Plastid genomes of higher plants and algae: Structure and functions

Molekulyarnaya Biologiya

Volumn 37, Issue 5, 2003, Pages 768-783

  Odintsova, M S ^a   Yurina, N P ^a  

^a BACH INSTITUTE OF BIOCHEMISTRY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPLAST DNA;

ALGA; CHLOROPLAST; DATA BASE; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENOME; HIGHER PLANT; HUMAN; PHOTOSYNTHESIS; PLANT METABOLISM; PLASTID; PUBLISHING; REVIEW; RNA TRANSLATION; GENETICS; PLANT; PROTEIN SYNTHESIS;

ALGAE; EMBRYOPHYTA;

ALGAE; CHLOROPLASTS; PLANTS; PLASTIDS; PROTEIN BIOSYNTHESIS; TRANSCRIPTION, GENETIC;

EID: 1542391587     PISSN: 00268984     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (53)

1. Wakasugi T., Tsudzuki T., Sugiura M. 2001. The genomics of land plant chloroplasts: gene content and alteration of genomic information by RNA editing. Photosynthesis Res. 70, 107-118.
2. Cosner M.E., Jansen R.K., Palmer J.D., Downie S.R. 1997. The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Current Genet. 31, 419-429.
3. Lilly J.W., Havey M.J., Jackson S.A., Jiang J. 2001. Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in higher plants. Plant Cell. 13, 245-254.
4. Shinozaki K., Ohme M., Tanaka M. et al. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5, 2043-2049.
5. Ohyama K., Fukuzawa H., Kohchi T. et al. 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature. 322, 572-574.
6. Hiratsuka J., Shimada H., Whittier R. et al. 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217, 185-194.
7. Ogihara Y., Isono K., Kojima T. et al. 2002. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol. Genet. Genomics. 266, 740-746.
8. Sugiura M., Hirose T., Sugita M. 1998. Evolution and mechanism of translation in chloroplasts. Annu. Rev. Genetics. 32, 437-459.
9. Sato Sh., Nakamura Y., Kaneko T. et al. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6, 283-290.
10. Kato T., Kaneko T., Sato S. et al. 2000. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 7, 323-330.
11. Knox E.B., Palmer J.D. 1999. The chloroplast genome arrangement of Lobelia thuliniana (Lobeliaceae): expansion of the inverted repeat in an ancestor of the Campanulales. Plant Syst. Evol. 214, 49-64.
12. Hupfer H., Swiatek M., Hornung S. et al. 2000. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable Euoenothera plastomes. Mol. Gen. Genet. 263, 581-585.
13. Schmitz-Linneweber Ch., Maier R., Alcaraz J.P. et al. 2001. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45, 307-315.
14. Katayama H., Ogihara Y. 1993. Structural alterations of the chloroplast genome found in grasses are not common in monocots. Current Genet. 23, 160-165.
15. Maier R.M., Neckermann K., Igloi G.L., Kössel H. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251, 614-628.
16. Douglas S.E. 1994. Chloroplast origins and evolution. In The Molecular Biology of Cyanobacteria. Ed. Bryant A. Amsterdam: Kluwer, pp. 91-118.
17. Wakasugi T., Sugita M., Tsudzuki T., Sugiura M. 1998. Updated gene map of tobacco chloroplast DNA. Plant Mol. Biol. Rep. 16, 231-241.
18. Kowallik K.V. 1997. Origin and evolution of chloroplasts: current status and future perspectives. In Eukaryotism and Symbiosis. Intertaxonic Combination versus Symbiotic Adaptation. Eds Schenk H., Herrmann R.G., Jeon K.W., Muller N.E., Schwemmler W. Berlin: Springer, pp. 3-23.
19. Wolfe K.H., Morden C.W., Palmer J.D. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc. Natl. Acad. Sci. USA. 89, 10648-10652.
20. Bommer D., Haberhausen G., Zetsche K. 1993. A large deletion in the plastid DNA of the holoparasitic flowering plant Cuscuta reflexa concerning two ribosomal proteins (rpl2, rpl23), one transfer RNA (trnI) and an ORF2280 homologue. Current Genet. 24, 171-176.
21. Schmitz-Linneweber C., Regel R., Du T.G. et al. 2002. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol. Biol. Evol. 19, 1602-1612.
22. Wakasugi T., Nagai M., Kapoor M. et al. 1997. Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc. Natl. Acad. Sci. USA. 94, 5967-5972.
23. Turmel M., Otis Ch., Lemieux C. 1999. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc. Natl. Acad. Sci. USA. 96, 10248-10253.
24. Sugiura M. 1998. The discovery of the complete sequence of tobacco and rice chloroplast genomes. in Discoveries in Plant Biology. Eds Kung S.-D., Yang S.-F., Singapore: World Scientific, H. pp. 45-60.
25. Freyer R., Neckermann K., Maier R.M., Kössel H. 1995. Structural and functional analysis of plastid genomes from parasitic plants: loss of an intron within the genus Cuscuta. Current Genet. 27, 580-586.
26. Wakasugi T., Tsudzuki J., Ito S. et al. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. USA. 91, 9794-9798.
27. Millen R.S., Olmstead R.G., Adams K.L. et al. 2001. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell. 13, 645-658.
28. Guera A., De Nova P.G., Sabater B. 2000. Identification of the Ndh(NAD(P)H-plastoquinone-oxidoreductase) complex in etioplast membranes of barley: changes during photomorphogenesis of chloroplasts. Plant Cell Physiol. 41, 49-59.
29. Stoebe B., Martin W., Kowallik K.V. 1998. Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes. Plant Mol. Biol. Rep. 16, 243-255.
30. Bhattacharya D., Medlin L. 1998. Algal phylogeny and the origin of land plants. Plant Physiol. 116, 9-15.
31. Douglas S.E. 1998. Plastid evolution: origins, diversity, trends. Current Opin. Genet. Dev. 8, 655-661.
32. Palmer J.D. 2000. A single birth of all plastids? Nature. 405, 32-33.
33. Simpson C.L., Stern D.B. 2002. The treasure trove of algal chloroplast genomes. Surprises in architecture and gene content, and their functional implications. Plant Physiol. 129, 957-966.
34. Kaneko T., Sato S., Kotani H. et al. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3, 109-136; 185-209.
35. Maul J.E., Lilly J.W., Liying Cui et al. 2002. The Chlamydomonas reinhardtii plastid chromosome. Islands of genes in a sea of repeats. Plant Cell. 14, 2659-2679.
36. Hallick R.B., Hong L., Drager R.G. et al. 1993. Com-plete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res. 21, 3537-3544.
37. Gockel G., Hachtel W. 2000. Complete gene map of the plastid genome of the nonphotosynthetic euglenoid flagellate Astasia longa. Protist. 151, 347-351.
38. Zhang Z., Green B.R., Cavalier-Smith T. 1999. Single gene circles in dinoflagellate chloroplast genomes. Nature. 400, 155-159.
39. Glockner G., Rosenthal A., Valentin K. 2000. The structure and gene repertoire of an ancient red algal plastid genome. J. Mol. Evol. 51, 382-390.
40. Lemieux C.X., Otis Ch., Turmel M. 2000. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature. 403, 649-652.
41. Douglas S.E., Penny S.L. 1999. The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. J. Mol. Evol. 48, 236-244.
42. Reith M., Munholland J. 1995. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Mol. Biol. Rep. 13, 333-335.
43. Baum M., Cordier A., Schon A. 1996. RNase P from a photosynthetic organelle contains an RNA homologous to the cyanobacterial counterpart. J. Mol. Biol. 257, 43-52.
44. Stirewalt V.L., Michalowski C.B., Löffelhardt W. et al. 1995. Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa. Plant Mol. Biol. Rep. 13, 327-332.
45. Ebel C., Frantz C., Paulus F., Imbault P. 1999. Trans-splicing and cis-splicing in the colourless euglenoid, Entosiphon sulcatum. Current Genet. 35, 542-550.
46. Osteryoung K.W. 2000. Organelle fission. Crossing the evolutionary divide. Plant Physiol. 123, 1213-1216.
47. Ohta N., Sato N., Kuroiwa T. 1998. Analysis of the plastid genome of protoflorideophyceous algae Cyanidioschizon merolae. Plant Cell Physiol. 39 (Suppl.01), 54.
48. Kobayashi T., Takahara M., Miyagishima S. et al. 2002. Detection and localization of a chloroplast-encoded HU-like protein that organizes chloroplast nucleoids. Plant Cell. 14, 1579-1589.
49. Martin W., Stoebe B., Goremykin V. et al. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature. 393, 162-165.
50. Martin W., Herrmann R.G. 1998. Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol. 118, 9-17.
51. Steiner J.M., Loffelhardt W. 2002. Protein import into cyanelles. Trends in Plant Sci. 7, 72-77.
52. Martin W., Rujan T., Richly E. et al. 2002. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. USA. 99, 12246-12251.