Ribosomal protein nomeclature
by Gary Olsen
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign
Historically, ribosomal proteins were identified in several important experimental organisms, including E. coli, Bacillus species, yeast, rat and Halobacterium. In each case, a unique nomeclature was developed. Now that the sequences are available and it has become possible to define the correspondences, several groups have sought unified nomenclatures. By and large the most complete efforts, including that of Swiss-Prot, have based prokaryotic names on those of E. coli, and eukaryotic names on those of rat and human. In the cases of Bacteria and Eucarya, these efforts have been hugely successful, and a great service. The most problematic aspects of the conventions were
1. the failure to uniformly indicate whether a given label is based upon the bacterial or the eukaryal numbering, and
2. the linking of equivalent eukaryal and bacterial terms. There are only two proteins (S3 and L3) for which the bacterial and eukaryal numbers are the same. This created a particularly schizophrenic situation when the bacterial nomenclature was applied to Archaea, except when no bacterial homolog existed, in which case the eukaryal label was applied.
While working on archaeal genomes, Nikos Kyrpides and Carl Woese (personal communication) were careful to track both the eukaryal homologs (which are nearly always more similar) and bacterial equivalents. This dual labeling was very attractive, and largely forms the basis for the nomenclature used here. In short, bacterial proteins are given the bacterial label (always explicitly including the "p", for example S5p), followed by the designation of the corresponding eukaryal protein in parentheses (always with the explicit "e", for example S2e). Thus, it is trivial for anyone to think in terms of whichever domain they are most familiar. Similarly, in the case of eukarya, the eukaryal protein designation is given first, followed by the bacterial label in parentheses. In the case of Archaea, in all but a few cases the proteins are clearly of the eukaryal genre, and the eukaryal term is given first.
One of the most important consequences of this nomenclature is that a text based search is always unambiguous as to whether the bacterial or eukaryal numbering is desired (something that is not true of any other convention that we are aware of). For example, a search for L11p will return bacterial L11 and eukaryal L12, but not bacterial L5 (the equivalent of eukaryal L11).
A second key decision was to use the terms LSU and SSU to distinguish the subunits, rather than 30S, 40S, 50S and 60S. In addition to further unifying the nomenclature, it avoids to key sources of confusion. Several eukaryal ribosomes (especially organellar ribosomes) have been assigned to "nonstandard" sizes. Thus, searching for 50S and/or 60S was not sufficient to ensure that all ribosomes were distinguished. But more importantly, it avoids the temptation to use 50S to designate the LSU of a eukaryal mitochondrial ribosomal, and distinguish it . Instead, we have explicitly identified all organellar proteins by "mitochondrial" or "chloroplast".
The mitochondrail nomenclature for proteins that lack clear correspondences in bacteria is a work in progress. First, this is an area with little consensus between organisms. Also it is likely that a few more bacterial homologs will be defined.
The Proposed Role Names
Ribosome SSU Bacterial
SSU ribosomal protein S1p
SSU ribosomal protein S2p (SAe)
SSU ribosomal protein S3p (S3e)
SSU ribosomal protein S4p (S9e)
SSU ribosomal protein S5p (S2e)
SSU ribosomal protein S6p
SSU ribosomal protein S7p (S5e)
SSU ribosomal protein S8p (S15Ae)
SSU ribosomal protein S9p (S16e)
SSU ribosomal protein S10p (S20e)
SSU ribosomal protein S11p (S14e)
SSU ribosomal protein S12p (S23e)
SSU ribosomal protein S13p (S18e)
SSU ribosomal protein S14p (S29e)
SSU ribosomal protein S15p (S13e)
SSU ribosomal protein S16p
SSU ribosomal protein S17p (S11e)
SSU ribosomal protein S18p
SSU ribosomal protein S19p (S15e)
SSU ribosomal protein S20p
SSU ribosomal protein S21p
SSU ribosomal protein S22p
SSU ribosomal protein Thx
Ribosome SSU Eukaryotic and Archaeal
SSU ribosomal protein S2e (S5p)
SSU ribosomal protein S3e (S3p)
SSU ribosomal protein S3Ae
SSU ribosomal protein S4e
SSU ribosomal protein S5e (S7p)
SSU ribosomal protein S6e
SSU ribosomal protein S7e
SSU ribosomal protein S8e
SSU ribosomal protein S9e (S4p)
SSU ribosomal protein S10e
SSU ribosomal protein S11e (S17p)
SSU ribosomal protein S12e
SSU ribosomal protein S13e (S15p)
SSU ribosomal protein S14e (S11p)
SSU ribosomal protein S15e (S19p)
SSU ribosomal protein S15Ae (S8p)
SSU ribosomal protein S16e (S9p)
SSU ribosomal protein S17e
SSU ribosomal protein S18e (S13p)
SSU ribosomal protein S19e
SSU ribosomal protein S20e (S10p)
SSU ribosomal protein S21e
SSU ribosomal protein S23e (S12p)
SSU ribosomal protein S24e
SSU ribosomal protein S25e
SSU ribosomal protein S26e
SSU ribosomal protein S27e
SSU ribosomal protein S27Ae
SSU ribosomal protein S28e
SSU ribosomal protein S29e (S14p)
SSU ribosomal protein S30e
SSU ribosomal protein SAe (S2p)
Ribosome SSU Chloroplast
SSU ribosomal protein S1p, chloroplast
SSU ribosomal protein S2p (SAe), chloroplast
SSU ribosomal protein S3p (S3e), chloroplast
SSU ribosomal protein S4p (S9e), chloroplast
SSU ribosomal protein S5p (S2e), chloroplast
SSU ribosomal protein S6p, chloroplast
SSU ribosomal protein S7p (S5e), chloroplast
SSU ribosomal protein S8p (S15Ae), chloroplast
SSU ribosomal protein S9p (S16e), chloroplast
SSU ribosomal protein S10p (S20e), chloroplast
SSU ribosomal protein S11p (S14e), chloroplast
SSU ribosomal protein S12p (S23e), chloroplast
SSU ribosomal protein S13p (S18e), chloroplast
SSU ribosomal protein S14p (S29e), chloroplast
SSU ribosomal protein S15p (S13e), chloroplast
SSU ribosomal protein S16p, chloroplast
SSU ribosomal protein S17p (S11e), chloroplast
SSU ribosomal protein S18p, chloroplast
SSU ribosomal protein S19p (S15e), chloroplast
SSU ribosomal protein S20p, chloroplast
Ribosome SSU Mitochondrial
SSU ribosomal protein S2p (SAe), mitochondrial
SSU ribosomal protein S3p (S3e), mitochondrial
SSU ribosomal protein S4p (S9e), mitochondrial
SSU ribosomal protein S5p (S2e), mitochondrial
SSU ribosomal protein S6p, mitochondrial
SSU ribosomal protein S7p (S5e), mitochondrial
SSU ribosomal protein S8p (S15Ae), mitochondrial
SSU ribosomal protein S9p (S16e), mitochondrial
SSU ribosomal protein S10p (S20e), mitochondrial
SSU ribosomal protein S11p (S14e), mitochondrial
SSU ribosomal protein S12p (S23e), mitochondrial
SSU ribosomal protein S13p (S18e), mitochondrial
SSU ribosomal protein S14p (S29e), mitochondrial
SSU ribosomal protein S15p (S13e), mitochondrial
SSU ribosomal protein S16p, mitochondrial
SSU ribosomal protein S17p (S11e), mitochondrial
SSU ribosomal protein S18p, mitochondrial
SSU ribosomal protein S19p (S15e), mitochondrial
SSU ribosomal protein S21p, mitochondrial
SSU ribosomal protein S22mt, mitochondrial
SSU ribosomal protein S23mt, mitochondrial
SSU ribosomal protein S24mt, mitochondrial
SSU ribosomal protein S25mt, mitochondrial
SSU ribosomal protein S26mt, mitochondrial
SSU ribosomal protein S27mt, mitochondrial
SSU ribosomal protein S28mt, mitochondrial
SSU ribosomal protein S29mt, mitochondrial
SSU ribosomal protein S30mt, mitochondrial
SSU ribosomal protein S31mt, mitochondrial
SSU ribosomal protein S33mt, mitochondrial
SSU ribosomal protein S34mt, mitochondrial
SSU ribosomal protein S35mt, mitochondrial
Ribosome LSU Bacterial
Functional Roles
LSU ribosomal protein L1p (L10Ae)
LSU ribosomal protein L2p (L8e)
LSU ribosomal protein L3p (L3e)
LSU ribosomal protein L4p (L1e)
LSU ribosomal protein L5p (L11e)
LSU ribosomal protein L6p (L9e)
LSU ribosomal protein L7/L12 (L23e)
LSU ribosomal protein L7Ae
LSU ribosomal protein L9p
LSU ribosomal protein L10p (P0)
LSU ribosomal protein L11p (L12e)
LSU ribosomal protein L13p (L13Ae)
LSU ribosomal protein L14p (L23e)
LSU ribosomal protein L15p (L27Ae)
LSU ribosomal protein L16p (L10e)
LSU ribosomal protein L17p
LSU ribosomal protein L18p (L5e)
LSU ribosomal protein L19p
LSU ribosomal protein L20p
LSU ribosomal protein L21p
LSU ribosomal protein L22p (L17e)
LSU ribosomal protein L23p (L23Ae)
LSU ribosomal protein L24p (L26e)
LSU ribosomal protein L25p
LSU ribosomal protein L27p
LSU ribosomal protein L28p
LSU ribosomal protein L29p (L35e)
LSU ribosomal protein L30p (L7e)
LSU ribosomal protein L31p
LSU ribosomal protein L32p
LSU ribosomal protein L33p
LSU ribosomal protein L34p
LSU ribosomal protein L35p
LSU ribosomal protein L36p
Ribosome LSU Eukaryotic and Archaeal
LSU ribosomal protein L1e (L4p)
LSU ribosomal protein L3e (L3p)
LSU ribosomal protein L5e (L18p)
LSU ribosomal protein L6e
LSU ribosomal protein L7e (L30p)
LSU ribosomal protein L7Ae
LSU ribosomal protein L8e (L2p)
LSU ribosomal protein L9e (L6p)
LSU ribosomal protein L10e (L16p)
LSU ribosomal protein L10Ae (L1p)
LSU ribosomal protein L11e (L5p)
LSU ribosomal protein L12e (L11p)
LSU ribosomal protein L11p (L12e)
LSU ribosomal protein L13e
LSU ribosomal protein L13Ae (L13p)
LSU ribosomal protein L14e
LSU ribosomal protein L15e
LSU ribosomal protein L17e (L22p)
LSU ribosomal protein L18e
LSU ribosomal protein L18Ae
LSU ribosomal protein L19e
LSU ribosomal protein L21e
LSU ribosomal protein L22e
LSU ribosomal protein L23e (L14p)
LSU ribosomal protein L23Ae (L23p)
LSU ribosomal protein L24e
LSU ribosomal protein L26e (L24p)
LSU ribosomal protein L27e
LSU ribosomal protein L27Ae (L15p)
LSU ribosomal protein L28e
LSU ribosomal protein L29e
LSU ribosomal protein L30e
LSU ribosomal protein L31e
LSU ribosomal protein L32e
LSU ribosomal protein L34e
LSU ribosomal protein L35e (L29p)
LSU ribosomal protein L35Ae
LSU ribosomal protein L36e
LSU ribosomal protein L37e
LSU ribosomal protein L37Ae
LSU ribosomal protein L38e
LSU ribosomal protein L39e
LSU ribosomal protein L40e
LSU ribosomal protein L41e
LSU ribosomal protein L44e
LSU ribosomal protein P0 (L10p)
LSU ribosomal protein P1
LSU ribosomal protein P2
LSU ribosomal protein L12a (P1/P2)
Ribosome LSU Chloroplast
LSU ribosomal protein L1p (L10Ae), chloroplast
LSU ribosomal protein L2p (L8e), chloroplast
LSU ribosomal protein L3p (L3e), chloroplast
LSU ribosomal protein L4p (L1e), chloroplast
LSU ribosomal protein L5p (L11e), chloroplast
LSU ribosomal protein L6p (L9e), chloroplast
LSU ribosomal protein L7/L12 (L23e), chloroplast
LSU ribosomal protein L9p, chloroplast
LSU ribosomal protein L10p (P0), chloroplast
LSU ribosomal protein L11p (L12e), chloroplast
LSU ribosomal protein L13p (L13Ae), chloroplast
LSU ribosomal protein L14p (L23e), chloroplast
LSU ribosomal protein L15p (L27Ae), chloroplast
LSU ribosomal protein L16p (L10e), chloroplast
LSU ribosomal protein L17p, chloroplast
LSU ribosomal protein L18p (L5e), chloroplast
LSU ribosomal protein L19p, chloroplast
LSU ribosomal protein L20p, chloroplast
LSU ribosomal protein L21p, chloroplast
LSU ribosomal protein L22p (L17e), chloroplast
LSU ribosomal protein L23p (L23Ae), chloroplast
LSU ribosomal protein L24p (L26e), chloroplast
LSU ribosomal protein L27p, chloroplast
LSU ribosomal protein L28p, chloroplast
LSU ribosomal protein L29p (L35e), chloroplast
LSU ribosomal protein L31p, chloroplast
LSU ribosomal protein L32p, chloroplast
LSU ribosomal protein L33p, chloroplast
LSU ribosomal protein L34p, chloroplast
LSU ribosomal protein L35p, chloroplast
LSU ribosomal protein L36p, chloroplast
Ribosome LSU Mitochondrial
LSU ribosomal protein L1p (L10Ae), mitochondrial
LSU ribosomal protein L2p (L8e), mitochondrial
LSU ribosomal protein L3p (L3e), mitochondrial
LSU ribosomal protein L4p (L1e), mitochondrial
LSU ribosomal protein L5p (L11e), mitochondrial
LSU ribosomal protein L6p (L9e), mitochondrial
LSU ribosomal protein L7/L12 (L23e), mitochondrial
LSU ribosomal protein L9p, mitochondrial
LSU ribosomal protein L10p (P0), mitochondrial
LSU ribosomal protein L11p (L12e), mitochondrial
LSU ribosomal protein L13p (L13Ae), mitochondrial
LSU ribosomal protein L14p (L23e), mitochondrial
LSU ribosomal protein L15p (L27Ae), mitochondrial
LSU ribosomal protein L16p (L10e), mitochondrial
LSU ribosomal protein L17p, mitochondrial
LSU ribosomal protein L18p (L5e), mitochondrial
LSU ribosomal protein L19p, mitochondrial
LSU ribosomal protein L20p, mitochondrial
LSU ribosomal protein L21p, mitochondrial
LSU ribosomal protein L22p (L17e), mitochondrial
LSU ribosomal protein L23p (L23Ae), mitochondrial
LSU ribosomal protein L24p (L26e), mitochondrial
LSU ribosomal protein L25p, mitochondrial
LSU ribosomal protein L27p, mitochondrial
LSU ribosomal protein L28p, mitochondrial
LSU ribosomal protein L29p (L35e), mitochondrial
LSU ribosomal protein L30p (L7e), mitochondrial
LSU ribosomal protein L31p, mitochondrial
LSU ribosomal protein L32p, mitochondrial
LSU ribosomal protein L33p, mitochondrial
LSU ribosomal protein L34p, mitochondrial
LSU ribosomal protein L35p, mitochondrial
LSU ribosomal protein L36p, mitochondrial
LSU ribosomal protein L37mt, mitochondrial
LSU ribosomal protein L38mt, mitochondrial
LSU ribosomal protein L39mt, mitochondrial
LSU ribosomal protein L40mt, mitochondrial
LSU ribosomal protein L41mt, mitochondrial
LSU ribosomal protein L42mt, mitochondrial
LSU ribosomal protein L43mt, mitochondrial
LSU ribosomal protein L44mt, mitochondrial
LSU ribosomal protein L45mt, mitochondrial
LSU ribosomal protein L46mt, mitochondrial
LSU ribosomal protein L47mt, mitochondrial
LSU ribosomal protein L48mt, mitochondrial
LSU ribosomal protein L49mt, mitochondrial
LSU ribosomal protein L50mt, mitochondrial
LSU ribosomal protein L51mt, mitochondrial
LSU ribosomal protein L52mt, mitochondrial
LSU ribosomal protein L53mt, mitochondrial
LSU ribosomal protein L54mt, mitochondrial
LSU ribosomal protein L55mt, mitochondrial