Skip to main content
PMC home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1985 Jan;5(1):46–51. doi: 10.1128/mcb.5.1.46

Concerted evolution of dispersed Neurospora crassa 5S RNA genes: pattern of sequence conservation between allelic and nonallelic genes.

E Morzycka-Wroblewska, E U Selker, J N Stevens, R L Metzenberg
PMCID: PMC366676  PMID: 2984554

Abstract

About 100 genes coding for 5S RNA in Neurospora crassa are dispersed throughout the genome (Selker et al., Cell 24:815-818, 1981; R. L. Metzenberg, J. N. Stevens, E. U. Selker, and E. Morzycka-Wroblewska, manuscript in preparation). The majority of them correspond to the most abundant species (alpha) of 5S RNA found in the cell. Gene conversion, gene transposition, or both may be responsible for the maintenance of sequence homogeneity (concerted evolution) of alpha-type 5S genes. To explore these possibilities, we isolated and characterized separate 5S regions from two distantly related laboratory strains of N. crassa. Restriction and sequence analyses revealed no differences in molecular location of allelic 5S genes between the two strains. However, the DNA sequences around the 5S genes are ca. 10% divergent. We concluded that transposition is not frequent enough to account for the concerted evolution of N. crassa alpha-5S genes. In contrast to sequence divergence in the flanking regions between the two strains, the 5S transcribed regions are identical (with one exception), suggesting that these genes are being corrected. We have found that flanking sequences of various N. crassa 5S genes within each strain are largely different. Thus, if the correction mechanism is based on gene conversion, it is limited to the transcribed regions of the genes. However, we did find a short region of consensus including the sequence TATA located 25 to 30 nucleotides preceding the position of transcription initiation. This region may be involved in the transcription of N. crassa 5S genes.

Full text

PDF
47

Images in this article

47Image
on p.47

Selected References

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

  1. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  2. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Blattner F. R., Blechl A. E., Denniston-Thompson K., Faber H. E., Richards J. E., Slightom J. L., Tucker P. W., Smithies O. Cloning human fetal gamma globin and mouse alpha-type globin DNA: preparation and screening of shotgun collections. Science. 1978 Dec 22;202(4374):1279–1284. doi: 10.1126/science.725603. [DOI] [PubMed] [Google Scholar]
  4. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  5. Davies J., Jacob F. Genetic mapping of the regulator and operator genes of the lac operon. J Mol Biol. 1968 Sep 28;36(3):413–417. doi: 10.1016/0022-2836(68)90165-4. [DOI] [PubMed] [Google Scholar]
  6. Dingermann T., Burke D. J., Sharp S., Schaack J., Söll D. The 5- flanking sequences of Drosophila tRNAArg genes control their in vitro transcription in a Drosophila cell extract. J Biol Chem. 1982 Dec 25;257(24):14738–14744. [PubMed] [Google Scholar]
  7. Dugaiczyk A., Boyer H. W., Goodman H. M. Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures. J Mol Biol. 1975 Jul 25;96(1):171–184. doi: 10.1016/0022-2836(75)90189-8. [DOI] [PubMed] [Google Scholar]
  8. Grosveld F. G., Dahl H. H., de Boer E., Flavell R. A. Isolation of beta-globin-related genes from a human cosmid library. Gene. 1981 Apr;13(3):227–237. doi: 10.1016/0378-1119(81)90028-7. [DOI] [PubMed] [Google Scholar]
  9. Indik Z. K., Tartof K. D. Glutamate tRNA genes are adjacent to 5S RNA genes in Drosophila and reveal a conserved upstream sequence (the ACT-TA box). Nucleic Acids Res. 1982 Jul 24;10(14):4159–4172. doi: 10.1093/nar/10.14.4159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Larson D., Bradford-Wilcox J., Young L. S., Sprague K. U. A short 5' flanking region containing conserved sequences is required for silkworm alanine tRNA gene activity. Proc Natl Acad Sci U S A. 1983 Jun;80(11):3416–3420. doi: 10.1073/pnas.80.11.3416. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Maniatis T., Jeffrey A., van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. doi: 10.1021/bi00688a010. [DOI] [PubMed] [Google Scholar]
  13. Mao J., Appel B., Schaack J., Sharp S., Yamada H., Söll D. The 5S RNA genes of Schizosaccharomyces pombe. Nucleic Acids Res. 1982 Jan 22;10(2):487–500. doi: 10.1093/nar/10.2.487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Maxam A. M., Tizard R., Skryabin K. G., Gilbert W. Promotor region for yeast 5S ribosomal RNA. Nature. 1977 Jun 16;267(5612):643–645. doi: 10.1038/267643a0. [DOI] [PubMed] [Google Scholar]
  16. Morton D. G., Sprague K. U. In vitro transcription of a silkworm 5S RNA gene requires an upstream signal. Proc Natl Acad Sci U S A. 1984 Sep;81(17):5519–5522. doi: 10.1073/pnas.81.17.5519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Morton D. G., Sprague K. U. Silkworm 5S RNA and alanine tRNA genes share highly conserved 5' flanking and coding sequences. Mol Cell Biol. 1982 Dec;2(12):1524–1531. doi: 10.1128/mcb.2.12.1524. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Munz P., Amstutz H., Kohli J., Leupold U. Recombination between dispersed serine tRNA genes in Schizosaccharomyces pombe. Nature. 1982 Nov 18;300(5889):225–231. doi: 10.1038/300225a0. [DOI] [PubMed] [Google Scholar]
  19. Murray N. E., Brammar W. J., Murray K. Lambdoid phages that simplify the recovery of in vitro recombinants. Mol Gen Genet. 1977 Jan 7;150(1):53–61. doi: 10.1007/BF02425325. [DOI] [PubMed] [Google Scholar]
  20. Nevins J. R. The pathway of eukaryotic mRNA formation. Annu Rev Biochem. 1983;52:441–466. doi: 10.1146/annurev.bi.52.070183.002301. [DOI] [PubMed] [Google Scholar]
  21. Nishikawa K., Takemura S. Structure and function of 5S ribosomal ribonucleic acid from Torulopsis utilis. II. Partial digestion with ribonucleases and derivation of the complete sequence. J Biochem. 1974 Nov;76(5):935–947. [PubMed] [Google Scholar]
  22. Piper P. W., Lockheart A., Patel N. A minor class of 5S rRNA genes in Saccharomyces cerevisiae X2180-1B, one member of which lies adjacent to a Ty transposable element. Nucleic Acids Res. 1984 May 25;12(10):4083–4096. doi: 10.1093/nar/12.10.4083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Rafalski J. A., Wiewiorowski M., Söll D. Organization and nucleotide sequence of nuclear 5S rRNA genes in yellow lupin (Lupinus luteus). Nucleic Acids Res. 1982 Dec 11;10(23):7635–7642. doi: 10.1093/nar/10.23.7635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  25. Sakonju S., Bogenhagen D. F., Brown D. D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell. 1980 Jan;19(1):13–25. doi: 10.1016/0092-8674(80)90384-0. [DOI] [PubMed] [Google Scholar]
  26. Selker E. U., Free S. J., Metzenberg R. L., Yanofsky C. An isolated pseudogene related to the 5S RNA genes in Neurospora crassa. Nature. 1981 Dec 10;294(5841):576–578. doi: 10.1038/294576a0. [DOI] [PubMed] [Google Scholar]
  27. Selker E. U., Yanofsky C., Driftmier K., Metzenberg R. L., Alzner-DeWeerd B., RajBhandary U. L. Dispersed 5S RNA genes in N. crassa: structure, expression and evolution. Cell. 1981 Jun;24(3):819–828. doi: 10.1016/0092-8674(81)90107-0. [DOI] [PubMed] [Google Scholar]
  28. Shaw K. J., Olson M. V. Effects of altered 5'-flanking sequences on the in vivo expression of a Saccharomyces cerevisiae tRNATyr gene. Mol Cell Biol. 1984 Apr;4(4):657–665. doi: 10.1128/mcb.4.4.657. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]
  30. Tabata S. Nucleotide sequences of the 5S ribosomal RNA genes and their adjacent regions in Schizosaccharomyces pombe. Nucleic Acids Res. 1981 Dec 11;9(23):6429–6437. doi: 10.1093/nar/9.23.6429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Thomas M., Davis R. W. Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975 Jan 25;91(3):315–328. doi: 10.1016/0022-2836(75)90383-6. [DOI] [PubMed] [Google Scholar]
  32. Valenzuela P., Bell G. I., Masiarz F. R., DeGennaro L. J., Rutter W. J. Nucleotide sequence of the yeast 5S ribosomal RNA gene and adjacent putative control regions. Nature. 1977 Jun 16;267(5612):641–643. doi: 10.1038/267641a0. [DOI] [PubMed] [Google Scholar]
  33. Woo S. L. A sensitive and rapid method for recombinant phage screening. Methods Enzymol. 1979;68:389–395. doi: 10.1016/0076-6879(79)68028-x. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES