• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of plntcellLink to Publisher's site
Plant Cell. Apr 1993; 5(4): 465–475.
PMCID: PMC160285

A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea.

Abstract

Extensive DNA sequencing of the chloroplast genome of the red alga Porphyra purpurea has resulted in the detection of more than 125 genes. Fifty-eight (approximately 46%) of these genes are not found on the chloroplast genomes of land plants. These include genes encoding 17 photosynthetic proteins, three tRNAs, and nine ribosomal proteins. In addition, nine genes encoding proteins related to biosynthetic functions, six genes encoding proteins involved in gene expression, and at least five genes encoding miscellaneous proteins are among those not known to be located on land plant chloroplast genomes. The increased coding capacity of the P. purpurea chloroplast genome, along with other characteristics such as the absence of introns and the conservation of ancestral operons, demonstrate the primitive nature of the P. purpurea chloroplast genome. In addition, evidence for a monophyletic origin of chloroplasts is suggested by the identification of two groups of genes that are clustered in chloroplast genomes but not in cyanobacteria.

Full Text

The Full Text of this article is available as a PDF (981K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • An G, Bendiak DS, Mamelak LA, Friesen JD. Organization and nucleotide sequence of a new ribosomal operon in Escherichia coli containing the genes for ribosomal protein S2 and elongation factor Ts. Nucleic Acids Res. 1981 Aug 25;9(16):4163–4172. [PMC free article] [PubMed]
  • Arizmendi JM, Runswick MJ, Skehel JM, Walker JE. NADH: ubiquinone oxidoreductase from bovine heart mitochondria. A fourth nuclear encoded subunit with a homologue encoded in chloroplast genomes. FEBS Lett. 1992 Apr 27;301(3):237–242. [PubMed]
  • Bachmann B, Lüke W, Hunsmann G. Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucleic Acids Res. 1990 Mar 11;18(5):1309–1309. [PMC free article] [PubMed]
  • Baldauf SL, Manhart JR, Palmer JD. Different fates of the chloroplast tufA gene following its transfer to the nucleus in green algae. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5317–5321. [PMC free article] [PubMed]
  • Bryant DA, Schluchter WM, Stirewalt VL. Ferredoxin and ribosomal protein S10 are encoded on the cyanelle genome of Cyanophora paradoxa. Gene. 1991 Feb 15;98(2):169–175. [PubMed]
  • Christopher DA, Hallick RB. Euglena gracilis chloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III. Nucleic Acids Res. 1989 Oct 11;17(19):7591–7608. [PMC free article] [PubMed]
  • Douglas SE. Unusual organization of a ribosomal protein operon in the plastid genome of Cryptomonas phi: evolutionary considerations. Curr Genet. 1991 Apr;19(4):289–294. [PubMed]
  • Douglas SE. Eukaryote-eukaryote endosymbioses: insights from studies of a cryptomonad alga. Biosystems. 1992;28(1-3):57–68. [PubMed]
  • Douglas SE, Murphy CA, Spencer DF, Gray MW. Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature. 1991 Mar 14;350(6314):148–151. [PubMed]
  • Erdmann R, Wiebel FF, Flessau A, Rytka J, Beyer A, Fröhlich KU, Kunau WH. PAS1, a yeast gene required for peroxisome biogenesis, encodes a member of a novel family of putative ATPases. Cell. 1991 Feb 8;64(3):499–510. [PubMed]
  • Falk G, Walker JE. DNA sequence of a gene cluster coding for subunits of the F0 membrane sector of ATP synthase in Rhodospirillum rubrum. Support for modular evolution of the F1 and F0 sectors. Biochem J. 1988 Aug 15;254(1):109–122. [PMC free article] [PubMed]
  • Fong SE, Surzycki SJ. Chloroplast RNA polymerase genes of Chlamydomonas reinhardtii exhibit an unusual structure and arrangement. Curr Genet. 1992 May;21(6):485–497. [PubMed]
  • Gray MW. The evolutionary origins of organelles. Trends Genet. 1989 Sep;5(9):294–299. [PubMed]
  • Gray MW, Doolittle WF. Has the endosymbiont hypothesis been proven? Microbiol Rev. 1982 Mar;46(1):1–42. [PMC free article] [PubMed]
  • Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, et al. 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. 1989 Jun;217(2-3):185–194. [PubMed]
  • Kessler U, Maid U, Zetsche K. An equivalent to bacterial ompR genes is encoded on the plastid genome of red algae. Plant Mol Biol. 1992 Feb;18(4):777–780. [PubMed]
  • Kostrzewa M, Zetsche K. Large ATP synthase operon of the red alga Antithamnion sp. resembles the corresponding operon in cyanobacteria. J Mol Biol. 1992 Oct 5;227(3):961–970. [PubMed]
  • Kusian B, Yoo JG, Bednarski R, Bowien B. The Calvin cycle enzyme pentose-5-phosphate 3-epimerase is encoded within the cfx operons of the chemoautotroph Alcaligenes eutrophus. J Bacteriol. 1992 Nov;174(22):7337–7344. [PMC free article] [PubMed]
  • Lang JD, Haselkorn R. Isolation, sequence and transcription of the gene encoding the photosystem II chlorophyll-binding protein, CP-47, in the cyanobacterium Anabaena 7120. Plant Mol Biol. 1989 Oct;13(4):441–457. [PubMed]
  • Li SJ, Rock CO, Cronan JE., Jr The dedB (usg) open reading frame of Escherichia coli encodes a subunit of acetyl-coenzyme A carboxylase. J Bacteriol. 1992 Sep;174(17):5755–5757. [PMC free article] [PubMed]
  • Linne von Berg KH, Kowallik KV. Structural organization of the chloroplast genome of the chromophytic alga Vaucheria bursata. Plant Mol Biol. 1992 Jan;18(1):83–95. [PubMed]
  • Maid U, Zetsche K. A 16 kb small single-copy region separates the plastid DNA inverted repeat of the unicellular red alga Cyanidium caldarium: physical mapping of the IR-flanking regions and nucleotide sequences of the psbD-psbC, rps16, 5S rRNA and rpl21 genes. Plant Mol Biol. 1992 Sep;19(6):1001–1010. [PubMed]
  • Margulis L, Obar R. Heliobacterium and the origin of chrysoplasts. Biosystems. 1985;17(4):317–325. [PubMed]
  • Mayes SR, Barber J. Primary structure of the psbN-psbH-petC-petA gene cluster of the cyanobacterium Synechocystis PCC 6803. Plant Mol Biol. 1991 Aug;17(2):289–293. [PubMed]
  • McCarn DF, Whitaker RA, Alam J, Vrba JM, Curtis SE. Genes encoding the alpha, gamma, delta, and four F0 subunits of ATP synthase constitute an operon in the cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol. 1988 Aug;170(8):3448–3458. [PMC free article] [PubMed]
  • Michalowski CB, Löffelhardt W, Bohnert HJ. An ORF323 with homology to crtE, specifying prephytoene pyrophosphate dehydrogenase, is encoded by cyanelle DNA in the eukaryotic alga Cyanophora paradoxa. J Biol Chem. 1991 Jun 25;266(18):11866–11870. [PubMed]
  • Neumann-Spallart C, Brandtner M, Kraus M, Jakowitsch J, Bayer MG, Maier TL, Schenk HE, Löffelhardt W. The petFI gene encoding ferredoxin I is located close to the str operon on the cyanelle genome of Cyanophora paradoxa. FEBS Lett. 1990 Jul 30;268(1):55–58. [PubMed]
  • Orsat B, Monfort A, Chatellard P, Stutz E. Mapping and sequencing of an actively transcribed Euglena gracilis chloroplast gene (ccsA) homologous to the Arabidopsis thaliana nuclear gene cs(ch-42). FEBS Lett. 1992 Jun 1;303(2-3):181–184. [PubMed]
  • O'Toole PW, Logan SM, Kostrzynska M, Wadström T, Trust TJ. Isolation and biochemical and molecular analyses of a species-specific protein antigen from the gastric pathogen Helicobacter pylori. J Bacteriol. 1991 Jan;173(2):505–513. [PMC free article] [PubMed]
  • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. [PMC free article] [PubMed]
  • Reinhold-Hurek B, Shub DA. Self-splicing introns in tRNA genes of widely divergent bacteria. Nature. 1992 May 14;357(6374):173–176. [PubMed]
  • Reith M. psaE and trnS(CGA) are encoded on the plastid genome of the red alga Porphyra umbilicalis. Plant Mol Biol. 1992 Feb;18(4):773–775. [PubMed]
  • Reith M, Munholland J. An hsp70 homolog is encoded on the plastid genome of the red alga, Porphyra umbilicalis. FEBS Lett. 1991 Dec 2;294(1-2):116–120. [PubMed]
  • Reith M, Munholland J. Two amino-acid biosynthetic genes are encoded on the plastid genome of the red alga Porphyra umbilicalis. Curr Genet. 1993 Jan;23(1):59–65. [PubMed]
  • Richard M, Bellemare G. Nucleotide sequence of Chlamydomonas moewusii chloroplastic tRNA(thr). Nucleic Acids Res. 1990 May 25;18(10):3061–3061. [PMC free article] [PubMed]
  • Sasaki Y, Nagano Y, Morioka S, Ishikawa H, Matsuno R. A chloroplast gene encoding a protein with one zinc finger. Nucleic Acids Res. 1989 Aug 11;17(15):6217–6227. [PMC free article] [PubMed]
  • Shen JR, Ikeuchi M, Inoue Y. Stoichiometric association of extrinsic cytochrome c550 and 12 kDa protein with a highly purified oxygen-evolving photosystem II core complex from Synechococcus vulcanus. FEBS Lett. 1992 Apr 20;301(2):145–149. [PubMed]
  • Shivji MS, Li N, Cattolico RA. Structure and organization of rhodophyte and chromophyte plastid genomes: implications for the ancestry of plastids. Mol Gen Genet. 1992 Mar;232(1):65–73. [PubMed]
  • Smith AG, Wilson RM, Kaethner TM, Willey DL, Gray JC. Pea chloroplast genes encoding a 4 kDa polypeptide of photosystem I and a putative enzyme of C1 metabolism. Curr Genet. 1991 May;19(5):403–410. [PubMed]
  • Stock JB, Ninfa AJ, Stock AM. Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol Rev. 1989 Dec;53(4):450–490. [PMC free article] [PubMed]
  • Suzuki JY, Bauer CE. Light-independent chlorophyll biosynthesis: involvement of the chloroplast gene chlL (frxC). Plant Cell. 1992 Aug;4(8):929–940. [PMC free article] [PubMed]
  • Torian BE, Flores BM, Stroeher VL, Hagen FS, Stamm WE. cDNA sequence analysis of a 29-kDa cysteine-rich surface antigen of pathogenic Entamoeba histolytica. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6358–6362. [PMC free article] [PubMed]
  • Urbach E, Robertson DL, Chisholm SW. Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature. 1992 Jan 16;355(6357):267–270. [PubMed]
  • Valentin K, Zetsche K. Rubisco genes indicate a close phylogenetic relation between the plastids of Chromophyta and Rhodophyta. Plant Mol Biol. 1990 Oct;15(4):575–584. [PubMed]
  • Willey DL, Gray JC. An open reading frame encoding a putative haem-binding polypeptide is cotranscribed with the pea chloroplast gene for apocytochrome f. Plant Mol Biol. 1990 Aug;15(2):347–356. [PubMed]
  • Yamamoto T, Matsui Y, Natori S, Obinata M. Cloning of a housekeeping-type gene (MER5) preferentially expressed in murine erythroleukemia cells. Gene. 1989 Aug 15;80(2):337–343. [PubMed]

Articles from The Plant Cell are provided here courtesy of American Society of Plant Biologists

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...