Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction

Phan, Anh Tuân; Kuryavyi, Vitaly; Darnell, Jennifer C.; Serganov, Alexander; Majumdar, Ananya; Il'in, S. G.; Raslin, Tanya; Polonskaia, Ann; Chen, Cynthia; Clain, David J.; Darnell, Robert B.; Patel, Dinshaw J.

doi:10.1038/nsmb.2064

Cited by 220 publications

(297 citation statements)

References 56 publications

Supporting

Mentioning

280

Contrasting

Unclassified

Order By: Relevance

“…Low-complexity and RGG/RG repeat sequences are present in a large number of proteins (Thandapani et al, 2013). To date, only a solution structure of the complex between a human fragile X mental retardation protein (FMRP) RGG peptide and a Gquadruplex RNA has been determined (Phan et al, 2011). The study shows that the RGG peptide changes from a random coil to a well ordered conformation upon RNA binding.…”

Section: Resultsmentioning

confidence: 99%

Bacterial expression and preliminary crystallographic studies of a 149-residue fragment of human Caprin-1

Zhu

Huang

et al. 2015

Acta Cryst Sect F

View full text Add to dashboard Cite

Caprin-1 is an RNA-binding protein which plays critical roles in several important biological processes, including cellular proliferation, the interferonmediated antiviral innate immune response, the maintenance of synaptic plasticity and the formation of RNA stress granules. Caprin-1 has been implicated in the pathogenesis of several human diseases, including osteosarcoma, breast cancer, viral infections, hearing loss and neurodegenerative disorders. Despite the emerging biological and physiopathological significance of Caprin-1, no structural information is available for this protein. Moreover, Caprin-1 does not have sequence similarity to any other protein with a known structure. It is therefore expected that structural studies will play a particularly crucial role in revealing the functional mechanisms of Caprin-1. Here, a protein fragment of human Caprin-1 consisting of residues 112-260 was expressed, purified and crystallized. Native and Se-SAD data sets were collected to resolutions to 2.05 and 2.65 Å , respectively, in different space groups.

show abstract

Section: Resultsmentioning

confidence: 99%

Bacterial expression and preliminary crystallographic studies of a 149-residue fragment of human Caprin-1

Zhu

Huang

et al. 2015

Acta Cryst Sect F

View full text Add to dashboard Cite

show abstract

“…S12). Such unusual local backbone conformations have recently been observed to occur in RNA quadruplex aptamers (27)(28)(29). Previously, quadruplexes with left-handed helicity have been artificially induced through full or partial incorporation of enantiomeric L-nucleotides (30,31).…”

Section: Resultsmentioning

confidence: 99%

Structure of a left-handed DNA G-quadruplex

Chung

Heddi

Schmitt

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

123

166

View full text Add to dashboard Cite

Aside from the well-known double helix, DNA can also adopt an alternative four-stranded structure known as G-quadruplex. Implications of such a structure in cellular processes, as well as its therapeutic and diagnostic applications, have been reported. The G-quadruplex structure is highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of a left-handed DNA G-quadruplex. The structure displays unprecedented features that can be exploited as unique recognition elements.G-quadruplex | left-handed helix | nucleic acid | NMR | X-ray crystallography

show abstract

“…The largest crystals, diffracted at 3.4 Å resolution, were grown with a 18-mer peptide (residues 3-20, numbering from ref. 37) and 35-mer RNA ( Fig. 1 A and B).…”

Section: Resultsmentioning

confidence: 99%

“…Crystals of RGG-sc1 complexes were obtained with several RNA variants and peptides centered on the Arg 10 -to-Arg 15 turn previously reported to contain determinants for sc1 RNA binding (37). The largest crystals, diffracted at 3.4 Å resolution, were grown with a 18-mer peptide (residues 3-20, numbering from ref.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, detailed structural information about RGG recognition of G-quadruplexes has been mostly obtained from studies on sc1 RNA (21), the RNA selected against the entire human FMRP but shown to require only the RGG motif of the protein for high affinity and specific binding (29,37,38). Previously, we determined the NMR solution structure of the RGG-sc1 complex that revealed an RNA fold composed of a three-layered G-quadruplex linked to a duplex RNA via a mixed junctional tetrad (37). The RGG peptide was found in the duplex-quadruplex junction, where it adopted a sharp turn specifically bound to guanines from two consecutive G-C base pairs.…”

Section: Significancementioning

confidence: 99%

See 1 more Smart Citation

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

Vasilyev

Polonskaia

Darnell

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

180

181

View full text Add to dashboard Cite

Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K + -stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex-quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation-π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex-quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG-RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.R NA-binding proteins (RBPs) control all aspects of RNA metabolism and are fundamental to core cellular processes. ∼14% of identified human RBPs are implicated in a broad spectrum of human pathologies, including neurodegenerative and muscular diseases, metabolic disorders, and cancers (1, 2). Fragile X Mental Retardation Protein (FMRP) is among the most important RBPs because of its central role in several human diseases (3). Loss of FMRP function due to CGG triplet repeat expansion-associated transcriptional silencing or missense mutations in the protein (4, 5) lead to fragile X syndrome (FXS), the most common cause of inherited intellectual disability. Mutations in FMRP are also the leading monogenic cause of autism (6, 7). Intermediate length repeat expansions in the FMR1 gene are linked to fragile X-associated tremor ataxia syndrome (8) and fragile X-associated primary ovarian insufficiency (9).FMRP contains four canonical nucleic acid-binding motifs, three KH domains and one arginine-glycine-rich (RGG) box, which mediate interactions with RNAs in mRNA transport, storage, stability, and regulation of translation (Fig. 1A) (3, 10). Each KH domain has been reported to have a mutation either causing FXS or found in patients with intellectual disability (4, 5, 11). In neurons, FMRP associates with a subset of mRNAs and represses their translation both in the cell body and near synapses (12). Loss of repression of these mRNAs is associated with alterations in synaptic plasticity and dendritic spine dynamics thought to underlie...

show abstract

Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction

Cited by 220 publications

References 56 publications

Bacterial expression and preliminary crystallographic studies of a 149-residue fragment of human Caprin-1

Bacterial expression and preliminary crystallographic studies of a 149-residue fragment of human Caprin-1

Structure of a left-handed DNA G-quadruplex

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

Contact Info

Product

Resources

About