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PMID: 2325628 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Transcription of tomato ribosomal DNA and the organization of the intergenic spacer.

Molecular & general genetics : MGG ·Vol. 221 ·No. 1 ·1990-03-00 ·Pages 103-12

Perry KL, Palukaitis P

Abstract

The organization of the intergenic spacer of a 9.04 kb tomato ribosomal RNA gene (rDNA) was determined. The 3258 bp spacer contains two major repeat elements enclosing a region which includes 351 bp of an 81.8% A --T rich sequence. A block of nine 53 bp repeats begins 388 bp downstream from the 3' end of the 25S rRNA. The A--T rich domain is followed by a block of six 141 bp repeats terminating 818 bp upstream from the 5' end of the 18S rRNA. Major pre-rRNAs of 7.6 and 6.5 kb were observed by Northern hybridization analysis. The 5' termini of these RNAs were identified through combined S1 nuclease and primer extension analyses. The 7.6 kb RNA is likely to be the primary transcript; its 5' terminus lies within a sequence motif. TATA(R)TA(N)GGG, conserved at the termini of transcripts mapped in three other plant species. The 6.5 kb RNA is interpreted as a 5' end processed transcript derived from the 7.6 kb RNA. Comparative analysis of transcribed sequences revealed a 25 bp domain of the intergenic spacer which is relatively conserved among five plant species. The conservation of spacer sequences in plants is in contrast to the extensive sequence divergence of the intergenic spacer in other non-plant systems and suggests a conserved function directed by these sequences.

MeSH Terms
Base Sequence Blotting, Northern DNA, Ribosomal/genetics Introns Molecular Sequence Data Plants/genetics RNA, Ribosomal/genetics Sequence Homology, Nucleic Acid Transcription, Genetic
Chemicals
DNA, Ribosomal RNA, Ribosomal
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Perry K L
Department of Plant Pathology, Cornell University, Ithaca, NY 14853-5908.
Palukaitis P
References (55)
55 references, click to expand
  1. The Relationship between Satellite Deoxyribonucleic Acid, Ribosomal Ribonucleic Acid Gene Redundancy, and Genome Size in Plants.
    Plant Physiol. 1975 Mar;55(3):496-501 PMID: 16659109
  2. Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
    Proc Natl Acad Sci U S A. 1984 Dec;81(24):8014-8 PMID: 6096873
  3. Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer.
    Plant Mol Biol. 1987 Sep;9(5):509-20 PMID: 24277137
  4. Transcription of mouse rDNA terminates downstream of the 3' end of 28S RNA and involves interaction of factors with repeated sequences in the 3' spacer.
    Cell. 1985 Dec;43(3 Pt 2):801-10 PMID: 4075406
  5. Chromosome and nucleotide sequence differentiation in genomes of polyploid Triticum species.
    Theor Appl Genet. 1982 Dec;63(4):349-60 PMID: 24270872
  6. Enhancer-like properties of the 60/81 bp elements in the ribosomal gene spacer of Xenopus laevis.
    Cell. 1984 May;37(1):285-9 PMID: 6722873
  7. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  8. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing.
    J Mol Biol. 1980 Oct 25;143(2):161-78 PMID: 6260957
  9. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease.
    Biochemistry. 1979 Nov 27;18(24):5294-9 PMID: 518835
  10. Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP.
    Nucleic Acids Res. 1986 Feb 11;14(3):1319-24 PMID: 3951988
  11. Transcription initiation site of rat ribosomal DNA.
    Nucleic Acids Res. 1982 Nov 25;10(22):7345-62 PMID: 6296773
  12. Transcription of tomato ribosomal DNA and the organization of the intergenic spacer.
    Mol Gen Genet. 1990 Mar;221(1):103-12 PMID: 2325628
  13. Determination of the sequence homology between the four RNA species of cucumber mosaic virus by hybridization analysis with complementary DNA.
    Nucleic Acids Res. 1977 Nov;4(11):3787-802 PMID: 593886
  14. Mapping of gene transcripts by nuclease protection assays and cDNA primer extension.
    Methods Enzymol. 1987;152:611-32 PMID: 2821358
  15. A transcriptional function for the repetitive ribosomal spacer in Xenopus laevis.
    Nature. 1983 Mar 17-23;302(5905):223-8 PMID: 6835360
  16. Repeated genes in eukaryotes.
    Annu Rev Biochem. 1980;49:727-64 PMID: 6996571
  17. The nucleotide sequence of the initiation and termination sites for ribosomal RNA transcription in X. laevis.
    Cell. 1979 Oct;18(2):485-99 PMID: 498280
  18. Detection of replication initiation by a replicon family in DNA of synchronized pea (Pisum sativum) root cells using benzoylated naphthoylated DEAE-cellulose chromatography.
    Plant Mol Biol. 1987 Mar;9(2):77-86 PMID: 24276897
  19. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity.
    Anal Biochem. 1983 Jul 1;132(1):6-13 PMID: 6312838
  20. Nucleotide sequence of a 25S rRNA gene from tomato.
    Nucleic Acids Res. 1989 Jan 25;17(2):796 PMID: 2915931
  21. 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):165-74 PMID: 7326749
  22. Spacer sequences regulate transcription of ribosomal gene plasmids injected into Xenopus embryos.
    Cell. 1983 Oct;34(3):989-96 PMID: 6627394
  23. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors.
    Gene. 1985;33(1):103-19 PMID: 2985470
  24. A comprehensive set of sequence analysis programs for the VAX.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387-95 PMID: 6546423
  25. Plasmids of Escherichia coli as cloning vectors.
    Methods Enzymol. 1979;68:245-67 PMID: 232214
  26. Structural and transcriptional characterization of the external spacer of a ribosomal RNA nuclear gene from a higher plant.
    Eur J Biochem. 1988 Mar 15;172(3):767-76 PMID: 3350023
  27. Nucleotide sequence of the 17S-25S spacer region from tomato rDNA.
    Nucleic Acids Res. 1988 Jul 25;16(14B):7179 PMID: 3405762
  28. Nucleotide sequence of tobacco mosaic virus RNA.
    Proc Natl Acad Sci U S A. 1982 Oct;79(19):5818-22 PMID: 6964389
  29. Structure and variation in ribosomal RNA genes of pea : Characterization of a cloned rDNA repeat and chromosomal rDNA variants.
    Plant Mol Biol. 1987 Jan;8(1):3-12 PMID: 24302519
  30. Nucleotide sequence of a 17S (18S) rRNA gene from tomato.
    Nucleic Acids Res. 1989 Mar 11;17(5):2127 PMID: 2928118
  31. Preferential homogenization between adjacent and alternate subrepeats in wheat rDNA.
    Nucleic Acids Res. 1986 Jul 11;14(13):5499-512 PMID: 3737408
  32. The ribosomal RNA promoter of Acanthamoeba castellanii determined by transcription in a cell-free system.
    Nucleic Acids Res. 1985 Sep 11;13(17):6237-48 PMID: 2995922
  33. Occurrence of 9 homologous repeat units in the external spacer region of a nuclear maize rRNA gene unit.
    Nucleic Acids Res. 1986 Jun 25;14(12):4969-86 PMID: 3014440
  34. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis.
    Gene. 1983 Dec;26(1):101-6 PMID: 6323249
  35. Heritability and Variability in Ribosomal RNA Genes of Vicia faba.
    Genetics. 1987 Oct;117(2):285-95 PMID: 17246404
  36. Nucleotide sequence determining the first cleavage site in the processing of mouse precursor rRNA.
    Proc Natl Acad Sci U S A. 1987 Feb;84(3):629-33 PMID: 3027694
  37. Nested control regions promote Xenopus ribosomal RNA synthesis by RNA polymerase I.
    Cell. 1983 Nov;35(1):199-206 PMID: 6684995
  38. Xenopsin: the neurotensin-like octapeptide from Xenopus skin at the carboxyl terminus of its precursor.
    Proc Natl Acad Sci U S A. 1984 Jan;81(2):380-4 PMID: 6582494
  39. The wheat ribosomal DNA spacer region: Its structure and variation in populations and among species.
    Theor Appl Genet. 1982 Dec;63(4):337-48 PMID: 24270871
  40. The structure of the maize ribosomal DNA spacer region.
    Nucleic Acids Res. 1986 Jun 25;14(12):4953-68 PMID: 3725589
  41. Complex organization of the length heterogeneous 5' external spacer of mung bean (Vigna radiata) ribosomal DNA.
    Genome. 1988 Oct;30(5):723-33 PMID: 3203889
  42. Analysis of single- and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange.
    Proc Natl Acad Sci U S A. 1977 Nov;74(11):4835-8 PMID: 73185
  43. Characterization of three sites of RNA 3' end formation in the Xenopus ribosomal gene spacer.
    Cell. 1986 May 9;45(3):431-43 PMID: 3453104
  44. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids.
    Cell. 1977 Nov;12(3):721-32 PMID: 922889
  45. Transcription of the tandem array of ribosomal DNA in Drosophila melanogaster does not terminate at any fixed point.
    EMBO J. 1986 Jun;5(6):1267-73 PMID: 16453684
  46. Human ribosomal RNA gene: nucleotide sequence of the transcription initiation region and comparison of three mammalian genes.
    Proc Natl Acad Sci U S A. 1982 May;79(10):3092-6 PMID: 6954460
  47. Transcription of cloned eukaryotic ribosomal RNA genes.
    Annu Rev Biochem. 1986;55:801-30 PMID: 3527052
  48. A specific replication origin in the chromosomal rDNA of Lytechinus variegatus.
    Nature. 1982 Sep 30;299(5882):453-6 PMID: 7121583
  49. Efficeint transcription of RNA into DNA by avian sarcoma virus polymerase.
    Biochim Biophys Acta. 1976 Sep 6;442(3):324-30 PMID: 183818
  50. Direct sequencing of denatured plasmid DNA.
    Methods Enzymol. 1987;152:556-62 PMID: 2443806
  51. Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat.
    J Mol Biol. 1988 May 5;201(1):1-17 PMID: 3418693
  52. Location of the replication origin in the 9-kb repeat size class of rDNA in pea (Pisum sativum).
    Plant Mol Biol. 1987 Mar;9(2):87-95 PMID: 24276898
  53. Enhancers and ribosomal gene spacers.
    Cell. 1984 Sep;38(2):349-51 PMID: 6467370
  54. Spacer promoters are essential for efficient enhancement of X. laevis ribosomal transcription.
    Cell. 1986 Jan 31;44(2):313-8 PMID: 3943126
  55. Production of single-stranded plasmid DNA.
    Methods Enzymol. 1987;153:3-11 PMID: 3323803
Article Info
Journal
Molecular & general genetics : MGG
Abbr.
Mol Gen Genet
ISSN
0026-8925
DOI
10.1007/BF00280374
Published
1990-03-00
Pages
103-12
Language
English
Region
Germany
NLM ID
0125036
Subset
IM
External Links
PubMed source DOI: 10.1007/BF00280374
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