ReviewThe expanding snoRNA world
Introduction
The biogenesis of eukaryotic ribosomes in the nucleolus involves an intricate series of pre-rRNA processing steps. This results in the removal of extended spacer regions from the primary transcript and production of stoichiometric amounts of mature small and large subunit rRNAs. Before its cleavage by endo- and exonucleases, the nascent pre-rRNA undergoes a complex pattern of nucleoside modifications of its mature small subunit (SSU) and large subunit (LSU) sequences. These modifications are of two prevalent types, 2-O-ribose methylation or pseudouridylation, each involving about 50–100 sites per eukaryotic ribosome 〚1〛, 〚2〛, 〚3〛. They are exclusively located within the most conserved, functionally important domains of mature RNAs, particularly into the structural elements contributing to the peptidyl-transfer region and its vicinity 〚4〛 and their positions are largely (but not perfectly) conserved among distant eukaryotes. While these modifications of elusive role are not absolutely essential, they are likely to fine-tune rRNA folding and interactions with ribosomal proteins, thereby modulating both the biogenesis and activity of the ribosomes. The two types of eukaryotic rRNA modifications are directed by two large families of snoRNAs (small nucleolar RNAs) which specify the sites to be modified, in both cases through the formation of a specific duplex at the rRNA modification site, while the catalytic function is provided by a common protein enzyme, methylase or pseudouridine synthase, associated with the snoRNA. Since a single snoRNA guide can direct one, or at most two rRNA modifications, the number of these RNA species was expected until recently to approach 200 in vertebrates.
However, recent studies show that the complexity of the two snoRNA guide families has been largely underestimated. Their diversity relates not only to their genetic organization and biosynthesis but also to the existence of variant snoRNA structures and multiple cellular RNA targets, reflecting a range of cellular functions beyond ribosome biogenesis. Novel members of the modification guide snoRNA families target spliceosomal snRNAs in vertebrates, tRNAs in Archaea and even probably eukaryotic mRNAs, in addition to rRNAs. Remarkably, an increasing number of “orphan” guides without known RNA targets have been identified. Several of them are expressed in a tissue-specific fashion and submitted to genomic imprinting, adding another level of complexity to the biological roles of snoRNA guides in mammals. Meanwhile, the identification of homologs of guide snoRNAs in organisms lacking a nucleus, Archaea, provides further insights into the evolutionary origin and function of these two large families of non-coding RNAs.
Fundamental properties of snoRNA guides for rRNA modification have been reviewed previously 〚2〛, 〚3〛, 〚5〛, 〚6〛, 〚7〛, 〚8〛, 〚9〛 and the reader is referred to these articles for further information on their gene organization, biogenesis and guide function, as well as to reviews dealing with pre-rRNA processing and nucleotide modification in eukaryotes 〚1〛, 〚10〛, 〚11〛, 〚12〛, 〚13〛. In this article, following an updated summary of the properties of rRNA modification guides, we will focus on recent breakthroughs revealing the unanticipated structural and functional diversity of the two families of guide snoRNAs in organisms ranging from Archaea to Eukarya.
Section snippets
Structure and function
Except for the RNA component for RNase MRP, all snoRNAs to date fall into two major classes, antisense box C/D and box H/ACA snoRNAs, based on the presence of short consensus sequence motifs 〚14〛. Most members of the two snoRNA families guide the 2′-O-ribose methylations and pseudouridylations, respectively, of rRNA. It is noteworthy, however, that a handful of them are involved instead in pre-rRNA cleavages 〚12〛. The two snoRNA guide families have been identified in a wide spectrum of eukaryal
Modification guides for spliceosomal snRNAs
Mammalian U1, U2, U4, U5 and U6 snRNAs contain a very substantial number of 2′-O-methylations and pseudouridylations, amounting collectively to 30 and 24, respectively 〚78〛. Interestingly, these modifications are mainly located in the snRNA segments involved in intermolecular RNA–RNA interactions or conformational switches during spliceosome assembly and function, suggesting that they play an important role in splicing control 〚78〛. In line with this notion, modifications in the 5′ terminal
Brain-specific snoRNAs and genomic imprinting
In contrast to all known rRNA or snRNA modification guides and unlike most orphan snoRNAs, an increasing number of recently identified snoRNAs, mostly of the C/D family, exhibit a tissue-specific expression pattern, being mainly expressed within the brain 〚106〛, 〚109〛, 〚110〛, 〚111〛, 〚112〛, 〚113〛. Intriguingly, the genes of all of them are subjected to genomic imprinting, an epigenetic phenomenon that restricts gene expression to only one chromosome, either the paternal or the maternal allele
Archaeal modification guides, tRNA targets and archaeal splicing
In contrast to eukaryotes, the rRNA of typical bacterium Escherichia coli contains only four 2′-O-methylations and 10 pseudouridines and each of these modifications appears to be catalyzed by a site-specific protein enzyme, ribose methylase or pseudouridine synthase, without any RNA cofactor 〚38〛, 〚122〛, 〚123〛. Among prokaryotic organisms, Archaea appear more closely related to Eukarya than to Bacteria by multiple aspects of the macromolecular machineries involved in DNA replication,
General conclusions
Methylation of 2′-hydroxyl groups may protect RNA from hydrolytic degradation, enhance hydrophobic surfaces and stabilize helical stems. Pseudouridines, through their flexible C–C glycosyl bonds and increased capacity, relative to uridines, to form H-bonds, may significantly contribute to RNA tertiary structure. Nucleotide modifications directed by snoRNA guides appear in most cases dispensable for cell viability or growth. However, they are likely to have an important biological role by
Acknowledgements
The work performed in J.P.B. laboratory was supported by laboratory funds from the Centre National de la Recherche Scientifique and Université Paul Sabatier, Toulouse, by grants from Association pour la Recherche sur le Cancer, the Toulouse Genopole and the Ministère de l’Education Nationale, de la Recherche et de la Technologie (Programme de Recherche Fondamentale en Microbiologie et Maladies Infectieuses et Parasitaires, 2001–2002) to J.P.B., and a grant from the Programme Interdisciplinaire
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