Microarray analysis confirms the specificity of a Chlamydomonas reinhardtii chloroplast RNA stability mutant

Plant Physiology

Volumn 137, Issue 2, 2005, Pages 534-544

  Erickson, Brian ^a   Stern, David B ^b   Higgs, David C ^a  

^a UNIVERSITY OF WISCONSIN PARKSIDE   (United States)

^b United States Department of Agriculture   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; PHOTOSYNTHESIS; PROTEINS; RNA;

CHLOROPLAST; MICROARRAY ANALYSIS; MITOCHONDRIAL GENES;

PLANTS (BOTANY);

NUCLEIC ACIDS; PHOTOSYNTHESIS; PLANTS; PROTEINS;

CHLAMYDOMONAS REINHARDTII;

ALGAL RNA; CHLOROPLAST RNA;

ANIMAL; ARTICLE; CHLAMYDOMONAS REINHARDTII; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; MUTATION; PHOTOSYNTHESIS;

ANIMALS; CHLAMYDOMONAS REINHARDTII; GENE EXPRESSION REGULATION; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOTOSYNTHESIS; RNA, ALGAL; RNA, CHLOROPLAST;

EID: 19044380495     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.053256     Document Type: Article

References (57)

1. Baena-Gonzalez E, Allahverdiyeva Y, Svab Z, Maliga P, Josse EM, Kuntz M, Maenpaa P, Aro EM (2003) Deletion of the tobacco plastid psbA gene triggers an upregulation of the thylakoid-associated NAD(P)H dehydrogenase complex and the plastid terminal oxidase (PTOX). Plant J 35: 704-716
2. Barkan A, Goldschmidt-Clermont M (2000) Participation of nuclear genes in chloroplast gene expression. Biochimie 82: 559-572
3. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al (2001) Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat Genet 29: 365-371
4. Chen X, Kindle K, Stern D (1993) Initiation codon mutations in the Chlamydomonas chloroplast petD gene result in temperature-sensitive photosynthetic growth. EMBO J 12: 3627-3635
5. Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81: 1991-1995
6. Danon A, Mayfield SP (1994) ADP-dependent phosphorylation regulates RNA-binding in vitro: implications in light-modulated translation. EMBO J 13: 2227-2235
7. Drager RG, Girard-Bascou J, Choquet Y, Kindle KL, Stern DB (1998) In vivo evidence for 5′Ø3′ exoribonuclease degradation of an unstable chloroplast mRNA. Plant J 13: 85-96
8. Drager RG, Higgs DC, Kindle KL, Stern DB (1999) 5′ to 3′ exoribo-nucleolytic activity is a normal component of chloroplast mRNA decay pathways. Plant J 19: 521-532
9. Drapier D, Girard-Bascou J, Stern DB, Wollman F-A (2002) A dominant nuclear mutation in Chlamydomonas identifies a factor controlling chloroplast mRNA stability by acting on the coding region of the atpA transcript. Plant J 31: 687-697
10. Drapier D, Girard-Bascou J, Wollman F-A (1992) Evidence for nuclear control of the expression of the atpA and atpB chloroplast genes in Chlamydomonas. Plant Cell 4: 283-295
11. Drapier D, Suzuki H, Levy H, Rimbault B, Kindle KL, Stern DB, Wollman F-A (1998) The chloroplast atpA gene cluster in Chlamydomonas reinhardtii, functional analysis of a polycistronic transcription unit. Plant Physiol 117: 629-641
12. Eberhard S, Draper D, Wollman F-A (2002) Searching limiting steps in the expression of chloroplast-encoded proteins: relations between gene copy number, transcription, transcript abundance and translation rate in the chloroplast of Chlamydomonas reinhardtii. Plant J 31: 149-160
13. Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210
14. Esposito D, Higgs DC, Drager RG, Stern DB, Girard-Bascou J (2001) A nucleus-encoded suppressor defines a new factor which can promote petD mRNA stability in the chloroplast of Chlamydomonas reinhardtii. Curr Genet 39: 40-48
15. Giege P, Hoffmann M, Binder S, Brennicke A (2000) RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria. EMBO Rep 1: 164-170
16. Girard-Bascou J, Pierre Y, Drapier D (1992) A nuclear mutation affects the synthesis of the chloroplast psbA gene product Chlamydomonas reinhardtii. Curr Genet 22: 47-52
17. Goldschmidt-Clermont M, Girard BJ, Choquet Y, Rochaix JD (1990) Transsplicing mutants of Chlamydomonas reinhardtii. Mol Gen Genet 223: 417-425
18. Gray MW, Boer PH (1988) Organization and expression of algal (Chlamydomonas reinhardtii) mitochondrial DNA. Philos Trans R Soc Lond B Biol Sci 319: 135-147
19. Grigull J, Mnaimneh S, Pootoolal J, Robinson M, Hughes T (2004) Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol 24: 5534-5547
20. Grivell LA, Artal-Sanz M, Hakkaart G, de Jong L, Nijtmans LGJ, van Oosterum K, Siep M, van der Spek H (1999) Mitochondrial assembly in yeast. FEBS Lett 452: 57-60
21. 6f complex. Plant Mol Biol 29: 921-932
22. Harris EH (1989) The Chlamydomonas Sourcebook. Academic Press, San Diego
23. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J (2000) A concise guide to cDNA microarray analysis. Biotechniques 29: 548-562
24. Higgs DC, Kuras R, Kindle KL, Wollman F-A, Stern DB (1998) Inversions in the Chlamydomonas chloroplast genome suppress a petD 5′ untranslated region deletion by creating functional chimeric mRNAs. Plant J 14: 663-671
25. Higgs DC, Shapiro RS, Kindle KL, Stern DB (1999) Small cis-acting sequences that specify secondary structures in a chloroplast mRNA are essential for RNA stability and translation. Mol Cell Biol 19: 8479-8491
26. Im CS, Zhang Z-D, Shrager J, Chang C-W, Grossman A (2003) Analysis of light and CO2 regulation in Chlamydomonas reinhardtii using genomewide approaches. Photosynth Res 75: 111-125
27. Jensen KH, Herrin DL, Plumley FG, Schmidt GW (1986) Biogenesis of photosystem II complexes: transcriptional, translational, and posttranslational regulation. J Cell Biol 103: 1315-1325
28. Kathir P, LaVoie M, Brazelton WJ, Haas NA, Lefebvre PA, Silflow CD (2003) Molecular map of the Chlamydomonas reinhardtii nuclear genome. Eukaryot Cell 2: 362-379
29. Kuchka MR, Goldschmidt-Clermont M, van Dillewijn J, Rochaix J-D (1989) Mutation in the Chlamydomonas nuclear NAC2 locus specifically affects stability of the chloroplast psbD transcript encoding polypeptide D2 of PSII. Cell 58: 869-876
30. Legen J, Kemp S, Krause K, Profanter B, Herrmann RG, Maier RM (2002) Comparative analysis of plastid transcription profiles of entire plastid chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries. Plant J 31: 171-188
31. Levy H, Kindle KL, Stern DB (1997) A nuclear mutation that affects the 3′ processing of several mRNAs in Chlamydomonas chloroplasts. Plant Cell 9: 825-836
32. Lilly JW, Maul JE, Stern DB (2002) The Chlamydomonas reinhardtii organellar genomes respond transcriptionally and post-transcriptionally to abiotic stress. Plant Cell 14: 2681-2706
33. Lilly JW, Maul JE, Stern DB (2002) The Chlamydomonas reinhardtii organellar genomes respond transcriptionally and post-transcriptionally to abiotic stimuli. Plant Cell 14: 2681-2706;
34. retraction Lilly JW, Maul JE, Stern DB (2004) Plant Cell 16: 785
35. Matsuo M, Obokata J (2002) Dual roles of photosynthetic electron transport in photosystem I biogenesis: light induction of mRNAs and chormatic regulation of post-mRNA level. Plant Cell Physiol 43: 1189-1197
36. Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, Harris EH, Stern DB (2002) The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Plant Cell 14: 2659-2679
37. Meurer J, Greveling C, Westhoff P, Reiss B (1998) The PAC protein affects the maturation of specific chloroplast mRNAs in Arabidopsis thaliana. Mol Gen Genet 258: 342-351
38. Mittelmeier TM, Dieckmann CL (1993) In vivo analysis of sequences necessary for CBP1-dependent accumulation of cytochrome b transcripts in yeast mitochondria. Mol Cell Biol 13: 4203-4213
39. Monde RA, Schuster G, Stern DB (2000) Processing and degradation of chloroplast mRNA. Biochimie 82: 573-582
40. Monod C, Goldschmidt-Clermont M, Rochaix J-D (1992) Accumulation of chloroplast psbB RNA requires a nuclear factor in Chlamydomonas reinhardtii. Mol Gen Genet 231: 449-459
41. Nagashima A, Hanaoka M, Motohashi R, Seki M, Shinozaki K, Kanamaru K, Takahashi H, Tanaka K (2004) DNA microarray analysis of plastid gene expression in an Arabidopsis mutant deficient in a plastid transcription factor sigma, SIG2. Biosci Biotechnol Biochem 68: 694-704
42. Pérez-Amador MA, Lidder P, Johnson MA, Landgraf J, Wisman E, Green PJ (2001) New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis. Plant Cell 13: 2703-2717
43. Pfannschmidt T (2003) Chloroplast redox signals: how photosynthesis controls its own genes. Trends Plant Sci 8: 33-41
44. Pfannschmidt T, Nilsson A, Allen JF (1999) Photosynthetic control of chloroplast gene expression. Nature 397: 625-628
45. Pfannschmidt T, Schütze K, Brost M, Oelmüller R (2001) A novel mechanism of nuclear photosynthesis gene regulation by redox signals from the chloroplast during photosystem stoichiometry adjustment. J Biol Chem 276: 36125-36130
46. Richly E, Dietzmann A, Biehl A, Kurth J, Laloi C, Apel K, Salamini F, Leister D (2003) Covariations in the nuclear chloroplast transcriptome reveal a regulatory master-switch. EMBO Rep 4: 491-498
47. Rochaix J-D, Kuchka M, Mayfield S, Schirmer-Rahire M, Girard-Bascou J, Bennoun P (1989) Nuclear and chloroplast mutations affect the synthesis or stability of the chloroplast psbC gene product in Chlamydomonas reinhardtii. EMBO J 8: 1013-1021
48. Rolland N, Dorne A-J, Amoroso G, Sültemeyer DF, Joyard J, Rochaix J-D (1997) Disruption of the plastid ycf10 open reading frame affects uptake of inorganic carbon in the chloroplast of Chlamydomonas. EMBO J 16: 6713-6726
49. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, et al (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378
50. Salvador ML, Klein U (1999) The redox state regulates RNA degradation in the chloroplast of Chlamydomonas reinhardtii. Plant Physiol 121: 1367-1374
51. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C (2003) Global RNA half-life analysis in Eschericia coli reveals positional patterns of transcript degradation. Genome Res 13: 216-223
52. Shepherd HS, Boynton JE, Gillham NW (1979) Mutations in nine chloroplast loci of Chlamydomonas affecting photosynthetic functions. Proc Natl Acad Sci USA 76: 1353-1357
53. Souret FF, Kastenmayer JP, Green PJ (2004) AtXrn4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15: 173-183
54. Stern DB, Radwanski ER, Kindle KL (1991) A 3′ stem/loop structure of the Chlamydomonas chloroplast atpB gene regulates mRNA accumulation in vivo. Plant Cell 3: 285-297
55. Wiesenberger G, Costanzo MC, Fox TD (1995) Analysis of the Saccharomyces cerevisiae mitochondrial COX3 mRNA 5′ untranslated leader: translational activation and mRNA processing. Mol Cell Biol 15: 3291-3300
56. Wollman F-A, Minai L, Nechushtai R (1999) The biogenesis and assembly of photosynthetic proteins in thylakoid membranes. Biochim Biophys Acta 1411: 21-85
57. Zerges W (2000) Translation of mRNAs encoded by chloroplast genomes. Biochimie 82: 583-601