molecular biology Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...

, U3 snoRNA is a

non-coding RNA A non-coding RNA (ncRNA) is a functional RNA molecule that is not Translation (genetics), translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally imp ...

found predominantly in the

nucleolus The nucleolus (; : nucleoli ) is the largest structure in the cell nucleus, nucleus of eukaryote, eukaryotic cell (biology), cells. It is best known as the site of ribosome biogenesis. The nucleolus also participates in the formation of signa ...

. U3 has C/D box motifs that technically make it a member of the box C/D class of

snoRNA In molecular biology, small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, t ...

s; however, unlike other C/D box snoRNAs, it has not been shown to direct 2'-''O''-

methylation Methylation, in the chemistry, chemical sciences, is the addition of a methyl group on a substrate (chemistry), substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replac ...

of other RNAs. Rather, U3 is thought to guide site-specific cleavage of

ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...

(rRNA) during pre-rRNA processing. The box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D.

Secondary Structure

The U3 snoRNA

secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

is characterized by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hyper-methylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

interactions and are necessary for the

rRNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...

processing functions of U3 snoRNA. Two potential mRNA binding motifs have been identified on U3 that base pair with the target sequences 5'-CUACCUCUCU-3' and 5'-CUCAGGAG-3'. mRNA targets bound by U3 appear to be involved in protein translation.

Species-specific secondary structure models

S. cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungal microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...

'' secondary structure determined by chemical mapping of U3A RNA in a purified snoRNP is available. A

human Humans (''Homo sapiens'') or modern humans are the most common and widespread species of primate, and the last surviving species of the genus ''Homo''. They are Hominidae, great apes characterized by their Prehistory of nakedness and clothing ...

structure model has also been proposed. Like yeast and human, protozoan protist Entamoeba histolytica : a primitive eukaryote adopted the same conserved secondary structure of U3 snoRNA.Srivastava A, Ahamad J, Ray AK, Kaur D, Bhattacharya A, Bhattacharya S (2014). Analysis of U3 snoRNA and small subunit processome components in the parasitic protist Entamoeba histolytica. Mol Biochem Parasitol. 193(2):82-92. doi: 10.1016/j.molbiopara.2014.03.001. Epub 2014 Mar 12 Four consensus structures specific to

metazoa Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia (). With few exceptions, animals consume organic material, breathe oxygen, have myocytes and are able to move, can reproduce sexually, and grow from a hol ...

fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...

plants Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars f ...

and basal eukaryotes have been proposed.

References

External links

*
uRNADB: U3 page (archive)

The UMASS snoRNAdb entry for U3

The SGD entry for U3a

The human snoRNAbase entry for U3
Small nuclear RNA {{molecular-biology-stub

Secondary Structure

Species-specific secondary structure models

See also

References

External links