The diurnal logic of the expression of the chloroplast genome in chlamydomonas reinhardtii

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Idoine, Adam D ^a   Boulouis, Alix ^a   Rupprecht, Jens ^a   Bock, Ralph ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL ORGANELLE; CHLAMYDOMONAS REINHARDTII; CHLOROPLAST GENOME; CIRCADIAN RHYTHM; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; LIGHT DARK CYCLE; MICROARRAY ANALYSIS; MITOCHONDRION; NONHUMAN; NORTHERN BLOTTING; PHOTOSYNTHESIS; PSAB GENE; PSBB GENE; QUANTITATIVE ANALYSIS; RNA TRANSLATION; RPOA GENE; RPOC2 GENE; RPS2 GENE; RPS3 GENE; CHLOROPLAST; CHLOROPLAST GENE; GENETICS; METABOLISM; THYLAKOID;

CHLAMYDOMONAS REINHARDTII;

CHLAMYDOMONAS REINHARDTII; CHLOROPLASTS; GENE EXPRESSION REGULATION, PLANT; GENES, CHLOROPLAST; GENOME, CHLOROPLAST; PHOTOSYNTHESIS; THYLAKOIDS; TRANSCRIPTION, GENETIC;

EID: 84907494013     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108760     Document Type: Article

References (38)

1. Harris EH (2001) Chlamydomonas as a model organism. Annu Rev Plant Physiol Plant Mol Biol 52: 363-406.
2. Rochaix J-D (2001) Assembly, functions, and dynamics of the photosynthetic machinery in Chlamydomonas reinhardtii. Plant Physiol 127: 1394-1398.
3. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-251.
4. Day A, Goldschmidt-Clermont M (2011) The chloroplast transformation toolbox: selectable markers and marker removal. Plant Biotechnol J 9: 540-553.
5. Terashima M, Specht M, Hippler M (2011) The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features. Curr Genet 57: 151-168.
6. 2production in microorganisms. Appl Microbiol Biotechnol 72: 442-449.
7. Hu Q, Sommerfeld M, Jarvis E, Ghirardi M, Posewitz M, et al. (2008) Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J 54: 621-639.
8. Beer LL, Boyd ES, Peters JW, Posewitz MC (2009) Engineering algae for biohydrogen and biofuel production. Curr Op Biotechnol 20: 264-271.
9. 2 production via Chlamydomonas reinhardtii. Trends Biotechnol 29: 595-600.
10. Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, et al. (2002) The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Plant Cell 14: 2659-2679.
11. Shimada H, Sugiura M (1991) Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Res 19: 983-995.
12. Shiina T, Tsunoyama Y, Nakahira Y, Khan MS (2005) Plastid RNA polymerases, promoters, and transcription regulators in higher plants. Int Rev Cytol 244: 1-68.
13. Liere K, Börner T (2007) Transcription and transcriptional regulation in plastids. Top Curr Genet 19: 121-174.
14. Carter ML, Smith AC, Kobayashi H, Purton S, Herrin DL (2004) Structure, circadian regulation and bioinformatic analysis of the unique sigma factor gene in Chlamydomonas reinhardtii. Photosynth Res 82: 339-349.
15. 70-like factor which likely functions in chloroplast transcription. Curr Genet 49: 333-340.
16. Klein U, De Camp JD, Bogorad L (1992) Two types of chloroplast gene promoters in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 89: 3453-3457.
17. Klein U, Salvador ML, Bogorad L (1994) Activity of the Chlamydomonas chloroplast rbcL gene promoter is enhanced by a remote sequence element. Proc Natl Acad Sci USA 91: 10819-10823.
18. Blowers AD, Ellmore GA, Klein U, Bogorad L (1990) Transcriptional analysis of endogenous and foreign genes in chloroplast transformants of Chlamydomonas. Plant Cell 2: 1059-1070.
19. Salvador ML, Klein U, Bogorad L (1998) Endogenous fluctuations of DNA topology in the chloroplast of Chlamydomonas reinhardtii. Mol Cell Biol 18: 7235-7242.
20. Salvador ML, Klein U (1999) The redox state regulates RNA degradation in the chloroplast of Chlamydomonas reinhardtii. Plant Physiol 121: 1367-1374.
21. Kawazoe R, Mahan KM, Venghaus BE, Carter ML, Herrin DL (2012) Circadian regulation of chloroplast transcription in Chlamydomonas is accompanied by little or no fluctuation in RPOD levels or core RNAP activity. Mol Biol Rep 39: 10565-10571.
22. Mettler T, Mühlhaus T, Hemme D, Schöttler MA, Rupprecht J, et al. (2014) Systems analysis of the response of photosynthesis, metabolism and growth to an increase in irradiance in the photosynthesis model organism Chlamydomonas reinhardtii. Plant Cell 26: 2310-2350.
23. Czechowski T, Bari RP, Stitt M, Scheible W-R, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38: 366-379.
24. Erickson B, Stern DB, Higgs DC (2005) Microarray analysis confirms the specificity of a Chlamydomonas reinhardtii chloroplast RNA stability mutant. Plant Physiol 137: 534-544.
25. Ramundo S, Rahire M, Schaad O, Rochaix J-D (2013) Repression of essential chloroplast genes reveals new signaling pathways and regulatory feedback loops in Chlamydomonas. Plant Cell 25: 167-186.
26. Baldauf SL, Manhart JR, Palmer JD (1990) Different fates of the chloroplast tufA gene following its transfer to the nucleus in green algae. Proc Natl Acad Sci USA 87: 5317-5321.
27. Hwang S, Kawazoe R, Herrin DL (1996) Transcription of tufA and other chloroplast-encoded genes is controlled by a circadian clock in Chlamydomonas. Proc Natl Acad Sci USA 93: 996-1000.
28. Matsuo T, Onai K, Okamoto K, Minagawa J, Ishiura M (2006) Real-time monitoring of chloroplast gene expression by a luciferase reporter: Evidence for nuclear regulation of chloroplast circadian period. Mol Cell Biol 26: 863-870.
29. Matsuo T, Okamoto K, Onai K, Niwa Y, Shimogawara K, et al. (2008) A systematic forward genetic analysis identified components of the Chlamydomonas circadian system. Genes & Dev 22: 918-930.
30. Eberhard S, Drapier 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.
31. Bräutigam K, Dietzel L, Pfannschmidt T (2007) Plastid-nucleus communication: anterograde and retrograde signalling in the development and function of plastids. Top Curr Genet 19: 409-455.
32. Berry JO, Yerramsetty P, Zielinski AM, Mure CM (2013) Photosynthetic gene expression in higher plants. Photosynth Res 117: 91-120.
33. Jarvis P, López-Juéz E (2013) Biogenesis and homeostasis of chloroplast and other plastids. Nat Rev Mol Cell Biol 14: 787-802.
34. Herrin DL, Michaels AS, Paul AL (1986) Regulation of genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase and the photosystem II polypeptides D-1 and D-2 during the cell cycle of Chlamydomonas reinhardtii. J Cell Biol 103: 1837-1845.
35. Leu S, White D, Michaels A (1990) Cell cycle-dependent transcriptional and post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii. Biochim Biophys Acta 1049: 311-317.
36. Salvador ML, Klein U, Bogorad L (1993) Light-regulated and endogenous fluctuations of chloroplast transcript levels in Chlamydomonas. Regulation by transcription and RNA degradation. Plant J 3: 213-219.
37. Harris EH (1989) The Chlamydomonas Sourcebook. Academic Press, San Diego, CA.
38. Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, opensource system for microarray data management and analysis. BioTechniques 34: 374-378.