Nomenclature of Ribosomal Proteins

Consistent with UniProt and the PDB

To consolidate the naming of the > 56,000 ribosomal protein entries in the external page UniProt database, the updated naming system is now implemented by UniProt and linked to the Protein Data Bank (external page PDB).

Currently, we suggest only one notable change to the originally proposed naming system: As protein eL41 is always found associated with the small ribosomal subunit (SSU) in archaeal and eukaryotic ribosome structures and is only present in a few fungi at the secondary binding side in the periphery of the large subunit (LSU), we propose to rename eL41 to eS32 to correctly account for its ribosomal location and evolutionary origin (see Table 3, Figure 4 and Figure 5 and accompanying text below).

Updated Nomenclature for Plant Ribosomal Proteins

Since the original proposal of the evolutionary-based naming system, the new names of ribosomal proteins have been widely adopted. However, for plant biologists the naming system turned out to be less useful due to the existence of multiple paralogous copies of ribosomal genes in plants, which require a specific indication of the gene locus. For this reason, external page Lan et al. (2022) and external page Scarpin et al. (2023) proposed a plant-specific extension of the naming system, and the plant community generally agreed to follow the nomenclature suggested by Scarpin et al. (2023). The new convention is also in accordance with public databases such as The Arabidopis Information Resource (external page TAIR), external page MaizeGDB and the external page Plant Cytoplasmic Ribosomal Proteins Database.

UniProt adopted this nomenclature with a minor change: In the UniProt database, no upper-case C or M is given in the suffix to specify organelle-encoded proteins as in Scarpin et al. (2023), because this would be inconsistent with the nomenclature of ribosomal proteins from non-plant sources and is a species-dependent trait. Note that until the new plant ribosomal protein nomenclature is well-established in the field, previous common ribosomal protein names should be additionally indicated in parentheses, and unique gene locus IDs should also be included.

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

Download Download high a resolution PDF file of all tables (PDF, 481 KB)

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 page Waltz et al., 2020). 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 page Dresios et al. 2003) was named based on its copurification with the LSU of baker’s yeast (Saccharomyces cerevisiae) (external page Otaka & Osawa, 1981 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 page Kisly and Tamm 2023), 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 to 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 page Hentschel et al. 2017, external page Jha et al. 2021, and external page Sharma et al. 2023). However, although the binding to the rRNA is also mediated by numerous positively charged residues and on the sequence level mS38 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.  

PyMOL Scripts and Sessions

We provide a number of scripts and sessions for "external page The PyMOL Molecular Graphics System" for ribosomes from different organisms. The updated nomenclature is implemented through the use of both the old and new ribosomal protein names.

The X-ray structure of the yeast cytosolic ribosome (PDB ID external page 4V88, large subunit B in the asymmetric unit, external page Ben-Shem et al. 2011) served as template to which all other structures were aligned in order to allow direct comparison of the proteins from different species.

How do I use the PyMOL scripts?

1. Download and install a current version of external page PyMOL (2.2.5 or higher).
2. Download the PyMOL session as a .zip file and unzip it
3. Double-click the file or open it from within PyMOL (File>Open...)
4. Alternatively, you can use the provided script files by copying the text into the command line of the PyMOL GUI. Please find further instructions in the header of each script.