Computational identification of RNA and protein components from the Signal Recognition Particle

Abstract

Problem. The signal recognition particle (SRP) is a ribonucleoprotein particle that targets proteins to the endoplasmic reticulum in eukaryotes, to the plasma membrane in Archaea and Bacteria and to the thylakoid membrane in chloroplasts of photosynthetic organisms. It has one RNA component and 1 6 proteins. The eukaryotic particle is composed of one S domain responsible for signal recognition and one Alu domain responsible for translation elongation arrest. In many phylogenetic groups the SRP is not characterized. Therefore, we aim to identify SRP component genes by computational screening of a large number of organisms where genomic information is available. Methods. For the protein gene identification, we relied on methods based on primary sequence alignments (BLAST, FASTA), profile searches (PSI-BLAST, HMMER, Profilescan), and secondary structure prediction (PSI-Pred). The main focus in this work is the identification of SRP RNA. It is highly diverse in its structure and has a low primary sequence conservation between different phylogenetic groups. As a consequence, standard sequence analysis tools, such as BLAST, are not useful. We have developed a tool for the identification of SRP RNA (SRPscan) using algorithms for pattern matching and covariance analysis of secondary structures.Results. We have carried out an extensive inventory of SRP components by screening available genomic sequences. As a result we have identified a large number of novel genes. The protein and RNA sequences are presented in the SRP database (SRPDB). We have identified full or partial SRP RNA genes in virtually all organisms where genomic sequences of nearly full genome coverage are available, and the findings have led to a proposal of a new nomenclature for SRP RNA.In an analysis of bacterial RNAs we found species with an unusual URRC tetraloop and we identified an RNA from deeply branching gram-negative bacterium Thermotoga that is of the gram-positive Bacillus type. It was previously believed that chloroplasts do not have an SRP RNA. However, we have shown that chloroplast genomes of red algae or red algal origin, as well as some green algae, encode a bacterial type SRP RNA.Eukaryotic SRP RNAs are highly divergent in their structures, mainly in the Alu domain. Based on an analysis of fungal RNAs we were able to present a novel secondary structure model of these RNAs. Analysis of eukaryotic RNAs includes a number of unexpected findings. In the fungal groups Basidiomycota and Zygomycota the SRP RNA has an Alu domain that conforms to the standard mammalian SRP RNA structure. The external loop of helix 8 is a tetraloop as a rule, but in several protists this sequence is a pentaloop. Finally, we suggest that some eukaryal species like Microsporidia might lack an SRP Alu domain.Conclusion. By computational screening of genomic sequences we have identified a large number of novel SRP RNA and proteins components. The results of these studies provide significant insights into the structure, function and phylogeny of the SRP.