Abstract
The pea chloroplast trnK gene which encodes tRNALys (UUU) was sequenced. TrnK is located 210 bp upstream from the promoter of psbA and immediately downstream from the 3′-end of rbcL. The gene is transcribed from the same DNA strand as psbA and rbcL. A 2447 bp intron with class II features is located in the trnK anticodon loop. The intron contains a 506 amino acid open reading frame which could encode an RNA maturase. The primary transcript of trnK is 2.9 kb long; its 5′-end was identified as a site of transcription initiation by in vitro transcription experiments. The 5′-terminus is adjacent to DNA sequences previously identified as transcription promoter elements. The most abundant trnK transcript is 2.5 kb long with termini corresponding to the 5′ and 3′ ends of the trnK exons. Intron specific RNAs were not detected. This suggests that RNA processing which produces tRNALys leads to rapid degradation of intron sequences.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bonitz S, Coruzzi G, Thalenfeld B, Tzagoloff A and Macino G (1980) Assembly of the mitochondrial system: structure and nucleotide sequence of the gene coding for subunit I of yeast cytochrome oxidase. J Biol Chem 225: 11927–11941.
Bonnard G, Michel F, Weil JH and Steinmetz A (1984) Nucleotide sequence of the split tRNALeu(AAA) gene from Vicia faba chloroplasts: evidence for structural homologies of the chloroplast tRNALeu intron with the intron from the autosplicable Tetrahymena ribosomal RNA precursor. Mol Gene Genet 194: 330–336.
Bonnard G, Weil JH and Steinmetz A (1985) The intragenic region between Vicia faba chloroplast tRNALeu(CAA) and tRNALeu(UAA) genes contains a partial copy of the split tRNALeu(UAA) gene. Curr Genet 9: 417–422.
Boyer SK and Mullet JE (1986) Characterization of P. sativum chloroplast psbA transcripts produced in vivo, in vitro and in E. coli. Plant Mol Biol 6: 229–43.
Bujard H (1980) The interactions of E. coli RNA polymerase with promoters. Trends Biochem Sci 5: 274–278.
Carignani G, Groudinsky O, Frezza D, Schiaron E, Bergantino E and Slonimski PP (1983) An RNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae. Cell 35: 733–742.
Chu NM, Shapiro DR, Oishi KK and Tewari KK (1985) Distribution of transfer RNA genes in the Psium sativum chloroplast DNA. Plant Mol Biol 4: 65–79.
Crouse EJ, Mubumbila M, Stummann BM, Bookjans G, Mickalowsi C, Bohnert HJ, Weil J-H and Henningsen KW (1986) Divergence of chloroplast geen organization in three legumes. Plant Mol Biol 7: 143–147.
Deno H, Kato A, Shinozaki K and Sigiura M (1982) Nucleotide sequences of tobacco chloroplast genes tRNAMet and tRNAVal(UAC): the tRNAVal(UAC) gene contains a long intron. Nuc Acids Res 10: 7511–7521.
Deno H and Sugiura M (1984) Chloroplast tRNAGly gene contains a long intron in the D stem: nucleotide sequences of tobacco chloroplast genes for tRNAGly(UCC) and tRNAArg(UCU). Proc Natl Acad Sci USA 81: 405–408.
Gauss DH and Sprinzel M (1984) Compilation of tRNA sequences. Nuc Acids Res 12: r1-rl31.
Gruissem W, Elsner-Menzelc, Latshaw S, Narita JO, Shaffer MA and Zurawski G (1987) A subpopulation of spinach chloroplast tRNA genes does not require upstream promoter elements for transcription. Nuc Acids Res 14: 7541–7556.
Gruissem W and Zurawski G (1985) Identification and mutational analysis of the promoter for a spinach chloroplast transfer RNA gene. EMBO J 4: 1637–1644.
Hallick RB, Hollingsworth MJ and Nickoloff JA (1984) Transfer RNA genes of Euglena gracilis chloroplast DNA. Plant Mol Biol 3: 169–175.
Hanley-Bowdoin L and Chua N-H (1987) Chloroplast promoters. Trends Biochem Sci 12: 67–70.
Koch W, Edwards K and Kössel H (1981) Sequencing of the 16S–23S spacer in a ribosomal RNA operon of Zea mays chloroplast DNA reveals two split tRNA genes. Cell 25: 203–213.
Krebbers E, Steinmetz A and Bogorad L (1984) DNA sequences for the Zea mays tRNA genes tV-UAC and tS-UGA: tV-UAC contains a large intron. Plant Mol Biol 3: 13–20.
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular Cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
Messing J (1980) New M13 vectors for cloning. In: Colowich SP, and Kaplan NO (eds) Methods in Enzymology, Vol 101C. Academic Press, New York, pp 20–77.
Michel F and Dujon B (1983) Conservation of RNA secondary structures in two intron families including mitochondrial, chloroplast and nuclear-encoded members EMBO J 2: 33–38.
Mullet JE, Orozco EM, Chua N-H (1985) Multiple transcripts for higher plant rbcL and atpB genes and localization of the transcription initiation site of rbcL gene. Plant Mol Biol 4: 39–54.
Neuhaus H and Link G (1987) The chloroplast tRNALys(UUU) gene from mustard (Sinapsis alba) contains a class II intron potentially coding for a maturase polypeptide. Curr Genet 11: 251–257.
Ogden RC, Knapp G, Peebles CL, Kang HS, Beckmann JS, Johnson PF, Fuhrman SA and Abelson JN (1980) In Söll D, Abelson JN and Schimmel PR (eds) Transfer RNA: Biological Aspects, pp 173–190, Cold Spring Harbor, NY, Cold Spring Harbor Laboratory.
Osiewacz HD and Esser K (1984) The mitochondrial plasmid of Podospora anserina: A mobile intron of a mitochondrial gene. Curr Genet 8: 299–305.
Schmelzer C, Schmidt C, May K and Schweyen RJ (1983) Determination of functional domains in intron b/l of yeast mitochondrial RNA by studies of mitochondrial mutations and a nuclear suppressor. EMBO J 2: 2047–2052.
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayash T, Zaita N, Chunwongse J, Obokato J, Yamaguchi-Shinozaki K, Ohto C, Torozawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusada J, Takaiwa F, Kato A, Tohdoh N, Shimada H and Sugiura M (1986) The complete nucleotide sequence of the tobacco chloroplast genome, its gene organization and expression EMBO J 5: 2043–2049.
Steinmetz A, Gubbins EJ and Bogorad L (1982) The anticodon of the maize chloroplast gene for tRNALeu(UAA) is split by a large intron. Nuc Acids Res 10: 3027–3037.
Sugita M, Shinozaki K and Sugiura M (1985) Tobacco chloroplast tRNALys(UUU) gene contains a 2.5-kilobase pair intron: An open reading frame and a conserved boundary sequence in the intron. Proc Natl Acad Sci 82: 3557–3561.
Van derVeen R, Arnberg AC, Van derHorst G, Bonen L, Tabak HF and Grivell LA (1986) Excised group II introns in yeast mitochondria are lariats and can be formed by self splicing in vitro. Cell 44: 225–234.
Wakasugi T, Ohme M, Shinozaki K and Sugiura M (1986) Structures of tobacco chloroplast genes for tRNAIle(CAU), tRNALeu(CAA), tRNACys(GCA), tRNASer(UGA), and tRNAThr(CGU): A complilation of tRNA genes from tobacco chloroplasts. Plant Mol Biol 7: 385–392.
Whitfield PR and Bottomley W (1983) Organization and structure of chloroplast genes. Ann Rev Plant Physiol 34: 279–310.
Yamaguchi-Shinozaki K, Shinozaki K and Sugiura M (1987) Processing of precursor tRNAs in a chloroplast lysate. FEBS Lett 215: 132–136.
Yamada K, Shinozaki K and Sugiura M (1986) DNA sequences of tobacco chloroplast genes for tRNASer(GAA), tRNAThr(UGU), tRNALeu(UAA): the tRNALeu gene contains a 503 bp intron. Plant Mol Biol 6: 193–199.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Boyer, S.K., Mullet, J.E. Pea chloroplast tRNALys (UUU) gene: transcription and analysis of an intron-containing gene. Photosynth Res 17, 7–22 (1988). https://doi.org/10.1007/BF00047679
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00047679