Insertional mutagenesis as a tool to study genes/functions in chlamydomonas

Advances in Experimental Medicine and Biology

Volumn 616, Issue , 2007, Pages 77-89

  Galván, Aurora ^a   González Ballester, David ^a,b   Fernández, Emilio ^a  

^a UNIVERSITY OF CÓRDOBA   (Spain)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BLEOMYCIN; PAROMOMYCIN; SPECTINOMYCIN;

CELL TRANSFORMATION; CHLAMYDOMONAS; DATA BASE; DIRECTED MOLECULAR EVOLUTION; FUNCTIONAL GENOMICS; GENE DISRUPTION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE INSERTION; GENE SILENCING; GENETIC ANALYSIS; GENETIC SCREENING; GENETIC SELECTION; GENETICS; HOMOLOGOUS RECOMBINATION; MUTAGENESIS; MUTANT; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RNA INTERFERENCE; RNA TRANSLATION; WILD TYPE; ANIMAL; CHLAMYDOMONAS REINHARDTII; GENE; PHOTOSYNTHESIS; PHYSIOLOGY;

ALGAE; ANIMALIA; CHLAMYDOMONAS; CHLAMYDOMONAS REINHARDTII; FUNGI;

ANIMALS; CHLAMYDOMONAS REINHARDTII; GENE EXPRESSION REGULATION; GENES; MUTAGENESIS, INSERTIONAL; PHENOTYPE; PHOTOSYNTHESIS;

EID: 38549143785     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-0-387-75532-8_7     Document Type: Review

References (83)

1. Harris EH. Chlamydomonas as a model organism. Annu Rev Plant Physiol Plant Mol Biol 2001; 52:363-406.
2. Gutman BL, Nigyogi KK. Chlamydomonas and Arabidopsis: A dynamic duo. Plant Physiol 2004; 135:607-610.
3. Kathir P, LaVoie M, Brazelton WJ et al. Molecular map of the Chlamydomonas reinhardtii nuclear genome. Eukaryot Cell 2003; 2:362-379.
4. Li JB, Lin SP, Jia HG et al. Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III. J Eukaryotic Microbiology 2003; 50:145-155.
5. Boyton JE, Gillham NW, Harris EH et al. Chloroplast transformation in Chlamydomonas with high velocity microprojectiles. Science 1988; 240:1534-1538.
6. Kindle KL. Nuclear transformation: Technology and applications. In: Rochaix JD et al, eds. The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas. Kluwer Academic Publishers, 1998:41-61.
7. Randolph-Anderson BL, Boynton JE, Gillham NW et al. Further characterization of the respiratory deficient dum-1 mutation of Chlamydomonas reinhardtii and its use as a recipient for mitochondrial transformation. Mol Gen Genet 1993; 236:235-244.
8. Remade C, Cardol P, Coosemans N et al. High-efficiency biolistic transformation of Chlamydomonas mitochondria can be used to insert mutations in complex I genes. Proc Natl Acad Sci USA 2006; 103:4771-4776.
9. Dent R, Haglund C, Chin B et al. Functional genomics of eukaryotic photosynthesis using insertional mutagenesis of Chlamydomonas reinhardtii. Plant Physiol 2005; 137:545-556.
10. González-Ballester D, de Montaigu A, Higuera JJ et al. Functional genomics of the regulation of the nitrate assimilation pathway in Chlamydomonas. Plant Physiol 2005; 137:522-533.
11. Harris EH. The Chlamydomonas Sourcebook. New York: Academic Press, 1989.
12. Rochaix JD. Chlamydomonas reinhardtii as the photosystthetic yeast. Annu Rev Genet 1995; 29:209-230.
13. Rochaix JD. Chlamydomonas, a model system for studying the assembly and dynamics of photosynthetic complexes. FEBS Lett 2002; 529:34-38.
14. Dutcher SK. Flagellar assembly in two hundred and fifty easy-to-follow steps. Trends Genet 1995; 11:398-404.
15. Rosembaum JL, Cole DC, Diener DR. Intraflagellar transport; the eyes have it. J Cell Biol 1999; 144:385-388.
16. Silflow C, Lefebvre PA. Assembly and motility of eukaryotic cilia and flagella: Lessons from Chlamydomonas reinhardtii. Plant Physiol 2001; 127:1500-1507.
17. Grossman A, Takahashi H, Macronutrient utilization by photosynthetic eukaryotes and the fabric of interactions. Annu Rev Plant Physiol Plant Mol Biol 2001; 52:163-210.
18. Galván A, Fernández E. Eukaryotic nitrate and nitrite transport. Cell Mol Life Sci 2001; 58:225-233.
19. Mittag M, Wagner V. The circadian clock of the unicellular eukaryotic model organism Chlamydomonas reinhardtii. Biol Chem 2003; 384:689-695.
20. Breton G, Kay SA. Circadian rhythms lit up in Chlamydomonas. Genome Biol 2006; 7:215.
21. Ferris PJ, Goodenough UW. Mating type in Chlamydomonas is specified by mid, the minus-dominance gene. Genetics 1997; 146:859-869.
22. In: Rochaix JD, Goldschmidt-Clermont M, Merchant S, eds. The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas. Dordrecht: Kluwer, 1998.
23. Fernández E, Galván A, Quesada A. Nitrogen assimilation and its regulation. In: Rochaix JD, Goldschmidt-Clermont M, Merchant S, eds. The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas. Dordrecht: Kluwer, 1998:637-659.
24. Moseley JL, Chang CW, Grossman AR. Genome-based approaches to understanding phosphorus deprivation responses and PSR1 control in Chlamydomonas reinhardtii. Eukaryot Cell 2006; 5:26-44.
25. Zhang Z, Shrager J, Jain M et al. Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryotic Cell 2004; 3:1331-1348.
26. Pollock SV, Pootakham W, Shibagaki N et al. Insights into the acclimation of Chlamydomonas reinhardtii to sulfur deprivation. Photosynth Res 2005; 86:475-489.
27. Rexach J, Fernández E, Galván A. The Chlamydomonas reinhardtii Nar1 gene encodes a chloroplast membrane protein involved in nitrite transport. Plant Cell 2000; 12:1441-1453.
28. Mariscal V, Moulin P, Orsel M et al. Differential Regulation of the Chlamydomonas Nar1 gene family by carbon and nitrogen. Protist 2006; 157:421-433.
29. 2-responsive genes regulated by CCM1 controlling a carbon-concentrating mechanism in Chlamydomonas reinhardtii. Plant Physiol 2004; 135:1595-1607.
30. Quesada A, Galván A, Schnell R et al. Five nitrate assimilation related loci are clustered in Chlamydomonas reinhardtii. Mol Gen Genet 1993; 240:387-394.
31. Quesada A, Galván A, Fernández E. Identification of nitrate transporter genes in Chlamydomonas reinhardtii. Plant J 1994; 5:407-419.
32. Galván A, Quesada A, Fernández E. Nitrate and nitrite are transported by different specific transport systems and by a bispecific transporter in Chlamydomonas reinhardtii. J Biol Chem 1996; 271:2088-2092.
33. Zhou JJ, Fernández E, Galván A et al. A high affinity nitrate transport system from Chlamydomonas requires two gene products. FEBS Lett 2000; 466:225-227.
34. Tong Y, Zhou JJ, Li ZS et al. A two-component high-affinity nitrate uptake system in barley. Plant J 2005; 41:442-450.
35. Okamoto M, Kumar A, Li W et al. High-affinity nitrate transport in roots of Arabidopsis depends on expression of the NAR2-like gene AtNRT3.1. Plant Physiol 2006; 140:1036-1046.
36. Zein LE, Omran H, Bouvagnet P. Lateralization defects and ciliary dyskinesia: Lessons from algae. Trends Genet 2003; 19:162-167.
37. Snell WJ, Pan J, Wang Q. Cilia and flagella revealed: From flagellar assembly in Chlamydomonas to human obesity disorders. Cell 2004; 117:693-697.
38. Pazour G, Agrin N, Leszyk J et al. Proteomic analysis of a eukaryotic cilium. J Cell Biol 2005; 170:103-113.
39. Gfeller RP, Gibbs M. Fermentative metabolism of Chlamydomonas reinhardtii: I. Analysis of fermentative products from starch in dark and light. Plant Physiol 1984; 75:212-218.
40. Hemschemeier A, Happe T. The exceptional photofermentative hydrogen metabolism of the green alga Chlamydomonas reinhardtii. Biochem Soc Trans 2005; 33:39-41.
41. León-Bañares R, González-Ballester D, Galván A et al. Transgenic microalgae as green cell-factories. Trends Biotechnol 2004; 22:45-52.
42. 2 regulation in Chlamydomonas reinhardtii using genome-wide approaches. Photosynth Res 2003; 75:111-125.
43. Kucho K, Okamoto K, Tabata S et al. Identification of novel clock-controlled genes by cDNA macroarray analysis in Chlamydomonas reinhardtii. Plant Mol Biol 2005; 57:889-906.
44. Abe J, Kubo T, Takagi Y et al. The transcriptional program of synchronous gametogenesis in Chlamydomonas reinhardtii. Curr Genet 2004; 46:304-315.
45. Prieto R, Fernández E. Toxicity of and mutagenesis by chlorate are independent of nitrate reductase activity in Chlamydomonas reinhardtii. Mol Gen Genet 1993; 237:429-438.
46. Ranum LPW, Thompson MD, Schloss JA et al. Mapping flagellar genes in Chlamydomonas using restriction fragment length polymorphisms. Genetics 1988; 120:109-122.
47. Rymarquis LA, Handley JM, Thomas M et al. Beyond complementation: Map-based cloning in Chlamydomonas reinhardtii. Plant Physiol 2005; 137:557-566.
48. Dykxhoorn DM, Novina CD, Sharp PA. Killing the messenger: Short RNAs that silence gene expression. Nat Rev Mol Cell Biol 2003; 4:457-467.
49. Waterhouse PM, Helliwell CA. Exploring plant genomes by RNA-induced gene silencing. Nat Rev Genet 2003; 4:29-38.
50. Cerutti H. RNA interference: Traveling in the cell and gaining functions? Trends Genet 2003; 19:39-46.
51. Schroda M. RNA silencing in Chlamydomonas: Mechanisms and tools. Curr Genet 2006; 49:69-84.
52. Fuhrmann M, Stahlberg A, Govorunova E et al. The abundant retinal protein of the Chlamydomonas eye is not the photoreceptor for phototaxis and photophobic responses. J Cell Sci 2001; 114:3857-3863.
53. Rohr J, Sarkar N, Balenger S et al. Tandem inverted repeat system for selection of effective transgenic RNAi strains in Chlamydomonas. Plant J 2004; 40:611-621.
54. Nelson JA, Lefebvre PA. Targeted disruption of the NIT8 gene in Chlamydomonas reinhardtii. Mol Cell Biol 1995; 15:5762-5769.
55. Sodeinde OA, Kindle KL. Homologous recombination in the nuclear genome of Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 1993; 90:9199-9203.
56. Zorin B, Hegemann P, Sizova I. Nuclear-gene targeting by using single-stranded DNA avoids illegitimate DNA integration in Chlamydomonas reinhardtii. Eukaryotic Cell 2005; 4:1264-1272.
57. Cenkci B, Petersen JL, Small GD. REX1, a novel gene required for DNA repair. J Biol Chem 2003; 278:22574-22577.
58. Tam LW, Lefebvre PA. Cloning of flagellar in Chlamydomonas reinhardtii by DNA insertional mutagenesis. Genetics 1993; 135:375-384.
59. Pazour GJ, Sineshchekov OA, Witman GB. Mutational analysis of the phototransduction pathway of Chlamydomonas reinhardtii. J Cell Biol 1995; 131:427-440.
60. Prieto R, Dubus A, Galván A et al. Isolation and characterization of two regulatory mutants for nitrate assimilation in Chlamydomonas reinhardtii. Mol Genet Genom 1996; 251:461-471.
61. Davies JP, Yildiz FH, Grossman A. Sac1, a putative regulator that is critical for survival of Chlamydomonas reinhardtii during sulfur deprivation. EMBO J 1996; 15:2150-2159.
62. 2-responsive gene Cah1, encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii. Plant Cell 2004; 16:1466-1477.
63. Zabawinski C, van den Koornhuyse N, d'Hulst N et al. Starchless mutants of Chlamydomonas reinhardtii lack the small subunit of a heterotetrameric ADP-glucose pyrophosphorylase. J Bacteriol 2001; 183:1069-1077.
64. Posewitz MC, Smolinski SL, Kanakagiri S et al. Hydrogen photoproduction is attenuated by disruption of an isoamylase gene in Chlamydomonas reinhardtii. Plant Ceil 2004; 16:2151-2163.
65. Horst CJ, Fishkind DJ, Pazour GJ et al. An insertional mutant of Chlamydomonas reinhardtii with defective microtubule positioning. Cell Motil Cytoskeleton 1999; 44:143-154.
66. Pazour GJ, Witman GB. Forward and reverse genetic analysis of microtubule motors in Chlamydomonas. Methods 2000; 22:285-298.
67. Kindle KL, Schnell RA, Fernández E et al. Stable nuclear transformation of Chlamydomonas using the Chlamydomonas gene for nitrate reductase. J Cell Biol 1989; 109:2589-2601.
68. Kindle KL. High-frequency nuclear transformation of Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 1990; 87:1228-1232.
69. Shimogawara K, Fujiwara S, Grossman A et al. High-efficiency transformation of Chlamydomonas reinhardtii by electroporation. Genetics 1998; 148:1821-1828.
70. Alonso JM, Stepanova AN, Leisse T H et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 2003; 301:653-657.
71. Prieto R, Pardo JM, Niu X et al. Salt-sensitive mutants of Chlamydomonas reinhardtii isolated after insertional tagging. Plant Physiol 1996; 112:99-104.
72. Cerutti H, Johnson AM, Gillham NW et al. A eubacterial gene conferring spectinomycin resistance on Chlamydomonas reinhardtii: Integration into the nuclear genome and gene expression. Genetics 1997; 145:97-110.
73. Sizova I, Fuhrmann M, Hegemann P. A Streptomyces rimosus aphVIII gene coding for a new type phosphotransferase provides stable antibiotic resistance to Chlamydomonas reinhardtii. Gene 2001; 277:221-229.
74. Hecht SM. Bleomycin: New perspectives on the mechanism of action. J Nat Prod 2000; 63:158-168.
75. Stevens DR, Rochaix JD, Purton S. The bacterial phleomycin resistance gene ble as a dominant selectable marker in Chlamydomonas. Mol Gen Genet 1996; 251:23-30.
76. Liu YG, Whittier RF. Thermal asymmetric interlaced PCR: Automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 1995; 25:674-681.
77. Liu YG, Mitsukawa N, Oosumi T et al. Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 1995; 8:457-463.
78. González-Ballester D, de Montaigu A, Galván A et al. Restriction enzyme site directed amplification (RESDA)-PCR: A tool to identify regions flanking a marker DNA. Anal Biochem 2005; 340:330-335.
79. Harrison RW, Miller JC, D'Souza MJ et al. Easy gene walking. Biotechniques 1997; 22:650-653.
80. González-Ballester D. Genómica functional de la señalización por amonio y nitrato, y caracterización de genes para el transporte de amonio en Chlamydomonas. PhD Thesis 2005, (Universidad de Córdoba, Spain).
81. Peréz-Alegre M, Dubus A, Fernández E. REM1, a new type of long terminal repeat retrotransposon in Chlamydomonas reinhardtii. Mol Cell Biol 2005; 25:10628-10638.
82. 2-concentrating mechanism. Planta 2003; 217:102-112.
83. Polle JE, Kanakagiri SD, Melis A. Tla1, a DNA insertional transformant of the green alga Chlamydomonas reinhardtii with a truncated light-harvesting chlorophyll antenna size. Planta 2003; 217:49-59.