Eukaryotic initiation factor

Eukaryotic initiation factors (eIFs) are proteins or protein complexes involved in the initiation phase of eukaryotic translation. These proteins help stabilize the formation of ribosomal preinitiation complexes around the start codon and are an important input for post-transcription gene regulation. Several initiation factors form a complex with the small 40S ribosomal subunit and Met-tRNA_i^Met called the 43S preinitiation complex (43S PIC). Additional factors of the eIF4F complex (eIF4A, E, and G) recruit the 43S PIC to the five-prime cap structure of the mRNA, from which the 43S particle scans 5'-->3' along the mRNA to reach an AUG start codon. Recognition of the start codon by the Met-tRNA_i^Met promotes gated phosphate and eIF1 release to form the 48S preinitiation complex (48S PIC), followed by large 60S ribosomal subunit recruitment to form the 80S ribosome.^[1] There exist many more eukaryotic initiation factors than prokaryotic initiation factors, reflecting the greater biological complexity of eukaryotic translation. There are at least twelve eukaryotic initiation factors, composed of many more polypeptides, and these are described below.^[2]

eIF1 and eIF1A

eIF1 and eIF1A both bind to the 40S ribosome subunit-mRNA complex. Together they induce an "open" conformation of the mRNA binding channel, which is crucial for scanning, tRNA delivery, and start codon recognition.^[3] In particular, eIF1 dissociation from the 40S subunit is considered to be a key step in start codon recognition.^[4] eIF1 and eIF1A are small proteins (13 and 16 kDa, respectively in humans) and are both components of the 43S PIC. eIF1 binds near the ribosomal P-site, while eIF1A binds near the A-site, in a manner similar to the structurally and functionally related bacterial counterparts IF3 and IF1, respectively.^[5]

eIF2

eIF2 is the main protein complex responsible for delivering the initiator tRNA to the P-site of the preinitiation complex, as a ternary complex containing Met-tRNA_i^Met and GTP (the eIF2-TC). eIF2 has specificity for the methionine-charged initiator tRNA, which is distinct from other methionine-charged tRNAs used for elongation of the polypeptide chain. The eIF2 ternary complex remains bound to the P-site while the mRNA attaches to the 40s ribosome and the complex begins to scan the mRNA. Once the AUG start codon is recognized and located in the P-site, eIF5 stimulates the hydrolysis of eIF2-GTP, effectively switching it to the GDP-bound form via gated phosphate release.^[2] The hydrolysis of eIF2-GTP provides the conformational change to change the scanning complex into the 48S Initiation complex with the initiator tRNA-Met anticodon base paired to the AUG. After the initiation complex is formed the 60s subunit joins and eIF2 along with most of the initiation factors dissociate from the complex allowing the 60S subunit to bind. eIF1A and eIF5B-GTP remain bound to one another in the A site and must be hydrolyzed to be released and properly initiate elongation.^[6]^{: 191–192}

eIF2 has three subunits, eIF2-α, β, and γ. The former α-subunit is a target of regulatory phosphorylation and is of particular importance for cells that may need to turn off protein synthesis globally as a response to cell signaling events. When phosphorylated, it sequesters eIF2B (not to be confused with eIF2β), a GEF. Without this GEF, GDP cannot be exchanged for GTP, and translation is repressed. One example of this is the eIF2α-induced translation repression that occurs in reticulocytes when starved for iron. In the case of viral infection, protein kinase R (PKR) phosphorylates eIF2α when dsRNA is detected in many multicellular organisms, leading to cell death.

The proteins eIF2A and eIF2D are both technically named 'eIF2' but neither are part of the eIF2 heterotrimer and they seem to play unique functions in translation. Instead, they appear to be involved in specialized pathways, such as 'eIF2-independent' translation initiation or re-initiation, respectively.

eIF3

eIF3 independently binds the 40S ribosomal subunit, multiple initiation factors, and cellular and viral mRNA.^[7]

In mammals, eIF3 is the largest initiation factor, made up of 13 subunits (a-m). It has a molecular weight of ~800 kDa and controls the assembly of the 40S ribosomal subunit on mRNA that have a 5' cap or an IRES. eIF3 may use the eIF4F complex, or alternatively during internal initiation, an IRES, to position the mRNA strand near the exit site of the 40S ribosomal subunit, thus promoting the assembly of a functional pre-initiation complex.

In many human cancers, eIF3 subunits are overexpressed (subunits a, b, c, h, i, and m) and underexpressed (subunits e and f).^[8] One potential mechanism to explain this disregulation comes from the finding that eIF3 binds a specific set of cell proliferation regulator mRNA transcripts and regulates their translation.^[9] eIF3 also mediates cellular signaling through S6K1 and mTOR/Raptor to effect translational regulation.^[10]

eIF4

The eIF4F complex is composed of three subunits: eIF4A, eIF4E, and eIF4G. Each subunit has multiple human isoforms and there exist additional eIF4 proteins: eIF4B and eIF4H.

eIF4G is a 175.5-kDa scaffolding protein that interacts with eIF3 and the Poly(A)-binding protein (PABP), as well as the other members of the eIF4F complex. eIF4E recognizes and binds to the 5' cap structure of mRNA, while eIF4G binds PABP, which binds the poly(A) tail, potentially circularizing and activating the bound mRNA. eIF4A – a DEAD box RNA helicase – is important for resolving mRNA secondary structures.

eIF4B contains two RNA-binding domains – one non-specifically interacts with mRNA, whereas the second specifically binds the 18S portion of the small ribosomal subunit. It acts as an anchor, as well as a critical co-factor for eIF4A. It is also a substrate of S6K, and when phosphorylated, it promotes the formation of the pre-initiation complex. In vertebrates, eIF4H is an additional initiation factor with similar function to eIF4B.

eIF5, eIF5A and eIF5B

eIF5 is a GTPase-activating protein, which helps the large ribosomal subunit associate with the small subunit. It is required for GTP-hydrolysis by eIF2.

eIF5A is the eukaryotic homolog of EF-P. It helps with elongation and also plays a role in termination. EIF5A contains the unusual amino acid hypusine.^[11]

eIF5B is a GTPase, and is involved in assembly of the full ribosome. It is the functional eukaryotic analog of bacterial IF2.^[12]

eIF6

eIF6 performs the same inhibition of ribosome assembly as eIF3, but binds with the large subunit.

References

^ Jackson RJ, Hellen CU, Pestova TV (February 2010). "The mechanism of eukaryotic translation initiation and principles of its regulation". Nature Reviews Molecular Cell Biology. 11 (2): 113–27. doi:10.1038/nrm2838. PMC 4461372. PMID 20094052.
^ ^a ^b Aitken CE, Lorsch JR (June 2012). "A mechanistic overview of translation initiation in eukaryotes". Nature Structural & Molecular Biology. 19 (6): 568–76. doi:10.1038/nsmb.2303. PMID 22664984. S2CID 9201095.
^ Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acker MG, Algire MA, Lorsch JR, Ramakrishnan V (April 2007). "The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome". Molecular Cell. 26 (1): 41–50. doi:10.1016/j.molcel.2007.03.018. PMID 17434125.
^ Cheung YN, Maag D, Mitchell SF, Fekete CA, Algire MA, Takacs JE, Shirokikh N, Pestova T, Lorsch JR, Hinnebusch AG (May 2007). "Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo". Genes & Development. 21 (10): 1217–30. doi:10.1101/gad.1528307. PMC 1865493. PMID 17504939.
^ Fraser CS (July 2015). "Quantitative studies of mRNA recruitment to the eukaryotic ribosome". Biochimie. 114: 58–71. doi:10.1016/j.biochi.2015.02.017. PMC 4458453. PMID 25742741.
^ Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Martin KC (2016). Molecular Cell Biology (8th ed.). New York: W. H. Freeman and Company. ISBN 978-1-4641-8339-3. LCCN 2015957295.
^ Hinnebusch AG (October 2006). "eIF3: a versatile scaffold for translation initiation complexes". Trends in Biochemical Sciences. 31 (10): 553–62. doi:10.1016/j.tibs.2006.08.005. PMID 16920360.
^ Hershey JW (July 2015). "The role of eIF3 and its individual subunits in cancer". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1849 (7): 792–800. doi:10.1016/j.bbagrm.2014.10.005. PMID 25450521.
^ Lee AS, Kranzusch PJ, Cate JH (June 2015). "eIF3 targets cell-proliferation messenger RNAs for translational activation or repression". Nature. 522 (7554): 111–4. Bibcode:2015Natur.522..111L. doi:10.1038/nature14267. PMC 4603833. PMID 25849773.
^ Holz MK, Ballif BA, Gygi SP, Blenis J (November 2005). "mTOR and S6K1 mediate assembly of the translation preinitiation complex through dynamic protein interchange and ordered phosphorylation events". Cell. 123 (4): 569–80. doi:10.1016/j.cell.2005.10.024. PMID 16286006.
^ Schuller, AP; Wu, CC; Dever, TE; Buskirk, AR; Green, R (20 April 2017). "eIF5A Functions Globally in Translation Elongation and Termination". Molecular Cell. 66 (2): 194–205.e5. doi:10.1016/j.molcel.2017.03.003. PMC 5414311. PMID 28392174.
^ Allen GS, Frank J (February 2007). "Structural insights on the translation initiation complex: ghosts of a universal initiation complex". Molecular Microbiology. 63 (4): 941–50. doi:10.1111/j.1365-2958.2006.05574.x. PMID 17238926.

External links

Eukaryotic+Initiation+Factors at the U.S. National Library of Medicine Medical Subject Headings (MeSH)

[jackson2010-1] Jackson RJ, Hellen CU, Pestova TV (February 2010). "The mechanism of eukaryotic translation initiation and principles of its regulation". Nature Reviews Molecular Cell Biology. 11 (2): 113–27. doi:10.1038/nrm2838. PMC 4461372. PMID 20094052.

[Aitken-2] Aitken CE, Lorsch JR (June 2012). "A mechanistic overview of translation initiation in eukaryotes". Nature Structural & Molecular Biology. 19 (6): 568–76. doi:10.1038/nsmb.2303. PMID 22664984. S2CID 9201095.

[Passmore-3] Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acker MG, Algire MA, Lorsch JR, Ramakrishnan V (April 2007). "The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome". Molecular Cell. 26 (1): 41–50. doi:10.1016/j.molcel.2007.03.018. PMID 17434125.

[Yuen-Nei-4] Cheung YN, Maag D, Mitchell SF, Fekete CA, Algire MA, Takacs JE, Shirokikh N, Pestova T, Lorsch JR, Hinnebusch AG (May 2007). "Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo". Genes & Development. 21 (10): 1217–30. doi:10.1101/gad.1528307. PMC 1865493. PMID 17504939.

[Fraser-5] Fraser CS (July 2015). "Quantitative studies of mRNA recruitment to the eukaryotic ribosome". Biochimie. 114: 58–71. doi:10.1016/j.biochi.2015.02.017. PMC 4458453. PMID 25742741.

[6] Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Martin KC (2016). Molecular Cell Biology (8th ed.). New York: W. H. Freeman and Company. ISBN 978-1-4641-8339-3. LCCN 2015957295.

[Hinnebusch-7] Hinnebusch AG (October 2006). "eIF3: a versatile scaffold for translation initiation complexes". Trends in Biochemical Sciences. 31 (10): 553–62. doi:10.1016/j.tibs.2006.08.005. PMID 16920360.

[8] Hershey JW (July 2015). "The role of eIF3 and its individual subunits in cancer". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1849 (7): 792–800. doi:10.1016/j.bbagrm.2014.10.005. PMID 25450521.

[Lee-9] Lee AS, Kranzusch PJ, Cate JH (June 2015). "eIF3 targets cell-proliferation messenger RNAs for translational activation or repression". Nature. 522 (7554): 111–4. Bibcode:2015Natur.522..111L. doi:10.1038/nature14267. PMC 4603833. PMID 25849773.

[Holz-10] Holz MK, Ballif BA, Gygi SP, Blenis J (November 2005). "mTOR and S6K1 mediate assembly of the translation preinitiation complex through dynamic protein interchange and ordered phosphorylation events". Cell. 123 (4): 569–80. doi:10.1016/j.cell.2005.10.024. PMID 16286006.

[11] Schuller, AP; Wu, CC; Dever, TE; Buskirk, AR; Green, R (20 April 2017). "eIF5A Functions Globally in Translation Elongation and Termination". Molecular Cell. 66 (2): 194–205.e5. doi:10.1016/j.molcel.2017.03.003. PMC 5414311. PMID 28392174.

[Allen-12] Allen GS, Frank J (February 2007). "Structural insights on the translation initiation complex: ghosts of a universal initiation complex". Molecular Microbiology. 63 (4): 941–50. doi:10.1111/j.1365-2958.2006.05574.x. PMID 17238926.

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