title: Influence of translation factor activities on start site selection in six different mRNAs.
abstract: Current literature using biochemical assays, structural analyses and genetic manipulations has reported that the key factors associated with the faithful matching of the initiator met-tRNA to the start codon AUG are eIF1, eIF1A and eIF5. However, these findings were in each case based upon the utilization of a single mRNA, perhaps with variations. In an effort to evaluate this general finding, we tested six different mRNAs. Our results confirm that these three proteins are important for start site selection. However, two additional findings would not have been predicted. The first is that eIF1 plays a major role in selecting against start codons that are in close proximity to the 5' end of the mRNA (i.e., less than 21 nucleotides). Second, the addition of eIF5B had nearly the same affect as the addition of eIF5. This is unexpected given the different roles that eIF5 and eIF5B have been proposed to play in the 80S initiation pathway. Finally, although many of the mRNAs appear to respond qualitatively in a similar manner, the quantitative differences noted suggest that there is still some mRNA specific character to our findings. This character may be the length of the 5' UTR, involvement of an IRES element, secondary structure either 5' or 3' of the start codon or specific sequence/structure elements that interact with RNA binding proteins or the ribosome.
authors.affiliation: Department of Biochemistry; School of Medicine; Case Western Reserve University; Cleveland, OH USA.
authors.forename: Daine
authors.initials: D
authors.lastname: Barth-Baus
authors.affiliation: Carlsbad, CA USA.
authors.forename: C Ramana
authors.initials: CR
authors.lastname: Bhasker
authors.affiliation: Biology Department; Montgomery County Community College; Blue Bell, PA USA.
authors.forename: Wendy
authors.initials: W
authors.lastname: Zoll
authors.affiliation: Department of Biochemistry; School of Medicine; Case Western Reserve University; Cleveland, OH USA.
authors.forename: William C
authors.initials: WC
authors.lastname: Merrick
keywords: eIF1; eIF1A; eIF5; eIF5B; mRNAs; protein synthesis; start site selection
references.citation: Genes Dev. 2010 Jan 1;24(1):97-110
references.pmid: 20048003
references.citation: Mol Cell Biol. 2008 Nov;28(22):6877-88
references.pmid: 18794367
references.citation: Genes Dev. 2007 Jun 1;21(11):1280-7
references.pmid: 17545463
references.citation: J Biol Chem. 2005 Feb 4;280(5):3433-40
references.pmid: 15561726
references.citation: J Mol Biol. 2010 Mar 5;396(4):1097-116
references.pmid: 20060839
references.citation: Nature. 1970 Aug 15;227(5259):680-5
references.pmid: 5432063
references.citation: Mol Cell. 2000 Jan;5(1):109-19
references.pmid: 10678173
references.citation: J Biol Chem. 1983 May 10;258(9):5804-10
references.pmid: 6853548
references.citation: Structure. 2009 Dec 9;17(12):1591-604
references.pmid: 20004163
references.citation: Proc Natl Acad Sci U S A. 1990 Nov;87(21):8301-5
references.pmid: 2236042
references.citation: EMBO J. 1999 May 4;18(9):2631-7
references.pmid: 10228174
references.citation: Proc Natl Acad Sci U S A. 1976 Aug;73(8):2584-8
references.pmid: 1066667
references.citation: Genetics. 1990 Mar;124(3):483-95
references.pmid: 2179049
references.citation: J Biol Chem. 1979 May 25;254(10):3708-11
references.pmid: 438155
references.citation: Nucleic Acids Res. 2012 Apr;40(7):2898-906
references.pmid: 22156057
references.citation: Mol Cell Biol. 2003 Jan;23(1):26-37
references.pmid: 12482958
references.citation: Gene. 2012 Jul 10;502(2):75-86
references.pmid: 22555019
references.citation: J Biol Chem. 2001 Mar 2;276(9):6720-6
references.pmid: 11092890
references.citation: Mol Cell Biol. 1992 Jan;12(1):248-60
references.pmid: 1729602
references.citation: J Biol Chem. 1982 May 10;257(9):5246-52
references.pmid: 7068683
references.citation: Genes Dev. 2000 Oct 1;14(19):2534-46
references.pmid: 11018020
references.citation: Genes Dev. 1997 Sep 15;11(18):2396-413
references.pmid: 9308967
references.citation: Methods Enzymol. 1979;60:108-23
references.pmid: 459892
references.citation: Mol Cell Biol. 1989 Nov;9(11):5134-42
references.pmid: 2601712
references.citation: Nature. 1998 Aug 27;394(6696):854-9
references.pmid: 9732867
references.citation: J Biol Chem. 1975 Dec 10;250(23):9083-9
references.pmid: 1194278
references.citation: Nucleic Acids Res. 2011 Sep 1;39(17):7598-609
references.pmid: 21705780
references.citation: Genes Dev. 2007 May 15;21(10):1217-30
references.pmid: 17504939
references.citation: J Biol Chem. 1991 Feb 25;266(6):3594-601
references.pmid: 1995620
references.citation: J Biol Chem. 1978 May 10;253(9):3070-7
references.pmid: 641055
references.citation: Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):18056-60
references.pmid: 20921384
references.citation: Genes Dev. 2006 Mar 1;20(5):624-36
references.pmid: 16510876
references.citation: J Mol Biol. 1977 Nov;116(4):755-67
references.pmid: 592399
references.citation: J Biol Chem. 1997 Dec 19;272(51):32061-6
references.pmid: 9405401
references.citation: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jun 1;67(Pt 6):730-3
references.pmid: 21636924
references.citation: Nat Struct Mol Biol. 2012 Jun 05;19(6):568-76
references.pmid: 22664984
references.citation: J Biol Chem. 1975 Dec 10;250(23):9067-75
references.pmid: 1194277
references.citation: Mol Cell Biol. 2011 Dec;31(23):4814-31
references.pmid: 21930786
references.citation: J Biol Chem. 2005 May 13;280(19):18610-22
references.pmid: 15755734
references.citation: J Biol Chem. 1976 Sep 25;251(18):5551-7
references.pmid: 965377
references.citation: J Biol Chem. 1979 Aug 25;254(16):7730-5
references.pmid: 468782
references.citation: RNA. 2011 Mar;17(3):439-52
references.pmid: 21220547
references.citation: Genes Dev. 2004 Dec 15;18(24):3078-93
references.pmid: 15601822
references.citation: Methods Enzymol. 1979;60:136-65
references.pmid: 459895
references.citation: EMBO J. 1991 Mar;10(3):655-64
references.pmid: 1825810
references.citation: Methods Enzymol. 2007;429:1-21
references.pmid: 17913616
references.citation: J Mol Biol. 1987 Aug 20;196(4):947-50
references.pmid: 3681984
references.citation: J Mol Biol. 2009 Jan 16;385(2):491-506
references.pmid: 18976658
references.citation: Mol Cell Biol. 1998 Sep;18(9):5021-31
references.pmid: 9710586
references.citation: Eur J Biochem. 1979 Aug 1;98(2):329-37
references.pmid: 488105
references.citation: Microbiol Mol Biol Rev. 2011 Sep;75(3):434-67, first page of table of contents
references.pmid: 21885680
references.citation: J Biol Chem. 1975 Jul 25;250(14):5556-62
references.pmid: 1095581
references.citation: J Biol Chem. 2003 Oct 10;278(41):39477-82
references.pmid: 12885778
references.citation: Science. 2011 Feb 11;331(6018):730-6
references.pmid: 21205638
references.citation: Mol Cell. 2005 Oct 28;20(2):251-62
references.pmid: 16246727
references.citation: Nature. 2000 Jan 20;403(6767):332-5
references.pmid: 10659855
references.citation: J Biol Chem. 1975 Feb 25;250(4):1197-206
references.pmid: 1112800
references.citation: EMBO J. 1995 Jun 1;14(11):2536-44
references.pmid: 7781606
references.citation: Cell Rep. 2012 Jun 28;1(6):689-702
references.pmid: 22813744