Publications:
A selected list of publications:
Roth Melissa S, Cokus Shawn J, Gallaher Sean D, Walter Andreas, Lopez David, Erickson Erika, Endelman Benjamin, Westcott Daniel, Larabell Carolyn A, Merchant Sabeeha S, Pellegrini Matteo, Niyogi Krishna K
Chromosome-level genome assembly and transcriptome of the green alga
Chromochloris zofingiensis illuminates astaxanthin production
Proceedings of the National Academy of Sciences of the United States of America,
2017; 114(21):
E4296-E4305.
Traller Jesse C, Cokus Shawn J, Lopez David A, Gaidarenko Olga, Smith Sarah R, McCrow John P, Gallaher Sean D, Podell Sheila, Thompson Michael, Cook Orna, Morselli Marco, Jaroszewicz Artur, Allen Eric E, Allen Andrew E, Merchant Sabeeha S, Pellegrini Matteo, Hildebrand Mark
Genome and methylome of the oleaginous diatom Cyclotella cryptica
reveal genetic flexibility toward a high lipid phenotype
Biotechnology for biofuels,
2016; 9(2):
258.
Yang Wenqiang, Wittkopp Tyler M, Li Xiaobo, Warakanont Jaruswan, Dubini Alexandra, Catalanotti Claudia, Kim Rick G, Nowack Eva C M, Mackinder Luke C M, Aksoy Munevver, Page Mark Dudley, D'Adamo Sarah, Saroussi Shai, Heinnickel Mark, Johnson Xenie, Richaud Pierre, Alric Jean, Boehm Marko, Jonikas Martin C, Benning Christoph, Merchant Sabeeha S, Posewitz Matthew C, Grossman Arthur R
Critical role of Chlamydomonas reinhardtii ferredoxin-5 in maintaining
membrane structure and dark metabolism
Proceedings of the National Academy of Sciences of the United States of America,
2015; 112(48):
14978-83.
Lopez David, Hamaji Takashi, Kropat Janette, De Hoff Peter, Morselli Marco, Rubbi Liudmilla, Fitz-Gibbon Sorel, Gallaher Sean D, Merchant Sabeeha S, Umen James, Pellegrini Matteo
Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas
reinhardtii throughout Its Life Cycle
Plant physiology,
2015; 169(4):
2730-43.
Ort Donald R, Merchant Sabeeha S, Alric Jean, Barkan Alice, Blankenship Robert E, Bock Ralph, Croce Roberta, Hanson Maureen R, Hibberd Julian M, Long Stephen P, Moore Thomas A, Moroney James, Niyogi Krishna K, Parry Martin A J, Peralta-Yahya Pamela P, Prince Roger C, Redding Kevin E, Spalding Martin H, van Wijk Klaas J, Vermaas Wim F J, von Caemmerer Susanne, Weber Andreas P M, Yeates Todd O, Yuan Joshua S, Zhu Xin Guang
Redesigning photosynthesis to sustainably meet global food and
bioenergy demand
Proceedings of the National Academy of Sciences of the United States of America,
2015; 112(28):
8529-36.
Allan Christopher M, Awad Agape M, Johnson Jarrett S, Shirasaki Dyna I, Wang Charles, Blaby-Haas Crysten E, Merchant Sabeeha S, Loo Joseph A, Clarke Catherine F
Identification of Coq11, a new coenzyme Q biosynthetic protein in the
CoQ-synthome in Saccharomyces cerevisiae
The Journal of biological chemistry,
2015; 290(12):
7517-34.
Hong-Hermesdorf Anne, Miethke Marcus, Gallaher Sean D, Kropat Janette, Dodani Sheel C, Chan Jefferson, Barupala Dulmini, Domaille Dylan W, Shirasaki Dyna I, Loo Joseph A, Weber Peter K, Pett-Ridge Jennifer, Stemmler Timothy L, Chang Christopher J, Merchant Sabeeha S
Subcellular metal imaging identifies dynamic sites of Cu accumulation
in Chlamydomonas
Nature chemical biology,
2015; 11(3):
235.
Hong-Hermesdorf Anne, Miethke Marcus, Gallaher Sean D, Kropat Janette, Dodani Sheel C, Chan Jefferson, Barupala Dulmini, Domaille Dylan W, Shirasaki Dyna I, Loo Joseph A, Weber Peter K, Pett-Ridge Jennifer, Stemmler Timothy L, Chang Christopher J, Merchant Sabeeha S
Subcellular metal imaging identifies dynamic sites of Cu accumulation
in Chlamydomonas
Nature chemical biology,
2014; 10(12):
1034-42.
Blaby Ian K, Blaby-Haas Crysten E, Tourasse Nicolas, Hom Erik F Y, Lopez David, Aksoy Munevver, Grossman Arthur, Umen James, Dutcher Susan, Porter Mary, King Stephen, Witman George B, Stanke Mario, Harris Elizabeth H, Goodstein David, Grimwood Jane, Schmutz Jeremy, Vallon Olivier, Merchant Sabeeha S, Prochnik Simon
The Chlamydomonas genome project: a decade on
Trends in plant science,
2014; 19(10):
672-80.
Goodenough Ursula, Blaby Ian, Casero David, Gallaher Sean D, Goodson Carrie, Johnson Shannon, Lee Jae-Hyeok, Merchant Sabeeha S, Pellegrini Matteo, Roth Robyn, Rusch Jannette, Singh Manmilan, Umen James G, Weiss Taylor L, Wulan Tuya
The path to triacylglyceride obesity in the sta6 strain of
Chlamydomonas reinhardtii
Eukaryotic cell,
2014; 13(5):
591-613.
Schmollinger Stefan, Mühlhaus Timo, Boyle Nanette R, Blaby Ian K, Casero David, Mettler Tabea, Moseley Jeffrey L, Kropat Janette, Sommer Frederik, Strenkert Daniela, Hemme Dorothea, Pellegrini Matteo, Grossman Arthur R, Stitt Mark, Schroda Michael, Merchant Sabeeha S
Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome,
the Proteome, and Photosynthetic Metabolism
The Plant cell,
2014; 26(4):
1410-1435.
Blaby Ian K, Glaesener Anne G, Mettler Tabea, Fitz-Gibbon Sorel T, Gallaher Sean D, Liu Bensheng, Boyle Nanette R, Kropat Janette, Stitt Mark, Johnson Shannon, Benning Christoph, Pellegrini Matteo, Casero David, Merchant Sabeeha S
Systems-level analysis of nitrogen starvation-induced modifications of
carbon metabolism in a Chlamydomonas reinhardtii starchless mutant
The Plant cell,
2013; 25(11):
4305-23.
Urzica Eugen I, Vieler Astrid, Hong-Hermesdorf Anne, Page M Dudley, Casero David, Gallaher Sean D, Kropat Janette, Pellegrini Matteo, Benning Christoph, Merchant Sabeeha S
Remodeling of membrane lipids in iron-starved Chlamydomonas
The Journal of biological chemistry,
2013; 288(42):
30246-58.
Block Anna, Fristedt Rikard, Rogers Sara, Kumar Jyothi, Barnes Brian, Barnes Joshua, Elowsky Christian G, Wamboldt Yashitola, Mackenzie Sally A, Redding Kevin, Merchant Sabeeha S, Basset Gilles J
Functional modeling identifies paralogous solanesyl-diphosphate
synthases that assemble the side chain of plastoquinone-9 in plastids
The Journal of biological chemistry,
2013; 288(38):
27594-606.
Ming Ray, VanBuren Robert, Liu Yanling, Yang Mei, Han Yuepeng, Li Lei-Ting, Zhang Qiong, Kim Min-Jeong, Schatz Michael C, Campbell Michael, Li Jingping, Bowers John E, Tang Haibao, Lyons Eric, Ferguson Ann A, Narzisi Giuseppe, Nelson David R, Blaby-Haas Crysten E, Gschwend Andrea R, Jiao Yuannian, Der Joshua P, Zeng Fanchang, Han Jennifer, Min Xiang Jia, Hudson Karen A, Singh Ratnesh, Grennan Aleel K, Karpowicz Steven J, Watling Jennifer R, Ito Kikukatsu, Robinson Sharon A, Hudson Matthew E, Yu Qingyi, Mockler Todd C, Carroll Andrew, Zheng Yun, Sunkar Ramanjulu, Jia Ruizong, Chen Nancy, Arro Jie, Wai Ching Man, Wafula Eric, Spence Ashley, Han Yanni, Xu Liming, Zhang Jisen, Peery Rhiannon, Haus Miranda J, Xiong Wenwei, Walsh James A, Wu Jun, Wang Ming-Li, Zhu Yun J, Paull Robert E, Britt Anne B, Du Chunguang, Downie Stephen R, Schuler Mary A, Michael Todd P, Long Steve P, Ort Donald R, Schopf J William, Gang David R, Jiang Ning, Yandell Mark, dePamphilis Claude W, Merchant Sabeeha S, Paterson Andrew H, Buchanan Bob B, Li Shaohua, Shen-Miller Jane
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
Genome biology,
2013; 14(5):
R41.
Duanmu Deqiang, Casero David, Dent Rachel M, Gallaher Sean, Yang Wenqiang, Rockwell Nathan C, Martin Shelley S, Pellegrini Matteo, Niyogi Krishna K, Merchant Sabeeha S, Grossman Arthur R, Lagarias J Clark
Retrograde bilin signaling enables Chlamydomonas greening and
phototrophic survival
Proceedings of the National Academy of Sciences of the United States of America,
2013; 110(9):
3621-6.
Hsieh Scott I, Castruita Madeli, Malasarn Davin, Urzica Eugen, Erde Jonathan, Page M Dudley, Yamasaki Hiroaki, Casero David, Pellegrini Matteo, Merchant Sabeeha S, Loo Joseph A
The proteome of copper, iron, zinc, and manganese micronutrient
deficiency in Chlamydomonas reinhardtii
Molecular & cellular proteomics : MCP,
2013; 12(1):
65-86.
Urzica Eugen I, Casero David, Yamasaki Hiroaki, Hsieh Scott I, Adler Lital N, Karpowicz Steven J, Blaby-Haas Crysten E, Clarke Steven G, Loo Joseph A, Pellegrini Matteo, Merchant Sabeeha S
Systems and trans-system level analysis identifies conserved iron
deficiency responses in the plant lineage
The Plant cell,
2012; 24(10):
3921-48.
Fischer Beat B, Ledford Heidi K, Wakao Setsuko, Huang ShihYau Grace, Casero David, Pellegrini Matteo, Merchant Sabeeha S, Koller Andreas, Eggen Rik I L, Niyogi Krishna K
SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to
singlet oxygen acclimation in Chlamydomonas reinhardtii
Proceedings of the National Academy of Sciences of the United States of America,
2012; 109(20):
E1302-11.
Boyle Nanette R, Page Mark Dudley, Liu Bensheng, Blaby Ian K, Casero David, Kropat Janette, Cokus Shawn J, Hong-Hermesdorf Anne, Shaw Johnathan, Karpowicz Steven J, Gallaher Sean D, Johnson Shannon, Benning Christoph, Pellegrini Matteo, Grossman Arthur, Merchant Sabeeha S
Three acyltransferases and nitrogen-responsive regulator are
implicated in nitrogen starvation-induced triacylglycerol accumulation
in Chlamydomonas
The Journal of biological chemistry,
2012; 287(19):
15811-25.
Bernal MarÃa, Casero David, Singh Vasantika, Wilson Grandon T, Grande Arne, Yang Huijun, Dodani Sheel C, Pellegrini Matteo, Huijser Peter, Connolly Erin L, Merchant Sabeeha S, Krämer Ute
Transcriptome sequencing identifies SPL7-regulated copper acquisition
genes FRO4/FRO5 and the copper dependence of iron homeostasis in
Arabidopsis
The Plant cell,
2012; 24(2):
738-61.
Castruita Madeli, Casero David, Karpowicz Steven J, Kropat Janette, Vieler Astrid, Hsieh Scott I, Yan Weihong, Cokus Shawn, Loo Joseph A, Benning Christoph, Pellegrini Matteo, Merchant Sabeeha S
Systems Biology Approach in Chlamydomonas Reveals Connections between
Copper Nutrition and Multiple Metabolic Steps
The Plant cell,
2011; 23(4):
1273-92.
Grossman Arthur R, Karpowicz Steven J, Heinnickel Mark, Dewez David, Hamel Blaise, Dent Rachel, Niyogi Krishna K, Johnson Xenie, Alric Jean, Wollman Francis-André, Li Huiying, Merchant Sabeeha S
Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation
Photosynthesis research,
2010; 106(1-2):
3-17.
Chodavarapu Ramakrishna K, Feng Suhua, Bernatavichute Yana V, Chen Pao-Yang, Stroud Hume, Yu Yanchun, Hetzel Jonathan A, Kuo Frank, Kim Jin, Cokus Shawn J, Casero David, Bernal Maria, Huijser Peter, Clark Amander T, Krämer Ute, Merchant Sabeeha S, Zhang Xiaoyu, Jacobsen Steven E, Pellegrini Matteo
Relationship between nucleosome positioning and DNA methylation
Nature,
2010; 466(7304):
388-92.
Hirasawa Masakazu, Tripathy Jatindra N, Sommer Frederik, Somasundaram Ramasamy, Chung Jung-Sung, Nestander Matthew, Kruthiventi Mahima, Zabet-Moghaddam Masoud, Johnson Michael K, Merchant Sabeeha S, Allen James P, Knaff David B
Enzymatic properties of the ferredoxin-dependent nitrite reductase
from Chlamydomonas reinhardtii. Evidence for hydroxylamine as a late
intermediate in ammonia production
Photosynthesis research,
2010; 103(2):
67-77.
Terauchi Aimee M, Lu Shu-Fen, Zaffagnini Mirko, Tappa Shane, Hirasawa Masakazu, Tripathy Jatindra N, Knaff David B, Farmer Patrick J, Lemaire Stéphane D, Hase Toshiharu, Merchant Sabeeha S
Pattern of expression and substrate specificity of chloroplast
ferredoxins from Chlamydomonas reinhardtii
The Journal of biological chemistry,
2009; 284(38):
25867-78.
Hanikenne, M., Merchant, S.S., Hamel, P.P.
Transition metal nutrition: a balance between deficiency and toxicity ,
The Chlamydomonas Sourcebook (2nd Edition),
2008; 2:
333-400.
Merchant Sabeeha S, Prochnik Simon E, Vallon Olivier, Harris Elizabeth H, Karpowicz Steven J, Witman George B, Terry Astrid, Salamov Asaf, Fritz-Laylin Lillian K, Maréchal-Drouard Laurence, Marshall Wallace F, Qu Liang-Hu, Nelson David R, Sanderfoot Anton A, Spalding Martin H, Kapitonov Vladimir V, Ren Qinghu, Ferris Patrick, Lindquist Erika, Shapiro Harris, Lucas Susan M, Grimwood Jane, Schmutz Jeremy, Cardol Pierre, Cerutti Heriberto, Chanfreau Guillaume, Chen Chun-Long, Cognat Valérie, Croft Martin T, Dent Rachel, Dutcher Susan, Fernández Emilio, Fukuzawa Hideya, González-Ballester David, González-Halphen Diego, Hallmann Armin, Hanikenne Marc, Hippler Michael, Inwood William, Jabbari Kamel, Kalanon Ming, Kuras Richard, Lefebvre Paul A, Lemaire Stéphane D, Lobanov Alexey V, Lohr Martin, Manuell Andrea, Meier Iris, Mets Laurens, Mittag Maria, Mittelmeier Telsa, Moroney James V, Moseley Jeffrey, Napoli Carolyn, Nedelcu Aurora M, Niyogi Krishna, Novoselov Sergey V, Paulsen Ian T, Pazour Greg, Purton Saul, Ral Jean-Philippe, Riaño-Pachón Diego Mauricio, Riekhof Wayne, Rymarquis Linda, Schroda Michael, Stern David, Umen James, Willows Robert, Wilson Nedra, Zimmer Sara Lana, Allmer Jens, Balk Janneke, Bisova Katerina, Chen Chong-Jian, Elias Marek, Gendler Karla, Hauser Charles, Lamb Mary Rose, Ledford Heidi, Long Joanne C, Minagawa Jun, Page M Dudley, Pan Junmin, Pootakham Wirulda, Roje Sanja, Rose Annkatrin, Stahlberg Eric, Terauchi Aimee M, Yang Pinfen, Ball Steven, Bowler Chris, Dieckmann Carol L, Gladyshev Vadim N, Green Pamela, Jorgensen Richard, Mayfield Stephen, Mueller-Roeber Bernd, Rajamani Sathish, Sayre Richard T, Brokstein Peter, Dubchak Inna, Goodstein David, Hornick Leila, Huang Y Wayne, Jhaveri Jinal, Luo Yigong, MartÃnez Diego, Ngau Wing Chi Abby, Otillar Bobby, Poliakov Alexander, Porter Aaron, Szajkowski Lukasz, Werner Gregory, Zhou Kemin, Grigoriev Igor V, Rokhsar Daniel S, Grossman Arthur R
The Chlamydomonas genome reveals the evolution of key animal and plant
functions
Science (New York, N.Y.),
2007; 318(5848):
245-50.
Allen, M.D., del Campo, J.A., Kropat, J. Merchant, S.S.
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,
2007; 6:
1841-1852.
Allen, M.D., Kropat, J. ,Tottey, S., Del Campo, J.A., Merchant, S.
Manganese Deficiency in Chlamydomonas Results in Loss of Photosystem II and MnSOD Function, Sensitivity to Peroxides, and Secondary Phosphorus and Iron Deficiency
Plant Physiology,
2007; 143:
263-277.
Grossman, A.R., Croft, M., Gladyshev, V.N., Merchant, S., Posewitz, M.C., Prochnik, S., Spalding, M.H.
Novel metabolism in Chlamydomonas through the lens of genomics
Current Opinion in Plant Biology,
2007; 10(2):
190-198.
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.
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
Science,
2007; 318:
245-250.
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.
Tiny eukaryotes provide genomic insights into the paradox of the plankton
Proc. Natl. Acad. Sci. USA,
2007; 104:
7705-7710.
Palenik Brian, Grimwood Jane, Aerts Andrea, Rouzé Pierre, Salamov Asaf, Putnam Nicholas, Dupont Chris, Jorgensen Richard, Derelle Evelyne, Rombauts Stephane, Zhou Kemin, Otillar Robert, Merchant Sabeeha S, Podell Sheila, Gaasterland Terry, Napoli Carolyn, Gendler Karla, Manuell Andrea, Tai Vera, Vallon Olivier, Piganeau Gwenael, Jancek Séverine, Heijde Marc, Jabbari Kamel, Bowler Chris, Lohr Martin, Robbens Steven, Werner Gregory, Dubchak Inna, Pazour Gregory J, Ren Qinghu, Paulsen Ian, Delwiche Chuck, Schmutz Jeremy, Rokhsar Daniel, Van de Peer Yves, Moreau Hervé, Grigoriev Igor V
The tiny eukaryote Ostreococcus provides genomic insights into the
paradox of plankton speciation
Proceedings of the National Academy of Sciences of the United States of America,
2007; 104(18):
7705-10.
Merchant, S., Allen, M.D., Kropat, J., Moseley, J.L., Long, J.C., Tottey, S., Terauchi, A.M.
Between a rock and a hard place: trace element nutrition in Chlamydomonas
Biochim. Biophys. Acta,
2006; 1763:
578-594.
Page M L Dudley, Hamel Patrice P, Gabilly Stéphane T, Zegzouti Hicham, Perea John V, Alonso José M, Ecker Joseph R, Theg Steven M, Christensen Sioux K, Merchant Sabeeha
A homolog of prokaryotic thiol disulfide transporter CcdA is required
for the assembly of the cytochrome b6f complex in Arabidopsis
chloroplasts
The Journal of biological chemistry,
2004; 279(31):
32474-82.
Page MD, Hamel PO, Gabilly ST, Zegzouti H, Perea JV, Alonso JM, Ecker JR, Theg S, Christiansen S, Merchant S
A homolog of prokaryotic thio-disulfide transporter CcdA is required for the assembly of the cytochrome c6f complex in Arabidopsis chloroplasts,
Journal of Biological Chemistry,
2004; 279:
32474-82.
Eriksson M, Mosely JL, Tottey S, del Campo JA, Quinn J, Kim Y, Merchant S
Molecular genetic dissection of nutritional copper signalling in Chlamydomonas distinguishes regulatory and target genes,
Genetics,
2004; 168:
795-807.
Tottey S, Block MA, Allen M, Westergren T, Albrieux C, Scheller HV, Merchant S, Jensen PE
Arabidopsis CHL27, located in both envelope and thylakoid membranes, is required for the synthesis of protochlorophyllide
Proceedings of the National Academy of Sciences of the United States of America,
2003; 100(26):
16119-24.
Tottey Stephen, Block Maryse A, Allen Michael, Westergren Tomas, Albrieux Catherine, Scheller Henrik V, Merchant Sabeeha, Jensen Poul Erik
Arabidopsis CHL27, located in both envelope and thylakoid membranes,
is required for the synthesis of protochlorophyllide
Proceedings of the National Academy of Sciences of the United States of America,
2003; 100(26):
16119-24.
Moseley JL, Page MD, Alder NP, Eriksson M, Quinn J, Soto F, Theg M, Hippler M, Merchant S
Reciprocal expression of two candidate di-iron enymes affecting photosystem I and light-harvesting complex accumulation,
Plant Cell,
2002; 14:
673-688.
Springer S, Chen E, Duden R, Marzioch M, Rowley A, Hamamoto S, Merchant S, Schekman R
The p24 proteins are not essential for vesicular transport in Saccharomyces cerevisiae,
Proc. Natl. Acad. Sci,
2000; 97:
4034-4039.
Koehler CM, Merchant S, Oppliger W, Schmid K, Jarosch E, Dolfini L, Junne T, Schatz G, Tokatlidis K
Tim9p, an essential partner subunit of Tim10p for the import of mitochondrial carrier proteins
The EMBO J,
1998; 17(22):
6477-86.