Merchant Group Publications 2010

Merchant Group Publications from 2011-2015

103. 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 187:793-802.

104. 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 23:1273-1292. Supplemental Data. Author Profile. In Brief.

105. 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. J. Biol. Chem. 286:21427-21439. Supplemental Data.

106. 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. 66:770-80.

107. 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.

108. Grossman, A.R., Gonzalez-Ballester, D., Bailey, S., Karpowicz, S.J., Merchant, S.S. (2012) Understanding photosynthetic electron transport using Chlamydomonas: The path from classical genetics to high throughput genomics in Advances in Photosynthesis and Respiration (ed. W. Burnap and W. Vermaas), vol. 33, pp. 139-176. 

109. Lee Y.J., Huang X., Kropat J., Henras A., Merchant S.S., Dickson R.C., Chanfreau G.F. (2012) Sphingolipid signaling mediates iron toxicity. Cell Metabol. 16:90-96.  

110. Bernal, M., Casero, D., Singh, V., Wilson, G.T., Grande, A., Yang, H., Connolly, E.L., Huijser, P., Pellegrini, M., Merchant, S.S., Krämer, U. (2012) Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis. The Plant Cell 24:738-61. Supplemental Data.

111. Page, M.D., Allen, M.D., Kropat, J., Urzica, E., Karpowicz, S., Hsieh, S.I., Loo, J.A., Merchant, S.S. (2012) Fe sparing and Fe recycling contribute to increased superoxide dismutase capacity in iron-starved Chlamydomonas reinhardtii. The Plant Cell 24:2649-2665. Supplemental Data.

112. Merchant, S.S., Kropat, J., Liu, B., Shaw, J., Warakanont, J. (2012) TAG, You're It! Chlamydomonas as a reference organism for understanding algal triacylglycerol  accumulation. Curr. Opin. Biotechnol. 23:352-363.

113. Fang, W., Si, Y., Douglass, S., Casero, D., Merchant, S.S., Pellegrini, M., Liu, P., Spalding, M.H. (2012) Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. The Plant Cell 24:1876-1893.

114. Fischer, B.B., Ledford, H.K., Wakao, S., Huang, S.G., Casero, D., Pellegrini, M., Merchant, S.S., Koller, A., Eggen, R.I.L, Niyogi, K.K. (2012) SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA. 109: E1302-1311.  

115. Boyle, N.R., Page, M.D., Liu, B., Blaby, I.K., Casero, D., Kropat, J., Cokus, S., Hong-Hermesdorf, A., Shaw, J., Karpowicz, S.J., Johnson, S., Benning, C., Pellegrini, M., Grossman, A.R., Merchant, S.S. (2012) Three acyltransferases and a nitrogen responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J. Biol. Chem. 287: 15811-25.

116. Urzica, E.I., Adler, L.N., Page, M.D., Linster. C.L., Arbing, M., Merchant, S.S., Clarke, S.G. (2012) Impact of Oxidative Stress on Ascorbate Biosynthesis in Chlamydomonas via Regulation of the VTC2 Gene Encoding a GDP-L-galactose Phosphorylase. J. Biol. Chem. 287: 14234-14245. Cover Image.

117. Merchant, S.S., Helmann, J.D. (2012) Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation. Adv. Microbiol. Physiol. 60: 91-210.

118. Blaby-Haas, C.E., Merchant, S.S. (2012) The ins and outs of algal metal transport. Biochim. Biophys. Acta, 1823:1531–1552.

119. Urzica E.I., Casero D., Yamasaki H., Hsieh S.I., Adler L.N., Karpowicz S.J., Blaby-Haas C.E., Clarke S.G., Loo J.A., Pellegrini M., Merchant S.S. (2012) Systems and Trans-System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage. The Plant Cell, 24: 3921-3948. Supplemental Data. In Brief. More Resources.

120. Hsieh S.I., Castruita M., Malasarn D., Urzica E., Erde J., Page M.D., Yamasaki H., Casero D., Pellegrini M., Merchant S.S., Loo J.A. (2012) The Proteome of Copper, Iron, Zinc, and Manganese Micronutrient Deficiency in Chlamydomonas reinhardtii. Mol. Cell. Proteomics, 12: 65-86. Supplemental Data.

122. Wang Q., Fristedt R., Yu X., Chen Z., Liu H., Lee Y., Guo H., Merchant S.S., Lin C. (2012) The γ-Carbonic Anhydrase Subcomplex of Mitochondrial Complex I Is Essential for Development and Important for Photomorphogenesis of Arabidopsis. Plant Physiol. 160:1373-1383.

123. Duanmu, D., Casero, D., Dent, R.M., Gallagher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R., Lagarias, J.C. (2013) Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival. Proc Natl Acad Sci U S A. 110:3621-6. Commentary.

124. Hemschemeier, A., Düner, M., Casero, D., Merchant, S.S., Winkler, M., Happe, T. (2013) Hypoxic survival requires a 2-on-2 hemoglobin in a process involving nitric oxide. Proc Natl Acad Sci U S A. 110:10854-9.

125. Hemschemeier, A., Casero, D., Liu, B., Benning, C., Pellegrini, M., Happe, T., Merchant, S.S. (2013) Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia. Plant Cell. 25(9):3186-211. Supplemental Data.

126. Malasarn, D., Kropat, J., Hsieh. S.I., Finazzi, G., Casero, D., Loo, J.A., Pellegrini, M., Wollman, F.A., Merchant, S.S. (2013) Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii. J. Biol. Chem. 288:10672-83. Supplemental Data.

127. Ming, R., Vanburen, R., Liu, Y., Yang, M., Han, Y., Li, L.-T., Zhang, Q., Kim, M.-J., Schatz, M.C., Campbell, M., Li, J., Bowers, J.E., Tang, H., Lyons, E., Ferguson, A.A., Narzisi, G., Nelson, D.R., Blaby-Haas, C.E., Gschwend, A.R., Jiao, Y., Der, J.P., Zeng, F., Han, J., Min, X.J., Hudson, K.A., Singh, R., Grennan, A.K., Karpowicz, S.J., Watling, J.R., Ito, K., Robinson, S.A., Hudson, M.E., Yu, Q., Mockler, T.C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R., Chen, N., Arro, J., Wai, C.M., Wafula, E., Spence, A., Han, Y., Xu, L., Zhang, J., Peery, R., Haus, M.J., Xiong, W., Walsh, J.A., Wu, J., Wang, M.L., Zhu, Y.J., Paull, R.E., Britt, A.B., Du, C., Downie, S.R., Schuler, M.A., Michael, T.P., Long, S.P., Ort, D.R., Somerville, C.R., Schopf, J.W., Gang, D.R., Jiang, N., Yandell, M., Depamphilis, C.W., Merchant, S.S., Paterson, A.H., Buchanan, B.B., Li, S., Shen-Miller, J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 14:R41.

128. Glaesener, A.G., Merchant, S.S., Blaby-Haas, C.E. (2013) Iron economy in Chlamydomonas reinhardtii. Front Plant Sci. 4:337.

129. Urzica, E.I., Vieler, A., Hong-Hermesdorf, A., Page, M.D., Casero, D., Gallaher, S.D., Kropat, J., Pellegrini, M., Benning, C., Merchant, S.S. (2013) Remodeling of membrane lipids in iron-starved Chlamydomonas. J Biol Chem. 288:30246-58.

130. Block, A., Fristedt, R., Rogers, S., Kumar, J., Barnes, B., Barnes, J., Elowsky, C.G., Wamboldt, Y., Mackenzie, S.A., Redding, K., Merchant, S.S., Basset, G. (2013) Functional modeling identifies paralogous solanesyl diphosphate synthases that assemble the side chain of plastoquinone-9 in plastids. J. Biol. Chem. 288:27594-27606.

131. Blaby, I.K, Casero, D., Glaesener, A.G., Fitz-Gibbon, S., Mettler, T., Gallaher, S., Liu, B., Boyle, N.R., Kropat, J., Stitt, M., Johnson, S., Benning, C., Pellegrini, M., Merchant, S.S. (2013) Systems-Level Analysis of Nitrogen Starvation–Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant. Plant Cell 25: 4305-4323.

133. Blaby-Haas, C.E., Merchant, S.S. (2013) Metal Homeostasis: Sparing and salvaging metals in chloroplasts, in Encyclopedia of Inorganic and Bioinorganic Chemistry, edited by R.A. Scott. John Wiley & Sons, Ltd: Chichester, UK. DOI: 10.1002/9781119951438.eibc2113.

134. Blaby-Haas, C.E., Merchant, S.S. (2013) Iron sparing and recycling in a compartmentalized cell. Curr Opin Microbiol. Dec;16(6):677-85.

135. Fristedt, R., Scharff, L.B., Clarke, C.A., Wang, Q., Lin, C., Merchant, S.S., Bock, R. (2014) RBF1, a plant homolog of the bacterial ribosome-binding factor RbfA, acts in processing of the chloroplast 16S ribosomal RNA. Plant Physiol. Jan;164(1):201-15.

136. Schmollinger, S., Mühlhaus, T., Boyle, N.R., Blaby, I.K., Casero, D., Mettler, T., Kropat, J., Sommer, F., Hemme, D., Stitt, M., Pellegrini, M., Schroda, M., Merchant, S.S. (2014) Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism. The Plant Cell, 2014 Apr 18;26(4):1410-1435.

137. Wakao, S., Chin, B.L., Ledford, H.K., Dent, R.M., Casero, D., Pellegrini, M., Merchant, S.S., Niyogi, K.K. (2014) Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii. eLife 3:e02286.

138. Goodenough, U., Blaby, I.K., Casero, D., Gallaher, S., Goodson, C., Johnson, S., Lee, J.-H., Merchant, S.S., Pellegrini, M., Roth, R., Rusch, J., Singh, M., Umen, J.G., Weiss, T.L, Wulan, T. (2014) The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot. Cell, May;13(5):591-613.

139. Blaby, I.K., Blaby-Haas, C.E., Tourasse, N., Hom, E.F., Lopez, D., Aksoy, M., Grossman, A., Umen, J., Dutcher, S., Porter, M., King, S., Witman, G.B., Stanke, M., Harris, E.H., Goodstein, D., Grimwood, J., Schmutz, J., Vallon, O., Merchant, S.S., Prochnik, S. (2014) The Chlamydomonas genome project: a decade on. Trends Plant Sci. 2014 19:672-80.

140. Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, Merchant SS. (2014) Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nat Chem Biol. 10:1034-42. News and Views. And more.

141. Fristedt, R., Williams-Carrier, R., Merchant, S.S., Barkan, A. (2014) A Thylakoid Membrane Protein Harboring a DnaJ-type Zinc Finger Domain is Required for Photosystem I Accumulation in Plants. J Biol Chem. 289:30657-67 [Available on 2015/10/31]

142. Blaby-Haas, C.E., Merchant, S.S. (2014) Lysosome-Related Organelles as Mediators of Metal Homeostasis. J Biol Chem. 289:28129-36.

143. Blaby-Haas CE, Padilla-Benavides T, Stübe R, Argüello JM, Merchant SS. (2014) Evolution of a plant-specific copper chaperone family for chloroplast copper homeostasis. Proc Natl Acad Sci U S A. 111:E5480-7.

144. Fristedt R, Herdean A, Blaby-Haas CE, Mamedov F, Merchant SS, Last RL, Lundin B. (2015) PHOTOSYSTEM II PROTEIN33, a Protein Conserved in the Plastid Lineage, Is Associated with the Chloroplast Thylakoid Membrane and Provides Stability to Photosystem II Supercomplexes in Arabidopsis. Plant Physiol. 167:481-92.

145. Kropat J, Gallaher SD, Urzica EI, Nakamoto SS, Strenkert D, Tottey S, Mason AZ, Merchant SS. (2015) Copper economy in Chlamydomonas: Prioritized allocation and reallocation of copper to respiration vs. photosynthesis. Proc Natl Acad Sci U S A. 112:2644-51 PMC4352834. News. Biography.

146. Allan CM, Awad AM, Johnson JS, Shirasaki DI, Wang C, Blaby-Haas CE, Merchant SS, Loo JA, Clarke CF. (2015) Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae. J Biol Chem. 290: 7517-34.

148. Fatihi, A., Latimer, S., Schmollinger, S., Block, A., Dussault, P., Vermaas, W., Merchant, S.S., Basset, G. (2015) A Dedicated Type II NADPH Dehydrogenase Performs a Hidden Penultimate Step in the Biosynthesis of Vitamin K in Photosynthetic Organisms. The Plant Cell, 27:1730-1741.

149. Ort, D.R., Merchant, S.S., Alric, J., Barkan, A., Blankenship, R.E., Bock, R., Croce, R., Hanson, M.R., Hibberd, J., Lindstrom, D.L., Long, S.P., Moore, T.A., Moroney, J., Niyogi, K.K., Parry, M., Peralta-Yahya, P., Price, R., Redding, K., Spalding, M., van Wijk, K., Vermaas, W.F.J., von Caemmerer, S., Weber, A., Yeates, T., Yuan, J., Zhu, X. (2015) Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc. Nat. Acad. Sci. USA, 112:8529-36. News

150. Pérez-Martín, M. Blaby-Haas, C.E., Pérez-Pérez, M.E., Andrés-Garrido, A., Blaby, I.K., Merchant, S. S., Crespo, J.L. (2015) Activation of autophagy by metals in Chlamydomonas reinhardtii. Eukaryot. Cell, 14(9):964-73.

151. Lopez, D., Hamaji, T., Kropat, J., Morselli, M., Rubbi, L., Fitz-Gibbon, S., Gallaher, S.D., Merchant, S.S., Umen, J., Pellegrini, M. (2015) Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its sexual life cycle, Plant Physiol., 169(4):2730-2743.

152. Gallaher, S.D., Fitz-Gibbon, S., Glaesener, A., Pellegrini, M., Merchant, S.S. (2015) Chlamydomonas laboratory strain genome resource reveals unexpected mosaic of dramatic sequence variation, identifies true strain histories and enables strain-specific studies. The Plant Cell, 27(9).

153. Zones, J.M., Blaby, I.K., Merchant, S.S., Umen, J.G. (2015) High-resolution profiling of a synchronized diurnal transcriptome from Chlamydomonas reinhardtii reveals continuous cell and metabolic differentiation. The Plant Cell, 27(10):2743-2769.

154. Barahimipour, R., Strenkert, D., Neupert, J., Schroda, M., Merchant, S., Bock, R. (2015) Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii. Plant J. 84:704-717. doi: 10.1111/tpj.13033

155. Blaby, I.K., Blaby, C.E., Perez-Perez, M., Schmollinger, S., Fitz-Gibbon, S., Lemaire, S., Merchant, S.S. (2015) Genome-wide analysis on Chlamydomonas reinhardtii reveals impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes. Plant J., 84:974-88. doi: 10.1111/tpj.13053  

156. Yang, W., Wittkopp, T.M., Li, X., Warakanont, J., Dubini, A., Catalanotti, C., Kim, R.G., Nowack, E.C.M., Mackinder, L., Aksoy, M., Page, M.D., D’Adamo, S., Saroussi, S., Heinnickel, M., Johnson, X., Richaud, P., Alric, J., Boehm, M., Jonikas, M.C., Benning, C., Merchant, S.S., Posewitz, M.C., Grossman, A.R. (2015) Critical Role of Chlamydomonas reinhardtii Ferredoxin-5 in Maintaining Membrane Structure and Dark Metabolism. Proc. Natl. Acad. Sci. USA. 112:14978-83