[1] | Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19: 47–56.
|
[2] | Schnell DJ, Blobel G, Keegstra K, Kessler F, Ko K, et al. (1997) A consensus nomenclature for the protein-import components of the chloroplast envelope. Trends Cell Biol 7: 303–304.
|
[3] | Li HM, Chiu CC (2010) Protein transport into chloroplasts. Annu Rev Plant Biol 61: 157–180.
|
[4] | Strittmatter P, Soll J, B?lter B (2010) The chloroplast protein import machinery: a review. Methods Mol Biol 619: 307–321.
|
[5] | Richter S, Zhong R, Lamppa G (2005) Function of the stromal processing peptidase in the chloroplast import pathway. Physiol Plant 123: 362–368.
|
[6] | Schünemann D (2007) Mechanisms of protein import into thylakoids of chloroplasts. Biol Chem 388: 907–915.
|
[7] | Aldridge C, Cain P, Robinson C (2009) Protein transport in organelles: Protein transport into and across the thylakoid membrane. FEBS J 276: 1177–1186.
|
[8] | 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.
|
[9] | Robinson C, Mant A (2005) Biogenesis of the thylakoid membrane. In: M?ller SG, editor. Plastids. Oxford, UK: Blackwell Publishing. pp. 180–213.
|
[10] | Voelker R, Barkan A (1995) Nuclear genes required for post-translational steps in the biogenesis of the chloroplast cytochrome b(6)f complex in maize. Mol Gen Genet 249: 507–514.
|
[11] | Nohara T, Asai T, Nakai M, Sugiura M, Endo T (1996) Cytochrome f encoded by the chloroplast genome is imported into thylakoids via the SecA-dependent pathway. Biochem Biophys Res Commun 224: 474–478.
|
[12] | Mould RM, Knight JS, Bogsch E, Gray JC (1997) Azide-sensitive thylakoid membrane insertion of chimeric cytochrome f polypeptides imported by isolated pea chloroplasts. Plant J 11: 1051–1058.
|
[13] | Smeekens S, Bauerle C, Hageman J, Keegstra K, Weisbeek (1986) The role of the transit peptide in the routing of precursors toward different chloroplast compartments. Cell 46: 365–375.
|
[14] | Hageman J, Robinson C, Smeekens S, Weisbeek P (1986) A thylakoid processing peptidase is required for complete maturation of the lumen protein plastocyanin. Nature 324: 567–569.
|
[15] | Kirwin PM, Elderfield PD, Robinson C (1987) Transport of proteins into chloroplasts. Partial purification of a thylakoidal processing peptidase involved in plastocyanin biogenesis. J Biol Chem 262: 16386–16390.
|
[16] | Kirwin PM, Elderfield PD, Williams RS, Robinson C (1988) Transport of proteins into chloroplasts. Organization, orientation, and lateral distribution of the plastocyanin processing peptidase in the thylakoid network. J Biol Chem 263: 18128–18132.
|
[17] | James HE, Bartling D, Musgrove JE, Kirwin PM, Herrmann RG, et al. (1989) Transport of proteins into chloroplasts. Import and maturation of precursors to the 33-, 23-, and 16-kDa proteins of the photosynthetic oxygen-evolving complex. J Biol Chem 264: 19573–19576.
|
[18] | Halpin C, Elderfield PD, James HE, Zimmermann R, Dunbar B, et al. (1989) The reaction specificities of the thylakoidal processing peptidase and Escherichia coli leader peptidase are identical. EMBO J 8: 3917–3921.
|
[19] | Wallace TP, Robinson C, Howe CJ (1990) The reaction specificities of the pea and a cyanobacterial thylakoid processing peptidase are similar but not identical. FEBS Lett 272: 141–144.
|
[20] | Shackleton JB, Robinson C (1991) Transport of proteins into chloroplasts. The thylakoidal processing peptidase is a signal-type peptidase with stringent substrate requirements at the ?3 and ?1 positions. J Biol Chem 266: 12152–12156.
|
[21] | Chaal BK, Ishida K, Green BR (2003) A thylakoidal processing peptidase from the heterokont alga Heterosigma akashiwo. Plant Mol Biol 52: 463–472.
|
[22] | Paetzel M, Karla A, Strynadka NC, Dalbey RE (2002) Signal peptidases. Chem Rev 102: 4549–4580.
|
[23] | Date T (1983) Demonstration by a novel genetic technique that leader peptidase is an essential enzyme of Escherichia coli. J Bacteriol 154: 76–83.
|
[24] | Dalbey RE, Wickner W (1985) Leader peptidase catalyzes the release of exported proteins from the outer surface of the Escherichia coli plasma membrane. J Biol Chem 260: 15925–15931.
|
[25] | Cregg KM, Wilding I, Black MT (1996) Molecular cloning and expression of the spsB gene encoding an essential type I signal peptidase from Staphylococcus aureus. J Bacteriol 178: 5712–5718.
|
[26] | Zhang YB, Greenberg B, Lacks SA (1997) Analysis of a Streptococcus pneumoniae gene encoding signal peptidase I and overproduction of the enzyme. Gene 194: 249–255.
|
[27] | Tjalsma H, Bolhuis A, van Roosmalen ML, Wiegert T, Schumann W, et al. (1998) Functional analysis of the secretory precursor processing machinery of Bacillus subtilis: identification of a eubacterial homolog of archaeal and eukaryotic signal peptidases. Genes Dev 12: 2318–2331.
|
[28] | Zhbanko M, Zinchenko V, Gutensohn M, Schierhorn A, Klosgen RB (2005) Inactivation of a predicted leader peptidase prevents photoautotrophic growth of Synechocystis sp. strain PCC 6803. J Bacteriol 187: 3071–3078.
|
[29] | Green N, Fang H, Miles S, Lively MO (2001) Structure and function of the endoplasmic reticulum signal peptidase complex. In: Dalbey R, Sigman DS, editors. Co- and Posttranslational Proteolysis of Poteins: the Enzymes vol XXII. San Diego, CA: Academic Press. pp. 57–75.
|
[30] | Howe CJ, Floyd KA (2001) Chloroplast and mitochondrial type I signal peptidases. In: Dalbey R, Sigman DS, editors. Co- and Posttranslational Proteolysis of Poteins: the Enzymes vol XXII. San Diego, CA: Academic Press. pp. 101–125.
|
[31] | Nunnari J, Fox TD, Walter P (1993) A mitochondrial protease with two catalytic subunits of nonoverlapping specificities. Science 262: 1997–2004.
|
[32] | Chaal BK, Mould RM, Barbrook AC, Gray JC, Howe CJ (1998) Characterization of a cDNA encoding the thylakoidal processing peptidase from Arabidopsis thaliana. Implications for the origin and catalytic mechanism of the enzyme. J Biol Chem 273: 689–692.
|
[33] | Tripathi LP, Sowdhamini R (2006) Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genomics 7: 200.
|
[34] | Inoue K, Baldwin AJ, Shipman RL, Matsui K, Theg SM, et al. (2005) Complete maturation of the plastid protein translocation channel requires a type I signal peptidase. J Cell Biol 171: 425–430.
|
[35] | Shipman-Roston RL, Ruppel NJ, Damoc C, Phinney BS, Inous K (2010) The significant of protein maturation by plastidic type I signal peptidase 1 for thylakoid development in Arabidopsis chloroplasts. Plant Physiol 152: 1297–1308.
|
[36] | Shipman RL, Inoue K (2009) Suborganellar localization of plastidic type I signal peptidase 1 depends on chloroplast development. FEBS Lett 583: 938–994.
|
[37] | Endow JK, Ruppel NJ, Inoue K (2010) Keep the balloon deflated: the significance of protein maturation for thylakoid flattening. Plant Signal Behav 5: 721–723.
|
[38] | Carlos JL, Paetzel M, Brubaker G, Karla A, Ashwell CM, et al. (2000) The role of the membrane-spanning domain of type I signal peptidases in substrate cleavage site selection. J Biol Chem 275: 38813–38822.
|
[39] | Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433–438.
|
[40] | Blanc G, Hokamp K, Wolfe KH (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137–144.
|
[41] | Yu F, Park S, Rodermel SR (2004) The Arabidopsis FtsH metalloprotease gene family: interchangeability of subunits in chloroplast oligomeric complexes. Plant J 37: 864–876.
|
[42] | Zaltsman A, Ori N, Adam Z (2005) Two types of FtsH protease subunits are required for chloroplast biogenesis and Photosystem II repair in Arabidopsis. Plant Cell 17: 2782–2790.
|
[43] | Coate JE, Schlueter J, Whaley A, Doyle J (2011) Comparative evolution of photosynthetic genes in response to polyploid and non-polyploid duplication. Plant Physiol 155: 2081–2095.
|
[44] | Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, et al. (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinform 2008: 420747.
|
[45] | Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W-R (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in arabidopsis. Plant Physiol 139: 5–17.
|
[46] | Murakami R, Ifuku K, Takabayashi A, Shikanai T, Endo T, et al. (2005) Functional dissection of two Arabidopsis PsbO proteins: PsbO1 and PsbO2. FEBS J 272: 2165–2175.
|
[47] | Lundin B, Nurmi M, Rojas-Stuetz M, Aro EM, Adamska I, et al. (2008) Towards understanding the functional difference between the two PsbO isoforms in Arabidopsis thaliana–insights from phenotypic analyses of psbo knockout mutants. Photosynth Res 98: 405–414.
|
[48] | Baldwin AJ, Inoue K (2006) The most C-terminal tri-glycine segment within the polyglycine stretch of the pea Toc75 transit peptide plays a critical role for targeting the protein to the chloroplast outer envelope membrane. FEBS J 273: 1547–1555.
|
[49] | Inoue K, Keegstra K (2003) A polyglycine stretch is necessary for proper targeting of the protein translocation channel precursor to the outer envelope membrane of chloroplasts. Plant J 34: 661–669.
|
[50] | Firlej-Kwoka E, Strittmatter P, Soll J, B?lter B (2008) Import of preproteins into the chloroplast inner envelope membrane. Plant Mol Biol 68: 505–519.
|
[51] | Tripp J, Inoue K, Keegstra K, Froehlich JE (2007) A novel serine/proline-rich domain in combination with a transmembrane domain is required for the insertion of AtTic40 into the inner envelope membrane of chloroplasts. Plant J 52: 824–838.
|
[52] | Whatley BJM (1983) Plastids in the roots of Paseolus vulgaris. New Phytol 94: 381–391.
|
[53] | Skalitzky CA, Martin JR, Harwood JH, Beirne JJ, Adamczyk BJ, et al. (2011) Plastids contain a second sec translocase system with essential functions. Plant Physiol 155: 354–369.
|
[54] | Rodrigues RAO, Silva-Filho MC, Cline K (2011) FtsH2 and FtsH5: two homologous subunits use different integration mechanisms leading to the same thylakoid multimeric complex. Plant J 65: 600–609.
|
[55] | Matsuzaki M, Misumi O, Shin IT, Maruyama S, Takahara M, et al. (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653–657.
|
[56] | Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, et al. (2005) The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138: 1310–1317.
|
[57] | Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, et al. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991–996.
|
[58] | Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183.
|
[59] | Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596–1604.
|
[60] | Lang D, Eisinger J, Reski R, Rensing SA (2005) Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses. Plant Biol (Stuttg) 7: 238–250.
|
[61] | Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205–217.
|
[62] | Felsenstein J (2009) PHYLIP (Phylogeny Inference Package) version 3.69. Department of Genome Sciences, University of Washington, Seattle.
|
[63] | Patel R, Hsu S-C, Bédard J, Inoue K, Jarvis P (2008) The Omp85-related chloroplast outer envelope protein OEP80 is essential for viability in Arabidopsis. Plant Physiol 148: 235–245.
|
[64] | Inoue K, Potter D (2004) The chloroplastic protein translocation channel Toc75 and its paralog OEP80 represent two distinct protein families and are targeted to the chloroplastic outer envelope by different mechanisms. Plant J 39: 354–365.
|
[65] | 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.
|
[66] | Becker D (1990) Binary vectors which allow the exchange of plant selectable markers and reporter genes. Nucleic Acids Res 18: 203.
|
[67] | Curtis MD, Grossniklaus U (2003) A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 33: 462–469.
|
[68] | Clough SJ, Bent AF (1998) Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735–743.
|
[69] | Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8: 978–984.
|