Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1984 Mar 26;12(6):2955–2968. doi: 10.1093/nar/12.6.2955

Structure and function of the nontranscribed spacer regions of yeast rDNA.

K G Skryabin, M A Eldarov, V L Larionov, A A Bayev, J Klootwijk, V C de Regt, G M Veldman, R J Planta, O I Georgiev, A A Hadjiolov
PMCID: PMC318718  PMID: 6369254

Abstract

The sequences of the nontranscribed spacers (NTS) of cloned ribosomal DNA (rDNA) units from both Saccharomyces cerevisiae and Saccharomyces carlsbergensis were determined. The NTS sequences of both species were found to be 93% homologous. The major disparities comprise different frequencies of reiteration of short tracts of six to sixteen basepairs. Most of these reiterations are found within the 1100 basepairs long NTS between the 3'-ends of 26S and 5S rRNA (NTS1). The NTS between the starts of 5S rRNA and 37S pre-rRNA (NTS2) comprises about 1250 basepairs. The first 800 basepairs of NTS NTS2 (adjacent to the 5S rRNA gene) are virtually identical in both strains whereas a variable region is present at about 250 basepairs upstream of the RNA polymerase A transcription start. In contrast to the situation in Drosophila and Xenopus no reiterations of the putative RNA polymerase A promoter are present within the yeast NTS. The strands of the yeast NTS reveal a remarkable bias of G and C-residues. Yeast rDNA was previously shown to contain a sequence capable of autonomous replication (ARS) (Szostak, J.W. and Wu, R (1979), Plasmid 2, 536-554). This ARS, which may correspond to a chromosomal origin of replication, was located on a fragment of 570 basepairs within NTS2.

Full text

PDF
2955

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bayev A. A., Georgiev O. I., Hadjiolov A. A., Kermekchiev M. B., Nikolaev N., Skryabin K. G., Zakharyev V. M. The structure of the yeast ribosomal RNA genes. 2. The nucleotide sequence of the initiation site for ribosomal RNA transcription. Nucleic Acids Res. 1980 Nov 11;8(21):4919–4926. doi: 10.1093/nar/8.21.4919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bayev A., Georgiev O. I., Hadjiolov A. A., Nikolaev N., Skryabin K. G., Zakharyev V. M. The structure of the yeast ribosomal RNA genes. 3. Precise mapping of the 18 S and 25 S rRNA genes and structure of the adjacent regions. Nucleic Acids Res. 1981 Feb 25;9(4):789–799. doi: 10.1093/nar/9.4.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bell G. I., DeGennaro L. J., Gelfand D. H., Bishop R. J., Valenzuela P., Rutter W. J. Ribosomal RNA genes of Saccharomyces cerevisiae. I. Physical map of the repeating unit and location of the regions coding for 5 S, 5.8 S, 18 S, and 25 S ribosomal RNAs. J Biol Chem. 1977 Nov 25;252(22):8118–8125. [PubMed] [Google Scholar]
  4. Bicknell J. N., Douglas H. C. Nucleic acid homologies among species of Saccharomyces. J Bacteriol. 1970 Feb;101(2):505–512. doi: 10.1128/jb.101.2.505-512.1970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Botchan P. M., Dayton A. I. A specific replication origin in the chromosomal rDNA of Lytechinus variegatus. Nature. 1982 Sep 30;299(5882):453–456. doi: 10.1038/299453a0. [DOI] [PubMed] [Google Scholar]
  6. Broach J. R., Li Y. Y., Feldman J., Jayaram M., Abraham J., Nasmyth K. A., Hicks J. B. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1165–1173. doi: 10.1101/sqb.1983.047.01.132. [DOI] [PubMed] [Google Scholar]
  7. Broach J. R., Strathern J. N., Hicks J. B. Transformation in yeast: development of a hybrid cloning vector and isolation of the CAN1 gene. Gene. 1979 Dec;8(1):121–133. doi: 10.1016/0378-1119(79)90012-x. [DOI] [PubMed] [Google Scholar]
  8. Cech T. R., Brehm S. L. Replication of the extrachromosomal ribosomal RNA genes of Tetrahymena thermophilia. Nucleic Acids Res. 1981 Jul 24;9(14):3531–3543. doi: 10.1093/nar/9.14.3531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Clark-Walker G. D., Azad A. A. Hybridizable sequences between cytoplasmic ribosomal RNAs and 3 micron circular DNAs of Saccharomyces cerevisiae and Torulopsis glabrata. Nucleic Acids Res. 1980 Mar 11;8(5):1009–1022. doi: 10.1093/nar/8.5.1009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Clarke L., Carbon J. Isolation of a yeast centromere and construction of functional small circular chromosomes. Nature. 1980 Oct 9;287(5782):504–509. doi: 10.1038/287504a0. [DOI] [PubMed] [Google Scholar]
  11. Clewell D. B., Helinski D. R. Properties of a supercoiled deoxyribonucleic acid-protein relaxation complex and strand specificity of the relaxation event. Biochemistry. 1970 Oct 27;9(22):4428–4440. doi: 10.1021/bi00824a026. [DOI] [PubMed] [Google Scholar]
  12. Coen E. S., Dover G. A. Multiple Pol I initiation sequences in rDNA spacers of Drosophila melanogaster. Nucleic Acids Res. 1982 Nov 11;10(21):7017–7026. doi: 10.1093/nar/10.21.7017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Coen E., Strachan T., Dover G. Dynamics of concerted evolution of ribosomal DNA and histone gene families in the melanogaster species subgroup of Drosophila. J Mol Biol. 1982 Jun 15;158(1):17–35. doi: 10.1016/0022-2836(82)90448-x. [DOI] [PubMed] [Google Scholar]
  14. Cramer J. H., Bhargava M. M., Halvorson H. O. Isolation and characterization of DNA of Saccharomyces cerevisiae. J Mol Biol. 1972 Oct 28;71(1):11–20. doi: 10.1016/0022-2836(72)90396-8. [DOI] [PubMed] [Google Scholar]
  15. Cramer J. H., Rownd R. H. Denaturation mapping of the ribosomal DNA of Saccharomyces cerevisiae. Mol Gen Genet. 1980 Jan;177(2):199–205. doi: 10.1007/BF00267430. [DOI] [PubMed] [Google Scholar]
  16. Georgiev O. I., Nikolaev N., Hadjiolov A. A., Skryabin K. G., Zakharyev V. M., Bayev A. A. The structure of the yeast ribosomal RNA genes. 4. Complete sequence of the 25 S rRNA gene from Saccharomyces cerevisae. Nucleic Acids Res. 1981 Dec 21;9(24):6953–6958. doi: 10.1093/nar/9.24.6953. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hsiao C. L., Carbon J. High-frequency transformation of yeast by plasmids containing the cloned yeast ARG4 gene. Proc Natl Acad Sci U S A. 1979 Aug;76(8):3829–3833. doi: 10.1073/pnas.76.8.3829. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Humphreys G. O., Willshaw G. A., Anderson E. S. A simple method for the preparation of large quantities of pure plasmid DNA. Biochim Biophys Acta. 1975 Apr 2;383(4):457–463. doi: 10.1016/0005-2787(75)90318-4. [DOI] [PubMed] [Google Scholar]
  19. Klein H. L., Petes T. D. Intrachromosomal gene conversion in yeast. Nature. 1981 Jan 15;289(5794):144–148. doi: 10.1038/289144a0. [DOI] [PubMed] [Google Scholar]
  20. Koch W., Edwards K., Kössel H. Sequencing of the 16S-23S spacer in a ribosomal RNA operon of Zea mays chloroplast DNA reveals two split tRNA genes. Cell. 1981 Jul;25(1):203–213. doi: 10.1016/0092-8674(81)90245-2. [DOI] [PubMed] [Google Scholar]
  21. Larionov V. L., Grishin A. V., Smirnov M. N. 3 micron DNA - an extrachromosomal ribosomal DNA in the yeast Saccharomyces cerevisiae. Gene. 1980 Dec;12(1-2):41–49. doi: 10.1016/0378-1119(80)90014-1. [DOI] [PubMed] [Google Scholar]
  22. Long E. O., Dawid I. B. Repeated genes in eukaryotes. Annu Rev Biochem. 1980;49:727–764. doi: 10.1146/annurev.bi.49.070180.003455. [DOI] [PubMed] [Google Scholar]
  23. Lund E., Dahlberg J. E., Lindahl L., Jaskunas S. R., Dennis P. P., Nomura M. Transfer RNA genes between 16S and 23S rRNA genes in rRNA transcription units of E. coli. Cell. 1976 Feb;7(2):165–177. doi: 10.1016/0092-8674(76)90016-7. [DOI] [PubMed] [Google Scholar]
  24. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Meyerink J. H., Retèl J. Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases. II. The physical map of EcoRI fragments. Nucleic Acids Res. 1976 Oct;3(10):2697–2707. doi: 10.1093/nar/3.10.2697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Miller J. R., Hayward D. C., Glover D. M. Transcription of the 'non-transcribed' spacer of Drosophila melanogaster rDNA. Nucleic Acids Res. 1983 Jan 11;11(1):11–19. doi: 10.1093/nar/11.1.11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Moss T. A transcriptional function for the repetitive ribosomal spacer in Xenopus laevis. Nature. 1983 Mar 17;302(5905):223–228. doi: 10.1038/302223a0. [DOI] [PubMed] [Google Scholar]
  28. Moss T., Birnstiel M. L. The putative promoter of a Xenopus laevis ribosomal gene is reduplicated. Nucleic Acids Res. 1979 Aug 24;6(12):3733–3743. doi: 10.1093/nar/6.12.3733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Nath K., Bollon A. P. Organization of the yeast ribosomal RNA gene cluster via cloning and restriction analysis. J Biol Chem. 1977 Sep 25;252(18):6562–6571. [PubMed] [Google Scholar]
  30. Nellen W., Donath C., Moos M., Gallwitz D. The nucleotide sequences of the actin genes from Saccharomyces carlsbergensis and Saccharomyces cerevisiae are identical except for their introns. J Mol Appl Genet. 1981;1(3):239–244. [PubMed] [Google Scholar]
  31. Petes T. D., Hereford L. M., Skryabin K. G. Characterization of two types of yeast ribosomal DNA genes. J Bacteriol. 1978 Apr;134(1):295–305. doi: 10.1128/jb.134.1.295-305.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Petes T. D. Unequal meiotic recombination within tandem arrays of yeast ribosomal DNA genes. Cell. 1980 Mar;19(3):765–774. doi: 10.1016/s0092-8674(80)80052-3. [DOI] [PubMed] [Google Scholar]
  33. Petes T. D. Yeast ribosomal DNA genes are located on chromosome XII. Proc Natl Acad Sci U S A. 1979 Jan;76(1):410–414. doi: 10.1073/pnas.76.1.410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Simeone A., de Falco A., Macino G., Boncinelli E. Sequence organization of the ribosomal spacer of D.melanogaster. Nucleic Acids Res. 1982 Dec 20;10(24):8263–8272. doi: 10.1093/nar/10.24.8263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Smith G. P. Evolution of repeated DNA sequences by unequal crossover. Science. 1976 Feb 13;191(4227):528–535. doi: 10.1126/science.1251186. [DOI] [PubMed] [Google Scholar]
  36. Swanson M. E., Holland M. J. RNA polymerase I-dependent selective transcription of yeast ribosomal DNA. Identification of a new cellular ribosomal RNA precursor. J Biol Chem. 1983 Mar 10;258(5):3242–3250. [PubMed] [Google Scholar]
  37. Szostak J. W., Wu R. Insertion of a genetic marker into the ribosomal DNA of yeast. Plasmid. 1979 Oct;2(4):536–554. doi: 10.1016/0147-619x(79)90053-2. [DOI] [PubMed] [Google Scholar]
  38. Szostak J. W., Wu R. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature. 1980 Apr 3;284(5755):426–430. doi: 10.1038/284426a0. [DOI] [PubMed] [Google Scholar]
  39. Truett M. A., Gall J. G. The replication of ribosomal DNA in the macronucleus of Tetrahymena. Chromosoma. 1977 Dec 6;64(4):295–303. doi: 10.1007/BF00294937. [DOI] [PubMed] [Google Scholar]
  40. Tschumper G., Carbon J. Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. Gene. 1980 Jul;10(2):157–166. doi: 10.1016/0378-1119(80)90133-x. [DOI] [PubMed] [Google Scholar]
  41. Valenzuela P., Bell G. I., Venegas A., Sewell E. T., Masiarz F. R., DeGennaro L. J., Weinberg F., Rutter W. J. Ribosomal RNA genes of Saccharomyces cerevisiae. II. Physical map and nucleotide sequence of the 5 S ribosomal RNA gene and adjacent intergenic regions. J Biol Chem. 1977 Nov 25;252(22):8126–8135. [PubMed] [Google Scholar]
  42. Veldman G. M., Klootwijk J., de Regt V. C., Planta R. J., Branlant C., Krol A., Ebel J. P. The primary and secondary structure of yeast 26S rRNA. Nucleic Acids Res. 1981 Dec 21;9(24):6935–6952. doi: 10.1093/nar/9.24.6935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Verbeet M. P., Klootwijk J., van Heerikhuizen H., Fontijn R., Vreugdenhil E., Planta R. J. Molecular cloning of the rDNA of Saccharomyces rosei and comparison of its transcription initiation region with that of Saccharomyces carlsbergensis. Gene. 1983 Jul;23(1):53–63. doi: 10.1016/0378-1119(83)90216-0. [DOI] [PubMed] [Google Scholar]
  44. Zamb T. J., Petes T. D. Analysis of the junction between ribosomal RNA genes and single-copy chromosomal sequences in the yeast Saccharomyces cerevisiae. Cell. 1982 Feb;28(2):355–364. doi: 10.1016/0092-8674(82)90353-1. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES