Genome-wide gene expression profiles in response to plastid division perturbations

Planta

Volumn 234, Issue 5, 2011, Pages 1055-1063

  Maple, Jodi ^a   Winge, Per ^b   Tveitaskog, Astrid Elisabeth ^a   Gargano, Daniela ^a   Bones, Atle M ^b   Møller, Simon Geir ^a,c  

^a UNIVERSITY OF STAVANGER   (Norway)

^b NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^c STAVANGER UNIVERSITY HOSPITAL   (Norway)

Author keywords

Arabidopsis; Chloroplast division; Microarray

Indexed keywords

ARABIDOPSIS PROTEIN; ARC3 PROTEIN, ARABIDOPSIS; ARC5 PROTEIN, ARABIDOPSIS; DYNAMIN; TRANSCRIPTOME;

ALGORITHM; ARABIDOPSIS; ARTICLE; CELL DIVISION; CYTOLOGY; CYTOSOL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MUTATION; PHENOTYPE; PHYSIOLOGICAL STRESS; PHYSIOLOGY; PLANT GENE; PLASTID;

ALGORITHMS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL DIVISION; CYTOSOL; DYNAMINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; PLASTIDS; STRESS, PHYSIOLOGICAL; TRANSCRIPTOME;

ARABIDOPSIS;

EID: 80255139940     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-011-1459-z     Document Type: Article

References (42)

1. 2+-ATPase stimulated by AtMinE1. J Biol Chem 280: 31673-31678.
2. Austin J II, Webber AN (2005) Photosynthesis in Arabidopsis thaliana mutants with reduced chloroplast number. Photosynth Res 85: 373-384.
3. Bernhardt A, Lechner E, Hano P, Schade V, Dieterle M, Anders M, Dubin MJ, Benvenuto G, Bowler C, Genschik P, Hellmann H (2006) CUL4 associates with DDB1 and DET1 and its downregulation affects diverse aspects of development in Arabidopsis thaliana. Plant J 47: 591-603.
4. Chen H, Shen Y, Tang X, Yu L, Wang J, Guo L, Zhang Y, Zhang H, Feng S, Strickland E, Zheng N, Deng XW (2006) Arabidopsis CULLIN4 forms an E3 ubiquitin ligase with RBX1 and the CDD complex in mediating light control of development. Plant Cell 18: 1991-2004.
5. Cookson PJ, Kiano JW, Shipton CA, Fraser PD, Romer S, Schuch W, Bramley PM, Pyke KA (2003) Increases in cell elongation, plastid compartment size and phytoene synthase activity underlie the phenotype of the high pigment-1 mutant of tomato. Planta 217: 896-903.
6. de Pater S, Caspers M, Kottenhagen M, Meima H, ter Stege R, de Vetten N (2006) Manipulation of starch granule size distribution in potato tubers by modulation of plastid division. Plant Biotechnol J 4: 123-134.
7. Dutta S, Mohanty S, Tripathy BC (2009) Role of temperature stress on chloroplast biogenesis and protein import in pea. Plant Physiol 150: 1050-1061.
8. Fujiwara MT, Nakamura A, Itoh R, Shimada Y, Yoshida S, Møller SG (2004) Chloroplast division site placement requires dimerization of the ARC11/AtMinD1 protein in Arabidopsis. J Cell Sci 117: 2399-2410.
9. Galpaz N, Wang Q, Menda N, Zamir D, Hirschberg J (2008) Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. Plant J 53: 717-730.
10. Gao H, Kadirjan-Kalbach D, Froehlich JE, Osteryoung KW (2003) ARC5, a cytosolic dynamin-like protein from plants, is part of the chloroplast division machinery. Proc Natl Acad Sci USA 100: 4328-4333.
11. Garton S, Knight H, Warren GJ, Knight MR, Thorlby GJ (2007) crinkled leaves 8-a mutation in the large subunit of ribonucleotide reductase-leads to defects in leaf development and chloroplast division in Arabidopsis thaliana. Plant J 50: 118-127.
12. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-W587.
13. Hudson M, Ringli C, Boylan MT, Quail PH (1999) The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling. Genes Dev 13: 2017-2027.
14. Jorstad TS, Langaas M, Bones AM (2007) Understanding sample size: what determines the required number of microarrays for an experiment? Trends Plant Sci 12: 46-50.
15. Jorstad TS, Midelfart H, Bones AM (2008) A mixture model approach to sample size estimation in two-sample comparative microarray experiments. BMC Bioinformatics 9: 117.
16. Kotting O, Pusch K, Tiessen A, Geigenberger P, Steup M, Ritte G (2005) Identification of a novel enzyme required for starch metabolism in Arabidopsis leaves. The phosphoglucan, water dikinase. Plant Physiol 137: 242-252.
17. Kusnierczyk A, Winge P, Jorstad TS, Troczynska J, Rossiter JT, Bones AM (2008) Towards global understanding of plant defence against aphids-timing and dynamics of early Arabidopsis defence responses to cabbage aphid (Brevicoryne brassicae) attack. Plant Cell Environ 31: 1097-1115.
18. Lascano HR, Casano LM, Martin M, Sabater B (2003) The activity of the chloroplastic Ndh complex is regulated by phosphorylation of the NDH-F subunit. Plant Physiol 132: 256-262.
19. Li L, Foster CM, Gan Q, Nettleton D, James MG, Myers AM, Wurtele ES (2009) Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves. Plant J 58: 485-498.
20. Makarova KS, Aravind L, Koonin EV (2002) SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes. Trends Biochem Sci 27: 384-386.
21. Maple J, Møller SG (2010) The complexity and evolution of the plastid-division machinery. Biochem Soc Trans 38: 783-788.
22. Maple J, Vojta L, Soll J, Møller SG (2007) ARC3 is a stromal Z-ring accessory protein essential for plastid division. EMBO Rep 8: 293-299.
23. Marrison JL, Rutherford SM, Robertson EJ, Lister C, Dean C, Leech RM (1999) The distinctive roles of five different ARC genes in the chloroplast division process in Arabidopsis. Plant J 18: 651-662.
24. Miyagishima SY, Froehlich JE, Osteryoung KW (2006) PDV1 and PDV2 mediate recruitment of the dynamin-related protein ARC5 to the plastid division site. Plant Cell 18: 2517-2530.
25. Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 37: D987-D991.
26. Okazaki K, Kabeya Y, Suzuki K, Mori T, Ichikawa T, Matsui M, Nakanishi H, Miyagishima SY (2009) The PLASTID DIVISION1 and 2 components of the chloroplast division machinery determine the rate of chloroplast division in land plant cell differentiation. Plant Cell 21: 1769-1780.
27. Peng L, Cai W, Shikanai T (2010) Chloroplast stromal proteins, CRR6 and CRR7, are required for assembly of the NAD(P)H dehydrogenase subcomplex A in Arabidopsis. Plant J 63: 203-211.
28. Pyke KA, Leech RM (1991) Rapid image analysis screening procedure for identifying chloroplast number mutants in mesophyll cells of Arabidopsis thaliana (L.) Heynh. Plant Physiol 96: 1193-1195.
29. Pyke KA, Leech RM (1994) A genetic analysis of chloroplast division and expansion in Arabidopsis thaliana. Plant Physiol 104: 201-207.
30. Raynaud C, Perennes C, Reuzeau C, Catrice O, Brown S, Bergounioux C (2005) Cell and plastid division are coordinated through the prereplication factor AtCDT1. Proc Natl Acad Sci USA 102: 8216-8221.
31. Rock CD, Bowlby NR, Hoffmann-Benning S, Zeevaart JA (1992) The aba mutant of Arabidopsis thaliana (L.) Heynh. has reduced chlorophyll fluorescence yields and reduced thylakoid stacking. Plant Physiol 100: 1796-1801.
32. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
33. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
34. Somanchi A, Mayfield SP (1999) Nuclear-chloroplast signalling. Curr Opin Plant Biol 2: 404-409.
35. Storey J (2002) A direct approach to false discovery rates. J Royal Statistical Society 64: 479-498.
36. Tetlow IJ, Rawsthorne S, Rines C, Emes MJ (2005) Plastid metabolic pathways. In: Møller SG (ed) Plastids. Blackwell, Oxford, pp 60-109.
37. Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914-939.
38. Tymms MJ, Steele Scott N, Possingham JV (1982) Chloroplast and nuclear DNA content of cultured spinach leaf discs. J Exp Bot 33: 831-837.
39. van Wijk KJ, Baginsky S (2011) Update on plastid proteomics in higher plants; current status and future goals. Plant Physiol 155: 1578-1588.
40. Vass I, Cser K, Cheregi O (2007) Molecular mechanisms of light stress of photosynthesis. Ann N Y Acad Sci 1113: 114-122.
41. Wang S, Liu J, Feng Y, Niu X, Giovannoni J, Liu Y (2008) Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4. Plant J 55: 89-103.
42. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30: e15.