Signal recognition particle RNA



The signal recognition particle RNA, also known as 7SL, 6S, ffs, or 4.5S RNA, is the is_associated_with::RNA component of the is_associated_with::signal recognition particle (SRP) is_associated_with::ribonucleoprotein complex. SRP is a universally conserved is_associated_with::ribonucleoprotein that directs the traffic of is_associated_with::proteins within the cell and allows them to be is_associated_with::secreted. The SRP RNA, together with one or more SRP is_associated_with::proteins contributes to the binding and release of the is_associated_with::signal peptide. The RNA and protein components of this complex are highly conserved but do vary between the different kingdoms of life.

The common is_associated_with::SINE family Alu probably originated from a 7SL RNA gene after deletion of a central sequence.

The is_associated_with::eukaryotic SRP consists of a 300-nucleotide 7S is_associated_with::RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. Eukaryotic and archaeal 7S RNAs have very similar secondary structures.

In most is_associated_with::bacteria, the SRP consists of an RNA molecule (4.5S) and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Some is_associated_with::Gram-positive bacteria (e.g. is_associated_with::Bacillus subtilis) have a longer eukaryote-like SRP RNA that includes an is_associated_with::Alu domain.

In eukaryotes and archaea, eight helical elements fold into the Alu and S domains, separated by a long linker region. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54 M domain mediates signal sequence recognition. The SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilises helix 8 for SRP54. binding The human genome in particular is known to contain a large amount of SRP RNA related sequence, including Alu repeats.

Discovery
SRP RNA was first detected in avian and murine is_associated_with::oncogenic is_associated_with::RNA (ocorna) is_associated_with::virus particles. Subsequently, SRP RNA was found to be a stable component of uninfected HeLa cells where it associated with membrane and is_associated_with::polysome fractions. In 1980, cell biologists purified from canine is_associated_with::pancreas an 11S "signal recognition protein" (fortuitously also abbreviated "SRP") which promoted the translocation of secretory proteins across the membrane of the is_associated_with::endoplasmic reticulum. It was then discovered that SRP contained an is_associated_with::RNA component. Comparing the SRP RNA is_associated_with::genes from different is_associated_with::species revealed helix 8 of the SRP RNA to be highly conserved in all domains of is_associated_with::life. The regions near the 5'- and 3'-ends of the is_associated_with::mammalian SRP RNA are similar to the dominant Alu family of middle repetitive sequences of the is_associated_with::human genome. It is now understood that Alu is_associated_with::DNA originated from SRP RNA by excision of the central SRP RNA-specific (S) fragment, followed by is_associated_with::reverse transcription and integration into multiple sites of the human is_associated_with::chromosomes. SRP RNAs have been identified also in some is_associated_with::organelles, for example in the is_associated_with::plastid SRPs of many photosynthetic organisms.

Transcription and processing
Eukaryotic SRP RNAs are transcribed from is_associated_with::DNA by is_associated_with::RNA polymerase III (Pol III). RNA polymerase III also transcribes the is_associated_with::genes for 5S is_associated_with::ribosomal RNA, is_associated_with::tRNA, is_associated_with::7SK RNA, and is_associated_with::U6 spliceosomal RNA. The promoters of the human SRP RNA genes include elements located downstream of the transcriptional start site. Plant SRP RNA promoters contain an is_associated_with::upstream stimulatory element (USE) and a is_associated_with::TATA box. is_associated_with::Yeast SRP RNA genes have a is_associated_with::TATA box and additional intragenic promoter sequences (referred to as A- and B-blocks) which play a role in regulating transcription of the SRP gene by Pol III. In the is_associated_with::bacteria, is_associated_with::genes are organized in is_associated_with::operons and transcribed by is_associated_with::RNA polymerase. The 5'-end of the small (4.5S) SRP RNA of many bacteria is cleaved by is_associated_with::RNase P. The ends of the is_associated_with::Bacillus subtilis SRP RNA are processed by is_associated_with::RNase III. So far, no SRP RNA is_associated_with::introns have been observed.

Co-translational translocation
The SRP RNA is an integral part of the small and the large domain of the SRP. The function of the small domain is to delay protein translation until the ribosome-bound SRP has an opportunity to associate with the membrane-resident is_associated_with::SRP receptor (SR). Within the large domain, the SRP RNA of the signal peptide-charged SRP promotes the hydrolysis of two is_associated_with::guanosine triphosphate (GTP) molecules. This reaction releases the SRP from the SRP receptor and the is_associated_with::ribosome, allowing translation to continue and the is_associated_with::protein to enter the is_associated_with::translocon. The protein transverses the membrane co-translationally (during translation) and enters into another cellular compartment or the extracellular space. In is_associated_with::eukaryotes, the target is the membrane of the is_associated_with::endoplasmic reticulum (ER). In is_associated_with::Archaea, SRP delivers proteins to the is_associated_with::plasma membrane. In the is_associated_with::bacteria, SRP primarily incorporates proteins into the inner membrane.

Post-translational transport
SRP participates also in the sorting of is_associated_with::proteins after their synthesis has been completed (post-translational protein sorting). In is_associated_with::eukaryotes, tail-anchored proteins possessing a is_associated_with::hydrophobic insertion sequence at their C-terminus are delivered to the is_associated_with::endoplasmic reticulum (ER) by the SRP. Similarly, the SRP assists post-translationally in the import of nuclear-encoded proteins to the is_associated_with::thylakoid membrane of is_associated_with::chloroplasts.

Structure


In 2005, a is_associated_with::nomenclature for all SRP RNAs proposed a numbering system of 12 helices. Helix sections are named with a lower case letter is_associated_with::suffix (e.g. 5a). Insertions, or helix "branches" are given dotted numbers (e.g. 9.1 and 12.1).

The SRP RNA spans a wide is_associated_with::phylogenetic spectrum with respect to size and the number of its structural features (see the SRP RNA Secondary Structure Examples, below). The smallest functional SRP RNAs have been found in is_associated_with::mycoplasma and related species. is_associated_with::Escherichia coli SRP RNA (also called 4.5S RNA) is composed of 114 is_associated_with::nucleotide residues and forms an RNA is_associated_with::stem-loop. The is_associated_with::gram-positive bacterium is_associated_with::Bacillus subtilis encodes a larger 6S SRP RNA which resemble the is_associated_with::Archaeal is_associated_with::homologs but lacks SRP RNA helix 6. is_associated_with::Archaeal SRP RNAs possess helices 1 to 8, lack helix 7, and are characterized by a is_associated_with::tertiary structure which involves the apical loops of helix 3 and helix 4. The is_associated_with::eukaryotic SRP RNAs lack helix 1 and contain a helix 7 of variable size. Some is_associated_with::protozoan SRP RNAs have reduced helices 3 and 4. The is_associated_with::ascomycota SRP RNAs have an altogether reduced small domain and lack helices 3 and 4. The largest SRP RNAs known to date are found in the is_associated_with::yeasts (is_associated_with::Saccharomycetes) which acquired helices 9 to 12 as insertions into helix 5, as well as an extended helix 7. Seed is_associated_with::plants express numerous highly divergent SRP RNAs.

Motifs
Four conserved features (motifs) have been identified (shown in the Figure in dark gray): the (1) SRP54 binding motif, (2) Helix 6 GNAR tetraloop motif, (3) 5e motif, and (4) UGU(NR) motif.

SRP54 binding
The asymmetric loop between helical sections 8a and 8b and the adjacent base paired 8b section are a prominent property of every SRP RNA. Helical section 8b contains non-is_associated_with::Watson-Crick base pairings which contribute to the formation of a flatted is_associated_with::minor groove in the RNA suitable for the binding of is_associated_with::protein SRP54 (called Ffh in the bacteria). The apical loop of helix 8 contains four, five, or six residues, depending on the is_associated_with::species. It has a highly conserved is_associated_with::guanosine as the first and an is_associated_with::adenosine as the last loop residue. This feature is required for the interaction with the third is_associated_with::adenosine residue of the helix 6 GNAR tetraloop motif.

Helix 6 GNAR tetraloop
The SRP RNAs of is_associated_with::eukaryotes and is_associated_with::Archaea have a GNAR tetraloop (N is for any is_associated_with::nucleotide, R is for a is_associated_with::purine) in helix 6. Its conserved is_associated_with::adenosine residue is important for the binding of is_associated_with::protein SRP19. This is_associated_with::adenosine makes a tertiary interaction with another is_associated_with::adenosine residue located in the apical loop of helix 8.

5e
The 11 nucleotides of the 5e motif form four is_associated_with::base pairs which are interrupted by a loop of three is_associated_with::nucleotides. In the is_associated_with::eukaryotes, the first nucleotide of the loop is an is_associated_with::adenosine which is needed for the binding of is_associated_with::protein SRP72.

UGU(NR)
The UGU(NR) motif connects helices 3 and 4 in the small (Alu) SRP domain. is_associated_with::Fungal SRP RNAs lacking helices 3 and 4 contain the motif within the loop of helix 2. It is important in the binding of the SRP9/14 is_associated_with::protein is_associated_with::heterodimer as part of an is_associated_with::RNA is_associated_with::U-turn.

Tertiary
is_associated_with::X-ray crystallography, is_associated_with::nuclear magnetic resonance (NMR), and is_associated_with::cryo-electron microscopy (cryo-EM] have been used to determine the is_associated_with::molecular structure of portions of the SRP RNAs from various is_associated_with::species. The available PDB structures show the RNA molecule either free or when bound to one or more SRP is_associated_with::proteins.

Binding proteins
One or more SRP is_associated_with::proteins bind to the SRP is_associated_with::RNA to assemble the functional SRP. The SRP proteins are named according to their approximate is_associated_with::molecular mass measured in is_associated_with::kilodalton. Most is_associated_with::bacterial SRPs are composed of SRP RNA and SRP54 (also named Ffh for "Fifty-four homolog"). The is_associated_with::Archaeal SRP contains proteins SRP54 and SRP19. In is_associated_with::eukaryotes, the SRP RNA combines with the imported SRP proteins SRP9/14, SRP19, and SRP68/72 in a region of the is_associated_with::nucleolus. This pre-SRP is transported to the is_associated_with::cytosol where it binds to protein SRP54. The is_associated_with::molecular structures of the free or SRP RNA-bound is_associated_with::proteins SRP9/14, SRP19, or SRP54 are known at high resolution.

SRP9 and SRP14
SRP9 and SRP14 are is_associated_with::structurally related and form the SRP9/14 is_associated_with::heterodimer which binds to the SRP RNA of the small (Alu) domain. is_associated_with::Yeast SRP lacks SRP9 and contains the is_associated_with::structurally related protein SRP21. is_associated_with::Yeast SRP14 forms a is_associated_with::homodimer. SRP9/14 is absent in the SRP of is_associated_with::trypanosoma which instead possess a is_associated_with::tRNA-like molecule.

SRP19
SRP19 is found in the SRP of is_associated_with::eukaryotes and is_associated_with::Archaea. Its primary role is in preparing the SRP RNA for the binding of SRP54, SRP68, and SRP72 by properly arranging SRP RNA helices 6 and 8. is_associated_with::Yeast SRP contains Sec65p, a larger is_associated_with::homolog of SRP19.

SRP54
Protein SRP54 (named Ffh in the is_associated_with::bacteria) is an essential component of every SRP. It is composed of three functional domains: the N-terminal (N) domain, the is_associated_with::GTPase (G) domain, and the is_associated_with::methionine-rich (M) domain.

SRP68 and SRP72
Proteins SRP68 and SRP72 are constituents of the large domain of the is_associated_with::eukaryotic SRP. They form a stable SRP68/72 heterodimer. About one third of the human SRP68 protein was shown to bind to the SRP RNA. A relatively small region located near the C-terminus of SRP72 binds to the 5e SRP RNA motif.