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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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
- 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.
- 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).
- 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.
- 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
- 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.
- 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.