Home LiteratureArticle Details
PMID: 8524279 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

An intramolecular recombination mechanism for the formation of the rRNA gene palindrome of Tetrahymena thermophila.

Molecular and cellular biology ·Vol. 15 ·No. 12 ·1995-12-00 ·Pages 7117-26

Butler DK, Yasuda LE, Yao MC

Abstract

Large palindromic DNAs are found in a wide variety of eukaryotic cells. In Tetrahymena thermophila, a large palindrome is formed from a single rRNA gene (rDNA) during nuclear differentiation. We present evidence that a key step in the formation of the rDNA palindrome of T. thermophila involves homologous intramolecular recombination. Heteroduplex micronuclear rDNA molecules were constructed in vitro and microinjected into developing macronuclei, where they formed palindromes. Analysis of the resulting palindromes indicated that both strands of the microinjected rDNA are used to form the same palindrome. This study, together with a previous study (L. F. Yasuda and M.-C. Yao, Cell 67:505-516, 1991), is the first to define a molecular pathway of palindrome formation. The process is initiated by chromosome breakage at sites flanking the micronuclear rDNA. An intramolecular recombination reaction, guided by a pair of short inverted repeats located at the 5' end of the excised rDNA, covalently joins the two strands of micronuclear rDNA in a giant hairpin molecule. Bidirectional DNA replication converts the giant hairpin molecule to a palindrome. We suggest that the general features of this pathway are applicable to palindrome formation in other cell types.

MeSH Terms
Animals Base Sequence Cloning, Molecular DNA, Protozoan/metabolism DNA, Ribosomal/metabolism Gene Expression Genes, Protozoan Models, Genetic Models, Structural Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Heteroduplexes/metabolism Oligodeoxyribonucleotides RNA, Protozoan/biosynthesis,genetics RNA, Ribosomal/biosynthesis,genetics Recombination, Genetic Restriction Mapping Tetrahymena thermophila/genetics,metabolism
Chemicals
DNA, Protozoan DNA, Ribosomal Nucleic Acid Heteroduplexes Oligodeoxyribonucleotides RNA, Protozoan RNA, Ribosomal
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Butler D K
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA.
Yasuda L E
Yao M C
References (46)
46 references, click to expand
  1. Nucleotide sequence structure and consistency of a developmentally regulated DNA deletion in Tetrahymena thermophila.
    Mol Cell Biol. 1987 Jan;7(1):435-43 PMID: 3031472
  2. Cleavage of cruciform DNA structures by an activity from Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 1985 Oct;82(19):6445-9 PMID: 3901001
  3. The Stability of Broken Ends of Chromosomes in Zea Mays.
    Genetics. 1941 Mar;26(2):234-82 PMID: 17247004
  4. Model for homologous recombination during transfer of DNA into mouse L cells: role for DNA ends in the recombination process.
    Mol Cell Biol. 1984 Jun;4(6):1020-34 PMID: 6330525
  5. Accurate processing and amplification of cloned germ line copies of ribosomal DNA injected into developing nuclei of Tetrahymena thermophila.
    Mol Cell Biol. 1989 Mar;9(3):1092-9 PMID: 2725489
  6. Partial purification of an enzyme from Saccharomyces cerevisiae that cleaves Holliday junctions.
    Proc Natl Acad Sci U S A. 1985 Nov;82(21):7247-51 PMID: 3903750
  7. Stabilization of dicentric chromosomes in Saccharomyces cerevisiae by telomere addition to broken ends or by centromere deletion.
    EMBO J. 1989 Jan;8(1):247-54 PMID: 2653811
  8. The controlling sequence for site-specific chromosome breakage in Tetrahymena.
    Cell. 1990 Nov 16;63(4):763-72 PMID: 2225076
  9. Allele-specific, selective amplification of a ribosomal RNA gene in Tetrahymena thermophila.
    Cell. 1982 Mar;28(3):595-604 PMID: 6280878
  10. Resolution of Holliday junctions by RuvC resolvase: cleavage specificity and DNA distortion.
    Cell. 1993 Sep 24;74(6):1021-31 PMID: 8402879
  11. A genetic analysis of dicentric minichromosomes in Saccharomyces cerevisiae.
    Cell. 1987 Mar 13;48(5):801-12 PMID: 3545498
  12. Two alternative pathways of double-strand break repair that are kinetically separable and independently modulated.
    Mol Cell Biol. 1992 Mar;12(3):1292-303 PMID: 1545810
  13. Formation of an inverted duplication can be an initial step in gene amplification.
    Mol Cell Biol. 1988 Oct;8(10):4302-13 PMID: 3185551
  14. Identifying functional regions of rRNA by insertion mutagenesis and complete gene replacement in Tetrahymena thermophila.
    EMBO J. 1989 Mar;8(3):933-8 PMID: 2542027
  15. The role of inverted duplication in the generation of gene amplification in mammalian cells.
    Biochim Biophys Acta. 1991 Oct 8;1090(2):143-55 PMID: 1932107
  16. Direct and inverted DNA repeats associated with P-glycoprotein gene amplification in drug resistant Leishmania.
    EMBO J. 1991 Apr;10(4):1009-16 PMID: 1672636
  17. An asymmetric nucleotide in the parvoviral 3' hairpin directs segregation of a single active origin of DNA replication.
    EMBO J. 1994 Sep 1;13(17):4145-52 PMID: 8076610
  18. Unstable DNA amplifications in methotrexate-resistant Leishmania consist of extrachromosomal circles which relocalize during stabilization.
    Cell. 1984 Sep;38(2):431-9 PMID: 6467372
  19. Healing of broken linear dicentric chromosomes in yeast.
    Genetics. 1984 Feb;106(2):207-26 PMID: 6365688
  20. A truncated human chromosome 16 associated with alpha thalassaemia is stabilized by addition of telomeric repeat (TTAGGG)n.
    Nature. 1990 Aug 30;346(6287):868-71 PMID: 1975428
  21. V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes.
    Cell. 1992 Sep 18;70(6):983-91 PMID: 1356077
  22. Sister chromatid fusion initiates amplification of the dihydrofolate reductase gene in Chinese hamster cells.
    Genes Dev. 1993 Apr;7(4):605-20 PMID: 8458577
  23. Co-amplified markers alternate in megabase long chromosomal inverted repeats and cluster independently in interphase nuclei at early steps of mammalian gene amplification.
    EMBO J. 1992 Jul;11(7):2665-73 PMID: 1628626
  24. Resistance to antimycin A in yeast by amplification of ADH4 on a linear, 42 kb palindromic plasmid.
    Cell. 1986 Sep 12;46(6):857-63 PMID: 3019553
  25. The multicopy appearance of a large inverted duplication and the sequence at the inversion joint suggest a new model for gene amplification.
    EMBO J. 1988 Feb;7(2):407-17 PMID: 3366118
  26. Resolution of linear minichromosomes with hairpin ends from circular plasmids containing vaccinia virus concatemer junctions.
    Cell. 1986 Jun 20;45(6):879-84 PMID: 3085958
  27. Phenotypic assortment in Tetrahymena thermophila: assortment kinetics of antibiotic-resistance markers, tsA, death, and the highly amplified rDNA locus.
    Genetics. 1988 Oct;120(2):389-95 PMID: 3197953
  28. Ribosomal DNA is a site of chromosome breakage in aneuploid strains of Neurospora.
    Genetics. 1992 Jul;131(3):581-92 PMID: 1385794
  29. Efficient homologous recombination of linear DNA substrates after injection into Xenopus laevis oocytes.
    Mol Cell Biol. 1986 Jun;6(6):2053-61 PMID: 2946937
  30. A distant 10-bp sequence specifies the boundaries of a programmed DNA deletion in Tetrahymena.
    Genes Dev. 1993 Dec;7(12A):2357-65 PMID: 8253382
  31. Resolution of recombination intermediates by a mammalian activity functionally analogous to Escherichia coli RuvC resolvase.
    J Biol Chem. 1994 Feb 18;269(7):5202-9 PMID: 8106502
  32. Recent progress in understanding mechanisms of mammalian DNA amplification.
    Cell. 1989 Jun 16;57(6):901-8 PMID: 2661014
  33. Identification of healed terminal DNA fragments in linear minichromosomes of Schizosaccharomyces pombe.
    Mol Cell Biol. 1987 Dec;7(12):4424-30 PMID: 2830493
  34. Short inverted repeats at a free end signal large palindromic DNA formation in Tetrahymena.
    Cell. 1991 Nov 1;67(3):505-16 PMID: 1934058
  35. Organization and genesis of dihydrofolate reductase amplicons in the genome of a methotrexate-resistant Chinese hamster ovary cell line.
    Mol Cell Biol. 1988 Jun;8(6):2316-27 PMID: 2841578
  36. In vitro resolution of covalently joined AAV chromosome ends.
    Cell. 1990 Jan 12;60(1):105-13 PMID: 2153052
  37. Free ribosomal DNA molecules from Tetrahymena pyriformis GL are giant palindromes.
    J Mol Biol. 1976 Jun 25;104(2):455-70 PMID: 820864
  38. New telomeres in yeast are initiated with a highly selected subset of TG1-3 repeats.
    Genes Dev. 1993 Dec;7(12A):2345-56 PMID: 8253381
  39. Large inverted duplications are associated with gene amplification.
    Cell. 1986 May 9;45(3):425-30 PMID: 2870814
  40. Transformation of Tetrahymena thermophila by microinjection of ribosomal RNA genes.
    Proc Natl Acad Sci U S A. 1986 Jun;83(12):4369-73 PMID: 3459180
  41. Structure of an inverted duplication formed as a first step in a gene amplification event: implications for a model of gene amplification.
    EMBO J. 1987 Jun;6(6):1697-703 PMID: 3038532
  42. Hairpin structures are the primary amplification products: a novel mechanism for generation of inverted repeats during gene amplification.
    Mol Cell Biol. 1994 Dec;14(12):7782-91 PMID: 7969119
  43. Yeast transformation: a model system for the study of recombination.
    Proc Natl Acad Sci U S A. 1981 Oct;78(10):6354-8 PMID: 6273866
  44. Large deletions result from breakage and healing of P. falciparum chromosomes.
    Cell. 1988 Dec 2;55(5):869-74 PMID: 3056622
  45. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans.
    Nature. 1994 Mar 3;368(6466):32-8 PMID: 7906398
  46. The macronuclear ribosomal DNA of Tetrahymena pyriformis is a palindrome.
    J Mol Biol. 1976 Jun 25;104(2):421-53 PMID: 820863
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/MCB.15.12.7117
Published
1995-12-00
Pages
7117-26
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC230967
Subset
IM
Grants
NIGMS NIH HHS · F32 GM13293-02 · United States
NIGMS NIH HHS · F32 GM1434-03 · United States
NHGRI NIH HHS · R01NIHGM26210 · United States
External Links
PubMed source DOI: 10.1128/MCB.15.12.7117 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2