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EMBO J. Jan 1985; 4(1): 185–195.
PMCID: PMC554169

RNA processing in Neurospora crassa mitochondria: use of transfer RNA sequences as signals.

Abstract

We have used RNA gel transfer hybridization, S1 nuclease mapping and primer extension to analyze transcripts derived from several genes in Neurospora crassa mitochondria. The transcripts studied include those for cytochrome oxidase subunit III, 17S rRNA and an unidentified open reading frame. In all three cases, initial transcripts are long, include tRNA sequences, and are subsequently processed to generate the mature RNAs. We find that endpoints of the most abundant transcripts generally coincide with those of tRNA sequences. We therefore conclude that tRNA sequences in long transcripts act as primary signals for RNA processing in N. crassa mitochondria. The situation is somewhat analogous to that observed in mammalian mitochondrial systems. The difference, however, is that in mammalian mitochondria, noncoding spacers between tRNA, rRNA and protein genes are very short and in many cases non-existent, allowing no room for intergenic RNA processing signals whereas, in N. crassa mtDNA, intergenic non-coding sequences are usually several hundred nucleotides long and contain highly conserved GC-rich palindromic sequences. Since these GC-rich palindromic sequences are retained in the processed mature RNAs, we conclude that they do not serve as signals for RNA processing.

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  • Akins RA, Lambowitz AM. The [poky] mutant of Neurospora contains a 4-base-pair deletion at the 5' end of the mitochondrial small rRNA. Proc Natl Acad Sci U S A. 1984 Jun;81(12):3791–3795. [PMC free article] [PubMed]
  • Aloni Y, Attardi G. Symmetrical in vivo transcription of mitochondrial DNA in HeLa cells. Proc Natl Acad Sci U S A. 1971 Aug;68(8):1757–1761. [PMC free article] [PubMed]
  • Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. [PubMed]
  • Berk AJ, Sharp PA. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. [PubMed]
  • Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA. Sequence and gene organization of mouse mitochondrial DNA. Cell. 1981 Oct;26(2 Pt 2):167–180. [PubMed]
  • Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801–4805. [PMC free article] [PubMed]
  • Brosius J, Dull TJ, Noller HF. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):201–204. [PMC free article] [PubMed]
  • Brown TA, Davies RW, Ray JA, Waring RB, Scazzocchio C. The mitochondnal genome of Aspergillus nidulans contains reading frames homologous to the human URFs 1 and 4. EMBO J. 1983;2(3):427–435. [PMC free article] [PubMed]
  • Browning KS, RajBhandary UL. Cytochrome oxidase subunit III gene in Neurospora crassa mitochondria. Location and sequence. J Biol Chem. 1982 May 10;257(9):5253–5256. [PubMed]
  • Buell GN, Wickens MP, Payvar F, Schimke RT. Synthesis of full length cDNAs from four partially purified oviduct mRNAs. J Biol Chem. 1978 Apr 10;253(7):2471–2482. [PubMed]
  • Burger G, Scriven C, Machleidt W, Werner S. Subunit 1 of cytochrome oxidase from Neurospora crassa: nucleotide sequence of the coding gene and partial amino acid sequence of the protein. EMBO J. 1982;1(11):1385–1391. [PMC free article] [PubMed]
  • Burke JM, RajBhandary UL. Intron within the large rRNA gene of N. crassa mitochondria: a long open reading frame and a consensus sequence possibly important in splicing. Cell. 1982 Dec;31(3 Pt 2):509–520. [PubMed]
  • Burke JM, Breitenberger C, Heckman JE, Dujon B, RajBhandary UL. Cytochrome b gene of Neurospora crassa mitochondria. Partial sequence and location of introns at sites different from those in Saccharomyces cerevisiae and Aspergillus nidulans. J Biol Chem. 1984 Jan 10;259(1):504–511. [PubMed]
  • Christianson T, Edwards J, Levens D, Locker J, Rabinowitz M. Transcriptional initiation and processing of the small ribosomal RNA of yeast mitochondria. J Biol Chem. 1982 Jun 10;257(11):6494–6500. [PubMed]
  • Christianson T, Edwards JC, Mueller DM, Rabinowitz M. Identification of a single transcriptional initiation site for the glutamic tRNA and COB genes in yeast mitochondria. Proc Natl Acad Sci U S A. 1983 Sep;80(18):5564–5568. [PMC free article] [PubMed]
  • Christianson T, Rabinowitz M. Identification of multiple transcriptional initiation sites on the yeast mitochondrial genome by in vitro capping with guanylyltransferase. J Biol Chem. 1983 Nov 25;258(22):14025–14033. [PubMed]
  • Helmer-Citterich M, Morelli G, Macino G. Nucleotide sequence and intron structure of the apocytochrome b gene of Neurospora crassa mitochondria. EMBO J. 1983;2(8):1235–1242. [PMC free article] [PubMed]
  • Cramer CL, Ristow JL, Paulus TJ, Davis RH. Methods for mycelial breakage and isolation of mitochondria and vacuoles of Neurospora. Anal Biochem. 1983 Feb 1;128(2):384–392. [PubMed]
  • de Bruijn MH. Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature. 1983 Jul 21;304(5923):234–241. [PubMed]
  • Dujon B. Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci. Cell. 1980 May;20(1):185–197. [PubMed]
  • Garriga G, Bertrand H, Lambowitz AM. RNA splicing in Neurospora mitochondria: nuclear mutants defective in both splicing and 3' end synthesis of the large rRNA. Cell. 1984 Mar;36(3):623–634. [PubMed]
  • Green MR, Grimm MF, Goewert RR, Collins RA, Cole MD, Lambowitz AM, Heckman JE, Yin S, RajBhandary UL. Transcripts and processing patterns for the ribosomal RNA and transfer RNA region of Neurospora crassa mitochondrial DNA. J Biol Chem. 1981 Feb 25;256(4):2027–2034. [PubMed]
  • Hansen U, Tenen DG, Livingston DM, Sharp PA. T antigen repression of SV40 early transcription from two promoters. Cell. 1981 Dec;27(3 Pt 2):603–613. [PubMed]
  • Heckman JE, RajBhandary UL. Organization of tRNA and rRNA genes in N. crassa mitochondria: intervening sequence in the large rRNA gene and strand distribution of the RNA genes. Cell. 1979 Jul;17(3):583–595. [PubMed]
  • Heckman JE, Yin S, Alzner-DeWeerd B, RajBhandary UL. Mapping and cloning of Neurospora crassa mitochondrial transfer RNA genes. J Biol Chem. 1979 Dec 25;254(24):12694–12700. [PubMed]
  • Heckman JE, Sarnoff J, Alzner-DeWeerd B, Yin S, RajBhandary UL. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3159–3163. [PMC free article] [PubMed]
  • Helser TL, Davies JE, Dahlberg JE. Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli. Nat New Biol. 1971 Sep 1;233(35):12–14. [PubMed]
  • Hudspeth ME, Vincent RD, Perlman PS, Shumard DS, Treisman LO, Grossman LI. Expandable var1 gene of yeast mitochondrial DNA: in-frame insertions can explain the strain-specific protein size polymorphisms. Proc Natl Acad Sci U S A. 1984 May;81(10):3148–3152. [PMC free article] [PubMed]
  • Jackl G, Sebald W. Identification of two products of mitochondrial protein synthesis associated with mitochondrial adenosine triphosphatase from Neurospora crassa. Eur J Biochem. 1975 May;54(1):97–106. [PubMed]
  • Köchel HG, Lazarus CM, Basak N, Küntzel H. Mitochondrial tRNA gene clusters in Aspergillus nidulans: organization and nucleotide sequence. Cell. 1981 Feb;23(2):625–633. [PubMed]
  • Levens D, Ticho B, Ackerman E, Rabinowitz M. Transcriptional initiation and 5' termini of yeast mitochondrial RNA. J Biol Chem. 1981 May 25;256(10):5226–5232. [PubMed]
  • Li M, Tzagoloff A, Underbrink-Lyon K, Martin NC. Identification of the paromomycin-resistance mutation in the 15 S rRNA gene of yeast mitochondria. J Biol Chem. 1982 May 25;257(10):5921–5928. [PubMed]
  • Macino G. Mapping of mitochondrial structural genes in Neurospora crassa. J Biol Chem. 1980 Nov 25;255(22):10563–10565. [PubMed]
  • Macino G, Morelli G. Cytochrome oxidase subunit 2 gene in Neurospora crassa mitochondria. J Biol Chem. 1983 Nov 10;258(21):13230–13235. [PubMed]
  • Martin FH, Tinoco I., Jr DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 1980 May 24;8(10):2295–2299. [PMC free article] [PubMed]
  • Maxam AM, Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. [PubMed]
  • Carmichael GG, McMaster GK. The analysis of nucleic acids in gels using glyoxal and acridine orange. Methods Enzymol. 1980;65(1):380–391. [PubMed]
  • Miller KG, Sollner-Webb B. Transcription of mouse rRNA genes by RNA polymerase I: in vitro and in vivo initiation and processing sites. Cell. 1981 Nov;27(1 Pt 2):165–174. [PubMed]
  • Ojala D, Merkel C, Gelfand R, Attardi G. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell. 1980 Nov;22(2 Pt 2):393–403. [PubMed]
  • Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981 Apr 9;290(5806):470–474. [PubMed]
  • Osinga KA, De Haan M, Christianson T, Tabak HF. A nonanucleotide sequence involved in promotion of ribosomal RNA synthesis and RNA priming of DNA replication in yeast mitochondria. Nucleic Acids Res. 1982 Dec 20;10(24):7993–8006. [PMC free article] [PubMed]
  • Palleschi C, Francisci S, Zennaro E, Frontali L. Expression of the clustered mitochondrial tRNA genes in Saccharomyces cerevisiae: transcription and processing of transcripts. EMBO J. 1984 Jun;3(6):1389–1395. [PMC free article] [PubMed]
  • Prunell A, Bernardi G. The mitochondrial genome of wild-type yeast cells. VI. Genome organization. J Mol Biol. 1977 Feb 15;110(1):53–74. [PubMed]
  • RajBhandary UL, Browning KS, Burke J, Yin S, Chang D. Structure and organization of tRNA, rRNA, and protein genes in neurospora crassa mitochondria. Princess Takamatsu Symp. 1982;12:41–51. [PubMed]
  • Sor F, Fukuhara H. Nature of an inserted sequence in the mitochondrial gene coding for the 15S ribosomal RNA of yeast. Nucleic Acids Res. 1982 Mar 11;10(5):1625–1633. [PMC free article] [PubMed]
  • Terpstra P, Holtrop M, Kroon AM. A complete cleavage map of Neurospora crassa mtDNA obtained with endonucleases Eco RI and Bam HI. Biochim Biophys Acta. 1977 Apr 19;475(4):571–588. [PubMed]
  • Thalenfeld BE, Bonitz SG, Nobrega FG, Macino G, Tzagoloff A. oli1 Transcripts in wild type and in a cytoplasmic "petite" mutant of yeast. J Biol Chem. 1983 Dec 10;258(23):14065–14068. [PubMed]
  • Thalenfeld BE, Hill J, Tzagoloff A. Assembly of the mitochondrial membrane system. Characterization of the oxi2 transcript and localization of its promoter in Saccharomyces cerevisiae D273-10B. J Biol Chem. 1983 Jan 10;258(1):610–615. [PubMed]
  • Thomas PS. Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5201–5205. [PMC free article] [PubMed]
  • van den Boogaart P, Samallo J, Agsteribbe E. Similar genes for a mitochondrial ATPase subunit in the nuclear and mitochondrial genomes of Neurospora crassa. Nature. 1982 Jul 8;298(5870):187–189. [PubMed]
  • Van Knippenberg PH, Van Kimmenade JM, Heus HA. Phylogeny of the conserved 3' terminal structure of the RNA of small ribosomal subunits. Nucleic Acids Res. 1984 Mar 26;12(6):2595–2604. [PMC free article] [PubMed]
  • Wong JF, Ma DP, Wilson RK, Roe BA. DNA sequence of the Xenopus laevis mitochondrial heavy and light strand replication origins and flanking tRNA genes. Nucleic Acids Res. 1983 Jul 25;11(14):4977–4995. [PMC free article] [PubMed]
  • Yin S, Heckman J, RajBhandary UL. Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria. Cell. 1981 Nov;26(3 Pt 1):325–332. [PubMed]
  • Ysebaert M, van Emmelo J, Fiers W. Total nucleotide sequence of a nearly full-size DNA copy of satellite tobacco necrosis virus RNA. J Mol Biol. 1980 Nov 5;143(3):273–287. [PubMed]
  • Zassenhaus HP, Martin NC, Butow RA. Origins of transcripts of the yeast mitochondrial var 1 gene. J Biol Chem. 1984 May 10;259(9):6019–6027. [PubMed]

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