Engineering <scp>RNA</scp>‐binding proteins with diverse activities

Wei, Huanhuan; Wang, Zefeng

doi:10.1002/wrna.1296

Cited by 31 publications

(15 citation statements)

References 101 publications

(211 reference statements)

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“…Because of the modular recognition of RNA sequences and the simple recognition code, PUF domains have been engineered to target designed RNA sequences for various purposes (43,44). These efforts have all been based on the classic PUF domains, which contain eight repeats and bind similar sequences that bear a 5΄ UGUR (where R is a purine) motif and a 3΄ UA motif.…”

Section: Discussionmentioning

confidence: 99%

Nop9 binds the central pseudoknot region of 18S rRNA

Wang

2017

Nucleic Acids Res

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The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3΄ side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode. Nop9 contains 10 Pumilio repeats arranged into a U-shaped scaffold. The target RNA is recognized by two stretches of repeats in a bipartite manner, and three central bases are unrecognized as a result of the degeneracy of repeats 6 and 7. Our data suggest that Nop9 regulates the folding of 18S rRNA at early assembly stages of 90S.

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Section: Discussionmentioning

confidence: 99%

Nop9 binds the central pseudoknot region of 18S rRNA

Wang

2017

Nucleic Acids Res

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“…As their fascinating properties and unusual evolutionary behaviour become better understood, other potential applications of RFL proteins besides fertility restoration are coming to the fore. PPR proteins are being investigated for their potential as custom-made RNA processing tools 24 62 , and of all the natural PPR proteins, RFL proteins are perhaps the best suited for biotechnological manipulation given their recurrent selection for diversity in binding site selection.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary plasticity of restorer-of-fertility-like proteins in rice

Melonek

Stone

Small

2016

Sci Rep

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Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised ‘restorer-of-fertility-like’ (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes. The RFL genomic cluster located on Oryza chromosome 10, the location of almost all known active rice RF genes, shows extreme variation in structure and gene content between species. We show evidence for homologous recombination events as an efficient mechanism for generating the huge repertoire of RNA sequence recognition motifs within RFL proteins and a major driver of RFL sequence evolution. The RFL sequences identified here will improve our understanding of the molecular basis of CMS and fertility restoration in plants and will accelerate the development of new breeding strategies.

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“…To validate the function of these proteins, we fused the candidate RBPs to a programmable RNA binding domain (i.e., Puf domain) that can be designed to bind any 8-nt RNA sequences 38 , and co-expressed the fusion proteins with the circRNAs containing their cognate targets. We found that the specific tethering of PABPC1 and hnRNP U clearly promoted translation of the circRNA, whereas the ELAVL1 (HuR) and hnRNP A1 did not affect translation when tethered to the same site ( Fig.…”

Section: Trans-acting Factors That Bind To Ires-like Short Elements Tmentioning

confidence: 99%

Pervasive translation of circular RNAs driven by short IRES-like elements

Xiu

Yang

Chen

et al. 2018

Preprint

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AbstractAlthough some circular RNAs (circRNAs) were found to be translated through IRES-driven mechanism, the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we developed a cell-based system to screen random sequences and identified 97 overrepresented hexamers that drive cap-independent circRNA translation. These IRES-like short elements are significantly enriched in endogenous circRNAs and sufficient to drive circRNA translation. We further identified multiple trans-acting factors that bind these IRES-like elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides were identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which were experimentally validated. Consistently, mutations of the IRES-like element in one circRNA reduced its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in translation control.

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Engineering RNA‐binding proteins with diverse activities

Cited by 31 publications

References 101 publications

Nop9 binds the central pseudoknot region of 18S rRNA

Nop9 binds the central pseudoknot region of 18S rRNA

Evolutionary plasticity of restorer-of-fertility-like proteins in rice

Pervasive translation of circular RNAs driven by short IRES-like elements

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