John Aitchison, PhD

Affiliate Faculty

Professor and Co-Director; Center for Global Infectious Disease Research, Seattle Children’s Research Institute

Dr. John Aitchison is an affiliate faculty member at the Institute for Systems Biology. He also holds an appointment at Seattle Children’s Research Institute as Professor and Co-Director of the Center for Global Infectious Disease Research. As a student, he studied biochemistry, specializing in biotechnology and genetic engineering at McMaster University in Ontario, Canada. There, in the laboratory of Dr. Richard Rachubinski, he investigated the molecular mechanisms responsible for sorting proteins into peroxisomes. After receiving his PhD, Dr. Aitchison performed his postdoctoral work in the laboratory of Nobel Laureate Dr. Günter Blobel at Rockefeller University. In Dr. Blobel’s lab, Dr. Aitchison applied classic cell biology techniques and yeast genetics to the study of protein import into the nucleus. During this time, he began to apply large-scale proteomics to the problem, which he continued as an Assistant Professor in the Faculty of Medicine and Dentistry at the University of Alberta until joining the ISB in 2000. Dr. Aitchison also holds affiliate appointments at the University of Washington, University of Alberta, and University of British Columbia and Rockefeller University. He is a member of the Molecular and Cellular Biology and Biomolecular Structural Design Graduate Programs at the University of Washington.

Since joining ISB in 2000, his laboratory has been exploiting systems-based assays and analyses to reveal and understand complex biological phenomena. Over the past ten years, his lab has focused on yeast as a model for developing systems biology approaches. At the Center for Global Infectious Disease Research, his lab is focused on enhancing our collective exposure to, and education in research of infectious diseases. With his position at ISB, he will remain at the cutting-edge of systems biology while bringing new developments to infectious disease research at Seattle Children’s Research Institute.

PhD, Biochemistry McMaster University, Ontario, Canada, 1992

Systems Cell Biology, Organelle Biogenesis, Host-pathogen Interactions

  

Aitchison, J. D., and M. P. Rout. 2000. “The Road to Ribosomes. Filling Potholes in the Export Pathway.” J Cell Biol 151 (5): F23-6. Cite
Marelli, M., D. J. Dilworth, R. W. Wozniak, and J. D. Aitchison. 2001. “The Dynamics of Karyopherin-Mediated Nuclear Transport.” Biochem Cell Biol 79 (5): 603–12. Cite
Pariyarath, R., H. Wang, J. D. Aitchison, H. N. Ginsberg, W. J. Welch, A. E. Johnson, and E. A. Fisher. 2001. “Co-Translational Interactions of Apoprotein B with the Ribosome and Translocon during Lipoprotein Assembly or Targeting to the Proteasome.” J Biol Chem 276 (1): 541–50. Cite
Iouk, T. L., J. D. Aitchison, S. Maguire, and R. W. Wozniak. 2001. “Rrb1p, a Yeast Nuclear WD-Repeat Protein Involved in the Regulation of Ribosome Biosynthesis.” Mol Cell Biol 21 (4): 1260–71. Cite
Marelli, M., C. P. Lusk, H. Chan, J. D. Aitchison, and R. W. Wozniak. 2001. “A Link between the Synthesis of Nucleoporins and the Biogenesis of the Nuclear Envelope.” J Cell Biol 153 (4): 709–24. Cite
Rout, M. P., and J. D. Aitchison. 2001. “The Nuclear Pore Complex as a Transport Machine.” J Biol Chem 276 (20): 16593–96. Cite
Dilworth, D. J., A. Suprapto, J. C. Padovan, B. T. Chait, R. W. Wozniak, M. P. Rout, and J. D. Aitchison. 2001. “Nup2p Dynamically Associates with the Distal Regions of the Yeast Nuclear Pore Complex.” J Cell Biol 153 (7): 1465–78. Cite
Aitchison, J. D., and M. P. Rout. 2002. “A Tense Time for the Nuclear Envelope.” Cell 108 (3): 301–4. Cite
Leslie, D. M., B. Grill, M. P. Rout, R. W. Wozniak, and J. D. Aitchison. 2002. “Kap121p-Mediated Nuclear Import Is Required for Mating and Cellular Differentiation in Yeast.” Mol Cell Biol 22 (8): 2544–55. Cite
Smith, J. J., M. Marelli, R. H. Christmas, F. J. Vizeacoumar, D. J. Dilworth, T. Ideker, T. Galitski, K. Dimitrov, R. A. Rachubinski, and J. D. Aitchison. 2002. “Transcriptome Profiling to Identify Genes Involved in Peroxisome Assembly and Function.” J Cell Biol 158 (2): 259–71. Cite
Yi, E. C., M. Marelli, H. Lee, S. O. Purvine, R. Aebersold, J. D. Aitchison, and D. R. Goodlett. 2002. “Approaching Complete Peroxisome Characterization by Gas-Phase Fractionation.” Electrophoresis 23 (18): 3205–16. Cite
Lusk, C. P., T. Makhnevych, M. Marelli, J. D. Aitchison, and R. W. Wozniak. 2002. “Karyopherins in Nuclear Pore Biogenesis: A Role for Kap121p in the Assembly of Nup53p into Nuclear Pore Complexes.” J Cell Biol 159 (2): 267–78. Cite
Aitchison, J. D. 2003. “Systems Biology and Elephants.” Nature Cell Biology 5: 285. Cite
Sydorskyy, Y., D. J. Dilworth, E. C. Yi, D. R. Goodlett, R. W. Wozniak, and J. D. Aitchison. 2003. “Intersection of the Kap123p-Mediated Nuclear Import and Ribosome Export Pathways.” Mol Cell Biol 23 (6): 2042–54. Cite
Vizeacoumar, F. J., J. C. Torres-Guzman, Y. Y. Tam, J. D. Aitchison, and R. A. Rachubinski. 2003. “YHR150w and YDR479c Encode Peroxisomal Integral Membrane Proteins Involved in the Regulation of Peroxisome Number, Size, and Distribution in Saccharomyces Cerevisiae.” J Cell Biol 161 (2): 321–32. Cite
Aitchison, J. D., and T. Galitski. 2003. “Inventories to Insights.” J Cell Biol 161 (3): 465–69. Cite
Steiner-Mosonyi, M., D. M. Leslie, H. Dehghani, J. D. Aitchison, and D. Mangroo. 2003. “Utp8p Is an Essential Intranuclear Component of the Nuclear TRNA Export Machinery of Saccharomyces Cerevisiae.” J Biol Chem 278 (34): 32236–45. Cite
Tam, Y. Y., J. C. Torres-Guzman, F. J. Vizeacoumar, J. J. Smith, M. Marelli, J. D. Aitchison, and R. A. Rachubinski. 2003. “Pex11-Related Proteins in Peroxisome Dynamics: A Role for the Novel Peroxin Pex27p in Controlling Peroxisome Size and Number in Saccharomyces Cerevisiae.” Mol Biol Cell 14 (10): 4089–4102. Cite
Rout, M. P., J. D. Aitchison, M. O. Magnasco, and B. T. Chait. 2003. “Virtual Gating and Nuclear Transport: The Hole Picture.” Trends Cell Biol 13 (12): 622–28. Cite
Makhnevych, T., C. P. Lusk, A. M. Anderson, J. D. Aitchison, and R. W. Wozniak. 2003. “Cell Cycle Regulated Transport Controlled by Alterations in the Nuclear Pore Complex.” Cell 115 (7): 813–23. Cite
Lausted, C., T. Dahl, C. Warren, K. King, K. Smith, M. Johnson, R. Saleem, J. D. Aitchison, L. Hood, and S. R. Lasky. 2004. “POSaM: A Fast, Flexible, Open-Source, Inkjet Oligonucleotide Synthesizer and Microarrayer.” Genome Biol 5 (8): R58. Cite
Vizeacoumar, F. J., J. C. Torres-Guzman, D. Bouard, J. D. Aitchison, and R. A. Rachubinski. 2004. “Pex30p, Pex31p, and Pex32p Form a Family of Peroxisomal Integral Membrane Proteins Regulating Peroxisome Size and Number in Saccharomyces Cerevisiae.” Mol Biol Cell 15 (2): 665–77. Cite
Leslie, D. M., W. Zhang, B. L. Timney, B. T. Chait, M. P. Rout, R. W. Wozniak, and J. D. Aitchison. 2004. “Characterization of Karyopherin Cargoes Reveals Unique Mechanisms of Kap121p-Mediated Nuclear Import.” Mol Cell Biol 24 (19): 8487–8503. Cite
Marelli, M., J. J. Smith, S. Jung, E. Yi, A. I. Nesvizhskii, R. H. Christmas, R. A. Saleem, et al. 2004. “Quantitative Mass Spectrometry Reveals a Role for the GTPase Rho1p in Actin Organization on the Peroxisome Membrane.” J Cell Biol 167 (6): 1099–1112. Cite
Tackett, A. J., D. J. Dilworth, M. J. Davey, M. O’Donnell, J. D. Aitchison, M. P. Rout, and B. T. Chait. 2005. “Proteomic and Genomic Characterization of Chromatin Complexes at a Boundary.” J Cell Biol 169 (1): 35–47. Cite
Fagarasanu, M., A. Fagarasanu, Y. Y. Tam, J. D. Aitchison, and R. A. Rachubinski. 2005. “Inp1p Is a Peroxisomal Membrane Protein Required for Peroxisome Inheritance in Saccharomyces Cerevisiae.” J Cell Biol 169 (5): 765–75. Cite
Sydorskyy, Y., D. J. Dilworth, B. Halloran, E. C. Yi, T. Makhnevych, R. W. Wozniak, and J. D. Aitchison. 2005. “Nop53p Is a Novel Nucleolar 60S Ribosomal Subunit Biogenesis Protein.” Biochem J 388 (Pt 3): 819–26. Cite
Scott, R. J., C. P. Lusk, D. J. Dilworth, J. D. Aitchison, and R. W. Wozniak. 2005. “Interactions between Mad1p and the Nuclear Transport Machinery in the Yeast Saccharomyces Cerevisiae.” Mol Biol Cell 16 (9): 4362–74. Cite
Hwang, D., J. J. Smith, D. M. Leslie, A. D. Weston, A. G. Rust, S. Ramsey, P. de Atauri, et al. 2005. “A Data Integration Methodology for Systems Biology: Experimental Verification.” Proc Natl Acad Sci U S A 102 (48): 17302–7. Cite
Dilworth, D. J., A. J. Tackett, R. S. Rogers, E. C. Yi, R. H. Christmas, J. J. Smith, A. F. Siegel, B. T. Chait, R. W. Wozniak, and J. D. Aitchison. 2005. “The Mobile Nucleoporin Nup2p and Chromatin-Bound Prp20p Function in Endogenous NPC-Mediated Transcriptional Control.” J Cell Biol 171 (6): 955–65. Cite
Niemisto, A., J. Selinummi, R. Saleem, I. Shmulevich, J. D. Aitchison, and O. Yli-Harja. 2006. “Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis.” Conf Proc IEEE Eng Med Biol Soc 1: 2353–56. Cite
Smith, J. J., Y. Sydorskyy, M. Marelli, D. Hwang, H. Bolouri, R. A. Rachubinski, and J. D. Aitchison. 2006. “Expression and Functional Profiling Reveal Distinct Gene Classes Involved in Fatty Acid Metabolism.” Mol Syst Biol 2: 2006 0009. Cite
Fagarasanu, A., M. Fagarasanu, G. A. Eitzen, J. D. Aitchison, and R. A. Rachubinski. 2006. “The Peroxisomal Membrane Protein Inp2p Is the Peroxisome-Specific Receptor for the Myosin V Motor Myo2p of Saccharomyces Cerevisiae.” Dev Cell 10 (5): 587–600. Cite
Vizeacoumar, F. J., W. N. Vreden, M. Fagarasanu, G. A. Eitzen, J. D. Aitchison, and R. A. Rachubinski. 2006. “The Dynamin-like Protein Vps1p of the Yeast Saccharomyces Cerevisiae Associates with Peroxisomes in a Pex19p-Dependent Manner.” J Biol Chem 281 (18): 12817–23. Cite
Vizeacoumar, F. J., W. N. Vreden, J. D. Aitchison, and R. A. Rachubinski. 2006. “Pex19p Binds Pex30p and Pex32p at Regions Required for Their Peroxisomal Localization but Separate from Their Peroxisomal Targeting Signals.” J Biol Chem 281 (21): 14805–12. Cite
Kowalewska, J., K. D. Smith, K. L. Hudkins, A. Chang, A. B. Fogo, D. Houghton, D. Leslie, J. D. Aitchison, R. F. Nicosia, and C. E. Alpers. 2006. “Membranous Glomerulopathy with Spherules: An Uncommon Variant with Obscure Pathogenesis.” Am J Kidney Dis 47 (6): 983–92. Cite
Pedrioli, P. G., B. Raught, X. D. Zhang, R. Rogers, J. D. Aitchison, M. Matunis, and R. Aebersold. 2006. “Automated Identification of SUMOylation Sites Using Mass Spectrometry and SUMmOn Pattern Recognition Software.” Nat Methods 3 (7): 533–39. Cite
Leslie, D. M., B. Timney, M. P. Rout, and J. D. Aitchison. 2006. “Studying Nuclear Protein Import in Yeast.” Methods 39 (4): 291–308. Cite
Ramsey, S. A., J. J. Smith, D. Orrell, M. Marelli, T. W. Petersen, P. de Atauri, H. Bolouri, and J. D. Aitchison. 2006. “Dual Feedback Loops in the GAL Regulon Suppress Cellular Heterogeneity in Yeast.” Nat Genet 38 (9): 1082–87. Cite
Saleem, R. A., J. J. Smith, and J. D. Aitchison. 2006. “Proteomics of the Peroxisome.” Biochim Biophys Acta 1763 (12): 1541–51. Cite
Taverna, S. D., S. Ilin, R. S. Rogers, J. C. Tanny, H. Lavender, H. Li, L. Baker, et al. 2006. “Yng1 PHD Finger Binding to H3 Trimethylated at K4 Promotes NuA3 HAT Activity at K14 of H3 and Transcription at a Subset of Targeted ORFs.” Mol Cell 24 (5): 785–96. Cite
Niemisto, A., T. Korpelainen, R. Saleem, O. Yli-Harja, J. D. Aitchison, and I. Shmulevich. 2007. “A K-Means Segmentation Method for Finding 2-D Object Areas Based on 3-D Image Stacks Obtained by Confocal Microscopy.” Conf Proc IEEE Eng Med Biol Soc 2007: 5559–62. Cite
Smith, J. J., S. A. Ramsey, M. Marelli, B. Marzolf, D. Hwang, R. A. Saleem, R. A. Rachubinski, and J. D. Aitchison. 2007. “Transcriptional Responses to Fatty Acid Are Coordinated by Combinatorial Control.” Mol Syst Biol 3: 115. Cite
Makhnevych, T., C. Ptak, C. P. Lusk, J. D. Aitchison, and R. W. Wozniak. 2007. “The Role of Karyopherins in the Regulated Sumoylation of Septins.” J Cell Biol 177 (1): 39–49. Cite
Oeffinger, M., K. E. Wei, R. Rogers, J. A. DeGrasse, B. T. Chait, J. D. Aitchison, and M. P. Rout. 2007. “Comprehensive Analysis of Diverse Ribonucleoprotein Complexes.” Nat Methods 4 (11): 951–56. Cite
Aitchison, J. D., and R. W. Wozniak. 2007. “Cell Biology: Pore Puzzle.” Nature 450 (7170): 621–22. Cite
Marelli, M., A. I. Nesvizhskii, and J. D. Aitchison. 2008. “Identifying Bona Fide Components of an Organelle by Isotope-Coded Labeling of Subcellular Fractions : An Example in Peroxisomes.” Methods Mol Biol 432: 357–71. Cite
Saleem, R. A., B. Knoblach, F. D. Mast, J. J. Smith, J. Boyle, C. M. Dobson, R. Long-O’Donnell, R. A. Rachubinski, and J. D. Aitchison. 2008. “Genome-Wide Analysis of Signaling Networks Regulating Fatty Acid-Induced Gene Expression and Organelle Biogenesis.” J Cell Biol 181 (2): 281–92. Cite
Gradolatto, A., R. S. Rogers, H. Lavender, S. D. Taverna, C. D. Allis, J. D. Aitchison, and A. J. Tackett. 2008. “Saccharomyces Cerevisiae Yta7 Regulates Histone Gene Expression.” Genetics 179 (1): 291–304. Cite
Hood, L., L. Rowen, D. J. Galas, and J. D. Aitchison. 2008. “Systems Biology at the Institute for Systems Biology.” Brief Funct Genomic Proteomic 7 (4): 239–48. Cite