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PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes.

Zhou C, Arslan F, Wee S, Krishnan S, Ivanov AR, Oliva A, Leatherwood J, Wolf DA - BMC Biol. (2005)

Bottom Line: Whereas neither eIF3e nor eIF3m contribute to the non-essential activities of CSN in cullin-RING ubiquitin ligase control, eif3m, unlike eif3e, is an essential gene required for global cellular protein synthesis and polysome formation.Using a ribonomic approach, this phenotypic distinction was correlated with a different set of mRNAs associated with the eIF3e and eIF3m complexes.We propose that the PCI proteins eIF3e and eIF3m define distinct eIF3 complexes that may assist in the translation of different sets of mRNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA. czhou@rics.bwh.harvard.edu

ABSTRACT

Background: PCI/MPN domain protein complexes comprise the 19S proteasome lid, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). The eIF3 complex is thought to be composed of essential core subunits required for global protein synthesis and non-essential subunits that may modulate mRNA specificity. Interactions of unclear significance were reported between eIF3 subunits and PCI proteins contained in the CSN.

Results: Here, we report the unexpected finding that fission yeast has two distinct eIF3 complexes sharing common core subunits, but distinguished by the PCI proteins eIF3e and the novel eIF3m, which was previously annotated as a putative CSN subunit. Whereas neither eIF3e nor eIF3m contribute to the non-essential activities of CSN in cullin-RING ubiquitin ligase control, eif3m, unlike eif3e, is an essential gene required for global cellular protein synthesis and polysome formation. Using a ribonomic approach, this phenotypic distinction was correlated with a different set of mRNAs associated with the eIF3e and eIF3m complexes. Whereas the eIF3m complex appears to associate with the bulk of cellular mRNAs, the eIF3e complex associates with a far more restricted set. The microarray findings were independently corroborated for a random set of 14 mRNAs by RT-PCR analysis.

Conclusion: We propose that the PCI proteins eIF3e and eIF3m define distinct eIF3 complexes that may assist in the translation of different sets of mRNAs.

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Association of mRNAs with eIF3 complexes. (A) Messenger RNAs associated with eIF3e and eIF3m complexes were identified by microarray hybridization as described in the Methods section. The graph indicates the numbers of mRNAs enriched more than three-fold over mock in both complexes. (B) Classification into functional groups of the 106 mRNAs most highly and uniquely enriched in complexes with eIF3e or eIF3m. (C) The relative expression ranks of the 106 most highly and uniquely enriched mRNAs in the eIF3e and eIF3m complexeswere determined using the relative hybridization signals obtained with total S. pombe cDNA ([see additional file 1]). The expression ranks were blotted against the factor of enrichment of each mRNA in the eIF3 complexes. No correlation between expression rank and enrichment is apparent, indicating that highly expressed mRNAs were not unspecifically enriched in eIF3 complexes. The 5407 individual features on the microarray slides represent the 4988 ORFs and transcripts predicted in the Sanger Centre S. pombe genome database and various controls. To simplify the analysis, expression ranks were also assigned to these control spots, thus resulting in expression ranks for some ORFs higher than the theoretically possible number of 4988.
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Figure 4: Association of mRNAs with eIF3 complexes. (A) Messenger RNAs associated with eIF3e and eIF3m complexes were identified by microarray hybridization as described in the Methods section. The graph indicates the numbers of mRNAs enriched more than three-fold over mock in both complexes. (B) Classification into functional groups of the 106 mRNAs most highly and uniquely enriched in complexes with eIF3e or eIF3m. (C) The relative expression ranks of the 106 most highly and uniquely enriched mRNAs in the eIF3e and eIF3m complexeswere determined using the relative hybridization signals obtained with total S. pombe cDNA ([see additional file 1]). The expression ranks were blotted against the factor of enrichment of each mRNA in the eIF3 complexes. No correlation between expression rank and enrichment is apparent, indicating that highly expressed mRNAs were not unspecifically enriched in eIF3 complexes. The 5407 individual features on the microarray slides represent the 4988 ORFs and transcripts predicted in the Sanger Centre S. pombe genome database and various controls. To simplify the analysis, expression ranks were also assigned to these control spots, thus resulting in expression ranks for some ORFs higher than the theoretically possible number of 4988.

Mentions: The microarray analysis suggested a global role for eIF3m and a more restricted function of eIF3e in translation. Using an arbitrary cut-off value of three-fold enrichment over mock, eIF3m associated with 2464 different mRNAs, whereas eIF3e associated with only 520 distinct species (Fig. 4A). We observed 414 mRNAs enriched more than three-fold in both samples. (Fig. 4A). In addition, our analysis revealed 106 mRNAs uniquely enriched in the eIF3e complex, whereas 2050 transcripts were uniquely enriched in the eIF3m complex (Fig. 4A,C).


PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes.

Zhou C, Arslan F, Wee S, Krishnan S, Ivanov AR, Oliva A, Leatherwood J, Wolf DA - BMC Biol. (2005)

Association of mRNAs with eIF3 complexes. (A) Messenger RNAs associated with eIF3e and eIF3m complexes were identified by microarray hybridization as described in the Methods section. The graph indicates the numbers of mRNAs enriched more than three-fold over mock in both complexes. (B) Classification into functional groups of the 106 mRNAs most highly and uniquely enriched in complexes with eIF3e or eIF3m. (C) The relative expression ranks of the 106 most highly and uniquely enriched mRNAs in the eIF3e and eIF3m complexeswere determined using the relative hybridization signals obtained with total S. pombe cDNA ([see additional file 1]). The expression ranks were blotted against the factor of enrichment of each mRNA in the eIF3 complexes. No correlation between expression rank and enrichment is apparent, indicating that highly expressed mRNAs were not unspecifically enriched in eIF3 complexes. The 5407 individual features on the microarray slides represent the 4988 ORFs and transcripts predicted in the Sanger Centre S. pombe genome database and various controls. To simplify the analysis, expression ranks were also assigned to these control spots, thus resulting in expression ranks for some ORFs higher than the theoretically possible number of 4988.
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Related In: Results  -  Collection

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Figure 4: Association of mRNAs with eIF3 complexes. (A) Messenger RNAs associated with eIF3e and eIF3m complexes were identified by microarray hybridization as described in the Methods section. The graph indicates the numbers of mRNAs enriched more than three-fold over mock in both complexes. (B) Classification into functional groups of the 106 mRNAs most highly and uniquely enriched in complexes with eIF3e or eIF3m. (C) The relative expression ranks of the 106 most highly and uniquely enriched mRNAs in the eIF3e and eIF3m complexeswere determined using the relative hybridization signals obtained with total S. pombe cDNA ([see additional file 1]). The expression ranks were blotted against the factor of enrichment of each mRNA in the eIF3 complexes. No correlation between expression rank and enrichment is apparent, indicating that highly expressed mRNAs were not unspecifically enriched in eIF3 complexes. The 5407 individual features on the microarray slides represent the 4988 ORFs and transcripts predicted in the Sanger Centre S. pombe genome database and various controls. To simplify the analysis, expression ranks were also assigned to these control spots, thus resulting in expression ranks for some ORFs higher than the theoretically possible number of 4988.
Mentions: The microarray analysis suggested a global role for eIF3m and a more restricted function of eIF3e in translation. Using an arbitrary cut-off value of three-fold enrichment over mock, eIF3m associated with 2464 different mRNAs, whereas eIF3e associated with only 520 distinct species (Fig. 4A). We observed 414 mRNAs enriched more than three-fold in both samples. (Fig. 4A). In addition, our analysis revealed 106 mRNAs uniquely enriched in the eIF3e complex, whereas 2050 transcripts were uniquely enriched in the eIF3m complex (Fig. 4A,C).

Bottom Line: Whereas neither eIF3e nor eIF3m contribute to the non-essential activities of CSN in cullin-RING ubiquitin ligase control, eif3m, unlike eif3e, is an essential gene required for global cellular protein synthesis and polysome formation.Using a ribonomic approach, this phenotypic distinction was correlated with a different set of mRNAs associated with the eIF3e and eIF3m complexes.We propose that the PCI proteins eIF3e and eIF3m define distinct eIF3 complexes that may assist in the translation of different sets of mRNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA. czhou@rics.bwh.harvard.edu

ABSTRACT

Background: PCI/MPN domain protein complexes comprise the 19S proteasome lid, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). The eIF3 complex is thought to be composed of essential core subunits required for global protein synthesis and non-essential subunits that may modulate mRNA specificity. Interactions of unclear significance were reported between eIF3 subunits and PCI proteins contained in the CSN.

Results: Here, we report the unexpected finding that fission yeast has two distinct eIF3 complexes sharing common core subunits, but distinguished by the PCI proteins eIF3e and the novel eIF3m, which was previously annotated as a putative CSN subunit. Whereas neither eIF3e nor eIF3m contribute to the non-essential activities of CSN in cullin-RING ubiquitin ligase control, eif3m, unlike eif3e, is an essential gene required for global cellular protein synthesis and polysome formation. Using a ribonomic approach, this phenotypic distinction was correlated with a different set of mRNAs associated with the eIF3e and eIF3m complexes. Whereas the eIF3m complex appears to associate with the bulk of cellular mRNAs, the eIF3e complex associates with a far more restricted set. The microarray findings were independently corroborated for a random set of 14 mRNAs by RT-PCR analysis.

Conclusion: We propose that the PCI proteins eIF3e and eIF3m define distinct eIF3 complexes that may assist in the translation of different sets of mRNAs.

Show MeSH
Related in: MedlinePlus