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. 1983 Sep;3(9):1615–1624. doi: 10.1128/mcb.3.9.1615

Transcriptional analysis of the Saccharomyces cerevisiae mitochondrial var1 gene: anomalous hybridization of RNA from AT-rich regions.

H P Zassenhaus, F Farrelly, M E Hudspeth, L I Grossman, R A Butow
PMCID: PMC370015  PMID: 6355829

Abstract

A family of mitochondrial RNAs hybridizes specifically to the var1 region on Saccharomyces cerevisiae mitochondrial DNA (Farrelly et al., J. Biol. Chem. 257:6581-6587, 1982). We constructed a fine-structure transcription map of this region by hybridizing DNA probes containing different portions of the var1 region and some flanking sequences to mitochondrial RNAs isolated from var1-containing petites. We also report the nucleotide sequence of more than 1.2 kilobases of DNA flanking the var1 gene. Our primary findings are: (i) The family of RNAs we detect with homology to var1 DNA is colinear with the var1 gene. Their direction of transcription is olil to cap, as it is for most other mitochondrial genes. (ii) Extensive hybridization anomalies are present, most likely due to the high A-T (A-U) content of the hybridizing species and to the asymmetric distribution of their G-C residues. An important conclusion is that failure to detect transcripts from A-T-rich regions of the yeast mitochondrial genome by standard blot transfer hybridizations cannot be interpreted to mean that such sequences, which are commonly supposed to be spacer DNA, are noncoding or lack direct function in the expression of mitochondrial genes.

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Selected References

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  1. Alwine J. C., Kemp D. J., Stark G. R. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5350–5354. doi: 10.1073/pnas.74.12.5350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Casey J., Davidson N. Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide. Nucleic Acids Res. 1977;4(5):1539–1552. doi: 10.1093/nar/4.5.1539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Douglas M. G., Butow R. A. Variant forms of mitochondrial translation products in yeast: evidence for location of determinants on mitochondrial DNA. Proc Natl Acad Sci U S A. 1976 Apr;73(4):1083–1086. doi: 10.1073/pnas.73.4.1083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Ehrlich S. D., Thiery J. P., Bernardi G. The mitochondrial genome of wild-type yeast cells. 3. The pyrimidine tracts of mitochondrial DNA. J Mol Biol. 1972 Mar 28;65(2):207–212. doi: 10.1016/0022-2836(72)90277-x. [DOI] [PubMed] [Google Scholar]
  5. Farrelly F., Zassenhaus H. P., Butow R. A. Characterization of transcripts from the Var1 region on mitochondrial DNA of Saccharomyces cerevisiae. J Biol Chem. 1982 Jun 10;257(11):6581–6587. [PubMed] [Google Scholar]
  6. Hensgens L. A., Grivell L. A., Borst P., Bos J. L. Nucleotide sequence of the mitochondrial structural gene for subunit 9 of yeast ATPase complex. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1663–1667. doi: 10.1073/pnas.76.4.1663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hudspeth M. E., Ainley W. M., Shumard D. S., Butow R. A., Grossman L. I. Location and structure of the var1 gene on yeast mitochondrial DNA: nucleotide sequence of the 40.0 allele. Cell. 1982 Sep;30(2):617–626. doi: 10.1016/0092-8674(82)90258-6. [DOI] [PubMed] [Google Scholar]
  8. Hudspeth M. E., Shumard D. S., Tatti K. M., Grossman L. I. Rapid purification of yeast mitochondrial DNA in high yield. Biochim Biophys Acta. 1980 Dec 11;610(2):221–228. doi: 10.1016/0005-2787(80)90003-9. [DOI] [PubMed] [Google Scholar]
  9. Locker J. Analytical and preparative electrophoresis of RNA in agarose-urea. Anal Biochem. 1979 Oct 1;98(2):358–367. doi: 10.1016/0003-2697(79)90154-4. [DOI] [PubMed] [Google Scholar]
  10. Locker J., Rabinowitz M. Transcription in yeast mitochondria: analysis of the 21 S rRNA region and its transcripts. Plasmid. 1981 Nov;6(3):302–314. doi: 10.1016/0147-619x(81)90038-x. [DOI] [PubMed] [Google Scholar]
  11. Martin F. H., 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. doi: 10.1093/nar/8.10.2295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  13. Perlman P. S., Douglas M. G., Strausberg R. L., Butow R. A. Localization of genes for variant forms of mitochondrial proteins on mitochondrial DNA of Saccharomyces cerevisiae. J Mol Biol. 1977 Oct 5;115(4):675–694. doi: 10.1016/0022-2836(77)90109-7. [DOI] [PubMed] [Google Scholar]
  14. 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. doi: 10.1016/s0022-2836(77)80098-3. [DOI] [PubMed] [Google Scholar]
  15. Prunell A., Kopecka H., Strauss F., Bernardi G. The mitochondrial genome of wild-type yeast cells. V. Genome evolution. J Mol Biol. 1977 Feb 15;110(1):17–47. doi: 10.1016/s0022-2836(77)80096-x. [DOI] [PubMed] [Google Scholar]
  16. Rubin C. M., Schmid C. W. Pyrimidine-specific chemical reactions useful for DNA sequencing. Nucleic Acids Res. 1980 Oct 24;8(20):4613–4619. doi: 10.1093/nar/8.20.4613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  18. Strausberg R. L., Vincent R. D., Perlman P. S., Butow R. A. Asymmetric gene conversion at inserted segments on yeast mitochondrial DNA. Nature. 1978 Dec 7;276(5688):577–583. doi: 10.1038/276577a0. [DOI] [PubMed] [Google Scholar]
  19. Terpstra P., Zanders E., Butow R. A. The association of var1 with the 38 S mitochondrial ribosomal subunit in yeast. J Biol Chem. 1979 Dec 25;254(24):12653–12661. [PubMed] [Google Scholar]
  20. Zassenhaus H. P., Butow R. A., Hannon Y. P. Rapid electroelution of nucleic acids from agarose and acrylamide gels. Anal Biochem. 1982 Sep 1;125(1):125–130. doi: 10.1016/0003-2697(82)90392-x. [DOI] [PubMed] [Google Scholar]

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