Signal recognition particle RNA

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

Some Gram-positive bacteria (e.g. Bacillus subtilis) have a longer eukaryote-like SRP RNA that includes an Alu domain.

[5] In eukaryotes and archaea, eight helical elements fold into the Alu and S domains, separated by a long linker region.

[6][7] The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP.

The human genome in particular is known to contain a large amount of SRP RNA related sequence, including Alu repeats.

[9] Subsequently, SRP RNA was found to be a stable component of uninfected HeLa cells where it associated with membrane and polysome fractions.

[14] The regions near the 5′- and 3′-ends of the mammalian SRP RNA are similar to the dominant Alu family of middle repetitive sequences of the human genome.

[3] SRP RNAs have been identified also in some organelles, for example in the plastid SRPs of many photosynthetic organisms,[16] and in the nuclear ribosomal internal transcribed spacer region of several ectomycorrhizal fungi.

The promoters of the human SRP RNA genes include elements located downstream of the transcriptional start site.

Plant SRP RNA promoters contain an upstream stimulatory element (USE) and a TATA box.

[citation needed] Yeast SRP RNA genes have a 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.

[21] The protein transverses the membrane co-translationally (during translation) and enters into another cellular compartment or the extracellular space.

In eukaryotes, tail-anchored proteins possessing a hydrophobic insertion sequence at their C-terminus are delivered to the endoplasmic reticulum (ER) by the SRP.

[24] Similarly, the SRP assists post-translationally in the import of nuclear-encoded proteins to the thylakoid membrane of chloroplasts.

Helical section 8b contains non-Watson–Crick base pairings which contribute to the formation of a flatted minor groove in the RNA suitable for the binding of protein SRP54 (called Ffh in the bacteria).

[30] X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy (cryo-EM] have been used to determine the molecular structure of portions of the SRP RNAs from various species.

The available PDB structures show the RNA molecule either free or when bound to one or more SRP proteins.

[32] Most bacterial SRPs are composed of SRP RNA and SRP54 (also named Ffh for "Fifty-four homolog").

SRP9 and SRP14 are structurally related and form the SRP9/14 heterodimer which binds to the SRP RNA of the small (Alu) domain.

Secondary structure of the human SRP RNA. Helices are numbered from 2 to 8. Helical sections in gray are named with lower case letters. Residues are numbered in increments of ten. The 5′- and 3′-ends are indicated. Highlighted are the two hinges and the small (Alu) and large (S, "specific") domain of the SRP RNA.
The classical function of SRP in translation-translocation. A membrane separates the cytosol from the endoplasmic reticulum . A ribosome (light gray with A, P, and E sites) synthesizes a protein with a signal peptide (green) encoded by messenger RNA (indicated by a line with 5′- and 3′-ends). The elongated SRP (blue), with its large (LD) and small (SD) domains, forms a complex with the membrane-resident SRP receptor (SR). When SRP separates, the protein crosses the membrane through a channel or translocon . The signal peptide may be removed by signal peptide peptidase (SP) and the protein modified by oligosaccharyl transferase (OT).
SRP RNA features and nomenclature. The human SRP RNA secondary structure is outlined in light gray, and the 5′- and 3′-ends are indicated. Conserved motifs are shown in dark gray. Helices are numbered from 1 to 12, helical sections are designated by lower case letters, and helix insertions by dotted numbers. Tertiary interactions between the apical loops of helices 3 and 4, and between helices 6 and 8 are indicated dotted lines.