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Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function.

ABSTRACT: Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nicotiana tabacum GR-RBP1. NMR studies of NtGR-RBP1 show that the glycine-rich domain, while intrinsically disordered, is responsible for mediating self-association by transient interactions with its RRM domain (NtRRM). Both NtGR-RBP1 and NtRRM bind specifically and with low micromolar affinity to RNA and single-stranded DNA. The solution structure of NtRRM shows that it is a canonical RRM domain. A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues. Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM. Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function.

SUBMITTER: Khan F

PROVIDER: S-EPMC4117745 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function.

Khan Fariha F Daniëls Mark A MA Folkers Gert E GE Boelens Rolf R Saqlan Naqvi S M SM van Ingen Hugo H

Nucleic acids research 20140623 13

Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nicotiana tabacum GR-RBP1. NMR studies of NtGR-RBP1 show that the glycine-rich domain, while intrinsically disordered, is responsible for mediating self- ...[more]

PMID: 24957607

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Project description:CP12 is a small nuclear encoded chloroplast protein that has been shown to form a complex with the Calvin cycle enzymes, PRK and GADPH. We have taken an antisense approach in order to address the importance of this regulatory protein on carbon assimilation. Transgenic Nicotiana tabacum cv. Samsun with reduced levels of the CP12 protein, produced by leaf disc transformation with a full length tobacco CP12 cDNA, regulated by the cauliflower mosaic virus 35S promoter. Agrobacterium tumefaciens-mediated transformation and selection on kanamycin produced primary transformants whose progeny segregate for severity of the antisense CP12 phenotype. Because of the impact of the antisense reductions in CP12 on carbon assimilation, these plants have abnormal morphology of leaves, floral organs, greatly reduced fertility and markedly slower growth rates. Our hypothesis is that the phenotype is exposing the regulatory nature of the CP12 protein. Intermediates leaving the Calvin cycle are essential for the synthesis of hormones and perturbation of hormone balances is a potential source of the morphological and development effects observed in the CP12 antisense plants. Our objective is to understand the CP12 phenotype by identifying changes in gene expression occurring at key stages in the life cycle of the CP12 antisense plants. CP12 antisense and wild type control plants for microarray analysis were germinated in a growth chamber in agar medium with 1% sucrose and 1/2 strength MS; with a 16 h light/8 h dark cycle at 25°C. At 20 days plants were transferred to a controlled environment greenhouse and grown in Fisons Levington F2 compost at 25°C, with light levels above 500 umol m-2 s-1 ;using supplementary lighting in a 16 h light/8 h dark cycle. 3 independent sets of plants (both wild type and CP12 antisense) were grown for preparation of three independent biological replicate RNA samples. RNA was extracted according to the TIGR protocol from plants in the early in all samples. Keywords: Direct comparison

Dataset Information

Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function.

Publications

Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function.

Similar Datasets

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