Dept Home | Biochem Home | Contact Info | Research | Publications  | Group | Collaborators

SABEEHA MERCHANT Professor of Biochemistry and Member, Molecular Biology Institute; BS and PhD, University of Wisconsin-Madison; Post-doctoral Scholar, Harvard University; Searle Scholar; National Institutes of Health Research Career Development Award; UCLA Faculty Career Development Awards;  Guggenheim Foundation Fellow; Charles Albert Shull Award of ASPB; Herbert Newby McCoy Award; AAAS Fellow; ASPB Fellow; NAS Gilbert Morgan Smith Medal; ASPB Charles F. Kettering Award, Humboldt Forschungspreis (Alexander von Humboldt Foundation), Darbaker Prize from the Botanical Society of America, Elected to the U.S. National Academy of Sciences.

RESEARCH DESCRIPTION      

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, especially mechanisms for reducing the quota or for recycling in situations of deficiency. Recently, the group in collaboration with the Pellegrini 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 transcriptome data, 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.

Positions for Ph.D. students and post-doctoral scholars may be available in late 2014 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: Biochemistry Division: Biochemistry and Molecular Biology (BMB) UCLA ACCESS Molecular Toxicology Interdepartmental program

PUBLICATIONS

From my Ph.D. thesis research

From my Post-Doctoral Research

From my Group 1990-1995

From my Group 1996-2000

From my Group 2001-2005

From my Group 2006-2009

From my Group 2010

From my Group 2011-Present

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.

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 N-starvation induced TAG accumulation in a Chlamydomonas starchless mutant. Plant Cell 25: 4305-4323.

133. Blaby-Haas, C.E., Merchant, S.S. (2013) Sparing and salvaging metals in chloroplasts. Encyclopedia of Inorganic and Bioinorganic Chemistry. (V. Culotta and R. Scott, eds.) John Wiley and Sons, in press.

134. 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) Systems analysis of nitrogen sparing mechanisms in Chlamydomonas. The Plant Cell, in press.

135. 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 obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot. Cell, in press.

From my sabbatical in the Schatz group at the Biozentrum in Basel

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.

From my sabbatical in the Schekman group at UC-Berkeley

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.

From my sabbatical in the Bock group at MPIMP-Potsdam

132. Fristedt, R., Scharff, L.B., Clarke, C.A., Wang, Q., Lin, C., Merchant, S.S., Bock, R. (2014) RBF1, a plant homologue of the bacterial ribosome-binding factor RbfA, acts in processing of the chloroplast 16S rRNA. Plant Physiol. 164:201-215.

Books

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.

Video

Sabeeha Merchant and Elaine Tobin interview Winslow Briggs

Online Articles

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.
 

CONTACT ME

 

Department of Chemistry and Biochemistry

UCLA

Box 951569 (post)

607 Charles E. Young Drive East (courier)

Los Angeles, CA  90095-1569

310-206-1035

310-825-8300

GROUP MEMBERS - Merchant Group Resources

• 1991
• 1993
• 1994
• 1998
• 1999
• 2000
• 2001
• 2002
• 2003   Pool Party
• 2004
• 2005
• 2006
• 2007
• 2009   Holiday Party
• 2010
• 2011   Farewell Party  Holiday Party
  
• 2012   NAS Election Party  Holiday Party - Movie (14 MB QuickTime file; may take time to download depending on connection speed)
• 2013   Holiday Party

Former Ph.D. Students
Michael Allen - mallen278@gmail.com - Commencement Ceremony and Party
Kent Hill - Graduation (1994) - Dinner (2003) - Voice of America Interview - Photos

Gregg Howe - Photos
Steven Karpowicz - skarp@chem.ucla.edu - Photos
Scott Hsieh - sihsieh@ucla.edu
Hong Hua Li - honghua_li2003@yahoo.com - Photos

Jeffrey Moseley - jmoseley@sbcglobal.net - Photos
Stacie Nakamoto - nakamoto@chem.ucla.edu - Photos
Aimee Terauchi - aimee.terauchi@gmail.com - Photos
Zhiyi Xie - Zhiyi.Xie@gen-probe.com - Photos

Former Post-Doctoral Scholars
Ute Boronowsky - ute.boronowsky@web.de
Nanette Boyle - nanette.boyle@gmail.com - Photos
Madeli Castruita - madeli@chem.ucla.edu - Photos
Duane Culler
Jose del Campo - joseantonio.delcampo@gmail.com - Photos
Jen-Chih Chen - jchchen@gmail.com - Jen Chih, Shu Fen, Sabeeha Merchant and Others at National Taiwan University
Beth Dreyfuss - beth.dreyfuss@dreyfussconstruction.com - Photos
Mats Eriksson - mats.eriksson@plantphys.umu.se - maer0003@student.umu.se - The Eriksson Family 2007
Maria Felix Vazquez-Bermudez - mvazber@yahoo.es
Patrice Hamel - hamel.16@osu.edu - Boyer Award Recipient - March 2003
Anja Hemschemeier - anja.hemschemeier@ruhr-uni-bochum.de - Algae in Santa Monica
Janette Kropat - kropat@chem.ucla.edu
Sharon La Fontaine - sharonl@deakin.edu.au - Visit with Sharon
Joanne Long - jcl_1111@yahoo.com - Jo is Co-Founder and President of IO Rodeo, Inc., an open source hardware consulting company for science and education.
Davin Malasarn - dmalasarn@gmail.com - Davin's Blog - Davin's First Book - Rey Martin with Sabeeha and Davin - Article on Rey's Research
Jeanette Quinn - jeanette.quinn@agilent.com
Frederik Sommer - derferdi@gmail.com; Sommer@mpimp-golm.mpg.de - Photos
Stephen Tottey - steve.tottey@hotmail.com
Eugen I. Urzica - urzica@chem.ucla.edu
Tomas Westergren - tomwest@chem.ucla.edu - Photos
Hiroaki Yamasaki - hiroaki@chem.ucla.edu - 2008 Visit

Former Visitors
Paola Barraco - Photos
Delphine Bernard - db490@cam.ac.uk
Diana Boy - dianaboy@chem.ucla.edu
Jan Cerveny - Jan.Cerveny@ucla.edu
Esperanza del Rio - esperanza@ibvf.csic.es

Petr Ent - petr.ent@seznam.cz

Mats Hansson - mats@crc.dk - Fulbright Scholar - Photos

Ph.D. Students presently in the group
Anne Glaesener - anneg@chem.ucla.edu

Post-doctoral Scholars presently in the group
Ian Blaby - ikb@chem.ucla.edu
Crysten Blaby-Haas - cblaby@chem.ucla.edu
Rikard Fristedt - rikard.fristedt@gmail.com - Photos
Sean Gallaher - gallaher@sent.com
Anne Hong-Hermesdorf - ahhong@chem.ucla.edu - Photos
Marcus Miethke - miethke@chem.ucla.edu
Stefan Schmollinger - schmolli@chem.ucla.edu
Daniela Strenkert - danielas@chem.ucla.edu
Roland Stube - rstuebe@chem.ucla.edu - Photos

 

Visiting Researchers
Patrice Salome - salome@chem.ucla.edu

Professional Staff
M. Dudley Page - dpage@chem.ucla.edu - Dudley's Trip to the Computer History Museum

Technicians
Maria Gutierrez
Simona Stube - sstuebe@chem.ucla.edu