Nomenclature of Ribosomal Proteins

Information about the Conversion Tables

• Proteins are colored based on their taxonomic range (cyan: universal, purple: bacterial, orange: archaeal/eukaryotic, red: eukaryotic, yellow: mitochondrial, and green: chloroplast).
• Abbreviations for the occurrence: A: Archaea, B: Bacteria, E: Eukaryotes, m: Mitochondria, c: Chloroplasts.
• Last update: April 2024

DownloadDownload high a resolution PDF file of all tables (PDF, 608 KB)vertical_align_bottom

Homologues or not?

Due to the evolutionary diversity of mitoribosomes and the lack of structural, biochemical and genetic information for many of them, the assignment of novel proteins is still ongoing. Exceptions are mammalian, yeast and plant mitoribosomes, the latter only being available since recently (external pageWaltz et al., 2020call_made). While most mammalian, yeast and plant mitoribosome-specific proteins can be unambiguously named based on both structural and sequence homology, for some the evolutionary relationship still remains unclear (Figure 3). For these, although some α helices colocalize in the structures after superposition, no obvious sequence homology can be detected. As UniProt relies on sequence homology to determine the evolutionary relationship of proteins, it was decided to attribute these with different names.

Renaming of eL41 to eS32

Historically, the non-essential ~25 amino acid eL41 peptide (external pageDresios et al. 2003call_made) was named based on its copurification with the LSU of baker’s yeast (Saccharomyces cerevisiae) (external pageOtaka & Osawa, 1981call_made and references therein). However, based on recent structural evidence (Table 3), it became clear that in those eukaryotic and archaeal species where the L41 gene is present in the genome, eL41 is always associated with the SSU at the subunit interface behind the functionally important rRNA helix h44, while its contact with the LSU at this position is only minor (external pageKisly and Tamm 2023call_made), rationalizing it’s renaming to eS32 (Table 3, Figure 4). Furthermore, in archaea and some protists, eS32 carries an N-terminal extension that proceeds further into the SSU rRNA and may serve as an additional hook or anchor (Table 3, Figure 4C).

Only in a few fungal species, including baker’s yeast, a second eS32 peptide can be found in some EM maps at a non-canonical rRNA binding pocket at the periphery of the LSU (Kisonaite et al. 2023, Table 3, Figure 5A & 5B). In structurally well-characterized ribosomes of all other eukaryotes, the corresponding rRNA area is occluded or adopts a different shape, and in archaea is even entirely absent (Figure 5C).

From these observations, it is plausible to assume that eS32 is a SSU protein of archaeal phylogenetic origin, and that its recruitment to the LSU of some fungi was a secondary event. The density for eS32 in EM or X-ray maps is typically also weaker compared to the areas in the vicinity, which indicates a sub-stoichiometric binding and that it could easily dissociate during purification depending on chosen buffer conditions.

In summary, eukaryotic ribosomal proteins were first assigned in ribosomal subunits of baker’s yeast (Otaka & Osaka, 1981 and references therein), which regarding the presence of eS32 in the LSU is rather the exception than the rule. Likely, eS32 was overseen as a component of the SSU for a long time either because it was lost from the subunit during purification or due its small size and highly basic nature (pI=13), both of which could lead to issues for detection depending on the experimental setup. Only with the resolution revolution in cryo-EM, which allows structure determination of ribosomes from numerous species under more physiological conditions, and recently even in situ (Xing et al. 2023), it became apparent that eL41 is actually a component of the small ribosomal subunit, reasoning its renaming to eS32.

eS32, bS22 or mS38?

Apart from eS32 found at the highly conserved canonical binding site at the cytosolic SSU, small helical proteins located behind helix h44 of the SSU were also detected in mammalian and fungal mitoribosomes (named mS38, Table 1a) and in Actinobacteria and Bacteroidetes (named bS22 in external pageHentschel et al. 2017call_made, external pageJha et al. 2021call_made, and external pageSharma et al. 2023call_made). However, although the binding to the rRNA is also mediated by numerous positively charged residues and on the sequence level mS30 and bS22 are distantly related, they do not share obvious homology with eS32 and are positioned differently in the SSU (Hentschel et al. 2017). Therefore, a common evolutionary origin of these helical peptide proteins remains unclear and their names are kept separate.