., T. Shideler, D.P. Nickerson, M. West, and G. Odorizzi. 2012. Class E compartments in yeast form in response to ESCRT dysfunction due to hyperactivity of the Vps21 Rab GTPase. J. Cell Sci., 125:5208-20.
Nickerson, D.P., M.R.G. Russell, S.-Y. Lo, H.C. Chapin, J.M. Milnes, and A.J. Merz. 2012. Termination of Isoform-selective Vps21/Rab5 signaling at endolysosomal organelles by Msb3/Gyp3. Traffic, 13:1411-28.
Nickerson, D.P., M. West, R. Henry, and G. Odorizzi. 2010. Regulators of Vps4 ATPase activity at endosomes differentially influence the size and rate of formation of lumenal vesicles. Mol. Biol. Cell, 21:1023-32.
Nickerson, D.P., C.L. Brett and A.J. Merz. 2009. Vps-C complexes: gatekeepers of endolysosomal transport. Curr. Opin. Cell Biol. 21:543-51.
Nickerson, D.P., M.R.G. Russell and G. Odorizzi. 2007. A concentric circle model of multivesicular body cargo sorting. EMBO Reports, 8:644-50.
Russell, M.R.G., D.P. Nickerson, and G. Odorizzi. 2006. Molecular mechanisms of late endosome morphology, identity, and sorting. Curr. Opin. Cell Biol. 18:422-28.
Nickerson, D.P., M. West and G. Odorizzi. 2006. Did2 coordinates Vps4-mediated dissociation of ESCRT-III from endosomes. J. Cell Biol. 175:715-20.