RDN5-4 Summary Help

Standard Name RDN5-4
Alias RDN5
Feature Type rRNA
Description Variant 5S ribosomal rRNA (5S rRNA) gene; located at a site distal to the RDN1 locus; unable to support cell viability when provided as sole source of 5S rRNA; identical in sequence to variant alleles RDN5-2, RDN5-3, and RDN5-5 (1, 2, 3, 4, 5, 6 and see Summary Paragraph)
Chromosomal Location
ChrXII:482045 to 482163 | ORF Map | GBrowse
Gene Ontology Annotations All RDN5-4 GO evidence and references
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
sequence information
ChrXII:482045 to 482163 | ORF Map | GBrowse
Last Update Coordinates: 2011-02-03 | Sequence: 2004-03-04
Subfeature details
Most Recent Updates
Coordinates Sequence
Noncoding exon 1..119 482045..482163 2011-02-03 2004-03-04
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
External Links All Associated Seq | Search all NCBI (Entrez)
Primary SGDIDS000029708

The ribosomal DNA (rDNA) of Saccharomyces cerevisiae is encoded by the RDN1 locus, an approximately 1-2 Mb region consisting of 100-200 tandem copies of a 9.1 kb repeat, on the right arm of chromosome XII (reviewed in 7). Each repeat contains the genes for 5S, 5.8S, 25S, and 18S rRNAs (RDN5, RDN58, RDN25, and RDN18), as well as three types of spacer regions: internal transcribed spacers (ITS1, ITS2), external transcribed spacers (5' ETS, 3' ETS) and nontranscribed spacers (NTS1, NTS2). As in other eukaryotes, genes encoding 18S, 5.8S, and 25S rRNAs are transcribed by RNA polymerase I as a single precursor, the 35S pre-rRNA, that also includes the ITS1 and ITS2 sequences. Transcription starts in the 5'ETS and terminates in the 3' ETS. The majority of transcripts terminate at a terminator 93 base pairs downstream of the 3' end of 25S rRNA, while a minority terminate at a site 211-250 nucleotides downstream (8, 9). The 5S rRNA is transcribed separately, and on the opposite strand, by RNA polymerase III.

Processing of the 35S pre-rRNA occurs in the nucleolus, and initiates with co-transcriptional cleavage in the 3' ETS. The transcript is then extensively modified and rapidly processed (reviewed in 7). Each ribosomal RNA is present in a single copy in a yeast ribosome: 18S rRNA is a component of the 40S ribosomal subunit, and the 25S, 5.8S, and 5S rRNAs are components of the 60S subunit (10).

Note that the systematic sequencing of the yeast genome included only two of the 100-200 rDNA repeats (3). Within SGD, each of the two annotated repeats is represented by several locus entries. The RDN1 locus represents the entire 1-2Mb repeat region. RDN37-1 and RDN37-2 represent the primary 35S transcripts of the two repeats. RDN25-1 and RDN25-2, RDN18-1 and RDN18-2, and RDN58-1 and RDN58-2 represent the 25S, 18S, and 5.8S rRNAs encoded by these transcripts, respectively.

RDN5-1 and RDN5-2 are within the RDN1 locus. RDN5-3 through RDN5-6 are located at sites distal to RDN1, in a 3.6 kb repeated region. Only RDN5-1 represents the complete 5S rDNA sequence. RDN5-2 through RDN5-6 are variant genes (11).

Click on the following figures for more details about the rDNA repeat (left) and the RDN1 locus (right):

figure 1 figure 2

About yeast ribosomes...

Ribosomes are highly conserved large ribonucleoprotein (RNP) particles, consisting in yeast of a large 60S subunit and a small 40S subunit, that perform protein synthesis. Yeast ribosomes contain one copy each of four ribosomal RNAs (5S, 5.8S, 18S, and 25S; produced in two separate transcripts encoded within the rDNA repeat present as hundreds of copies on Chromosome 12) and 78 different ribosomal proteins (r-proteins), which are encoded by 137 different genes scattered about the genome, 59 of which are duplicated (7). The 60S subunit contains 42 proteins and three RNA molecules: 25S RNA of 3392 nt, hydrogen bonded to the 5.8S RNA of 158 nt and associated with the 5S RNA of 121 nt. The 40S subunit has a single 18S RNA of 1798 nt and 32 proteins (12). All yeast ribosomal proteins have a mammalian homolog (13).

In a rapidly growing yeast cell, 60% of total transcription is devoted to ribosomal RNA, and 50% of RNA polymerase II transcription and 90% of mRNA splicing are devoted to the production of mRNAs for r-proteins. Coordinate regulation of the rRNA genes and 137 r-protein genes is affected by nutritional cues and a number of signal transduction pathways that can abruptly induce or silence the ribosomal genes, whose transcripts have naturally short lifetimes, leading to major implications for the expression of other genes as well (14, 15, 16). The expression of some r-protein genes is influenced by Abf1p (17), and most are directly induced by binding of Rap1p to their promoters, which excludes nucleosomes and recruits Fhl1p and Ifh1p to drive transcription (18).

Ribosome assembly is a complex process, with different steps occurring in different parts of the cell. Ribosomal protein genes are transcribed in the nucleus, and the mRNA is transported to the cytoplasm for translation. The newly synthesized r-proteins then enter the nucleus and associate in the nucleolus with the two rRNA transcripts, one of which is methylated and pseudouridylated (view sites of modifications), and then cleaved into three individual rRNAs (18S, 5.8S, and 25S) as part of the assembly process (7). Separate ribosomal subunits are then transported from the nucleolus to the cytoplasm where they assemble into mature ribosomes before functioning in translation (19, 20). Blockage of subunit assembly, such as due to inhibition of rRNA synthesis or processing, results in degradation of newly synthesized r-proteins (21, 20). (For more information on the early steps of rRNA processing and small ribosomal subunit assembly, see the summary paragraph for the U3 snoRNA, encoded by snR17A and snR17B.)

Last updated: 2004-03-25 Contact SGD

References cited on this page View Complete Literature Guide for RDN5-4
1) Dinman JD and Wickner RB  (1995) 5 S rRNA is involved in fidelity of translational reading frame. Genetics 141(1):95-105
2) Camier S, et al.  (1995) The only essential function of TFIIIA in yeast is the transcription of 5S rRNA genes. Proc Natl Acad Sci U S A 92(20):9338-42
3) Johnston M, et al.  (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature 387(6632 Suppl):87-90
4) Michael WM and Dreyfuss G  (1996) Distinct domains in ribosomal protein L5 mediate 5 S rRNA binding and nucleolar localization. J Biol Chem 271(19):11571-4
5) Kiparisov S, et al.  (2005) Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae. Mol Genet Genomics 274(3):235-47
6) Dieci G, et al.  (2009) Positive modulation of RNA polymerase III transcription by ribosomal proteins. Biochem Biophys Res Commun 379(2):489-93
7) Venema J and Tollervey D  (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311
8) Reeder RH, et al.  (1999) Saccharomyces cerevisiae RNA polymerase I terminates transcription at the Reb1 terminator in vivo. Mol Cell Biol 19(11):7369-76
9) van der Sande CA, et al.  (1989) Termination of transcription by yeast RNA polymerase I. Nucleic Acids Res 17(22):9127-46
10) Spahn CM, et al.  (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell 107(3):373-86
11) McMahon ME, et al.  (1984) Tandemly arranged variant 5S ribosomal RNA genes in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 12(21):8001-16
12) Verschoor A, et al.  (1998) Three-dimensional structure of the yeast ribosome. Nucleic Acids Res 26(2):655-61
13) Mager WH, et al.  (1997) A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic Acids Res 25(24):4872-5
14) Li B, et al.  (1999) Transcriptional elements involved in the repression of ribosomal protein synthesis. Mol Cell Biol 19(8):5393-404
15) Zhao Y, et al.  (2003) Autoregulation in the biosynthesis of ribosomes. Mol Cell Biol 23(2):699-707
16) Warner JR  (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24(11):437-40
17) Mager WH and Planta RJ  (1990) Multifunctional DNA-binding proteins mediate concerted transcription activation of yeast ribosomal protein genes. Biochim Biophys Acta 1050(1-3):351-5
18) Zhao Y, et al.  (2006) Fine-structure analysis of ribosomal protein gene transcription. Mol Cell Biol 26(13):4853-62
19) Moritz M, et al.  (1990) Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly. J Cell Biol 111(6 Pt 1):2261-74
20) Milgrom E, et al.  (2007) Loss of vacuolar proton-translocating ATPase activity in yeast results in chronic oxidative stress. J Biol Chem 282(10):7125-36
21) Wang S, et al.  (2007) Influence of Substrate Conformation on the Deglycosylation of Ribonuclease B by Recombinant Yeast Peptide:N-glycanase. Acta Biochim Biophys Sin (Shanghai) 39(1):8-14