Cleavage Specificity of Chloroplast and Nuclear tRNA 3′-Processing Nucleases

REFERENCES

• Adeniyi-Jones, S., P. H. Romeo, and M. Zasloff. 1984. Generation of long read-through transcripts in vivo and in vitro by deletion of 3′ termination and processing signals in the human tRNAMeti gene. Nucleic Acids Res. 12:1101–1115.
   PubMedGoogle Scholar
• Akama, K., and S. Tanifuji. 1989. Nucleotide sequence of a methionine initiator tRNA gene of Arabidopsis thaliana. Plant Mol. Biol. 13:599–600.
   PubMedGoogle Scholar
• Akama, K., and S. Tanifuji. 1990. Sequence analysis of three tRNAPhe nuclear genes and a mutated gene, and one gene for tRNAAla from Arabidopsis thaliana. Plant Mol. Biol. 15:337–346.
   PubMedGoogle Scholar
• Bikoff, E. K., B. F. LaRue, and M. L. Gefter. 1975. In vitro synthesis of transfer RNA. II. Identification of required enzymatic activities. J. Biol. Chem. 250:6248–6255.
   PubMed Web of Science ®Google Scholar
• Canaday, J., P. Guillemaut, R. Gloeckler, and J.-H. Weil. 1980. Comparison of the nucleotide sequences of chloroplast tRNAsphe and tRNAseu from spinach and bean. Plant Sci. Lett. 20:57–62.
   Google Scholar
• Castano, J. G., Tobian, J. A., and M. Zasloff. 1985. Purification and characterization of an endonuclease from Xenopus laevis ovaries which accurately processes the 3′ terminus of human pre-tRNA-*et (3′ pre-tRNase). J. Biol. Chem. 260:9002–9008.
   PubMedGoogle Scholar
• Chen, J.-Y., and N. C. Martin. 1988. Biosynthesis of tRNA in yeast mitochondria. An endonuclease is responsible for the 3′-processing of tRNA precursors. J. Biol. Chem. 263:13677–13682.
   PubMedGoogle Scholar
• Cudny, H., and M. P. Deutscher. 1980. Apparent involvement of ribonuclease D in the 3′ processing of tRNA precursors. Proc. Natl. Acad. Sci. USA 77:837–841.
   PubMed Web of Science ®Google Scholar
• Deutscher, M. P. 1982. tRNA nucleotidyltransferase, p. 183–215. In P. D. Boyer (ed.), The enzymes, vol. XV. Academic Press, New York.
   Google Scholar
• Deutscher, M. P. 1983. tRNA nucleotidyltransferase and the -C-C-A terminus of transfer RNA, p. 159–183. In S. T. Jacob (ed.), Enzymes of nucleic acid synthesis and modification, vol. II. CRC Press, Boca Raton, Fla.
   Google Scholar
• Deutscher, M. P. 1984. Processing of tRNA in prokaryotes and eukaryotes. Crit. Rev. Biochem. 17:45–71.
   PubMed Web of Science ®Google Scholar
• Engelke, D. R., P. Gegenheimer, and J. Abelson. 1985. Nucleo- lytic processing of a tRNAAr8-tRNAAsp dimeric precursor by a homologous component from Saccharomyces cerevisiae. J. Biol. Chem. 260:1271–1279.
   PubMedGoogle Scholar
• Fournier, M. J., and H. Ozeki. 1985. Structure and organization of the transfer ribonucleic acid genes of Escherichia coli K-12. Microbiol. Rev. 49:379–397.
   PubMedGoogle Scholar
• Frendewey, D., T. Dingerman, L. Cooley, and D. Söll. 1985. Processing of precursor tRNAs in Drosophila. Processing of the 3′ end involves an endonucleolytic cleavage and occurs after 5′ end maturation. J. Biol. Chem. 260:449–454.
   PubMedGoogle Scholar
• Garber, R. L., and S. Altman. 1979. In vitro processing of B. mori transfer RNA precursor molecules. Cell 17:389–397.
   PubMed Web of Science ®Google Scholar
• Garber, R. L., and L. P. Gage. 1979. Transcription of a cloned Bombyx mori tRNAAla2 gene: nucleotide sequence of the tRNA precursor and its processing in vitro. Cell 18:817–828.
   PubMed Web of Science ®Google Scholar
• Gegenheimer, P. 1990. Preparation of extracts from plants. Methods Enzymol. 182:174–193.
   PubMed Web of Science ®Google Scholar
• Gegenheimer, P., and D. Apirion. 1981. Processing of procaryotic ribonucleic acids. Microbiol. Rev. 45:502–541.
   PubMedGoogle Scholar
• Greenberg, B. M., W. Gruissem, and R. B. Hallick. 1984. Accurate processing and pseudouridylation of chloroplast transfer RNA in a chloroplast transcription system. Plant Mol. Biol. 3:97–109.
   PubMed Web of Science ®Google Scholar
• Greenberg, B. M., and R. B. Hallick. 1986. Accurate transcription and processing of 19 Euglena chloroplast tRNAs in a Euglena soluble extract. Plant Mol. Biol. 6:89–100.
   PubMed Web of Science ®Google Scholar
• Gruissem, W., B. M. Greenberg, G. Zurawski, and R. B. Hallick. 1986. Chloroplast gene expression and promoter identification in chloroplast extracts. Methods Enzymol. 118:253–270.
   PubMedGoogle Scholar
• Gruissem, W., B. M. Greenberg, G. Zurawski, D. M. Prescott, and R. B. Hallick. 1983. Biosynthesis of chloroplast transfer RNA in a spinach chloroplast transcription system. Cell 35:815–828.
   PubMed Web of Science ®Google Scholar
• Hagenbüchle, O., D. Larson, G. I. Hall, and K. U. Sprague. 1979. The primary transcription product of a silkworm alanine tRNA gene: identification of in vitro sites of initiation, termination, and processing. Cell 18:1217–1229.
   PubMed Web of Science ®Google Scholar
• Hallick, R. B., and W. Bottomley. 1983. Proposals for the naming of chloroplast genes. Plant Mol. Biol. Rep. 1:38–43.
   Google Scholar
• Hiratsuka, J., H. Shimada, R. Whittier, T. Ishibashi, M. Sakamoto, M. Mori, C. Kondo, Y. Honji, C. R. Sun, B. Y. Meng, Y. Q. Ki, A. Kanno, Y. Nishizawa, A. Hirai, K. Shinozaki, and M. Sugiura. 1989. The complete sequence of the rice (Oryza saliva) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of cereals. Mol. Gen. Genet. 217:185–194.
   PubMedGoogle Scholar
• Hollingsworth, M. J., and N. C. Martin. 1986. RNase P activity in the mitochondria of Saccharomyces cerevisiae depends on both mitochondrion and nucleus-encoded components. Mol. Cell. Biol. 6:1058–1064.
   PubMedGoogle Scholar
• King, T. C., R. Sirdeskmukh, and D. Schlessinger. 1986. Nucle- olytic processing of ribonucleic acid transcripts in procaryotes. Microbiol. Rev. 50:428–451.
   PubMedGoogle Scholar
• Manam, S., and G. C. Van Tuyle. 1987. Separation and characterization of 5′- and 3′-tRNA processing nucleases from rat liver mitochondria. J. Biol. Chem. 262:10272–10279.
   PubMedGoogle Scholar
• Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual, p. 88–89. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Marion-Poll, A., C. Hibbert, C. Radebaugh, and R. Hallick. 1988. Processing of mono-, di-, and tricistronic transfer RNAs precursors in a spinach or pea chloroplast soluble extract. Plant Mol. Biol. 11:45–56.
   PubMed Web of Science ®Google Scholar
• Micard, D., M. L. Sobrier, J. L. Couderc, and B. Dastugue. 1985. Purification of RNA-free plasmid DNA using alkaline extraction followed by Ultrogel A2 column chromatography. Anal. Biochem. 148:121–126.
   PubMedGoogle Scholar
• Ohyama, K., H. Fukuzawa, T. Kohchi, H. Shirai, T. Sano, S. Sano, K. Umesono, Y. Shiki, M. Takeuchi, Z. Chang, S.-I. Aota, H. Inokuchi, and H. Ozeki. 1986. Complete nucletide sequence of liverwort Marchantía polymorpha chloroplast DNA. Plant Mol. Biol. Rep. 4:149–175.
   Google Scholar
• Oommen, A. 1991. Ph.D. dissertation. University of Kansas, Lawrence.
   Google Scholar
• Piper, P. W., and K. B. Sträby. 1989. Processing of transcripts of a dimeric tRNA gene in yeast uses the nuclease responsible for maturation of the 3′ termini upon 5 S and 37 S precursor rRNAs. FEBS Lett. 250:311–316.
   PubMedGoogle Scholar
• Quigley, F., and J.-H. Weil. 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.
   PubMedGoogle Scholar
• Robertson, H. D., S. Altman, and J. D. Smith. 1972. Purification and properties of a specific Escherichia coli ribonuclease which cleaves a tyrosine transfer ribonucleic acid precursor. J. Biol. Chem. 247:5243–5251.
   PubMed Web of Science ®Google Scholar
• Rooney, R. J., and J. D. Harding. 1986. Processing of mammalian tRNA transcripts in vitro: different pre-tRNAs are processed along alternative pathways that contain a common ratelimiting step. Nucleic Acids Res. 14:4849–4864.
   PubMedGoogle Scholar
• Sampson, J. R., and O. C. Uhlenbeck. 1988. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc. Natl. Acad. Sci. USA 85:1033–1037.
   PubMed Web of Science ®Google Scholar
• Schimmel, P. R., D. Soil, and J. N. Abelson. 1979. Proposed numbering system of nucleotides in tRNAs based on yeast tRNAPhe, p. 518–519. In P. R. Schimmel, D. Söll, and J. N. Abelson (ed.), Transfer RNA: structure, properties, and recognition. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Sekiya, T., R. Contreras, T. Takeya, and H. G. Khorana. 1979. Total synthesis of a tyrosine suppressor transfer RNA gene. XVII. Transcription, in vitro, of the synthetic gene and processing of the primary transcript to transfer RNA. J. Biol. Chem. 254:5802–5816.
   PubMed Web of Science ®Google Scholar
• Shinozaki, K., M. Ohme, M. Tanaka, T. Wakasugi, N. Hayashida, T. Matsubayasha, N. Zaita, J. Chunwongse, J. Obokata, K. Yamaguchi-Shinozaki, C. Ohto, K. Torazawa, B. Y. Meng, M. Sugita, H. Deno, T. Kamogashira, K. Yamada, J. Kusuda, F. Takaiwa, A. Kato, N. Todoh, H. Shimada, and M. Sugiura. 1986. The complete nucleotide sequence of the tobacco chloroplast genome. Plant Mol. Biol. Rep. 4:111–147.
   Google Scholar
• Solari, A., and M. P. Deutscher. 1983. Identification of multiple RNases in Xenopus laevis oocytes and their possible role in tRNA processing. Mol. Cell. Biol. 3:1711–1717.
   PubMed Web of Science ®Google Scholar
• Stange, N., H. J. Gross, and H. Beier. 1988. Wheat germ splicing endonuclease is highly specific for plant pre-tRNAs. EMBO J. 7:3823–3828.
   PubMedGoogle Scholar
• Steinmetz, A. A., E. T. Krebbers, Z. Schwartz, E. J. Gubbins, and L. Bogorad. 1983. Nucleotide sequence of five maize chloroplast transfer RNA genes and their flanking regions. J. Biol. Chem. 258:5503–5511.
   PubMedGoogle Scholar
• Wang, M. J., N. W. Davis, and P. Gegenheimer. 1988. Novel mechanisms for maturation of chloroplast transfer RNA precursors. EMBO J. 7:1567–1574.
   PubMedGoogle Scholar
• Yamaguchi-Shinozaki, K., K. Shinozaki, and M. Sugiura. 1987. Processing of precursor tRNAs in a chloroplast lysate: processing of the 5′ end involves endonucleolytic cleavage by an RNase P-like enzyme and precedes 3′ end maturation. FEBS Lett. 215:131–136.
   Google Scholar
• Zasloff, M., T. Santos, P. Romeo, and M. Rosenberg. 1982. Transcription and precursor processing of normal and mutant human tRNA,Meti genes in a homologous cell-free system. J. Biol. Chem. 257:7857–7863.
   PubMed Web of Science ®Google Scholar
• Zhang, J. R., and M. P. Deutscher. 1988. Transfer RNA is a substrate for RNase D in vivo. J. Biol. Chem. 263:17909–17912.
   PubMed Web of Science ®Google Scholar