Prokaryotic and eukaryotic translation factors

(Recommendations 1995)

https://iubmb.qmul.ac.uk/misc/trans.html

World Wide Web version prepared by G. P. Moss

School of Physical and Chemical Sciences, 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-tRNA_i 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.

Name	Subunits	Former names	Mass (kDa)		Accession number	Species	Function
			SDS	Sequence
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-tRNA_f; GTPase
IF2-2		IF-2b	90	79.7		E coli	Binds fmet-tRNA_f; GTPase
IF3		IF-3	20	20.7	Ko2844	E coli	Prevents Rb association; monitors correct fMet-tRNA_f-initiation codon interaction
Prokaryotic elongation factors
EF1A		EF-Tu		43.2	J01690 J01770	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
eIF1		eIF-1	15	12.6	Z19334 Z21478	Human	Enhances initiation complex formation
eIF1A		eIF-1A eIF-4C	17	16.5	L18960	Human	Pleiotropic; dissociates Rbs; stabilizes Met-tRNA_i binding to 40S Rbs.
eIF2		eIF-2	125				GTP-dependent Met-tRNA_i binding to 40S Rbs.
	a		36	36.2	J02646	Human	Regulated by phosphorylation
	b		50	38.4	M29536	Human	Binds Met-tRNA_i
	g		55	51.8	L19161	Human	Binds GTP, Met-tRNA_i
eIF2B		eIF-2B GEF	270				Promotes guanine nucleotide exchange on eIF2
	a		26	33.7	U05821	Rat
	b		39	39.0	U31880	Rat	Binds GTP
	g		58				Binds ATP
	d		67	57.8	Z48225	Rat	Binds ATP
	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-tRNA_i and mRNA binding
	p35	a	35
	p36	b	36
	p40	g	40
	p44	d	44
	p47	e	47
	p66	x	66				Binds RNA
	p115	h	115				Major phosphorylated subunit
	p170	q	170
eIF4A		eIF-4A eIF-4b	46	44.4	S00985 S00986	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.
eIF4E		eIF-4E eIF-4a CBP-1	25	25.1	M 15353	Human	Binds to mRNA-caps
eIF4G		p220 eIF-4g	220	153.4	D12686	Human	Binds 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
eIF5		eIF-5	49	48.9	L11651	Rat	Promotes GTPase of eIF2, ejection of eIFs
eIF6		eIF-6 eIF-3A	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 Rb.A-site; GTPase
eEF1B		eEF-1bgd	114
	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
	g	eEF-1b	48	50.1	Z11531	Human
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.

Name Mass (kDa) Accession
number Species Function

SDS Sequence

eIF2A 65 Rabbit Promotes GTP-independent binding of
Met-tRNA_i to 40S ribosomes.

eIF5A 17 16.7 M23419 Human Contains hypusine; stimulates methionyl-puromycin synthesis

4E-BPI 22 12.6 L36055
U28656 Human
Mouse 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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