Research Summary

My group has long-standing, extensive expertise and experience in mass spectrometry, proteomics and systems biology, especially focused on sequencing, identification and study of unknown proteins, and the detection, assignment and site-specific dynamics of posttranslational modifications of proteins, particularly OGlcNAcylation, phosphorylation, acetylation, methylation and ubiquitinylation. Over many years we have collaborated with the neurobiological community extensively, including structural characterization of the GPI membrane anchor of the prion protein, structure of the lysyl oxidase co-factor, identification and PTM regulation of proteins in the retrograde signaling complexes in damaged axons, the O-GlcNAc/phosphorylation dynamics at the murine synapse, identification of new proteins involved in the Nodes of Ranvier, etc.

In addition to the work in proteomics and epigenetics above, we have focused significant effort on other studies concerning the architecture of protein complexes and machines for which angstrom resolution structural information has not yet been tractable. For example we have developed a new lysine-lysine cross-linking strategy based on chemical reductive amination that provides comprehensive sequence and cross-link site assignments using electron transfer dissociation (ETD). This information provides accurate distance constraints that complement cryoEM and computer modeling efforts. In parallel software algorithms and scoring strategies have been developed that greatly facilitates the assignment of cross-linked peptides in general. Very recently we have initiated a thrust into development and application of methodology to measure protein complexes directly in the gas phase using a newly acquired high mass Orbitrap Exactive instrument (m/z < 22,000). This effort will complement our long-standing work on chemical cross-linking of protein complexes and machines.

Finally, we have developed a general suite of programs and software tools required for processing large scale mass spectral data sets (HCD, ETD, etc) and stable isotopic labeling experiments (SILAC, iTRAQ, etc) called Protein Prospector.

Research Funding

  • July 1, 1985 - May 31, 2023 - UCSF Liver Center , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P30DK026743
  • August 1, 2002 - April 30, 2020 - Genetic Biochemical Studies of Plant Steroid Signaling , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM066258
  • September 30, 1987 - March 31, 2017 - Toxic Substances in the Environment , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P42ES004705
  • March 15, 1997 - May 31, 2016 - Bio-Organic Biomedical Mass Spectrometry Resource , Principal Investigator . Sponsor: NIH, Sponsor Award ID: P41GM103481

Education

University of Rhode Island, Kingston, RI, B.S. 1959, Chemistry
MIT, Cambridge, MA, Ph.D., 1962, Chemistry, Physics

Honors & Awards

  • 1970-72
    Guggenheim Fellow, Karolinska Institute, Stockholm
  • 1990-
    Elected Fellow, American Association for the Advancement of Science1999-2006
    Deputy Editor, Molecular and Cellular Proteomics
  • 2002-04
    Physiological Chemistry Study Section CSR, NIH
  • 2006-
    Co-editor, Molecular and Cellular Proteomics
  • 2013-
    Editor-in-chief, Molecular and Cellular Proteomics
  • 2012
    International Forum of Proteomics, Achievement Award
  • 2013
    Awarded the MCP lectureship Plenary at the Society for Glycobiology, St Petersburg, FL, November 17-20, 2013
  • 2018
    Albert Nelson Marquis Lifetime Achievement Award

Selected Publications

  1. Yang T, Cuesta A, Wan X, Craven GB, Hirakawa B, Khamphavong P, May JR, Kath JC, Lapek JD, Niessen S, Burlingame AL, Carelli JD, Taunton J. Reversible lysine-targeted probes reveal residence time-based kinase selectivity. Nat Chem Biol. 2022 May 19.  View on PubMed
  2. Patel P, Buchanan CN, Zdradzinski MD, Sahoo PK, Kar AN, Lee SJ, Vaughn LS, Urisman A, Oses-Prieto J, Dell'Orco M, Cassidy DE, Costa ID, Miller S, Thames E, Smith TP, Burlingame AL, Perrone-Bizzozero N, Twiss JL. Intra-axonal translation of Khsrp mRNA slows axon regeneration by destabilizing localized mRNAs. Nucleic Acids Res. 2022 May 12.  View on PubMed
  3. Zhao M, Ren K, Xiong X, Xin Y, Zou Y, Maynard JC, Kim A, Battist AP, Koneripalli N, Wang Y, Chen Q, Xin R, Yang C, Huang R, Yu J, Huang Z, Zhang Z, Wang H, Wang D, Xiao Y, Salgado OC, Jarjour NN, Hogquist KA, Revelo XS, Burlingame AL, Gao X, von Moltke J, Lin Z, Ruan HB. Epithelial STAT6 O-GlcNAcylation drives a concerted anti-helminth alarmin response dependent on tuft cell hyperplasia and Gasdermin C. Immunity. 2022 Apr 12; 55(4):623-638.e5.  View on PubMed
  4. Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ. Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters. Sci Adv. 2022 01 28; 8(4):eabi7711.  View on PubMed
  5. Zhou J, Hamdan H, Yalamanchili HK, Pang K, Pohodich AE, Lopez J, Shao Y, Oses-Prieto JA, Li L, Kim W, Durham MA, Bajikar SS, Palmer DJ, Ng P, Thompson ML, Bebin EM, Müller AJ, Kuechler A, Kampmeier A, Haack TB, Burlingame AL, Liu Z, Rasband MN, Zoghbi HY. Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders. Proc Natl Acad Sci U S A. 2022 01 25; 119(4).  View on PubMed
  6. Cibichakravarthy B, Oses-Prieto JA, Ben-Yosef M, Burlingame AL, Karr TL, Gottlieb Y. Comparative Proteomics of Coxiella like Endosymbionts (CLEs) in the Symbiotic Organs of Rhipicephalus sanguineus Ticks. Microbiol Spectr. 2022 02 23; 10(1):e0167321.  View on PubMed
  7. Zille M, Oses-Prieto JA, Savage SR, Karuppagounder SS, Chen Y, Kumar A, Morris JH, Scheidt KA, Burlingame AL, Ratan RR. Hemin-Induced Death Models Hemorrhagic Stroke and Is a Variant of Classical Neuronal Ferroptosis. J Neurosci. 2022 03 09; 42(10):2065-2079.  View on PubMed
  8. Alquezar C, Schoch KM, Geier EG, Ramos EM, Scrivo A, Li KH, Argouarch AR, Mlynarski EE, Dombroski B, DeTure M, Dickson DW, Yokoyama JS, Cuervo AM, Burlingame AL, Schellenberg GD, Miller TM, Miller BL, Kao AW. TSC1 loss increases risk for tauopathy by inducing tau acetylation and preventing tau clearance via chaperone-mediated autophagy. Sci Adv. 2021 Nov 05; 7(45):eabg3897.  View on PubMed
  9. Peters JJ, Leitz J, Oses-Prieto JA, Burlingame AL, Brunger AT. Molecular Characterization of AMPA-Receptor-Containing Vesicles. Front Mol Neurosci. 2021; 14:754631.  View on PubMed
  10. Rye KA, Davidson NO, Burlingame AL, Guengerich FP. Working Toward Reducing Bias in Peer Review. Mol Cell Proteomics. 2021; 20:100152.  View on PubMed
  11. Rye KA, Davidson NO, Burlingame AL, Guengerich FP. Working toward reducing bias in peer review. J Biol Chem. 2021 10; 297(4):101243.  View on PubMed
  12. Rye KA, Davidson NO, Burlingame AL, Guengerich FP. Working toward reducing bias in peer review. J Lipid Res. 2021; 62:100124.  View on PubMed
  13. Xu Y, Huangyang P, Wang Y, Xue L, Devericks E, Nguyen HG, Yu X, Oses-Prieto JA, Burlingame AL, Miglani S, Goodarzi H, Ruggero D. ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance. Cell. 2021 09 30; 184(20):5215-5229.e17.  View on PubMed
  14. Doron-Mandel E, Koppel I, Abraham O, Rishal I, Smith TP, Buchanan CN, Sahoo PK, Kadlec J, Oses-Prieto JA, Kawaguchi R, Alber S, Zahavi EE, Di Matteo P, Di Pizio A, Song DA, Okladnikov N, Gordon D, Ben-Dor S, Haffner-Krausz R, Coppola G, Burlingame AL, Jungwirth P, Twiss JL, Fainzilber M. The glycine arginine-rich domain of the RNA-binding protein nucleolin regulates its subcellular localization. EMBO J. 2021 10 18; 40(20):e107158.  View on PubMed
  15. Roehrig AE, Klupsch K, Oses-Prieto JA, Chaib S, Henderson S, Emmett W, Young LC, Surinova S, Blees A, Pfeiffer A, Tijani M, Brunk F, Hartig N, Muñoz-Alegre M, Hergovich A, Jennings BH, Burlingame AL, Rodriguez-Viciana P. Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex. PLoS One. 2021; 16(8):e0254697.  View on PubMed
  16. Moradi A, Dai S, Wong EOY, Zhu G, Yu F, Lam HM, Wang Z, Burlingame A, Lin C, Afsharifar A, Yu W, Wang T, Li N. Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars. Biomolecules. 2021 08 16; 11(8).  View on PubMed
  17. Mohan S, Sampognaro PJ, Argouarch AR, Maynard JC, Welch M, Patwardhan A, Courtney EC, Zhang J, Mason A, Li KH, Huang EJ, Seeley WW, Miller BL, Burlingame A, Jacobson MP, Kao AW. Processing of progranulin into granulins involves multiple lysosomal proteases and is affected in frontotemporal lobar degeneration. Mol Neurodegener. 2021 08 03; 16(1):51.  View on PubMed
  18. Stevens SR, Longley CM, Ogawa Y, Teliska LH, Arumanayagam AS, Nair S, Oses-Prieto JA, Burlingame AL, Cykowski MD, Xue M, Rasband MN. Ankyrin-R regulates fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K+ channels. Elife. 2021 06 28; 10.  View on PubMed
  19. Qu J, Fourman S, Fitzgerald M, Liu M, Nair S, Oses-Prieto J, Burlingame A, Morris JH, Davidson WS, Tso P, Bhargava A. Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue. Sci Rep. 2021 06 24; 11(1):13289.  View on PubMed
  20. Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Sci Rep. 2021 06 22; 11(1):13084.  View on PubMed

Go to UCSF Profiles, powered by CTSI