Analysis of light and CO2 regulation in Chlamydomonas reinhardtii using genome-wide approaches

Photosynthesis Research

Volumn 75, Issue 2, 2003, Pages 111-125

  Im, Chung Soon ^a   Zhang, Zhaoduo ^a   Shrager, Jeffrey ^a   Chang, Chiung Wen ^a   Grossman, Arthur R ^a  

^a GEOPHYSICAL LABORATORY   (United States)

Author keywords

Carbon concentrating mechanism; Differential display; Global gene expression; High light; Microarray

Indexed keywords

ALGAE; CHLAMYDOMONAS REINHARDTII; CHLOROPHYTA; EUKARYOTA;

EID: 0037251317     PISSN: 01668595     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1022800630430     Document Type: Article

References (100)

1. Adamska I, Ohad I and Kloppstech K (1992) Synthesis of the early light-inducible protein is controlled by blue-light and related to light stress. Proc Natl Acad Sci USA 89: 2610-2613
2. Beckmann K, Dzuibany C, Biehler K, Fock H, Hell R, Migge A and Becker TW (1997) Photosynthesis and fluorescence quenching, and the mRNA levels of plastidic glutamine synthetase or of mitochondrial serine hydroxymethyltransferase (SHMT) in the leaves of the wild-type and of the SHMT-deficient stm mutant of Arabidopsis thaliana in relation to the rate of photorespiration. Planta 202: 379-386
3. Beier M and Hoheisel JD (2002) Analysis of DNA-microarrays produced by inverse in situ oligonucleotide synthesis. J Biotechnol 94: 15-22
4. Bhaya D, Vaulot D, Amin P, Takahashi AW and Grossman AR (2000) Isolation of regulated genes of the cyanobacterium Synechocystis sp strain PCC 6803 by differential display. J Bacteriol 182: 5692-5699
5. Bhaya D, Takahashi A and Grossman AR (2001) Light regutation of type IV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC6803. Proc Natl Acad Sci USA 98: 7540-7545
6. - transporter in the cyanobacterium Synechococcus sp. strain PCC 7942. FEBS Lett 430: 236-240
7. Bowtell DD (1999) Options available - from start to finish - for obtaining expression data by microarray. Nat Genet 21: 25-32
8. Brown PO and Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21: 33-37
9. Burke HB (2000) Discovering patterns in microarray data. Mol Diagn 5: 349-357
10. 2. Plant Mol Biol 31: 443-448
11. Castellino AM (1997) When the chips are down. Genome Res 7: 943-946
12. 2-inducible chloroplast envelope protein LIP-36 from Chlamydomonas reinhardtii. Plant Physiol 114: 265-273
13. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R and Childs G (1999) Making and reading microarrays. Nat Genet 21: 15-19
14. Cho RJ, FromontRacine M, Wodicka L, Feierbach B, Stearns T, Legrain P, Lockhart DJ and Davis RW (1998) Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc Natl Acad Sci USA 95: 3752-3757
15. Christopher DA (1996) Leaf development and phytochrome modulate the activation of psbD-psbC transcription by high-fluence blue light in barley chloroplasts. Photosynth Res 47: 239-251
16. Dantuma NP, Lindsten K, Glas R, Jellne M and Masucci MG (2000) Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysls in living cells. Nat Biotechnol 18: 538-543
17. Dargeviciute A, Roux C, Decreux A, Sitbon F and Perrot-Rechenmann C (1998) Molecular cloning and expression of the early auxin-responsive Aux/1AA gene family in Nicotiana tabacum. Plant Cell Physiol 39: 993-1002
18. DeRisi JL, Iyer VR and Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686
19. Diehn M and Relman DA (2001) Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions. Curr Opin Microbiol 4: 95-101
20. Dietmaier W, Fabry S, Huber H and Schmitt R (1995) Analysis of a family of ypt genes and their products from Chlamydomonas reinhardtii. Gene 158: 41-50
21. Dionisiosese ML, Fukuzawa H and Miyachi S (1990) Light-induced carbonic-anhydrase expression in Chlamydomonas reinhardtii. Plant Physiol 94: 1103-1110
22. Dolganov NAM, Bhaya D and Grossman AR (1995) Cyanobacterial protein with similarity to the chlorophyll a/b binding-proteins of higher-plants: evolution and regulation. Proc Natl Acad Sci USA 92: 636-640
23. Duggan DJ, Bittner M, Chen Y, Meltzer P and Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet 21: 10-14
24. Eisen MB and Brown PO (1999) DNA arrays for analysis of gene expression. Methods Enzymot 303: 179-205
25. Eisen MB, Spellman PT, Brown PO and Botstein D (1998) Ctuster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868
26. Epstein CB and Butow RA (2000) Microarray technology - enhanced versatility, persistent challenge. Curr Opin Biotechnol 11: 36-41
27. 2-induced polypeptide in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 93: 12031-12034
28. 2-induced mitochondrial carbonic anhydrase in Chlamydomonas reinhardtii. Plant Physiol 116: 637-641
29. Escoubas JM, Lomas M, Laroche J and Falkowski PG (1995) Light-intensity regulation of cab gene-transcription is signaled by the redox state of the plastoquinone pool. Proc Natl Acad Sci USA 92: 10237-10241
30. Finkelstein D, Ewing R, Gollub J, Sterky F, Cherry JM and Somerville S (2002) Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium. Plant Mol Biol 48: 119-131
31. Fujiwara S, Fukuzawa H, Tachiki A and Miyachi S (1990) Structure and differential expression of two genes encoding carbonic anhydrase in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 87: 9779-9783
32. Fukuzawa H, Fujiwara S, Tachiki A and Miyachi S (1990) Nucleotide sequences of two genes CAH1 and CAH2 which encode carbonic anhydrase polypeptides in Chlamydomonas reinhardtii. Nucleic Acids Res 18: 6441-6442
33. Fukuzawa H, Suzuki E, Komukai Y and Miyachi S (1992) A gene homologous to chloroplast carbonic anhydrase (icfA) is essential to photosynthetic carbon dioxide fixation by Synechococcus PCC7942. Proc Natl Acad Sci USA 89: 4437-4441
34. 2 availability. Proc Natl Acad Sci USA 98: 5347-5352
35. Funk C, and Vermaas W (1999) A cyanobacterial gene family coding for single-helix proteins resembling part of the light-harvesting proteins from higher plants. Biochemistry 38: 9397-9404
36. Graßes T, Grimm B, Koroleva O and Jahns P (2001) Loss of alpha-tocopherol in tobacco plants with decreased geranylgeranyl reductase activity does not modify photosynthesis in optimal growth conditions but increases sensitivity to high-light stress. Planta 213: 620-628
37. Harkin DP (2000) Uncovering functionally relevant signaling pathways using microarray-based expression profiling. Oncologist 5: 501-507
38. Hautefort I and Hinton JC (2000) Measurement of bacterial gene expression in vivo. Philos Trans R Soc London B Biol Sci 355: 601-611
39. Havaux M, Guedeney G, He Q and Grossman AR (2003) Elimination of high-light-inducible polypeptides related to eukaryotic chlorophyll a/b binding proteins results in aberrant photoacclimation in Synechocystis PCC 6803. Biochim Biophys Acta (in press)
40. He Q, Dolganov N, Bjorkman O, Grossman AR (2001) The high light-inducible polypeptides in Synechocystis PCC6803. Expression and function in high light. J Biol Chem 276: 306-14
41. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N and Quackenbush J (2000) A concise guide to cDNA microarray analysis. Biotechniques 29: 548-556
42. Im CS and Grossman AR (2002) Identification and regulation of high light-induced genes in Chlamydomonas reinhardtii. The Plant J 30: 301-313
43. 2+-dependent nuclease of Arabidopsis that is similar to staphylococcal nuclease. Biochim et Biophys Acta-Gene Struct Express 1491: 267-272
44. Jansson S, Andersson J, Kim SJ and Jackowski G (2000) An Arabidopsis thaliana protein homologous to cyanobacterial high-light-inducible proteins. Plant Mol Biol 42: 345-351
45. Kadyrzhanova DK, Vlachonasios KE, Ververidis P and Dilley DR (1998) Molecular cloning of a novel heat induced chilling tolerance related cDNA in tomato fruit by use of mRNA differential display. Plant Mol Biol 36: 885-895
46. 2 concentrating mechanisms in photosynthetic microorganisms. Ann Rev Plant Physiol Plant Mol Biol 50: 539-570
47. 2. EMBO J 17: 1208-1216
48. Karpinski S, Escobar C, Karpinska B, Creissen G and Mullineaux PM (1997) Photosynthetic electron transport regulates the expression of cytosolic ascorbate peroxidase genes in Arabidopsis during excess light stress. Plant Cell 9: 627-640
49. Kallioniemi OP (2001) Biochip technologies in cancer research. Ann Med 33: 142-147
50. Kauraniemi P, Barlund M, Monni O and Kalfioniemi A (2001) New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res 61: 8235-8240
51. Kozaki A and Takeba G (1996) Photorespiration protects C3 plants from photooxidation. Nature 384: 557-560
52. Kurella M, Hsiao LL, Yoshida T, Randall JD, Chow G, Sarang SS, Jensen RV and Gullans SR (2001) DNA microarray analysis of complex biologic processes. J Am Soc Nephrol 12: 1072-1078
53. Kurian KM, Watson CJ and Wyllie AH (1999) DNA chip technology. J Pathol 187: 267-271
54. Lashkari DA, McCusker JH and Davis RW (1997) Whole genome analysis: experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR. Proc Natl Acad Sci USA 94: 8945-8947
55. Lee ML, Kuo FC, Whitmore GA and Sklar J (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 97: 9834-9839
56. Li HM, Kaneko Y and Keegstra K (1994) Molecular-cloning of a chloroplastic protein associated with both the envelope and thylakoid membranes. Plant Mol Biol 25: 619-632
57. Liang P and Pardee AB (1992) Differential display of eukaryotic mRNA by means of the polymerase chain-reaction. Science 257: 967-971
58. Lipshutz RJ, Fodor SP, Gingeras TR and Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21: 20-24
59. Metzlaff MM, OD Cluster PD and Flavell RB (1997) RNA-mediated RNA degradation and chalcone synthase A silencing in Petunia. Cell 88: 845-854
60. Mi H, Endo T, Schrelber U, Ogawa T and Asada K (1994) NAD(P)H dehydrogenase-dependent cyclic electron flow around Photosystem-I in the cyanobacterium Synechocystis PCC-6803: a study of dark-starved cells and spheroplasts. Plant Cell Physiol 35: 163-173
61. Mittler R and Lam E (1997) Characterization of nuclease activities and DNA fragmentation induced upon hypersensitive response cell death and mechanical stress. Plant Mol Biol 24: 209-221
62. Montane MH, Tardy F, Kloppstech K and Havaux M (1998) Differential control of xanthophylls and light-induced stress proteins, as opposed to light-harvesting chlorophyll a/b proteins, during photosynthetic acclimation of barley leaves to light irradiance. Plant Physiol 118: 227-235
63. 2 to increase the efficiency of photosynthetic carbon fixation? Plant Physiol 119: 9-16
64. 2 concentrating mechanism. Plant Physiol 89: 897-903
65. Moseley J, Quinn J, Eriksson M and 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. EMBO J 19: 2139-2151
66. Moseley JL, Page MD, Alder NP, Eriksson M, Qinn J, Soto F, Theg SM, Hippler M and Merchant S (2002) Reciprocal expression of two candidate di-iron enzymes affecting Photosystem I and light harvesting complex accumulation. Plant Cell 14: 673-688
67. Muramoto Y, Watanabe A, Nakamura T and Takabe T (1999) Enhanced expression of a nuclease gene in leaves of barley plants under salt stress. Gene 234: 315-321
68. O'Mahony PJ and Oliver MJ (1999) Characterization of a desiccation-responsive small GTP-binding protein (Rab2) from the desiccation-tolerant grass Sporobolus stapfanus. Plant Mol Biol 39: 809-821
69. Ogawa M, Kusano T, Koizumi N, Katsumi M and Sano H (1999) Gibberellin-responsive genes: high level of transcript accumulation in leaf sheath meristematic tissue from Zea mays L. Plant Mol Biol 40: 645-657
70. Ohkawa H, Pakrasi HB and Ogawa T (2000) Two types of functionally distinct NAD(P)H dehydrogenases in Synechocystis sp. strain PCC6803. J Biol Chem 275: 31630-31634
71. Omata T, Price GD, Badger MR, Okamura M, Gehta S and Ogawa T (1999) Identification of an ATP-binding cassette transporter involved in bicarbonate uptake in the cyanobacterium Synechococcus sp. strain PCC 7942. Proc Natl Acad Sci USA 96: 13571-13576
72. Osmond CB (1981) Photo-respiration and photoinhibition. Some implications for the energetics of photosynthesis. Biochim et Biophys Acta 639: 77-98
73. Osmond B, Badger M, Maxwell K, Bjorkman O and Leegood R (1997) Too many photons: Photorespiration, photoinhibition and photooxidation. Trends Plant Sci 2: 119-121
74. Pallen MJ (1999) Microbial genomes. Mol Microbiol 32: 907-912
75. Petracek ME, Dickey LF, Nguyen TT, Gatz C, Sowinski DA, Allen GC and Thompson WF (1998) Ferredoxin-1 mRNA is destabilized by changes in photosynthetic electron transport. Proc Natl Acad Sci USA 95: 9009-9013
76. Petrik J (2001) Microarray technology: the future of blood testing? Vox Sang 80: 1-11
77. Pfeffer SR (2001) Rab GTPases: specifying and deciphering organelle identity and function. Trends Cell Biol 11: 487-491
78. Quinn JM, Eriksson M, Moseley JL, Merchant S (2002) Oxygen deficiency responsive gene expression in Chlamydomonas reinhardtii through a copper-sensing signal transduction pathway. Plant Physiol 128: 463-471
79. Richmond T and Somerville S (2000) Chasing the dream: plant EST microarrays. Curr Opin Plant Biol 3: 108-116
80. Rudert F, Ge L and Ilag LL (2000) Functional genomics with protein-protein interactions. Biotechnol Annu Rev 5: 45-86
81. Sambrook J, Fritsch EF and Maniatis T (1989) Molecular Cloning, a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
82. Schaller A, Schmid J and Amrhein N (1992) Plant cDNA similar to a bacterial plasmid partition locus. Plant Physiol 99: 777-778
83. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E and Davis RW (1998) Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol 16: 301-306
84. Schirch L (1982) Serine hydroxymethyltransferase. Adv Enzymol Rel Areas Mol Biol 53: 83-112
85. Sherlock G (2000) Analysis of large-scale gene expression data. Curr Opin Immunol 12: 201-205
86. Shibata M, Katoh H, Sonoda M, Ohkawa H, Shimoyama M, Fukuzawa H, Kaplan A and Ogawa T (2002) Genes essential to sodium-dependent bicarbonate transport in cyanobacteria: function and phylogenetic analysis. J Biol Chem 277: 28981-28986
87. 2-requiring mutant of Chlamydomonas reinhardii. Plant Physiol 73: 273-276
88. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D and Futcher B (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297
89. Tanaka R, Oster U, Kruse E, Rudiger W and Grimm B (1999) Reduced activity of geranylgeranyl reductase leads to loss of chlorophyll and tocopherol and to partially geranylgeranylated chlorophyll in transgenic tobacco plants expressing antisense RNA for geranylgeranyl reductase. Plant Physiol 120: 695-704
90. Toguri T, Muto S and Miyachi S (1986) Biosynthesis and intracellular processing of carbonic anhydrase in Chlamydomonas reinhardtii. Eur J Biochem 158: 443-450
91. 2-flux mechanism operating via pH-polarity in Hydrilla verticillata leaves with C-3 and C-4 photosynthesis. Photosynth Res 68: 81-88
92. Villand P, Eriksson M and Samuelsson G (1997) Carbon dioxide and light regulation of promoters controlling the expression of mitochondrial carbonic anhydrase in Chlamydomonas reinhardtii. Biochem J 327: 51-57
93. Watson SJ, Meng F, Thompson RC and Akil H (2000) The 'chip' as a specific genetic tool. Biol Psychiatry 48: 1147-1156
94. Wodicka L, Dong H, Mittmann M, Ho MH and Lockhart DJ (1997) Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 15: 1359-1367
95. Wu J, Neimanis S and Heber U (1991) Photorespiration is more effective than the Mehler reaction in protecting the photosynthetic apparatus against photoinhibition. Botanica Acta 104: 283-291
96. Xiang Y, Zhang J and Weeks DP (2001) The Cia5 gene controls formation of the carbon concentrating mechanism in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 98: 5341-5346
97. Xu H, Vavilin D, Funk C and Vermaas W (2002) Small Cab-like proteins regulating tetrapyrrole biosynthesis in the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol Biol 49: 149-160
98. Yang YH, Buckley MJ, Luu P, and Speed TP (2001) Normalization for cDNA microarray data. Technical 589, Department of Statistics, University of California, Berkeley
99. Zhao J, Williams CC and Last RL (1998) Induction of Arabidopsis tryptophan pathway enzymes and camalexin by amino acid starvation, oxidative stress, and an abiotic elicitor. Plant Cell 10: 359-370
100. Zwick MB, Shen J and Scott JK (1998) Phage-displayed peptide libraries. Curr Opin Biotechnol 9: 427-436