SUMMARY PARAGRAPH for SNR17A
The small nucleolar RNAs (snoRNAs) are stable RNAs that are found within small nucleolar ribonucleoprotein complexes (snoRNPs) and localized to the nucleoli of eukaryotic cells. The majority of the snoRNAs are involved in ribosomal RNA processing, though some are also involved in processing of other RNAs and a couple have not yet been characterized as to their role in cells. Based on conserved sequence elements and association with conserved nucleolar proteins, the snoRNAs can be divided into three classes: box C/D snoRNAs, box H/ACA snoRNAs, and snoRNA MRP. Both the box C/D and box H/ACA families have many members, while MRP (produced by the NME1 gene) is the sole RNA of its type (2, 3). The box C/D and box H/ACA snoRNPs are found in all eukaryotes and even in Archaea, indicating that these are ancient and highly conserved complexes (4) For a complete listing of all the snoRNA genes in S cerevisiae, see the table of snoRNAs.
About the U3 snoRNA
The U3 snoRNA is one of the most abundant RNA molecules in S. cerevisiae, present at about 400-1000 copies per cell (1). U3 is a box C/D snoRNA (3) encoded by two genes, snR17A and snR17B, both of which contain an intron with an atypical branch point sequence (5). Both U3 genes are transcribed, though snR17A is 5-10 fold more abundant than snR17B (1, 5). Each is 328 nucleotides long and they are 96% identical in the region of the mature RNA (1). U3 from S. cerevisiae is over 100 nucleotides longer than U3 from most other eukaryotes, e.g. human, rat, or dictystelium, but shares conserved primary and secondary structure elements (1), including perfect complementarity to a conserved sequence within the 5'-ETS of the primary rRNA transcript(6) and to three highly conserved sequences within the 18S rRNA which form the conserved pseudoknot found at the core of all small subunit rRNAs (7). While either snR17A or snR17B can be deleted without any effect, the double deletion is inviable, indicating that U3 is essential (1).
Box C/D snoRNAs
The box C/D snoRNAs are characterized by two short conserved sequence elements, called boxes C and D, near the 5' or 3'-end of the snoRNA respectively. The middle part may contain additional imperfect copies of the C and D boxes, referred to as C' and D' boxes. In addition, the C/D snoRNAs contain one or more sequences, from 10-22 nucleotides long, of perfect complementarity to the sequence of their target RNA molecule, most often either the 18S or 25S rRNAs (3, 4). Each box C/D snoRNA is bound by four evolutionarily conserved proteins to form a box C/D type small nucleolar ribonucleoprotein complex, or snoRNP (8): Nop1p (the homolog of vertebrate fibrillarin, 9), Nop58p, Nop56p, and Snu13p.
Most of the box C/D snoRNPs methylate the ribose moieties of nucleotides within the 18S or 25S rRNAs, a modification which, along with pseudouridylation, occurs immediately after transcription and prior to various cleavages to generate the mature 18S, 25S, and 5.8S rRNAs (2, 10, 11). See the tables of Modified Nucleotides in RNAs to view known methylation sites. The site of methylation is directed by base pairing between the snoRNA and the target RNA and occurs within the hybrid at a specific distance from the box D or D', but is catalyzed by the Nop1p methyltransferase (8). The function of methylating the ribosomal RNAs is not quite clear and loss of any particular methylation site, or the specific snoRNA that directs it, is generally tolerated with no phenotype (12). However, a total lack of 2'-O-ribose methylation may be lethal as a temperative sensitive allele of the Nop1p catalytic subunit that prevents methylation without preventing the cleavage steps is lethal (10). It is notable that the sites of modification are in functionally important regions and many are conserved across species (2, 13). In mammals, snRNAs involved in mRNA splicing are also methylated and mRNAs may also be methylated by box C/D snoRNPs with regulatory consequences (13).
The role of snoRNAs in converting the primary rRNA transcript into mature rRNAs
While most of the snoRNAs are not essential and are involved in RNA modification, either 2'-O-ribose methylation or pseudouridylation, a few, including members of each of the three families, are required for endonucleolytic cleavage steps in the processing to convert the primary rRNA transcript into the mature 18S, 5.8S, and 25S rRNA molecules (2, 11). Two box C/D snoRNAs, U3 (produced by two genes SNR17A and SNR17B) and U14 (produced by SNR128) and two box H/ACA snoRNPs, snR30 and snR10 are required for cleavage of the primary rRNA transcript. Depletion of U3, U14, or snR30 results in depletion of the 18S rRNA and complete lack of any one of these snoRNAs is lethal (2, 11). The snR10 snoRNA is not essential and its deletion produces only a mild reduction in 18S rRNA accumulation (11). U14 and snR10 are involved in both endonucleolytic cleavage steps and in targeting RNA modification reactions (11). In addition, RNase MRP is involved in endonucleolytic cleavage to produce the mature 5.8S rRNA molecule; its depletion produces lessened accumulation of the 5.8S rRNA. However, while RNase MRP is essential, it is not essential for rRNA processing as there is an alternative minor processing pathway (11).
The genomic organization of snoRNAs
The genomic organization of the box C/D snoRNAs in S. cerevisiae is notable in that it is quite variable. Some of these genes are encoded within the introns of protein coding genes, as is the case for vertebrate snoRNAs. Other snoRNA genes are found in polycistronic arrays, containing from two to seven snoRNA genes, a common organization for plant snoRNAs. Additionally, S. cerevisiae also has independently transcribed monocistronic box C/D snoRNA genes (12). The genomic organization of the box H/ACA snoRNAs is not as variable as that of the box C/D snoRNAs, and none are found within polycistronic transcripts. Almost all of them are monocistronic genes, though a couple are found within the introns of protein coding genes (2). In addition, while almost all of the snoRNA genes in S. cerevisiae are transcribed by RNA polymerase II, snR52 is transcribed by RNA polymerase III (14).
About the early stages of rRNA processing and 40S small ribosomal subunit assembly
The early stages of ribosome assembly occur in conjunction with processing of the 35S pre-ribosomal RNA transcript into the mature 18S, 5.8S, and 25S rRNA molecules. The first three cleavages at A0, A1, and A2 (see diagram) are essential for production of the 18S rRNA and the 40S small ribosomal subunit, but mutations which interfere with these cleavages have little effect on production of the 60S large ribosomal subunit (11). These three early cleavages occur in a series of large U3-associated ribonucleoprotein complexes (15, 16) and require base pairing of the U3 snoRNA with sequences in the 5'-ETS and the 18S rRNA (6, 7).
Click on the following figure for more details about the rDNA repeat and cleavage sites within the rRNA transcript:
About the 90S preribosome and SSU processome complexes
A number of U3-containing early ribosome assembly and rRNA processing complexes have been identified that contain the 35S pre-rRNA transcript and have overlapping but not identical protein compositions (15, 16). Both the 90S preribosome and the small subunit (SSU) processome complexes contain ribosomal proteins, primarily of the small subunit, and non-ribosomal proteins presumably involved in rRNA processing and assembly of the small 40S ribsomal subunit. While many proteins are found in both complexes, some are found in only one or the other (see lists below). It may be that the 90S preribosome and SSU processome complexes are both intermediates in a series of complexes leading to the assembly of the small ribosomal subunit (15), or it may be that the SSU processome lies on an alternate assembly pathway (16).
The 90S preribosome complex is described as corresponding to the earliest detectable rRNA processing and ribosome assembly complex (17). The 90S is itself assembled from a number of stable subcomplexes including the t-UTP subcomplex (Utp5p, Utp4p, Nan1p, Utp8p, Utp9p, Utp10p, and Utp15p), the Pwp2p/UTP-B subcomplex (Utp6p, Pwp2p, Utp18p, Utp21p, Utp13p, and Dip2p) which interacts directly with the 5'-ETS of the 35S pre-rRNA (18), the UTP-C subcomplex (Rrp7p, Utp22p, Ckb1p, Cka1p, Ckb2p, and Cka2p), and the Mpp10 subcomplex (Mpp10p, Imp3p, and Imp4p) (19). The t-UTP subcomplex is also found as part of the SSU processome complex, which is slightly smaller at 80S (20, 21). Depletion of any of the members of the t-UTP subcomplex results in decreased transcription of rDNA leading to decreased levels of the primary 35S rRNA transcript (22). In contrast, mutation or depletion of most other members of either the 90S preribosome or SSU processome complexes causes decreased 18S rRNA levels without affecting the levels of the 25S or 5.8S rRNAs.
Non-ribosomal protein components of the 90S preribosome and SSU processome
Subunits of both the 90S preribosome (17) and SSU processome (20, 21) include: Bud21p, Dip2p, Ecm16p, Emg1p, Imp3p, Imp4p, Krr1p, Mpp10p, Nan1p, Noc4p, Nop1p, Nop14p, Nop58p, Pwp2p, Rrp5p, Rrp9p, Nop56p, Sof1p, Utp4p, Utp6p, Utp7p, Utp8p, Utp9p, Utp10p, Utp13p, Utp15p, Utp18p, Utp20p, Utp21p, and Utp22p
Additional subunits of the 90S preribosome (17) include: Bfr2p, Bms1p, Cbf5p, Cms1p, Dbp8p, Dim1p, Enp1p, Enp2p, Has1p, Kre33p, Mrd1p, Nop9p (23), Pno1p, Prp43p, Rcl1p, Rok1p, Rrp12p, Scl1p, Slx9p (24), Tsr1p, and Utp30p
Additional subunits of the SSU processome (20, 21) include: Fcf1p, Utp23p, Sas10p, Snu13p, Utp5p, Utp11p, and Utp14p
Last updated: 2007-06-29