title: Probing the closed-loop model of mRNA translation in living cells.
abstract: The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence in vivo is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression.
authors.affiliation: a Genome Biology Department; The John Curtin School of Medical Research (JCSMR); The Australian National University ; Acton (Canberra), Australian Capital Territory , Australia.
authors.forename: Stuart K
authors.initials: SK
authors.lastname: Archer
authors.forename: Nikolay E
authors.initials: NE
authors.lastname: Shirokikh
authors.forename: Claus V
authors.initials: CV
authors.lastname: Hallwirth
authors.forename: Traude H
authors.initials: TH
authors.lastname: Beilharz
authors.forename: Thomas
authors.initials: T
authors.lastname: Preiss
mesh_terms: D001665:Binding Sites; D039561:Eukaryotic Initiation Factor-4E / Q000235:genetics / Q000378:metabolism; D039603:Eukaryotic Initiation Factor-4G / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D009690:Nucleic Acid Conformation; D039102:Poly(A)-Binding Proteins / Q000235:genetics / Q000378:metabolism; D011132:Polyribosomes / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D014176:Protein Biosynthesis; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D039561:Eukaryotic Initiation Factor-4E; D039603:Eukaryotic Initiation Factor-4G; D039102:Poly(A)-Binding Proteins; D012331:RNA, Fungal; D012333:RNA, Messenger; D011994:Recombinant Proteins; D029701:Saccharomyces cerevisiae Proteins; C450100:pab1 protein, S cerevisiae
keywords: cap-poly(A) synergy; eukaryotic translation; mRNA closed-loop; polysomes, ribosomal recycling
references.citation: Microbiology. 2001 Feb;147(Pt 2):411-7
references.pmid: 11158358
references.citation: Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3889-94
references.pmid: 12660367
references.citation: Cold Spring Harb Symp Quant Biol. 2001;66:293-300
references.pmid: 12762031
references.citation: Nature. 2003 Oct 16;425(6959):686-91
references.pmid: 14562095
references.citation: Nature. 2003 Oct 16;425(6959):737-41
references.pmid: 14562106
references.citation: Mol Cell Biol. 2004 Feb;24(4):1779-90
references.pmid: 14749392
references.citation: Yeast. 2004 Aug;21(11):947-62
references.pmid: 15334558
references.citation: Eur J Biochem. 1971 Dec 22;24(1):156-62
references.pmid: 5138645
references.citation: Genes Dev. 1991 Nov;5(11):2108-16
references.pmid: 1682219
references.citation: Nucleic Acids Res. 1995 Jun 25;23(12):2198-205
references.pmid: 7610048
references.citation: Genes Dev. 1995 Dec 1;9(23):2997-3007
references.pmid: 7498795
references.citation: EMBO J. 1996 Dec 16;15(24):7168-77
references.pmid: 9003792
references.citation: Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9046-51
references.pmid: 9256432
references.citation: J Biol Chem. 1997 Aug 29;272(35):21677-80
references.pmid: 9268293
references.citation: Nature. 1998 Apr 2;392(6675):516-20
references.pmid: 9548259
references.citation: Mol Cell. 1998 Jul;2(1):135-40
references.pmid: 9702200
references.citation: Yeast. 1998 Sep 15;14(12):1089-104
references.pmid: 9778795
references.citation: EMBO J. 1998 Dec 15;17(24):7480-9
references.pmid: 9857202
references.citation: Anat Rec. 1999 Jun 1;255(2):116-29
references.pmid: 10359513
references.citation: Yeast. 1999 Jul;15(10B):963-72
references.pmid: 10407276
references.citation: J Biophys Biochem Cytol. 1955 Jan;1(1):59-68
references.pmid: 14381428
references.citation: Nature. 1965 Feb 6;205:567-70
references.pmid: 14298546
references.citation: Methods Enzymol. 2007;429:163-83
references.pmid: 17913623
references.citation: J Cell Biol. 2007 Oct 8;179(1):65-74
references.pmid: 17908917
references.citation: Nucleic Acids Res. 2008 May;36(8):2476-88
references.pmid: 18310103
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Nature. 2008 Jun 26;453(7199):1276-80
references.pmid: 18496529
references.citation: Nat Rev Mol Cell Biol. 2010 Feb;11(2):113-27
references.pmid: 20094052
references.citation: Nucleic Acids Res. 2010 Nov;38(20):7054-67
references.pmid: 20571082
references.citation: PLoS One. 2010;5(11):e15442
references.pmid: 21103382
references.citation: Mol Syst Biol. 2011 Jan 4;7:458
references.pmid: 21206491
references.citation: BMC Genomics. 2011;12:68
references.pmid: 21269496
references.citation: Cold Spring Harb Perspect Biol. 2012 Jul;4(7):a012245
references.pmid: 22751153
references.citation: Cell. 2012 Jul 6;150(1):111-21
references.pmid: 22770215
references.citation: BMC Mol Biol. 2012;13:19
references.pmid: 22720784
references.citation: PLoS One. 2012;7(12):e52824
references.pmid: 23285195
references.citation: Genome Res. 2014 Mar;24(3):422-30
references.pmid: 24318730
references.citation: Mol Cell. 2014 May 22;54(4):547-58
references.pmid: 24856220
references.citation: Annu Rev Biochem. 2014;83:779-812
references.pmid: 24499181
references.citation: Wiley Interdiscip Rev RNA. 2014 Nov-Dec;5(6):747-63
references.pmid: 24944158