5S ribosomal RNA
The 5S ribosomal RNA (5S rRNA) is an approximately 120 nucleotide-long ribosomal RNA molecule with a mass of 40 kDa. It is a structural and functional component of the large subunit of the ribosome in all domains of life (bacteria, archaea, and eukaryotes), with the exception of mitochondrial ribosomes of fungi and animals. The designation 5S refers to the molecule's sedimentation velocity in an ultracentrifuge, which is measured in Svedberg units (S).[1]
5S ribosomal RNA
5S_rRNA
Biosynthesis[edit]
In prokaryotes, the 5S rRNA gene is typically located in the rRNA operons downstream of the small and the large subunit rRNA, and co-transcribed into a polycistronic precursor.[3] A particularity of eukaryotic nuclear genomes is the occurrence of multiple 5S rRNA gene copies (5S rDNA) clustered in tandem repeats, with copy number varying from species to species.[4][5] Eukaryotic 5S rRNA is synthesized by RNA polymerase III, whereas other eukaryotic rRNAs are cleaved from a 45S precursor transcribed by RNA polymerase I. In Xenopus oocytes, it has been shown that fingers 4–7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA.[6][7] Binding between 5S rRNA and TFIIIA serves to both repress further transcription of the 5S RNA gene and stabilize the 5S RNA transcript until it is required for ribosome assembly.[8]
Structure[edit]
The secondary structure of 5S rRNA consists of five helices (denoted I–V in roman numerals), four loops (B-E), and one hinge (A), which form together a Y-like structure. Loops C and D are terminal hairpins and loops B and E are internal.[4] According to phylogenetic studies, helices I and III are likely ancestral.[9] Helix III includes two highly conserved adenosines.[10] Helix V, with its hairpin structure, is thought to interact with TFIIIA.[4]
Ribosomal functions[edit]
The exact function of 5S rRNA is not yet clear. In Escherichia coli, 5S rRNA gene deletions reduce the protein synthesis rate and have a more profound detrimental effect on cell fitness than deletions of a comparable number of copies of other (16S and 23S) rRNA genes.[16] Crystallographic studies indicate that 5S rRNA-binding proteins and other proteins of the central protuberance of the LSU plays a role in binding tRNAs.[15] Also, the topographical and physical proximity between 5S rRNA and 23S rRNA, which forms the peptidyl transferase and GTPase-associating center, suggests that 5S rRNA acts as a mediator between the two functional centers of the ribosome by forming, together with 5S rRNA-binding proteins and other components of the central protuberance, intersubunit bridges and tRNA-binding sites.[15]
Roles in ribosomal assembly[edit]
In eukaryotes, the cytosolic ribosome is assembled from four rRNAs and over 80 proteins.[14][17] Once transcribed, the 3' ends of 5S rRNA can only be trimmed to mature length by functional homologues of RNase T, for example Rex1p in Saccharomyces cerevisiae.[18] The 60S and 40S ribosomal subunits are exported from the nucleus to the cytoplasm where they join to form the mature and translation-competent 80S ribosome. When exactly 5S rRNA is integrated into the ribosome remains controversial,[4] but it is generally accepted that 5S rRNA is incorporated into the 90S particle, which is a precursor to 60S particle, as part of a small ribosome-independent RNP complex formed by 5S rRNA and ribosomal protein L5.[17]