IUBMB Ad Hoc Nomenclature Subcommittee
World Wide Web version prepared by G. P. Moss
School of Biological and Chemical Sciences, Queen Mary University of London,
Mile End Road, London, E1 4NS, UK
This document is as close as possible to the published version prepared by Brian FC Clark, Marianne Grunberg-Manago (Chair), Naba K Gupta, John WB Hershey, Alan G Hinnebusch, Richard J Jackson, Umadas Maltra, Michael B Mathews, William C. Merrick, Robert E Rhoads, Nahum Sonenberg, Linda L Spremulli, Hans Trachsel, Harry O Voorma [see Biochimie 1996, 78, 1119-1122; Copyright IUBMB; reproduced with the permission of IUBMB]. If you need to cite these rules please quote this reference as their source.
The following principles were recognized as important in formulating a nomenclature: whenever possible, changes in factor names should be minimized; the nomenclature should be systematic; the prokaryotic and eukaryotic names should be similar but distinguishable; when a factor is renamed, the old name should not be used for a different factor; no polypeptide should have more than one name. In some cases, a compromise between adhering to historical names and taking a strictly systematic approach was necessary.
Some general rules were applied. All initiation, elongation and termination factors begin with IF, EF and RF, respectively, for prokaryotes, whereas an 'e' precedes the same symbols for eukaryotes. The symbols are followed by either an Arabic numeral or, in cases where a number of factors possess related functions, by an Arabic numeral plus an upper case letter. Subunits found in complex factors are identified by Greek letters, beginning with the lowest molecular weight subunit. No hyphens are used in factor names, except when isoforms are found, which are identified as: -1, -2, etc.
The well-established translation factors
Translation factors whose roles in translation are well established are listed in Table I. All of the proteins in table I have met nearly all of the following criteria: purification of the factor to near-homogeneity; stimulation in vitro of protein synthesis or a partial reaction thereof; cloning of its cDNA or gene. Demonstration of a role in translation in intact cells is highly desirable, but many factors have not yet met this criterion.
The names of the prokaryotic initiation factors listed in Table I have not changed, except for deletion of the hyphens. The general scheme developed previously for naming eukaryotic initiation factors was maintained:
eIF1 class: pleiotropic; general stimulation of initiation complex formation.Only a few changes in the eukaryotic names were made, in particular in the eIF4 group of proteins. Each of the proteins of the eIF4F complex should be given its own name (i.e. eIF4A, eIF4E and eIF4G), since there is uncertainty that the complex functions exclusively as a heterotrimeric complex. The term eIF4F may continue to be used, but its composition (dimer, trimer?) should be defined each time since the number of components differs between species. The term eIF4, with and without Greek letters for subunits, is retired. The isoforms of eIF4A are designated eIF4A-1 and eIF4A-2. The cap binding isoforms found in plants are namcd eIFiso4E and eIFiso4G. In the case of the eight subunits of eIF3, an exception was made by defining the subunit proteins according to their apparent molecular weights rather than by Greek letters, since the higher Greek letters are not generally familiar and the relationships of the subunits across species may not be straightforward.
eIF2 class: promotes Met-tRNAi binding to ribosomes.
eIF3 class: binds 40S, dissociates ribosomes, promotes initiation complex formation.
eIF4 class: promotes mRNA binding to ribosomes.
eIF5 class: promotes eIF ejection and 60S junction reaction.
eIF6 class: interacts with 60S subunits.
It is proposed to change the long-term and well established names used for the prokaryotic elongation factors to conform to the general principles of using numbers following the EF designation and to have parallel names for both prokaryotic and eukaryotic proteins. The EF1/eEF1 group of proteins is concerned with aminoacyl-tRNA binding to ribosomes, where 1A refers to the protein that promotes the binding and 1B is concemed with catalyzing the guanine exchange reaction on EF1A. The EF2/eEF2 group promotes the translocation reaction on the ribosome.
The termination factor names follow previous usage and are straightforward; no significant changes have been made except to include the ribosome release factor, RF4, in the systematic nomenclature.
Other proteins associated with translation
A number of proteins not listed in Table I nevertheless may be involved in the translation pathway. These are proteins (see Table II) either whose functions are not sufficiently well established to be included as a translation factor, that interact with translation factors to modify their activities, or that are thought to function at steps not generally considered a part of the pathway of translation. Some of these proteins eventually may be placed in Table I, whereas others may be dropped entirely.
New translation factors and future revisions
The nomenclature system is designed to accommodate new proteins. Such proteins should carry the general designation (eg IF, EF) followed by the number indicating its function and a new upper case letter. Previously used and now obsolete names should be avoided. A systematic name signifying inclusion in table I should be give to a protein factor only after it has satisfied the criteria described above. To avoid confusion in the field, all researchers are urged to employ this nomenclature system.
W.F. Anderson, L. Bosch, W.E. Cohn, H. Lodish, W.C. Merrick, H. Weissbach, H.G.Wittman and I.G. Wool, FEBS Lett., 1977, 76, 1-10
B. Safer, Eur. J. Biochem., 1989, 186, 1-3.
Table I. Well-established translation factors.
|Prokaryotic initiation factors|
|IF1||IF-1||8||7.1||Y00373||E coli||Stimulates IF2 and IF3|
|IF2-1||IF-2a||120||97.3||X00513||E coli||Binds fMet-tRNAf; GTPase|
|IF2-2||IF-2b||90||79.7||E coli||Binds fmet-tRNAf; GTPase|
|IF3||IF-3||20||20.7||Ko2844||E coli||Prevents Rb association; monitors correct|
fMet-tRNAf-initiation codon interaction
|Prokaryotic elongation factors|
|E coli||Forms ternary complex with aa-tRNA and GTP;|
binds aa-tRNA to Rb A-site; GTPase
|EF1B||EF-Ts||30.3||V00343||E coli||Promotes guanine nucleotide exchange on EF1A|
|EF2||EF-G||77.4||X00415||E coli||Promotes translocation reaction, GTPase|
|Prokaryotic termination factors|
|RF1||RF-1||44||35.9||D28567||E coli||Promotes termination at UAA, UAG|
|RF2||RF-2||47||38.4||X76613||E coli||Promotes termination at UAA, UGA|
|RF3||RF-3||59.6||Z26313||E coli||Promotes action of RFI and RF2; GTPase|
|RF4||RRF||23||20.6||J05113||E coli||Dissociates mRNA and tRNAs from Rb|
|Eukaryotic initiation factors|
|Human||Enhances initiation complex formation|
|17||16.5||L18960||Human||Pleiotropic; dissociates Rbs; stabilizes|
Met-tRNAi binding to 40S Rbs.
|eIF2||eIF-2||125||GTP-dependent Met-tRNAi binding to 40S Rbs.|
|a||36||36.2||J02646||Human||Regulated by phosphorylation|
|g||55||51.8||L19161||Human||Binds GTP, Met-tRNAi|
|270||Promotes guanine nucleotide exchange on eIF2|
|e||82||80.2||U19511||Rat||Regulated by phosphorylation|
|eIF2C||Co-eIF-2||94||Rabbit||Stabilizes ternary complex in presence of RNA|
|eIF3||eIF-3||550||Dissociates Rbs, promotes Met-tRNAi|
and mRNA binding
|p115||h||115||Major phosphorylated subunit|
|Mouse||Binds RNA; ATPase; RNA helicase;|
promotes mRNA binding to 40S Rbs
|eIF4B||eIF-4B||80||69.2||S12566||Human||Binds mRNA; promotes RNA helicase activity|
and mRNA binding to 40S Rbs.
|25||25.1||M 15353||Human||Binds to mRNA-caps|
|220||153.4||D12686||Human||Binds eIF4A, eIF4E and eIF3;|
cleaved by picornavirus proteases
|Complex binds to mRNA-caps; RNA helicase|
activity; promotes mRNA binding to 40S Rbs
|eIF5||eIF-5||49||48.9||L11651||Rat||Promotes GTPase of eIF2, ejection of eIFs|
|25||Dissociates 80S Rbs.; binds to 60S Rb.|
|Eukaryotic elongation factors|
|eEF1A||eEF-1a||51||50.1||X16869||Human||Forms ternary complex, binds aa-tRNAs to|
|a||eEF-1d||30||24.8||X60489||Human||Promotes guanine nucleotide exchange on eEF1A|
|b||eEF-1g||36||31.2||P29692||Human||Possesses major exchange activity|
|eEF2||eEF-2||100||95.3||11692||Human||Promotes translocation reaction; GTPase|
|Eukaryotic termination factors|
|eRF1||eRF-1||55||48.0||M75715||Human||Promotes termination at UAA, UAG, UGA|
|eRF3||55||55.8||X17644||Human||GTPase; stimulates eRF1|
Table II. Other proteins associated with protein synthesis.
|eIF2A||65||Rabbit||Promotes GTP-independent binding of|
Met-tRNAi to 40S ribosomes.
|eIF5A||17||16.7||M23419||Human||Contains hypusine; stimulates methionyl-puromycin synthesis|
|Binds to eIF4E, prevents eIF4E binding to eIF4G;|
regulated by phosphorylation.
|4E-BP2||12.9||L36056||Human||Same as 4E-BP1|
|p67||67||52.9||U13261||Human||Binds to eIF2, prevents phosphorylation by eIF2a kinases.|
|PABP||72||70.6||X65553||Mouse||Poly (A) binding protein; binds to poly(A) tails,|
stimulates translation synergistically with mRNA-caps.
|p50||50||35||U16821||Rabbit||Major protein in mRNP particles.|
|La||46.8||J04205||Human||Found in RNPs; binds to IRES elements.|
|PTB||58||57.2||X60648||Human||Polypyrimidine tract binding protein; binds to IRES elements.|
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