Functional variants of 5S rRNA in the ribosomes of common sea urchin Paracentrotus lividus

Gene

Volumn 508, Issue 1, 2012, Pages 21-25

  Dimarco, Eufrosina ^a   Cascone, Eleonora ^a   Bellavia, Daniele ^a   Caradonna, Fabio ^a  

^a UNIVERSITY OF PALERMO   (Italy)

Author keywords

5S gene; 5S rRNA variants; Paracentrotus lividus; Sea urchin; Single strand conformation polymorphism (SSCP)

Indexed keywords

DNA 5S; RNA 5S;

AMPLICON; ARTICLE; CONTROLLED STUDY; CYTOGENETICS; ELUTION; GENE CLUSTER; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; MOLECULAR CLONING; MOLECULAR GENETICS; NONHUMAN; PARACENTROTUS LIVIDUS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBOSOME; SEA URCHIN; SINGLE STRAND CONFORMATION POLYMORPHISM;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; OOCYTES; PARACENTROTUS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; RIBOSOMES; RNA, RIBOSOMAL, 5S; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ANIMALIA; ECHINOIDEA; PARACENTROTUS LIVIDUS;

EID: 84865542836     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.07.067     Document Type: Article

References (33)

1. Appels R., Gerlach W.L., Dennis E.S., Swift H., Peacock W.J. Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals. Chromosoma 1980, 78:293-311.
2. Barbieri R., Duro G., Morgante A., Izzo V. Rapid DNA elution procedure from agarose gels. Anal. Biochem. 1996, 235:106-107.
3. Bellavia D., Barbieri R. Evidence for a novel cytoplasmic processing event in ribosome maturation in the sea urchin Paracentrotus lividus. Cell. Mol. Life Sci. 2010, 67:1871-1879.
4. Cantone M., Barbieri R., Duro G., Izzo V., Giudice G. Sequence analysis of the rDNA spacer of Paracentrotus lividus and observations about pre-rRNA processing. Mol. Biol. Rep. 1993, 18:177-182.
5. Caradonna F., Bellavia D., Clemente A.M., Sisino G., Barbieri R. Chromosomal localization and molecular characterization of three different 5S ribosomal DNA clusters in the sea urchin Paracentrotus lividus. Genome 2007, 50:867-870.
6. Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 1987, 162:156-159.
7. Cloix C., et al. Analysis of 5S rDNA Arrays in Arabidopsis thaliana-mapping e chromosome specific polymorph. Genome Res. 2000, 10:679-690.
8. Cloix C., et al. Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA. Genome Res. 2002, 12:132-144.
9. Cronn R.C., Zhao X., Paterson A.H., Wendel J.F. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J. Mol. Evol. 1996, 42:685-705.
10. Del Pino E.M., Murphy C., Masson P.H., Gall J.G. 5S rRNA-encoding genes of the marsupial frog Gastrotheca riobambae. Gene 1992, 111:235-238.
11. Doran J.L., Bingle W.H., Roy K.L. The nucleotide sequences of two human 5S rRNA pseudogenes. Nucleic Acids Res. 1987, 15:6297.
12. Douet J., Tormente S. Transcription of the 5S rRNA heterochromatic genes is epigenetically controlled in Arabidopsis thaliana and Xenopus laevis. Heredity 2007, 99:5-13.
13. Ellis T.N., et al. 5S rRNA genes in pisum: sequence, long range and chromosomal organization. Mol. Gen. Genet. 1988, 214:333-342.
14. Ford P.J., Southern E.M. Different sequences for 5S RNA in kidney cells and ovaries of Xenopus laevis. Nat. New Biol. 1973, 241:7-12.
15. Ghose R., Malik M., Huber P.W. Restricted specificity of Xenopus TFIIIA for Transcription of Somatic 5S rRNA Genes. Mol. Cell. Biol. 2004, 24:2467-2477.
16. Izzo V., et al. Electrophoresis of proteins and DNA on horizontal sodium dodecyl sulfate polyacrylamide gels. Immun. Ageing 2006, 10.1186/1742-4933-3-7.
17. Komiya H., Shimizu N., Kawakami M., Takemura S. Nucleotide sequence of 5S ribosomal RNA from Lingula anatina. A study on the molecular evolution of 5S ribosomal RNA from a living fossil. J. Biochem. 1980, 88:1449-1456.
18. Leah R., Frederiksen S., Engberg J., Sørensen P.D. Nucleotide sequence of a mouse 5S rRNA variant gene. Nucleic Acids Res. 1990, 18:7441.
19. Long E.O., Dawid I.B. Repeated genes in eukaryotes. Annu. Rev. Biochem. 1980, 49:727-764.
20. Lu A.L., Steege D.A., Stafford D.W. Nucleotide sequence of a 5S ribosomal RNA gene in the sea urchin Lytechinus variegatus. Nucleic Acids Res. 1980, 8:1839-1853.
21. Lu A.L., Blin N., Stafford D.W. Cloning and organization of genes for 5S ribosomal RNA in the sea urchin. Lytechinus variegatus. Gene 1981, 14:51-62.
22. Martins C., Galetti P.M. Organization of 5S rDNA in species of the fish Leporinus: two different genomic locations are characterized by distinct nontranscribed spacers. Genome 2001, 44:903-910.
23. Negi M.S., Rajagopal J., Chauhan N., Cronn R., Lakshmikumaran M. Length and sequence heterogeneity in 5S rDNA of Populus deltoides. Genome 2002, 45:1181-1188.
24. Pasolini P., Costagliola D., Rocco L., Tinti F. Molecular organization of 5S rDNAs in Rajidae (Chondrichthyes): structural features and evolution of piscine 5S rRNA genes and nontranscribed intergenic spacers. J. Mol. Evol. 2006, 62:564-574.
25. Peterson R.C., Doering J.L., Brown D.D. Characterization of two Xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA. Cell 1980, 20:131-141.
26. Pinhal D., Yoshimura T.S., Araki C.S., Martins C. The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays. BMC Evol. Biol. 2011, 10.1186/1471-2148-11-151.
27. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 2nd edn.
28. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. 1977, 77:5463-5467.
29. Singh K., Bhatia S., Lakshmikumaran M. Novel variants of the 5S rRNA genes in Eruca sativa. Genome 1994, 37:121-128.
30. Sørensen P.D., Frederiksen S. Characterization of human 5S rRNA genes. Nucleic Acids Res. 1991, 19:4147-4151.
31. Szymanski M., Barciszewska M.Z., Erdmann V.A., Barciszewski J. 5S Ribosomal RNA database. Nucleic Acids Res. 2002, 30:176-178.
32. Vahidi H., Purac A., LeBlanc J.M., Honda B.M. Characterization of potentially functional 5S rRNA-encoding genes within ribosomal DNA repeats of the nematode Meloidogyne arenaria. Gene 1991, 108:281-284.
33. Wildeman A.G., Nazar R.N. Structural studies of 5S ribosomal RNAs from a thermophilic fungus, Thermomyces lanuginosus. A comparison of generalized models for eukaryotic 5S RNAs. J. Biol. Chem. 1982, 257:11395-11404.