Archaea signal recognition particle shows the way

Abstract

Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only with the hydrophobic signal sequence as it emerges from the ribosomal exit tunnel, but also interacts with the membrane-associated SRP receptor (FtsY). Comparative analyses of the archaea genomes and their SRP component sequences, combined with structural and biochemical data, support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an archaea SRP72 homolog. The primary function of the 5e region may be to serve as a hinge, strategically positioned between the small and large SRP domain, allowing the elongated SRP to bind simultaneously to distant ribosomal sites. SRP19, required in eukaryotes for initiating SRP assembly, appears to play a subordinate role in the archaea SRP or may be defunct. The N-terminal A region and a novel C-terminal R region of the archaea SRP receptor (FtsY) are strikingly diverse or absent even among the members of a taxonomic subgroup.

Figure 1

Hypothetical steps in the SRP-mediated targeting of archaea proteins. Step 1: A ribosome (gray, with A, P and E tRNA binding sites) in the cytoplasm translates a mRNA molecule (black, 5′ and 3′ ends are indicated) which encodes a N-terminal signal or membrane-anchor sequence (black dots). Step 2: As the signal emerges from the large ribosomal subunit, it is recognized by the elongated SRP and further translation may be halted. Step 3: The SRP-bound ribosome nascent chain complex (RNC) binds to free or membrane-associated FtsY (arrow). Step 4: After GTP hydrolysis, SRP has been released, translation resumes, and the targeted protein is threaded through the protein-conducting channel (PCC). The surface (S) layer, present in most archaea, is anchored to a glycerol-ether lipids-containing cell membrane.

Figure 2

Archaea SRP RNA features. (a) Secondary structure of Archaeoglobus fulgidus SRP RNA. (b) Consensus-matching 5e motifs sorted by their taxonomic membership. (c) Mismatching 5e motifs. Helices are numbered from 1 to 8 and helical sections are labeled with letters a to f [33]. For example, helix 1 is composed of residues one to seven which are base paired with residues 303 to 310; helix 2 consists of residues at positions ten to 13 base paired with the residues at positions 59 to 62. The extended helix 5 contains six helical sections, 5a to 5f. Helix 7 is lacking in the SRP RNAs of the archaea. The 5′- and 3′-ends are shown, and residues are labeled in ten-residue increments. Base pairs were determined by comparative sequence analysis [32] and by considering high-resolution data (Table 1). The approximate extents of the large (S) and the small (Alu) domains are indicated. Shown in dark gray are the UGUNR motif (labeled UGU) in the small domain, the 5e motif within helical section 5e at the indicated hinge [34], the GNAR apical tetraloop of helix 6 and the SRP54 binding motif of helix 8 in the large domain. Dashed lines suggest tertiary interactions.

Figure 3

Features of SRP19 (top), SRP54 (center) and the FtsY SRP receptor (bottom). Indicated are the N- and C-termini. Helices are shown as cylinders, beta-sheets as arrows, and some loops are labeled with an arch and the letter L. Invariant or highly conserved residues are shown boxed, and several amino acid residue inserts which are characteristic for the indicated taxonomic groups are shown as bold letters. Numbering is according to the column positions of each protein alignment accessible as listed in Supplementary Materials 2 and at the SRP database at http://rnp.uthct.edu/rnp/SRPDB/SRPDB.html). Regions and sites which interact with other SRP components or the signal sequence are marked with brackets below each panel.

Figure 4

Interactions between the components of archaea SRP-mediated protein targeting. Schematic drawing of the coaxially-arranged SRP RNA helices 6 and 8 bound together by SRP19 and two tertiary interactions (dashed lines). The M-domain of the SRP54 protein (dark gray) binds to SRP RNA helix 8 as well as the signal sequence (black). The NG-domains of SRP54 and the FtsY SRP receptor are arranged quasisymmetrically and poised to separate upon the hydrolysis of two G-domain-bound GTP molecules. The N-terminal region labeled A (for acidic) and the C-terminal repeat region (R) of FtsY are variable or may be absent (see Table 2).