Sandbox Reserved 327: Difference between revisions
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=Introduction= | =Introduction= | ||
Translation is an essential process for both prokaryotes and eukaryotes to make various proteins from nucleic acid. It requires three different steps: initiation, elongation, and termination. Many proteins are needed in the initiation phase to form an initiation complex with the ribosome and promote the translation. In eukaryotes, these proteins are also known as eukaryotic initiation factors (eIF). The eIFs were first studied through the genetic analyzed of yeast ''Saccharomyces cerevisiae'' | Translation is an essential process for both prokaryotes and eukaryotes to make various proteins from nucleic acid. It requires three different steps: initiation, elongation, and termination. Many proteins are needed in the initiation phase to form an initiation complex with the ribosome and promote the translation. In eukaryotes, these proteins are also known as eukaryotic initiation factors (eIF). The eIFs were first studied through the genetic analyzed of yeast | ||
[http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae| ''Saccharomyces cerevisiae''] showed that the initiation process is complex since it involves at least 12 eIFs containing more than 30 polypeptides , including eIF1, eIF2, eIF3, eIF4, and eIF5 <ref name="elegans"/>. | |||
=Structure and the binding sites= | |||
{{STRUCTURE_2ogh|PDB=2ogh|SCENE}} | {{STRUCTURE_2ogh|PDB=2ogh|SCENE}} | ||
eIF1 is a small protein (12 kDa) that is encode by ''sui1'' which is one of the component of multifactor complex (MFC) that plays an important role in regulating translation initiation <ref name="eIF1"/><ref name="asano"/>. eIF1 is a universal translation factor across organisms which make eIF1 homologs can be found in other eukayotes, archaea, and some bacteria <ref name="flet"/>. Yeast eIF1 contains a | eIF1 is a small protein (12 kDa) that is encode by ''sui1'' which is one of the component of multifactor complex (MFC) that plays an important role in regulating translation initiation <ref name="eIF1"/><ref name="asano"/>. eIF1 is a universal translation factor across organisms which make eIF1 homologs can be found in other eukayotes, archaea, and some bacteria <ref name="flet"/>. Yeast eIF1 contains a | ||
<scene name='Sandbox_Reserved_327/Ribbon_structure/1'>β-sheet with α helices</scene> | <scene name='Sandbox_Reserved_327/Ribbon_structure/1'>β-sheet with α helices</scene> | ||
on one side with N-terminal tail (aa 1-23) or NTT <ref name="eIF1"/>. It is homolog to | on one side with N-terminal tail (aa 1-23) or NTT <ref name="eIF1"/>. It is homolog to | ||
<scene name='Sandbox_Reserved_327/Human_eif1/1'>human eIF1</scene> | <scene name='Sandbox_Reserved_327/Human_eif1/1'>human eIF1</scene> | ||
since | since it has 87% structure similarity and 63% identity (DNA sequence) to the human eIF1 <ref name="eIF1"/> <ref name="flet"/>. However, yeast eIF1 has two different conformations with two clear sets of backbone resonances that interconverting with each other and 20 different possible models for the N-terminal tail structure <ref name="eIF1"/>. So far, only the binding sites of eIF1 to ribosome and eIF5 have been determined, while the exact binding site interactions with other initiation proteins are still unknown <ref name="eIF1"/> <ref name="flet"/>. | ||
==eIF1-ribosome binding site== | ==eIF1-ribosome binding site== | ||
eIF1 would bind near the P-site region of the ribosomal 40S, changes the conformation of the 40S subunit, the position of mRNA and the start codon initiation <ref name="lomakin"/>. This binding site region is unexpectedly similar to the binding site of prokaryotic initiation factor IF3 to the ribosome, despite their unrelated structure <ref name="lomakin"/>. Together with eIF1A, eIF5, eIF3, and the eIF2.GTP.Met-tRNA<sub>i</sub><sup>Met</sup> ternary complex (TC), eIF1 would form a 43S preinitiation complex (PIC) or also known as multi factor complex (MFC)<ref name="eIF1"/><ref name="lomakin"/><ref name="cheung"/>. | |||
==eIF1-eIF5 binding sites== | ==eIF1-eIF5 binding sites== | ||
There are two | There are two | ||
<scene name='Sandbox_Reserved_327/Basic_eif1/3'>eIF1-eIF5 binding sites</scene>: at the NTT site of eIF1 and at a KH surface area, a specific region that rich in Lysine (K) and hydrophobic (H) residues <ref name="eIF1"/>. These bindings are different from the eIF1-ribosome binding site and are salt dependent, with high salt concentration would make the interaction weaker <ref name="eIF1"/>. The eIF1-NTT area is believed to play role in stimulating the MFC assembly by promoting the eIF5- eIF2β <ref name="eIF1"/>. The other binding site area | <scene name='Sandbox_Reserved_327/Basic_eif1/3'>eIF1-eIF5 binding sites</scene>: at the NTT site of eIF1 and at a KH surface area, a specific region that rich in Lysine (K) and hydrophobic (H) residues <ref name="eIF1"/>. These bindings are different from the eIF1-ribosome binding site and are salt dependent, with high salt concentration would make the interaction weaker <ref name="eIF1"/>. | ||
===eIF1-NTT=== | |||
The eIF1-NTT area is believed to play role in stimulating the MFC assembly by promoting the eIF5- eIF2β <ref name="eIF1"/>. | |||
''In vitro'' mutation in the eIF1-NTT area would alter the binding of eIF5 and eIF2β, but not eIF3c which supported that this area played role in stimulating the MFC assembly <ref name="eIF1"/>. ''In vivo'' study also supported that eIF1-NTT would allow the binding of eIF1 to the eIF5 and eIF2β <ref name="eIF1"/>. | |||
===eIF1-KH=== | |||
The other binding site area of eIF1 to eIF5 which is believed to play role in the AUG start codon selection since ''in vitro'' mutation in this area by altering the basic part of the KH region would relax the start codon selection <ref name="eIF1"/>.The mutation would also alter the formation of MFC, but not like mutation in the eIF1-NTT area, eIF1-NTT mutation is lethal to the yeast growth <ref name="eIF1"/>. Mutation that alter the hydrophobic residue would disrupt a critical link to the PIC and prevent the eIF1 dissociation <ref name="cheung"/>. The critical link is believed to be strongly associate with eIF5 <ref name="eIF1"/>. | |||
=Function and Mechanism= | =Function and Mechanism= | ||
[[Image:640px-Eukaryotic_initiation.png|thumb|left|Simplified model of eukaryotic initiation by [http://commons.wikimedia.org/wiki/User:Webridge Webridge]]] | [[Image:640px-Eukaryotic_initiation.png|thumb|left|570px|Simplified model of eukaryotic initiation by [http://commons.wikimedia.org/wiki/User:Webridge Webridge]]] | ||
= | eIF1 is essential to control the ribosome conformational rearrangement in translation initiation by stimulating the formation of MFC and controlling the start codon selection which allow the translation elongation process to occur | ||
==eIF1 | <ref name="eIF1"/><ref name="asano"/>.Start codon selection is a key step for translation elongation to occur because recognition of the right AUG start codon would lead to the binding of 60S subunit to form the 80 S initiation complex, a precursor for elongation <ref name="eIF1"/>. Study showed eIF1 dissociation plays a critical role in start codon selection <ref name="cheung"/>. | ||
Initially, eIF1 in the 43S PIC would interact with the 5’end of mRNA to form 48S PIC and promotes scanning until the Met-tRNA<sub>i</sub><sup>Met</sup> recognizes the right AUG codon from the mRNA <ref name="eIF1"/><ref name="cheung"/>. Once the right codon is recognized, there would be a conformational change on the ribosome and the Met-tRNA<sub>i</sub><sup>Met</sup> would be released to the P-site, ready for the elongation process (paper, cheung). Also, hydrolysis of eIF2.GTP to GDP by the action of N-terminal residues of eIF5 in the PIC complex would occur, leading to a Pi being released <ref name="eIF1"/><ref name="cheung"/>. These two events would let the eIF1 and eIF2.GDP to be released from the PIC. Then, eIF5 GTPase would promote the binding of the ribosomal 60S forming the 80S ribosome, get it ready for elongation <ref name="eIF1"/>. The eIF2-GDP is then going to be re-used for another TC formation when it is recycled back to eIF2-GTP by eIF2B.GEF <ref name="eIF1"/>. However, when the codon-anticodon pair is mismatched, eIF1 would avoid the recognition by preventing the hydrolysis through blocking the Pi release at non-AUG codons and repressing the activity of eIF5 GTPase <ref name="eIF1"/><ref name="lomakin"/><ref name="cheung"/>. | |||
Mutations in eIF1 would alter the function and mechanism of eIF1 in the cell. There are two classesof mutations in yeast eIF1: ''Mof2'' and ''Sui1'' mutations <ref name="flet"/>. Mof2 mutation in eIF1 would increase the ribosome frameshifting in the translation process <ref name="flet"/>. As for ''Sui1'' mutation, | |||
''in vitro'' and ''in vivo'' mutations would let the mismatched pairing of Met-tRNA<sub>i</sub><sup>Met</sup> with non-AUG codons to occur <ref name="flet"/>. Initiation at UUG codons would be increased instead, while the binding of eIF1 to 40S subunits would be reduced <ref name="cheung"/>. However, this mutation would increase the eIF1 dissociation and Pi release rate from the PIC while another mutation that is completely the opposite, suppress the expression of ''Sui'' mutation (hyperaccuracy mutation in eIF1A), would decrease the dissociation rate <ref name="cheung"/>. | |||
=See also= | |||
[http://en.wikibooks.org/wiki/An_Introduction_to_Molecular_Biology/Protein_synthesis#Initiation_2| Eukaryotic Translation] | |||
=References= | =References= | ||
<ref name="elegans"> DOI:10.1534/genetics.110.121541 </ref> | |||
<ref name="eIF1"> PMID:17974565 </ref> | <ref name="eIF1"> PMID:17974565 </ref> | ||
<ref name="asano"> DOI:10.1101/gad.1562707 </ref> | |||
<ref name="flet"> PMID: 10228174 </ref> | <ref name="flet"> PMID: 10228174 </ref> | ||
<ref name="lomakin"> DOI:10.1101/gad.1141803 </ref> | <ref name="lomakin"> DOI:10.1101/gad.1141803 </ref> | ||
<ref name="cheung"> DOI:10.1101/gad.1528307 </ref> | <ref name="cheung"> DOI:10.1101/gad.1528307 </ref> | ||
<references/> | <references/> | ||