INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY

IUBMB Ad Hoc Nomenclature Subcommittee

Prokaryotic and eukaryotic translation factors

(Recommendations 1995)

http://www.chem.qmul.ac.uk/iubmb/misc/trans.html

World Wide Web version prepared by G. P. Moss

Department of Chemistry, Queen Mary University of London,
Mile End Road, London, E1 4NS, UK
e-mail g.p.moss@qmul.ac.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.


It has been nearly 20 years since the nomenclature of all of the translation factors from prokaryotic and eukaryotic cells was addressed at the same time (Anderson et al., 1977). Since then, a new nomenclature of eukaryotic initiation factors was proposed in 1988 and adopted by the IUBMB (Safer, 1989). Although the current nomenclature has been generally accepted by researchers in the field, there remain a number of problems or ambiguities that require attention. The Nomenclature Committee of the IUBMB asked Dr Marianne Grunberg-Manago to convene an ad hoc subcommittee to address the current state of translation factor nomenclature, leading to this report.

General principles

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.

Initiation factors

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.

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.

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.

Elongation factors

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.

Termination factors

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.

References

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.

NameSubunitsFormer
names
Mass (kDa)Accession
number
SpeciesFunction
SDSSequence
Prokaryotic initiation factors
IF1IF-187.1Y00373E coliStimulates IF2 and IF3
IF2-1IF-2a12097.3X00513E coliBinds fMet-tRNAf; GTPase
IF2-2IF-2b9079.7E coliBinds fmet-tRNAf; GTPase
IF3IF-32020.7Ko2844E coliPrevents Rb association; monitors correct
fMet-tRNAf-initiation codon interaction
Prokaryotic elongation factors
EF1AEF-Tu43.2J01690
J01770
E coliForms ternary complex with aa-tRNA and GTP;
binds aa-tRNA to Rb A-site; GTPase
EF1BEF-Ts30.3V00343E coliPromotes guanine nucleotide exchange on EF1A
EF2EF-G77.4X00415E coliPromotes translocation reaction, GTPase
Prokaryotic termination factors
RF1RF-14435.9D28567E coliPromotes termination at UAA, UAG
RF2RF-24738.4X76613E coliPromotes termination at UAA, UGA
RF3RF-359.6Z26313E coliPromotes action of RFI and RF2; GTPase
RF4RRF2320.6J05113 E coliDissociates mRNA and tRNAs from Rb
Eukaryotic initiation factors
eIF1eIF-11512.6Z19334
Z21478
HumanEnhances initiation complex formation
eIF1AeIF-1A
eIF-4C
1716.5L18960HumanPleiotropic; dissociates Rbs; stabilizes
Met-tRNAi binding to 40S Rbs.
eIF2eIF-2125GTP-dependent Met-tRNAi binding to 40S Rbs.
a3636.2J02646 HumanRegulated by phosphorylation
b5038.4M29536HumanBinds Met-tRNAi
g5551.8L19161HumanBinds GTP, Met-tRNAi
eIF2BeIF-2B
GEF
270Promotes guanine nucleotide exchange on eIF2
a2633.7U05821Rat
b3939.0U31880RatBinds GTP
g58 Binds ATP
d6757.8Z48225RatBinds ATP
e8280.2U19511RatRegulated by phosphorylation
eIF2CCo-eIF-294RabbitStabilizes ternary complex in presence of RNA
eIF3eIF-3550Dissociates Rbs, promotes Met-tRNAi
and mRNA binding
p35a35
p36b36
p40g40
p44d44
p47e47
p66x66Binds RNA
p115h115Major phosphorylated subunit
p170q170
eIF4AeIF-4A
eIF-4
b
4644.4S00985
S00986
MouseBinds RNA; ATPase; RNA helicase;
promotes mRNA binding to 40S Rbs
eIF4BeIF-4B8069.2S12566HumanBinds mRNA; promotes RNA helicase activity
and mRNA binding to 40S Rbs.
eIF4EeIF-4E
eIF-4
a
CBP-1
2525.1M 15353HumanBinds to mRNA-caps
eIF4Gp220
eIF-4
g
220153.4D12686HumanBinds eIF4A, eIF4E and eIF3;
cleaved by picornavirus proteases
eIF4F*eIF-4F
eIF-4
CBP-II
Complex binds to mRNA-caps; RNA helicase
activity; promotes mRNA binding to 40S Rbs
eIF5eIF-54948.9L11651RatPromotes GTPase of eIF2, ejection of eIFs
eIF6eIF-6
eIF-3A
25Dissociates 80S Rbs.; binds to 60S Rb.
Eukaryotic elongation factors
eEF1AeEF-1a5150.1X16869HumanForms ternary complex, binds aa-tRNAs to
Rb.A-site; GTPase
eEF1BeEF-1bgd114
aeEF-1d3024.8X60489Human Promotes guanine nucleotide exchange on eEF1A
beEF-1g3631.2P29692Human Possesses major exchange activity
geEF-1b4850.1Z11531Human
eEF2eEF-210095.311692HumanPromotes translocation reaction; GTPase
Eukaryotic termination factors
eRF1eRF-15548.0M75715HumanPromotes termination at UAA, UAG, UGA
eRF35555.8X17644HumanGTPase; stimulates eRF1

Table II. Other proteins associated with protein synthesis.

NameMass (kDa)Accession
number
SpeciesFunction
SDSSequence
eIF2A65RabbitPromotes GTP-independent binding of
Met-tRNAi to 40S ribosomes.
eIF5A1716.7M23419Human Contains hypusine; stimulates methionyl-puromycin synthesis
4E-BPI2212.6L36055
U28656
Human
Mouse
Binds to eIF4E, prevents eIF4E binding to eIF4G;
regulated by phosphorylation.
4E-BP212.9L36056HumanSame as 4E-BP1
p676752.9U13261HumanBinds to eIF2, prevents phosphorylation by eIF2a kinases.
PABP7270.6X65553MousePoly (A) binding protein; binds to poly(A) tails,
stimulates translation synergistically with mRNA-caps.
p505035U16821Rabbit Major protein in mRNP particles.
La46.8J04205Human Found in RNPs; binds to IRES elements.
PTB5857.2X60648Human Polypyrimidine tract binding protein; binds to IRES elements.


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