title: Physical evidence supporting a ribosomal shunting mechanism of translation initiation for BACE1 mRNA.
abstract: In Alzheimer disease, elevated levels of the BACE1 enzyme are correlated with increased production of amyloid peptides and disease pathology. The increase in BACE1 levels is post-transcriptional and may involve altered translation efficiency. Earlier studies have indicated that translation of BACE1 mRNA is cap-dependent. As ribosomal subunits move from the cap-structure to the initiation codon, they fail to recognize several AUG codons in the 5' leader. In this study, we looked for physical evidence of the mechanism underlying ribosomal scanning or shunting along the BACE1 5' leader by investigating structural stability in the 5' leaders of endogenous mRNAs in vivo. To perform this analysis, we probed RNAs using lead(II) acetate, a cell-permeable chemical that induces cleavage of unpaired nucleotides having conformational flexibility. The data revealed that the ≈440-nt 5' leader was generally resistant to cleavage except for a region upstream of the initiation codon. Cleavage continued into the coding region, consistent with destabilization of secondary structures by translating ribosomes. Evidence that a large segment of the BACE1 5' leader was not cleaved indicates that this region is structurally stable and suggests that it is not scanned. The data support a mechanism of translation initiation in which ribosomal subunits bypass (shunt) part of the BACE1 5' leader to reach the initiation codon. We suggest that a nucleotide bias in the 5' leader may predispose the initiation codon to be more accessible than other AUG codons in the 5' leader, leading to an increase in its relative utilization.
authors.affiliation: Department of Cell and Molecular Biology; The Scripps Research Institute; La Jolla, CA USA.
authors.forename: Dora C
authors.initials: DC
authors.lastname: Koh
authors.affiliation: Department of Cell and Molecular Biology; The Scripps Research Institute; La Jolla, CA USA.
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Edelman
authors.affiliation: Department of Cell and Molecular Biology; The Scripps Research Institute; La Jolla, CA USA.
authors.forename: Vincent P
authors.initials: VP
authors.lastname: Mauro
keywords: BACE1; Initiation; RNase P; Ribosome; Shunt; Translation; mRNA
references.citation: Prog Nucleic Acid Res Mol Biol. 2002;72:307-31
references.pmid: 12206455
references.citation: RNA. 1997 Jun;3(6):557-60
references.pmid: 9174091
references.citation: RNA. 2005 Sep;11(9):1348-54
references.pmid: 16043496
references.citation: Nucleic Acids Res. 2010 Dec;38(22):7885-94
references.pmid: 20716516
references.citation: Nucleic Acids Res. 2007;35(9):2975-85
references.pmid: 17439957
references.citation: Mol Cell. 2006 Nov 3;24(3):445-56
references.pmid: 17081993
references.citation: Annu Rev Neurosci. 2011;34:185-204
references.pmid: 21456963
references.citation: Nat Chem Biol. 2006 Apr;2(4):213-20
references.pmid: 16532013
references.citation: Nat Rev Mol Cell Biol. 2011 Apr;12(4):235-45
references.pmid: 21427765
references.citation: RNA Biol. 2009 Sep-Oct;6(4):362-9
references.pmid: 19738420
references.citation: Trends Biochem Sci. 2006 Jun;31(6):333-41
references.pmid: 16679018
references.citation: Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2794-9
references.pmid: 14981268
references.citation: J Mol Biol. 1998 Jan 16;275(2):211-20
references.pmid: 9466904
references.citation: Bioinformatics. 2010 Nov 1;26(21):2651-5
references.pmid: 20819958
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1808-17
references.pmid: 15034149
references.citation: Eur J Biochem. 1994 Jan 15;219(1-2):49-56
references.pmid: 8307015
references.citation: Methods Enzymol. 2007;429:323-54
references.pmid: 17913630
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18077-82
references.pmid: 17110442
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9488-93
references.pmid: 16769881
references.citation: RNA. 2002 Apr;8(4):534-41
references.pmid: 11991646
references.citation: J Cell Biol. 1989 Feb;108(2):229-41
references.pmid: 2645293
references.citation: RNA. 2000 Dec;6(12):1895-904
references.pmid: 11142387
references.citation: Nucleic Acids Res. 1981 Jan 10;9(1):133-48
references.pmid: 6163133
references.citation: J Neurochem. 2012 Jan;120 Suppl 1:9-21
references.pmid: 22122372
references.citation: Nucleic Acids Res. 1999 Jan 1;27(1):314
references.pmid: 9847214
references.citation: Nucleic Acids Res. 1989 Aug 11;17(15):6419
references.pmid: 2771659
references.citation: Can J Neurol Sci. 2012 May;39(3):286-98
references.pmid: 22547507
references.citation: Microbiol Mol Biol Rev. 2011 Sep;75(3):434-67, first page of table of contents
references.pmid: 21885680
references.citation: J Neurochem. 2012 Jan;120 Suppl 1:62-70
references.pmid: 22122349
references.citation: Mol Microbiol. 2004 Feb;51(4):987-1001
references.pmid: 14763975
references.citation: PLoS One. 2010 Nov 24;5(11):e15057
references.pmid: 21124832
references.citation: J Mol Biol. 1999 May 21;288(5):911-40
references.pmid: 10329189
references.citation: RNA Biol. 2009 Jan-Mar;6(1):54-8
references.pmid: 19106624
references.citation: FASEB J. 2004 Jun;18(9):1034-6
references.pmid: 15059975
references.citation: EMBO Rep. 2004 Jun;5(6):620-5
references.pmid: 15167888