MOLECULAR EVOLUTION OF SRP CYCLE COMPONENTS - FUNCTIONAL IMPLICATIONS

Signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein t hat targets a subset of nascent presecretory proteins to the endoplasm ic reticulum membrane. We have considered the SRP cycle from the persp ective of molecular evolution, using recently determined sequences of genes or cDNAs encoding homologs of SRP (7SL) RNA, the Srp54 protein ( Srp54p), and the alpha subunit of the SRP receptor (SR alpha) from a b road spectrum of organisms, together with the remaining five polypepti des of mammalian SRP. Our analysis provides insight into the significa nce of structural variation in SRP RNA and identifies novel conserved motifs in protein components of this pathway. The lack of congruence b etween an established phylogenetic tree and size variation in 7SL homo logs implies the occurrence of several independent events that elimina ted more than half the sequence content of this RNA during bacterial e volution. The apparently non-essential structures are domain I, a tRNA -like element that is constant in archaea, varies in size among eucary otes, and is generally missing in bacteria, and domain III, a tightly base-paired hairpin that is present in all eucaryotic and archeal SRP RNAs but is invariably absent in bacteria. Based on both structural an d functional considerations, we propose that the conserved core of SRP consists minimally of the 54 kDa signal sequence-binding protein comp lexed with the loosely base-paired domain IV helix of SRP RNA, and is also likely to contain a homolog of the Srp68 protein. Comparative seq uence analysis of the methionine-rich M domains from a diverse array o f Srp54p homologs reveals an extended region of amino acid identity th at resembles a recently identified RNA recognition motif. Multiple seq uence alignment of the G domains of Srp54p and SR alpha homologs indic ates that these two polypeptides exhibit significant similarity even o utside the four GTPase consensus motifs, including a block of nine con tiguous amino acids in a location analogous to the binding site of the guanine nucleotide dissociation stimulator (GDS) for E.coli EF-Tu. Th e conservation of this sequence, in combination with the results of ea rlier genetic and biochemical studies of the SRP cycle, leads us to hy pothesize that a component of the Srp68/72p heterodimer serves as the GDS for both Srp54p and SR alpha. Using an iterative alignment procedu re, we demonstrate similarity between Srp68p and sequence motifs conse rved among GDS proteins for small Ras-related GTPases. The conservatio n of SRP cycle components in organisms from all three major branches o f the phylogenetic tree suggests that this pathway for protein export is of ancient evolutionary origin.