Full Publication List
1980-2000
1. Selman-Reimer, S., Merchant, S., Selman, B.R. (1981)
Isolation, Purification and Characterization of Coupling Factor 1 from Chlamydomonas reinhardi.
Biochemistry 20:5476-5482.
2. Kneusel, R.E., Merchant, S., Selman, B.R. (1982)
Properties of the Solvent-Stimulated ATPase Activity of Chloroplast Coupling Factor 1 from Chlamydomonas reinhardii.
Biochim. Biophys. Acta 681:337-344.
3. Merchant, S., Shaner, S.L., Selman, B.R. (1983)
Molecular Weight and Subunit Stoichiometry of the Chloroplast Coupling Factor 1 in Chlamydomonas reinhardi.
J. Biol. Chem. 258:1026-1031.
4. Merchant, S., Selman, B.R. (1983)
Identification of the a and β Subunits of the Chloroplast Coupling Factor One in Chlamydomonas reinhardi.
Eur. J. Biochem. 137:373-376.
5. Merchant, S., Selman, B.R. (1984)
Synthesis and Turnover of the Chloroplast Coupling Factor 1 in Chlamydomonas reinhardi.
Plant Physiol. 75:781-787.
6. Merchant, S., Selman, B.R. (1985)
Photosynthetic ATPases: Purification, Properties, Subunit Isolation and Function.
Photosyn. Res. 6:3-31.
7. Merchant, S., Bogorad, L. (1986)
Regulation by Copper of the Expression of Plastocyanin and Cytochrome c552 in Chlamydomonas reinhardi.
Mol. Cell. Biol. 6:462-469.
8. Merchant, S., Bogorad, L. (1986)
Rapid Degradation of Apoplastocyanin in Cu(II)-deficient Cells of Chlamydomonas reinhardtii.
J. Biol. Chem. 261:15850-15853.
9. Merchant, S., Bogorad, L. (1987)
The Cu(II)-repressible Plastidic Cytochrome c: Cloning and Sequence of a Complementary DNA for the Pre-apoprotein.
J. Biol. Chem. 262:9062-9067.
10. Merchant, S., Bogorad, L. (1987)
Metal Ion Regulated Gene Expression: Use of a Plastocyanin-less Mutant of Chlamydomonas reinhardtii to Study the Cu(II)-dependent Expression of Cytochrome c-552.
The EMBO J. 6:2531-2535.
11. Yu, L., Merchant, S., Theg, S.M., Selman, B.R. (1988)
Isolation of a cDNA Clone for the γ-Subunit of the Chloroplast ATP Synthase of Chlamydomonas reinhardtii: Import and Cleavage of the Precursor Protein.
Proc. Natl. Acad. Sci. USA 85:1369-1373.
12. Merchant, S., Hill, K., Kim, J.-H., Thompson, J. Zaitlin, D., Bogorad, L. (1990)
Isolation and Characterization of a Complementary DNA Clone for an Algal Pre-apoplastocyanin.
J. Biol. Chem. 265:12372-12379.
13. Merchant, S., Hill, K., Howe, G. (1991)
Dynamic Interplay between Two Copper-titrating Components in the Transcriptional Regulation of Cyt c6.
The EMBO J. 10:1383-1389.
14. Hill, K., Li, H.H., Singer, J., Merchant, S. (1991)
Isolation and Structural Characterization of the Chlamydomonas reinhardtii Gene for Cytochrome c6: Analysis of the Kinetics and Metal Specificity of its Copper-responsive Expression.
J. Biol. Chem. 266:15060-15067.
15. Howe, G., Merchant, S. (1992)
Heavy Metal-activated Synthesis of Peptides in Chlamydomonas reinhardtii.
Plant Physiol. 98:127-136.
16. Howe, G., Quinn, J., Hill, K., Merchant, S. (1992)
Control of the Biosynthesis of Cytochrome c6 in Chlamydomonas reinhardtii.
Plant Physiol. Biochem. 30:299-307.
17. Li, H.H., Merchant, S. (1992)
Two Metal-dependent Steps in the Biosynthesis of Scenedesmus obliquus Plastocyanin: Differential mRNA Accumulation and Holoprotein Formation.
J. Biol. Chem. 267:9368-9375.
18. Howe, G., Merchant, S. (1992)
The Biosynthesis of Soluble and Membrane-associated Plastidic c-type Cytochromes of Chlamydomonas reinhardtii is Dependent on Multiple Common Gene Products.
The EMBO J. 11:2789-2801.
19. Hill, K., Merchant, S. (1992)
In vivo Competition between Plastocyanin and a Copper-dependent Regulator of the Cytochrome c6 Gene.
Plant Physiol. 100:319-326.
20. Quinn, J., Li, H.H., Singer, J., Morimoto, B., Mets, L.J., Kindle, K., Merchant, S. (1993)
The Plastocyanin-Deficient Phenotype of Chlamydomonas reinhardtii Ac-208 Results from a Frame-shift Mutation in the Nuclear Gene Encoding Preapoplastocyanin.
J. Biol. Chem. 268:7832-7841.
21. Howe, G., Merchant, S. (1993)
The Maturation of Thylakoid Lumenal Proteins in Chlamydomonas reinhardtii Proceeds Post-Translationally Through an Intermediate In Vivo.
Proc. Natl. Acad. Sci. USA 90:1862-1866.
22. Redinbo, M., Cascio, D., Choukair, M., Rice, D., Merchant, S., Yeates, T.O. (1993)
The 1.5Å Crystal Structure of Plastocyanin from the Green Alga Chlamydomonas reinhardtii.
Biochemistry 32:10560-10567.
23. Howe, G., Merchant, S. (1994)
Role of Heme in the Biosynthesis of Cytochrome c6.
J. Biol. Chem. 269:5824-5832.
24. Redinbo, M., Yeates, T.O., Merchant, S. (1994)
Plastocyanin: Structural and Functional Analysis.
J. Bioenerg. Biomembr. 26: 49-66.
25. Howe, G., Merchant, S. (1994)
The Biosynthesis of Bacterial and Plastidic c-type Cytochromes.
Photosyn. Res. 40: 147-165.
26. Howe, G., Mets, L., Merchant, S. (1995)
Biosynthesis of Cytochrome f in Chlamydomonas reinhardtii: Analysis of the Pathway in Gabaculine-Treated Cells and in the Heme Attachment Mutant B6.
Mol. Gen. Genet. 246:156-165.
27. Kerfeld, C., Anwar, H., Interrante, R., Merchant, S., Yeates, T.O. (1995)
The Structure of Chloroplast Cytochrome c6 at 1.9 A resolution.
J. Mol. Biol. 250:627-647.
28. Hill, K.L., Merchant, S. (1995)
Coordinate Expression of Coproporphyrinogen Oxidase and Cytochrome c6 in the Green Alga Chlamydomonas reinhardtii in Response to Changes in Copper Availability.
The EMBO J. 14:857-865.
29. Quinn, J., Merchant, S. (1995)
Two Copper-Responsive Elements Associated with the Chlamydomonas Cyc6 Gene Function as Targets for Transcriptional Activators.
Plant Cell 7:623-638.
30. Li, H.H., Merchant, S. (1995)
Degradation of Plastocyanin in Copper-Deficient Chlamydomonas reinhardtii: Evidence for a Protease-Susceptible Conformation of the Apoprotein and Regulated Proteolysis.
J. Biol. Chem. 270:23504-23510.
33. Li, H.H., Quinn, J.M., Culler, D., Girard-Bascou, J., Merchant, S. (1996)
Molecular Genetic Analysis of Plastocyanin Biosynthesis in Chlamydomonas reinhardtii.
J. Biol. Chem. 271:31283-31289.
34. Kuras, R., de Vitry, C., Choquet, Y., Girard-Bascou, J., Culler, D., Buschlen, S., Merchant, S., Wollman, F.-A. (1997)
Molecular Genetic Identification of a Pathway for Heme Binding to Cytochrome b6.
J. Biol. Chem. 272:32427-32435.
35. Inoue, K., Dreyfuss, B.W., Kindle, K.L., Stern, D.B., Merchant, S., Sodeinde, O.A. (1997)
Ccs1, a Nuclear Gene Required for the Maturation of Chloroplast c-type Cytochromes.
J. Biol. Chem. 272:31747-31754
36. Xie, Z.Y., Culler, D., Dreyfuss, B.W., Girard-Bascou, J., Kuras, R., Wollman, F.A., Merchant, S. (1998)
Genetic analysis of Chloroplast c-type Cytochrome Assembly: One Chloroplast Locus and At Least Four Nuclear Loci Are Required for Heme Attachment.
Genetics 148: 681-692.
37. Merchant, S., Dreyfuss, B.W. (1998)
Posttranslational assembly of photosynthetic metalloproteins.
Annu. Rev. Plant Physiol. Plant Mol. Biol. 49: 25-51.
38. Xie, Z., Merchant, S. (1998)
A novel pathway for cytochromes c biogenesis in chloroplasts.
Biochim. Biophys. Acta 1365: 309-318.
39. Kranz, R., Lill, R., Goldman, B., Bonnard, G., Merchant, S. (1998)
Molecular mechanisms of cytochromes c biogenesis: three distinct systems.
Molecular Microbiol. 29:383-396
40. Quinn, J.M., Merchant, S. (1998)
Copper-Responsive Gene Expression in Photosynthetic Microorganisms.
Methods in Enzymology 297:263-279.
41. 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.
42. 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.
43. Quinn, J.M., Merchant, S. (1999)
Adaptation of Scenedesmus obliquus (Chlorophyceae) to Copper-Deficiency: Transcriptional Regulation of Pcy1 but not Cpx1.
J. Phycol. 35:1253-1263.
44. Quinn, J.M., Nakamoto, S.S., Merchant, S. (1999)
Induction of Coproporphyrinogen Oxidase in Chlamydomonas Chloroplasts Occurs via Transcriptional Regulation of Cpx1 Mediated by Copper Response Elements and Increased Translation from a Copper-Deficiency-specific Form of the Transcript.
J. Biol. Chem. 274:14444-14454.
45. Koehler, C.M., Merchant, S., Schatz, G. (1999)
How membrane proteins travel across the mitochondrial intermembrane space.
Trends in Biochem. Sci. 24: 428-432.
46. Quinn, J.M., Barraco, P., Eriksson, M., Merchant, S. (2000)
Coordinate Copper- and Oxygen-responsive Cyc6 and Cpx1 Expression in Chlamydomonas is Mediated by the Same Element.
J. Biol. Chem. 275:6080-6089.
47. Moseley, J.L., Quinn, J.M., Eriksson, M., Merchant, S. (2000)
The Crd1 Gene Encodes a Putative Di-iron Enzyme Required for Photosystem I Accumulation in Copper Deficiency and Hypoxia in Chlamydomonas reinhardtii.
The EMBO J. 19:2139-2151.
48. 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. 96: 2141-2146.
49. Nakamoto, S., Hamel, P., Merchant, S. (2000)
Assembly of Chloroplast Cytochromes b and c.
Biochimie 82: 603-614.
2001-2010
50. Quinn, J.M., Eriksson, M., Moseley, J.L., Merchant, S. (2002)
Oxygen-deficiency gene expression in Chlamydomonas through a copper signal transduction pathway.
Plant Physiol. 128:463-471.
51. Moseley, J.L., Page, M.D., Alder, N.P., Eriksson, M., Quinn, J., Soto, F., Theg, M., Hippler, M., Merchant, S. (2002)
Reciprocal expression of two candidate di-iron enzymes affecting photosystem I and light-harvesting complex accumulation.
Plant Cell 14:673-688.
52. LaFontaine, S., Quinn, J.M. Nakamoto, S.S., Page, M.D., Göhre, V., Moseley, J.L., Kropat, J., Merchant, S. (2002)
Copper-dependent iron assimilation pathway in the model photosynthetic eukaryote Chlamydomonas reinhardtii.
Eukaryot. Cell. 1:736-757.
53. Moseley, J., Allinger, T., Herzog, S., Hoerth, P., Wehinger, E., Merchant, S., Hippler, M. (2002)
Adaptation to Fe-deficiency requires remodeling of the photosynthetic apparatus.
EMBO J. 21:6709-6720.
54. Dreyfuss, B.W., Hamel, P., Nakamoto, S.S., Merchant, S. (2003)
Functional analysis of a divergent system II protein, Ccs1, involved in c-type cytochrome biogenesis.
J. Biol. Chem. 278: 2604-2613.
55. Hamel, P., Dreyfuss, B.W., Xie, Z., Gabilly, S., Merchant, S. (2003)
Essential histidine and tryptophan residues in CcsA, a system II polytopic cytochrome c biogenesis protein.
J. Biol. Chem. 278: 2593-2603.
56. Quinn, J.M., Kropat, J., Merchant, S. (2003)
A Copper Response Element and Crr1-dependent Ni2+-responsive promoter for induced, reversible gene expression in Chlamydomonas reinhardtii.
Eukaryot. Cell 2: 995-1002.
57. Bernard, D., Gabilly, S., Dujardin, G., Merchant, S., Hamel, P. (2003)
Overlapping specificities of the mitochondrial cytochrome c and c1 heme lyases.
J. Biol. Chem. 278:49732-42.
58. Tottey, S., Block, M., Allen, M., Westergren, T., Albrieux, C., Scheller, H.V., Merchant, S., Jensen, P.E. (2003)
Arabidopsis CHL27, located in both envelope and thylakoid membranes, is required for the synthesis of protochlorophyllide.
Proc. Natl. Acad. Sci. USA, 100:16119-24.
59. Del Campo, J.A., Quinn, J.M., Merchant, S. (2004)
Evaluation of oxygen response involving differential gene expression in Chlamydomonas reinhardtii.
Methods in Enzymol., 381:604-617.
60. Eriksson, M., Moseley, J.L., Tottey, S., del Campo, J.A., Quinn, J., Kim, Y., Merchant, S. (2004)
Genetic dissection of nutritional copper signaling in Chlamydomonas distinguishes regulatory and target genes.
Genetics 168: 795-807.
61. Page, M.D., Hamel, P. P., Gabilly, S. T., Zegzouti, H., Perea, J.V., Alonso, J. M., Ecker, J. R., Theg, S., Christiansen, S., Merchant, S. (2004)
A homolog of prokaryotic thiol-disulfide transporter CcdA is required for the assembly of the cytochrome b6f complex in Arabidopsis chloroplasts.
J. Biol. Chem. 279:32474-82.
62. Merchant, S., Sawaya, M. (2005)
The light reactions: a guide to recent acquisitions for the picture gallery.
The Plant Cell 17:648-663.
63. Rzeznicka, K., Walker, C.J., Westergren, T., Kannangara, G.C., von Wettstein, D., Merchant, S., Gough, S.P., Hansson, M. (2005)
Xantha-l encodes one of at least three subunits of the aerobic Mg-protoporphyrin IX monomethyl ester cyclase in the chlorophyll biosynthetic pathway.
Proc. Natl. Acad. Sci. USA 102: 5886-5891.
64. Bernard, D.G., Quevillon-Cheruel, S., Merchant, S., Guiard, B., Hamel, P.P. (2005)
Cyc2p, a membrane-bound flavoprotein involved in the maturation of mitochondrial c-type cytochromes.
J. Biol. Chem. 280:39852-39859.
65. Kropat, J., Tottey, S., Birkenbihl, R., Depège, N., Huijser, P., Merchant, S. (2005)
A regulator of nutritional copper signaling in Chlamydomonas is an SBP-domain protein that recognizes the GTAC core of the CuRE.
Proc. Natl. Acad. Sci. USA. 102: 18730-5.
66. Merchant, S.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.
67. Merchant, S.S., Sagasti, A. (2006)
Precious metal economy.
Cell Metabolism. 4:99-101.
68. Allen, M.D., Kropat, J., Tottey, S., delCampo, J.A., Merchant, S.S. (2007)
Manganese deficiency in Chlamydomonas results in loss of PSII and MnSOD function, sensitivity to peroxides, and secondary phosphorus- and iron-deficiency.
Plant Physiol. 143:263-277.
69. Grossman, A.R., Croft, M., Gladyshev, V.N., Posewitz. M., Merchant, S.S., Prochnik, S., Spalding, M.H. (2007)
Novel metabolism in Chlamydomonas through the lens of genomics.
Curr. Opin. Plant Biol. 10:199-203
70. 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.
72. 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.
73. Long, J.C., Sommer, F., Allen, M.D., Lu, S.-F., Merchant, S.S. (2008)
Two ferritin complexes in Chlamydomonas reinhardtii chloroplasts are regulated by iron.
Genetics, 179:137-147.
74. Chen, J.-C., Hsieh, S.I., Kropat, J., Merchant, S.S. (2008)
A ferroxidase encoded by FOX1 contributes to iron assimilation under conditions of poor iron nutrition in Chlamydomonas.
Eukaryot. Cell 7: 541-545.
75. Long, J.C., Merchant, S.S. (2008)
Photo-oxidative stress impacts the expression of genes encoding iron metabolism components in Chlamydomonas.
Photochem. Photobiol. 84: 1395-1403.
76. Allen, M.D., Kropat, J., Merchant, S.S. (2008)
Regulation and localization of isoforms of the aerobic oxidative cyclase in Chlamydomonas reinhardtii.
Photochem. Photobiol. 84: 1336-1342.
77. Page, M.L.D., Kropat, J., Hamel, P. Merchant, S. (2009)
Two Chlamydomonas CTR transporters with a novel Cys-Met motif are localized to the plasma membrane and function in copper assimilation.
Plant Cell 21:928-943.
78. Merchant, S.S. (2009)
His protects heme as it crosses the membrane.
Proc. Natl. Acad. Sci. USA 106: 10069-10070.
79. 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. 284:25867-25878.
80. 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.
81. 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.
82. 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)
Expression and Enzymatic Properties of a Ferredoxin-Dependent Nitrite Reductase from Chlamydomonas reinhardtii.
Photosyn. Res. 103: 67-77.
83. Gonzalez-Ballester, D., Casero, D., Cokus, S., Pellegrini, M., Merchant, S.S., Grossman, A.R. (2010)
RNA-seq Analysis of the Transcriptome from Sulfur Deprived Chlamydomonas Cells.
Plant Cell 22:2058-2084.
84. Grossman, A. R., Karpowicz, S. J., Heinnickel, M., Dewez, D., Hamel, B., Dent, R., Niyogi, K.K., Johnson, X., Alric, J., Wollman, F.A., Li, H., Merchant, S.S. (2010)
Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation.
Photosyn. Res. 106:3-17.
85. 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.
86. 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.
87. Terauchi, A., Peers, G., Kobayashi, M., Niyogi, K.K., Merchant, S.S. (2010)
Trophic status of Chlamydomonas influences the impact of Fe-deficiency on photosynthesis.
Photosyn. Res.105:39-49.
88. Merchant, S.S. (2010)
The elements of plant micronutrients.
Plant Physiol. 154:512-515.
89. 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.
Biochemistry. 49:9667-9676.
90. Sommer, F., Kropat, J., Malasarn, D., Grossoehme, N.E., Chen, X., Giedroc, D.P., Merchant, S.S. (2010)
The CRR1 nutritional copper sensor in Chlamydomonas contains two distinct metal-responsive domains.
Plant Cell 22:4098-4113.
2011-2020
91. Gabilly, S., 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.
92. 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.
93. 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.
94. 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.
95. 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.
96. 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.
97. Bernal, M., Casero, D., Singh, V., Wilson, G.T., Grande, A., Yang, H., Dodani, S.C., Pellegrini, M., Huijser, P., Connolly, E.L., 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.
Plant Cell 24:738-61.
98. 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.
Plant Cell 24:2649-2665.
99. 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.
100. Fang, W., Si, Y., Douglass, S., Casero, D., Merchant, S.S., Pellegrini, M., Ladunga, I., Liu, P., Spalding, M.H. (2012)
Global changes in Chlamydomonas gene expression regulated by carbon dioxide and CIA5/CCM1.
Plant Cell 24:1876-1893.
101. 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.
102. Boyle, N.R., Page, M.D., Liu, B., Blaby, I.K., Casero, D., Kropat, J., Cokus, S.J., Hong-Hermesdorf, A., Shaw, J., Karpowicz, S.J., Gallaher, S.D., 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.
103. Urzica, E.I., Adler, L.N., Page, M.D., Linster. C.L., Arbing, M., Casero, D., Pellegrini, 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.
104. 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.
105. Blaby-Haas, C.E., Merchant, S.S. (2012)
The ins and outs of algal metal transporters.
Biochim. Biophys. Acta 1823:1531-1552.
106. 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.
Plant Cell 24:3921-48.
107. Wang, Q., Fristedt, R., Yu, X., Chen, Z., Liu, H., Lee, Y., Guo, H., Merchant, S.S., Lin, C. (2012)
Plant Physiol. 160:1373-1383.
108. Hsieh, S.I., Castruita, M., Malasarn, D., Urzica, E.I., Erde, J., Page, M.D., Yamasaki, H., Casero, D., Pellegrini, M., Merchant, S.S., Loo, J.A. (2013)
The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii.
Mol. Cell. Proteomics 12: 65-86.
109. Duanmu, D., Casero, D., Dent, R.M, Gallaher, 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. USA. 110:3621-26.
110. 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. USA. 110: 10854-10859.
111. Hemschemeier, A., Casero, D., Liu, B., Benning, C., Pellegrini, M., Happe, T., Merchant, S.S. (2013)
Copper response regulator 1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark-anoxia.
Plant Cell 25:3186-3211.
112. 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.
113. 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., 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., 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., Jian, 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
114. Glaesener, A.G., Merchant, S.S., Blaby-Haas, C. (2013)
Iron economy in Chlamydomonas.
Front. Plant Sci. 4: 337.
115. 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. 288:30246-30258.
116. 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.
117. 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.
118. Blaby-Haas, C.E., Merchant, S.S. (2013)
Iron sparing and recycling in a compartmentalized cell.
Curr. Opin. Microbiol. 16:677-85.
119. 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.
120. 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 26:1410-1435.
121. 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.
122. 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 13:591-613.
123. Blaby, I.K., Blaby-Haas, C.E., Tourasse, N., Hom, E., Lopez, D., Aksoy, M., Grossman, A., Umen, J., Dutcher, S., Porter, M., King, S., Witman, G., Stanke, M., Harris, E.H., Goodstein, D., Grimwood, J., Schmutz, J., Vallon, O., Merchant, S.S., Prochnik, S.I. (2014)
The Chlamydomonas genome: a decade of improvement.
Trends in Plant Sci. 19: 672-680.
124. Hong-Hermesdorf, A., Miethke, M., Gallaher, S.D., Kropat, J., Dodani, S.C., Barupala, D., Chan, J., Domaille, D.W., Shirasaki, D.I., Loo, J.A., Weber, P.K., Pett-Ridge, J., Stemmler, T.L., Chang, C.J., Merchant, S.S. (2014)
Selective sub-cellular visualization of trace metals identifies dynamic sites of Cu accumulation in Chlamydomonas.
Nat. Chem. Biol. 10:1034-42.
125. 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 biogenesis in plants.
J. Biol. Chem. 289:30657-67.
126. Blaby-Haas, C.E., Merchant, S.S. (2014)
Lysosome related organelles as mediators of metal homeostasis.
J. Biol. Chem. 289:28129-28136.
127. Blaby-Haas, C. E., Padilla-Benavides, T., Stübe, R., Argüello, J.M., Merchant, S.S. (2014)
Evolution of a plant-specific copper chaperone for chloroplast copper homeostasis.
Proc. Natl. Acad. Sci. USA 111:E5480-7.
128. Fristedt, R., Mamedov, F., Blaby-Haas, C.E. Merchant, S.S., Last R.L, Lundin, B. (2015)
PSB33, 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.
129. Kropat, J., Gallaher, S.D., Urzica, E.I., Nakamoto, S.S., Tottey, S., Mason, A.Z., Merchant, S.S. (2015)
Copper economy in Chlamydomonas: prioritized allocation and re-allocation of copper to respiration versus photosynthesis.
Proc. Natl. Acad. Sci. USA 112:2644-51.
130. Allan, C.M., Awad, A.M., Johnson, J.S., Shirasaki, D.I., Wang, C., Blaby-Haas. C.E., Merchant, S.S., Loo, J.A., Clarke, C.F. (2015)
Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae.
J. Biol. Chem. 290:7517-34.
131. Fristedt, R., Martins, N.F., Strenkert, D., Clarke, C.A., Suchoszek, M., Thiele, W., Schöttler, M.A., Merchant, S.S. (2015)
The thylakoid membrane protein CGL160 supports CF1CF0 ATP synthase accumulation in Arabidopsis thaliana.
PLoS One: 10:e0121658.
132. 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.
133. 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
134. 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 14:964-273.
135. 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. 169:2730-43.
136. Gallaher, S.D., Fitz-Gibbon, S., Glaesener, A., Pellegrini, M., Merchant, S.S. (2015)
Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies.
The Plant Cell 27:2335-2352.
137. 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. 27:2743-69
138. 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.
139. 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.
140. 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.
141. Anderson, A. Laohavisit, A., Blaby, I.K, Bombelli, P., Howe, C.J., Merchant, S.S., Davies, J.M, Smith, A.G. (2016)
Exploiting algal NADPH oxidase for biophotovoltaic energy.
Plant Biotech. J. 14:24-28.
142. Reyes, V., Spitzmiller, M., Hong-Hermesdorf, A., Kropat, J., Damoiseaux, R., Merchant, S.S., Mahendra, S. (2016)
Copper Status of Exposed Microorganisms Influences Susceptibility to Metallic Nanoparticles.
Env. Toxicol. Chem. 35:1148-1158.
143. Kumar, D., Blaby-Haas, C.E., Merchant, S.S., Mains, R.E., King, S.M., Eipper, B.A. (2016)
Early eukaryotic origins for cilia-associated bioactive peptide-amidating activity.
J. Cell. Sci. 129:143-156.
144. Blaby-Haas, C.E., Castruita, M., Fitz-Gibbon, S.T., Kropat, J. and Merchant, S.S. (2016)
Ni induces the CRR1-dependent regulon revealing overlap and distinction between hypoxia and Cu deficiency responses in Chlamydomonas reinhardtii.
Metallomics 8:679-691.
145. Strenkert, D., Limso, C.A., Fatihi, A., Schmollinger, S., Basset, G.J., Merchant, S.S. (2016)
Genetically programmed changes in photosynthetic cofactor metabolism in copper deficient Chlamydomonas.
J. Biol. Chem. 291:19118 –19131.
146. Wells, M.L., Potin, P., Craigie, J., Raven, J.A., Merchant, S.S., Helliwell, K.E., Smith, A.G., Camire, M.E., Brawley, S.H. (2016)
Algae as Nutritional and Functional Food Sources: Revisiting Our Understanding.
J. Appl. Phycol. 29: 949-982.
147. Traller, J.C., Cokus, S.J., Lopez, D.A., Gaidarenko, O., Smith, S.R., McCrow, J.P., Gallaher, S.D., Podell, S. , Thompson, M., Cook, O., Morselli, M., Jaroszewicz, A., Allen, E.E., Allen, A.E., Merchant, S.S., Pellegrini, M., Hildebrand, M. (2016)
Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype.
Biotechnol. Biofuels. 9:258.
148. 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
149. Roth, M.S., Cokus, S.J., Gallaher, S.D., Walter, A., Lopez, D., Erickson, E., Endelman, B., Westcott, D., Larabell, C., 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 14:E4296-E4305.
150. 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.
151. 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.
152. Blaby-Haas, C.E., Merchant, S.S. (2017)
Regulating trace metal economy in algae.
Curr. Opin. Plant Biol. 39:88-96.
153. 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.
154. 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.
155. Fristedt, R., Hu, C., Wheatley, N., Roy, L., Wachter, R., Savage, L., Kramer, D., Merchant, S.S., Yeates, T.O., Croce, R. (2018).
RAF2 is a Rubisco assembly factor in Arabidopsis thaliana.
The Plant J. 94:146-156.
156. 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.
157. 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.
158. Li, M., van Zee, M., Riche, C.T., Tofig, B., Gallaher, S.D., Merchant, S.S., Damoiseaux, R., Goda, K., Di Carlo, D. (2018)
A gelatin microdroplet platform for high-throughput sorting of hyperproducing single-cell-derived microalgal clones.
Small. 14:e1803315.
159. Blaby-Haas, C.E., Merchant, S.S. (2019)
Comparative and functional algal genomics.
Annu. Rev. Plant Biol. 70:605-638.
160. 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.
161. Armaleo, D., Mueller, O., Lutzoni, F., Andrésson, Ó., Blanc, G., Bode, H.B., Collart, F.R., Dal Grande, F., Dietrich, F., Grigoriev, I.V., Joneson, S., Kuo, A., Larsen, P.E., Logsdon, J.M., Lopez, D., Martin, F., May, S.P., McDonald, T.R., Merchant, S.S., Miao, V., Morin, E., Oono, R., Pellegrini, M., Rubinstein, N., Sanchez-Puerta, M.V., Savelkoul, E., Schmitt, I., Slot, J.C., Soanes, D., Szövényi, P., Talbot, N., Veneault-Fourrey, C., Xavier, B.B. (2019)
The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.
BMC Genomics, 20:605.
162.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. doi.org/10.1105/tpc.18.00742
163. Salomé, P.A., Merchant, S.S. (2019)
A series of fortunate events: Introducing Chlamydomonas as a reference organism.
The Plant Cell, 31:1682-1707.
164. Tsednee, M., Castruita, M., Salome, P.A., Sharma, A., Lewis, B.E., Schmollinger, S.R., Holbrook, K., Otegui, M., Khatua, K., Das, S., Datta, A., Chen, S., Ramon, C., Ralle, M., Weber, P.K., Stemmler, T.L., Pett-Ridge, J., Hoffman, B.M., Merchant, S.S. (2019)
Hyper-accumulated Mn, co-localized in acidocalcisomes with Ca and P, can be mobilized in Mn-deficient situations.
J. Biol. Chem. 294, 17626-17641.
165. Amstutz, C.L., Fristedt, R., Schultink, A., Merchant, S.S., Niyogi, K.K., Malnoë, A. (2020)
An atypical short-chain dehydrogenase–reductase functions in the relaxation of photoprotective qH in Arabidopsis
Nature Plants 6, 154-166.
166. Attar, N., Campos, O.A., Vogelauer, M., Cheng, C., Xue, Y., Schmollinger, S., Salwinski, L., Mallipeddi, N.V., Boone, B.A., Yen, L., Yang, S., Zikovich, S., Dardine, J., Carey, M.F., Merchant S.S., Kurdistani, S.K. (2020) The histone H3-H4 tetramer is a copper reductase enzyme. Science. 369, 59-64.
167. Neupert, J., Lu, Y., Strenkert, D., Gallaher, S.D., Segal, N., Barahimipour, R., Fitz-Gibbon, S.T., Schroda, M., Merchant, S.S., Bock, R. (2020) An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas. Nat. Comm. 11, 6269.
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168. Ramundo, S., Askakura, Y., Salome, P.A., Strenkert, D., Boone, M., Mackinder, L., Takafuji, K., Dinc, E., Rahire, M., Crevecoeur, M., Magneschi, L., Schaad, O., Hippler, M., Jonikas, M.C., Merchant, S.S., Nakai, M., Rochaix, J.-D. Walter, P. (2020). Co-expressed subunits of dual genetic origin define a conserved supercomplex mediating essential protein import into chloroplasts. Proc. Natl. Acad. Sci. USA 117: 32739-32749 https://doi.org/10.1073/pnas.2014294117
169. Merchant, S.S., Schmollinger S, Strenkert D, Moseley JL, Blaby-Haas CE (2020) From economy to luxury: Copper homeostasis in Chlamydomonas and other algae. Biochim Biophys Acta 1867:118822. doi: 10.1016/j.bbamcr.2020.118822. Epub 2020 Aug 13. PMID: 32800924
2021-Present
170. Ma, F., Salome, P.A., Merchant, S.S., Pellegrini, M. Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures Reveals Heterogeneity in their Diurnal Cycle Phase (2021) Plant Cell, 31:1042-1057. doi: https://doi.org/10.1101/2020.09.15.298844
171. Gallaher, S.D., Craig, R.J., Ganesan, I., Purvine, S.O., McCorkle, S.R., Grimwood, J., Strenkert, D., Davidi, L., Roth, M.S., Jeffers, T.L., Lipton, M., Niyogi, K.K., Schmutz, J., Theg, S.M., Blaby-Haas,C.E., Merchant, S.S. (2021). Proc. Natl. Acad. Sci. USA. Widespread polycistronic gene expression in green algae. 118: e2017714118 https://doi.org/10.1073/pnas.2017714118
172. Salome, P.A., Merchant, S.S. (2021) Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery. Plant Cell 33:1058-1082. https://www.biorxiv.org/content/10.1101/2020.10.05.326611v1
173. Schmollinger, S., Chen, S., Strenkert, D., Hui, C., Ralle, M., Merchant, S.S. (2021) Single-cell visualization and quantification of trace metals in Chlamydomonas lysosome related organelles, Proc. Natl. Acad. Sci. USA 118:e2026811118 https://doi.org/10.1073/pnas.2026811118
174. Campos, O.A., Attar, N.K., Cheng, C., Vogelauer, M., Mallipeddi, N.V., Schmollinger, S., Matulionis, N., Christofk, H. R., Merchant, S.S., Kurdistani, S.K. (2021) A pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich’s ataxia. Sci. Adv. 7: eabj9889. doi: 10.1126/sciadv.abj9889. Epub 2021 Dec 17.
175. Pham, K., Schmollinger, S., Merchant, S.S., Strenkert, D. (2022) Chlamydomonas ATX1 is essential for Cu distribution to multiple cupro-enzymes and maintenance of biomass in conditions demanding cupro-enzyme-dependent metabolic pathways. Plant Direct 6:e383. https://doi.org/10.1002/pld3.383
176. Strenkert, D., Mingay, M., Schmollinger, S., Chen, C., O’Malley, R.C., Merchant, S.S. (2022) An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis. Plant Direct 6:e392. doi: 10.1002/pld3.392 PMC8961045
177. Hui, C., Schmollinger, S., Strenkert, D., Holbrook, K., Montgomery, H., Chen, S., Nelson, H., Weber, P., Merchant, S.S. (2022) Simple steps to enable reproducibility: Culture conditions affecting Chlamydomonas growth and elemental composition. Plant J. 111:995-1014. doi: 10.1111/tpj.15867
178. Strenkert, D., Yildirim, A., Yan, J., Yoshinaga, Y., Pellegrini, M., O’Malley, R.C., Merchant, S.S., Umen, J.G. (2022) The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle. Plant J. 112:352-68.
179. Fauser, F., Vilarrasa-Blasi, J., Onishi, M., Ramundo, S., Patena, W., Millican, M., Osaki, J., Philp, C., Nemeth, M., Salomé, P.A., Li, X., Wakao, S., Kim, R.G., Kaye, Y., Grossman, A.R., Niyogi, K.K., Merchant, S.S., Cutler, S.R., Walter, P., Dinneny, J.R., Jonikas, M.C., Jinkerson, R.E. (2022) Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii. Nat. Genet. 54:705-714. doi: 10.1038/s41588-022-01052-9. Epub 2022 May 5 PMC9110296
180. Craig, R.J., Gallaher, S.D., Shu, S., Salome, P., Jenkins, J.W., Blaby-Haas, C.E., Purvine, S.O., O’Donnell, S., Barry, K., Grimwood, J., Strenkert, D., Daum, C., Yoshinaga, Y., Goodstein, D.M., Vallon, O., Schmutz, J., Merchant, S.S. (2023) The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory. The Plant Cell 35:644-672.
181. Long, H., Fang, J., Ye, L., Zhang, B., Hui, C., Deng, X., Merchant, S.S., Huang, K. (2023) Structural and functional regulation of lysosome-related organelles in response to environmental changes in Chlamydomonas reinhardtii. Plant Physiol.192:927-944. doi: 10.1093/plphys/kiad189.
182. Schmollinger, S., Merchant, S.S. (2023) Quantitative elemental imaging in eukaryotic algae. Metallomics, in press. doi: 10.1093/mtomcs/mfad025
183. Davidi, L., Gallaher, S.D., Ben-David, E., Purvine, S.O., Filmore, T.L., Nicora, C.D., Craig, R.J., Schmollinger, S., Roje, S., Blaby-Haas, C.E., Auber, R.P., Wisecaver, J., Merchant, S.S. (2023) Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Mechanisms of Iron Economy. Proc. Natl. Acad. Sci. USA, in press.
https://www.biorxiv.org/content/10.1101/2023.02.09.527888v1
184. Sreedasyam, A., Plott, C., Hossain, M.S., Lovell, J.T., Grimwood, J., Jenkins, J.W., Daum, C., Barry, K., Carlson, J., Shu, S., Phillips, J., Amirebrahimi, M., Zane, M., Wang, M., Goodstein, D., Haas, F.B., Hiss, M., Perroud, P.-F., Jawdy, S.S., Hu, R., Johnson, J., Kropat, J., Gallaher, S., Lipzen, A., Tillman, R., Shakirov, E., Weng, X., Torres-Jerez, I., Weers, B., Conde, D., Pappas, M.R., Liu, L., Muchlinski, A., Jiang, H., Shyu, C., Huang, P., Sebastian, J., Laiben, C., Medlin, A., Carey, S., Carrell, A.A., Perales, M., Swaminathan, K., Allona, I., Grattapaglia, D., Cooper, E.A., Tholl, D., Vogel, J.P., Kellogg, E.A., Baxter, I., Udvardi, M., Tang, Y., Mockler, T.C., Juenger, T.E., Mullet, J., Rensing, S.A., Tuskan, G.A., Merchant, S.S., Stacey, G., Schmutz, J. (2023) JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional descriptions across the plant kingdom. Nucl. Acids Res. in press.
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185. Strenkert, D., Schmollinger, S., Hu, Y., Hofmann, C., Holbrook, K., Liu, H., Purvine, S., Nicora, C.D., Chen, S., Lipton, M.S., Northern, T., Clemens, S., Merchant, S.S. (2023) Zn deficiency disrupts Cu and S homeostasis in Chlamydomonas resulting in over accumulation of Cu and Cysteine. Metallomics, in press.
BioRxiv 2023.03.15.532757.full