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Steve Briggs

Research

We study molecular signaling networks with a focus on the innate immune system of plants. To support our studies, we developed a proteomics capability that is sensitive enough to: discover new genes and gene models (1); discover genes based solely on comparison between the proteomes of mutant and wild type plants (2), and discover mechanisms of signaling mediated by protein phosphorylation (3). We used mass spectrometry to generate a proteomics atlas, elements of which have been published (4, 5, 6). When combined with RNA-seq data generated by our collaborator, Joe Ecker (Salk), our integrated gene expression atlas was used to derive co-expression networks and gene regulatory networks from the proteome and transcriptome alone and from integration of the data. We found that the transcriptome does not predict the proteome either quantitatively or qualitatively (4) and now we are pursuing explanations for certain discrepancies. Recent reports on host-microbe interactions include studies of host peptide signaling (7) and pathogen effector secretion (8, 9).

  1. Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays. Mol Cell Proteomics. 2014 Jan;13(1):157-67. doi: 10.1074/mcp.M113.031260.
  2. Zhang X, Facette M, Humphries JA, Shen Z, Park Y, Sutimantanapi D, Sylvester AW, Briggs SP, Smith LG. Identification of PAN2 by quantitative proteomics as a leucine-rich repeat-receptor-like kinase acting upstream of PAN1 to polarize cell division in maize. Plant Cell. 2012 Nov;24(11):4577-89. doi: 10.1105/tpc.112.104125. Epub 2012 Nov 21. PubMed PMID: 23175742; PubMed Central PMCID: PMC3531853.
  3. Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas. Science. 2012 Oct 19;338(6105):390-3. doi: 10.1126/science.1225974. Epub 2012 Aug 30. PubMed PMID: 22936567; PubMed Central PMCID: PMC3523706.
  4. Walley JW, Shen Z, Sartor R, Wu KJ, Osborn J, Smith LG, Briggs SP. Reconstruction of protein networks from an atlas of maize seed proteotypes. Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4808-17. doi: 10.1073/pnas.1319113110. Epub 2013 Nov 18. PubMed PMID: 24248366; PubMed Central PMCID: PMC3856832.
  5. Facette MR, Shen Z, Björnsdóttir FR, Briggs SP, Smith LG. Parallel proteomic and phosphoproteomic analyses of successive stages of maize leaf development. Plant Cell. 2013 Aug;25(8):2798-812. doi: 10.1105/tpc.113.112227. Epub 2013 Aug 9. PubMed PMID: 23933881; PubMed Central PMCID: PMC3784581.
  6. Marcon C, Malik WA, Walley JW, Shen Z, Paschold A, Smith LG, Piepho HP, Briggs SP, Hochholdinger F. A high resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axis. Plant Physiol. 2015 Mar 16. pii: pp.00138.2015
  7. Huffaker A, Pearce G, Veyrat N, Erb M, Turlings TC, Sartor R, Shen Z, Briggs SP, Vaughan MM, Alborn HT, Teal PE, Schmelz EA. Plant elicitor peptides are conserved signals regulating direct and indirect antiherbivore defense. Proc Natl Acad Sci U S A. Apr 2;110(14):5707-12. doi: 10.1073/pnas.1214668110. 2013
  8. Chaudhary R, Atamian HS, Shen Z, Briggs SP, Kaloshian I. Potato aphid salivary proteome: enhanced salivation using resorcinol and identification of aphid phosphoproteins. J Proteome Res. 2015 Apr 3;14(4):1762-78. doi: 10.1021/pr501128k.
  9. Chaudhary R, Atamian HS, Shen Z, Briggs SP, Kaloshian I. GroEL from the endosymbiont Buchnera aphidicola betrays the aphid by triggering plant defense. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8919-24. doi: 10.1073/pnas.1407687111.

We collaborate with several labs to understand problems in signaling that are less central to our interests but that can be uniquely addressed using our expertise. These include understanding endoplasmic reticulum stress (1) and circadian signaling in plants (2); chemotactic signaling in Dictyostelium (3); and the molecular determinants of chronic lymphocytic leukemia (4).

  1. Walley J, Xiao Y, Wang JZ, Baidoo EE, Keasling JD, Shen Z, Briggs SP, Dehesh K. Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum. Proc Natl Acad Sci U S A. 2015 May 12;112(19):6212-7. doi: 10.1073/pnas.1504828112. Epub 2015 Apr 28. PubMed PMID: 25922532; PubMed Central PMCID: PMC4434691.
  2. Huang H, Alvarez S, Bindbeutel RK, Shen Z, Naldrett MJ, Evans BS, Briggs SP, Hicks LM, Kay SA, Nusinow DA. Identification of evening complex associated proteins in Arabidopsis by affinity purification and mass spectrometry. Mol Cell Proteomics. 2015 Nov 6. pii: mcp.M115.054064
  3. Kölsch V, Shen Z, Lee S, Plak K, Lotfi P, Chang J, Charest PG, Romero JL, Jeon TJ, Kortholt A, Briggs SP, Firtel RA. Daydreamer, a Ras effector and GSK-3 substrate, is important for directional sensing and cell motility. Mol Biol Cell. 2013 Jan;24(2):100-14. doi: 10.1091/mbc.E12-04-0271. Epub 2012 Nov 7. PubMed PMID: 23135995; PubMed Central PMCID: PMC3541958.
  4. Yu J, Chen L, Cui B, Widhopf GF 2nd, Shen Z, Wu R, Zhang L, Zhang S, Briggs SP, Kipps TJ. Wnt5a induces ROR1/ROR2 hetero-oligomerization to enhance leukemia chemotaxis and proliferation. J Clin Invest. 2015 Dec 21. pii: 83535. doi: 10.1172/JCI83535.
Briggs Figure 1

Publications

  • Huang H, Alvarez S, Bindbeutel RK, Shen Z, Naldrett MJ, Evans BS, Briggs SP, Hicks LM, Kay SA, Nusinow DA. Identification of evening complex associated proteins in Arabidopsis by affinity purification and mass spectrometry. Mol Cell Proteomics. 2015 Nov 6. pii: mcp.M115.054064
  • Yu J, Chen L, Cui B, Widhopf GF 2nd, Shen Z, Wu R, Zhang L, Zhang S, Briggs SP, Kipps TJ. Wnt5a induces ROR1/ROR2 heterooligomerization to enhance leukemia chemotaxis and proliferation. J Clin Invest. 2015 Dec 21. pii: 83535. doi: 10.1172/JCI83535.
  • Nakasaki M, Hwang Y, Xie Y, Kataria S, Gund R, Hajam EY, Samuel R, George R, Danda D, M J P, Nakamura T, Shen Z, Briggs S, Varghese S, Jamora C. The matrix protein Fibulin-5 is at the interface of tissue stiffness and inflammation in fibrosis. Nat Commun. 2015 Oct 15;6:8574. doi: 10.1038/ncomms9574.
  • Pineda G, Shen Z, Ponte de Albuquerque C, Reynoso E, Chen J, Tu C-C, Tang W, Briggs S, Zhou H, Wang JY. Proteomics Studies of the Interactome of RNA Polymerase II C-Terminal Repeated Domain. BMC Research Notes 2015 Oct 29;8:616. doi: 10.1186/s13104-015-1569-y
  • Walley J, Xiao Y, Wang J-Z, Baidoo EE, Keasling JD, Shen Z, Briggs SP, Dehesh K. Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum. Proc Natl Acad Sci USA April 28, 2015 doi: 10.1073/pnas.1504828112
  • Marcon C, Malik WA, Walley JW, Shen Z, Paschold A, Smith LG, Piepho HP, Briggs SP, Hochholdinger F. A high resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axis. Plant Physiol. 2015 Mar 16. pii: pp.00138.2015
  • Xiong J, Todorova D, Su NY, Kim J, Lee PJ, Shen Z, Briggs SP, Xu Y. Stemness factor Sall4 is required for DNA damage response in embryonic stem cells. J Cell Biol. 2015 Mar 2;208(5):513-20. doi: 10.1083/jcb.201408106.
  • Chaudhary R, Atamian HS, Shen Z, Briggs SP, Kaloshian I. Potato aphid salivary proteome: enhanced salivation using resorcinol and identification of aphid phosphoproteins. J Proteome Res. 2015 Apr 3;14(4):1762-78. doi: 10.1021/pr501128k.
  • Wang Q, Sun T, Xu J, Shen Z, Briggs SP, Zhou D, Wang L. Response and Adaptation of Escherichia coli to Suppression of the Amber Stop Codon. Chembiochem. 2014 Aug 18;15(12):1744-9. doi: 10.1002/cbic.201402235.
  • Chaudhary R, Atamian HS, Shen Z, Briggs SP, Kaloshian I. GroEL from the endosymbiont Buchnera aphidicola betrays the aphid by triggering plant defense. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8919-24. doi: 10.1073/pnas.1407687111.
  • Widhopf GF 2nd, Cui B, Ghia EM, Chen L, Messer K, Shen Z, Briggs SP, Croce CM, Kipps TJ. ROR1 can interact with TCL1 and enhance leukemogenesis in Eμ-TCL1 transgenic mice. Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):793-8. doi: 10.1073/pnas.1308374111.
  • Almenar-Queralt A, Falzone T, Shen Z, Lillo C, Killian R, Arreola A, Niederst E, Ng K, Kim S, Briggs S, Williams D, Goldstein L. UV Irradiation Accelerates Amyloid Precursor Protein (APP) Processing and Disrupts APP Axonal Transport. Journal of Neuroscience 2014 Feb 26;34(9):3320-39. doi: 10.1523/JNEUROSCI.1503-13.2014
  • Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays. Mol Cell Proteomics. 2014 Jan;13(1):157-67. doi: 10.1074/mcp.M113.031260.
  • Walley JW, Shen Z, Sartor R, Wu KJ, Osborn J, Smith LG, Briggs SP. Reconstruction of protein networks from an atlas of maize seed proteotypes. Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4808-17. doi: 10.1073/pnas.1319113110.
  • Guo Y, Darshi M, Ma Y, Perkins GA, Shen Z, Kristofer KJ, Saito R, Chen A, Lee YS, Patel HH, Briggs SP, Ellisman MH, Olefsky JM, Taylor SS. Quantitative Proteomic and Functioanl Analysis of Liver Mitochondria from High Fat Diet Diabetic Mice. Mol Cell Proteomics. 2013 Sep 12
  • Facette MR, Shen Z, Björnsdóttir FR, Briggs SP, Smith LG. Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development. Plant Cell. 2013 Aug 9.
  • Huffaker A, Pearce G, Veyrat N, Erb M, Turlings TC, Sartor R, Shen Z, Briggs SP, Vaughan MM, Alborn HT, Teal PE, Schmelz EA. Plant elicitor peptides are conserved signals regulating direct and indirect antiherbivore defense. Proc Natl Acad Sci U S A. Apr 2;110(14):5707-12. doi: 10.1073/pnas.1214668110. 2013
  • Jones CS, Luong T, Hannon M, Tran M, Gregory JA, Shen Z, Briggs SP, Mayfield SP. Heterologous expression of the C-terminal antigenic domain of the malaria vaccine candidate Pfs48/45 in the green algae Chlamydomonas reinhardtii. Appl Microbiol Biotechnol. Mar;97(5):1987-95. doi: 10.1007/s00253-012-4071-7. 2013
  • Kölsch V, Shen Z, Lee S, Plak K, Lotfi P, Chang J, Charest PG, Romero JL, Jeon TJ, Kortholt A, Briggs SP, Firtel RA. Daydreamer, a Ras effector and GSK-3 substrate, is important for directional sensing and cell motility. Mol Biol Cell. Jan;24(2):100-14. doi: 10.1091/mbc.E12-04-0271. 2013
  • Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas. Science. Oct 19;338(6105):390-3. doi: 10.1126/science.1225974. 2012
  • Zhang X, Facette M, Humphries JA, Shen Z, Park Y, Sutimantanapi D, Sylvester AW, Briggs SP, Smith LG. Identification of PAN2 by Quantitative Proteomics as a Leucine-Rich Repeat-Receptor-Like Kinase Acting Upstream of PAN1 to Polarize Cell Division in Maize. Plant Cell. Nov;24(11):4577-89. doi: 10.1105/tpc.112.104125. 2012
  • Ng DW, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ. Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity (Edinb). Apr;108(4):419-30. doi: 10.1038/hdy.2011.92. 2012
  • Rasala BA, Lee PA, Shen Z, Briggs SP, Mendez M, Mayfield SP. Robust expression and secretion of Xylanase1 in Chlamydomonas reinhardtii by fusion to a selection gene and processing with the FMDV 2A peptide. PLoS One;7(8):e43349. doi: 10.1371/journal.pone.0043349. 2012
  • Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. Accurate mass spectrometry based protein quantification via shared peptides. J Comput Biol. Apr;19(4):337-48. doi: 10.1089/cmb.2009.0267. 2012
  • Parrish AR, She X, Xiang Z, Coin I, Shen Z, Briggs SP, Dillin A, Wang L. Expanding the genetic code of Caenorhabditis elegans using bacterial aminoacyl-tRNA synthetase/tRNA pairs. ACS Chem Biol. Jul 20;7(7):1292-302. doi: 10.1021/cb200542j. Epub 2012 May 11. 2012
  • Teachenor R, Beck K, Wright LY, Shen Z, Briggs SP, Murre C. Biochemical and phosphoproteomic analysis of the helix-loop-helix protein E47. Mol Cell Biol. May;32(9):1671-82. doi: 10.1128/MCB.06452-11. Epub 2012 Feb 21. 2012

Biography

Steve Briggs received his Ph.D. from Michigan State University and spent the first half of his career in industry, most recently as Sr. Vice President for Corporate Research at Diversa. Previously he was President of Torrey Mesa Research Institute and before that he was Director at Pioneer/DuPont for several research areas including genomics. Briggs has been Co-editor of The Plant Cell; he serves on the Scientific Advisory Board, Keystone Symposia and the Board of Advisors, Plant Sciences Institute, Iowa State University; he is a member of the National Academy of Sciences.