Ribosomes in RNA Granules Are Stalled on mRNA Sequences That Are Consensus Sites for FMRP Association.
cryo-EM
elongation
neuroscience
protein synthesis
ribosome profiling
stalled ribosome
Journal
The Journal of neuroscience : the official journal of the Society for Neuroscience
ISSN: 1529-2401
Titre abrégé: J Neurosci
Pays: United States
ID NLM: 8102140
Informations de publication
Date de publication:
05 04 2023
05 04 2023
Historique:
received:
23
05
2022
revised:
07
02
2023
accepted:
13
02
2023
medline:
7
4
2023
pubmed:
28
2
2023
entrez:
27
2
2023
Statut:
ppublish
Résumé
Local translation in neurons is partly mediated by the reactivation of stalled polysomes. Stalled polysomes may be enriched within the granule fraction, defined as the pellet of sucrose gradients used to separate polysomes from monosomes. The mechanism of how elongating ribosomes are reversibly stalled and unstalled on mRNAs is still unclear. In the present study, we characterize the ribosomes in the granule fraction using immunoblotting, cryogenic electron microscopy (cryo-EM), and ribosome profiling. We find that this fraction, isolated from 5-d-old rat brains of both sexes, is enriched in proteins implicated in stalled polysome function, such as the fragile X mental retardation protein (FMRP) and Up-frameshift mutation 1 homologue. Cryo-EM analysis of ribosomes in this fraction indicates they are stalled, mainly in the hybrid state. Ribosome profiling of this fraction reveals (1) an enrichment for footprint reads of mRNAs that interact with FMRPs and are associated with stalled polysomes, (2) an abundance of footprint reads derived from mRNAs of cytoskeletal proteins implicated in neuronal development, and (3) increased ribosome occupancy on mRNAs encoding RNA binding proteins. Compared with those usually found in ribosome profiling studies, the footprint reads were longer and were mapped to reproducible peaks in the mRNAs. These peaks were enriched in motifs previously associated with mRNAs cross-linked to FMRP
Identifiants
pubmed: 36849416
pii: JNEUROSCI.1002-22.2023
doi: 10.1523/JNEUROSCI.1002-22.2023
pmc: PMC10082463
doi:
Substances chimiques
Fragile X Mental Retardation Protein
139135-51-6
RNA, Messenger
0
Banques de données
PDB
['6XIQ']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2440-2459Subventions
Organisme : CIHR
ID : 374967
Pays : Canada
Informations de copyright
Copyright © 2023 the authors.
Références
Science. 2009 Apr 10;324(5924):218-23
pubmed: 19213877
Science. 2020 Jan 31;367(6477):
pubmed: 32001627
Int J Mol Sci. 2014 Dec 16;15(12):23377-88
pubmed: 25522169
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
Nat Neurosci. 2006 Oct;9(10):1247-56
pubmed: 16980963
J Neurosci. 2011 Mar 9;31(10):3914-25
pubmed: 21389246
Curr Opin Neurobiol. 2017 Aug;45:169-177
pubmed: 28633045
Nature. 2012 May 02;485(7396):109-13
pubmed: 22552098
Nature. 2020 Jul;583(7818):711-719
pubmed: 32728246
Elife. 2020 Jun 08;9:
pubmed: 32510328
BMC Bioinformatics. 2017 Sep 2;18(1):391
pubmed: 28865429
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Nature. 2015 Apr 30;520(7549):640-5
pubmed: 25901680
Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16205-10
pubmed: 24043809
Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22157-22166
pubmed: 32855298
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
J Neurosci. 2015 Mar 11;35(10):4403-17
pubmed: 25762683
Nucleic Acids Res. 2015 Apr 20;43(7):3680-7
pubmed: 25805170
Hum Mol Genet. 2003 Dec 15;12(24):3295-305
pubmed: 14570712
J Cell Sci. 1995 Aug;108 ( Pt 8):2781-90
pubmed: 7593319
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Genome Biol. 2021 Jan 5;22(1):16
pubmed: 33402206
Cell Rep. 2020 Mar 31;30(13):4459-4472.e6
pubmed: 32234480
Curr Opin Neurobiol. 2018 Aug;51:86-94
pubmed: 29549711
Traffic. 2006 Dec;7(12):1581-9
pubmed: 17054760
J Med Genet. 2018 Feb;55(2):104-113
pubmed: 29097605
RNA. 2019 Apr;25(4):407-422
pubmed: 30655309
J Struct Biol. 2015 Nov;192(2):216-21
pubmed: 26278980
Nat Rev Genet. 2014 Mar;15(3):205-13
pubmed: 24468696
Nat Neurosci. 2018 Jul;21(7):1004-1014
pubmed: 29950670
Genes (Basel). 2020 Sep 27;11(10):
pubmed: 32992647
Neuron. 2001 Nov 20;32(4):683-96
pubmed: 11719208
Nucleic Acids Res. 2019 Mar 18;47(5):e25
pubmed: 30590705
Nat Methods. 2019 Jun;16(6):471-477
pubmed: 31086343
Nucleic Acids Res. 2016 Aug 19;44(14):6649-59
pubmed: 27378784
J Biol Chem. 2019 Dec 27;294(52):19889-19895
pubmed: 31753916
Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2180-5
pubmed: 15684045
J Neurosci. 2005 Mar 16;25(11):2992-3001
pubmed: 15772359
Mol Cell. 2014 May 8;54(3):407-417
pubmed: 24746697
J Neurosci. 2017 Sep 20;37(38):9116-9131
pubmed: 28821679
Nature. 2012 Dec 20;492(7429):382-6
pubmed: 23235829
Nucleic Acids Res. 2018 Jul 6;46(12):6344-6355
pubmed: 29668986
Philos Trans R Soc Lond B Biol Sci. 2017 Mar 19;372(1716):
pubmed: 28138069
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
pubmed: 12824337
Protein Sci. 2021 Jan;30(1):70-82
pubmed: 32881101
J Biol Chem. 2010 Feb 12;285(7):4747-56
pubmed: 20007716
Nat Struct Mol Biol. 2016 Feb;23(2):110-5
pubmed: 26751643
J Neurosci. 2003 Nov 12;23(32):10433-44
pubmed: 14614102
Sci Rep. 2020 Jul 1;10(1):10781
pubmed: 32612155
J Neurochem. 2016 Jan;136(2):276-84
pubmed: 26485687
Prog Neurobiol. 2013 Jul-Aug;106-107:1-16
pubmed: 23583307
Mol Cell. 2018 Nov 1;72(3):469-481.e7
pubmed: 30293783
Hum Mol Genet. 2018 Nov 15;27(22):3936-3950
pubmed: 30107516
Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7
pubmed: 23161672
J Neurochem. 2018 Oct;147(2):137-152
pubmed: 29873074
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Cold Spring Harb Perspect Biol. 2019 Aug 1;11(8):
pubmed: 30082469
Mol Cell. 2019 Mar 7;73(5):959-970.e5
pubmed: 30686592
Neuron. 2004 Aug 19;43(4):513-25
pubmed: 15312650
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Sci Adv. 2020 Apr 01;6(14):eaay9572
pubmed: 32270040
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Learn Mem. 2019 Aug 15;26(9):351-362
pubmed: 31416908
J Neurosci. 2018 Feb 21;38(8):2118-2133
pubmed: 29367404
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Elife. 2018 Nov 09;7:
pubmed: 30412051
Eur J Hum Genet. 2008 Jun;16(6):666-72
pubmed: 18398441
Cell. 2011 Jul 22;146(2):247-61
pubmed: 21784246
PLoS Genet. 2016 Jul 27;12(7):e1006192
pubmed: 27462983
Nat Neurosci. 2014 Aug;17(8):1073-82
pubmed: 24974795
Nucleic Acids Res. 2016 Jul 8;44(W1):W83-9
pubmed: 27098042
J Neurosci. 2010 Oct 20;30(42):14059-67
pubmed: 20962227
PLoS Comput Biol. 2018 Aug 13;14(8):e1006169
pubmed: 30102689
Nat Methods. 2017 Apr;14(4):331-332
pubmed: 28250466
Nat Commun. 2021 Oct 21;12(1):6127
pubmed: 34675203
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nat Cell Biol. 2021 Jan;23(1):40-48
pubmed: 33420492
J Mol Biol. 2022 Oct 30;434(20):167801
pubmed: 36038000
Protein Sci. 2018 Jan;27(1):14-25
pubmed: 28710774
Mol Cell Proteomics. 2006 Apr;5(4):635-51
pubmed: 16352523