Sabeeha Merchant

Professor of Plant and Microbial Biology

Sabeeha Merchant

Professor of Plant and Microbial Biology*
*and Professor of Biochemistry, Biophsyics and Structural Biology (Department of Molecular and Cell Biology)

Lab Homepage: https://merchant.berkeley.edu

Full Directory Information

Current Projects

Elemental Economy

More than 80 of the 92 naturally occurring elements are found in living organisms, but 12 of the low mass elements, which are also high abundance elements on Earth, constitute > 99% of the biomass. Yet, the others, despite their occurrence at trace levels, are essential for life because they enable the diverse chemistries of living cells. Organisms use metals like copper, iron, manganese, molybdenum, vanadium, which have multiple stable oxidation states, for reducing nitrogen gas to ammonium, for using light to convert carbon-dioxide and water to carbohydrate, and for extracting energy from inorganic or organic chemicals to sustain life. At the same time, their reactivity can make these very elements harmful in the biological environment, especially in the presence of oxygen. Too little means that enzymes that use the trace metals as catalytic cofactors will not function, and too much means that the metals may react promiscuously. For this reason, there are homeostatic mechanisms to maintain elemental quotas in biology. One evolutionary adaptation to limitation in a particular element is the reduce, reuse, recycle paradigm. For instance, when faced with Fe deficiency, an organism can reduce its inventory of iron-containing proteins by replacing them with iron-independent catalysts. In situations of Fe starvation or sustained deficiency, an organism can remove Fe from one protein and reuse it in a different - more critical for life - protein. These mechanisms have been discovered through classical genetics and biochemistry in multiple microbes, revealing metabolic signatures for elemental economy. Comparative genomics and metagenomics indicate widespread utilization of these economies in nature.
Also see 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. for more information.

Photosynthesis and comparative algal genomics

Algae are distributed throughout the tree of life with polyphyletic origin; their defining characteristic is the presence of a photosynthetic plastid. There is remarkable diversity among the algae. They inhabit temperate and tropical soils and fresh waters, polar permafrost, as well as marine environments. Extremophile algae, like Dunaliella species, may inhabit the oversaturated salt lakes or acid lakes at pH 0! Advances in sequencing technology and computational methods are giving us a breadth of genomic data that can be used to understand the breadth of metabolism in this important group in the microbial world. The proteomes of diverse algae can be used to infer a paleontological record of environments experienced by their ancestors. Algae in Archaeplastida contain primary plastids that originated from an endosymbiotic relationship with a cyanobacterium. These algae share a common ancestor with land plants. Outside this group, there are algae that originated from one or more endosymbiotic relationships with a eukaryotic alga, giving rise to organisms with secondary or tertiary plastids. Among the algae in Archaeplastida are Chlamydomonas, a key reference organism for fundamental discovery in photosynthesis and chloroplast metabolism, halotolerant Dunaliella spp., of commercial interest as a rich natural source of beta-carotene, and Chromochloris zofingiensis, which we are lifting up as a biofuels reference organism for its remarkable capacity for accumulating triacylglycerols (biodiesel precursors). For each organism, we have high quality chromosome-level genome assemblies, and transcript-based structural annotations. For Chlamydomonas, we use highly synchronized cultures in flat panel bioreactors to generate multi-layered genome-wide datasets anchored to physiology to dissect daily metabolic rhythms and patterns. Similar approaches in Chr. zofingiensis will enable the application of synthetic biology in phototrophs for biofuels and high value bioproducts. For Dunaliella, our interest is in using cryo-EM approaches to get a view of the dynamics of the photosynthetic apparatus during acclimation to extreme environments.
Also see Blaby-Haas, C.E., Merchant, S.S. (2019) Comparative and functional algal genomics. Annu. Rev. Plant Biol. 70:605-638. for more information.

Selected Publications

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.

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.

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.

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.

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 USA. 111:E5480-7.

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 USA. 112:2644-51.

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

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.

159. Kumar, D., Blaby-Haas, C.E., Merchant, S.S., Mains, R.E., King, S.M., Eipper, B.A. (2016) Cilia-associated bioactive peptide amidating activity preceded the emergence of multicellularity. J. Cell. Sci. 129:143-156.

162. Kumar, D., Strenkert, D., Patel-King, R.S., Leonard, M.T., Merchant, S.S., Mains, R.E., King, S.M., Eipper, B.A. (2017) A bioactive peptide amidating enzyme is required for ciliogenesis.eLife. 6. pii:e25728

163. Roth, M.S., Cokus, S.J., Gallaher, S.D., Walter, A., Lopez, D., Erickson, E., Endelman, B., Westcott, D., Larabell, C.A., Merchant, S.S., Pellegrini, M., Niyogi, K.K. (2017) Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. Proc Natl Acad Sci USA. 114(21).

164. Wittkopp, T.M., Schmollinger, S., Saroussia, S.I., Hu, W., Fane, Q., Gallaher, S.D., Leonard, M.T., Soubeyrand, E., Basset, G.J., Merchant, S.S., Grossman, A.R., Duanmu, D., Lagarias, J.C. (2017) Bilin-dependent photoacclimation in Chlamydomonas reinhardtii. The Plant Cell, 29:2711-2726.

165. Xue, Y., Schmollinger, S., Attar, N., Campos, O.A., Vogelauer, M., Carey, M.F., Merchant, S.S., Kurdistani, S.K. (2017) Endoplasmic reticulum–mitochondria junction is required for iron homeostasis. J. Biol. Chem., 292:13197-13204.

166. Lojek, L.J., Farrand, A.J., Wisecaver, J.H., Blaby-Haas, C.E., Michel, B.W., Merchant, S.S., Rokas, A., Skaar, E.P. (2017) Chlamydomonas reinhardtii LFO1 is an IsdG family heme oxygenase. mSphere. 2: e00176-17.

167. Blaby-Haas, C.E., Merchant, S.S. (2017) Regulating trace metal economy in algae. Curr. Opin. Plant Biol. 39:88-96.

168. Gallaher, S.D., Fitz-Gibbon, S.T., Strenkert, D., Purvine, S.O., Pellegrini, M., Merchant, S.S. (2018) High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates, The Plant J. 93:545-565.

170. Mosalaganti, S., Kosinski, J., Albert, S., Schaffer, M., Strenkert, D., Salomé, P.A., Merchant, S.S., Plitzko, J.M., Baumeister, W., Engel, B.D., Beck, M. (2018). In situ architecture of the algal nuclear pore complex. Nature Comm. 9:2361.

171. Blaby-Haas, C.E., M.D. Page, Merchant, S.S. (2018) Using YFP as a reporter of gene expression in the green alga Chlamydomonas reinhardtii. Methods Mol. Biol. 1755, 135-148.

173. Blaby-Haas, C.E., Merchant, S.S. (2019) Comparative and functional algal genomics. Annu. Rev. Plant Biol. 70:605-638.

174. Strenkert, D., Schmollinger, S., Gallaher, S.D., Salomé, P., Purvine, S.O., Nicora, C., Mettler-Altmann, T., Soubeyrand, E., Weber, A.P.M., Lipton, M., Basset, G.J., Merchant, S.S. (2019). Multi-omics resolution of molecular events of a day in the life of Chlamydomonas. Proc. Natl. Acad. Sci. USA 116: 2374-2385.

176. Roth, M.S., Gallaher, S.D., Westcott, D.J., Iwai, M., Louie, K.B., Mueller, M., Walter, A., Foflonker, F., Bowen, B.P., Ataii, N.N., Song, J., Chen, J.-H., Blaby-Haas, C., Larabell, C., Auer, M., Northen, T., Merchant, S.S., Niyogi, K.K. (2019) Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis. The Plant Cell, 31:579-601.

A full list of Publications is available at http://merchant.berkeley.edu

Last Updated 2020-03-11