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Chapter 12 : The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function
Authors:
James Ofengand1,
Maurille J. Fournier2
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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
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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
Figures
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function
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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
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Tables
The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function
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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