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Jeffrey Johnson, PhD

Title(s)Research Protein Chemist, Cellular Molecular Pharmacology
SchoolSchool of Medicine
Phone415-476-3068
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    Collapse Biography 
    Collapse Education and Training
    The Scripps Research InstitutePh.D.2008Cell Biology
    University of Illinois Urbana-ChampaignB.S.2002Biochemistry
    University of Illinois Urbana-ChampaignB.S.2002Bioengineering

    Collapse Research 
    Collapse Research Activities and Funding
    Decoding the Chlamydia inclusion membrane protein-host protein interactome
    NIH/NIAID R01AI122747Dec 1, 2015 - Nov 30, 2020
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Faust TB, Li Y, Jang GM, Johnson JR, Yang S, Weiss A, Krogan NJ, Frankel AD. PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription. Sci Rep. 2017 03 27; 7:45394. PMID: 28345603.
      View in: PubMed
    2. Elwell CA, Czudnochowski N, von Dollen J, Johnson JR, Nakagawa R, Mirrashidi K, Krogan NJ, Engel JN, Rosenberg OS. Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction. Elife. 2017 03 02; 6. PMID: 28252385.
      View in: PubMed
    3. Celona B, Dollen JV, Vatsavayai SC, Kashima R, Johnson JR, Tang AA, Hata A, Miller BL, Huang EJ, Krogan NJ, Seeley WW, Black BL. Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106. Elife. 2017 01 10; 6. PMID: 28072389.
      View in: PubMed
    4. Tsvetanova NG, Trester-Zedlitz M, Newton BW, Riordan DP, Sundaram AB, Johnson JR, Krogan NJ, von Zastrow M. G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands. Mol Pharmacol. 2017 Feb; 91(2):145-156. PMID: 27879340.
      View in: PubMed
    5. Jayaraman D, Kodani A, Gonzalez DM, Mancias JD, Mochida GH, Vagnoni C, Johnson J, Krogan N, Harper JW, Reiter JF, Yu TW, Bae BI, Walsh CA. Microcephaly Proteins Wdr62 and Aspm Define a Mother Centriole Complex Regulating Centriole Biogenesis, Apical Complex, and Cell Fate. Neuron. 2016 Nov 23; 92(4):813-828. PMID: 27974163.
      View in: PubMed
    6. Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP. Non-degradative Ubiquitination of Protein Kinases. PLoS Comput Biol. 2016 06; 12(6):e1004898. PMID: 27253329; PMCID: PMC4890936.
      View in: PubMed, PubMed Central
    7. Inclan YF, Persat A, Greninger A, Von Dollen J, Johnson J, Krogan N, Gitai Z, Engel JN. A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa. Mol Microbiol. 2016 08; 101(4):590-605. PMID: 27145134; PMCID: PMC4980298 [Available on 08/01/17].
      View in: PubMed, PubMed Central
    8. Tripathi S, Pohl MO, Zhou Y, Rodriguez-Frandsen A, Wang G, Stein DA, Moulton HM, DeJesus P, Che J, Mulder LC, Yángüez E, Andenmatten D, Pache L, Manicassamy B, Albrecht RA, Gonzalez MG, Nguyen Q, Brass A, Elledge S, White M, Shapira S, Hacohen N, Karlas A, Meyer TF, Shales M, Gatorano A, Johnson JR, Jang G, Johnson T, Verschueren E, Sanders D, Krogan N, Shaw M, König R, Stertz S, García-Sastre A, Chanda SK. Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. Cell Host Microbe. 2015 Dec 09; 18(6):723-35. PMID: 26651948; PMCID: PMC4829074 [Available on 12/09/16].
      View in: PubMed, PubMed Central
    9. Costa HA, Leitner MG, Sos ML, Mavrantoni A, Rychkova A, Johnson JR, Newton BW, Yee MC, De La Vega FM, Ford JM, Krogan NJ, Shokat KM, Oliver D, Halaszovich CR, Bustamante CD. Discovery and functional characterization of a neomorphic PTEN mutation. Proc Natl Acad Sci U S A. 2015 Nov 10; 112(45):13976-81. PMID: 26504226; PMCID: PMC4653168.
      View in: PubMed, PubMed Central
    10. Min SW, Chen X, Tracy TE, Li Y, Zhou Y, Wang C, Shirakawa K, Minami SS, Defensor E, Mok SA, Sohn PD, Schilling B, Cong X, Ellerby L, Gibson BW, Johnson J, Krogan N, Shamloo M, Gestwicki J, Masliah E, Verdin E, Gan L. Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits. Nat Med. 2015 Oct; 21(10):1154-62. PMID: 26390242.
      View in: PubMed
    11. Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P. Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PLoS Comput Biol. 2015 Aug; 11(8):e1004362. PMID: 26312481; PMCID: PMC4552029.
      View in: PubMed, PubMed Central
    12. Kodani A, Yu TW, Johnson JR, Jayaraman D, Johnson TL, Al-Gazali L, Sztriha L, Partlow JN, Kim H, Krup AL, Dammermann A, Krogan NJ, Walsh CA, Reiter JF. Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication. Elife. 2015 Aug 22; 4. PMID: 26297806; PMCID: PMC4574112.
      View in: PubMed, PubMed Central
    13. Mark KG, Meza-Gutierrez F, Johnson JR, Newton BW, Krogan NJ, Toczyski DP. Prb1 Protease Activity Is Required for Its Recognition by the F-Box Protein Saf1. Biochemistry. 2015 Jul 28; 54(29):4423-6. PMID: 26161950; PMCID: PMC4816488.
      View in: PubMed, PubMed Central
    14. Mirrashidi KM, Elwell CA, Verschueren E, Johnson JR, Frando A, Von Dollen J, Rosenberg O, Gulbahce N, Jang G, Johnson T, Jäger S, Gopalakrishnan AM, Sherry J, Dunn JD, Olive A, Penn B, Shales M, Cox JS, Starnbach MN, Derre I, Valdivia R, Krogan NJ, Engel J. Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. Cell Host Microbe. 2015 Jul 08; 18(1):109-21. PMID: 26118995; PMCID: PMC4540348.
      View in: PubMed, PubMed Central
    15. Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Cell Rep. 2015 May 26; 11(8):1236-50. PMID: 25981045; PMCID: PMC4613747.
      View in: PubMed, PubMed Central
    16. Sidrauski C, Tsai JC, Kampmann M, Hearn BR, Vedantham P, Jaishankar P, Sokabe M, Mendez AS, Newton BW, Tang EL, Verschueren E, Johnson JR, Krogan NJ, Fraser CS, Weissman JS, Renslo AR, Walter P. Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response. Elife. 2015 Apr 15; 4:e07314. PMID: 25875391; PMCID: PMC4426669.
      View in: PubMed, PubMed Central
    17. Blakely CM, Pazarentzos E, Olivas V, Asthana S, Yan JJ, Tan I, Hrustanovic G, Chan E, Lin L, Neel DS, Newton W, Bobb KL, Fouts TR, Meshulam J, Gubens MA, Jablons DM, Johnson JR, Bandyopadhyay S, Krogan NJ, Bivona TG. NF-?B-activating complex engaged in response to EGFR oncogene inhibition drives tumor cell survival and residual disease in lung cancer. Cell Rep. 2015 Apr 07; 11(1):98-110. PMID: 25843712; PMCID: PMC4394036.
      View in: PubMed, PubMed Central
    18. Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M. A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Mol Cell. 2015 Jan 22; 57(2):329-340. PMID: 25616068; PMCID: PMC4305532.
      View in: PubMed, PubMed Central
    19. Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, Von Dollen J, Maher MC, Johnson T, Newton W, Jäger S, Shales M, Horner J, Hernandez RD, Krogan NJ, Glaunsinger BA. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell. 2015 Jan 22; 57(2):349-60. PMID: 25544563; PMCID: PMC4305015.
      View in: PubMed, PubMed Central
    20. Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map. Cancer Discov. 2015 Feb; 5(2):154-67. PMID: 25501949.
      View in: PubMed
    21. Lin C, Yao E, Wang K, Nozawa Y, Shimizu H, Johnson JR, Chen JN, Krogan NJ, Chuang PT. Regulation of Sufu activity by p66ß and Mycbp provides new insight into vertebrate Hedgehog signaling. Genes Dev. 2014 Nov 15; 28(22):2547-63. PMID: 25403183; PMCID: PMC4233246.
      View in: PubMed, PubMed Central
    22. Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts. Mol Cell Biol. 2015 Jan; 35(2):468-78. PMID: 25384976; PMCID: PMC4272423.
      View in: PubMed, PubMed Central
    23. Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP. Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1. Mol Cell Proteomics. 2015 Jan; 14(1):162-76. PMID: 25381059; PMCID: PMC4288252.
      View in: PubMed, PubMed Central
    24. Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov; 9(11):2539-54. PMID: 25275790; PMCID: PMC4332878.
      View in: PubMed, PubMed Central
    25. Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q. AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):E15-24. PMID: 24367103; PMCID: PMC3890890.
      View in: PubMed, PubMed Central
    26. Monroe KM, Yang Z, Johnson JR, Geng X, Doitsh G, Krogan NJ, Greene WC. IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV. Science. 2014 Jan 24; 343(6169):428-32. PMID: 24356113.
      View in: PubMed
    27. Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M, Lenstra TL, Holstege FC, Johnson JR, Bloom K, Krogan NJ. Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. Cell Rep. 2013 Jun 27; 3(6):2168-78. PMID: 23746449; PMCID: PMC3718395.
      View in: PubMed, PubMed Central
    28. Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS. Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F. J Mol Biol. 2013 Apr 12; 425(7):1172-82. PMID: 23318957; PMCID: PMC3602375.
      View in: PubMed, PubMed Central
    29. Li M, Shandilya SM, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK, Parniak MA, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris RS. First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. ACS Chem Biol. 2012 Mar 16; 7(3):506-17. PMID: 22181350; PMCID: PMC3306499.
      View in: PubMed, PubMed Central
    30. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. PMID: 22190034; PMCID: PMC3310911.
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    31. Naji S, Ambrus G, Cimermancic P, Reyes JR, Johnson JR, Filbrandt R, Huber MD, Vesely P, Krogan NJ, Yates JR, Saphire AC, Gerace L. Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production. Mol Cell Proteomics. 2012 Apr; 11(4):M111.015313. PMID: 22174317; PMCID: PMC3322577.
      View in: PubMed, PubMed Central
    32. Dinglasan RR, Devenport M, Florens L, Johnson JR, McHugh CA, Donnelly-Doman M, Carucci DJ, Yates JR, Jacobs-Lorena M. The Anopheles gambiae adult midgut peritrophic matrix proteome. Insect Biochem Mol Biol. 2009 Feb; 39(2):125-34. PMID: 19038338; PMCID: PMC2684889.
      View in: PubMed, PubMed Central
    33. Le Roch KG, Johnson JR, Ahiboh H, Chung DW, Prudhomme J, Plouffe D, Henson K, Zhou Y, Witola W, Yates JR, Mamoun CB, Winzeler EA, Vial H. A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum. BMC Genomics. 2008 Oct 30; 9:513. PMID: 18973684; PMCID: PMC2596145.
      View in: PubMed, PubMed Central
    34. Patra KP, Johnson JR, Cantin GT, Yates JR, Vinetz JM. Proteomic analysis of zygote and ookinete stages of the avian malaria parasite Plasmodium gallinaceum delineates the homologous proteomes of the lethal human malaria parasite Plasmodium falciparum. Proteomics. 2008 Jun; 8(12):2492-9. PMID: 18563747; PMCID: PMC2637033.
      View in: PubMed, PubMed Central
    35. Kato N, Sakata T, Breton G, Le Roch KG, Nagle A, Andersen C, Bursulaya B, Henson K, Johnson J, Kumar KA, Marr F, Mason D, McNamara C, Plouffe D, Ramachandran V, Spooner M, Tuntland T, Zhou Y, Peters EC, Chatterjee A, Schultz PG, Ward GE, Gray N, Harper J, Winzeler EA. Gene expression signatures and small-molecule compounds link a protein kinase to Plasmodium falciparum motility. Nat Chem Biol. 2008 Jun; 4(6):347-56. PMID: 18454143.
      View in: PubMed
    36. Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA. In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics. 2008 Feb 07; 9:70. PMID: 18257930; PMCID: PMC2268928.
      View in: PubMed, PubMed Central
    37. Dong MQ, Venable JD, Au N, Xu T, Park SK, Cociorva D, Johnson JR, Dillin A, Yates JR. Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science. 2007 Aug 03; 317(5838):660-3. PMID: 17673661.
      View in: PubMed
    38. Cass CL, Johnson JR, Califf LL, Xu T, Hernandez HJ, Stadecker MJ, Yates JR, Williams DL. Proteomic analysis of Schistosoma mansoni egg secretions. Mol Biochem Parasitol. 2007 Oct; 155(2):84-93. PMID: 17644200; PMCID: PMC2077830.
      View in: PubMed, PubMed Central
    39. Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch K, Sarr O, Ndir O, Mboup S, Batalov S, Wirth DF, Winzeler EA. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog. 2006 Jun; 2(6):e57. PMID: 16789840; PMCID: PMC1480597.
      View in: PubMed, PubMed Central
    40. Hu K, Johnson J, Florens L, Fraunholz M, Suravajjala S, DiLullo C, Yates J, Roos DS, Murray JM. Cytoskeletal components of an invasion machine--the apical complex of Toxoplasma gondii. PLoS Pathog. 2006 Feb; 2(2):e13. PMID: 16518471; PMCID: PMC1383488.
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    41. Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR, Winzeler EA. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004 Nov; 14(11):2308-18. PMID: 15520293; PMCID: PMC525690.
      View in: PubMed, PubMed Central
    42. Trueman HE, Raine JD, Florens L, Dessens JT, Mendoza J, Johnson J, Waller CC, Delrieu I, Holders AA, Langhorne J, Carucci DJ, Yates JR, Sinden RE. Functional characterization of an LCCL-lectin domain containing protein family in Plasmodium berghei. J Parasitol. 2004 Oct; 90(5):1062-71. PMID: 15562607.
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    43. Sam-Yellowe TY, Florens L, Johnson JR, Wang T, Drazba JA, Le Roch KG, Zhou Y, Batalov S, Carucci DJ, Winzeler EA, Yates JR. A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling. Genome Res. 2004 Jun; 14(6):1052-9. PMID: 15140830; PMCID: PMC419783.
      View in: PubMed, PubMed Central
    44. Ling IT, Florens L, Dluzewski AR, Kaneko O, Grainger M, Yim Lim BY, Tsuboi T, Hopkins JM, Johnson JR, Torii M, Bannister LH, Yates JR, Holder AA, Mattei D. The Plasmodium falciparum clag9 gene encodes a rhoptry protein that is transferred to the host erythrocyte upon invasion. Mol Microbiol. 2004 Apr; 52(1):107-18. PMID: 15049814.
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    45. Johnson JR, Florens L, Carucci DJ, Yates JR. Proteomics in malaria. J Proteome Res. 2004 Mar-Apr; 3(2):296-306. PMID: 15113107.
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    46. McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom. 2004; 18(18):2162-8. PMID: 15317041.
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    47. Johnson JR, Meng F, Forbes AJ, Cargile BJ, Kelleher NL. Fourier-transform mass spectrometry for automated fragmentation and identification of 5-20 kDa proteins in mixtures. Electrophoresis. 2002 Sep; 23(18):3217-23. PMID: 12298093.
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    48. Meng F, Cargile BJ, Patrie SM, Johnson JR, McLoughlin SM, Kelleher NL. Processing complex mixtures of intact proteins for direct analysis by mass spectrometry. Anal Chem. 2002 Jul 01; 74(13):2923-9. PMID: 12141648.
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    49. Meng F, Cargile BJ, Miller LM, Forbes AJ, Johnson JR, Kelleher NL. Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat Biotechnol. 2001 Oct; 19(10):952-7. PMID: 11581661.
      View in: PubMed
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