Evolution of the large-subunit ribosomal RNA binding site for protein L23/25

Molecular Biology and Evolution

Volumn 14, Issue 5, 1997, Pages 578-588

  Chenuil, Anne ^a   Solignac, Michel ^a   Bernard, Michot ^a  

^a CNRS   (France)

Author keywords

divergent domain; evolution; invertebrates; large subunit rRNA; protein rRNA interaction; secondary structure; sequence

Indexed keywords

RIBOSOME RNA; RNA BINDING PROTEIN;

ANNELID WORM; ARTHROPOD; ARTICLE; ESCHERICHIA COLI; EVOLUTION; GENETIC CONSERVATION; INVERTEBRATE; MOLLUSC; NONHUMAN; PHYLOGENY; PROTEIN DOMAIN; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE;

EID: 0030971364     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025795     Document Type: Article

References (47)

1. BACHELLERIE, J. P., and B. MICHOT. 1989. Evolution of large subunit rRNA structure. The 3′ terminal domain contains elements of secondary structure specific to major phylogenetic groups. Biochimie 71:701-709.
2. BRUSCA, R. C., and G. J. BRUSCA. 1990. Invertebrates. Sinauer, Sunderland, Mass.
3. CHAN, Y. L., J. OLVERA, and I. G. WOOL. 1983. The structure of rat 28S ribonucleic acids inferred from the sequence of nucleotides in a gene. Nucleic Acids Res. 11:7819-7831.
4. CLARK, C. G., B. W. TAGUE, V. C. WARE, and S. A. GERBI. 1984. Xenopus laevis ribosomal RNA: a secondary structure model and its evolutionary and functional implications. Nucleic Acids Res. 12:6197-6220.
5. CORPET, F. 1989. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16:10881-10890.
6. CORPET, F., and B. MICHOT. 1994. RNAlign program: alignment of RNA sequences using both primary and secondary structures. Comput. Appl. Biosci. 10:389-399.
7. DABBS, E. R. 1980. On the mechanism of chloramphenicol-induced changes in the photoinduced affinity labeling of Escherichia coli ribosomes by puromycin. Evidence for puromycin and chloramphenicol sites. Mol. Gen. Genet. 177: 271-276.
8. DE LANVERSIN, G., and B. JACQ. 1989. Sequence and secondary structure of the central domain of Drosophila 26S rRNA: a universal model for the central domain of the large rRNA containing the region in which the central break may happen. J. Mol. Evol. 28:403-417.
9. EERNISSE, D. J., J. S. ALBERT, and F. E. ANDERSON. 1992. Annelida and Arthropoda are not sister taxa: a phylogenetic analysis of Spiralian metazoan morphology. Syst. Biol. 4: 305-330.
10. EGEBJERG, J., A. CHRISTIANSEN, and R. A. GARRETT. 1991. Attachment sites of primary binding proteins L1, L2 and L23 and 23S ribosomal RNA Escherichia coli. J. Mol. Biol. 222:251-264.
11. EL-BARADI, T. T. A. L., V. C. H. F. DE REGT, R. J. PLANTA, K. H. NIERHAUS, and H. A. RAUÉ. 1987. Interaction of ribosomal protein L25 from yeast and EL23 from E. coli with yeast 26S and mouse 28S rRNA. Biochimie 69:939-948.
12. EL-BARADI, T. T. A. L., A. H. RAUÉ, V. C. H. F. DE REGT, E. C. VERBREE, and R. J. PLANTA. 1985. Yeast ribosomal protein L25 binds to an evolutionary conserved site on yeast 26S and E. coli 23S rRNA. EMBO J. 4:2101-2107.
13. FIELD, K. G., G. J. OLSEN, D. J. LANE, S. J. GIOVANNONI, M. T. GHISELIN, E. C. RAFF, N. R. PACE, and R. A. RAFF. 1988. Molecular phylogeny of the animal kingdom. Science 239: 748-753.
14. FUJIWAR, H., and H. ISHIKAWA. 1986. Molecular mechanism of introduction of the hidden break into the 28S rRNA of insects: implication based on structural studies. Nucleic Acids Res. 14:6393-6401.
15. GERBI, S. A. 1985. Evolution of ribosomal DNA. Pp. 419-517 in R. J. MCINTYRE, ed. Molecular evolutionary genetics. Plenum Publishing, New York, N.Y.
16. _. 1996. Expansion segments: regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. Pp. 71-87 in R. A. ZIMMERMAN and A. E. DAHLBERG, eds. Ribosomal RNA. Structure, evolution, processing and function in protein biosynthesis. CRC Press.
17. GORSKI, J. L., I. L. GONZALEZ, and R. D. SCHMICKEL. 1987. The secondary structure of human 28S rRNA: the structure and evolution of a mosaic rRNA gene. J. Mol. Evol. 24: 236-251.
18. GRANT, P. G., W. Z. STRYCHARZ, E. N. JAYNES, and B. S. COOPERMAN. 1979. Antibiotic effects on the photoinduced affinity labeling of Escherichia coli ribosomes by puromycin. Biochemistry 18:2149-2154.
19. GRAY, M. W., and M. N. SCHNARE. 1996. Evolution of rRNA gene organization. Pp. 49-69 in ZIMMERMAN and A. E. DAHLBERG, eds. Ribosomal RNA. Structure, evolution, processing and function in protein biosynthesis. CRC Press.
20. GUTELL, R. R. 1996. Comparative sequence analysis and the structure of 16S and 23S rRNA. Pp. 111-128 in R. A. ZIMMERMAN and A. E. DAHLBERG, eds. Ribosomal RNA. Structure, evolution, processing and function in protein biosynthesis. CRC Press.
21. HASSOUNA, N., B. MICHOT, and J.-P. BACHELLERIE. 1984. The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA eukaryotes. Nucleic Acids Res. 12:3563-3583.
22. HEUS, H. A., and A. PARDI. 1991. Structural features that give rise to the unusual stability for RNA hairpins containing GNRA loops. Science 253:191.
23. KOCHER, T. D., W. K. THOMAS, A. MEYER, S. V. EDWARDS, S. PÄÄBO, F. X. VILLABLANCA, and A. C. WILSON. 1989. Dynamics of the mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86:6196-6200.
24. KOOI, E. A., C. A. RUTGERS, M. J. KLEIJMEER, J. VAN'T RIET, J. VENEMA, and H. A. RAUÉ. 1994. Mutational analysis of the C-terminal region of Saccharomyces cerevisiae ribosomal protein L25 in vitro and in vivo demonstrates the presence of two distinct functional elements. J. Mol. Biol. 240: 243-255.
25. LAKE, J. A. 1990. Origin of the metazoa. Proc. Natl. Acad. Sci. USA 87:763-766.
26. METZENBERG, S., C. JOBLET, P. VERSPIEREN, and N. AGABIAN. 1993. Ribosomal protein L25 from Trypanosoma brucei: phylogeny and molecular co-evolution of an rRNA-binding protein and its binding site. Nucleic Acids Res. 21:4936-4940.
27. MICHOT, B., and J. P. BACHELLERIE. 1987. Comparisons of large subunit rRNAs reveal some eukaryote-specific elements of secondary structure. Biochimie 69:11-23.
28. MICHOT, B., N. HASSOUNA, and J. P. BACHELLERIE. 1984. Secondary structure of mouse 28S rRNA and general model for the folding of the large rRNA in eukaryotes. Nucleic Acids Res. 12:4259-4279.
29. MICHOT, B., L. H. Qu, and J. P. BACHELLERIE. 1990. Evolution of large-subunit rRNA structure. The diversification of divergent D3 domain among major phylogenic groups. Eur. J. Biochem. 188:219-252.
30. MUSTERS, W., K. BOON, C. A. F. M. VAN DER SANDE, H. VAN HEERIKHUIZEN, and R. J. PLANTA. 1990. Functional analysis of transcribed spacers of yeast ribosomal DNA. EMBO J. 9:3989-3996.
31. MUSTERS, W., P. M. GONÇALVES, K. BOON, H. A. RAUÉ, H. VAN HEERIKHUISEN, and R. J. PLANTA. 1991. The conserved GTPase center and variable region V9 from Saccharomyces cerevisiae 26S rRNA can be replaced by their equivalents from other parokaryotes or eukaryotes without detectable loss of ribosomal function. Proc. Natl. Acad. Sci. USA 88: 1469-1473.
32. OTTEN, L., P. DERUFFRAY, P. LAJUDIE, and B. MICHOT. 1996. Sequence and characterisation of a ribosomal RNA operon from Agrobacterium vitis. Mol. Gen. Genet. 251:99-107.
33. PELANDAKIS, M., and M. SOLIGNAC. 1993. Molecular phylogeny of Drosophila based on ribosomal sequences. J. Mol. Evol. 37:525-543.
34. PERASSO, R., A. BAROIN, L. H. QU, J. P. BACHELLERIE, and A. ADOUTTE. 1989. Origin of the algae. Nature 339:142-144.
35. PEROCHON-DORISSE, J., F. CHETOUANI, S. AUREL, N. ISCOLO, and B. MICHOT. 1995. RNA_d2: a computer program for editing and display of RNA secondary structures. Comput. Appl. Biosci. 11:101-109.
36. PHILIPPE, H., A. CHENUIL, and A. ADOUTTE. 1994. Can the Cambrian explosion be inferred through molecular phylogeny? Development 120:15-25.
37. QU, L. H., M. NICOLOSO, and J. P. BACHELLERIE. 1988. Phylogenetic calibration of the 5′ terminal domain of large rRNA achieved by determining twenty eucaryotic sequences. J. Mol. Evol. 28:113-124.
38. RAUÉ, H. A., W. MUSTER, C. RUTGERS, J. V. RIET, and R. J. PLANTA. 1990. rRNA: from structure to function. Pp. 217-235 in W. E. HILL, A. DAHLBERG, R. A. GARRETT, P. B. MOORE, D. SCHLESSINGER, and J. R. WARNER, eds. The ribosome. Structure, function and evolution. American Society for Microbiology, Washington, D.C.
39. ROUSSET, F. M. PÉLANDAKIS, and M. SOLIGNAC. 1991. Evolution of compensatory substitutions through G.U intermediate state in Drosophila ribosomal RNA. Proc Natl. Acad. Sci. USA 88:10032-10036.
40. RUTGERS, C. A., M. J. RIENTJES, J. VAN'T RIET, and H. A. RAUÉ. 1991. rRNA binding domain of yeast ribosomal protein L25. Identification of its border and a key leucine residue. J. Mol. Biol. 218:375-385.
41. SCHNARE, M. N., S. H. DAMBERGER, W. GRAY, and R. R. GUTELL. 1996. Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA. J. Mol. Biol. 256-701-719.
42. SWEENEY, R., L. CHEN, and M. C. YAO. 1994. An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence. Mol. Cell. Biol. 14-4203-4215.
43. SWEENEY, R., and M. C. YAO. 1989. Identifying functional regions of rRNA by insertion mutagenesis and complete gene replacement in Tetrahymena thermophyla. EMBO J. 8:933-938.
44. VARANI, G., C. CHEONG, and I. TINOCO. 1991. Structure of an unusually stable RNA hairpin. Biochemistry 30:3280.
45. VESTER, B., and R. A. GARRETT. 1984. Structure of a protein L23-RNA complex located at the A-site domain of the ribosomal peptidyl transferase centre. J. Mol. Biol. 179-431-452.
46. WARE, V. C., R. RENKAWITZ, and S. A. GERBI. 1985. rRNA processing: removal of only nineteen bases at the gap between 28S alpha and 38S beta rRNA in Sciara coprophila. Nucleic Acids Res. 13:3581-3597.
47. WOESE, C. R., and N. PACE. 1993. Probing RNA structure, function, and history by comparative analysis. Pp. 91-117 in R. F. GESTELAND and J. E ATKINS, eds. The RNA world. CSHL Press.