Light induced changes in protein expression and uniform regulation of transcription in the thylakoid lumen of Arabidopsis thaliana

PLoS ONE

Volumn 4, Issue 5, 2009, Pages

  Granlund, Irene ^a,c   Hall, Michael ^a   Kieselbach, Thomas ^a   Schröder, Wolfgang P ^a,b  

^a UMEÅ UNIVERSITY   (Sweden)

^b Umea Plant Science Center   (Sweden)

^c SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

PLASTOCYANIN; PROTEIN PSBP; PROTEIN PSBQ; PROTEOME; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN;

ARABIDOPSIS; ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; GEL ELECTROPHORESIS; GENE EXPRESSION REGULATION; LIGHT ADAPTATION; LIGHT EXPOSURE; NONHUMAN; PHOTOACTIVATION; PHOTOSTIMULATION; PHOTOSYNTHESIS; PLANT GENETICS; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN QUATERNARY STRUCTURE; PROTEOMICS; REACTION TIME; THYLAKOID; TRANSCRIPTION REGULATION; ADAPTATION; CLUSTER ANALYSIS; DARKNESS; GENETIC TRANSCRIPTION; GENETICS; LIGHT; METABOLISM; PLANT GENE; RADIATION EXPOSURE; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ARABIDOPSIS THALIANA;

ADAPTATION, PHYSIOLOGICAL; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CLUSTER ANALYSIS; DARKNESS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; LIGHT; PROTEOME; THYLAKOIDS; TRANSCRIPTION, GENETIC;

EID: 66249134957     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005649     Document Type: Article

References (40)

1. Kovalenko IB, Abaturova AM, Gromov PA, Ustinin DM, Grachev EA, et al. (2006) Direct simulation of plastocyanin and cytochrome f interactions in solution. Phys Biol 3: 121-129.
2. Schubert M, Petersson UA, Haas BJ, Funk C, Schroder WP, et al. (2002) Proteome map of the chloroplast lumen of Arabidopsis thaliana. J Biol Chem 277: 8354-8365.
3. Peltier JB, Emanuelsson O, Kalume DE, Ytterberg J, Friso G, et al. (2002) Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell 14: 211-236.
4. Ishihara S, Takabayashi A, Ido K, Endo T, Ifuku K, et al. (2007) Distinct functions for the two PsbP-like proteins PPL1 and PPL2 in the chloroplast thylakoid lumen of Arabidopsis. Plant Physiol 145: 668-679.
5. Sirpio S, Allahverdiyeva Y, Suorsa M, Paakkarinen V, Vainonen J, et al. (2007) TLP18.3, a novel thylakoid lumen protein regulating photosystem II repair cycle. Biochem J 406: 415-425.
6. Fu A, He Z, Cho HS, Lima A, Buchanan BB, et al. (2007) A chloroplast cyclophilin functions in the assembly and maintenance of photosystem II in Arabidopsis thaliana. Proc Natl Acad Sci U S A 104: 15947-15952.
7. Pfannschmidt T, Allen JF, Iler RO (2001) Principles of redox control in photosynthesis gene expression. Physiol Plant 112: 1-9.
8. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, et al. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110-2113.
9. Blasing OE, Gibon Y, Gunther M, Hohne M, Morcuende R, et al. (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17: 3257-3281.
10. Dodd AN, Salathia N, Hall A, Kevei E, Toth R, et al. (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630-633.
11. Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18: 2071-2077.
12. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, et al. (2003) A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3: 36-44.
13. Kieselbach T, Hagman, Andersson B, Schroder WP (1998) The thylakoid lumen of chloroplasts. Isolation and characterization. J Biol Chem 273: 6710-6716.
14. Yonekura-Sakakibara K, Tohge T, Niida R, Saito K (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem 282: 14932-14941.
15. Saito K, Hirai MY, Yonekura-Sakakibara K (2008) Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'. Trends Plant Sci 13: 36-43.
16. Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48: 381-390.
17. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, et al. (2007) An "electronic fluorescent pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2: e718.
18. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, et al. (2008) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14.
19. Ifuku K, Yamamoto Y, Ono TA, Ishihara S, Sato F (2005) PsbP protein, but not PsbQ protein, is essential for the regulation and stabilization of photosystem II in higher plants. Plant Physiol 139: 1175-1184.
20. Yi X, Hargett SR, Frankel LK, Bricker TM (2006) The PsbQ protein is required in Arabidopsis for photosystem II assembly/stability and photo autotrophy under low light conditions. J Biol Chem 281: 26260-26267.
21. Meurer J, Plucken H, Kowallik KV, Westhoff P (1998) A nuclear-encoded protein of prokaryotic origin is essential for the stability of photosystem II in Arabidopsis thaliana. Embo J 17: 5286-5297.
22. Lintala M, Allahverdiyeva Y, Kidron H, Piippo M, Battchikova N, et al. (2007) Structural and functional characterization of ferredoxin-NADP+-oxidoreductase using knock-out mutants of Arabidopsis. Plant J 49: 1041-1052.
23. Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, et al. (2008) Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE 3: e1994.
24. Manfield IW, Jen CH, Pinney JW, Michalopoulos I, Bradford JR, et al. (2006) Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res 34: W504-509.
25. Sun XW, Peng LW, Guo JK, Chi W, Ma JF, et al. (2007) Formation of DEG5 and DEG8 complexes and their involvement in the degradation of photodamaged photosystem II reaction center D1 protein in Arabidopsis. Plant Cell 19: 1347-1361.
26. Kapri-Pardes E, Naveh L, Adam Z (2007) The thylakoid lumen protease Deg1 is involved in the repair of photosystem II from photoinhibition in Arabidopsis. Plant Cell 19: 1039-1047.
27. Kieselbach T, Schroder WP (2003) The proteome of the chloroplast lumen of higher plants. Photosynthesis Res 78: 249-264.
28. Lima A, Lima S, Wong JH, Phillips RS, Buchanan BB, et al. (2006) A redoxactive FKBP-type immunophilin functions in accumulation of the photosystem II supercomplex in Arabidopsis thaliana. Proc Natl Acad Sci U S A 103: 12631-12636.
29. Sun Q, Zybailov B, Majeran W, Friso G, Olinares PDB, et al. (2009) PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res 37: D969-D974.
30. Fankhauser C, Staiger D (2002) Photoreceptors in Arabidopsis thaliana: light perception, signal transduction and entrainment of the endogenous clock. Planta 216: 1-16.
31. Thompson W, White M (1991) Physiological and molecular studies of light-regulated nuclear genes in higher plants. Annu Rev Plant Physiol Plant Mol Biol 42: 423-466.
32. Plucken H, Muller B, Grohmann D, Westhoff P, Eichacker LA (2002) The HCF136 protein is essential for assembly of the photosystem II reaction center in Arabidopsis thaliana. FEBS Lett 532: 85-90.
33. Hashimoto A, Yamamoto Y, Theg SM (1996) Unassembled subunits of the photosynthetic oxygen-evolving complex present in the thylakoid lumen are long-lived and assembly-competent. FEBS Lett 391: 29-34.
34. Melis A (1999) Photosystem-II damage and repair cycle in chloroplasts: what modulates the rate of photodamage ? Trends Plant Sci 4: 130-135.
35. Vorst O, Kock P, Lever A, Weterings B, Weisbeek P, et al. (1993) The promoter of the Arabidopsis thaliana plastocyanin gene contains a far upstream enhancer-like element involved in chloroplast-dependent expression. Plant J 4: 933-945.
36. Schutze K, Steiner S, Pfannschmidt T (2008) Photosynthetic redox regulation of the plastocyanin promoter in tobacco. Physiol Plant 133: 557-565.
37. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
38. Porra R, Thompson W, Kreidmann P (1989) Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four diffferent solvents: verification of the concentration of chlorophyll standards y atomic mass spectroscopy. Biochim Biophys Acta 972: 163-170.
39. Westermeier R, Naven T (2002) Proteomics in Practice. A laboratory manual for proteome analysis, Wiley-VCH, Weinheim, Germany.
40. Pesaresi P, Scharfenberg M, Weigel M, Granlund I, Schroder WP, et al. (2009) Mutants, overexpressors, and interactors of Arabidopsis plastocyanin Isoforms: revised roles of plastocyanin in photosynthetic electron flow and thylakoid redox State. Mol Plant 2: 236-248.