Peroxisomes and photomorphogenesis

Subcellular Biochemistry

Volumn 69, Issue , 2013, Pages 195-211

  Kaur, Navneet ^a   Li, Jiying ^a   Hu, Jianping ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

COP; De etiolated 1; Glyoxylate cycle; HYH; Nitric oxide; Peroxisome proliferation; PEX11; PEX2; Photomorphogenesis; Photorespiration; Phytochrome A; oxidation

Indexed keywords

NITRIC OXIDE; UBIQUITIN PROTEIN LIGASE;

GENE EXPRESSION REGULATION; GROWTH, DEVELOPMENT AND AGING; LIGHT; METABOLISM; PEROXISOME; PLANT DEVELOPMENT; RADIATION EXPOSURE; REVIEW; SEEDLING; SIGNAL TRANSDUCTION;

GENE EXPRESSION REGULATION, PLANT; LIGHT; NITRIC OXIDE; PEROXISOMES; PLANT DEVELOPMENT; SEEDLING; SIGNAL TRANSDUCTION; UBIQUITIN-PROTEIN LIGASES;

EID: 84888869119     PISSN: 03060225     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-007-6889-5_11     Document Type: Article

References (80)

1. Babujee L, Wurtz V, Ma C, Lueder F, Soni P, van Dorsselaer A, Reumann S (2010) The proteome map of spinach leaf peroxisomes indicates partial compartmentalization of phylloquinone (vitamin K1) biosynthesis in plant peroxisomes. J Exp Bot 61:1441-1453
2. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res 39:D1005-D1010
3. Beligni MV, Lamattina L (2000) Nitric oxide stimulates seed germination and de-etiolation, and inhibits hypocotyl elongation, three light-inducible responses in plants. Planta 210:215-221
4. Benvenuto G, Formiggini F, Laflamme P,Malakhov M, Bowler C (2002) The photomorphogenesis regulator DET1 binds the amino-terminal tail of histone H2B in a nucleosome context. Curr Biol 12:1529-1534
5. Carrie C, Kuhn K, Murcha MW, Duncan O, Small ID, O'Toole N,Whelan J (2009) Approaches to defining dual-targeted proteins in Arabidopsis. Plant J 57:1128-1139
6. Casal JJ, Mazzella MA (1998) Conditional synergism between cryptochrome 1 and phytochrome B is shown by the analysis of phyA, phyB, and hy4 simple, double, and triple mutants in Arabidopsis. Plant Physiol 118:19-25
7. Castillo MC, Sandalio LM, del Río LA, Léon J (2008) Peroxisome proliferation, wound-activated responses and expression of peroxisome-associated genes are cross-regulated but uncoupled in Arabidopsis thaliana. Plant Cell Environ 31:492-505
8. Chandler JW (2008) Cotyledon organogenesis. J Exp Bot 59:2917-2931
9. Chen M, Chory J (2011) Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol 21:664-671
10. Chen M, Chory J, Fankhauser C (2004) Light signal transduction in higher plants. Annu Rev Genet 38:87-117
11. Chory J (2010) Light signal transduction: an infinite spectrum of possibilities. Plant J 61:982-991
12. Chory J, Peto C, Feinbaum R, Pratt L, Ausubel F (1989) Arabidopsis thaliana mutant that develops as a light-grown plant in the absence of light. Cell 58:991-999
13. Corpas FJ, Palma JM, del Río LA, Barroso JB (2009) Evidence supporting the existence of L-arginine-dependent nitric oxide synthase in plants. New Phytol 184:9-14
14. Cousins AB, Pracharoenwattana I, Zhou W, Smith SM, Badger MR (2008) Peroxisomal malate dehydrogenase is not essential for photorespiration in Arabidopsis but its absence causes an increase in the stoichiometry of photorespiratory CO2 release. Plant Physiol 148:786-795
15. de Felipe MR, Lucas MM, Pozuelo JM (1988) Cytochemical study of catalase and peroxidase in the mesophyll of Lolium rigidum plants treated with isoproturon. J Plant Physiol 132:67-73
16. del Río LA (2011) Peroxisomes as a cellular source of reactive nitrogen species signal molecules. Arch Biochem Biophys 506:1-11
17. del Río LA, Pastori GM, Palma JM, Sandalio LM, Sevilla F, Corpas FJ, Jimenez A, López-Huertas E, Hernandez JA (1998) The activated oxygen role of peroxisomes in senescence. Plant Physiol 116:1195-1200
18. del Río LA, Sandalio LM, Corpas FJ, Palma JM, Barroso JB (2006) Reactive oxygen species and reactive nitrogen species in peroxisomes. Production, scavenging, and role in cell signaling. Plant Physiol 141:330-335
19. Desai M, Hu J (2008) Light induces peroxisome proliferation in Arabidopsis seedlings through the photoreceptor phytochrome A, the transcription factor HY5 HOMOLOG, and the peroxisomal protein PEROXIN11b. Plant Physiol 146:1117-1127
20. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210
21. Eubel H, Meyer EH, Taylor NL, Bussell JD, O'Toole N, Heazlewood JL, Castleden I, Small ID, Smith SM,Millar AH (2008) Novel proteins, putative membrane transporters, and an integrated metabolic network are revealed by quantitative proteomic analysis of Arabidopsis cell culture peroxisomes. Plant Physiol 148:1809-1829
22. Fernández-Marcos M, Sanz L, Lorenzo O (2012) Nitric oxide: an emerging regulator of cell elongation during primary root growth. Plant Signal Behav 7:196-200
23. Ferreira MB, Bird B, Davies DD (1989) The effect of light on the structure and organization of Lemna peroxisomes. J Exp Bot 40:1029-1035
24. Foyer CH, Bloom AJ, Queval G, Noctor G (2009) Photorespiratory metabolism: genes, mutants, energetics, and redox signaling. Annu Rev Plant Biol 60:455-484
25. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80
26. Gross J, Cho WK, Lezhneva L, Falk J, Krupinska K, Shinozaki K, Seki M, Herrmann RG, Meurer J (2006) A plant locus essential for phylloquinone (vitamin K1) biosynthesis originated from a fusion of four eubacterial genes. J Biol Chem 281:17189-17196
27. Hancock JT (2012) NO synthase? Generation of nitric oxide in plants. Period Biol 114:19-24
28. Heijde M, Ulm R (2012) UV-B photoreceptor-mediated signalling in plants. Trends Plant Sci 17:230-237
29. Hu J (2009) Molecular basis of peroxisome division and proliferation in plants. Int Rev Cell Mol Biol 279:79-99
30. Hu J, Desai M (2008) Light control of peroxisome proliferation during Arabidopsis photomorphogenesis. Plant Signal Behav 3:801-803
31. Hu J, Aguirre M, Peto C, Alonso J, Ecker J, Chory J (2002) A role for peroxisomes in photomorphogenesis and development of Arabidopsis. Science 297:405-409
32. Hu J, Baker A, Bartel B, Linka N, Mullen RT, Reumann S, Zolman BK (2012) Plant peroxisomes: biogenesis and function. Plant Cell 24:2279-2303
33. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264
34. Jiao Y, Lau OS, Deng XW (2007) Light-regulated transcriptional networks in higher plants. Nat Rev 8:217-230
35. Kamada-Nobusada T, Hayashi M, Fukazawa M, Sakakibara H, Nishimura M (2008) A putative peroxisomal polyamine oxidase, AtPAO4, is involved in polyamine catabolism in Arabidopsis thaliana. Plant Cell Physiol 49:1272-1282
36. Kami C, Lorrain S, Hornitschek P, Fankhauser C (2010) Light-regulated plant growth and development. Curr Top Dev Biol 91:29-66
37. Kaur N, Hu J (2011) Defining the plant peroxisomal proteome: from Arabidopsis to rice. Front Plant Sci 3. doi:10.3389/fpls.2011.00103
38. Kaur N, Reumann S, Hu J (2009) Peroxisome biogenesis and function. Arabidopsis Book 7:e0123. doi:0110.1199/tab.0123
39. Kaur N, Zhao Q, Xie Q, Hu J (2013) Arabidopsis RING peroxins are E3 ubiquitin ligases that interact with two homologous ubiquitin receptor proteins. J Integr Plant Biol 55:108-120. doi:10.1111/jipb.12014
40. Kim HU, van Oostende C, Basset GJ, Browse J (2008) The AAE14 gene encodes the Arabidopsis o-succinylbenzoyl-CoA ligase that is essential for phylloquinone synthesis and photosystem-I function. Plant J 54:272-283
41. Lau OS, Deng XW (2012) The photomorphogenic repressors COP1 and DET1: 20 years later. Trends Plant Sci 17:584-593
42. Lau OS, Huang X, Charron JB, Lee JH, Li G, Deng XW (2011) Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock. Mol Cell 43:703-712
43. Leivar P, Quail PH (2011) PIFs: pivotal components in a cellular signaling hub. Trends Plant Sci 16:19-28
44. Leivar P, Tepperman JM, Monte E, Calderon RH, Liu TL, Quail PH (2009) Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings. Plant Cell 21:3535-3553
45. Lingard MJ, Gidda SK, Bingham S, Rothstein SJ, Mullen RT, Trelease RN (2008) Arabidopsis PEROXIN11c-e, FISSION1b, and DYNAMIN-RELATED PROTEIN3A cooperate in cell cycle-associated replication of peroxisomes. Plant Cell 20:1567-1585
46. Liu H, Liu B, Zhao C, Pepper M, Lin C (2011) The action mechanisms of plant cryptochromes. Trends Plant Sci 16:684-691
47. Lozano-Juste J, Léon J (2010) Enhanced abscisic acid-mediated responses in nia1nia2noa1-2. triple mutant impaired in NIA/NR- and AtNOA1-dependent nitric oxide biosynthesis in Arabidopsis. Plant Physiol 152:891-903
48. Lozano-Juste J, Léon J (2011) Nitric oxide regulates DELLA content and PIF expression to promote photomorphogenesis in Arabidopsis. Plant Physiol 156:1410-1423
49. Mitsuya S, El-Shami M, Sparkes IA, Charlton WL, Lousa Cde M, Johnson B, Baker A (2010) Salt stress causes peroxisome proliferation, but inducing peroxisome proliferation does not improve NaCl tolerance in Arabidopsis thaliana. PLoS One 5:e9408
50. Moschou PN, Sanmartin M, Andriopoulou AH, Rojo E, Sánchez-Serrano JJ, Roubelakis- Angelakis KA (2008) Bridging the gap between plant and mammalian polyamine catabolism: a novel peroxisomal polyamine oxidase responsible for a full back-conversion pathway in Arabidopsis. Plant Physiol 147:1845-1857
51. Nayidu NK, Wang L, Xie W, Zhang C, Fan C, Lian X, Zhang Q, Xiong L (2008) Comprehensive sequence and expression profile analysis of PEX11 gene family in rice. Gene 412:59-70
52. Neff MM, Chory J (1998) Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during Arabidopsis development. Plant Physiol 118:27-35
53. Neff MM, Fankhauser C, Chory J (2000) Light: an indicator of time and place. Genes Dev 14: 257-271
54. Nezames CD, Deng XW(2012) The COP9 signalosome: its regulation of cullin-based E3 ubiquitin ligases and role in photomorphogenesis. Plant Physiol 160:38-46
55. Nila AG, Sandalio LM, López MG, Gómez M, del Río LA, Gómez-Lim MA (2006) Expression of a peroxisome proliferator-activated receptor gene (xPPARalpha) from Xenopus laevis in tobacco (Nicotiana tabacum) plants. Planta 224:569-581
56. Oksanen E, Haikio E, Sober J, Karnosky DF (2003) Ozone-induced H2O2 accumulation in fieldgrown aspen and birch is linked to foliar ultrastructure and peroxisomal activity. New Phytol 161:791-799
57. Orth T, Reumann S, Zhang X, Fan J, Wenzel D, Quan S, Hu J (2007) The PEROXIN11 protein family controls peroxisome proliferation in Arabidopsis. Plant Cell 19:333-350
58. Palma JM, Garrido M, Rodriguez-Garcia MI, del Río LA (1991) Peroxisome proliferation and oxidative stress mediated by activated oxygen species in plant peroxisomes. Arch Biochem Biophys 287:68-74
59. Pepper AE, Chory J (1997) Extragenic suppressors of the Arabidopsis det1 mutant identify elements of flowering-time and light-response regulatory pathways. Genetics 145:1125-1137
60. Pepper A, Delaney T, Washburn T, Poole D, Chory J (1994) DET1, a negative regulator of lightmediated development and gene expression in Arabidopsis, encodes a novel nuclear-localized protein. Cell 78:109-116
61. Peschke F, Kretsch T (2011) Genome-wide analysis of light-dependent transcript accumulation patterns during early stages of Arabidopsis seedling deetiolation. Plant Physiol 155:1353-1366
62. Peterhansel C, Horst I, Niessen M, Blume C, Kebeish R, Kurkcuoglu S, Kreuzaler F (2010) Photorespiration. Arabidopsis Book/Am Soc Plant Biol, Rockville. doi:10.1199/tab.0130
63. Poppe C, Sweere U, Drumm-Herrel H, Schafer E (1998) The blue light receptor cryptochrome 1 can act independently of phytochrome A and B in Arabidopsis thaliana. Plant J 16:465-471
64. Reumann S, Quan S, Aung K, Yang P, Manandhar-Shrestha K, Holbrook D, Linka N, Switzenberg R,Wilkerson CG,Weber AP, Olsen LJ, Hu J (2009) In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes. Plant Physiol 150:125-143
65. Rocha M, Licausi F, Araujo WL, Nunes-Nesi A, Sodek L, Fernie AR, van Dongen JT (2010) Glycolysis and the tricarboxylic acid cycle are linked by alanine aminotransferase during hypoxia induced by waterlogging of Lotus japonicus. Plant Physiol 152:1501-1513
66. Rucktaschel R, Girzalsky W, Erdmann R (2011) Protein import machineries of peroxisomes. Biochim Biophys Acta 1808:892-900
67. Schrader M, Bonekamp NA, Islinger M (2012) Fission and proliferation of peroxisomes. Biochim Biophys Acta. doi:10.1016/j.bbadis.2011.1012.1014
68. Schultz CJ, Coruzzi GM (1995) The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subcellular compartments. Plant J 7:61-75
69. Shimada H, Ohno R, Shibata M, Ikegami I, Onai K, Ohto MA, Takamiya K (2005) Inactivation and deficiency of core proteins of photosystems I and II caused by genetical phylloquinone and plastoquinone deficiency but retained lamellar structure in a T-DNA mutant of Arabidopsis. Plant J 41:627-637
70. Sinclair AM, Trobacher CP, Mathur N, Greenwood JS, Mathur J (2009) Peroxule extension over ER defined paths constitutes a rapid subcellular response to hydroxyl stress. Plant J 59:231-242
71. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:1544-6115
72. Tonon C, Cecilia Terrile M, José Iglesias M, Lamattina L, Casalongue C (2010) Extracellular ATP, nitric oxide and superoxide act coordinately to regulate hypocotyl growth in etiolated Arabidopsis seedlings. J Plant Physiol 167:540-546
73. Wang H, Deng XW (2003) Dissecting the phytochrome A-dependent signaling network in higher plants. Trends Plant Sci 8:172-178
74. Warnes G, Bolker B, Lumley T (2011) gplots: Various R programming tools for plotting data. R package version 2.11.0. http://cran.r-project.org/web/packages/gplots/index.html
75. Weitbrecht K, Muller K, Leubner-Metzger G (2011) First off the mark: early seed germination. J Exp Bot 62:3289-3309
76. Widhalm JR, Ducluzeau AL, Buller NE, Elowsky CG, Olsen LJ, Basset GJ (2012) Phylloquinone (vitamin K(1)) biosynthesis in plants: two peroxisomal thioesterases of lactobacillales origin hydrolyze 1,4-dihydroxy-2-naphthoyl-coa. Plant J 71:205-215
77. Wimalasekera R, Tebartz F, Scherer GF (2011a) Polyamines, polyamine oxidases and nitric oxide in development, abiotic and biotic stresses. Plant Sci 181:593-603
78. Wimalasekera R, Villar C, Begum T, Scherer GF (2011b) COPPER AMINE OXIDASE1 (CuAO1) of Arabidopsis thaliana contributes to abscisic acid- and polyamine-induced nitric oxide biosynthesis and abscisic acid signal transduction. Mol Plant 4:663-678
79. Yu X, Liu H, Klejnot J, Lin C (2010) The cryptochrome blue light receptors. The Arabidopsis Book 8. doi:10.1199/tab.0135
80. Zemojtel T, Fröhlich A, Palmieri MC, Kolanczyk M,Mikula I, Wyrwicz LS,Wanker EE, Mundlos S, Vingron M, Martasek P, Durner J (2006) Plant nitric oxide synthase: a never-ending story? Trends Plant Sci 11:526-527