Highlighted Text:
Show |
Hide
Full text loading...
Chapter 12 : The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function
Authors:
James Ofengand1,
Maurille J. Fournier2
VIEW AFFILIATIONS
HIDE AFFILIATIONS
Affiliations:
1: Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33101;
2: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
Content Type: Monograph
Publication Year:
1998
Category: Microbial Genetics and Molecular Biology
Book DOI:
10.1128/9781555818296
Chapter DOI:
10.1128/9781555818296.ch12
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Preview this chapter:
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function, Page 1 of 2
< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap12-1.gif /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap12-2.gif
Abstract:
This chapter focuses on the pseudouridine (5-β-D-ribofuranosyluracil; Ψ) residues in rRNA. This subject has been reviewed previously both in a detailed analysis of the work on eukaryotic rRNA up to circa 1990, which also includes methylated nucleosides, and in a review of more recent work. The chapter talks about number and locations of Ψ in small-subunit (SSU) and large-subunit (LSU) rRNAs. Synthesis of cytoplasmic rRNAs in eukaryotic cells involves the action of a large population of small nucleolar RNAs (snoRNAs). Site selection in each case involves base pairing of a guide snoRNA with the rRNA segment to be modified, and selection of a nucleotide located at a constant distance from an additional determinant(s) in the snoRNA. The two types of guide function are provided by snoRNAs in separate families known as the box C/D and H/ACA box families, respectively. Each family contains snoRNAs required for rRNA processing, but the main function of these RNAs is the modification of rRNA nucleotides. There is no firm evidence so far for an essential role for any in the cell, and a number of cases are known where deletion of a single Ψ has no obvious effect. It is likely that additional pseudouridine synthases will be identified and characterized and that they will come from new and familiar sources.
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
Key Concept Ranking
- Small Nucleolar RNA
- 0.44404793
- Sodium Dodecyl Sulfate
- 0.4305956
- Small Nuclear RNA
- 0.4189934
0.44404793
Figures
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap12-1,webId=/content/author/10.1128/9781555818296.chap12-1,properties={foaf_givenname=James, foaf_name=James Ofengand, foaf_surname=Ofengand, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap12-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap12-2,webId=/content/author/10.1128/9781555818296.chap12-2,properties={foaf_givenname=Maurille J., foaf_name=Maurille J. Fournier, foaf_surname=Fournier, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap12-aff2]]}]]
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.fig12-1
Figure 1
Location of Ψ and other modified residues in SSU RNA. The secondary structure is that of S. cerevisiae. Ψ and insert symbol, pseudouridines in S. cerevisiae ( Bakin and Ofengand, 1995 ); ○ and insert symbol, mammalian pseudouridine positions ( Maden, 1990 ; Ganot et al., 1997a ); ©, pseudouridines at the same site in both S. cerevisiae and mammals; Ψ*, m1acp3Ψ ( Saponara and Enger, 1974 ; Maden et al., 1975 ); Δ, base-methylated, and ▲, 2′-O-methyl, nucleosides in S. cerevisiae ( Maden, 1990 ); arrow, site of Ψ in E. coli ( Bakin et al., 1994a ) and B. subtilis ( Wrzesinski et al., 1995a ). Adapted from Bakin and Ofengand (1995) .
10.1128/9781555818296/fig12-1_thmb.gif
10.1128/9781555818296/fig12-1.gif
Figure 1
Location of Ψ and other modified residues in SSU RNA. The secondary structure is that of S. cerevisiae. Ψ and insert symbol, pseudouridines in S. cerevisiae ( Bakin and Ofengand, 1995 ); ○ and insert symbol, mammalian pseudouridine positions ( Maden, 1990 ; Ganot et al., 1997a ); ©, pseudouridines at the same site in both S. cerevisiae and mammals; Ψ*, m1acp3Ψ ( Saponara and Enger, 1974 ; Maden et al., 1975 ); Δ, base-methylated, and ▲, 2′-O-methyl, nucleosides in S. cerevisiae ( Maden, 1990 ); arrow, site of Ψ in E. coli ( Bakin et al., 1994a ) and B. subtilis ( Wrzesinski et al., 1995a ). Adapted from Bakin and Ofengand (1995) .
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.fig12-3
Figure 3
Comparative positions of Ψ residues in the 5′ region of LSU RNAs. The sequence is that of S. cerevisiae. E, E..coli; Y, S. cerevisiae; D, D. melanogaster; Μ, M. musculus; Η, H. sapiens. Reprinted from Ofengand et al. (1995) with permission.
10.1128/9781555818296/fig12-3_thmb.gif
10.1128/9781555818296/fig12-3.gif
Figure 3
Comparative positions of Ψ residues in the 5′ region of LSU RNAs. The sequence is that of S. cerevisiae. E, E..coli; Y, S. cerevisiae; D, D. melanogaster; Μ, M. musculus; Η, H. sapiens. Reprinted from Ofengand et al. (1995) with permission.
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.fig12-5
Figure 5
Comparative positions of Ψ residues in the 3′ region, including the PTC, of LSU RNAs. The sequence is that of S. cerevisiae. Ε, E. coli; Β, B. subtilis; A, H. halobium; Ζ, Z. mays chloroplasts; Y, S. cerevisiae; D, D. melanogaster; Μ, M. musculus; Η, H. sapiens; Ym, S. cerevisiae mitochondria; Mm, M. musculus mitochondria; Hm, H. sapiens mitochondria; T, T. brucei mitochondria. The two sets of paired dashed ovals denote two semi-invariant sites. Reprinted from Ofengand and Bakin (1997) with permission.
10.1128/9781555818296/fig12-5_thmb.gif
10.1128/9781555818296/fig12-5.gif
Figure 5
Comparative positions of Ψ residues in the 3′ region, including the PTC, of LSU RNAs. The sequence is that of S. cerevisiae. Ε, E. coli; Β, B. subtilis; A, H. halobium; Ζ, Z. mays chloroplasts; Y, S. cerevisiae; D, D. melanogaster; Μ, M. musculus; Η, H. sapiens; Ym, S. cerevisiae mitochondria; Mm, M. musculus mitochondria; Hm, H. sapiens mitochondria; T, T. brucei mitochondria. The two sets of paired dashed ovals denote two semi-invariant sites. Reprinted from Ofengand and Bakin (1997) with permission.
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.fig12-2
Figure 2
Location of Ψ and other modified residues in E. coli LSU RNA. The secondary structure is from Gutell et al. (1993) . Location of the Ψ residues is from Bakin and Ofengand (1993) and Bakin et al. (1994b) . Open circles, base-methyl, and filled circles, 2′-O-methyl nucleosides (see Table II of Bakin and Ofengand, 1993 ); D, dihydrouridine ( Kowalak et al., 1995 ); Ψ*, N 3-methyl Ψ ( Kowalak et al., 1996 ).
10.1128/9781555818296/fig12-2_thmb.gif
10.1128/9781555818296/fig12-2.gif
Figure 2
Location of Ψ and other modified residues in E. coli LSU RNA. The secondary structure is from Gutell et al. (1993) . Location of the Ψ residues is from Bakin and Ofengand (1993) and Bakin et al. (1994b) . Open circles, base-methyl, and filled circles, 2′-O-methyl nucleosides (see Table II of Bakin and Ofengand, 1993 ); D, dihydrouridine ( Kowalak et al., 1995 ); Ψ*, N 3-methyl Ψ ( Kowalak et al., 1996 ).
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.fig12-6
Figure 6
Hypothetical pairing of a guide snoRNA with rRNA sites of Ψ formation. Targeting involves base pairing of the guide RNA with complementary rRNA sequences which flank the uridine to be modified. The lengths of the guide sequences vary, but the target uridine sits in an unpaired pocket that is quite constant in size. Pairing on the 5′ side of the uridine involves 4 to 10 base pairs, and that on the 3′ side involves 3 to 10. The distance between the target uridine and the helix on the 5′ side is mostly 0 but occasionally 1 residue and that on the 3′ side is mostly one and rarely 2. In addition to the guide sequences, the distance to the Η or ACA box is also a determinant in site selection. This spacing is a nearly constant 14 to 16 nucleotides. One or both domains shown in Fig. 7 can function in site selection. Adapted from Ganot et al. (1997a) .
10.1128/9781555818296/fig12-6_thmb.gif
10.1128/9781555818296/fig12-6.gif
Figure 6
Hypothetical pairing of a guide snoRNA with rRNA sites of Ψ formation. Targeting involves base pairing of the guide RNA with complementary rRNA sequences which flank the uridine to be modified. The lengths of the guide sequences vary, but the target uridine sits in an unpaired pocket that is quite constant in size. Pairing on the 5′ side of the uridine involves 4 to 10 base pairs, and that on the 3′ side involves 3 to 10. The distance between the target uridine and the helix on the 5′ side is mostly 0 but occasionally 1 residue and that on the 3′ side is mostly one and rarely 2. In addition to the guide sequences, the distance to the Η or ACA box is also a determinant in site selection. This spacing is a nearly constant 14 to 16 nucleotides. One or both domains shown in Fig. 7 can function in site selection. Adapted from Ganot et al. (1997a) .
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.fig12-7
Figure 7
Consensus secondary structure of the H/ACA box snoRNAs. snoRNAs in this family share common secondary structure domains, which can be represented schematically in a simple ‘hairpin-hinge-hairpin’ arrangement. Adapted from Balakin et al. (1996) and Ganot et al. (1997b) .
10.1128/9781555818296/fig12-7_thmb.gif
10.1128/9781555818296/fig12-7.gif
Figure 7
Consensus secondary structure of the H/ACA box snoRNAs. snoRNAs in this family share common secondary structure domains, which can be represented schematically in a simple ‘hairpin-hinge-hairpin’ arrangement. Adapted from Balakin et al. (1996) and Ganot et al. (1997b) .
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.fig12-4
Figure 4
Comparative positions of Ψ residues in the central region of LSU RNAs. The sequence is that of S. cerevisiae. Ε, E. coli; Β, B. subtilis; Α, H. halobium; Ζ, Z. mays chloroplasts; Y, S. cerevisiae; D, D. melanogaster; Μ, M. musculus; Η, H. sapiens. Ε*, B*, and Z*, see legend to Fig. 5 . The boxed residues are invariant among the tested cytoplasmic and chloroplast species. Also shown are all of the sequence variations at the sites for Ψ in each of the examined species with the uppercase letter(s) indicating the organism(s) and the subscript letter indicating the nucleoside in those species. Reprinted from Ofengand and Bakin (1997) with permission.
10.1128/9781555818296/fig12-4_thmb.gif
10.1128/9781555818296/fig12-4.gif
Figure 4
Comparative positions of Ψ residues in the central region of LSU RNAs. The sequence is that of S. cerevisiae. Ε, E. coli; Β, B. subtilis; Α, H. halobium; Ζ, Z. mays chloroplasts; Y, S. cerevisiae; D, D. melanogaster; Μ, M. musculus; Η, H. sapiens. Ε*, B*, and Z*, see legend to Fig. 5 . The boxed residues are invariant among the tested cytoplasmic and chloroplast species. Also shown are all of the sequence variations at the sites for Ψ in each of the examined species with the uppercase letter(s) indicating the organism(s) and the subscript letter indicating the nucleoside in those species. Reprinted from Ofengand and Bakin (1997) with permission.
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
References
/content/book/10.1128/9781555818296.chap12
1.
Arena, F.,, G. Ciliberto,, S. Ciampi,, and R. Cortese. 1978. Purification of pseudouridylate synthetase I from Salmonella typhimurium. Nucleic Acids Res. 5: 4523– 4536.
2.
Arnez, J. G.,, and T. A. Steirz. 1994. Crystal structure of unmodified tRNA Gln complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry 33: 7560– 7567.
3.
Arps, P. J.,, C. C. Marvel,, B.C. Rubin,, D. A. Tolan, E. E. Penhoet, and M. E. Winkler. 1985. Structural features of the hisT operon of Escherichia coli K-12. Nucleic Acids Res. 13: 5297– 5315.
4.
Bakin, A.,, and J. Ofengand. 1993. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyl transferase center: analysis by the application of a new sequencing technique. Biochemistry 32: 9754– 9762.
5.
Bakin, A.,, and J. Ofengand. 1995. Mapping of the thirteen pseudouridine residues in Saccharomyces cerevisiae small subunit ribosomal RNA to nucleotide resolution. Nucleic Acids Res. 23: 3290– 3294.
6.
Bakin, A.,, J. A. Kowalak,, J. A. McCloskey,, and J. Ofengand. 1994a. The single pseudouridine residue in Escherichia coli 16S RNA is located at position 516. Nucleic Acids Res. 22: 3681– 3684.
7.
Bakin, A.,, B. G. Lane,, and J. Ofengand. 1994b. Clustering of pseudouridine residues around the peptidyl transferase center of yeast cytoplasmic and mitochondrial ribosomes. Biochemistry 33: 13475– 13483.
8.
Balakin, A. G.,, L. Smith,, and M. J. Fournier. 1996. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86: 823– 834.
9.
Bally, M.,, J. Hughes,, and G. Cesareni. 1988. snR30: a new essential small nuclear RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 16: 5291– 5303.
10.
Bandaru, R.,, H. Hashimoto,, and C. Switzer. 1995. An inverted motif for oligonucleotide triplexes: adenosine-pseudouridine-adenosine (A-Ψ-A). J. Org. Chem. 60: 786– 787.
11.
Becker, H. F.,, Y. Motorin,, R. J. Planta,, and H. Grosjean. 1997. The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of Ψ55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res. 25: 4493– 4499.
12.
Bousquet-Antonelli, C.,, Y. Henry,, J.-P. Gelugne,, M. Caizergues-Ferrer,, and T. Kiss. 1997. A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. EMBO J. 16: 4770– 4776.
13.
Brand, R. C.,, J. Klootwijk,, R. J. Planta,, and B. E. Maden. 1978. Biosynthesis of a hypermodified nucleotide in Saccharomyces carlsbergensis 17S and HeLa-cell 18S ribosomal ribonucleic acid. Biochem. J. 169: 71– 77.
14.
Brand, R. C.,, J. Klootwijk,, C. P. Sibum,, and R. J. Planta. 1979. Pseudouridylation of yeast ribosomal precursor RNA. Nucleic Acids Res. 7: 121– 134.
15.
Branlant, C.,, A. Krol,, M. A. Machatt,, J. Pouyet,, and J. P. Ebel. 1981. Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs. Nucleic Acids Res. 9: 4303– 4324.
16.
Brimacombe, R. 1995. The structure of ribosomal RNA: a three-dimensional jigsaw puzzle. Eur. J. Biochem. 230: 365– 383.
17.
Ciampi, M. S.,, F. Arena,, R. Cortese, and V. Daniel. 1977. Biosynthesis of pseudouridine in the in vitro transcribed tRNA Tyr precursor. FEBS Lett. 77: 75– 82.
18.
Cohn, W. E. 1959. 5-Ribosyl uracil, a carbon-carbon ribofuranosyl nucleoside in ribonucleic acids. Biochim. Biophys. Acta 32: 569– 571.
19.
Cohn, W. E. 1960. Pseudouridine, a carbon-carbon linked ribonucleoside in ribonucleic acids: isolation, structure, and chemical characteristics. J. Biol. Chem. 235: 1488– 1498.
20.
Conrad, J.,, S. Raychaudhuri,, B. Hall,, and J. Ofengand. Unpublished results.
21.
Cortese, R.,, H. O. Kammen,, S. J. Spengler,, and B. N. Ames. 1974. Biosynthesis of pseudouridine in transfer ribonucleic acid. J. Biol. Chem. 249: 1103– 1108.
22.
Crain, P. F.,, and J. A. McCloskey. 1997. The RNA modification database. Nucleic Acids Res. 25: 126– 127.
23.
Cunningham, P. R.,, R. B. Richard,, C. J. Weitzmann,, K. Nurse,, and J. Ofengand. 1991. The absence of modified nucleotides affects both in vitro assembly and in vitro function of the 3 OS ribosomal subunit of Escherichia coli. Biochimie 73: 789– 796.
24.
Dahlberg, J. E. , N. Nikolaev, and D. Schlessinger. 1975. Posttranscriptional modification of nucleotides in E. coli ribosomal RNAs. Brookhaven Symp. Biol. 26: 194– 200.
25.
Davis, D. R. 1995. Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res. 23: 5020– 5026.
26.
Davis, F. F.,, and F. W. Allen. 1957. Ribonucleic acids from yeast which contain a fifth nucleotide. J. Biol. Chem. 227: 907– 915.
27.
Denman, R.,, J. Colgan,, K. Nurse,, and J. Ofengand. 1988. Cross-linking of the anticodon of P site bound tRNA to C-1400 of E. coli 16S RNA does not require the participation of the 50S subunit. Nucleic Acids Res. 16: 165– 178.
28.
Denman, R.,, C. Weitzmann,, P. R. Cunningham,, D. Negre,, K. Nurse,, J. Colgan,, Y. C. Pan,, M. Miedel,, and J. Ofengand. 1989a. In vitro assembly of 30S and 70S bacterial ribosomes from 16S RNA containing single base substitutions, insertions, and deletions around the decoding site (C1400). Biochemistry 28: 1002– 1011.
29.
Denman, R.,, D. Negre,, P. R. Cunningham,, K. Nurse,, J. Colgan,, C. Weitzmann,, and J. Ofengand. 1989b. Effect of point mutations in the decoding site (C1400) region of 16S ribosomal RNA on the ability of ribosomes to carry out individual steps of protein synthesis. Biochemistry 28: 1012– 1019.
30.
Dokudovskaya, S.,, O. Dontsova,, O. Shpanchenko,, A. Bogdanov,, and R. Brimacombe. 1996. Loop IV of 5S ribosomal RNA has contacts both to domain II and to domain V of the 23S RNA. RNA 2: 146– 152.
31.
Foster, P. G.,, L. Huang,, D. V. Santi,, and R. M. Stroud. 1997. The crystal structure of E. coli tRNA pseudouridine synthase I. FASEB J. 11: A862.
32.
Ganot, P.,, M.-L. Bortolin,, and T. Kiss. 1997a. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89: 799– 809.
33.
Ganot, P.,, M. Caizergues-Ferrer,, and T. Kiss. 1997b. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 11: 941– 956.
34.
Gehrke, C. W.,, and K. C. Kuo. 1989. Ribonucleoside analysis by reversed-phase high-performance liquid chromatography. J. Chromatogr. 47: 3– 36.
35.
Girard, J.-P.,, H. Lehtonen,, M. Caizergues-Ferrer,, F. Amalric,, D. Tollervey,, and B. Lapeyre. 1992. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J. 11: 673– 682.
36.
Gray, M. W. 1976. 02'-Methylinosine, a constituent of the ribosomal RNA of Crithidia fasciculata. Nucleic Acids Res. 3: 977– 988.
37.
Gray, M. W. 1974. The presence of O-2'-methylpseudouridine in the 18S + 26S ribosomal ribonucleates of wheat embryo. Biochemistry 13: 5453– 5463.
38.
Green, R.,, and H. F. Noller. 1996. In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA 2: 1011– 1021.
39.
Green, R.,, and H. F. Noller. 1997. Ribosomes and translation. Annu. Rev. Biochem. 66: 679– 716.
40.
Green, C. J.,, H. O. Kammen,, and E. E. Penhoet. 1982. Purification and properties of a mammalian tRNA pseudouridine synthase. J. Biol. Chem. 257: 3045– 3052.
41.
Grosjean, H.,, Z. Szweykowska-Kulinska,, Y. Motorin,, F. Fasiolo,, and G. Simos. 1997. Intron-dependent enzymatic formation of modified nucleosides in eukaryotic tRNAs: a review. Biochimie 79: 293– 302.
42.
Gu, J.,, and R. Reddy. 1997. Small RNA database. Nucleic Acids Res. 25: 98– 101.
43.
Gustafsson, C.,, R. Reid,, P. J. Greene,, and D. V. Santi. 1996. Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes. Nucleic Acids Res. 24: 3756– 3762.
44.
Gutell, R. R.,, M. W. Gray,, and M. N. Schnare. 1993. A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures. Nucleic Acids Res. 21: 3055– 3074.
45.
Ho, N. W. Y.,, and P. T. Gilham. 1971. Reaction of pseudouridine and inosine with N-cyclohexyl-N'- β-(4-methylmorpholinium)ethylcarbodiimide. Biochemistry 10: 3651– 3657.
46.
Huang, L.,, M. Pookanjanatavip,, X. Gu,, and D. V. Santi. 1998. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry 37: 344– 351.
47.
Jeanteur, P.,, F. Amaldi,, and G. Attardi. 1968. Partial sequence analysis of ribosomal RNA from HeLa cells. II. Evidence for sequences of non-ribosomal type in 45S and 32S ribosomal RNA precursors. J. Mol. Biol. 33: 757– 775.
48.
Jiang, W.,, K. Middleton,, H.-J. Yoon,, C. Fouquet,, and J. Carbon. 1993. An essential yeast protein, CBF5, binds in vitro to centromeres and microtubules. Mol. Cell. Biol. 13: 4884– 4893.
49.
Johnson, L.,, and D. Soli. 1970. In vitro biosynthesis of pseudouridine at the polynucleotide level by an enzyme extract from Escherichia coli. Proc. Natl. Acad. Sci. USA 67: 943– 950.
50.
Joseph, S.,, and H. F. Noller. 1996. Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome. EMBO J. 15: 910– 916.
51.
Kammen, H. O.,, C. C. Marvel,, L. Hardy,, and E. E. Penhoet. 1988. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J. Biol. Chem. 263: 2255– 2263.
52.
Khan, M. S. N.,, and B. E. H. Maden. 1977. Nucleotide sequence relationships between vertebrate 5.8 S ribosomal RNAs. Nucleic Acids Res. 4: 2495– 2505.
53.
Kiss-Laszlo, Z.,, Y. Henry,, J. P. Bachellerie,, M. Caizergues-Ferrer,, and T. Kiss. 1996. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85: 1077– 1088.
54.
Klootwijk, J.,, I. Klein,, and L. A. Grivell. 1975. Minimal posttranscriptional modification of yeast mitochondrial ribosomal RNA. J. Mol. Biol. 97: 337– 350.
55.
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: 2411– 2415.
56.
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: 17758– 17764.
57.
Kowalak, J. A., , E. Bruenger,, T. Hashizume,, J. M. Peltier,, J. Ofengand,, and J. A. McCloskey. 1996. Structural characterization of 3-methylpseudouridine in domain IV from E. coli 23S ribosomal RNA. Nucleic Acids Res. 24: 688– 693.
58.
Krzyzosiak, W.,, R. Denman,, K. Nurse,, M. Hellmann,, 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 3 OS ribosome. Biochemistry 26: 2353– 2364.
59.
Lafontaine, D. L. J.,, C. Bousquet-Antonelli,, Y. Henry,, M. Caizergues-Ferrer,, and D. Tollervey. 1998. The box H+ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev. 12: 527– 537.
60.
Lane, B. G.,, J. Ofengand,, and M. W. Gray. 1995. Pseudouridine and 0 2-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins. Biochimie 77: 7– 15.
61.
Lankat-Buttgereit, B.,, H. J. Gross,, and G. Krupp. 1987. Detection of modified nucleosides by rapid RNA sequencing methods. Nucleic Acids Res. 15: 7649.
62.
Lecointe, F.,, G. Simos,, A. Sauer,, E. C. Hurt,, Y. Motorin,, and H. Grosjean. 1997. Characterization of yeast protein Degl as pseudouridine synthase (Pus3) catalyzing the formation of Ψ 38 and Ψ 39 in tRNA anticodon loop. J. Biol. Chem. 273: 1316– 1323.
63.
Li, H. V.,, J. Zagorski,, and M. J. Fournier. 1990. Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 10: 1145– 1152.
64.
Liang, W.-Q.,, and M. J. Fournier. 1995. U14 base pairs with 18S rRNA: a novel snoRNA interaction required for rRNA processing. Genes Dev. 9: 2433– 2443.
65.
Maden, B. E. H. 1988. Locations of methyl groups in 28S rRNA of Xenopus laevis and man. Clustering in the conserved core of the molecule. J. Mol. Biol. 201: 289– 314.
66.
Maden, B. E. H. 1990. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 39: 241– 300.
67.
Maden, B. E. H. 1997. Guides to 95 new angles. Nature 389: 129– 131.
68.
Maden, B. E. H.,, J. Forbes,, P. de Jong,, and J. Klootwijk. 1975. Presence of a hypermodified nucleotide in HeLa cell 18S and Saccharomyces carlsbergensis 17S ribosomal RNAs. FEBS Lett. 59: 60– 63.
69.
Maden, B. E. H.,, and M. Salim. 1974. The methylated nucleotide sequences in HeLa cell ribosomal RNA and its precursors. J. Mol. Biol. 88: 133– 164.
70.
Maxwell, E. S.,, and M. J. Fournier. 1995. The small nucleolar RNAs. Annu. Rev. Biochem. 35: 897– 934.
71.
Meier, U. T.,, and G. Blobel. 1994. NAP57, a mammalian nucleolar protein with a putative homolog in yeast and bacteria. J. Cell Biol. 127: 1505– 1514.
72.
Mitchell, P.,, M. Osswald,, D. Schiller,, and R. Brimacombe. 1990. Selective isolation and detailed analysis of intra-RNA cross-links induced in the large ribosomal subunit of E. coli; a model for the tertiary structure of the tRNA binding domain in 23 S RNA. Nucleic Acids Res. 18: 4325– 4333.
73.
Mitchell, P.,, M. Osswald,, and R. Brimacombe. 1992. Identification of intermolecular RNA cross-links at the subunit interface of the Escherichia coli ribosome. Biochemistry 31: 3004– 3011.
74.
Moazed, D.,, and H. F. Noller. 1990. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. J. Mol. Biol. 211: 135– 145.
75.
Morrissey, J. P.,, and D. Tollervey. 1993. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol. Cell. Biol. 13: 2469– 2477.
76.
Nazar, R. N.,, T. O. Sitz,, and H. Busch. 1976. Sequence homologies in mammalian 5.8S ribosomal RNA. Biochemistry IS: 505– 508.
77.
Ni, J.,, A. L. Tien,, and M. J. Fournier. 1997. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89: 565– 573.
78.
Ni, J.,, A. L. Tien,, and M. Fournier. Unpublished results.
79.
Niu, L.,, and J. Ofengand. Unpublished results.
80.
Nurse, K.,, and J. Ofengand. Unpublished results.
81.
Nurse, K.,, J. Wrzesinski,, A. Bakin,, B. G. Lane,, and J. Ofengand. 1995. Purification, cloning, and properties of the tRNA Ψ55 synthase from Escherichia coli. RNA 1: 102– 112.
82.
O'Connor, M.,, and A. E. Dahlberg. 1995. The involvement of two distinct regions of 23 S ribosomal RNA in tRNA selection. J. Mol. Biol. 254: 838– 847.
83.
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: 246– 268.
84.
Ofengand, J.,, A. Bakin,, and K. Nurse,. 1993. The functional role of conserved sequences of 16S ribosomal RNA in protein synthesis, p. 489– 500. In K. H. Nierhaus,, A. R. Subramanian,, V. A. Erdmann,, F. Franceschi,, and B. Wittman-Liebold (ed.), The Translational Apparatus. Plenum Press, New York, N.Y.
85.
Ofengand, J.,, A. Bakin,, J. Wrzesinski,, K. Nurse,, and B. G. Lane. 1995. The pseudouridine residues of ribosomal RNA. Biochem. Cell Biol. 73: 915– 924.
86.
Olsen, G. J.,, and C. R. Woese. 1997. Archaeal genomics: an overview. Cell 89: 991– 994.
87.
Parker, R.,, T. Simmons,, E. O. Shuster,, P. G. Siliciano,, and C. Guthrie. 1988. Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable sextuplet mutant. Mol. Cell. Biol. 8: 3150– 3159.
88.
Peculis, B. 1997. RNA processing: pocket guides to ribosomal RNA. Curr. Biol. 7: R480– R482.
89.
Pennisi, E. 1997. Microbial genomes come tumbling in. Science 277: 1433.
90.
Rudd, K. Personal communication.
91.
Rudd, K.,, and J. Ofengand. Unpublished results.
92.
Samarsky, D. A.,, A. G. Balakin,, and M. J. Fournier. 1995. Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34, snR35 and snR36. Nucleic Acids Res. 23: 2548– 2554.
93.
Samuelsson, T.,, and M. Olsson. 1990. Transfer RNA pseudouridine synthases in Saccharomyces cerevisiae. J. Biol. Chem. 265: 8782– 8787.
94.
Saponara, A. G.,, and M. D. Enger. 1974. The isolation from ribonucleic acid of substituted uridines containing α-aminobutyrate moieties derived from methionine. Biochim. Biophys. Acta 349: 61– 77.
95.
Scannell, J. P.,, A. M. Crestfield,, and F. W. Allen. 1959. Methylation studies on various uracil derivatives and on an isomer of uridine isolated from ribonucleic acids. Biochim. Biophys. Acta 32: 406– 412.
96.
Schaefer, K. P.,, S. Altman,, and D. Soil. 1973. Nucleotide modification in vitro of the precursor of transfer RNA Tyr of Escherichia coli. Proc. Natl. Acad. Set. USA 70: 3626– 3630.
97.
Simos, G.,, H. Tekotte,, H. Grosjean,, A. Segref,, K. Sharma,, D. Tollervey,, and E. C. Hurt. 1996. Nuclear pore proteins are involved in the biogenesis of functional tRNA. EMBO J. 15: 2270– 2284.
98.
Smith, C. M.,, and J. A. Steitz. 1997. Sno storm in the nucleolus: new roles for myriad small RNPs. Cell 89: 669– 672.
99.
Smith, J. E.,, B. S. Cooperman,, and P. Mitchell. 1992. Methylation sites in Escherichia coli. Ribosomal RNA: localization and identification of four new sites of methylation in 23S RNA. Biochemistry 31: 10825– 10834.
100.
Sollner-Webb, B.,, K. Tyc,, and J. A. Steitz,. 1995. Ribosomal RNA processing in eukaryotes. In R. A. Zimmermann, and A. E. Dahlberg (ed.), Ribosomal RNA Structure, Evolution, Processing, and Function in Protein Biosynthesis. Telford, Cadwell, N.J.
101.
Sprinzl, M.,, C. Steegborn,, F. Hubel,, and S. Steinberg. 1996. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 24: 68– 72.
102.
Sun, D.,, F. Nallaseth,, and J. Ofengand. Unpublished results.
103.
Szweykowska-Kulinska, Z.,, B. Senger,, G. Keith,, F. Fasiolo,, and H. Grosjean. 1994. Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile). EMBO J. 13: 4636– 4644.
104.
Thomas, G.,, J. Gordon,, and H. Rogg. 1978. N 4-Acetylcytidine. A previously unidentified labile component of the small subunit of eukaryotic ribosomes. J. Biol. Chem. 253: 1101– 1105.
105.
Tollervey, D. 1987. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J. 13: 4169– 4175.
106.
Tollervey, D.,, and C. Guthrie. 1985. Deletion of a yeast small nuclear RNA gene impairs growth. EMBOJ. 6: 4169– 4175.
107.
Tollervey, D.,, and T. Kiss. 1997. Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol. 9: 337– 342.
108.
Trapane, T. L.,, M. S. Christopherson,, C. D. Roby,, P. O. P. Ts'o,, and D. Wang. 1994. DNA triple helices with C-nucleosides (deoxypseudouridine) in the second strand. J. Am. Chem. Soc. 116: 8412– 8413.
109.
Tscherne, J.,, P. Popieniek,, K. Nurse,, H. Michel,, M. Sochacki,, and J. Ofengand. Unpublished results.
110.
Tycowski, K. T.,, Z. You,, and J. A. Steitz. Personal communication.
111.
Van de Peer, Y.,, J. Jansen,, P. De Rijk,, and R. De Wachter. 1997. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 25: 111– 116.
112.
Veldman, G. M.,, J. Planta,, C. Branlant,, A. Krol,, and J. P. Ebel, 1981. The primary and secondary structure of yeast 26S rRNA. Nucleic Acids Res. 9: 6935– 6952.
113.
Venema, J.,, and D. Tollervey. 1995. Processing of pre-ribosomal RNA in Saccharomyces cerevisiae. Yeast 11: 1629– 1650.
114.
Weitzmann, C.,, P. R. Cunningham,, K. Nurse,, and J. Ofengand. 1993. Chemical evidence for domain assembly of the E. coli 30S ribosome. FASEB J. 7: 177– 180.
115.
Wrzesinski, J.,, A. Bakin,, K. Nurse,, B. G. Lane,, and J. Ofengand. 1995a. Purification, cloning, and properties of the 16S RNA Ψ516 synthase from Escherichia coli. Biochemistry 34: 8904– 8913.
116.
Wrzesinski, J.,, K. Nurse,, A. Bakin,, B. G. Lane,, and J. Ofengand. 1995b. A dual-specificity pseudouridine synthase: purification and cloning of a synthase from Escherichia coli which is specific for both Ψ746 in 23S RNA and for Ψ32 in tRNA Phe. RNA 1: 437– 448.
117.
Yu, C. T.,, and F. W. Allen. 1959. Studies on an isomer of uridine isolated from ribonucleic acids. Biochim. Biophys. Acta 32: 393– 405.
Tables
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap12-1,webId=/content/author/10.1128/9781555818296.chap12-1,properties={foaf_givenname=James, foaf_name=James Ofengand, foaf_surname=Ofengand, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap12-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap12-2,webId=/content/author/10.1128/9781555818296.chap12-2,properties={foaf_givenname=Maurille J., foaf_name=Maurille J. Fournier, foaf_surname=Fournier, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap12-aff2]]}]]
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.tab12-1
Table 1
Reactivity of U-derived modified nucleosides with CMC/OH and hydrazine-aniline
10.1128/9781555818296/tab12-1_thmb.gif
10.1128/9781555818296/tab12-1.gif
Table 1
Reactivity of U-derived modified nucleosides with CMC/OH and hydrazine-aniline
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.tab12-2
Table 2
Number of pseudouridine and modified pseudouridine residues in small subunit rRNAs and number positioned in the RNA sequence
10.1128/9781555818296/tab12-2_thmb.gif
10.1128/9781555818296/tab12-2.gif
Table 2
Number of pseudouridine and modified pseudouridine residues in small subunit rRNAs and number positioned in the RNA sequence
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.tab12-3
Table 3
Number of pseudouridine and modified pseudouridine residues in large subunit rRNAs and number positioned in the RNA sequence
10.1128/9781555818296/tab12-3_thmb.gif
10.1128/9781555818296/tab12-3.gif
Table 3
Number of pseudouridine and modified pseudouridine residues in large subunit rRNAs and number positioned in the RNA sequence
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.tab12-4
Table 4
Structural environment of Ψ and modified Ψ residues in SSU and LSU RNAs f
10.1128/9781555818296/tab12-4_thmb.gif
10.1128/9781555818296/tab12-4.gif
Table 4
Structural environment of Ψ and modified Ψ residues in SSU and LSU RNAs f
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.tab12-5
Table 5
Cloned pseudouridine synthases
10.1128/9781555818296/tab12-5_thmb.gif
10.1128/9781555818296/tab12-5.gif
Table 5
Cloned pseudouridine synthases
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.tab12-6
Table 6
Pseudouridine synthases in E. coli identified by sequence homology
10.1128/9781555818296/tab12-6_thmb.gif
10.1128/9781555818296/tab12-6.gif
Table 6
Pseudouridine synthases in E. coli identified by sequence homology
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12
/content/10.1128/9781555818296.chap12.tab12-7
Table 7
ACA snoRNAs in Saccharomyces cerevisiae
10.1128/9781555818296/tab12-7_thmb.gif
10.1128/9781555818296/tab12-7.gif
Table 7
ACA snoRNAs in Saccharomyces cerevisiae
Citation:
Ofengand J, Fournier M.
1998.
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function,
p 229-253.
In
Grosjean H, Benne R (ed),
Modification and Editing of RNA.
ASM Press, Washington, DC.
doi: 10.1128/9781555818296.ch12