SmY RNA

Last updated
SmY spliceosomal RNA
SmY-structure.png
Consensus secondary structure of SmY RNAs. A count of base pair substitutions observed in 68 structurally aligned sequences in the Rfam seed alignment is shown for each base pair, illustrating the extensive support for this predicted structure. [1]
Identifiers
SymbolSmY
Rfam RF01844
Other data
RNA typesnRNA, splicing
Domain(s) Chromadorea
PDB structures PDBe

SmY ribonucleic acids (SmY RNAs) are a family of small nuclear RNAs found in some species of nematode worms. They are thought to be involved in mRNA trans-splicing.

Contents

SmY RNAs are about 70–90 nucleotides long and share a common secondary structure, with two stem-loops flanking a consensus binding site for Sm protein. [2] [3] Sm protein is a shared component of spliceosomal snRNPs.

Phylogenetic distribution of known and predicted SmY RNA genes, and the number of genes and pseudogenes found in each species. Gene numbers are based on computational analysis (using the program Infernal) of genome assemblies; in some cases these are draft genomes that may be incomplete. SmY-phylogeny.png
Phylogenetic distribution of known and predicted SmY RNA genes, and the number of genes and pseudogenes found in each species. Gene numbers are based on computational analysis (using the program Infernal) of genome assemblies; in some cases these are draft genomes that may be incomplete.

SmY RNAs have been found in nematodes of class Chromadorea, which includes the most commonly studied nematodes (such as Caenorhabditis , Pristionchus , and Ascaris ), but not in the more distantly related Trichinella spiralis in class Dorylaimia. The number of SmY genes in each species varies, with most Caenorhabditis and Pristionchus species having 10–26 related paralogous copies, while other nematodes have 1–5. [1]

Discovery

The first SmY RNA was discovered in 1996 in purified Ascaris lumbricoides spliceosome preparations, as was another called SmX RNA that is not detectably homologous to SmY. [2] Twelve SmY homologs were identified computationally in Caenorhabditis elegans , and ten in Caenorhabditis briggsae . [3] Several transcripts from these SmY genes were cloned and sequenced in a systematic survey of small non-coding RNA transcripts in C. elegans. [4]

A systematic survey of 2,2,7-trimethylguanosine (TMG) 5′ capped transcripts in C.elegans using anti TMG antibodies identified two TMG capped SmY transcripts. [5] Sequence analysis of the potential Sm binding sites in these transcripts indicated the SmY, U5 snRNA, U3 snoRNA and the spliced leader RNAs transcripts (SL1 and SL2) all contain a very similar consensus SM binding sequence (AAU4–5GGA). The predicted SM binding sites identified in the U1, U2 and U4 snRNA transcripts varied from this consensus. [5]

Function

In C. elegans , SmY RNAs copurify with spliceosome and with Sm, SL75p, and SL26p proteins, while the better-characterized C. elegans SL1 trans-splicing snRNA copurifies in a complex with Sm, SL75p, and SL21p (a paralog of SL26p). [2] [3] Loss of function of either SL21p or SL26p individually causes only a weak cold-sensitive phenotype, whereas knockdown of both is lethal, as is a SL75p knockdown. Based on these results, the SmY RNAs are believed to have a function in trans-splicing.

Related Research Articles

RNA splicing Processing primary RNA to remove intron sequences and join the remaining exon sections

RNA splicing, in molecular biology, is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing, introns are removed and exons are joined together. For nuclear-encoded genes, splicing takes place within the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually required in order to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing is carried out in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). Self-splicing introns, or ribozymes capable of catalyzing their own excision from their parent RNA molecule, also exist.

Spliceosome Molecular machine that removes intron RNA from the primary transcript

A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. The spliceosome removes introns from a transcribed pre-mRNA, a type of primary transcript. This process is generally referred to as splicing. An analogy is a film editor, who selectively cuts out irrelevant or incorrect material from the initial film and sends the cleaned-up version to the director for the final cut.

Trans-splicing is a special form of RNA processing where exons from two different primary RNA transcripts are joined end to end and ligated. It is usually found in eukaryotes and mediated by the spliceosome, although some bacteria and archaea also have "half-genes" for tRNAs.

snRNPs, or small nuclear ribonucleoproteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs. The action of snRNPs is essential to the removal of introns from pre-mRNA, a critical aspect of post-transcriptional modification of RNA, occurring only in the nucleus of eukaryotic cells. Additionally, U7 snRNP is not involved in splicing at all, as U7 snRNP is responsible for processing the 3′ stem-loop of histone pre-mRNA.

Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III. Their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. They have also been shown to aid in the regulation of transcription factors or RNA polymerase II, and maintaining the telomeres.

U11 spliceosomal RNA

The U11 snRNA is an important non-coding RNA in the minor spliceosome protein complex, which activates the alternative splicing mechanism. The minor spliceosome is associated with similar protein components as the major spliceosome. It uses U11 snRNA to recognize the 5' splice site while U12 snRNA binds to the branchpoint to recognize the 3' splice site.

U1 spliceosomal RNA

U1 spliceosomal RNA is the small nuclear RNA (snRNA) component of U1 snRNP, an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs. Splicing, or the removal of introns, is a major aspect of post-transcriptional modification, and takes place only in the nucleus of eukaryotes.

U2 spliceosomal RNA

U2 spliceosomal snRNAs are a species of small nuclear RNA (snRNA) molecules found in the major spliceosomal (Sm) machinery of virtually all eukaryotic organisms. In vivo, U2 snRNA along with its associated polypeptides assemble to produce the U2 small nuclear ribonucleoprotein (snRNP), an essential component of the major spliceosomal complex. The major spliceosomal-splicing pathway is occasionally referred to as U2 dependent, based on a class of Sm intron—found in mRNA primary transcripts—that are recognized exclusively by the U2 snRNP during early stages of spliceosomal assembly. In addition to U2 dependent intron recognition, U2 snRNA has been theorized to serve a catalytic role in the chemistry of pre-RNA splicing as well. Similar to ribosomal RNAs (rRNAs), Sm snRNAs must mediate both RNA:RNA and RNA:protein contacts and hence have evolved specialized, highly conserved, primary and secondary structural elements to facilitate these types of interactions.

U4 spliceosomal RNA Non-coding RNA component of the spliceosome

The U4 small nuclear Ribo-Nucleic Acid is a non-coding RNA component of the major or U2-dependent spliceosome – a eukaryotic molecular machine involved in the splicing of pre-messenger RNA (pre-mRNA). It forms a duplex with U6, and with each splicing round, it is displaced from the U6 snRNA in an ATP-dependent manner, allowing U6 to re-fold and create the active site for splicing catalysis. A recycling process involving protein Brr2 releases U4 from U6, while protein Prp24 re-anneals U4 and U6. The crystal structure of a 5′ stem-loop of U4 in complex with a binding protein has been solved.

U5 spliceosomal RNA

U5 snRNA is a small nuclear RNA (snRNA) that participates in RNA splicing as a component of the spliceosome. It forms the U5 snRNP by associating with several proteins including Prp8 - the largest and most conserved protein in the spliceosome, Brr2 - a helicase required for spliceosome activation, Snu114, and the 7 Sm proteins. U5 snRNA forms a coaxially-stacked series of helices that project into the active site of the spliceosome. Loop 1, which caps this series of helices, forms 4-5 base pairs with the 5'-exon during the two chemical reactions of splicing. This interaction appears to be especially important during step two of splicing, exon ligation.

U6 spliceosomal RNA

U6 snRNA is the non-coding small nuclear RNA (snRNA) component of U6 snRNP, an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a large RNA-protein molecular complex that catalyzes the excision of introns from pre-mRNA. Splicing, or the removal of introns, is a major aspect of post-transcriptional modification and takes place only in the nucleus of eukaryotes.

U4atac minor spliceosomal RNA

U4atac minor spliceosomal RNA is a ncRNA which is an essential component of the minor U12-type spliceosome complex. The U12-type spliceosome is required for removal of the rarer class of eukaryotic introns.

snRNP70

snRNP70 also known as U1 small nuclear ribonucleoprotein 70 kDa is a protein that in humans is encoded by the SNRNP70 gene. snRNP70 is a small nuclear ribonucleoprotein that associates with U1 spliceosomal RNA, forming the U1snRNP a core component of the spliceosome. The U1-70K protein and other components of the spliceosome complex form detergent-insoluble aggregates in both sporadic and familial human cases of Alzheimer's disease. U1-70K co-localizes with Tau in neurofibrillary tangles in Alzheimer's disease.

SNRPB

Small nuclear ribonucleoprotein-associated proteins B and B' is a protein that in humans is encoded by the SNRPB gene.

SF3A2

Splicing factor 3A subunit 2 is a protein that in humans is encoded by the SF3A2 gene.

SF3B2

Splicing factor 3B subunit 2 is a protein that in humans is encoded by the SF3B2 gene.

Small RNAs (sRNAs) have been identified within the C. elegans genome and comparative genomics has shown that they are conserved across several nematode species. These sRNAs contain a characteristic 2,2,7-trimethylguanosine (TMG) cap structure that identifies them as non-coding RNAs that have a functional role within the cell but at present the exact function of these sRNAs is unknown. Immunoprecipitation using antibodies against TMG and RNA microarrays were used to identify these sRNA.

sbRNA

sbRNA is a family of non-coding RNA first discovered in Caenorhabditis elegans. It was identified during a full transcriptome screen of the C. elegans cDNA library. Subsequent experimentation characterised sbRNA as having conserved 5' and 3' internal motifs which form a long paired stem which is interrupted with a bulge.

Prp8

Prp8 refers to both the Prp8 protein and Prp8 gene. Prp8's name originates from its involvement in pre-mRNA processing. The Prp8 protein is a large, highly conserved, and unique protein that resides in the catalytic core of the spliceosome and has been found to have a central role in molecular rearrangements that occur there. Prp8 protein is a major central component of the catalytic core in the spliceosome, and the spliceosome is responsible for splicing of precursor mRNA that contains introns and exons. Unexpressed introns are removed by the spliceosome complex in order to create a more concise mRNA transcript. Splicing is just one of many different post-transcriptional modifications that mRNA must undergo before translation. Prp8 has also been hypothesized to be a cofactor in RNA catalysis.

Kiyoshi Nagai Japanese structural biologist

Kiyoshi Nagai was a Japanese structural biologist at the MRC Laboratory of Molecular Biology Cambridge, UK. He was known for his work on the mechanism of RNA splicing and structures of the spliceosome.

References

  1. 1 2 3 Jones TA, Otto W, Marz M, Eddy SR, Stadler PF (2009). "A survey of nematode SmY RNAs". RNA Biol. 6 (1): 5–8. doi: 10.4161/rna.6.1.7634 . PMID   19106623.
  2. 1 2 3 Maroney PA, Yu YT, Jankowska M, Nilsen TW (August 1996). "Direct analysis of nematode cis- and trans-spliceosomes: a functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPs". RNA. 2 (8): 735–745. PMC   1369411 . PMID   8752084.
  3. 1 2 3 MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T (April 2007). "A novel family of C. elegans snRNPs contains proteins associated with trans-splicing". RNA. 13 (4): 511–520. doi:10.1261/rna.426707. PMC   1831854 . PMID   17283210.
  4. ↑ Deng W, Zhu X, Skogerbø G, et al. (January 2006). "Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression". Genome Research. 16 (1): 20–29. doi:10.1101/gr.4139206. PMC   1356125 . PMID   16344563.
  5. 1 2 Jia D, Cai L, He H, Skogerbø G, Li T, Aftab N, Chen R (September 2007). "Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans". BMC Molecular Biology. 8: 86. doi:10.1186/1471-2199-8-86. PMC   2200864 . PMID   17903271.
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