SmY ribonucleic acids (SmY RNAs) are a family of small nuclear RNAs found in some species of

nematode The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant-Parasitism, parasitic nematodes also known as eelworms. They are a diverse animal phylum inhab ...

worms. They are thought to be involved in

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

trans-splicing ''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 ...

. SmY RNAs are about 70–90

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

s long and share a common

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

, with two

stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when ...

s flanking a consensus binding site for

Sm protein In molecular biology, LSm proteins are a family of RNA-binding proteins found in virtually every cellular organism. LSm is a contraction of 'like Sm', because the first identified members of the LSm protein family were the Sm proteins. LSm pro ...

. Sm protein is a shared component of spliceosomal

snRNP snRNPs (pronounced "snurps"), 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- ...

SmY RNAs have been found in nematodes of class

Chromadorea The Chromadorea are a class of the roundworm phylum, Nematoda. They contain a single subclass (Chromadoria) and several orders. With such a redundant arrangement, the Chromadoria are liable to be divided if the orders are found to form several c ...

, which includes the most commonly studied nematodes (such as '' Caenorhabditis'', ''

Pristionchus ''Pristionchus'' is a genus of nematodes (roundworms) in the family Diplogastridae that currently includes more than 50 described species. They are known mainly as non-parasitic associates of insects, especially beetles, while others have been r ...

'', and ''

Ascaris ''Ascaris'' is a genus of parasite, parasitic nematode worms known as the "small intestinal roundworms", which is a type of parasitic worm. One species, ''Ascaris lumbricoides'', affects humans and causes the disease ascariasis. Another species ...

''), but not in the more distantly related '' Trichinella spiralis'' in class

Dorylaimia Dorylaimia is a subclass of nematodes. Description In general, members of subclass Dorylaimia exhibit a great diversity of terrestrial and freshwater species, most of which are large predators or omnivorous free-living species. Some are plant ...

. The number of SmY genes in each species varies, with most ''Caenorhabditis'' and ''Pristionchus'' species having 10–26 related

paralogous Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...

copies, while other nematodes have 1–5.

Discovery

The first SmY RNA was discovered in 1996 in purified ''

Ascaris lumbricoides ''Ascaris lumbricoides'' is a large parasitic worm that causes ascariasis in humans. A Nematoda, roundworm of genus ''Ascaris'', it is the most common parasitic worm in humans. An estimated one-sixth of the human population is at some point infe ...

spliceosome 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. Small nuclear RNA (snRNA) molecules bind to specifi ...

preparations, as was another called

SmX RNA SMX may refer to: As an abbreviation: * SMX (operating system), a Unix-like simulator on SPARC, the "SunOS/Solaris MINIX" * Standard Musical Expression, a representation of simple music in ASCII that was used in some DOS software such as QBasic ...

that is not detectably homologous to SmY. Twelve SmY homologs were identified computationally in ''

Caenorhabditis elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (ro ...

'', and ten in '' Caenorhabditis briggsae''. Several transcripts from these SmY

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s were

cloned Cloning is the process of producing individual organisms with identical or virtually identical DNA, either by natural or artificial means. In nature, some organisms produce clones through asexual reproduction. In the field of biotechnology, c ...

and sequenced in a systematic survey of small non-coding RNA transcripts in ''C. elegans''. A systematic survey of 2,2,7-trimethylguanosine (TMG)

5′ cap In molecular biology, the five-prime cap (5′ cap) is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is highly regulated and vital in the creation o ...

ped transcripts in ''C.elegans'' using anti TMG

antibodies An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...

identified two TMG capped SmY transcripts. 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.

Function

In ''

C. elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (r ...

'', SmY RNAs copurify with

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). Loss of function of either SL21p or SL26p individually causes only a weak cold-sensitive

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...

, 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.

References

External links

* {{Rfam, id=RF01844, name=SmY spliceosomal RNA Non-coding RNA Small nuclear RNA RNA splicing Nematode nucleic acids