Abstract
The complete nucleotide sequence of chloroplast DNA from a liverwort, Marchantia polymorpha has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. Other genes involved in photosynthesis, respiratory electron transport, and membrane-associated transport in chloroplasts were predicted by the amino acid sequence homology and secondary structure of gene products. Thirty-three open reading frames in the liverwort chloroplast genome remain unidentified. However, most of these open reading frames are also conserved in the chloroplast genomes of two species, a liverwort, Marchantia polymorpha, and tobacco, Nicotiana tabacum, indicating their active functions in chloroplasts.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Abbreviations
- bp:
-
base pair
- kDa:
-
kilodalton
- IR:
-
inverted repeat
- ORF:
-
open reading frame
- DALA:
-
δ-aminolevulinate
References
Alt J and Herrmann RG (1984) Nucleotide sequence of the gene for preapocytochrome f in the spinach plastid chromosome. Curr Genet 8: 551–557
Alt J, Morris J, Westhoff P and Herrmann RG (1984) Nucleotide sequence of the clustered genes for the 44 kd chlorophyll a apoprotein and the ‘32 kd’-like protein of the photosystem II reaction center in the spinach plastid chromosome. Curr Genet 8: 597–606
Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R and Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290: 457–465
Bedwell D, Davis G, Gosink M, Post L, Nomura M, Kestler H, Zengel JM and Lindahl L (1985) Nucleotide sequence of the alpha ribosomal protein Operon of Escherichia coli. Nucl Acids Res 13: 3891–3903
Bennoun P (1982) Evidence for a respiratory chain in the chloroplast. Proc Natl Acad Sci USA 79: 4352–4356
Bonitz SG, Berlani R, Coruzzi G, Li M, Macino G, Nobrega FG, Nobrega MP, Thalenfeld BE and Tzagoloff A (1980) Codon recognition rules in yeast mitochondria. Proc Natl Acad Sci USA 77: 3167–3170
Cerretti DP, Dean D, Davis GR, Bedwell DM and Nomura M (1983) The spc ribosomal protein Operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene. Nucl Acids Res 11: 2599–2616
Chomyn A, Mariottini P, Cleeter MWJ, Ragan CI, Matsuno-Yagi A, Hatefi Y, Doolittle RF and Attardi G (1985) Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase. Nature 314: 592–597
Chomyn A, Cleeter MWJ, Ragan CI, Riley M, Doolittle RF and Attardi G (1986) URF6, last unidentified reading frame of human mtDNA, codes for an NADH dehydrogenase subunit. Science 234: 614–618
Cozens AL, Walker JE, Phillips AL, Huttly AK and Gray JC (1986) A sixth subunit of ATP synthase, an F0 component, is encoded in the pea chloroplast genome. EMBO J 5: 217–222
Crick FHC (1966) The genetic code: III. Sci Amer 254(4): 55–62.
Crouse EJ, Schmitt JM and Bohnert HJ (1985) Chloroplast and cyanobacterial genomes, genes and RNAs: a compilation. Plant Mol Biol Reporter 3: 43–89
Deno H and Sugiura M (1983) The nucleotide sequences of tRNASer(GCU) and tRNAGln(UUG) genes from tobacco chloroplasts. Nucl Acids Res 11: 2185–2192
Dorne AM, Lescure AM and Mache R (1984) Site of synthesis of spinach chloroplast ribosomal proteins and formation of incomplete ribosomal particles in isolated chloroplasts. Plant Mol Biol 3: 83–90
Ellis RJ (1981) Chloroplast proteins: synthesis, transport and assembly. Ann Rev Plant Physiol 32: 111–137
Fish LE, Kuck U and Bogorad L (1985) Two partially homologous adjacent light-inducible maize chloroplast genes encoding polypeptides of the p700 chlorophyll a-protein complex of photosystem I. J Biol Chem 260: 1413–1421
Fournier MJ and Ozeki H (1985) Structure and organization of the transfer ribonucleic acid genes of Escherichia coli K-12. Microbiol Rev 49: 379–397
Froshauer S and Beckwith J (1984) The nucleotide sequence of the gene for malF protein, an inner membrane component of the maltose transport system of Escherichia coli. J Biol Chem 259: 10896–10903
Fukuzawa H, Kohchi T, Shirai H, Ohyama K, Umesono K, Inokuchi H and Ozeki H (1986) Coding sequences for chloroplast ribosomal protein S12 from the liverwort, Marchantia polymorpha, are separated far apart on the different DNA strands. FEBS Lett 198: 11–15
Fukuzawa H, Yoshida T, Kohchi T, Okumura T, Sawano Y and Ohyama K (1987) Splicing of group II introns in mRNAs coding cytochrome b6 and subunit IV in the liverwort Marchantia polymorpha chloroplast genome: Exon specifying a region coding for two genes with the spacer region. FEBS Lett 220: 61–66
Gilson E, Nikaido H and Hofnung M (1982) Sequence of the malK gene in E. coli K12. Nucl Acids Res 10: 7449–7458
Hausinger RP and Howard JB (1982) The amino acid sequence of the nitrogenase iron protein from Azotobacter vinelandii. J Biol Chem 257: 2483–2487
Hayashida N, Matsubayashi T, Shinozaki K, Sugiura M, Inoue K and Hiyama T (1987) The gene for the 9 kd polypeptide, a possible apoprotein for the iron-sulfur centers A and B of the photosystem I complex, in tobacco chloroplast DNA. Curr Genet 12: 247–250
Hearst JE, Alberti M and Doolittle RF (1985) A putative nitrogenase reductase gene found in the nucleotide sequences from the photosynthetic gene cluster of R. capsulata. Cell 40: 219–220
Heinemeyer W, Alt J and Herrmann RG (1984) Nucleotide sequence of the clustered genes for apocytochrome b6 and subunit 4 of the cytochrome b/f complex in the spinach plastid chromosome. Curr Genet 8: 543–549
Henning J and Herrmann RG (1986) Chloroplast ATP synthase of spinach contains nine nonidentical subunit species, six of which are encoded by plastid chromosomes in two operons in a phylogenetically conserved arrangement. Mol Gen Genet 203: 117–128
Herrmann RG, Alt J, Schiller B, Widger WR and Cramer WA (1984) Nucleotide sequence of the gene for apocytochrome b-559 on the spinach plastid chromosome: implications for the structure of the membrane protein. FEBS Lett 176: 239–244
Higgins CF, Haag PD, Nikaido K, Ardeshir F, Garcia G and Ames GFL (1982) Complete nucleotide sequence and identification of membrane components of the histidine transport operon of S. typhimurium. Nature 298: 723–727
Higgins CF, Hiles ID, Whalley K and Jamieson DJ (1985) Nucleotide binding by membrane components of bacterial periplasmic binding protein-dependent transport systems. EMBO J 4: 1033–1040
Higgins CF, Hiles ID, Salmond GPC, Gill DR, Downie JA, Evans IJ, Holland IB, Gray L, Buckel SD, Bell AW and Hermodson MA (1986) A family of related ATP-binding subunits coupled to many distinct biological processes in bacteria. Nature 323: 448–450
Hirschberg J and Mcintosh L (1983) Molecular basis of herbicide resistance in Amaranthus hybridus. Science 222: 1346–1349
Høj PB, Svendsen I, Scheller HV and Moller BL (1987) Identification of a chloroplast-encoded 9-kDa polypeptide as a 2[4Fe-4S] protein carrying centers A and B of photosystem I. J Biol Chem 262: 12676–12684
Holschuh K, Bottomley W and Whitfeld PR (1984) Structure of the spinach chloroplast genes for the D2 and 44 kd reaction-center proteins of photosystem II and for tRNASer(UGA). Nucl Acids Res 12: 8819–8834
Howard JB, Lorsbach TW, Ghosh D, Melis K and Stout CD (1983) Structure of Azotobacter vinelandii 7Fe ferredoxin. J Biol Chem 258: 508–522
Klein P, Kanehisa M and DeLisi C (1985) The detection and classification of membrane-spanning proteins. Biochim Biophys Acta 815: 468–476
Maione TE and Gibbs M (1986) Association of the chloroplastic respiratory and photosyn-thetic electron transport chains of Chlamydomonas reinhardtii with photoreduction and the oxyhydrogen reaction. Plant Physiol 80: 364–368
Minami Y, Wakabayashi S, Wada K, Matsubara H, Kerscher L and Oesterhelt D (1985) Amino acid sequence of a ferredoxin from thermoacidophilic Archaebacterium, Sulfolobus acidocaldarius. Presence of an N6-monomethyllysine and phyletic consideration of Arch-aebacteria. J Biochem 97: 745–753
Montandon PE and Stutz E (1983) Nucleotide sequence of a Euglena gracilis chloroplast genome region coding for the elongation factor Tu; evidence for a spliced mRNA. Nucl Acids Res 11: 5877–5891
Morris J and Herrmann RG (1984) Nucleotide sequence of the gene for the P680 chlorophyll a apoprotein of the photosystem II reaction center from spinach. Nucl Acids Res 12: 2837–2850
Oh-oka H, Takahashi Y, Wada K, Matsubara H, Ohyama K and Ozeki H (1987) The 8 kDa polypeptide in photosystem I is a probable candidate of an iron-sulfur center protein coded by the chloroplast gene frx A. FEBS Lett 218: 52–54
Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S, Inokuchi H and Ozeki H (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322: 572–574
Phillips AL and Gray JC (1984) Location and nucleotide sequence of the gene for the 15.2 kDa polypeptide of the cytochrome b-f complex from pea chloroplasts. Mol Gen Genet 194: 477–484
Quigley F and Weil JH (1985) Organization and sequence of five tRNA genes and of an unidentified reading frame in the wheat chloroplast genome: evidence for gene rearrangements during the evolution of chloroplast genomes. Curr Genet 9: 495–503
Schon A, Krupp G, Gough S, Berry-Lowe S, Kannangara CG and Soll D (1986) The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nature 322: 281–284
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H and Sugiura M (1986) The Complete nucleotide sequence of the tobacco chloroplast genomes: its gene organization and expression. EMBO J 5: 2043–2049
Steinback KE, Bonitz S, Arntzen CJ and Bogorad L (1985) (eds) Molecular Biology of the Photosynthetic Apparatus. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Steinmetz AA, Castroviejo M, Sayre RT and Bogorad L (1986) Protein PSII-G: An additional component of photosystem II identified through its plasmid gene in maize. J Biol Chem 261: 2485–2488
Stern DB, Bang AG and Thompson WF (1986) The watermelon mitochondrial URF-1 gene: evidence for a complex structure. Curr Genet 10: 857–869
Sugita M, Shinozaki K and Sugiura M (1985) Tobacco chloroplast tRNALys(UUU) conserved boundary sequence in the intron. Proc Natl Acad Sci USA 82: 3557–3561
Wada A and Sako T (1987) Primary structures of and genes for new ribosomal proteins A and B in Escherichia coli. J Biochem 101: 817–820
Westhoff P (1985) Transcription of the gene encoding the 51 kd chlorophyll a-apoprotein of the photosystem II reaction center from spinach. Mol Gen Genet 201: 115–123
Westhoff P, Farchaus JW and Herrmann RG (1986) The gene for the M r 10,000 phosphopro-tein associated with photosystem II is part of the psbB Operon of the spinach plastid chromosome. Curr Genet 11: 165–169
Wittmann HG (1983) Architecture of prokaryotic ribosomes. Ann Rev Biochem 52: 35–65
Youvan DC, Bylina EJ, Alberti M, Begusch H and Hearst JE (1984) Nucleotide and deduced polypeptide sequences of the photosynthetic reaction-center, B8970 antenna, and flanking polypeptides from R. capsulata. Cell 37: 949–957
Zurawski G, Bohnert HJ, Whitfeld PR and Bottomley W (1982) Nucleotide sequence of the gene for the M r 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of M r 38,950. Proc Natl Acad Sci USA 79: 7699–7703
Zurawski G and Zurawski SM (1985) Structure of the Escherichia coli S10 ribosomal protein Operon. Nucl Acids Res 13: 4521–4526
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1988 Kluwer Academic Publishers
About this chapter
Cite this chapter
Ohyama, K., Kohchi, T., Fukuzawa, H., Sano, T., Umesono, K., Ozeki, H. (1988). Gene organization and newly identified groups of genes of the chloroplast genome from a liverwort, Marchantia polymorpha . In: Govindjee (eds) Molecular Biology of Photosynthesis. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-2269-3_2
Download citation
DOI: https://doi.org/10.1007/978-94-009-2269-3_2
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-010-7517-6
Online ISBN: 978-94-009-2269-3
eBook Packages: Springer Book Archive