U.S. Department of Energy

Pacific Northwest National Laboratory

Ernesto Nakayasu

Ernesto Nakayasu
Professional Title: 

2003 - Bachelor in Biological Sciences, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil.

2008 - Doctor of Philosophy, Pathobiology Program, Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA.


M.T. Thomas Award for Outstanding Postdoctoral Achievement for his protein degradation studies in biological systems that have, according to the selection committee, "a large potential for real societal impact". Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA. August 19, 2014.

Outstanding Graduate Student in Biological Science Award. College of Science, University of Texas at El Paso, El Paso, TX. December 5, 2008.

Professional Memberships and Activities: 

Biological Sciences Division, Earth and Biolgical Sciences Directorate, Pacific Northwest National Laboratory.



  • Burnum-Johnson KE, JE Kyle, AJ Eisfeld, CP Casey, KG Stratton, JF Gonzalez, F Habyarimana, NM Negretti, AC Sims, S Chauhan, LB Thackray, P Halfmann, KB Walters, YM Kim, EM Zink, CD Nicora, KK Weitz, BJM Webb-Robertson, ES Nakayasu, B Ahmer, M Konkel, VL Motin, R Baric, MS Diamond, Y Kawaoka, KM Waters, RD Smith, and TO Metz. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142(3):442-448.  doi:10.1039/c6an02486f
  • Liu Y, W Zhu, Y Tan, ES Nakayasu, CJ Staiger, and ZQ Luo. 2017. "A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin." PLoS Pathogens 13(1):e1006186. doi:10.1371/journal.ppat.1006186
  • Muralimanoharan S, C Li, ES Nakayasu, CP Casey, TO Metz, PW Nathanielsz, and A Maloyan. 2017. "Sexual dimorphism in the fetal cardiac response to maternal nutrient restriction." Journal of Molecular and Cellular Cardiology 108:181-193. doi:10.1016/j.yjmcc.2017.06.006
  • Qiu J, K Yu, X Fei, Y Liu, ES Nakayasu, PD Piehowski, JB Shaw, K Puvar, C Das, X Liu, and ZQ Luo. 2017. "A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination." Cell Research 27(7):865-881.  doi:10.1038/cr.2017.66
  • Shakya B, WD Penn, ES Nakayasu, and DJ Lacount. 2017. "The Plasmodium falciparum exported protein PF3D7_0402000 binds to erythrocyte ankyrin and band 4.1." Molecular and Biochemical Parasitology 216:5-13.  doi:10.1016/j.molbiopara.2017.06.002
  • Wang L, X Cai, S Wu, R Bomjan, ES Nakayasu, K H�ndler, JC Hinton, and D Zhao. 2017. "InvS Coordinates Expression of PrgH and FimZ and Is Required for Invasion of Epithelial Cells by Salmonella enterica serovar Typhimurium." Journal of Bacteriology 199(13):00824-16.  doi:10.1128/JB.00824-16
  • Yang J, L Yin, FH Lessner, ES Nakayasu, SH Payne, K Fixen, LA Gallagher, and C Harwood. 2017. "Genes essential for phototrophic growth by a purple alphaproteobacterium." Environmental Microbiology 19(9):3567-3578.  doi:10.1111/1462-2920.13852


  • Sontag RL, ES Nakayasu, RN Brown, GS Niemann, MA Sydor, O Sanchez, C Ansong, SY Lu, H Choi, D Valleau, KK Weitz, A Savchenko, E Cambronne, and JN Adkins. 2016. "Identification of novel host interactors of effectors secreted by Salmonella and Citrobacter: SrfH regulates host kinase ERK2 phosphorylation." mSystems 1(4):e00032-15. doi:10.1128/mSystems.00032-15
  • Baltazar LM, ES Nakayasu, T Sobreira, H Choi, A Casadevall, L Nimrichter, and JD Nosanchuk. 2016. "Antibody Binding Alters the Characteristics and Contents of Extracellular Vesicles Released by Histoplasma Capsulatum." mSphere 1(2):Article No. e00085-15. doi:10.1128/mSphere.00085-15
  • Nakayasu ES, CD Nicora, AC Sims, KE Burnum-Johnson, YM Kim, JE Kyle, MM Matzke, AK Shukla, RK Chu, AA Schepmoes, JM Jacobs, R Baric, BJM Webb-Robertson, RD Smith, and TO Metz. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1(3):e00043-16. doi:10.1128/mSystems.00043-16
  • Qiu J, MJ Sheedlo, K Yu, Y Tan, ES Nakayasu, C Das, X Liu, and ZQ Luo. 2016. "Ubiquitination independent of E1 and E2 enzymes by bacterial effectors." Nature 533(7601):120-124.  doi:10.1038/nature17657


  • Elfenbein JR, LA Knodler, ES Nakayasu, C Ansong, HM Brewer, L Bogomolnaya, LG Adams, M McClelland, JN Adkins, and HL Andrews-Polymenis. 2015. "Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens." PLoS Genetics 11(9):e1005472. doi:10.1371/journal.pgen.1005472
  • Li J, CC Overall, ES Nakayasu, AS Kidwai, MB Jones, R Johnson, NT Nguyen, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in sE-regulated SPI-2 gene expression." Frontiers in Microbiology 6:Artcle No. 27.  doi:10.3389/fmicb.2015.00027
  • Li J, ES Nakayasu, CC Overall, R Johnson, AS Kidwai, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14(4):1716-1726. doi:10.1021/pr5010423
  • Nakayasu ES, MA Sydor, RN Brown, RL Sontag, T Sobreira, GW Slysz, DR Humphrys, T Skarina, O Onoprienko, R Di Leo, BLD Kaiser, J Li, C Ansong, E Cambronne, RD Smith, A Savchenko, and JN Adkins. 2015. "Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis." Journal of Proteome Research 14(9):4029-4038.  doi:10.1021/acs.jproteome.5b00574


  • Malouli D, SG Hansen, ES Nakayasu, EE Marshall, CM Hughes, AB Ventura, RM Gilbride, MS Lewis, G Xu, CN Kreklywich, N Whizin, M Fischer, AW Legasse, K Viswanathan, D Siess, DG Camp, II, MK Axthelm, C Kahl, VR DeFilippis, RD Smith, DN Streblow, LJ Picker, and K Fruh. 2014. "Cytomegalovirus pp65 limits dissemination but is dispensable for persistence." Journal of Clinical Investigation 124(5):1928-1944.  doi:10.1172/JCI67420
  • Nakayasu ES, S Wu, MA Sydor, AK Shukla, KK Weitz, RJ Moore, KK Hixson, JS Kim, VA Petyuk, ME Monroe, L Pasa-Tolic, W Qian, RD Smith, JN Adkins, and C Ansong. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014:Article No. 730725.  doi:10.1155/2014/730725


  • Ansong C, S Wu, D Meng, X Liu, HM Brewer, BLD Kaiser, ES Nakayasu, JR Cort, PA Pevzner, RD Smith, F Heffron, JN Adkins, and L Pasa-Tolic. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions." Proceedings of the National Academy of Sciences of the United States of America 110(25):10153-10158.  doi:10.1073/pnas.1221210110
  • Conlon BP, ES Nakayasu, LE Fleck, MD LaFleur, VM Isabella, K Coleman, SN Leonard, RD Smith, JN Adkins, and K Lewis. 2013. "Activated ClpP kills persisters and eradicates a chronic biofilm infection." Nature 503(7476):365-370.  doi:10.1038/nature12790
  • Nakayasu ES, C Ansong, JN Brown, F Yang, D Lopez-Ferrer, W Qian, RD Smith, and JN Adkins. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry 24(8):1214-1223. doi:10.1007/s13361-013-0619-8
  • Nakayasu ES, R Tempel, XA Cambronne, VA Petyuk, MB Jones, MA Gritsenko, ME Monroe, F Yang, RD Smith, JN Adkins, and F Heffron. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Molecular and Cellular Proteomics 12(11):3297-3309. doi:10.1074/mcp.M113.029850
  • Nakayasu ES, RN Brown, C Ansong, MA Sydor, S Imtiaz, C Mihai, RL Sontag, KK Hixson, ME Monroe, T Sobreira, G Orr, VA Petyuk, F Yang, RD Smith, and JN Adkins. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12(8):2136-2147.  doi:10.1074/mcp.M112.026138
  • Su D, AK Shukla, B Chen, JS Kim, ES Nakayasu, Y Qu, UK Aryal, KK Weitz, TRW Clauss, ME Monroe, DG Camp, II, DJ Bigelow, RD Smith, RN Kulkarni, and W Qian. 2013. "Quantitative Site-specific Reactivity Profiling of S-Nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radical Biology & Medicine 57:68-78.  doi:10.1016/j.freeradbiomed.2012.12.010


  • Bordbar A, ML Mo, ES Nakayasu, AC Rutledge, YM Kim, TO Metz, MB Jones, BC Frank, RD Smith, SN Peterson, DR Hyduke, JN Adkins, and BO Palsson. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8:Article No. 558.  doi:10.1038/msb.2012.21
  • Malouli D, ES Nakayasu, K Viswanathan, DG Camp, II, WL Chang, PA Barry, RD Smith, and K Fruh. 2012. "Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1." Journal of Virology 86(17):8959-8973. doi:10.1128/JVI.01132-12


  • McDermott JE, H Yoon, ES Nakayasu, TO Metz, DR Hyduke, AS Kidwai, BO Palsson, JN Adkins, and F Heffron. 2011. "Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella." Frontiers in Microbiology 2:121. doi:10.3389/fmicb.2011.00121
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