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Chapter 16 : Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes

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Abstract:

rRNAs contain a number of different modified nucleosides, mainly, but not exclusively, pseudouridine (ψ, 5-ribosyl-uracil) and nucleosides methylated on either the base or the 2'-hydroxyl of the ribose. This chapter focuses on the rRNAs of bacteria, archaea, and organelles, including the last because of their presumed evolutionary relationship to bacterial organisms. With a single exception in , all of the available information on the rRNA ψ synthases comes from . Deletion of the synthase gene and subsequent RNA analysis for ψ can also be misleading if another synthase shares the specificity for forming a particular ψ. The effects of the absence of RluC or RsuA were much less marked but still significant. The strong effect of RluA deletion might be due to the loss of ψ from both large-subunit (LSU) RNA and tRNA. It is also important to note that the family designations based on amino acid sequence homology do not necessarily define the specificities of the member synthases. In , the locations of the 10 methylated nucleosides in the small-subunit (SSU) RNA and the 14 methylated nucleosides (one is mψ) plus one dihydrouridine in the LSU RNA are known.

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16

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Figures

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Figure 1

Conversion of uridine (left) to pseudouridine (right). The reaction results in the release of the C-5 H of uridine (shown as H) to water. Two axes are shown about which the uracil ring could rotate so as to place C-5 at the position previously occupied by N-1.

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
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Image of Figure 2
Figure 2

Secondary structure of 16S RNA showing the site of the single Ψ along with the designation of the synthase which forms it.

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
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Image of Figure 3
Figure 3

Secondary structure of 23S RNA showing the locations of the nine Ψ in this RNA along with the assignments of the five synthases which form them.

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
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Figure 4

Diminished growth of lacking a functional RluD. The gene was disrupted and inactivated by a mini-Tn:: insertion two-thirds of the way along the gene ( ). The defect was rescued by supplying an intact gene in on a plasmid. Wild-type /pTRC, MG1655 ( ) containing the plasmid vector pTrc; Wild-type /pTRC-SfhB, same, except the pTrc vector contained the gene; Mutant/pTRC, MG1655 ( minus) containing the plasmid vector pTrc; Mutant/pTRC-SfhB, same, except the pTrc vector contained the gene. (Reprinted from , with the permission of Cambridge University Press.)

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
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Figure 5

Alignment of 132 motif II sequences of the Ψ synthase superfamily I and 43 TruB motif II-like sequences. The 14 amino acids of motif II are aligned and grouped according to families. The motif consensus shown above the sequences summarizes the sequence patterns but does not indicate all pattern variations. Motif conventions: single capital letters, invariant or nearly invariant; vertical letter pairs indicate the two most common amino acids at that position; $, usually one of ILVM; +, charged. The YTZF/BASCU protein sequence is a reconstruction of a probable frameshift mutation that fuses two adjacent protein sequences, YTZF BACSU (O32068) and YTZG BACSU (O32069). There is also a human orthologue to the YD36 YEAST subgroup of the RluA family (tr, Q92939) which is not listed because it is a C-terminal partial sequence with the motif II region still unsequenced. Two TruA sequences were omitted from the alignment. The conserved motif in the TruA homologue YQN3 CAEEL (sp, Q09524) appears to have two gaps and therefore was not aligned. A TruA homologue found in the database of expressed sequence tags, db EST, supposedly from (gb, N37304), is very similar to the sequence, and we suspect it represents a bacterial contaminant in that particular EST library. The database record accession numbers are taken from a variety of databases abbreviated as follows: sp, SWISSPROT; pi, PIR; tr, TREMBL, em, EMBL; gb, GenBank; dd, DDBJ. The citations to the original sequence papers can be found within the database records. Locus names were taken from SWISS-PROT or are provisional designations (if Gene and Organism are connected by a backslash instead of an underline). When no orthologue was obvious and no other name was available, a generic family name was given to the protein as a temporary identifier, e.g., RLUX or RSUX. The SWISS-PROT organism codes used are as follows: ACICA, ; AQUAE, ; ARATH, ; ARCFU, ; ASPFU, ; BACHD, ; BACSP, sp. strain KSM-64; BACSU, ; BARBA, ; BUCAP, ; BORBU, ; CHLTR, ; CHLPN, ; CAEEL, ; CAMJE, ; CANAL, ; CHLAU, ; CHLVI, ; CRYPV, ; DEIRA, ; DROME, ; ECOLI, ; EMENI, ; ERWCA, ; HAEIN, ; HELPY, ; HUMAN, ; KLULA, ; LACLA, ; LEIDO, ; LEIMA, ; METJA, ; METTH, MOUSE, ; MYCGE, ; MYCLE, ; MYCPN, ; MYCTU, ; PLAFA, ; PSEAE, ; PYRAB, ; PYRFU, ; PYRHO, ; RAT, ; RICPR, ; SCHPO, ; STRCO, ; SYNP6, sp. strain PCC 6301; SYNP7, sp. strain PCC 7942; SYNY3, sp. strain PCC 6803; THEMA, ; TREPA, ; YEAST, ; YEREN, ; ZYMMO, . HELP2 is a second strain (J99) of that has been recently sequenced. The motif II sequence from this strain was included, since it differed from the HELPY version. Other motif II sequences from different strains of the same species were identical and have been omitted from this compilation. The complete genome sequences for (SANG), (TIGR), (GENO), and (UGC) were taken from the following private databases indicated in parentheses: SANG, sequence data produced by the Sequencing Group at the Sanger Centre (they can be obtained from ftp://ftp.sanger.ac.uk/pub/pathogens.cj/); TIGR, preliminary sequence data obtained from The Institute for Genome Research website at http://www.tigr.org; sequencing of was accomplished with support from the U.S. Department of Energy; UGC, the Utah Genome Center, Department of Human Genetics, University of Utah; GENO, the GENOSCOPE website (www.genoscope.cns.fr).

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
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Tables

Generic image for table
Table 1

Number of pseudouridine residues in LSU and SSU ribosomal RNAs of bacteria, archaea, and organelles

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
Generic image for table
Table 2

Properties of known bacterial rRNA and tRNA pseudouridine synthases

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
Generic image for table
Table 3

Effect of deletion and conserved aspartate mutation of pseudouridine synthases on cell growth and synthase activity in vivo and in vitro

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16
Generic image for table
Table 4

Number and family distribution of pseudouridine synthases in sequenced genomes

Citation: Ofengand J, Rudd K. 2000. Bacterial, Archaeal, and Organellar rRNA Pseudouridines and Methylated Nucleosides and Their Enzymes, p 175-190. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch16

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