Plant Molecular Biology

, Volume 73, Issue 3, pp 309–323 | Cite as

Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant

  • Ching-Chih Tseng
  • Tzu-Ying Sung
  • Yi-Chiou Li
  • Shih-Jui Hsu
  • Chien-Li Lin
  • Ming-Hsiun Hsieh


The vanilla cream1 (vac1) albino mutant is defective in a gene encoding a chloroplast-localized pentatricopeptide repeat protein of the DYW subgroup. However, the carboxyl-terminal DYW motif is truncated in VAC1. To identify vac1-specific phenotypes, we compared 34 chloroplast RNA editing sites and ~90 chloroplast gene expression patterns among wild type, vac1 and another albino mutant ispH, which is defective in the plastid isoprenoid biosynthesis pathway. We found that the editing of accD and ndhF transcripts is partially affected in vac1. In addition, steady-state levels of chloroplast rRNAs are significantly decreased in vac1. The expression of plastid-encoded RNA polymerase transcribed genes is down-regulated, whereas the expression of nucleus-encoded RNA polymerase transcribed genes is up-regulated in vac1. Although the development and function of mutant chloroplasts are severely impaired, steady-state mRNA levels of nucleus-encoded photosynthetic genes are not affected or are only slightly decreased in vac1. The ZAT10 gene encodes a transcription factor and its expression is down-regulated by norflurazon treatment in wild type. This norflurazon effect was not observed in vac1. These results suggest that the VAC1 protein may be involved in plastid-to-nucleus retrograde signaling in addition to its role in chloroplast RNA editing and gene expression. A defect in a key biosynthetic pathway can have many indirect effects on chloroplast gene expression as is seen in the ispH mutant. Similarly, the vac1 mutant has pleiotropic molecular phenotypes and most of which may be indirect effects.


Arabidopsis Chloroplast Albino Pentatricopeptide repeat protein Chloroplast gene expression Chloroplast RNA editing 



We thank Dr. J. Sheen for the GFP vector, T.Y. Chung for technical assistance and M.J. Fang for assistance in confocal microscopy. This work was supported by grants to M.-H. H. from National Science Council and Academia Sinica of Taiwan.

Supplementary material

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  1. Allison LA, Simon LD, Maliga P (1996) Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J 15:2802–2809PubMedGoogle Scholar
  2. Barkan A, Walker M, Nolasco M, Johnson D (1994) A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO J 13:3170–3181PubMedGoogle Scholar
  3. Beick S, Schmitz-Linneweber C, Williams-Carrier R, Jensen B, Barkan A (2008) The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts. Mol Cell Biol 28:5337–5347CrossRefPubMedGoogle Scholar
  4. Cai W, Ji D, Peng L, Guo J, Ma J, Zou M, Lu C, Zhang L (2009) LPA66 is required for editing psbF chloroplast transcripts in Arabidopsis. Plant Physiol 150:1260–1271CrossRefPubMedGoogle Scholar
  5. Chateigner-Boutin AL, Small I (2007) A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res 35:e114CrossRefPubMedGoogle Scholar
  6. Chateigner-Boutin AL, Ramos-Vega M, Guevara-García A, Andrés C, de la Luz Gutiérrez-Nava M, Cantero A, Delannoy E, Jiménez LF, Lurin C, Small I, León P (2008) CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts. Plant J 56:590–602CrossRefPubMedGoogle Scholar
  7. Chi W, Ma J, Zhang D, Guo J, Chen F, Lu C, Zhang L (2008) The pentratricopeptide repeat protein DELAYED GREENING1 is involved in the regulation of early chloroplast development and chloroplast gene expression in Arabidopsis. Plant Physiol 147:573–584CrossRefPubMedGoogle Scholar
  8. Chiu W, Niwa Y, Zeng W, Hirano T, Kobayashi H, Sheen J (1996) Engineered GFP as a vital reporter in plants. Curr Biol 6:325–330CrossRefPubMedGoogle Scholar
  9. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743CrossRefPubMedGoogle Scholar
  10. de Longevialle AF, Meyer EH, Andrés C, Taylor NL, Lurin C, Millar AH, Small ID (2007) The pentatricopeptide repeat gene OTP43 is required for trans-splicing of the mitochondrial nad1 Intron 1 in Arabidopsis thaliana. Plant Cell 19:3256–3265CrossRefPubMedGoogle Scholar
  11. de Longevialle AF, Hendrickson L, Taylor NL, Delannoy E, Lurin C, Badger M, Millar AH, Small I (2008) The pentatricopeptide repeat gene OTP51 with two LAGLIDADG motifs is required for the cis-splicing of plastid ycf3 intron 2 in Arabidopsis thaliana. Plant J 56:157–168CrossRefPubMedGoogle Scholar
  12. De Santis-MacIossek G, Kofer W, Bock A, Schoch S, Maier RM, Wanner G, Rudiger W, Koop HU, Herrmann RG (1999) Targeted disruption of the plastid RNA polymerase genes rpoA, B and C1: molecular biology, biochemistry and ultrastructure. Plant J 18:477–489CrossRefPubMedGoogle Scholar
  13. Delannoy E, Stanley WA, Bond CS, Small ID (2007) Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles. Biochem Soc Trans 35:1643–1647CrossRefPubMedGoogle Scholar
  14. Fisk DG, Walker MB, Barkan A (1999) Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression. EMBO J 18:2621–2630CrossRefPubMedGoogle Scholar
  15. Gong Z, Koiwa H, Cushman MA, Ray A, Bufford D, Kore-eda S, Matsumoto TK, Zhu J, Cushman JC, Bressan RA, Hasegawa PM (2001) Genes that are uniquely stress regulated in salt overly sensitive (sos) mutants. Plant Physiol 126:363–375CrossRefPubMedGoogle Scholar
  16. Hajdukiewicz PT, Allison LA, Maliga P (1997) The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J 16:4041–4048CrossRefPubMedGoogle Scholar
  17. Hammani K, Okuda K, Tanz SK, Chateigner-Boutin AL, Shikanai T, Small I (2009) A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites. Plant Cell 21:3686–3699CrossRefPubMedGoogle Scholar
  18. Hanaoka M, Kanamaru K, Fujiwara M, Takahashi H, Tanaka K (2005) Glutamyl-tRNA mediates a switch in RNA polymerase use during chloroplast biogenesis. EMBO Rep 6:545–550CrossRefPubMedGoogle Scholar
  19. Hashimoto M, Endo T, Peltier G, Tasaka M, Shikanai T (2003) A nucleus-encoded factor, CRR2, is essential for the expression of chloroplast ndhB in Arabidopsis. Plant J 6:541–549CrossRefGoogle Scholar
  20. Hattori M, Miyake H, Sugita M (2007) A pentatricopeptide repeat protein is required for RNA processing of clpP Pre-mRNA in moss chloroplasts. J Biol Chem 282:10773–10782CrossRefPubMedGoogle Scholar
  21. Hedtke B, Börner T, Weihe A (1997) Mitochondrial and chloroplast phage type RNA polymerases in Arabidopsis. Science 277:809–811CrossRefPubMedGoogle Scholar
  22. Hess WR, Börner T (1999) Organellar RNA polymerases of higher plants. Int Rev Cytol 190:1–59CrossRefPubMedGoogle Scholar
  23. Hess WR, Prombona A, Fieder B, Subramanian AR, Börner T (1993) Chloroplast rps15 and the rpoB/C1/C2 gene cluster are strongly transcribed in ribosome-deficient plastids: evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J 12:563–571PubMedGoogle Scholar
  24. Hsieh MH, Goodman HM (2002) Molecular characterization of a novel gene family encoding ACT domain repeat proteins in Arabidopsis. Plant Physiol 130:1797–1806CrossRefPubMedGoogle Scholar
  25. Hsieh MH, Goodman HM (2005) The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis. Plant Physiol 138:641–653CrossRefPubMedGoogle Scholar
  26. Hu J, Bogorad L (1990) Maize chloroplast RNA polymerase: The 180-, 120-, and 38-kilodalton polypeptides are encoded in chloroplast genes. Proc Natl Acad Sci USA 87:1531–1535CrossRefPubMedGoogle Scholar
  27. Igloi GL, Kössel H (1992) The transcriptional apparatus of chloroplast. CRC Crit Rev Plant Sci 10:525–558CrossRefGoogle Scholar
  28. Jackson AO, Larkins BA (1976) Influence of ionic strength, pH, and chelation of divalent metals on isolation of polyribosomes from tobacco leaves. Plant Physiol 57:5–10CrossRefPubMedGoogle Scholar
  29. Kishine M, Takabayashi A, Munekage Y, Shikanai T, Endo T, Sato F (2004) Ribosomal RNA processing and an RNase R family member in chloroplasts of Arabidopsis. Plant Mol Biol 55:595–606CrossRefPubMedGoogle Scholar
  30. Kode V, Mudd EA, Iamtham S, Day A (2005) The tobacco plastid accD gene is essential and is required for leaf development. Plant J 44:237–244CrossRefPubMedGoogle Scholar
  31. Kotera E, Tasaka M, Shikanai T (2005) A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433:326–330CrossRefPubMedGoogle Scholar
  32. Koussevitzky S, Nott A, Mockler TC, Hong F, Sachetto-Martins G, Surpin M, Lim J, Mittler R, Chory J (2007) Signals from chloroplasts converge to regulate nuclear gene expression. Science 316:715–719CrossRefPubMedGoogle Scholar
  33. Krause K, Maier RM, Kofer W, Krupinska K, Herrmann RG (2000) Disruption of plastid-encoded RNA polymerase genes in tobacco: expression of only a distinct set of genes is not based on selective transcription of the plastid chromosome. Mol Gen Genet 263:1022–1030CrossRefPubMedGoogle Scholar
  34. Larkin RM, Alonso JM, Ecker JR, Chory J (2003) GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science 299:902–906CrossRefPubMedGoogle Scholar
  35. Lee H, Guo Y, Ohta M, Xiong LM, Stevenson B, Zhu JK (2002) LOS2, a genetic locus required for cold-responsive gene transcription encodes a bi-functional enolase. EMBO J 21:2692–2702CrossRefPubMedGoogle Scholar
  36. 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 31:171–188CrossRefPubMedGoogle Scholar
  37. Leon P, Arroyo A, Mackenzie S (1998) Nuclear control of plastid and mitochondrial development in higher plants. Annu Rev Plant Physiol Plant Mol Biol 49:453–480CrossRefPubMedGoogle Scholar
  38. Lichtenthaler HK, Wellburn AR (1983) Determination of total carotenoids and chlorophylls a and b of leaf extracts in different solvents. Biochem Soc Trans 11:591–592Google Scholar
  39. Liere K, Maliga P (1999) In vitro characterization of the tobacco rpoB promoter reveals a core sequence motif conserved between phage-type plastid and plant mitochondrial promoters. EMBO J 18:249–257CrossRefPubMedGoogle Scholar
  40. Liu YG, Mitsukawa N, Oosumi T, Whittier RF (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 8:457–463CrossRefPubMedGoogle Scholar
  41. Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B et al (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16:2089–2103CrossRefPubMedGoogle Scholar
  42. Maier RM, Zeltz P, Kössel H, Bonnard G, Gualberto JM, Grienenberger JM (1996) RNA editing in plant mitochondria and chloroplasts. Plant Mol Biol 32:343–365CrossRefPubMedGoogle Scholar
  43. Meierhoff K, Felder S, Nakamura T, Bechtold N, Schuster G (2003) HCF152, an Arabidopsis RNA binding pentatricopeptide repeat protein involved in the processing of chloroplast psbB-psbT-psbH-petB-petD RNAs. Plant Cell 15:1480–1495CrossRefPubMedGoogle Scholar
  44. Mochizuki N, Brusslan JA, Larkin R, Nagatani A, Chory J (2001) Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proc Natl Acad Sci USA 98:2053–2058CrossRefPubMedGoogle Scholar
  45. Mullet JE (1988) Chloroplast development and gene expression. Annu Rev Plant Physiol Plant Mol Biol 39:475–502CrossRefGoogle Scholar
  46. Nott A, Jung HS, Koussevitzky S, Chory J (2006) Plastid-to-nucleus retrograde signaling. Annu Rev Plant Biol 57:739–759CrossRefPubMedGoogle Scholar
  47. O’Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M, Small I (2008) On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol 25:1120–1128CrossRefPubMedGoogle Scholar
  48. Okuda K, Myouga F, Motohashi R, Shinozaki K, Shikanai T (2007) Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proc Natl Acad Sci USA 104:8178–8183CrossRefPubMedGoogle Scholar
  49. Okuda K, Habata Y, Kobayashi Y, Shikanai T (2008) Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids. Nucleic Acids Res 36:6155–6164CrossRefPubMedGoogle Scholar
  50. Okuda K, Chateigner-Boutin AL, Nakamura T, Delannoy E, Sugita M, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T (2009) Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts. Plant Cell 21:146–156CrossRefPubMedGoogle Scholar
  51. Pfalz J, Liere K, Kandlbinder A, Dietz KJ, Oelmüller R (2006) pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. Plant Cell 18:176–197CrossRefPubMedGoogle Scholar
  52. Pfalz J, Bayraktar OA, Prikryl J, Barkan A (2009) Site-specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts. EMBO J 28:2042–2052CrossRefPubMedGoogle Scholar
  53. Pogson BJ, Woo NS, Förster B, Small ID (2008) Plastid signaling to the nucleus and beyond. Trends Plant Sci 13:602–609CrossRefPubMedGoogle Scholar
  54. Robbins JC, Heller WP, Hanson MR (2009) A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript. RNA 15:1142–1153CrossRefPubMedGoogle Scholar
  55. Rossel JB, Wilson PB, Hussain D, Woo NS, Gordon MJ, Mewett OP, Howell KA, Whelan J, Kazan K, Pogson BJ (2007) Systemic and intracellular response to photooxidative stress in Arabidopsis. Plant Cell 19:4091–4110CrossRefPubMedGoogle Scholar
  56. Sakamoto H, Araki T, Meshi T, Iwabuchi M (2000) Expression of a subset of the Arabidopsis Cys(2)/His(2)-type zinc-finger protein gene family under water stress. Gene 248:23–32CrossRefPubMedGoogle Scholar
  57. Sakamoto H, Maruyama K, Sakuma Y, Meshi T, Iwabuchi M, Shinozaki K, Yamaguchi-Shinozaki K (2004) Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol 136:2734–2746CrossRefPubMedGoogle Scholar
  58. Salone V, Rüdinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C (2007) A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Lett 581:4132–4138CrossRefPubMedGoogle Scholar
  59. Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 6:283–290CrossRefPubMedGoogle Scholar
  60. Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13:663–670CrossRefPubMedGoogle Scholar
  61. Schmitz-Linneweber C, Williams-Carrier R, Barkan A (2005) RNA immunoprecipitation and microarray analysis show a chloroplast pentatricopeptide repeat protein to be associated with the 5′ region of mRNAs whose translation it activates. Plant Cell 17:2791–2804CrossRefPubMedGoogle Scholar
  62. Schmitz-Linneweber C, Williams-Carrier RE, Williams-Voelker PM, Kroeger TS, Vichas A, Barkan A (2006) A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA. Plant Cell 18:2650–2663CrossRefPubMedGoogle Scholar
  63. Silhavy D, Maliga P (1998) Mapping of promoters for the nucleus-encoded plastid RNA polymerase (NEP) in the iojap maize mutant. Curr Genet 33:340–344CrossRefPubMedGoogle Scholar
  64. Small ID, Peeters N (2000) The PPR motif—a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 25:46–47CrossRefPubMedGoogle Scholar
  65. Sugita M, Sugiura M (1996) Regulation of gene expression in chloroplasts of higher plants. Plant Mol Biol 32:315–326CrossRefPubMedGoogle Scholar
  66. Sugiura M, Hirose T, Sugita M (1998) Evolution and mechanism of translation in chloroplasts. Annu Rev Genet 32:437–459CrossRefPubMedGoogle Scholar
  67. Susek RE, Ausubel FM, Chory J (1993) Signal transduction mutants of Arabidopsis uncouple nuclear CAB and RBCS gene expression from chloroplast development. Cell 74:787–799CrossRefPubMedGoogle Scholar
  68. Swiatecka-Hagenbruch M, Liere K, Börner T (2007) High diversity of plastidial promoters in Arabidopsis thaliana. Mol Genet Genomics 277:725–734CrossRefPubMedGoogle Scholar
  69. Swiatecka-Hagenbruch M, Emanuel C, Hedtke B, Liere K, Börner T (2008) Impaired function of the phage-type RNA polymerase RpoTp in transcription of chloroplast genes is compensated by a second phage-type RNA polymerase. Nucleic Acids Res 36:785–792CrossRefPubMedGoogle Scholar
  70. Williams PM, Barkan A (2003) A chloroplast-localized PPR protein required for plastid ribosome accumulation. Plant J 36:675–686CrossRefPubMedGoogle Scholar
  71. Woodson JD, Chory J (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9:383–395CrossRefPubMedGoogle Scholar
  72. Yamazaki H, Tasaka M, Shikanai T (2004) PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis. Plant J 38:152–163CrossRefPubMedGoogle Scholar
  73. Yu QB, Jiang Y, Chong K, Yang ZN (2009) AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana. Plant J 59:1011–1023CrossRefPubMedGoogle Scholar
  74. Zhou W, Cheng Y, Yap A, Chateigner-Boutin AL, Delannoy E, Hammani K, Small I, Huang J (2009) The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth. Plant J 58:82–96CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Ching-Chih Tseng
    • 1
  • Tzu-Ying Sung
    • 1
  • Yi-Chiou Li
    • 1
  • Shih-Jui Hsu
    • 1
  • Chien-Li Lin
    • 1
  • Ming-Hsiun Hsieh
    • 1
  1. 1.Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan

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