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Biochemistry, Genetics and Genomics of Metal Nutrition and Chloroplast Metabolism |
 The Merchant research program focuses on trace metal metabolism using Chlamydomonas as a reference organism. A large fraction of proteins require metals (e.g. Zn, Cu, Fe, Mn) or metal-cofactors (hemes, FeS centers, chlorophylls, molydopterin, cobalamin) for function. Besides its essential function as a catalyst, the metal is also an important structural constituent of the protein. Metalloproteins are found in every cellular compartment and they function in diverse metabolic pathways. Therefore, elements like Zn, Cu, Fe, Mn are essential nutrients for all organisms. Nevertheless, the chemical reactivity, exploited in biology to make desirable catalysts, can cause intracellular damage if it is not controlled. Therefore, metal and metal-cofactor metabolism is subject to tight homeostatic control, involving regulation of assimilation, distribution and storage with high selectivity and specificity for each metal. The Merchant group uses a combination of classical genetics, genomics and biochemistry to discover mechanisms of trace metal homeostasis in Chlamydomonas. Recently, the group is exploiting next generation sequencing technology (RNA-Seq) to define the transcriptome of wild-type and mutant Chlamydomonas strains under various nutrient, environmental and developmental conditions with the goal of identifying the pattern of expression of every gene in the genome, divining co-expressed genes and cis-regulatory sequences that determine the patterns, and using transcriptome information for genome annotation. While the fundamental methodology is being developed in the context of projects with Chlamydomonas, the group is applying the approaches, in collaboration with the Pellegrini group, to the study of a range of eukaryotic algae that have potential as producers of biodiesel. |
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Positions for Ph.D. students and post-doctoral scholars may be available in mid-2011 for all Merchant laboratory projects. Candidates with demonstrated research productivity (publication record) and expertise in genetics or biochemistry are especially encouraged to apply for post-doctoral positions. Ph.D. candidates should apply to one of the following: |
From my Group 2006-Present
76. Merchant, S. (2006) Trace Metal Utilization in Chloroplasts in The Structure and Function of Plastids (ed. Robert R. Wise and J. Kenneth Hoober), Springer, Netherlands, pp. 199-218.
77. Merchant, S., Allen, M.D., Kropat, J., Moseley, J.L., Long, J.C., Tottey, S., Terauchi, A.M. (2006) Between a rock and a hard place: trace element nutrition in Chlamydomonas. Biochim. Biophys. Acta 1763:578-594.
78. Merchant, S., Sagasti, A. (2006) Precious metal economy. Cell Metabolism. 4:99-101.
79. Grossman, A.R., Croft, M., Gladyshev, V.N., Merchant, S., Posewitz, M.C., Prochnik, S., Spalding, M.H. (2007) Novel metabolism in Chlamydomonas through the lens of genomics. Current Opinion in Plant Biology 10(2):190-198.
80. Allen, M.D., Kropat, J. ,Tottey, S., Del Campo, J.A., Merchant, S. (2007) Manganese Deficiency in Chlamydomonas Results in Loss of Photosystem II and MnSOD Function, Sensitivity to Peroxides, and Secondary Phosphorus and Iron Deficiency. Plant Physiology 143:263-277. Online supporting information.
81. Palenik, B., Grimwood, J., Aerts, A., Rouze, P., Salamov, A., Putnam, N., Dupont C., Jorgensen, R., Derelle, E., Rombauts, S., Zhou, K., Otillar, R., Merchant, S., Podell, S., Gaasterland, T., Napoli, C., Gendler, K., Manuell, A., Tai, V., Vallon, O., Piganeau, G., Jancek, S., Heijde, M., Jabbari, K., Bowler, C., Lohr, M., Robbens, S., Werner, G., Dubchak, I., Pazour, G.J., Ren, Q., Paulsen, I., Delwiche, C., Schmutz, J., Rokhsar, D., van de Peer, Y., Moreau, H., Grigoriev, I. (2007) Tiny eukaryotes provide genomic insights into the paradox of the plankton. Proc. Natl. Acad. Sci. USA 104, 7705-7710. Online supporting information.
82. Merchant, S.S., Prochnik, S.E., Vallon, O., Harris, E.H., Karpowicz, S.J., Witman, G.B., Terry, A., Salamov, A., Fritz-Laylin, L.K., Marechal-Drouard, L., Marshall, W.F., Qu, L.-H., Nelson, D.R., Sanderfoot, A.A., Spalding, M.H., Kapitonov, V.V., Ren, Q., Ferris, P., Lindquist, E., Shapiro, H., Grimwood, J., Schmutz, J., Lucas, S., Chlamydomonas community annotation team, JGI annotation team, Grigoriev, I.V., Rokhsar, D.S., Grossman, A.R. (2007) The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions. Science 318:245 - 250. Online supporting information. Press Releases: JGI, Carnegie, UCLA.
83. Allen, M.D., del Campo, J.A., Kropat, J. Merchant, S.S. (2007) FEA1, FEA2 and FRE1, Encoding Two Homologous Secreted Proteins and a Candidate Ferrireductase, are Expressed Coordinately with FOX1 and FTR1 in Iron-Deficient Chlamydomonas reinhardtii. Eukaryot. Cell 6: 1841-1852.
84. Chen, J.-C., Hsieh, S.I., Kropat, J., Merchant, S. (2008) A Ferroxidase Encoded by FOX1 Contributes to Iron Assimilation under Conditions of Poor Iron Nutrition in Chlamydomonas. Eukaryot. Cell 7: 541-545.
85. Long, J., Sommer, F., Allen, M., Lu, S., Merchant, S.S. (2008) FER1 and FER2 Encoding Two Ferritin Complexes in Chlamydomonas reinhardtii Chloroplasts Are Regulated by Iron. Genetics. 179(1): 137-147.
86. Hanikenne, M., Merchant, S.S., Hamel, P.P. (2008) Transition metal nutrition: a balance between deficiency and toxicity in The Chlamydomonas Sourcebook, ed. 2nd edition, Vol. 2, D. Stern, 333-400. Request a copy.
87. Long, J.C., Merchant, S. (2008) Photo-oxidative stress impacts the expression of genes encoding iron metabolism components in Chlamydomonas. Photochem. Photobiol. 84: 1395-1403.
88. Allen, M.D., Kropat, J., Merchant, S. (2008) Regulation and localization of isoforms of the aerobic oxidative cyclase in Chlamydomonas reinhardtii. Photochem. Photobiol. 84: 1336-1342.
89. Page, D, M., Kropat, J., Hamel, P., Merchant, S. (2009) Two Chlamydomonas CTR Copper Transporters with a Novel Cys-Met Motif Are Localized to the Plasma Membrane and Function in Copper Assimilation. Plant Cell: 21 928-943.
90. Merchant, S.S. (2009) His protects heme as it crosses the membrane. Proc. Natl. Acad. Sci. USA 106: 10069-10070.
91. Terauchi, A.M., Lu, S.F., Zaffagno, M., Tappa, S., Hirasawa, M., Tripathy, J.N., Knaff, D.B., Farmer, P.J., Lemaire, S., Hase, T., Merchant, S.S. (2009) Pattern of Expression and Substrate Specificity of Chlamydomonas Chloroplast Ferredoxins. J. Biol. Chem. 2009; 284: 25867-25878.
49. Koehler, C. M., Merchant, S., Oppliger, W., Schmid, K., Jarosch, E., Dolfini, L., Junne, T., Schatz, G., Tokatlidis, K. (1998) Tim9p, An Essential Partner Subunit of Tim10p for the Import of Mitochondrial Carrier Proteins. EMBO J. 17:6477-6486.
50. Koehler, C.M., Leuenberger, D., Merchant, S., Renold, A., Junne, T., Schatz, G. (1999) Human Deafness Dystonia Syndrome is a Mitochondrial Disease. Proc. Natl. Acad. Sci USA 96:2141-2146. see commentary
56. Springer, S., Chen, E., Duden, R., Marzioch, M., Rowley, A., Hamamoto, S., Merchant, S., Schekman, R. (2000) The p24 proteins are not essential for vesicular transport in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97:4034-4039. see commentary.
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