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Unified nomenclature for the subunits of eukaryotic initiation factor 31
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284
TRENDS in Biochemical Sciences Vol.26 No.5 May 2001
Letters
Unified nomenclature for the subunits of eukaryotic initiation factor 3 †
Translation initiation in eukaryotes is an intricate process requiring at least 11 eukaryotic initiation factors (eIFs)1. Among these initiation factors, eIF3 is the largest as it comprises up to 11 non-identical subunits. Several functions have been ascribed to eIF3, including the binding to and stabilization of ternary complex, binding to the 40S ribosome, facilitating the binding of mRNA to the 40S ribosome, and promoting dissociation of 40S and 60S ribosomal subunits2. Other initiation factors (e.g. eIF4G, eIF4B, eIF5 and eIF1) are known to interact with eIF3, suggesting that this factor might have a role in ‘organizing’ proteins on the surface of the 40S ribosome2. The subunits from the human, plant and Saccharomyces cerevisiae eIF3 complexes have been identified and sequenced. Surprisingly, there are substantial differences in their subunit composition. Mammalian eIF3 appears to contain 11 subunits – p170, p116, p110, p66, p44, p48, p47, p40, p36, p35 and p28 (Ref. 1). By contrast, S. cerevisiae eIF3 contains a core complex of five subunits – Tif32p, Prt1p, Nip1p, Tif35p and Tif34p (Refs 1,2) – which are orthologs of the †This letter arises from the Cold Spring Harbor Translational Control meeting held on September 6–10 2000 in Cold Spring Harbor, NY, USA.
mammalian subunits p170, p116, p110, p44 and p36, respectively (see Table 1). Other proteins associated with the S. cerevisiae eIF3 core complex [i.e. Tif31p (also known as Clu1p), Gcd10p, eIF5 and Sui1p (eIF1)] are not present in mammalian or plant eIF3 (Refs 1,3); however, direct interaction of eIF3c with eIF5 and eIF1 has been shown in both S. cerevisiae and mammals2. The subunit composition of plant eIF3 is more similar to mammalian eIF3 than to S. cerevisiae eIF3 as 10 out of its 11 subunits are equivalent to mammalian eIF3 subunits on the basis of amino acid sequence similarity3. The subunit composition of eIF3 from wheat (a monocot) and Arabidopsis thaliana (a dicot) is conserved, suggesting that eIF3 from all higher plants will share a similar composition. Plant eIF3 does differ from mammalian eIF3 in that the plant factor does not appear to contain a protein comparable to mammalian eIF3j and has a novel subunit, eIF3l, not present in mammalian eIF3 (Ref. 3). Genes encoding orthologs of most of the subunits of mammalian and plant eIF3 complexes are present in the genomes of Schizosaccharomyces pombe, Drosophila melanogaster and Caenorhabditis elegans; however, eIF3 complexes from these organisms have not been purified and so their subunit compositions have not been confirmed. The conservation of eIF3 between mammals and plants suggests that S. cerevisiae eIF3 might have diverged significantly from other eukaryotes. Clearly, more genetic and biochemical work is necessary to identify the functional
components of eIF3 complexes from a variety of eukaryotic organisms. To date, ad hoc nomenclatures for eIF3 subunits have been derived from subunit molecular weights or gene names. To eliminate confusion surrounding cross-species comparisons of eIF3 subunits, a unified nomenclature is proposed in which the subunits are provided letter designations based on the order of the mammalian subunits by molecular weights (see Table 1). Assignment of the plant and S. cerevisiae proteins is through their amino acid sequence similarity to the mammalian subunits. The nomenclature is flexible enough to accommodate any species-specific subunits (e.g. eIF3j and eIF3l) as they arise. References 1 Hershey, J.W.B. and Merrick, W.C. (2000) Pathway and mechanism of initiation of protein synthesis. In Translational Control of Gene Expression (Sonenberg, N. et al., eds), pp. 33–88, Cold Spring Harbor Laboratory Press, NY, USA 2 Hinnebusch, A.G. (2000) Mechanism and regulation of initiator methionyl-tRNA binding to ribosomes. In Translational Control of Gene Expression (Sonenberg, N. et al., eds), pp. 185–243, Cold Spring Harbor Laboratory Press, NY, USA 3 Burks, E.A. et al. (2001) Plant initiation factor 3 subunit composition resembles mammalian initiation factor 3 and has a novel subunit. J. Biol. Chem. 276, 2131–2133 4 Aravind, L. and Ponting, C.P. (1998) Homologues of 26S proteasome subunits are regulators of transcription and translation. Protein Sci. 7, 1250–1254 5 Hofmann, K. and Bucher, P. (1998) The PCI domain: a common theme in three multiprotein complexes. Trends Biochem. Sci. 23, 204–205 6 Aravind, L. and Koonin, E.V. (2000) Eukaryotespecific domains in translation initiation factors: implications for translation regulation and evolution of the translation system. Genome Res. 10, 1172–1184
Table 1. Proposed nomenclature for eIF3 subunitsa Human
Wheat
A. thaliana
S. cerevisiae
MWd
MWd
MWe
MWe
170 116 110 66 (INT6) 48 47 TIF35 44 40 TIF34 (TRIP1) 36 HCR1g 35 28 None
116 83 107 87 45 34 36 41b 41a None 28 56
114 82 105 66 51 32 33 38 36 None 25 60
110 90 93 None None None 33 None 39 30g None None
Subunit name Consensus motif b Gene namec eIF3a eIF3b eIF3c eIF3d eIF3e eIF3f eIF3g eIF3h eIF3i eIF3jf eIF3k eIF3lh
PCI RRM PCI None PCI MPN RBD, Zn finger MPN WD repeats None None None
TIF32/RPG1 PRT1 NIP1
aAbbreviations: eIF3, eukaryotic initiation factor 3; MW, molecular weight. bSee Refs 1,4–6. cBlank entries represent genes that have not yet been named. Gene names in parentheses are mammalian; all others are from yeast. dMass (kDa) determined from SDS PAGE mobility. eMass (kDa) calculated from deduced protein sequence. f This protein is not found in the plant eIF3 complex. gThis subunit is not part of the Saccharomyces cerevisiae core eIF3 complex. hThis protein is not found in the mammalian eIF3 complex.
Karen S. Browning* Depts of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA. *e-mail: [email protected] Daniel R. Gallie University of California, Riverside, CA 92521-0129, USA. John W.B. Hershey University of California, Davis, CA 95616, USA. Alan G. Hinnebusch National Institutes of Health, Bethesda, MD 20892-2716, USA. Umadas Maitra Albert Einstein College of Medicine, Bronx, NY 10461-1975, USA. William C. Merrick Case Western Reserve University Medical School, Cleveland, OH 44106-4935, USA. Chris Norbury Imperial Cancer Research Fund, Oxford, UK OX3 9DS.
http://tibs.trends.com 0968-0004/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved. PII: S0968-0004(01)01825-4
284
TRENDS in Biochemical Sciences Vol.26 No.5 May 2001
Letters
Unified nomenclature for the subunits of eukaryotic initiation factor 3 †
Translation initiation in eukaryotes is an intricate process requiring at least 11 eukaryotic initiation factors (eIFs)1. Among these initiation factors, eIF3 is the largest as it comprises up to 11 non-identical subunits. Several functions have been ascribed to eIF3, including the binding to and stabilization of ternary complex, binding to the 40S ribosome, facilitating the binding of mRNA to the 40S ribosome, and promoting dissociation of 40S and 60S ribosomal subunits2. Other initiation factors (e.g. eIF4G, eIF4B, eIF5 and eIF1) are known to interact with eIF3, suggesting that this factor might have a role in ‘organizing’ proteins on the surface of the 40S ribosome2. The subunits from the human, plant and Saccharomyces cerevisiae eIF3 complexes have been identified and sequenced. Surprisingly, there are substantial differences in their subunit composition. Mammalian eIF3 appears to contain 11 subunits – p170, p116, p110, p66, p44, p48, p47, p40, p36, p35 and p28 (Ref. 1). By contrast, S. cerevisiae eIF3 contains a core complex of five subunits – Tif32p, Prt1p, Nip1p, Tif35p and Tif34p (Refs 1,2) – which are orthologs of the †This letter arises from the Cold Spring Harbor Translational Control meeting held on September 6–10 2000 in Cold Spring Harbor, NY, USA.
mammalian subunits p170, p116, p110, p44 and p36, respectively (see Table 1). Other proteins associated with the S. cerevisiae eIF3 core complex [i.e. Tif31p (also known as Clu1p), Gcd10p, eIF5 and Sui1p (eIF1)] are not present in mammalian or plant eIF3 (Refs 1,3); however, direct interaction of eIF3c with eIF5 and eIF1 has been shown in both S. cerevisiae and mammals2. The subunit composition of plant eIF3 is more similar to mammalian eIF3 than to S. cerevisiae eIF3 as 10 out of its 11 subunits are equivalent to mammalian eIF3 subunits on the basis of amino acid sequence similarity3. The subunit composition of eIF3 from wheat (a monocot) and Arabidopsis thaliana (a dicot) is conserved, suggesting that eIF3 from all higher plants will share a similar composition. Plant eIF3 does differ from mammalian eIF3 in that the plant factor does not appear to contain a protein comparable to mammalian eIF3j and has a novel subunit, eIF3l, not present in mammalian eIF3 (Ref. 3). Genes encoding orthologs of most of the subunits of mammalian and plant eIF3 complexes are present in the genomes of Schizosaccharomyces pombe, Drosophila melanogaster and Caenorhabditis elegans; however, eIF3 complexes from these organisms have not been purified and so their subunit compositions have not been confirmed. The conservation of eIF3 between mammals and plants suggests that S. cerevisiae eIF3 might have diverged significantly from other eukaryotes. Clearly, more genetic and biochemical work is necessary to identify the functional
components of eIF3 complexes from a variety of eukaryotic organisms. To date, ad hoc nomenclatures for eIF3 subunits have been derived from subunit molecular weights or gene names. To eliminate confusion surrounding cross-species comparisons of eIF3 subunits, a unified nomenclature is proposed in which the subunits are provided letter designations based on the order of the mammalian subunits by molecular weights (see Table 1). Assignment of the plant and S. cerevisiae proteins is through their amino acid sequence similarity to the mammalian subunits. The nomenclature is flexible enough to accommodate any species-specific subunits (e.g. eIF3j and eIF3l) as they arise. References 1 Hershey, J.W.B. and Merrick, W.C. (2000) Pathway and mechanism of initiation of protein synthesis. In Translational Control of Gene Expression (Sonenberg, N. et al., eds), pp. 33–88, Cold Spring Harbor Laboratory Press, NY, USA 2 Hinnebusch, A.G. (2000) Mechanism and regulation of initiator methionyl-tRNA binding to ribosomes. In Translational Control of Gene Expression (Sonenberg, N. et al., eds), pp. 185–243, Cold Spring Harbor Laboratory Press, NY, USA 3 Burks, E.A. et al. (2001) Plant initiation factor 3 subunit composition resembles mammalian initiation factor 3 and has a novel subunit. J. Biol. Chem. 276, 2131–2133 4 Aravind, L. and Ponting, C.P. (1998) Homologues of 26S proteasome subunits are regulators of transcription and translation. Protein Sci. 7, 1250–1254 5 Hofmann, K. and Bucher, P. (1998) The PCI domain: a common theme in three multiprotein complexes. Trends Biochem. Sci. 23, 204–205 6 Aravind, L. and Koonin, E.V. (2000) Eukaryotespecific domains in translation initiation factors: implications for translation regulation and evolution of the translation system. Genome Res. 10, 1172–1184
Table 1. Proposed nomenclature for eIF3 subunitsa Human
Wheat
A. thaliana
S. cerevisiae
MWd
MWd
MWe
MWe
170 116 110 66 (INT6) 48 47 TIF35 44 40 TIF34 (TRIP1) 36 HCR1g 35 28 None
116 83 107 87 45 34 36 41b 41a None 28 56
114 82 105 66 51 32 33 38 36 None 25 60
110 90 93 None None None 33 None 39 30g None None
Subunit name Consensus motif b Gene namec eIF3a eIF3b eIF3c eIF3d eIF3e eIF3f eIF3g eIF3h eIF3i eIF3jf eIF3k eIF3lh
PCI RRM PCI None PCI MPN RBD, Zn finger MPN WD repeats None None None
TIF32/RPG1 PRT1 NIP1
aAbbreviations: eIF3, eukaryotic initiation factor 3; MW, molecular weight. bSee Refs 1,4–6. cBlank entries represent genes that have not yet been named. Gene names in parentheses are mammalian; all others are from yeast. dMass (kDa) determined from SDS PAGE mobility. eMass (kDa) calculated from deduced protein sequence. f This protein is not found in the plant eIF3 complex. gThis subunit is not part of the Saccharomyces cerevisiae core eIF3 complex. hThis protein is not found in the mammalian eIF3 complex.
Karen S. Browning* Depts of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA. *e-mail: [email protected] Daniel R. Gallie University of California, Riverside, CA 92521-0129, USA. John W.B. Hershey University of California, Davis, CA 95616, USA. Alan G. Hinnebusch National Institutes of Health, Bethesda, MD 20892-2716, USA. Umadas Maitra Albert Einstein College of Medicine, Bronx, NY 10461-1975, USA. William C. Merrick Case Western Reserve University Medical School, Cleveland, OH 44106-4935, USA. Chris Norbury Imperial Cancer Research Fund, Oxford, UK OX3 9DS.
http://tibs.trends.com 0968-0004/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved. PII: S0968-0004(01)01825-4