An indexed, mapped mutant library enables reverse genetics studies of biological processes in chlamydomonas reinhardtii

Plant Cell

Volumn 28, Issue 2, 2015, Pages 367-387

  Li, Xiaobo ^a   Zhang, Ru ^a   Patena, Weronika ^a   Gang, Spencer S ^a   Blum, Sean R ^a   Ivanova, Nina ^a   Yue, Rebecca ^a   Robertson, Jacob M ^a   Lefebvre, Paul A ^b   Fitz Gibbon, Sorel T ^c   Grossman, Arthur R ^a   Jonikasa, Martin C ^a  

^a GEOPHYSICAL LABORATORY   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FATTY ACID; LIPID; PLANT PROTEIN; PROTEOME; TRIACYLGLYCEROL;

CHLAMYDOMONAS REINHARDTII; CHLOROPLAST; CHROMOSOMAL MAPPING; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MUTATION; PHENOTYPE; PHYSIOLOGY; REVERSE GENETICS;

CHLAMYDOMONAS REINHARDTII; CHLOROPLASTS; CHROMOSOME MAPPING; FATTY ACIDS; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIPIDS; MUTAGENESIS, INSERTIONAL; MUTATION; PHENOTYPE; PLANT PROTEINS; PROTEOME; REVERSE GENETICS; SEQUENCE ANALYSIS, DNA; TRIGLYCERIDES;

EID: 84960392782     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.15.00465     Document Type: Article

References (161)

1. Aksoy, M., Pootakham, W., and Grossman, A.R. (2014). Critical function of a Chlamydomonas reinhardtii putative polyphosphate polymerase subunit during nutrient deprivation. Plant Cell 26: 4214-4229
2. Albee, A.J., Kwan, A.L., Lin, H., Granas, D., Stormo, G.D., and Dutcher, S.K. (2013). Identification of cilia genes that affect cellcycle progression using whole-genome transcriptome analysis in Chlamydomonas reinhardtti. G3 (Bethesda) 3: 979–991
3. Alonso, J.M., et al. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653–657
4. Andrews, J., and Keegstra, K. (1983). Acyl-CoA synthetase is located in the outer membrane and acyl-CoA thioesterase in the inner membrane of pea chloroplast envelopes. Plant Physiol. 72: 735-740
5. Athenstaedt, K., and Daum, G. (2003). YMR313c/TGL3 encodes a novel triacylglycerol lipase located in lipid particles of Saccharomyces cerevisiae. J. Biol. Chem. 278: 23317–23323
6. Athenstaedt, K., and Daum, G. (2005). Tgl4p and Tgl5p, two triacylglycerol lipases of the yeast Saccharomyces cerevisiae are localized to lipid particles. J. Biol. Chem. 280: 37301–37309
7. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., and Mori, H. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2: 2006.0008
8. Badger, M.R., Kaplan, A., and Berry, J.A. (1980). Internal inorganic carbon pool of Chlamydomonas reinhardtii: Evidence for a carbon dioxide-concentrating mechanism. Plant Physiol. 66: 407–413
9. Baldari, C.T., and Rosenbaum, J. (2010). Intraflagellar transport: it’s not just for cilia anymore. Curr. Opin. Cell Biol. 22: 75–80
10. Beale, S.I. (2009). Biosynthesis of chlorophylls and hemes. In The Chlamydomonas Sourcebook, E.H. Harris, D.B. Stern, and G.B. Witman, eds (San Diego, CA: Academic Press), pp. 731–798
11. Beel, B., Prager, K., Spexard, M., Sasso, S., Weiss, D., Müller, N., Heinnickel, M., Dewez, D., Ikoma, D., Grossman, A.R., Kottke, T., and Mittag, M. (2012). A flavin binding cryptochrome photoreceptor responds to both blue and red light in Chlamydomonas reinhardtii. Plant Cell 24: 2992–3008
12. Belcher, S., Williams-Carrier, R., Stiffler, N., and Barkan, A. (2015). Large-scale genetic analysis of chloroplast biogenesis in maize. Biochim. Biophys. Acta 1847: 1004–1016
13. Berthold, P., Schmitt, R., and Mages, W. (2002). An engineered Streptomyces hygroscopicus aph 7" gene mediates dominant resistance against hygromycin B in Chlamydomonas reinhardtii. Protist 153: 401–412
14. Blaby, I.K., et al. (2013). Systems-level analysis of nitrogen starvationinduced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. Plant Cell 25: 4305–4323
15. Boyle, N.R., et al. (2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J. Biol. Chem. 287: 15811–15825
16. Boynton, J.E., et al. (1988). Chloroplast transformation in Chlamydomonas with high velocity microprojectiles. Science 240: 1534–1538
17. Bragg, J.N., Wu, J., Gordon, S.P., Guttman, M.E., Thilmony, R., Lazo, G.R., Gu, Y.Q., and Vogel, J.P. (2012). Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One 7: e41916
18. Brueggeman, A.J., Gangadharaiah, D.S., Cserhati, M.F., Casero, D., Weeks, D.P., and Ladunga, I. (2012). Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii. Plant Cell 24: 1860–1875
19. Calderon, R.H., García-Cerdán, J.G., Malnoë, A., Cook, R., Russell, J.J., Gaw, C., Dent, R.M., de Vitry, C., and Niyogi, K.K. (2013). A conserved rubredoxin is necessary for photosystem II accumulation in diverse oxygenic photoautotrophs. J. Biol. Chem. 288: 26688-26696
20. Carette, J.E., Guimaraes, C.P., Wuethrich, I., Blomen, V.A., Varadarajan, M., Sun, C., Bell, G., Yuan, B., Muellner, M.K., Nijman, S.M., Ploegh, H.L., and Brummelkamp, T.R. (2011). Global gene disruption in human cells to assign genes to phenotypes by deep sequencing. Nat. Biotechnol. 29: 542–546
21. 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., and Merchant, S.S. (2011). Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell 23: 1273–1292
22. Catalanotti, C., Dubini, A., Subramanian, V., Yang, W., Magneschi, L., Mus, F., Seibert, M., Posewitz, M.C., and Grossman, A.R. (2012). Altered fermentative metabolism in Chlamydomonas reinhardtii mutants lacking pyruvate formate lyase and both pyruvate formate lyase and alcohol dehydrogenase. Plant Cell 24: 692–707
23. Catalanotti, C., Yang, W., Posewitz, M.C., and Grossman, A.R. (2013). Fermentation metabolism and its evolution in algae. Front. Plant Sci. 4: 150
24. Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., and Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819–823
25. Costanzo, M., et al. (2010). The genetic landscape of a cell. Science 327: 425–431
26. Cross, F.R., and Umen, J.G. (2015). The Chlamydomonas cell cycle. Plant J. 82: 370–392.
27. de Azevedo Souza, C., Kim, S.S., Koch, S., Kienow, L., Schneider, K., McKim, S.M., Haughn, G.W., Kombrink, E., and Douglas, C.J. (2009). A novel fatty Acyl-CoA Synthetase is required for pollen development and sporopollenin biosynthesis in Arabidopsis. Plant Cell 21: 507–525
28. Deng, X.D., Gu, B., Li, Y.J., Hu, X.W., Guo, J.C., and Fei, X.W. (2012). The roles of acyl-CoA: diacylglycerol acyltransferase 2 genes in the biosynthesis of triacylglycerols by the green algae Chlamydomonas reinhardtii. Mol. Plant 5: 945–947
29. Dent, R.M., Haglund, C.M., Chin, B.L., Kobayashi, M.C., and Niyogi, K.K. (2005). Functional genomics of eukaryotic photosynthesis using insertional mutagenesis of Chlamydomonas reinhardtii. Plant Physiol. 137: 545–556
30. Dent, R.M., Sharifi, M.N., Malnoë, A., Haglund, C., Calderon, R.H., Wakao, S., and Niyogi, K.K. (2015). Large-scale insertional mutagenesis of Chlamydomonas supports phylogenomic functional prediction of photosynthetic genes and analysis of classical acetaterequiring mutants. Plant J. 82: 337–351
31. Dubini, A., Mus, F., Seibert, M., Grossman, A.R., and Posewitz, M.C. (2009). Flexibility in anaerobic metabolism as revealed in a mutant of Chlamydomonas reinhardtii lacking hydrogenase activity. J. Biol. Chem. 284: 7201–7213
32. Eastmond, P.J. (2006). SUGAR-DEPENDENT1 encodes a patatin domain triacylglycerol lipase that initiates storage oil breakdown in germinating Arabidopsis seeds. Plant Cell 18: 665–675
33. Engel, B.D., Ishikawa, H., Feldman, J.L., Wilson, C.W., Chuang, P.T., Snedecor, J., Williams, J., Sun, Z., and Marshall, W.F. (2011). A cell-based screen for inhibitors of flagella-driven motility in Chlamydomonas reveals a novel modulator of ciliary length and retrograde actin flow. Cytoskeleton (Hoboken) 68: 188–203
34. Fan, J., Andre, C., and Xu, C. (2011). A chloroplast pathway for the de novo biosynthesis of triacylglycerol in Chlamydomonas reinhardtii. FEBS Lett. 585: 1985–1991
35. Fang, W., Si, Y., Douglass, S., Casero, D., Merchant, S.S., Pellegrini, M., Ladunga, I., Liu, P., and Spalding, M.H. (2012). Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell 24: 1876–1893
36. Farese, R.V., Jr., and Walther, T.C. (2009). Lipid droplets finally get a little R-E-S-P-E-C-T. Cell 139: 855–860
37. Fliegauf, M., Benzing, T., and Omran, H. (2007). When cilia go bad: cilia defects and ciliopathies. Nat. Rev. Mol. Cell Biol. 8: 880–893
38. Fulda, M., Schnurr, J., Abbadi, A., Heinz, E., and Browse, J. (2004). Peroxisomal Acyl-CoA synthetase activity is essential for seedling development in Arabidopsis thaliana. Plant Cell 16: 394–405
39. Fulda, M., Shockey, J., Werber, M., Wolter, F.P., and Heinz, E. (2002). Two long-chain acyl-CoA synthetases from Arabidopsis thaliana involved in peroxisomal fatty acid beta-oxidation. Plant J. 32: 93–103
40. Gallaher, S.D., Fitz-Gibbon, S.T., Glaesener, A.G., Pellegrini, M., and 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. Plant Cell 27: 2335–2352
41. Galván, A., González-Ballester, D., and Fernández, E. (2007). Insertional mutagenesis as a tool to study genes/functions in Chlamydomonas. Adv. Exp. Med. Biol. 616: 77–89
42. Geng, S., De Hoff, P., and Umen, J.G. (2014). Evolution of sexes from an ancestral mating-type specification pathway. PLoS Biol. 12: e1001904
43. Ghirardi, M.L., Posewitz, M.C., Maness, P.C., Dubini, A., Yu, J., and Seibert, M. (2007). Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms. Annu. Rev. Plant Biol. 58: 71–91
44. Giaever, G., et al. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387–391
45. González-Ballester, D., Casero, D., Cokus, S., Pellegrini, M., Merchant, S.S., and Grossman, A.R. (2010). RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell 22: 2058–2084
46. González-Ballester, D., de Montaigu, A., Galván, A., and Fernández, E. (2005a). Restriction enzyme site-directed amplification PCR: a tool to identify regions flanking a marker DNA. Anal. Biochem. 340: 330–335
47. González-Ballester, D., de Montaigu, A., Higuera, J.J., Galván, A., and Fernández, E. (2005b). Functional genomics of the regulation of the nitrate assimilation pathway in Chlamydomonas. Plant Physiol. 137: 522–533
48. Gonzalez-Ballester, D., Pootakham, W., Mus, F., Yang, W., Catalanotti, C., Magneschi, L., de Montaigu, A., Higuera, J.J., Prior, M., Galván, A., Fernandez, E., and Grossman, A.R. (2011). Reverse genetics in Chlamydomonas: a platform for isolating insertional mutants. Plant Methods 7: 24
49. Goodenough, U. (2015). Historical perspective on Chlamydomonas as a model for basic research: 1950-1970. Plant J. 82: 365–369
50. Goodman, A.L., McNulty, N.P., Zhao, Y., Leip, D., Mitra, R.D., Lozupone, C.A., Knight, R., and Gordon, J.I. (2009). Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6: 279–289
51. Goold, H., Beisson, F., Peltier, G., and Li-Beisson, Y. (2015). Microalgal lipid droplets: composition, diversity, biogenesis and functions. Plant Cell Rep. 34: 545–555
52. Grossman, A.R., Catalanotti, C., Yang, W., Dubini, A., Magneschi, L., Subramanian, V., Posewitz, M.C., and Seibert, M. (2011). Multiple facets of anoxic metabolism and hydrogen production in the unicellular green alga Chlamydomonas reinhardtii. New Phytol. 190: 279–288
53. Grossman, A.R., Harris, E.E., Hauser, C., Lefebvre, P.A., Martinez, D., Rokhsar, D., Shrager, J., Silflow, C.D., Stern, D., Vallon, O., and Zhang, Z. (2003). Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryot. Cell 2: 1137–1150
54. 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., and Merchant, S.S. (2010). Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation. Photosynth. Res. 106: 3–17
55. Gutman, B.L., and Niyogi, K.K. (2004). Chlamydomonas and Arabidopsis. A dynamic duo. Plant Physiol. 135: 607–610
56. Harris, E.H. (2001). Chlamydomonas as a model organism. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52: 363–406
57. Heinnickel, M.L., Alric, J., Wittkopp, T., Yang, W., Catalanotti, C., Dent, R., Niyogi, K.K., Wollman, F.A., and Grossman, A.R. (2013). Novel thylakoid membrane GreenCut protein CPLD38 impacts accumulation of the cytochrome b6f complex and associated regulatory processes. J. Biol. Chem. 288: 7024–7036
58. Hemme, D., et al. (2014). Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii. Plant Cell 26: 4270–4297
59. Hemschemeier, A., Casero, D., Liu, B., Benning, C., Pellegrini, M., Happe, T., and Merchant, S.S. (2013). Copper response regulator1- dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia. Plant Cell 25: 3186–3211
60. Hemschemeier, A., Jacobs, J., and Happe, T. (2008). Biochemical and physiological characterization of the pyruvate formate-lyase Pfl1 of Chlamydomonas reinhardtii, a typically bacterial enzyme in a eukaryotic alga. Eukaryot. Cell 7: 518–526
61. Hsing, Y.I., et al. (2007). A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol. Biol. 63: 351–364
62. Hu, Q., Sommerfeld, M., Jarvis, E., Ghirardi, M., Posewitz, M., Seibert, M., and Darzins, A. (2008). Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J. 54: 621–639
63. Hung, C.H., Ho, M.Y., Kanehara, K., and Nakamura, Y. (2013). Functional study of diacylglycerol acyltransferase type 2 family in Chlamydomonas reinhardtii. FEBS Lett. 587: 2364–2370
64. Hunter, C.T., Suzuki, M., Saunders, J., Wu, S., Tasi, A., McCarty, D.R., and Koch, K.E. (2014). Phenotype to genotype using forwardgenetic Mu-seq for identification and functional classification of maize mutants. Front. Plant Sci. 4: 545
65. Hwang, S.W., and Hudock, G.A. (1971). Stability of Chlamydomonas reinhardtii in liquid nitrogen storage. J. Phycol. 7: 300–303
66. Jarvik, J.W., and Rosenbaum, J.L. (1980). Oversized flagellar membrane protein in paralyzed mutants of Chlamydomonas reinhardrii. J. Cell Biol. 85: 258–272
67. Jessen, D., Olbrich, A., Knüfer, J., Krüger, A., Hoppert, M., Polle, A., and Fulda, M. (2011). Combined activity of LACS1 and LACS4 is required for proper pollen coat formation in Arabidopsis. Plant J. 68: 715–726
68. Jessen, D., Roth, C., Wiermer, M., and Fulda, M. (2015). Two activities of long-chain acyl-coenzyme A synthetase are involved in lipid trafficking between the endoplasmic reticulum and the plastid in Arabidopsis. Plant Physiol. 167: 351–366
69. Jiang, W., Brueggeman, A.J., Horken, K.M., Plucinak, T.M., and Weeks, D.P. (2014). Successful transient expression of Cas9 and single guide RNA genes in Chlamydomonas reinhardtii. Eukaryot. Cell 13: 1465–1469
70. Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., and Doudna, J. (2013). RNA-programmed genome editing in human cells. eLife 2: e00471
71. Johnson, X., Vandystadt, G., Bujaldon, S., Wollman, F.A., Dubois, R., Roussel, P., Alric, J., and Béal, D. (2009). A new setup for in vivo fluorescence imaging of photosynthetic activity. Photosynth. Res. 102: 85–93
72. Kajikawa, M., Sawaragi, Y., Shinkawa, H., Yamano, T., Ando, A., Kato, M., Hirono, M., Sato, N., and Fukuzawa, H. (2015). Algal dual-specificity tyrosine phosphorylation-regulated kinase, triacylglycerol accumulation regulator1, regulates accumulation of triacylglycerol in nitrogen or sulfur deficiency. Plant Physiol. 168: 752–764
73. Karpowicz, S.J., Prochnik, S.E., Grossman, A.R., and Merchant, S.S. (2011). The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J. Biol. Chem. 286: 21427–21439
74. Kates, J.R., and Jones, R.F. (1964). Fluoroacetate inhibition of amino acids during photosynthesis of Chlamydomonas reinhardti. Science 143: 145–146
75. Keller, L.C., Romijn, E.P., Zamora, I., Yates, J.R., Marshall, W.F. (2005). Proteomic analysis of isolated chlamydomonas centrioles reveals orthologs of ciliary-disease genes. Curr. Biol. 15: 1090–1098
76. Kindle, K.L., Schnell, R.A., Fernández, E., and Lefebvre, P.A. (1989). Stable nuclear transformation of Chlamydomonas using the Chlamydomonas gene for nitrate reductase. J. Cell Biol. 109: 2589–2601
77. Koo, A.J., Ohlrogge, J.B., and Pollard, M. (2004). On the export of fatty acids from the chloroplast. J. Biol. Chem. 279: 16101–16110
78. Kourmpetis, Y.A., van Dijk, A.D., van Ham, R.C., and ter Braak, C.J. (2011). Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources. Plant Physiol. 155: 271–281
79. Kozminski, K.G., Johnson, K.A., Forscher, P., and Rosenbaum, J.L. (1993). A motility in the eukaryotic flagellum unrelated to flagellar beating. Proc. Natl. Acad. Sci. USA 90: 5519–5523
80. Kropat, J., Hong-Hermesdorf, A., Casero, D., Ent, P., Castruita, M., Pellegrini, M., Merchant, S.S., and Malasarn, D. (2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J. 66: 770–780
81. Kurat, C.F., Natter, K., Petschnigg, J., Wolinski, H., Scheuringer, K., Scholz, H., Zimmermann, R., Leber, R., Zechner, R., and Kohlwein, S.D. (2006). Obese yeast: triglyceride lipolysis isfunctionally conserved from mammals to yeast. J. Biol. Chem. 281: 491–500
82. LaRussa, M., Bogen, C., Uhmeyer, A., Doebbe, A., Filippone, E., Kruse, O., and Mussgnug, J.H. (2012). Functional analysis of three type-2 DGAT homologue genes for triacylglycerol production in the green microalga Chlamydomonas reinhardtii. J. Biotechnol. 162: 13–20
83. Levine, R.P. (1960). Genetic control of photosynthesis in Chlamydomonas reinhardi. Proc. Natl. Acad. Sci. USA 46: 972–978
84. Lewin, R.A. (1953). Studies on the flagella of algae. Il. Formation of flagella by Chlamydomonas in light and darkness. Ann. N. Y. Acad. Sci. 56: 1091–1093
85. Li, J.B., et al. (2004). Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell 117: 541–552
86. Li, X., Benning, C., and Kuo, M.H. (2012a). Rapid triacylglycerol turnover in Chlamydomonas reinhardtii requires a lipase with broad substrate specificity. Eukaryot. Cell 11: 1451–1462
87. Li, X., Moellering, E.R., Liu, B., Johnny, C., Fedewa, M., Sears, B.B., Kuo, M.H., and Benning, C. (2012b). A galactoglycerolipid lipase is required for triacylglycerol accumulation and survival following nitrogen deprivation in Chlamydomonas reinhardtii. Plant Cell 24: 4670–4686
88. Li, Y., Rosso, M.G., Viehoever, P., and Weisshaar, B. (2007). GABIKat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. Nucleic Acids Res. 35: D874–D878
89. Li-Beisson, Y., Beisson, F., and Riekhof, W. (2015). Metabolism of acyl-lipids in Chlamydomonas reinhardtii. Plant J. 82: 504–522
90. Liu, B., and Benning, C. (2013). Lipid metabolism in microalgae distinguishes itself. Curr. Opin. Biotechnol. 24: 300–309
91. Liu, Y., Pei, J., Grishin, N., and Snell, W.J. (2015). The cytoplasmic domain of the gamete membrane fusion protein HAP2 targets the protein to the fusion site in Chlamydomonas and regulates the fusion reaction. Development 142: 962–971
92. Lohr, M. (2009). Carotenoids. In The Chlamydomonas Sourcebook, H. E.H., S. E.B., and W. G.B., eds (Academic Press), pp. 799–817
93. Lohr, M., Im, C.S., and Grossman, A.R. (2005). Genome-based examination of chlorophyll and carotenoid biosynthesis in Chlamydomonas reinhardtii. Plant Physiol. 138: 490–515
94. Lü, S., Song, T., Kosma, D.K., Parsons, E.P., Rowland, O., and Jenks, M.A. (2009). Arabidopsis CER8 encodes LONG-CHAIN ACYL-COA SYNTHETASE 1 (LACS1) that has overlapping functions with LACS2 in plant wax and cutin synthesis. Plant J. 59: 553–564
95. Magneschi, L., Catalanotti, C., Subramanian, V., Dubini, A., Yang, W., Mus, F., Posewitz, M.C., Seibert, M., Perata, P., and Grossman, A.R. (2012). A mutant in the ADH1 gene of Chlamydomonas reinhardtii elicits metabolic restructuring during anaerobiosis. Plant Physiol. 158: 1293–1305
96. Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., Norville, J.E., and Church, G.M. (2013). RNA-guided human genome engineering via Cas9. Science 339: 823–826
97. Matsuo, T., Okamoto, K., Onai, K., Niwa, Y., Shimogawara, K., and Ishiura, M. (2008). A systematic forward genetic analysis identified components of the Chlamydomonas circadian system. Genes Dev. 22: 918–930
98. Maul, J.E., Lilly, J.W., Cui, L., dePamphilis, C.W., Miller, W., Harris, E.H., and Stern, D.B. (2002). The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Plant Cell 14: 2659–2679
99. May, B.P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P.D., Roh, D., Pan, X., Stein, L., Freeling, M., Alexander, D., and Martienssen, R. (2003). Maize-targeted mutagenesis: A knockout resource for maize. Proc. Natl. Acad. Sci. USA 100: 11541–11546
100. McCarty, D.R., Latshaw, S., Wu, S., Suzuki, M., Hunter, C.T., Avigne, W.T., and Koch, K.E. (2013). Mu-seq: sequence-based mapping and identification of transposon induced mutations. PLoS One 8: e77172
101. McCarty, D.R., et al. (2005). Steady-state transposon mutagenesis in inbred maize. Plant J. 44: 52–61
102. McDonald, J.H. (2009). Handbook of Biological Statistics, 2nd ed. (Baltimore, MD: Sparky House Publishing).
103. Merchant, S.S., Kropat, J., Liu, B., Shaw, J., and Warakanont, J. (2012). TAG, you’re it! Chlamydomonas as a reference organism for understanding algal triacylglycerol accumulation. Curr. Opin. Biotechnol. 23: 352–363
104. Merchant, S.S., et al. (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-250
105. Meslet-Cladière, L., and Vallon, O. (2012). A new method to identify flanking sequence tags in chlamydomonas using 39-RACE. Plant Methods 8: 21
106. Miller, R., et al. (2010). Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol. 154: 1737–1752
107. Mintz, R.H., and Lewin, R.A. (1954). Studies on the flagella of algae. V. Serology of paralyzed mutants of Chlamydomonas. Can. J. Microbiol. 1: 65–67
108. Mitchell, D.R. (2004). Speculations on the evolution of 9+2 organelles and the role of central pair microtubules. Biol. Cell 96: 691–696
109. Moellering, E.R., and Benning, C. (2010). RNA interference silencing of a major lipid droplet protein affects lipid droplet size in Chlamydomonas reinhardtii. Eukaryot. Cell 9: 97–106
110. Molnar, A., Bassett, A., Thuenemann, E., Schwach, F., Karkare, S., Ossowski, S., Weigel, D., and Baulcombe, D. (2009). Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. Plant J. 58: 165–174
111. Murthy, U.M., Wecker, M.S., Posewitz, M.C., Gilles-Gonzalez, M.A., and Ghirardi, M.L. (2012). Novel FixL homologues in Chlamydomonas reinhardtii bind heme and O(2). FEBS Lett. 586: 4282-4288
112. Mus, F., Dubini, A., Seibert, M., Posewitz, M.C., and Grossman, A.R. (2007). Anaerobic acclimation in Chlamydomonas reinhardtii: anoxic gene expression, hydrogenase induction, and metabolic pathways. J. Biol. Chem. 282: 25475–25486
113. Nguyen, H.M., Baudet, M., Cuiné, S., Adriano, J.M., Barthe, D., Billon, E., Bruley, C., Beisson, F., Peltier, G., Ferro, M., and Li- Beisson, Y. (2011). Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: with focus on proteins involved in lipid metabolism. Proteomics 11: 4266–4273
114. Nguyen, R.L., Tam, L.W., and Lefebvre, P.A. (2005). The LF1 gene of Chlamydomonas reinhardtii encodes a novel protein required for flagellar length control. Genetics 169: 1415–1424
115. Ohlrogge, J.B., Kuhn, D.N., and Stumpf, P.K. (1979). Subcellular localization of acyl carrier protein in leaf protoplasts of Spinacia oleracea. Proc. Natl. Acad. Sci. USA 76: 1194–1198
116. O’Malley, R.C., and Ecker, J.R. (2010). Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J. 61: 928–940
117. Pazour, G.J., Agrin, N., Leszyk, J., and Witman, G.B. (2005). Proteomic analysis of a eukaryotic cilium. J. Cell Biol. 170: 103–113
118. Pazour, G.J., Dickert, B.L., Vucica, Y., Seeley, E.S., Rosenbaum, J.L., Witman, G.B., and Cole, D.G. (2000). Chlamydomonas IFT88 and its mouse homologue, polycystic kidney disease gene tg737, are required for assembly of cilia and flagella. J. Cell Biol. 151: 709–718
119. Philipps, G., Krawietz, D., Hemschemeier, A., and Happe, T. (2011). A pyruvate formate lyase-deficient Chlamydomonas reinhardtiistrain provides evidence for a link between fermentation and hydrogen production in green algae. Plant J. 66: 330–340
120. Piasecki, B.P., Diller, K.R., and Brand, J.J. (2009). Cryopreservation of Chlamydomonas reinhardtii: a cause of low viability at high cell density. Cryobiology 58: 103–109
121. Pootakham, W., Gonzalez-Ballester, D., and Grossman, A.R. (2010). Identification and regulation of plasma membrane sulfate transporters in Chlamydomonas. Plant Physiol. 153: 1653–1668
122. Qin, H., Rosenbaum, J.L., and Barr, M.M. (2001). An autosomal recessive polycystic kidney disease gene homolog is involved in intraflagellar transport in C. elegans ciliated sensory neurons. Curr. Biol. 11: 457–461
123. Randolph-Anderson, B.L., Boynton, J.E., Gillham, N.W., Harris, E.H., Johnson, A.M., Dorthu, M.P., and Matagne, R.F. (1993). Further characterization of the respiratory deficient dum-1 mutation of Chlamydomonas reinhardtii and its use as a recipient for mitochondrial transformation. Mol. Gen. Genet. 236: 235–244
124. Riekhof, W.R., Sears, B.B., and Benning, C. (2005). Annotation of genes involved in glycerolipid biosynthesis in Chlamydomonas reinhardtii: discovery of the betaine lipid synthase BTA1Cr. Eukaryot. Cell 4: 242–252
125. Sager, R., and Zalokar, M. (1958). Pigments and photosynthesis in a carotenoid-deficient mutant of Chlamydomonas. Nature 182: 98-100
126. Sanjaya, M., Miller, R., Durrett, T.P., Kosma, D.K., Lydic, T.A., Muthan, B., Koo, A.J., Bukhman, Y.V., Reid, G.E., Howe, G.A., Ohlrogge, J., and Benning, C. (2013). Altered lipid composition and enhanced nutritional value of Arabidopsis leaves following introduction of an algal diacylglycerol acyltransferase 2. Plant Cell 25: 677–693
127. Schmollinger, S., et al. (2014). Nitrogen-sparing mechanisms in Chlamydomonas affect the transcriptome, the proteome, and photosynthetic metabolism. Plant Cell 26: 1410–1435
128. Shockey, J., and Browse, J. (2011). Genome-level and biochemical diversity of the acyl-activating enzyme superfamily in plants. Plant J. 66: 143–160
129. Shockey, J.M., Fulda, M.S., and Browse, J.A. (2002). Arabidopsis contains nine long-chain acyl-coenzyme a synthetase genes that participate in fatty acid and glycerolipid metabolism. Plant Physiol. 129: 1710–1722
130. Shoemaker, D.D., Lashkari, D.A., Morris, D., Mittmann, M., and Davis, R.W. (1996). Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14: 450–456
131. Sizova, I., Fuhrmann, M., and Hegemann, P. (2001). A Streptomyces rimosus aphVIII gene coding for a new type phosphotransferase provides stable antibiotic resistance to Chlamydomonas reinhardtii. Gene 277: 221–229
132. Sizova, I., Greiner, A., Awasthi, M., Kateriya, S., and Hegemann, P. (2013). Nuclear gene targeting in Chlamydomonas using engineered zinc-finger nucleases. Plant J. 73: 873–882
133. Slaninová, M., Hroššová, D., Vlcek, D., and Wolfgang, W. (2008). Is it possible to improve homologous recombination in Chlamydomonas reinhardtii? Biologia 63: 941–946
134. Strizhov, N., Li, Y., Rosso, M.G., Viehoever, P., Dekker, K.A., and Weisshaar, B. (2003). High-throughput generation of sequence indexes from T-DNA mutagenized Arabidopsis thaliana lines. Biotechniques 35: 1164–1168
135. Tam, L.W., and Lefebvre, P.A. (1993). Cloning of flagellar genes in Chlamydomonas reinhardtii by DNA insertional mutagenesis. Genetics 135: 375–384
136. Terashima, M., Freeman, E.S., Jinkerson, R.E., and Jonikas, M.C. (2015). A fluorescence-activated cell sorting-based strategy for rapid isolation of high-lipid Chlamydomonas mutants. Plant J. 81: 147–159
137. Terashima, M., Specht, M., and Hippler, M. (2011). The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features. Curr. Genet. 57: 151–168
138. Toepel, J., Illmer-Kephalides, M., Jaenicke, S., Straube, J., May, P., Goesmann, A., and Kruse, O. (2013). New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. Plant Biotechnol. J. 11: 717–733
139. Tsai, C.H., Warakanont, J., Takeuchi, T., Sears, B.B., Moellering, E.R., and Benning, C. (2014). The protein Compromised Hydrolysis of Triacylglycerols 7 (CHT7) acts as a repressor of cellular quiescence in Chlamydomonas. Proc. Natl. Acad. Sci. USA 111: 15833-15838
140. Tulin, F., and Cross, F.R. (2014). A microbial avenue to cell cycle control in the plant superkingdom. Plant Cell 26: 4019–4038
141. Umen, J.G. (2011). Evolution of sex and mating loci: an expanded view from Volvocine algae. Curr. Opin. Microbiol. 14: 634–641
142. Urbański, D.F., Małolepszy, A., Stougaard, J., and Andersen, S.U. (2012). Genome-wide LORE1 retrotransposon mutagenesis and highthroughput insertion detection in Lotus japonicus. Plant J. 69: 731–741
143. 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., and Merchant, S.S. (2012). Systems and transsystem level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell 24: 3921–3948
144. Urzica, E.I., Vieler, A., Hong-Hermesdorf, A., Page, M.D., Casero, D., Gallaher, S.D., Kropat, J., Pellegrini, M., Benning, C., and Merchant, S.S. (2013). Remodeling of membrane lipids in ironstarved Chlamydomonas. J. Biol. Chem. 288: 30246–30258
145. Varshney, G.K., et al. (2013). A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome Res. 23: 727–735
146. Venken, K.J., Schulze, K.L., Haelterman, N.A., Pan, H., He, Y., Evans-Holm, M., Carlson, J.W., Levis, R.W., Spradling, A.C., Hoskins, R.A., and Bellen, H.J. (2011). MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes. Nat. Methods 8: 737–743
147. Voss, B., Meinecke, L., Kurz, T., Al-Babili, S., Beck, C.F., and Hess, W.R. (2011). Hemin and magnesium-protoporphyrin IX induce global changes in gene expression in Chlamydomonas reinhardtii. Plant Physiol. 155: 892–905
148. Wang, Y., Duanmu, D., and Spalding, M.H. (2011). Carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii: inorganic carbon transport and CO2 recapture. Photosynth. Res. 109: 115–122
149. Wang, Z.T., Ullrich, N., Joo, S., Waffenschmidt, S., and Goodenough, U. (2009). Algal lipid bodies: stress induction, purification, and biochemical characterization in wild-type and starchless Chlamydomonas reinhardtii. Eukaryot. Cell 8: 1856–1868
150. Weng, H., Molina, I., Shockey, J., and Browse, J. (2010). Organ fusion and defective cuticle function in a lacs1 lacs2 double mutant of Arabidopsis. Planta 231: 1089–1100
151. Wilfling, F., et al. (2013). Triacylglycerol synthesis enzymes mediate lipid droplet growth by relocalizing from the ER to lipid droplets. Dev. Cell 24: 384–399
152. Williams-Carrier, R., Stiffler, N., Belcher, S., Kroeger, T., Stern, D.B., Monde, R.A., Coalter, R., and Barkan, A. (2010). Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J. 63: 167–177
153. Winzeler, E.A., et al. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901–906
154. Wirschell, M., Zhao, F., Yang, C., Yang, P., Diener, D., Gaillard, A., Rosenbaum, J.L., and Sale, W.S. (2008). Building a radial spoke: flagellar radial spoke protein 3 (RSP3) is a dimer. Cell Motil. Cytoskeleton 65: 238–248
155. Yang, P., Diener, D.R., Yang, C., Kohno, T., Pazour, G.J., Dienes, J.M., Agrin, N.S., King, S.M., Sale, W.S., Kamiya, R., Rosenbaum, J.L., and Witman, G.B. (2006). Radial spoke proteins of Chlamydomonas flagella. J. Cell Sci. 119: 1165–1174
156. Yang, W., et al. (2014). Alternative acetate production pathways in Chlamydomonas reinhardtii during dark anoxia and the dominant role of chloroplasts in fermentative acetate production. Plant Cell 26: 4499–4518
157. Yoon, K., Han, D., Li, Y., Sommerfeld, M., and Hu, Q. (2012). Phospholipid:diacylglycerol acyltransferase is a multifunctional enzyme involved in membrane lipid turnover and degradation while synthesizing triacylglycerol in the unicellular green microalga Chlamydomonas reinhardtii. Plant Cell 24: 3708–3724
158. Zhang, J., Li, C., Wu, C., Xiong, L., Chen, G., Zhang, Q., and Wang, S. (2006). RMD: a rice mutant database for functional analysis of the rice genome. Nucleic Acids Res. 34: D745–D748
159. Zhang, R., Patena, W., Armbruster, U., Gang, S.S., Blum, S.R., and Jonikas, M.C. (2014). High-throughput genotyping of green algal mutants reveals random distribution of mutagenic insertion sites and endonucleolytic cleavage of transforming DNA. Plant Cell 26: 1398–1409
160. Zhao, L., Katavic, V., Li, F., Haughn, G.W., and Kunst, L. (2010). Insertional mutant analysis reveals that long-chain acyl-CoA synthetase 1 (LACS1), but not LACS8, functionally overlaps with LACS9 in Arabidopsis seed oil biosynthesis. Plant J. 64: 1048–1058
161. Zhao, T., Wang, W., Bai, X., and Qi, Y. (2009). Gene silencing by artificial microRNAs in Chlamydomonas. Plant J. 58: 157–164.