A new system for naming ribosomal proteins

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A system for naming ribosomal proteins is described that the authors intend to use in the future. They urge others to adopt it. The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as ‘new system’ names.

Introduction

We take it as given that homologous macromolecules that perform the same functions in different organisms should be assigned the same name. Homologous macromolecules are the products of genes that have evolved from a common ancestor. The fact that two macromolecules are homologous can often be established simply by comparing their sequences, but sometimes it becomes apparent only after their three-dimensional structures have been determined so that comparisons can be done using structure-based sequence alignments.

It has long been a challenge to devise a system for naming ribosomal proteins that respects this principle. The reason is that the characterization of ribosomal proteins began in the 1960s, at a time when there were no structures and the only way to obtain protein sequences was by sequencing them directly, an enterprise that in those days could consume hundreds of milligrams of pure protein and many man years of labor. By the time enough sequences had been obtained to begin identifying homologies, several different conventions for naming ribosomal proteins had become embedded in the literature.

Here we propose a new naming system that we hope will ultimately replace its predecessors. We know that at first many will be disinclined to use it because they find it disruptive, but we hope that the logic behind it will ultimately carry the day. We view this as a sensible next step in a process that has been moving forward for over 40 years.

Section snippets

The origins of the naming problem

The naming of ribosomal proteins first emerged as a problem in the mid-1960s, when several groups began purifying and characterizing the ribosomal proteins from Escherichia coli. Each laboratory devised its own naming system, which made it hard even for members of that in-group to make sense of the data being published, let alone for anyone else. That chaos ended in 1971 when a standard experimental method for identifying these proteins was agreed upon, as well as a naming system [1].

Discussion

Some further comments are in order. The protein in eukaryotic ribosomes that is equivalent to protein L10 in bacteria is somewhat larger, and is referred to in the literature as P0. We propose that the name uL10 be assigned to this molecule. Furthermore, only bacteria have proteins that correspond to the protein called L7/L12 in E. coli. In addition the acetylated variant of L12, L7, is not found in all bacterial species. Therefore we suggest that this protein be called bL12 unless its

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