1887

Chapter 14 : Functional Aspects of the Three Modified Nucleotides in Yeast Mitochondrial Large-Subunit rRNA

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Functional Aspects of the Three Modified Nucleotides in Yeast Mitochondrial Large-Subunit rRNA, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap14-1.gif /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap14-2.gif

Abstract:

This chapter focuses on the possible functional significance of the three highly conserved modified nucleotides in the otherwise minimally modified yeast mitochondrial large-subunit rRNA (LSU rRNA). The three modified nucleotides in yeast mitochondrial LSU rRNA, Gm2270, Um2791, and pseudouridine 2819, are equivalent to the Gm2251, Um2552, and pseudouridine 2580, respectively, in peptidyl transferase center (PTC) of LSU rRna. The PET56 nuclear gene encodes an rRNA ribose methyltransferase (Pet56p) required for the formation of 2’-O-methylguanosine at G2270 in yeast mitochondrial LSU rRNA (G2251 in numbering), and PET56 function is essential for the formation of functional mitochondrial ribosomes. While PET56 is normally essential for the formation of functional yeast mitochondrial ribosomes, a dominant extragenic mutation has been isolated (SRM1-1) that suppresses, albeit very weakly, pet56 loss-of-function mutations without restoring methylation at G2270 in yeast mitochondrial LSU rRNA. The presence of only three modified nucleotides at highly conserved positions in the PTC of yeast mitochondrial LSU rRNA has fueled speculation that these particular modification might have special functional significance. The recent progress in the identification of genes responsible for specific modifications in , yeast mitochondrial, and yeast cytoplasmic rRNAs will accelerate the genetic analysis of rRNA modification in these systems. It will be particularly informative to compare the in vivo effects of depleting pseudouridine 2580 in and yeast mitochondria and Gm2251 and Um2552 in all three ribosomal systems.

Citation: Mason T. 1998. Functional Aspects of the Three Modified Nucleotides in Yeast Mitochondrial Large-Subunit rRNA, p 273-280. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch14

Key Concept Ranking

Small Nucleolar RNA
0.45647967
0.45647967
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

The three modified nucleotides in yeast mitochondrial LSU rRNA are located at positions implicated in binding the 3′-terminal end of either Α-site- or P-site-bound tRNA. The secondary structure is that of domain V from mitochondrial LSU rRNA. The circled A, B, and C indicate the positions of variable sequences that are not shown. The locations of three modified nucleotides are indicated by arrows, and the sequences corresponding to the equivalent modifications in 23S rRNA are boxed. The closed arrowheads indicate sites that are protected from chemical modification by P-site-bound tRNA; the open arrowheads indicate protections by A-site-bound tRNA; positions where base substitutions cause strong dominant negative growth phenotypes are underlined. The region corresponding to the binding site for ribosomal protein L1 in 23S rRNA is enclosed by the dashed line. See the text for references.

Citation: Mason T. 1998. Functional Aspects of the Three Modified Nucleotides in Yeast Mitochondrial Large-Subunit rRNA, p 273-280. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818296.chap14
1. Bachellerie, J.-P.,, and J. Cavaille. 1997. Guiding ribose methylation of rRNA. Trends Biochem. Sci. 22:257261.
2. Draper, D. E., 1996. Ribosomal-protein interactions, p. 171197. In R. A. Zimmermann, and A. E. Dahlberg (ed.), Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis. CRC Press, Boca Raton, Fla.
3. Garrett, R. A., , and C. Rodriguez-Fonseca,. 1996. The peptidyl transferase center, p. 327-355. In R. A. Zimmermann, and A. E. Dahlberg (ed.), Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis. CRC Press, Boca Raton, Fla.
4. Green, R.,, and H. F. Noller. 1996. In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli SOS ribosomal subunit assembly and function. RNA 2:10111021.
5. Green, R.,, and H. F. Noller. 1997. Ribosomes and translation. Annu. Rev. Biochem. 66:679716.
6. Green, R.,, R. S. Samaha,, and H. F. Noller. 1997. Mutations at nucleotides G2251 and U2585 of 23S rRNA perturb the peptidyl transferase center of the ribosome.J. Mol. Biol. 266:4050.
7. Gregory, S.,, and A. Dahlberg. Personal communication.
8. Gregory, S.,, K. Sirum-Connolly,, T. Mason,, and A. Dahlberg. Unpublished results.
9. Gregory, S. T.,, K. R. Lieberman,, and A. E. Dahlberg. 1994. Mutations in the peptidyl transferase region of E. coli 23S rRNA affecting translational accuracy. Nucleic Acids Res. 22: 279284.
10. Gustafsson, C.,, R. Reid,, P. J. Greene,, and D. Santi. 1996. Identification of new modifying enzymes by iterative genome search using known modifying enzymes as probes. Nucleic Acids Res. 24:37563762.
11. Klootwijk, J.,, I. Klein,, and L. A. Grivell. 1975. Minimal posttranscriptional modification of yeast mitochondrial ribosomal RNA. J. Mol. Biol. 97:337350.
12. Koonin, E. V. 1996. Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Acids Res. 24:24112415.
13. Kowalak, J. A.,, E. Bruenger,, and J. A. McCloskey. 1995. Posttranscriptional modification of the central loop of domain V in Escherichia coli 23S ribosomal RNA. J. Biol. Chem. 270: 1775817764.
14. Krzyzosiak, W. R.,, R. Denman,, K. Nurse,, W. Hellman,, M. Boublik,, C. W. Gehrke,, P. F. Agris,, and J. Ofengand. 1987. In vitro synthesis of 16S ribosomal RNA containing single base changes and assembly into a functional 30S ribosome. Biochemistry 26: 23532364.
15. Lafontaine, D.,, J. Vandenhaute,, and D. Tollervey. 1995. The 18S rRNA dimethylase Dimlp is required for pre-ribosomal RNA processing in yeast. Genes Dev. 9:24702481.
16. Lane, B. G.,, J. Ofengand,, and M. W. Gray. 1995. Pseudouridine and O2 -methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins. Biochimie 77:715.
17. Lieberman, K. R.,, and A. E. Dahlberg. 1995. Ribosome-catalyzed peptide-bond formation. Prog. Nucleic Acid Res. Mol. Biol. 50: 123.
18. Maden, B. E. H.,, M. E. Corbett,, P. A. Heeney,, K. Pugh,, and P. M. Ajuh. 1995. Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie 77:2229.
19. Mason, T. Unpublished data.
20. Mason, T. L.,, C. Pan,, M. E. Sanchirico,, and K. Sirum-Connolly. 1996. Molecular genetics of the peptidyl transferase center and the unusual Varl protein in yeast mitochondrial ribosomes. Experientia 52:11481157.
21. Moazed, D.,, and H. F. Noller. 1989. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 57:585597.
22. Nicol, S. M.,, and F. V. Fuller-Pace. 1995. The "DEAD box" protein Dbp interacts specifically with the peptidyltransferase center in 23S rRNA. Proc. Natl. Acad. Sci. USA 92:1168111685.
23. Nicoloso, M.,, L.-H. Qu,, B. Michot,, and J.-P. Bachellerie. 1996. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs. J. Mol. Biol. 260: 178195.
24. Nierhaus, K.,, and F. Dohme. 1974. Total reconstitution of functionally active 50S ribosomal subunits from E. coli. Proc. Natl. Acad. Sci. USA 71:47134717.
25. Ofengand, J.,, and A. Bakin. 1997. Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts.J. Mol. Biol. 266:246268.
26. Pinkham, J. L.,, A. M. Dudley,, and T. L. Mason. 1994. T7 RNA polymerase-dependent expression of COXII in yeast mitochondria. Mol. Cell. Biol. 14:46434652.
27. Porse, B. T.,, and R. A. Garrett. 1995. Mapping important nucleotides in the peptidyl transferase center of 23S rRNA using a random mutagenesis approach.J. Mol. Biol. 249:110.
28. Porse, B. T.,, H. P. Thi-Ngoc,, and R. A. Garrett. 1996. The donor substrate site within the peptidyl transferase loop of 23S rRNA and its putative interactions with the CCA-end of N-blocked aminoacyl-tRNA(Phe).J. Mol. Biol. 264:472483.
29. Saarma, U.,, and J. Remme. 1992. Novel mutants of 23S RNA: characterization of functional properties. Nucleic Acids Res. 20: 31473152.
30. Samaha, R. R.,, R. R. Green,, and H. F. Noller. 1995. A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377:309314.
31. Sirum-Connolly, K.,, and T. L. Mason. Unpublished data.
32. Sirum-Connolly, K.,, and T. L. Mason. 1993. Functional requirement of a site-specific ribose methylation in ribosomal RNA. Science 262:18861889.
33. Sirum-Connolly, K.,, J. M. Peltier,, P. F. Crain,, J. McCloskey,, and T. L. Mason. 1995. Implications of a functional large ribosomal RNA with only three modified nucleotides. Biochimie 77:3039.
34. Spahn, C. M. T.,, J. Remme,, M. A. Schafer,, and K. H. Nierhaus. 1996a. Mutational analysis of two highly conserved UGG sequences of 23S rRNA from Escherichia coli. J. Biol. Chem. 271: 3284932856.
35. Spahn, C. M. T., , M. A. Schafer,, A. A. Krayevsky,, and K. H. Nierhaus. 1996b. Conserved nucleotides of 23S rRNA located at the ribosomal peptidyltransferase center. J. Biol. Chem. 271: 3285732862.
36. Thompson, J.,, and E. Cundliffe, 1991. The binding of thiostrepton to 23S RNA. Biochimie 73:11311135.
37. Traub, P.,, and M. Nomura. 1968. Structure and function of E. coli ribosomes. V. Reconstitution of functionally active 30S ribosomal particles from RNA and protein. Proc. Natl. Acad. Sci. USA 59:777784.
38. Tycowski, K. T.,, M. D. Shu,, and J. A. Steitz. 1996. A mammalian gene with introns instead of exons generating stable RNA products. Nature 379:464466.
39. Walleczek, J.,, B. Redl,, M. Stöffler-Meilicke,, and G. Stuffier. 1989. Protein-protein cross-linking of the 50S ribosomal subunit of Escherichia coli using 2-iminothiolane. Identification of cross-links by immunoblotting techniques.J. Biol. Chem. 264:42314237.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error