Structure of a PLS-class Pentatricopeptide Repeat Protein Provides Insights into Mechanism of RNA Recognition

Ban, Ting; Ke, Jiyuan; Chen, Runze; Gu, Xin; Tan, Mingyue; Zhou, Xin; Kang, Ying; Melcher, Karsten; Zhu, Jian‐Kang; Xu, H. Eric

doi:10.1074/jbc.m113.496828

Cited by 55 publications

(52 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Its C-terminal half comprises four OPR repeats followed by a RAP (RNA binding domain abundant in apicomplexans) domain (Figure 1; Supplemental Figure 1A; Lee and Hong, 2004), which is probably related to OPR repeats (Eberhard et al, 2011). Secondary structure analysis with the Jpred algorithm (www.compbio.dundee.ac.uk/www.jpred; Cole et al 2008) predicted the presence of two a-helices in each of the OPR repeats identified ( Figure 1B), as in the case of PPR and TPR repeats (Das et al, 1998;Ban et al, 2013). This a-helical structure of the OPR repeats is further supported by the prediction of the 3D structure of the region representing OPR repeats 1 to 3 ( Figure 1C).…”

mentioning

confidence: 99%

RAP, the Sole Octotricopeptide Repeat Protein in Arabidopsis, Is Required for Chloroplast 16S rRNA Maturation

Kleinknecht¹,

Wang²,

Stübe³

et al. 2014

The Plant Cell

View full text Add to dashboard Cite

The biogenesis and activity of chloroplasts in both vascular plants and algae depends on an intracellular network of nucleus-encoded, trans-acting factors that control almost all aspects of organellar gene expression. Most of these regulatory factors belong to the helical repeat protein superfamily, which includes tetratricopeptide repeat, pentatricopeptide repeat, and the recently identified octotricopeptide repeat (OPR) proteins. Whereas green algae express many different OPR proteins, only a single orthologous OPR protein is encoded in the genomes of most land plants. Here, we report the characterization of the only OPR protein in Arabidopsis thaliana, RAP, which has previously been implicated in plant pathogen defense. Loss of RAP led to a severe defect in processing of chloroplast 16S rRNA resulting in impaired chloroplast translation and photosynthesis. In vitro RNA binding and RNase protection assays revealed that RAP has an intrinsic and specific RNA binding capacity, and the RAP binding site was mapped to the 5' region of the 16S rRNA precursor. Nucleoid localization of RAP was shown by transient green fluorescent protein import assays, implicating the nucleoid as the site of chloroplast rRNA processing. Taken together, our data indicate that the single OPR protein in Arabidopsis is important for a basic process of chloroplast biogenesis.

show abstract

mentioning

confidence: 99%

RAP, the Sole Octotricopeptide Repeat Protein in Arabidopsis, Is Required for Chloroplast 16S rRNA Maturation

Kleinknecht¹,

Wang²,

Stübe³

et al. 2014

The Plant Cell

View full text Add to dashboard Cite

show abstract

“…The tha8 gene encodes a small PPR protein that is localized to chloroplasts, where it is required for the splicing of the ycf3-2 and trnA group II introns 3 . A. thaliana has a THA8 ortholog with conserved functions in the biogenesis of chloroplast thylakoid membranes 3 and a THA8-like (THA8L) protein, which shares 26% sequence identity with THA8 but has unknown functions 18 . Whereas most PPR proteins have more than ten PPR motifs, THA8 belongs to a subfamily of small PPR proteins that are involved in the splicing of group II introns through specific RNA binding.…”

mentioning

confidence: 99%

Structural basis for RNA recognition by a dimeric PPR-protein complex

Chen

Ban

et al. 2013

Nat Struct Mol Biol

Self Cite

View full text Add to dashboard Cite

Thylakoid assembly 8 (THA8) is a pentatricopeptide repeat (PPR) RNA-binding protein required for the splicing of the transcript of ycf3, a gene involved in chloroplast thylakoid-membrane biogenesis. Here we report the identification of multiple THA8-binding sites in the ycf3 intron and present crystal structures of Brachypodium distachyon THA8 either free of RNA or bound to two of the identified RNA sites. The apostructure reveals a THA8 monomer with five tandem PPR repeats arranged in a planar fold. The complexes of THA8 bound to the two short RNA fragments surprisingly reveal asymmetric THA8 dimers with the bound RNAs at the dimeric interface. RNA binding induces THA8 dimerization, with a conserved G nucleotide of the bound RNAs making extensive contacts with both monomers. Together, these results establish a new model of RNA recognition by RNA-induced formation of an asymmetric dimer of a PPR protein.

show abstract

“…PPR proteins generally contain an array of 2-30 tandem repeats, and each canonical repeat is composed of 35 amino acids arranged into a hairpin of ␣-helices (15)(16)(17). The system of RNA recognition code was tentatively disclosed by bioinformatic analysis in conjunction with biochemical assays and recently corroborated by structural elucidation (see Figs.…”

mentioning

confidence: 99%

Examination of the Dimerization States of the Single-stranded RNA Recognition Protein Pentatricopeptide Repeat 10 (PPR10)

Yan

et al. 2014

Journal of Biological Chemistry

View full text Add to dashboard Cite

Structure of a PLS-class Pentatricopeptide Repeat Protein Provides Insights into Mechanism of RNA Recognition

Cited by 55 publications

References 25 publications

RAP, the Sole Octotricopeptide Repeat Protein in Arabidopsis, Is Required for Chloroplast 16S rRNA Maturation

RAP, the Sole Octotricopeptide Repeat Protein in Arabidopsis, Is Required for Chloroplast 16S rRNA Maturation

Structural basis for RNA recognition by a dimeric PPR-protein complex

Examination of the Dimerization States of the Single-stranded RNA Recognition Protein Pentatricopeptide Repeat 10 (PPR10)

Contact Info

Product

Resources

About