Origin and Evolution of Plastids: Genomic View on the Unification and Diversity of Plastids

  • Naoki Sato
Part of the Advances in Photosynthesis and Respiration book series (AIPH, volume 23)

The notion “plastid” unifies the diversity of various plastids in diverse photosynthetic eukaryotes and certain non-photosynthetic parasites. Plastid diversity can be seen in the photosynthetic or metabolic capacities, the photosynthetic accessory pigments, the architecture of plastid membranes, and the size and content of plastid genomes. The central unifying principle is that all plastids are bound by two envelope membranes and possess plastid DNA, which was inherited from an ancestral cyanobacterial endosymbiont. Although phylogenetic analysis of the relationship between cyanobacteria and plastids does not identify the cyanobacterial species nearest to the plastid origin or the branching order of various plastids lineages, the radiation of both extant cyanobacteria and plastids is estimated to have occurred on a similar geological timescale. In addition to two major secondary endosymbiogenesis each involving a red and a green algal endosymbionts, tertiary endosymbiotic events have been proposed to explain the origin of diverse dinoflagellates. A new concept of plants suggests that all hosts of secondary or tertiary plastid endosymbiogenesis had once possessed primary plastids and subsequently lost them, and thereby they had been prepared to accept new plastids. In spite of these recent developments in plastid phylogeny that demonstrate continuity of plastid genomes, discontinuous evolution of plastid genomic machinery is another aspect of plastid evolution. Plastids gained various regulatory mechanisms from their host organisms during the evolution of land plants such that the genomic machinery that runs the plastid genome of the flowering plants no longer looks like red algal counterparts, nor even the cyanobacterial genomic machinery.


Plastid Genome Envelope Membrane Single Origin Photosynthetic Eukaryote Plastid Evolution 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Abdallah F, Salamini F and Leister D (2000) A prediction of the size and evolutionary origin of the proteome of chloroplasts of Arabidopsis. Trends Plant Sci 5: 141-142PubMedGoogle Scholar
  2. Adachi J and Hasegawa M (1996) MOLPHY: programs for molecular phylogenetics, version 2.3. Institute of Statistical Mathematics, TokyoGoogle Scholar
  3. Aitken A and Stanier RY (1979) Characterization of peptido- glycan from the cyanelles of Cyanophora paradoxa. J Gen Microbiol 112: 219-223Google Scholar
  4. Andersson JO (2000) Evolutionary genomics: Is Buchnera a bac- terium or an organelle? Curr Biol 10: R866-R868PubMedGoogle Scholar
  5. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815Google Scholar
  6. Archibald JM and Keeling PJ (2002) Recycled plastids: a “green movement” in eukaryotic evolution. Trends Genet 18: 577-584PubMedGoogle Scholar
  7. Baba K, Nakano T, Yamagishi K. and Yoshida S (2001) Involve- ment of a nuclear-encoded basic helix-loop-helix protein in transcription of the light-responsive promoter of psbD. Plant Physiol 125: 595-603PubMedGoogle Scholar
  8. Baldauf SL, Roger AJ, Wenk-Siefert I and Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977PubMedGoogle Scholar
  9. Besendahl A, Qiu Y-L, Lee J, Palmer JD and Bhattacharya D (2000) The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I intron. Curr Genet 37: 12-23PubMedGoogle Scholar
  10. Bligny M, Courtois F, Thaminy S, Chang CC, Lagrange T, Baruah-Wolff J, Stern D and Lerbs-Mache S (2000) Regu- lation of plastid rDNA transcription by interaction of CDF2 with two different RNA polymerase. EMBO J 19: 1851-1860PubMedGoogle Scholar
  11. Boivin R, Richard M, Beauseigle D, Bousquet J and Bellemare G (1996) Phylogenetic inferences from chloroplast chlB gene sequences of Nephrolepis exaltata (Filicopsida), Ephedra al- tissima (Gnetopsida), and diverse land plants. Mol Phylogenet Evol 6: 19-29PubMedGoogle Scholar
  12. Browse J, Warwick N, Somerville CR and Slack CR (1986) Fluxes through the prokaryotic and eukaryotic pathways of lipid synthesis in the “16:3” plant Arabidopsis thaliana. Biochem J 235: 25-31PubMedGoogle Scholar
  13. Cavalier-Smith T (1982) The origins of plastids. Biol J Linn Soc 17: 289-306Google Scholar
  14. Cavalier-Smith T (2003) Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). Phil Trans R Soc Lond B 358: 109-134Google Scholar
  15. Chew O, Lister R, Qbadou S, Heazlewood JL, Soll J, Schleiff E, Millar AH and Whelan J (2004) A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor. FEBS Lett 557: 109-114PubMedGoogle Scholar
  16. Cummings MP, Nugent JM, Olmstead RG and Palmer JD (2003) Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in an-giosperms. Curr Genet 43: 131-138PubMedGoogle Scholar
  17. Delwiche CF and Palmer JD (1996) Rampant horizontal transfer and duplication of Rubisco genes in eubacteria and plastids. Mol Biol Evol 13: 873-882PubMedGoogle Scholar
  18. Dodge JD (1973) The Fine Structure of Algal Cells. Academic Press, LondonGoogle Scholar
  19. Dolganov NAM, Bhaya D and Grossman AR (1995) Cyanobacterial protein with similarity to the chlorophyll a/b- binding proteins of higher plants: Evolution and regulation. Proc Natl Acad Sci USA 92: 636-640PubMedGoogle Scholar
  20. Douce R and Joyard J (1990) Biochemistry and function of the plastid envelope. Annu Rev Cell Biol 6: 173-216PubMedGoogle Scholar
  21. Douglas SE and Turner S (1991) Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor. J Mol Evol 33: 267-273PubMedGoogle Scholar
  22. Douglas SE, Murphy CA, Spencer DF and Gray MW (1991) Cryptomonad algae are evolutionary chimaeras of two phylo- genetically distinct unicellular eukaryotes. Nature 350: 148-151PubMedGoogle Scholar
  23. Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng L-T, Wu X, Reith M, Cavalier-Smith T and Maier U-G (2001) The highly reduced genome of an enslaved algal nucleus. Na-ture 410: 1091-1096Google Scholar
  24. Durnford DG, Deane JA, Tan S, McFadden GI, Gantt E and Green BR (1999) A phylogenetic assessment of the eukaryotic light-harvesting antenna proteins, with implications for plastid evolution. J Mol Evol 48: 59-68PubMedGoogle Scholar
  25. Eckart K, Eichacker L, Sohrt K, Schleiff E, Heins L and Soll J (2002) A Toc75-like protein import channel is abundant in chloroplasts. EMBO Rep 3: 557-562PubMedGoogle Scholar
  26. Ellis J (1982) Promiscuous DNA-chloroplast genes inside plant mitochondria. Nature 299: 678-679PubMedGoogle Scholar
  27. Erwin JA (1973) Comparative biochemistry of fatty acids in eukaryotic microorganisms. In: Erwin JA (ed) Lipids and Biomembranes of Eukaryotic Microorganisms, pp 41-143. Academic Press, New YorkGoogle Scholar
  28. Fast NM, Kissinger JC, Roos DS and Keeling PJ (2001) Nuclear- encoded, plastid-targeted genes suggest a single common ori- gin for apicomplexan and dinoflagellate plastids. Mol Biol Evol 18: 418-426PubMedGoogle Scholar
  29. Fichera ME and Roos DS (1997) A plastid organelle as a drug target in apicomplexan parasites. Nature 390: 407-409PubMedGoogle Scholar
  30. Fliée J, Forterre P, Sen-Lin T and Laurent J (2002) Evolution of DNA polymerase families: Evidence for multiple gene ex- change between cellular and viral proteins. J Mol Evol 54: 763-773Google Scholar
  31. Fujita Y (1996) Protochlorophyllide reduction: a key step in the greening of plants. Plant Cell Physiol 37: 411-421PubMedGoogle Scholar
  32. Funes S, Davidson E, Reyes-Prieto A, Magall ón S, Herion P, King MP and Gonz ález-Halphen D (2002) A green algal apicoplast ancestor. Science 298: 2155PubMedGoogle Scholar
  33. Gaikwad A, Hop DV and Mukherjee SK (2002) A 70-kDa chloro- plast DNA polymerase from pea (Pisum sativum) that shows high processivity and displays moderate fidelity. Mol Genet Genomics 267: 45-56PubMedGoogle Scholar
  34. Grasser KD, Ritt C, Krieg M, Fern ádez S, Alonso JC and Grimm R (1997) The recombinant product of the Cryptomonas [Phi] plastid gene hlpA is an architectural HU-like protein that promotes the assembly of complex nucleoprotein structures. Eur J Biochem 249: 70-76PubMedGoogle Scholar
  35. Gray MW and Doolittle WF (1982) Has the endosymbiont hy- pothesis been proven? Microbiol Rev 46: 1-42PubMedGoogle Scholar
  36. Gupta RS (1998) Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebac- teria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62: 1435-1491PubMedGoogle Scholar
  37. Hallick RB, Hong L, Drager RG, Favreau MR, Monfort A, Orsat B, Spielmann A and Stutz E (1993) Complete sequence of Eu- glena gracilis chloroplast DNA. Nucleic Acids Res 21: 3537-3544PubMedGoogle Scholar
  38. Hannaert V, Saavedra E, Duffieux F, Szikora J-P, Rigden DJ, Michels PAM and Opperdoes FR (2003) Plant-like traits as- sociated with metabolism of Trypanosoma parasites. Proc Natl Acad Sci USA 100: 1067-1071PubMedGoogle Scholar
  39. Harwood JL and Jones AL (1989) Lipid metabolism in algae. Adv Bot Res 16: 1-53Google Scholar
  40. Hedges SB, Chen H, Kumar S, Wang DY-C, Thompson AS and Watanabe H (2001) A genomic timescale for the origin of eukaryotes. BMC Evol Biol 1: 4-13PubMedGoogle Scholar
  41. Hedtke B, B örner T and Weihe A (1997) Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Sci- ence 277: 809-811Google Scholar
  42. Hess WR, Partensky F, van der Staay GWM, Garcia-Fernandez JM, B örner T and Vaulot D (1996) Coexistence of phycoery- thrin and a chlorophyll a/b antenna in a marine prokaryote. Proc Natl Acad Sci USA 93: 11126-11130PubMedGoogle Scholar
  43. Hess WR, Rocap G, Ting CS, Larimer F, Stilwagen S, Lamerdin J and Chisholm SW (2001) The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics. Photosynth Res 70: 53-71PubMedGoogle Scholar
  44. Honda D, Yokota A and Sugiyama J (1999) Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new se-quences of five marine Synechococcus strains. J Mol Evol 48: 723-739PubMedGoogle Scholar
  45. Huang CY, Ayliffe MA and Timmis JN (2003) Direct measure- ment of the transfer rate of chloroplast DNA into the nucleus. Nature 422: 72-76PubMedGoogle Scholar
  46. Ishida K and Green BR (2002) Second- and third-hand chloroplasts in dinoflagellates: Phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear- encoded plastid gene by that of a haptophyte tertiary endosym-biont. Proc Natl Acad Sci USA 99: 9294-9299PubMedGoogle Scholar
  47. Jarvis P and Soll J (2001) Toc, Tic, and chloroplast import. Biochim Biophys Acta 1541: 64-79PubMedGoogle Scholar
  48. Jeong SY, Rose A, Meier I (2003) MFP1 is a thylakoid- associated, nucleoid-binding protein with a coiled-coil struc- ture. Nucleic Acids Res 31: 5175-5185PubMedGoogle Scholar
  49. Kabeya Y and Sato N (2005) Unique translation initiation at the second AUG codon determines mitochondrial localization of the phage-type RNA polymerases in the moss Physcomitrella patens. Plant Physiol 138: 369-382PubMedGoogle Scholar
  50. Kabeya Y, Hashimoto K and Sato N (2002) Identification and characterization of two phage-type RNA polymerase cDNAs in the moss Physcomitrella patens: Implication of recent evo-lution of nuclear-encoded RNA polymerase of plastids in plants. Plant Cell Physiol 43: 245-255PubMedGoogle Scholar
  51. Kabeya Y, Sekine K and Sato N (2004) Evolution of organellar transcription machinery in bryophytes and vascular plants. In: Wood AJ (ed) New Frontiers in Bryology, pp inpress. Kluwer Academic Publishers, DordrechtGoogle Scholar
  52. Kenrick P and Crane PR (1997) The origin and early evolution of plants on land. Nature 389: 33-39Google Scholar
  53. Kenyon CN (1972) Fatty acid composition of unicellular strains of blue-green algae. J Bacteriol 109: 827-834PubMedGoogle Scholar
  54. Kimura S, Uchiyama Y, Kasai N, Namekawa S, Saotome A, Ueda T, Ando T, Ishibashi T, Oshige M, Furukawa T, Yamamoto T, Hashimoto J and Sakaguchi K (2002) A novel DNA poly-merase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa). Nucleic Acids Res 30: 1585-1592PubMedGoogle Scholar
  55. Kirk JTO and Tilney-Bassett RAE (1967) The Plastids, Freeman, LondonGoogle Scholar
  56. Kobayashi T, Takahara M, Miyagishima S, Kuroiwa H, Sasaki N, Ohta N, Matsuzaki M and Kuroiwa T (2002) Detection and localization of a chloroplast-encoded HU-like protein that organizes chloroplast nucleoids. Plant Cell 14: 1579-1589PubMedGoogle Scholar
  57. Kolodner RD and Tewari KK (1975). Chloroplast DNA from higher plants replicates by both the Cairns and the rolling circle mechanism. Nature 256: 708-711PubMedGoogle Scholar
  58. Kumar S, Tamura K, Jakobsen IB and Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinfor- matics 17: 1244-1245Google Scholar
  59. Kusumi J, Tsumura Y, Yoshimaru H and Tachida H (2000) Phylo- genetic relationships in Taxodiaceae and Cupressaceae sensu based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences. Amer J Bot 87: 1480-1488Google Scholar
  60. Lemieux C, Otis C and Turmel M (2000) Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature 403: 649-652PubMedGoogle Scholar
  61. Lewin (1976) Prochlorophyta as a proposed new division of al- gae. Nature 261: 697-698PubMedGoogle Scholar
  62. Lutziger I and Oliver DJ (2000) Molecular evidence of a unique lipoamide dehydrogenase in plastids: analysis of plastidic lipoamide dehydrogenase from Arabidopsis thaliana. FEBS Lett 484: 12-16PubMedGoogle Scholar
  63. McConn M and Browse J (1996) The critical requirement for linolenic acid is pollen development, not photosynthesis, in an Arabidopsis mutant. Plant Cell 8: 403-416PubMedGoogle Scholar
  64. Maliga P (1998) Two plastid RNA polymerases of higher plants: an evolving story. Trends Plant Sci 3: 4-6Google Scholar
  65. Margulis L (1970) Origin of the Eukaryotic Cells. Yale University Press, New HavenGoogle Scholar
  66. Marin B, Palm A, Klingberg M and Melkonian M (2003) Phylogeny and taxonomic revision of plastid-containing eu- glenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary struc- ture. Protist 154: 99-145PubMedGoogle Scholar
  67. Martin W and Schnarrenberger C (1997) The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis. Curr Genet 32: 1-18PubMedGoogle Scholar
  68. Martin W, Stoebe B, Goremykin V, Hapsmann S, Hasegawa M and Kowallik KV (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393: 162-165PubMedGoogle Scholar
  69. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M and Penny D (2002) Evolu- tionary analysis of Arabidopsis, cyanobacterial, and chloro-plast genomes reveals plastid phylogeny and thousands of cyanobactgerial genes in the nucleus. Proc Natl Acad Sci USA 99: 12246-12251PubMedGoogle Scholar
  70. Maruyama K, Sato N and Ohta N (1999) Conservation of structure and cold-regulation of RNA-binding proteins in cyanobacteria: probable convergent evolution with eukaryotic glycine-rich RNA-binding proteins. Nucleic Acids Res 27: 2029-2036PubMedGoogle Scholar
  71. Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y and Kuroiwa T (2004) Genome sequence of the ultra-small unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653-657PubMedGoogle Scholar
  72. McFadden GI (2001) Chloroplast origin and integration. Plant Physiol 125: 50-53PubMedGoogle Scholar
  73. Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermiin LS and Wolfe KH (2001) Many parallel losses of infA from chloroplast DNA during angiosperm evo- lution with multiple independent transfers to the nucleus. Plant Cell 13: 645-658PubMedGoogle Scholar
  74. Miras S, Salvi D, Ferro M, Grunwald D, Garin J, Joyard J and Rolland N (2002) Non-canonical transit peptide for import into the chloroplast. J Biol Chem 277: 47770-47778PubMedGoogle Scholar
  75. Miyagishima S, Nishida K and Kuroiwa T (2003) An evolu- tionary puzzle: chloroplast and mitochondrial division rings. Trends Plant Sci 8: 432-438PubMedGoogle Scholar
  76. Miyajima K, Sekine K, Kabeya Y, Ehira S, Togawa Y and Sato N (2004) Comparative structural and functional analysis of cyanobacterial nucleoids. Roles of HU and SiR in the nu-cleoids. Plant Cell Physiol 45: s209Google Scholar
  77. Montgomery BL and Lagarias JC (2002) Phytochrome ances- try: sensors of bilins and light. Trends Plant Sci 7: 357-366PubMedGoogle Scholar
  78. Moreira D, Le Guyader H and Philippe H (2000) The origin of red algae and the evolution of chloroplasts. Nature 405: 69-72PubMedGoogle Scholar
  79. Moretti A and Nazzaro R (1980) Fatty acids in thermoacidophilic algae. Delpinoa 21: 4-11Google Scholar
  80. Moriyama T, Miyajima K, Kuroiwa T and Sato N (2003) Detection of organellar localized DNA polymerases from a unicellular red alga Cyanidioschyzon merolae. J Plant Res 116 supplement: abstract 323Google Scholar
  81. M ühlbauer SK, L össl A, Tzekova L, Zou Z and Koop H-U (2002) Functional analysis of plastid DNA replication origins in to- bacco by targeted inactivation. Plant J 32: 175-184Google Scholar
  82. Murata N and Sato N (1983) Analysis of lipids in Prochloron sp.: Occurrence of monoglucosyl diacylglycerol. Plant Cell Physiol 24: 133-138.Google Scholar
  83. Nakamura T, Ohta M, Sugiura M and Sugita M (2001) Chloro- plast ribonucleoproteins function as a stabilizing factor of ribosome-free mRNAs in the stroma. J Biol Chem 276: 147-152PubMedGoogle Scholar
  84. Nelissen B, Van de Peer Y, Wilmotte A and De Wachter R (1995) An early origin of plastids within the cyanobacterial diver- gence is suggested by evolutionary trees based on complete 16S rRNA sequences. Mol Biol Evol 12: 1166-1173PubMedGoogle Scholar
  85. Nomata T, Kabeya Y and Sato N (2004) Cloning and charac- terization of glycine-rich RNA-binding protein cDNAs in the moss Physcomitrella patens. Plant Cell Physiol 45: 48-56PubMedGoogle Scholar
  86. Nozaki H, Matsuzaki M, Takahara M, Misumi O, Kuroiwa H, Hasegawa M, Shin-i T, Kohara Y, Ogasawara N and Kuroiwa T (2003a) The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukary- otes and an alternative hypothesis on the origin of plastids. J Mol Evol 56: 485-497Google Scholar
  87. Nozaki H, Ohta N, Matsuzaki M, Misumi O and Kuroiwa T (2003b) Phylogeny of plastids based on cladistic analysis of gene loss inferred from complete plastid genome sequences. J Mol Evol 57: 377-382Google Scholar
  88. Ohta N, Sato N, Kawano S and Kuroiwa T (1991) Methylation of DNA in the chloroplasts and amyloplasts of the pea, Pisum sativum. Plant Sci 78: 33-42Google Scholar
  89. Ohta N, Sato N, Nozaki H and Kuroiwa T (1997) Analysis of the cluster of ribosomal protein genes in the plastid genome of a unicellular red alga Cyanidioschyzon merolae: Translo-cation of the str cluster as an early event in the Rhodophyte- Chromophyte lineage of plastid evolution. J Mol Evol 45: 688-695PubMedGoogle Scholar
  90. Osteryoung KW and Nunnari J (2003) The division of endosym- biotic organelles. Science 302: 1698-1704PubMedGoogle Scholar
  91. Palmer JD (2003) The symbiotic birth and spread of plastids: How many times and whodunit? J Phycol 39: 4-11Google Scholar
  92. Parkinson CL, Adams KL and Palmer JD (1999) Multigene anal- yses identify the three earliest lineages of extant flowering plants. Curr Biol 9: 1485-1488PubMedGoogle Scholar
  93. Peeters N and Small I (2001) Dual targeting to mitochondria and chloroplasts. Biochim Biophys Acta 1541: 54-63PubMedGoogle Scholar
  94. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY and Blankenship RE (2002) Whole-genome analysis of photosyn- thetic prokaryotes. Science 298: 1616-1620PubMedGoogle Scholar
  95. Richter U, Kiessling J, Hedtke B, Decker E, Reski R, B örner T and Weihe A (2002) Two RpoT genes of Physcomitrella patens encode phage-type RNA polymerases with dual targeting to mitochondria and plastids. Gene 290: 95-105PubMedGoogle Scholar
  96. Ronquist F and Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574PubMedGoogle Scholar
  97. Roughan G and Slack CR (1982) Cellular organization of glyc- erolipid metabolism. Annu Rev Plant Physiol 33: 97-132Google Scholar
  98. Routaboul J-M, Fischer SF and Browse J (2000) Trienoic fatty acids are required to maintain chloroplast function at low tem- perature. Plant Physiol 124: 1697-1705PubMedGoogle Scholar
  99. Sakai A (2001) In vitro transcription / DNA synthesis system using isolated organelle-nuclei: Application to the analysis on the mechanisms regulating the function of organelle genomes. J Plant Res 114: 199-211Google Scholar
  100. Sakurai I, Hagio M, Gombos Z, Tyystj ärvi T, Paakkarinen V, Aro E-M and Wada H (2003) Requirement of phosphatidyl- glycerol for maintenance of photosynthetic machinery. Plant Physiol 133: 1-9Google Scholar
  101. Sato N (1991) Lipids in Cryptomonas CR-1. II. Biosynthesis of betaine lipids and galactolipids. Plant Cell Physiol 32: 845-851Google Scholar
  102. Sato N (1992) Betaine lipids. Bot Mag Tokyo 105: 185-197Google Scholar
  103. Sato N (2001) Was the evolution of plastid genetic machinery discontinuous? Trends Plant Sci 6: 151-156PubMedGoogle Scholar
  104. Sato N (2002) Comparative analysis of the genomes of cyanobac- teria and plants. Genome Inform 13: 173-182PubMedGoogle Scholar
  105. Sato N (2003a) Gclust: genome-wide clustering of protein se- quences for identification of photosynthesis-related genes re- sulting from massive horizontal gene transfer. Genome Inform 14: 585-586Google Scholar
  106. Sato N (2003b) Bioinformatics of evolution of metabolic sys- tem. Tanpakushitsu Kakusan Koso (in Japanese) 48: 2211-2217Google Scholar
  107. Sato N and Murata N (1982) Lipid biosynthesis in the blue-green alga, Anabaena variabilis I. Lipid classes. Biochim Biophys Acta 710: 271-278Google Scholar
  108. Sato N, Sonoike K, Tsuzuki M and Kawaguchi A (1995) Impaired photosyntem II in a mutant of Chlamydomonas reinhardtii defective in sulfoquinovosyl diacylglycerol. Eur J Biochem 234: 16-23PubMedGoogle Scholar
  109. Sato N, Ohshima K, Watanabe A, Ohta N, Nishiyama Y, Jo- yard J and Douce R (1998) Molecular characterization of the PEND protein, a novel bZIP protein present in the envelope membrane that is the site of nucleoid replication in developing plastids. Plant Cell 10: 859-872PubMedGoogle Scholar
  110. Sato N, Nakayama M and Hase T (2001) The 70-kDa major DNA-compacting protein of the chloroplast nucleoid is sulfite reductase. FEBS Lett 487: 347-350PubMedGoogle Scholar
  111. Sato N, Terasawa K, Miyajima K and Kabeya Y (2003) Organi- zation, developmental dynamics and evolution of the plastid nucleoids. Int Rev Cytol 232: 217-262PubMedGoogle Scholar
  112. Sato N, Sekine K, Kabeya Y, Ehira S, Onuma M and Ohta N (2004) Discontinuous evolution of plastid genomic machin- ery: Radical replacement of major DNA-binding proteins. En-docytobiosis Cell Res 15: 286-293Google Scholar
  113. Savolainen V, Chase MW, Hoot SB, Morton CM, Soltis DE, Bayer C, Fay MF, de Bruijn AY, Sullivan S and Qiu YL (2000) Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst Biol 49: 306-62PubMedGoogle Scholar
  114. Schimper AFW (1885) Untersuchungen über die Chloro- phyllk örper und die ihnen homologen Gebilde. J Wissen Bot 1-247Google Scholar
  115. Schopf JW (1993) Microfossils of the early Archean apex chert: New evidence of the antiquity of life. Science 260: 640-646PubMedGoogle Scholar
  116. Schuster W and Brennicke A (1987) Plastid, nuclear and re- verse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between or- ganelles via RNA? EMBO J 6: 2857-2863PubMedGoogle Scholar
  117. Sekine K, Hase T and Sato N (2002) Reversible DNA com- paction by sulfite reductase regulates transcriptional activity of chloroplast nucleoids. J Biol Chem 277: 24399-24404PubMedGoogle Scholar
  118. Selstam E and Campbell D (1996) Membrane lipid composi- tion of the unusual cyanobacterium Gloeobacter violaceus sp. PCC 7421, which lacks sulfoquinovosyl diacylglycerol. Arch Microbiol 166: 132-135Google Scholar
  119. Shahmuradov IA, Akbarova YY, Solovyev VV and Aliyev JA (2003) Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Plant Mol Biol 52: 923-934PubMedGoogle Scholar
  120. Steiner JM and L öffelhardt W (2002) Protein import into cyanelles. Trends Plant Sci 7: 72-77PubMedGoogle Scholar
  121. Stegemann S, Hartmann S, Ruf S and Bock R (2003) High- frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci USA 100: 8828-8833PubMedGoogle Scholar
  122. Stern DB and Lonsdale DM (1982) Mitochondrial and chloro- plast genomes of maize have a 12-kilobase DNA sequence in common. Nature 299: 698-702PubMedGoogle Scholar
  123. Stiller JW, Reel DC and Johnson JC (2003) A single origin of plastids revisited: Convergent evolution in organellar genome content. J Phycol 39: 95-105Google Scholar
  124. Stirewalt VL, Michalowski CB, L öfelhardt W, Bohnert HJ and Bryant DA (1995) Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa. Plant Mol Biol Rept 13: 327-332Google Scholar
  125. Stoebe B and Kowallik KV (1999) Gene-cluster analysis in chloroplast genomics. Trends Genet 15: 344-347PubMedGoogle Scholar
  126. Strimmer K and von Haeseler A (1996) Quartet puzzling: a quar- tet maximum likelihood method for reconstructing tree topolo- gies. Mol Biol Evol 13: 964-996Google Scholar
  127. Sugiura C, Kobayashi Y, Aoki S, Sugita C and Sugita M (2003) Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Res 31: 5324-5331PubMedGoogle Scholar
  128. Swofford DL (2002) PAUP: Phylogenetic analysis using par- simony. Version 4. Sinauer Associates, Sunderland, Mas- sachusettsGoogle Scholar
  129. Tabita FR (1999) Microbial ribulose-1,5-bisphosphate carboxy- lase/oxygenase: A different perspective. Photosynth Res 60: 1-28Google Scholar
  130. Tanaka K, Tozawa Y, Mochizuki N, Shinozaki K, Nagatani A, Wakasa K and Takahashi H (1997) Characterization of three cDNA species encoding plastid RNA polymerase sigma fac-tors in Arabidopsis thaliana: evidence for the sigma factor heterogeneity in higher plant plastids. FEBS Lett 413: 309-313PubMedGoogle Scholar
  131. Tanaka A, Ito H, Tanaka R, Tanaka NK, Yoshida K and Okada K (1998) Chlorophyll a oxygenase (CAO) is involved in chloro- phyll b formation from chlorophyll a. Proc Natl Acad Sci USA 95: 12719-12723PubMedGoogle Scholar
  132. Thorsness PE and Weber ER (1996) Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nu- cleus. Int Rev Cytol 165: 207-234PubMedGoogle Scholar
  133. Turner S, Pryer KM, Miao VP and Palmer JD (1999) Investigat- ing deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 46: 327-338PubMedGoogle Scholar
  134. Wang DYC, Kumar S and Hedges SB (1999) Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc R Soc Lond B 266: 163-171Google Scholar
  135. von Wettstein D (1959) The formation of plastid structure. Brookhaven Symp Biol 11: 138Google Scholar
  136. Westphal S, Soll J and Vothknecht UC (2003) Evolution of chloroplast vesicle transport. Plant Cell Physiol 44: 217-222PubMedGoogle Scholar
  137. Whatley JM (1983) Plastids—past, present, and future. Int Rev Cytol 14: 329-373Google Scholar
  138. Wilson RJM (2002) Progress with parasite plastids. J Mol Biol 319: 257-274PubMedGoogle Scholar
  139. Wilson RJM, Denny PW, Preiser PR, Rangachari K, Roberts K, Roy A, Whyte A, Strath M, Moore DJ, Moore PW and Williamson DH (1996) Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. J Mol Biol 261: 155-172PubMedGoogle Scholar
  140. Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221-271PubMedGoogle Scholar
  141. Wolfe KH, Morden CW and Palmer JD (1992) Function and evo- lution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci USA 89: 10648-10652PubMedGoogle Scholar
  142. Wu H and Liu X-Q (1997) DNA binding and bending by a chloroplast-encoded HU-like protein overexpressed in Escherichia coli. Plant Mol Biol 34: 339-343PubMedGoogle Scholar
  143. Xiong J, Fischer WM, Inoue K, Nakahara M and Bauer CE (2000) Molecular evidence for the early evolution of photosynthesis. Science 289: 1724-1730PubMedGoogle Scholar
  144. Xu H, Vavilin D and Vermaas W (2001) Chlorophyll b can serve as the major pigment in functional photosystem II com- plexes of cyanobacteria. Proc Natl Acad Sci USA 98: 14168-14173PubMedGoogle Scholar
  145. Yoon HS, Hackett JD and Bhattacharya D (2002a) A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis. Proc Natl Acad Sci USA 99: 11724-11729Google Scholar
  146. Yoon HS, Hackett JD, Pinto G and Bhattacharya D (2002b) The single, ancient origin of chromist plastids. Proc Natl Acad Sci USA 99: 15507-15512Google Scholar
  147. Yuan Q, Hill J, Hsiao J, Moffat K, Ouyang S, Cheng Z, Jiang J and Buell CR (2002) Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol Genet Genomics 267: 713-720PubMedGoogle Scholar
  148. Zhang Z, Green BR and Cavalier-Smith T (1999) Single gene cir- cles in dinoflagellate chloroplast genomes. Nature 400: 155-159PubMedGoogle Scholar
  149. Zhang Z, Cavalier-Smith T and Green BR (2002) Evolution of dinoflagellate unigene minicircles and the partially concerted divergence of their putative replicon origins. Mol Biol Evol 19: 489-500PubMedGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Naoki Sato
    • 1
  1. 1.Department of Life Sciences, Graduate School of Arts and SciencesThe University of TokyoMeguroJapan

Personalised recommendations