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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 requires 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 in collaboration with the Pelligrini 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. To view alignments of 454 ESTs on the Chlamydomonas genome assemblies and to download sequence files, please click here. To view the S deficiency transcriptome, please click here. To view the copper deficiency transcriptome, please click here. Rising concerns about energy security and the environmental impacts of fossil fuel dependence has created a resurgence in interest in alternative fuel sources. "Biodiesel Fuel" by Prof. Suzanne Paulson of the UCLA Department of Atmospheric & Oceanic Sciences and the Institute of the Environment examines the different types of biodiesel fuel source material, the resources needed to produce this fuel, climate impacts and future applications. The Merchant laboratory has recently initiated a program, in collaboration with the Pellegrini laboratory, to deduce the metabolic pathways and regulatory factors that promote the synthesis of triglycerides in Chlamydomonas, which serves as a reference system for chlorophyte algae. Metabolomics, proteomics and transcriptomics approaches are exploited in particular. |
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Positions for Ph.D. students and post-doctoral scholars may be available in early 2013 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, USDA.
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.
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.
92. Haas, C.E., Rodionov, D., Kropat, J., Malasarn, D., Merchant, S.S., de Crécy-Lagard, V. (2009) A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics. 10:470.
93. Petroutsos, D., Terauchi, A.M., Busch, A., Hirschmann, I., Merchant, S.S., Finazzi, G., Hippler, M. (2009) PGRL1 participates in iron-induced remodeling of the photosynthetic apparatus and in energy metabolism in Chlamydomonas reinhardtii. J. Biol. Chem. 284, 32770-32781.
94. Hirasawa, M., Tripathy, J.N., Sommer, F., Somasundaram, R., Chung, J.-S., Nestander, M., Kruthiventi, M., Zabet-Moghaddam, M., Johnson, M.K., Merchant, S.S., Allen, J.P., Knaff, D.B. (2010) Enzymatic Properties of a Ferredoxin-Dependent Nitrite Reductase from Chlamydomonas reinhardtii. Photosyn. Res. 103:67-77.
95. Terauchi, A., Peers, G., Kobayashi, M., Niyogi, K., Merchant, S.S. (2010) Trophic status of Chlamydomonas reinhardtii influences the impact of iron deficiency on photosynthesis. Photosyn. Res. 105: 39-49.
96. Grossman AR, Karpowicz SJ, Heinnickel M, Dewez D, Hamel B, Dent R, Niyogi KK, Johnson X, Alric J, Wollman FA, Li H, Merchant SS. (2010) Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation. Photosynth Res. 106:3-17.
97. González-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR. (2010) RNA-Seq Analysis of Sulfur-Deprived Chlamydomonas Cells Reveals Aspects of Acclimation Critical for Cell Survival. Plant Cell. 22: 2058-2084. F1000 evaluation.
98. Chodavarapu, R.K., Feng, S., Bernatavichute, Y.V., Chen, P.-Y., Stroud, H., Yu, Y., Hetzel, J.A., Kuo, F., Kim, J., Cokus, S.J., Casero, D., Bernal, M., Huijser, P., Clark, A.T., Krämer, U., Merchant, S.S., Zhang, X., Jacobsen, S.E., Pellegrini, M. (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466:388-392.
99. Gabilly, S., Dreyfuss, B.W., Karamoko, M., Corvest, V., Kropat, J., Page, M.D., Merchant, S.S., Hamel, P. (2010) Ccs5, a thioredoxin-like protein involved in the assembly of plastid c-type cytochromes. J. Biol. Chem. 285:29738-29749.
100. Merchant, S.S. (2010) The elements of plant micronutrients. Plant Physiol. 154:512-515.
101. Merchant, S.S. (2010) Green with envy: on citation of the chlorophyll assay. Commentary on Arnon DI (1949) Copper enzymes in isolated chloroplasts. Plant Physiol. 24:1-15.
102. Knight, M.J., Baron, M.K., Plotkowski, M.L., Kropat, J., Gingery, M., Sakane, F., Merchant, S.S., Bowie, J.U. (2010) Zinc binding drives sheet formation by the SAM domain of diacylglycerol kinase d. Biochemistry. 49:9667-9676.
103. Sommer, F., Kropat, J., Malasarn, D., Grossoehme, N., Chen, X., Giedroc, D., Merchant, S.S. (2010) The CRR1 Nutritional Copper Sensor in Chlamydomonas Contains Two Distinct Metal-Responsive Domains. Plant Cell 22:4098-4113.
104. Kropat J., Hong-Hermesdorf A., Casero D., Ent P., Castruita M., Pellegrini M., Merchant, S.S., Malasarn D. (2011) A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J. Feb 11. doi: 10.1111/j.1365-313X.2011.04537.x. [Epub ahead of print] PMID: 21309872.
105. Gabilly S.T., Kropat J., Karamoko M., Page M.D., Nakamoto S.S., Merchant S.S., Hamel P.P. (2011) A Novel Component of the Disulfide Reducing Pathway Required for Cytochrome c Assembly in Plastids. Genetics 2011 187: 793–802. PMID: 21220358.
106. Castruita, M., Casero, D., Karpowicz,S.J., Kropat, J., Vieler, A., Hsieh, S.I., Yan, W., Cokus, S., Loo, J.A., Benning, C., Pellegrini, M., Merchant, S.S. (2011) Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps. Plant Cell. April 2011, doi: 10.1105/tpc.111.084400 [Epub ahead of print]. Supplemental Data. Author Profile.
107. Karpowicz, S. J., Prochnik, S. E., Grossman, A. R., Merchant, S. S. (2011) The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage. The Journal of Biological Chemistry, 2011, 286 (24), 21427-39.
108. Kropat, J., Hong-Hermesdorf, A., Casero, D., Ent, P., Pellegrini, M., Merchant, S.S., Malasarn, D. (2011) A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J. 66:770-80.
109. Lopez, D., Casero, D., Cokus, S., Merchant, S.S., Pellegrini, M. (2011) Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinformatics 2011, 12:282. Highly Accessed.
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
51. Koehler, C.M., Merchant, S., Schatz, G. (1999) How membrane proteins travel across the mitochondrial intermembrane space. Trends in Biochem. Sci. 24: 428-432.
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.
1. Rochaix, J.-D., Goldschmidt-Clermont, M., Merchant, S., eds. (1998) Molecular Biology of Chlamydomonas: Chloroplasts and Mitochondria. Advances in Photosynthesis (Govindjee, series ed.), Kluwer Academic Publishers.
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Former Ph.D. Students
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