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Chapter 12 : The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function

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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

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Figures

Image of Figure 1
Figure 1

Location of Ψ and other modified residues in SSU RNA. The secondary structure is that of . Ψ and insert symbol, pseudouridines in . ( ); ○ and insert symbol, mammalian pseudouridine positions ( ); ©, pseudouridines at the same site in both S. and mammals; Ψ, macpΨ ( ); Δ, base-methylated, and ▲, 2-O-methyl, nucleosides in . ( ); arrow, site of Ψ in ( ) and ( ). Adapted from .

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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Image of Figure 3
Figure 3

Comparative positions of Ψ residues in the 5′ region of LSU RNAs. The sequence is that of .. E, .. Y, . D, . Μ, . Η, .. Reprinted from 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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Image of Figure 5
Figure 5

Comparative positions of Ψ residues in the 3′ region, including the PTC, of LSU RNAs. The sequence is that of Ε, ., . A, . Ζ, Z. chloroplasts; Y, . D, . Μ, M. Η, . Ym, . mitochondria; Mm, . mitochondria; Hm, . mitochondria; T, T. mitochondria. The two sets of paired dashed ovals denote two semi-invariant sites. Reprinted from 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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Image of Figure 2
Figure 2

Location of Ψ and other modified residues in LSU RNA. The secondary structure is from . Location of the Ψ residues is from and . Open circles, base-methyl, and filled circles, 2-O-methyl nucleosides (see Table II of ); D, dihydrouridine ( ); Ψ, -methyl Ψ ( ).

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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Image of Figure 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 .

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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Image of Figure 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 and .

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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Image of Figure 4
Figure 4

Comparative positions of Ψ residues in the central region of LSU RNAs. The sequence is that of .. Ε, . , . Α, . Ζ, . chloroplasts; Y, . D, . Μ, M. Η, .. 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 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

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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
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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
Generic image for table
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
Generic image for table
Table 4

Structural environment of Ψ and modified Ψ residues in SSU and LSU RNAs

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
Generic image for table
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
Generic image for table
Table 6

Pseudouridine synthases in 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
Generic image for table
Table 7

ACA snoRNAs in

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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