Sequence Analysis of 28S Ribosomal DNA from the Amphibian Xenopus Laevis

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1983 Nov 25

PMID 6359063

Citations 73

Authors

V C Ware

B W Tague

C G Clark

R L Gourse

R C Brand

S A Gerbi

Affiliations

Soon will be listed here.

Abstract

We have determined the complete nucleotide sequence of Xenopus laevis 28S rDNA (4110 bp). In order to locate evolutionarily conserved regions within rDNA, we compared the Xenopus 28S sequence to homologous rDNA sequences from yeast, Physarum, and E. coli. Numerous regions of sequence homology are dispersed throughout the entire length of rDNA from all four organisms. These conserved regions have a higher A + T base composition than the remainder of the rDNA. The Xenopus 28S rDNA has nine major areas of sequence inserted when compared to E. coli 23S rDNA. The total base composition of these inserts in Xenopus is 83% G + C, and is generally responsible for the high (66%) G + C content of Xenopus 28S rDNA as a whole. Although the length of the inserted sequences varies, the inserts are found in the same relative positions in yeast 26S, Physarum 26S, and Xenopus 28S rDNAs. In one insert there are 25 bases completely conserved between the various eukaryotes, suggesting that this area is important for eukaryotic ribosomes. The other inserts differ in sequence between species and may or may not play a functional role.

Citing Articles

Ribosome Structural Changes Dynamically Affect Ribosome Function.

Lindahl L Int J Mol Sci. 2024; 25(20).

PMID: 39456968 PMC: 11508205. DOI: 10.3390/ijms252011186.

rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles.

Biesiada M, Hu M, Williams L, Purzycka K, Petrov A Nucleic Acids Res. 2022; 50(18):10717-10732.

PMID: 36200812 PMC: 9561286. DOI: 10.1093/nar/gkac844.

Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes.

Wilson K, Kung R, Dsouza S, Wetmore S Nucleic Acids Res. 2021; 49(4):2213-2225.

PMID: 33544852 PMC: 7913691. DOI: 10.1093/nar/gkab008.

Interaction Networks of Ribosomal Expansion Segments in Kinetoplastids.

Vicens Q, Bochler A, Jobe A, Frank J, Hashem Y Subcell Biochem. 2020; 96:433-450.

PMID: 33252739 DOI: 10.1007/978-3-030-58971-4_13.

Supersized Ribosomal RNA Expansion Segments in Asgard Archaea.

Penev P, Fakhretaha-Aval S, Patel V, Cannone J, Gutell R, Petrov A Genome Biol Evol. 2020; 12(10):1694-1710.

PMID: 32785681 PMC: 7594248. DOI: 10.1093/gbe/evaa170.

References

Sege R, Soll D, Ruddle F, Queen C . A conversational system for the computer analysis of nucleic acid sequences. Nucleic Acids Res. 1981; 9(2):437-44. PMC: 326703. DOI: 10.1093/nar/9.2.437. View

Gourse R, Gerbi S . Fine structure of ribosomal RNA. IV. Extraordinary evolutionary conservation in sequences that flank introns in rDNA. Nucleic Acids Res. 1980; 8(16):3623-37. PMC: 324180. DOI: 10.1093/nar/8.16.3623. View

Muller F, Clarkson S . Nucleotide sequence of genes coding for tRNAPhe and tRNATyr from a repeating unit of X. laevis DNA. Cell. 1980; 19(2):345-53. DOI: 10.1016/0092-8674(80)90509-7. View

Georgiev O, Nikolaev N, HADJIOLOV A, Skryabin K, Zakharyev V, Bayev 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; 9(24):6953-8. PMC: 327653. DOI: 10.1093/nar/9.24.6953. View

Nazar R, Sitz T . Role of the 5'-terminal sequence in the RNA binding site of yeast 5.8 S rRNA. FEBS Lett. 1980; 115(1):71-6. DOI: 10.1016/0014-5793(80)80729-0. View

Machatt M, Ebel J, Branlant C . The 3'-terminal region of bacterial 23S ribosomal RNA: structure and homology with the 3'-terminal region of eukaryotic 28S rRNA and with chloroplast 4.5s rRNA. Nucleic Acids Res. 1981; 9(7):1533-49. PMC: 326779. DOI: 10.1093/nar/9.7.1533. View

Queen C, Korn L . Computer analysis of nucleic acids and proteins. Methods Enzymol. 1980; 65(1):595-609. DOI: 10.1016/s0076-6879(80)65062-9. View

Brosius J, Dull T, Noller H . Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1980; 77(1):201-4. PMC: 348236. DOI: 10.1073/pnas.77.1.201. View

Brownlee G, Cartwright E, McShane T, Williamson R . The nucleotide sequence of somatic 5 S RNA from Xenopus laevis. FEBS Lett. 1972; 25(1):8-12. DOI: 10.1016/0014-5793(72)80442-3. View

10.

Salim M, Maden B . Nucleotide sequence encoding the 5' end of Xenopus laevis 18S rRNA. Nucleic Acids Res. 1980; 8(13):2871-84. PMC: 324131. DOI: 10.1093/nar/8.13.2871. View

11.

Salim M, Maden B . Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from gene sequence. Nature. 1981; 291(5812):205-8. DOI: 10.1038/291205a0. View

12.

Sinclair J, Brown D . Retention of common nucleotide sequences in the ribosomal deoxyribonucleic acid of eukaryotes and some of their physical characteristics. Biochemistry. 1971; 10(14):2761-9. DOI: 10.1021/bi00790a017. View

13.

Amaldi F, Posta A . Base composition of ribosomal RNA and evolution. J Mol Evol. 1972; 2(1):44-55. DOI: 10.1007/BF01653942. View

14.

Peacock A, DINGMAN C . Molecular weight estimation and separation of ribonucleic acid by electrophoresis in agarose-acrylamide composite gels. Biochemistry. 1968; 7(2):668-74. DOI: 10.1021/bi00842a023. View

15.

Moss T, Boseley P, Birnstiel M . More ribosomal spacer sequences from Xenopus laevis. Nucleic Acids Res. 1980; 8(3):467-85. PMC: 327284. DOI: 10.1093/nar/8.3.467. View

16.

Amaldi F . Non-random variability in evolution of base compositions of ribosomal RNA. Nature. 1969; 221(5175):95-6. DOI: 10.1038/221095a0. View

17.

Hall L, Maden B . Nucleotide sequence through the 18S-28S intergene region of a vertebrate ribosomal transcription unit. Nucleic Acids Res. 1980; 8(24):5993-6005. PMC: 328067. DOI: 10.1093/nar/8.24.5993. View

18.

Glotz C, Zwieb C, Brimacombe R, Edwards K, Kossel H . Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes. Nucleic Acids Res. 1981; 9(14):3287-306. PMC: 327352. DOI: 10.1093/nar/9.14.3287. View

19.

Orgel L . Evolution of the genetic apparatus. J Mol Biol. 1968; 38(3):381-93. DOI: 10.1016/0022-2836(68)90393-8. View

20.

BIRNSTIEL M, Speirs J, PURDOM I, Jones K, Loening U . Properties and composition of the isolated ribosomal DNA satellite of Xenopus laevis. Nature. 1968; 219(5153):454-63. DOI: 10.1038/219454a0. View