What this resource is about?
Ribosomal proteins are invariant components of every living species with known genome sequence1. And yet structure of these universally abundant proteins is astonishingly distinct in different species2. In many organisms, including human pathogens and microorganisms used in biotechnology, ribosomal proteins carry unique structural features – such as additional domains, extended loops, and elongated N- or C-termini3. A growing evidence suggests that these species-specific protein segments mediate species-specific strategies of protein synthesis and ribosome biogenesis4-7. However, we only begin to uncover this barely explored aspect of protein synthesis.
With this database, we systematize our knowledge about unique structural features of homologous ribosomal proteins in four major taxonomic groups: bacteria, archaea, eukaryoteis and eukaryotic plastids. We also compare and contrast structure of homologous ribosomal proteins between ~30 most common model organisms, including pathogenic microorganisms and parasitic cells with minimal bacterial (Mycoplasma) and eukaryotic (Microsporidia) genomes. Providing this accurate description of the unique structural segments in ribosomal proteins we are striving to go ahead and explore biology underlying structural innovations in ribosomal proteins.
Why it is important? Biomedical Angle
Ribosomal proteins carry two essential functions that make them indispensable for a living cell: during ribosome biogenesis, they govern ribosomal RNA folding into a functional rybozime8, and once the ribosome is assembled, they mediate ribosome interactions with translation factors9. It is therefore not surprising that structural differences between homologous ribosomal proteins are used to enable unique strategies of protein synthesis or ribosome biogenesis in different species. However, although the physiological function of structural diversity of homologous ribosomal proteins is being gradually revealed, most species-specific features of ribosomal proteins still remain uncharacterized.
Numerous studies have illustrated that species-specific features of ribosomal proteins povide a precious understanding of functional specialization of translation apparatus across species10-15. Because ribosome activity and ribosome biogenesis are both targeted by drugs16-20, understanding species-specific features in ribosomal proteins may help develop species-specific drugs.
Why it is important? Synthetic Biology Angle
There are very few universally abundant proteins in nature. Comparative analysis of genomes shows that only ~60 protein-coding genes are present in every sequenced genome without exceptions: core subunits of DNA and RNA polymerases, 15 aminoacyl-tRNA synthetases, ~2 factors of tRNA biogenesis and ~30 ribosomal proteins are the only invariant protein components of a living cell1. These proteins remain in focus of synthetic biology projects aimed to create a minimal cell and an artificial microorganism21-24. Therefore, understanding of the extent to which essential cellular proteins can be reduced without loss of function may facilitate constructing a minimal living cell with synthetic genome.