Proteomics & Mass Spectrometry

The Danforth Center’s Proteomics & Mass Spectrometry Facility develops new tools and provides high quality sample analysis in proteomics, mass spectrometry and related analytical fields.

DESCRIPTION | RESEARCH TEAM | PUBLICATIONS | FEES | FACILITY NEWS

Publications

Alvarez, S., Hicks, L.M., and Pandey, S. (2011). ABA-dependent and -independent G-protein signaling in Arabidopsis roots revealed through an iTRAQ proteomics approach. J Proteome Res 10, 3107-22.
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Alvarez, S., Galant, A., Jez, J.M., and Hicks, L.M. (2011). Redox-regulatory mechanisms induced by oxidative stress in Brassica juncea roots monitored by 2-DE proteomics. Proteomics 11, 1346-50.
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Alvarez, S., and Hicks, L.M. (2011). Survey in plant root proteomics. In Sustainable Agriculture and New Biotechnologies (CRC Press), pp. 215-56.
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Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., Wang, J., Zhang, L., Looney, T.J., Zhang, B., Godley, L.A., Hicks, L.M., Lahn, B.T., Jin, P., and He, C. (2011). Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29, 68-72.
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Chen, H., Saksa, K., Zhao, F., Qiu, J., and Xiong, L. (2010). Genetic analysis of pathway regulation for enhancing branched-chain amino acid biosynthesis in plants. Plant J 63, 573-583.
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Chen, Q., Westfall, C.S., Hicks, L.M., Wang, S., and Jez, J.M. (2010). Kinetic basis for the conjugation of auxin by a GH3 family indole acetic acid-amido synthetase. J Biol Chem 285, 29780-29786.
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de Crecy-Lagard, V., Brochier-Armanet, C., Urbonavicius, J., Fernandez, B., Phillips, G., Lyons, B., Noma, A., Alvarez, S., Droogmans, L., Armengaud, J., and Grosjean, H. (2010). Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol 27, 2062-2077.
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Ernst, L., Goodger, J.Q., Alvarez, S., Marsh, E.L., Berla, B., Lockhart, E., Jung, J., Li, P., Bohnert, H.J., and Schachtman, D.P. (2010). Sulphate as a xylem-borne chemical signal precedes the expression of ABA biosynthetic genes in maize roots. J Exp Bot 61, 3395-3405.
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Grobe, N., Lamshoft, M., Orth, R.G., Drager, B., Kutchan, T.M., Zenk, M.H., and Spiteller, M. (2010). Urinary excretion of morphine and biosynthetic precursors in mice. Proc Natl Acad Sci U S A 107, 8147-8152.
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Gutierrez-Gonzalez, J.J., Guttikonda, S.K., Tran, L.S., Aldrich, D.L., Zhong, R., Yu, O., Nguyen, H.T., and Sleper, D.A. (2010). Differential expression of isoflavone biosynthetic genes in soybean during water deficits. Plant Cell Physiol 51, 936-948.
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Gutierrez-Gonzalez, J.J., Wu, X., Gillman, J.D., Lee, J.D., Zhong, R., Yu, O., Shannon, G., Ellersieck, M., Nguyen, H.T., and Sleper, D.A. (2010). Intricate environment-modulated genetic networks control isoflavone accumulation in soybean seeds. BMC Plant Biol 10, 105.
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Han, X., Lamshoft, M., Grobe, N., Ren, X., Fist, A.J., Kutchan, T.M., Spiteller, M., and Zenk, M.H. (2010). The biosynthesis of papaverine proceeds via (S)-reticuline. Phytochemistry 71, 1305-1312.
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Li, H., Deng, Y., Wu, T., Subramanian, S., and Yu, O. (2010). Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiol 153, 1759-1770.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20508137
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Marsh, E., Alvarez, S., Hicks, L.M., Barbazuk, W.B., Qiu, W., Kovacs, L., and Schachtman, D. (2010). Changes in protein abundance during powdery mildew infection of leaf tissues of Cabernet Sauvignon grapevine (Vitis vinifera L.). Proteomics 10, 2057-2064.
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Ning, J., Li, X., Hicks, L.M., and Xiong, L. (2010). A Raf-like MAPKKK gene DSM1 mediates drought resistance through reactive oxygen species scavenging in rice. Plant Physiol 152, 876-890.
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Nomura, T., and Kutchan, T.M. (2010). Three new O-methyltransferases are sufficient for all O-methylation reactions of ipecac alkaloid biosynthesis in root culture of Psychotria ipecacuanha. J Biol Chem 285, 7722-7738.
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Pan, X., Welti, R., and Wang, X. (2010). Quantitative analysis of major plant hormones in crude plant extracts by high-performance liquid chromatography-mass spectrometry. Nat Protoc 5, 986-992.
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Waller, J.C., Alvarez, S., Naponelli, V., Lara-Nunez, A., Blaby, I.K., Da Silva, V., Ziemak, M.J., Vickers, T.J., Beverley, S.M., Edison, A.S., Rocca, J.R., Gregory, J.F., 3rd, de Crecy-Lagard, V., and Hanson, A.D. (2010). A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life. Proc Natl Acad Sci U S A 107, 10412-10417.
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Wu, B., Zhang, B., Feng, X., Rubens, J.R., Huang, R., Hicks, L.M., Pakrasi, H.B., and Tang, Y.J. (2010). Alternative isoleucine synthesis pathway in cyanobacterial species. Microbiology 156, 596-602.
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Yamaguchi, M., Valliyodan, B., Zhang, J., Lenoble, M.E., Yu, O., Rogers, E.E., Nguyen, H.T., and Sharp, R.E. (2010). Regulation of growth response to water stress in the soybean primary root. I. Proteomic analysis reveals region-specific regulation of phenylpropanoid metabolism and control of free iron in the elongation zone. Plant Cell Environ 33, 223-243.
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Zhang, B., Tolstikov, V., Turnbull, C., Hicks, L.M., and Fiehn, O. (2010). Divergent metabolome and proteome suggest functional independence of dual phloem transport systems in cucurbits. Proc Natl Acad Sci U S A 107, 13532-13537.
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Alvarez, S., Berla, B.M., Sheffield, J., Cahoon, R.E., Jez, J.M., and Hicks, L.M. (2009). Comprehensive analysis of the Brassica juncea root proteome in response to cadmium exposure by complementary proteomic approaches. Proteomics 9, 2419-2431.
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Alvarez, S., Wilson, G.H., and Chen, S. (2009). Determination of in vivo disulfide-bonded proteins in Arabidopsis. J Chromatogr B Analyt Technol Biomed Life Sci 877, 101-104.
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Alvarez, S., Zhu, M., and Chen, S. (2009). Proteomics of Arabidopsis redox proteins in response to methyl jasmonate. J Proteomics 73, 30-40.
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Beaudoin, F., Wu, X., Li, F., Haslam, R.P., Markham, J.E., Zheng, H., Napier, J.A., and Kunst, L. (2009). Functional characterization of the Arabidopsis b-ketoacyl-coenzyme A reductase candidates of the fatty acid elongase. Plant Physiol 150, 1174-1191.
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Chen, H., and Xiong, L. (2009). Enhancement of vitamin B(6) levels in seeds through metabolic engineering. Plant Biotechnol J 7, 673-681.
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Chen, Q., Zhang, B., Hicks, L.M., Wang, S., and Jez, J.M. (2009). A liquid chromatography-tandem mass spectrometry-based assay for indole-3-acetic acid-amido synthetase. Anal Biochem 390, 149-154.
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Feng, X., Mouttaki, H., Lin, L., Huang, R., Wu, B., Hemme, C.L., He, Z., Zhang, B., Hicks, L.M., Xu, J., Zhou, J., and Tang, Y.J. (2009). Characterization of the central metabolic pathways in Thermoanaerobacter sp. strain X514 via isotopomer-assisted metabolite analysis. Appl Environ Microbiol 75, 5001-5008.
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Gesell, A., Rolf, M., Ziegler, J., Diaz Chavez, M.L., Huang, F.C., and Kutchan, T.M. (2009). CYP719B1 is salutaridine synthase, the C-C phenol-coupling enzyme of morphine biosynthesis in opium poppy. J Biol Chem 284, 24432-24442.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19567876
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Grobe, N., Zhang, B., Fisinger, U., Kutchan, T.M., Zenk, M.H., and Guengerich, F.P. (2009). Mammalian cytochrome P450 enzymes catalyze the phenol-coupling step in endogenous morphine biosynthesis. J Biol Chem 284, 24425-24431.
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Gutierrez-Gonzalez, J.J., Wu, X., Zhang, J., Lee, J.D., Ellersieck, M., Shannon, J.G., Yu, O., Nguyen, H.T., and Sleper, D.A. (2009). Genetic control of soybean seed isoflavone content: importance of statistical model and epistasis in complex traits. Theor Appl Genet 119, 1069-1083.
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Kavazis, A.N., Alvarez, S., Talbert, E., Lee, Y., and Powers, S.K. (2009). Exercise training induces a cardioprotective phenotype and alterations in cardiac subsarcolemmal and intermyofibrillar mitochondrial proteins. Am J Physiol Heart Circ Physiol 297, H144-152.
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Kempe, K., Higashi, Y., Frick, S., Sabarna, K., and Kutchan, T.M. (2009). RNAi suppression of the morphine biosynthetic gene salAT and evidence of association of pathway enzymes. Phytochemistry 70, 579-589.
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Kumaran, S., Yi, H., Krishnan, H.B., and Jez, J.M. (2009). Assembly of the cysteine synthase complex and the regulatory role of protein-protein interactions. J Biol Chem 284, 10268-10275.
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Martyniuk, C.J., Alvarez, S., McClung, S., Villeneuve, D.L., Ankley, G.T., and Denslow, N.D. (2009). Quantitative proteomic profiles of androgen receptor signaling in the liver of fathead minnows (Pimephales promelas). J Proteome Res 8, 2186-2200.
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Michaelson, L.V., Zauner, S., Markham, J.E., Haslam, R.P., Desikan, R., Mugford, S., Albrecht, S., Warnecke, D., Sperling, P., Heinz, E., and Napier, J.A. (2009). Functional characterization of a higher plant sphingolipid Delta4-desaturase: defining the role of sphingosine and sphingosine-1-phosphate in Arabidopsis. Plant Physiol 149, 487-498.
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Pan, X., and Wang, X. (2009). Profiling of plant hormones by mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 877, 2806-2813.
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Reyes, L., Alvarez, S., Allam, A., Reinhard, M., and Brown, M.B. (2009). Complicated urinary tract infection is associated with uroepithelial expression of proinflammatory protein S100A8. Infect Immun 77, 4265-4274.
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Subramanian, S., Cho, U.H., Keyes, C., and Yu, O. (2009). Distinct changes in soybean xylem sap proteome in response to pathogenic and symbiotic microbe interactions. BMC Plant Biol 9, 119.
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Zhang, J., Subramanian, S., Stacey, G., and Yu, O. (2009). Flavones and flavonols play distinct critical roles during nodulation of Medicago truncatula by Sinorhizobium meliloti. Plant J 57, 171-183.
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Alvarez, S., Marsh, E.L., Schroeder, S.G., and Schachtman, D.P. (2008). Metabolomic and proteomic changes in the xylem sap of maize under drought. Plant Cell Environ 31, 325-340.
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Bach, L., Michaelson, L.V., Haslam, R., Bellec, Y., Gissot, L., Marion, J., Da Costa, M., Boutin, J.P., Miquel, M., Tellier, F., Domergue, F., Markham, J.E., Beaudoin, F., Napier, J.A., and Faure, J.D. (2008). The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO2 is essential and limiting for plant development. Proc Natl Acad Sci U S A 105, 14727-14731.
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Chen, H., Hu, J., Chen, P.R., Lan, L., Li, Z., Hicks, L.M., Dinner, A.R., and He, C. (2008). The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A 105, 13586-13591.
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Chen, M., Markham, J.E., Dietrich, C.R., Jaworski, J.G., and Cahoon, E.B. (2008). Sphingolipid long-chain base hydroxylation is important for growth and regulation of sphingolipid content and composition in Arabidopsis. Plant Cell 20, 1862-1878.
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Hong, Y., Pan, X., Welti, R., and Wang, X. (2008). Phospholipase Da3 is involved in the hyperosmotic response in Arabidopsis. Plant Cell 20, 803-816.
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Jindaprasert, A., Springob, K., Schmidt, J., De-Eknamkul, W., and Kutchan, T.M. (2008). Pyrone polyketides synthesized by a type III polyketide synthase from Drosophyllum lusitanicum. Phytochemistry 69, 3043-3053.
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Kopycki, J.G., Stubbs, M.T., Brandt, W., Hagemann, M., Porzel, A., Schmidt, J., Schliemann, W., Zenk, M.H., and Vogt, T. (2008). Functional and structural characterization of a cation-dependent O-methyltransferase from the cyanobacterium Synechocystis sp. strain PCC 6803. J Biol Chem 283, 20888-20896.
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Nagamune, K., Hicks, L.M., Fux, B., Brossier, F., Chini, E.N., and Sibley, L.D. (2008). Abscisic acid controls calcium-dependent egress and development in Toxoplasma gondii. Nature 451, 207-210.
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Nomura, T., Quesada, A.L., and Kutchan, T.M. (2008). The new beta-D-glucosidase in terpenoid-isoquinoline alkaloid biosynthesis in Psychotria ipecacuanha. J Biol Chem 283, 34650-34659.
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Pan, X., Welti, R., and Wang, X. (2008). Simultaneous quantification of major phytohormones and related compounds in crude plant extracts by liquid chromatography-electrospray tandem mass spectrometry. Phytochemistry 69, 1773-1781.
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Phillips, G., El Yacoubi, B., Lyons, B., Alvarez, S., Iwata-Reuyl, D., and de Crecy-Lagard, V. (2008). Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP cyclohydrolase I. J Bacteriol 190, 7876-7884.
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Sarma, A.D., Oehrle, N.W., and Emerich, D.W. (2008). Plant protein isolation and stabilization for enhanced resolution of two-dimensional polyacrylamide gel electrophoresis. Anal Biochem 379, 192-195.
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Schmidt, M.A., and Herman, E.M. (2008). Proteome rebalancing in soybean seeds can be exploited to enhance foreign protein accumulation. Plant Biotechnol J 6, 832-842.
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Schmidt, M.A., and Herman, E.M. (2008). Suppression of soybean oleosin produces micro-oil bodies that aggregate into oil body/ER complexes. Mol Plant 1, 910-924.
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Schroeder, A.C., Kumaran, S., Hicks, L.M., Cahoon, R.E., Halls, C., Yu, O., and Jez, J.M. (2008). Contributions of conserved serine and tyrosine residues to catalysis, ligand binding, and cofactor processing in the active site of tyrosine ammonia lyase. Phytochemistry 69, 1496-1506.
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Wang, W., Yang, X., Tangchaiburana, S., Ndeh, R., Markham, J.E., Tsegaye, Y., Dunn, T.M., Wang, G.L., Bellizzi, M., Parsons, J.F., Morrissey, D., Bravo, J.E., Lynch, D.V., and Xiao, S. (2008). An inositolphosphorylceramide synthase is involved in regulation of plant programmed cell death associated with defense in Arabidopsis. Plant Cell 20, 3163-3179.
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Brendza, K.M., Haakenson, W., Cahoon, R.E., Hicks, L.M., Palavalli, L.H., Chiapelli, B.J., McLaird, M., McCarter, J.P., Williams, D.J., Hresko, M.C., and Jez, J.M. (2007). Phosphoethanolamine N-methyltransferase (PMT-1) catalyses the first reaction of a new pathway for phosphocholine biosynthesis in Caenorhabditis elegans. Biochem J 404, 439-448.
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Earley, K.W., Shook, M.S., Brower-Toland, B., Hicks, L., and Pikaard, C.S. (2007). In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation. Plant J 52, 615-626.
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Graham, T.L., Graham, M.Y., Subramanian, S., and Yu, O. (2007). RNAi silencing of genes for elicitation or biosynthesis of 5-deoxyisoflavonoids suppresses race-specific resistance and hypersensitive cell death in Phytophthora sojae infected tissues. Plant Physiol 144, 728-740.
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Hicks, L.M., Cahoon, R.E., Bonner, E.R., Rivard, R.S., Sheffield, J., and Jez, J.M. (2007). Thiol-based regulation of redox-active glutamate-cysteine ligase from Arabidopsis thaliana. Plant Cell 19, 2653-2661.
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Jez, J.M., Schachtman, D.P., Berg, R.H., Taylor, C.G., Chen, S., Hicks, L.M., Jaworski, J.G., Smith, T.J., Nielsen, E., and Pikaard, C.S. (2007). Developing a new interdisciplinary lab course for undergraduate and graduate students: plant cells and proteins. Biochem Mol Biol Educ 35, 410-415
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Katpally, U., and Smith, T.J. (2007). Pocket factors are unlikely to play a major role in the life cycle of human rhinovirus. J Virol 81, 6307-6315.
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Livingstone, D., Beilinson, V., Kalyaeva, M., Schmidt, M.A., Herman, E.M., and Nielsen, N.C. (2007). Reduction of protease inhibitor activity by expression of a mutant Bowman-Birk gene in soybean seed. Plant Mol Biol 64, 397-408.
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Markham, J.E., and Jaworski, J.G. (2007). Rapid measurement of sphingolipids from Arabidopsis thaliana by reversed-phase high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom 21, 1304-1314.
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Moravec, T., Schmidt, M.A., Herman, E.M., and Woodford-Thomas, T. (2007). Production of Escherichia coli heat labile toxin (LT) B subunit in soybean seed and analysis of its immunogenicity as an oral vaccine. Vaccine 25, 1647-1657.
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Shin, R., Alvarez, S., Burch, A.Y., Jez, J.M., and Schachtman, D.P. (2007). Phosphoproteomic identification of targets of the Arabidopsis sucrose nonfermenting-like kinase SnRK2.8 reveals a connection to metabolic processes. Proc Natl Acad Sci U S A 104, 6460-6465.
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Tsegaye, Y., Richardson, C.G., Bravo, J.E., Mulcahy, B.J., Lynch, D.V., Markham, J.E., Jaworski, J.G., Chen, M., Cahoon, E.B., and Dunn, T.M. (2007). Arabidopsis mutants lacking long chain base phosphate lyase are fumonisin-sensitive and accumulate trihydroxy-18:1 long chain base phosphate. J Biol Chem 282, 28195-28206.
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Yang, W., Devaiah, S.P., Pan, X., Isaac, G., Welti, R., and Wang, X. (2007). AtPLAI is an acyl hydrolase involved in basal jasmonic acid production and Arabidopsis resistance to Botrytis cinerea. J Biol Chem 282, 18116-18128.
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Zhang, J., Subramanian, S., Zhang, Y., and Yu, O. (2007). Flavone synthases from Medicago truncatula are flavanone-2-hydroxylases and are important for nodulation. Plant Physiol 144, 741-751.
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Zhu, J., Alvarez, S., Marsh, E.L., Lenoble, M.E., Cho, I.J., Sivaguru, M., Chen, S., Nguyen, H.T., Wu, Y., Schachtman, D.P., and Sharp, R.E. (2007). Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically bound proteins under water deficit. Plant Physiol 145, 1533-1548.
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Alvarez, S., Goodger, J.Q., Marsh, E.L., Chen, S., Asirvatham, V.S., and Schachtman, D.P. (2006). Characterization of the maize xylem sap proteome. J Proteome Res 5, 963-972.
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Chen, S. (2006). Rapid protein identification using direct infusion nanoelectrospray ionization mass spectrometry. Proteomics 6, 16-25.
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Herman, E.M., Rotter, K., Premakumar, R., Elwinger, G., Bae, H., Ehler-King, L., Chen, S., and Livingston, D.P., 3rd. (2006). Additional freeze hardiness in wheat acquired by exposure to -3 degreesC is associated with extensive physiological, morphological, and molecular changes. J Exp Bot 57, 3601-3618.
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Joseph, L.M., Hymowitz, T., Schmidt, M.A., and Herman, E.M. (2006). Evaluation of glycine germplasm for nulls of the immunodominant allergen p34/Gly m BD 30k. Crop Sci 46, 1755-1763
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Markham, J.E., Li, J., Cahoon, E.B., and Jaworski, J.G. (2006). Separation and identification of major plant sphingolipid classes from leaves. J Biol Chem 281, 22684-22694.
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Palavalli, L.H., Brendza, K.M., Haakenson, W., Cahoon, R.E., McLaird, M., Hicks, L.M., McCarter, J.P., Williams, D.J., Hresko, M.C., and Jez, J.M. (2006). Defining the role of phosphomethylethanolamine N-methyltransferase from Caenorhabditis elegans in phosphocholine biosynthesis by biochemical and kinetic analysis. Biochemistry 45, 6056-6065.
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Sheffield, J., Taylor, N., Fauquet, C., and Chen, S. (2006). The cassava (Manihot esculenta Crantz) root proteome: protein identification and differential expression. Proteomics 6, 1588-1598.
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Subramanian, S., Stacey, G., and Yu, O. (2006). Endogenous isoflavones are essential for the establishment of symbiosis between soybean and Bradyrhizobium japonicum. Plant J 48, 261-273.
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Zhang, Y., Li, S.Z., Li, J., Pan, X., Cahoon, R.E., Jaworski, J.G., Wang, X., Jez, J.M., Chen, F., and Yu, O. (2006). Using unnatural protein fusions to engineer resveratrol biosynthesis in yeast and Mammalian cells. J Am Chem Soc 128, 13030-13031.
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Zhu, J., Chen, S., Alvarez, S., Asirvatham, V.S., Schachtman, D.P., Wu, Y., and Sharp, R.E. (2006). Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins. Plant Physiol 140, 311-325.
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Bonner, E.R., Cahoon, R.E., Knapke, S.M., and Jez, J.M. (2005). Molecular basis of cysteine biosynthesis in plants: structural and functional analysis of O-acetylserine sulfhydrylase from Arabidopsis thaliana. J Biol Chem 280, 38803-38813.
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