Identification of RNA-Binding Proteins Associated to RNA Structural Elements.
Aptamers, Nucleotide
Electrophoresis, Polyacrylamide Gel
Humans
Internal Ribosome Entry Sites
Mass Spectrometry
Nucleotide Motifs
/ genetics
Protein Biosynthesis
Proteomics
/ methods
RNA
/ isolation & purification
RNA, Transfer
/ biosynthesis
RNA-Binding Proteins
/ isolation & purification
Streptavidin
Substrate Specificity
IRES elements
Pull-down
RNA structure
RNA-binding proteins
Streptavidin aptamer
Translation control
tRNA scaffold
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
4
6
2021
pubmed:
5
6
2021
medline:
20
8
2021
Statut:
ppublish
Résumé
RNA motifs guide the interaction with specific proteins leading to the assembly of ribonucleoprotein complexes that perform key functions in cellular processes. Internal ribosome entry site (IRES) elements are organized in structural domains that determine internal initiation of translation. In this chapter we describe a pull-down assay using streptavidin-aptamer tagged RNAs that combines RNA structure-dependent protein isolation with proteomic analysis to identify novel interactors recognizing RNA structural domains. This approach takes advantage of tRNA-scaffold guided expression, allowing the identification of factors belonging to networks involved in RNA and protein metabolism.
Identifiants
pubmed: 34086277
doi: 10.1007/978-1-0716-1499-0_9
doi:
Substances chimiques
Aptamers, Nucleotide
0
Internal Ribosome Entry Sites
0
RNA, recombinant
0
RNA-Binding Proteins
0
RNA
63231-63-0
Streptavidin
9013-20-1
RNA, Transfer
9014-25-9
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
109-119Références
Hinnebusch AG (2017) Structural insights into the mechanism of scanning and start codon recognition in eukaryotic translation initiation. Trends Biochem Sci 42:589–611
doi: 10.1016/j.tibs.2017.03.004
Lozano G, Francisco-Velilla R, Martinez-Salas E (2018) Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences. Open Biol 8(11):180155
doi: 10.1098/rsob.180155
Lozano G, Martinez-Salas E (2015) Structural insights into viral IRES-dependent translation mechanisms. Curr Opin Virol 12:113–120
doi: 10.1016/j.coviro.2015.04.008
Lozano G, Fernandez N, Martinez-Salas E (2016) Modeling three-dimensional structural motifs of viral IRES. J Mol Biol 428:767–776
doi: 10.1016/j.jmb.2016.01.005
Fernandez-Miragall O, Ramos R, Ramajo J, Martinez-Salas E (2006) Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation. RNA 12:223–234
doi: 10.1261/rna.2153206
Jung S, Schlick T (2013) Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site. Nucleic Acids Res 41:1483–1495
doi: 10.1093/nar/gks1302
Yu Y, Abaeva IS, Marintchev A, Pestova TV, Hellen CU (2011) Common conformational changes induced in type 2 picornavirus IRESs by cognate trans-acting factors. Nucleic Acids Res 39:4851–4865
doi: 10.1093/nar/gkr045
Sweeney TR, Abaeva IS, Pestova TV, Hellen CU (2014) The mechanism of translation initiation on type 1 picornavirus IRESs. EMBO J 33:76–92
doi: 10.1002/embj.201386124
Pineiro D, Fernandez N, Ramajo J, Martinez-Salas E (2013) Gemin5 promotes IRES interaction and translation control through its C-terminal region. Nucleic Acids Res 41:1017–1028
doi: 10.1093/nar/gks1212
Lee KM, Chen CJ, Shih SR (2017) Regulation mechanisms of viral IRES-driven translation. Trends Microbiol 25:546–561
doi: 10.1016/j.tim.2017.01.010
Lozano G, Francisco-Velilla R, Martinez-Salas E (2018) Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE. Sci Rep 8:5545
doi: 10.1038/s41598-018-23845-x
Ponchon L, Beauvais G, Nonin-Lecomte S, Dardel F (2009) A generic protocol for the expression and purification of recombinant RNA in Escherichia coli using a tRNA scaffold. Nat Protoc 4:947–959
doi: 10.1038/nprot.2009.67
Fernandez-Chamorro J, Francisco-Velilla R, Ramajo J, Martinez-Salas E (2019) Rab1b and ARF5 are novel RNA-binding proteins involved in FMDV IRES-driven RNA localization. Life Sci Alliance 2(1):e201800131
doi: 10.26508/lsa.201800131
Martinez-Salas E, Francisco-Velilla R, Fernandez-Chamorro J, Lozano G, Diaz-Toledano R (2015) Picornavirus IRES elements: RNA structure and host protein interactions. Virus Res 206:62–73
doi: 10.1016/j.virusres.2015.01.012
Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD (2017) PANTHER version 11: expanded annotation data from gene ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res 45:D183–D189
doi: 10.1093/nar/gkw1138
Francisco-Velilla R, Fernandez-Chamorro J, Lozano G, Diaz-Toledano R, Martinez-Salas E (2015) RNA-protein interaction methods to study viral IRES elements. Methods 91:3–12
doi: 10.1016/j.ymeth.2015.06.023
Lopez de Quinto S, Martinez-Salas E (2000) Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo. RNA 6:1380–1392
doi: 10.1017/S1355838200000753
Francisco-Velilla R, Fernandez-Chamorro J, Ramajo J, Martinez-Salas E (2016) The RNA-binding protein Gemin5 binds directly to the ribosome and regulates global translation. Nucleic Acids Res 44:8335–8351
doi: 10.1093/nar/gkw702