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

Li, Quanxiu; Yan, Chuangye; Xu, Honglei; Wang, Zheng; Long, Jiafu; Li, Wenqi; Wu, Jianping; Yin, Ping; Yan, Nieng

doi:10.1074/jbc.m114.575472

Cited by 16 publications

(16 citation statements)

References 43 publications

(72 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This structure captured a subset of the predicted modular repeat/nucleotide contacts as well as two "nonmodular" protein/RNA contacts that do not conform to the PPR code. Other evidence supports the view that a 1:1 PPR10:RNA complex reflects the native state (Li et al 2014;Gully et al 2015), a view that gains further support from the findings presented here.…”

Section: Introductionsupporting

confidence: 87%

RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10

Miranda

Rojas

Montgomery

et al. 2017

RNA

View full text Add to dashboard Cite

Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that influence gene expression in mitochondria and chloroplasts. PPR tracts can bind RNA via a modular one repeat-one nucleotide mechanism in which the nucleotide is specified by the identities of several amino acids in each repeat. This mode of recognition, the so-called PPR code, offers opportunities for the prediction of native PPR binding sites and the design of proteins to bind specified RNAs However, a deep understanding of the parameters that dictate the affinity and specificity of PPR-RNA interactions is necessary to realize these goals. We report a comprehensive analysis of the sequence specificity of PPR10, a protein that binds similar RNA sequences of ∼18 nucleotides (nt) near the chloroplast and genes in maize. We assessed the contribution of each nucleotide in the binding site to PPR10 affinity in vitro by analyzing the effects of single-nucleotide changes at each position. In a complementary approach, the RNAs bound by PPR10 from partially randomized RNA pools were analyzed by deep sequencing. The results revealed three patches in which nucleotide identity has a major impact on binding affinity. These include 5 nt for which protein contacts were not observed in a PPR10-RNA crystal structure and 4 nt that are not explained by current views of the PPR code. These findings highlight aspects of PPR-RNA interactions that pose challenges for binding site prediction and design.

show abstract

Section: Introductionsupporting

confidence: 87%

RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10

Miranda

Rojas

Montgomery

et al. 2017

RNA

View full text Add to dashboard Cite

show abstract

“…PPR motif containing proteins can exist as homodimers, exemplified by HCF152 28 and PPR10 29; 30 , or monomers, such as PPR4 and PPR5 29; 30; 31; 32 . In our crystal structure PRORP2 appears as a homodimer.…”

Section: Resultsmentioning

confidence: 99%

“…The PPR domain of PRORP2 consists of five and a half PPR motifs corresponding to eleven consecutive α-helices similar to PRORP1. Based on the available structures of PPR motif containing proteins 8; 29; 30; 34; 35; 36 sequential PPR motifs packing in a parallel fashion results in a spiral of anti-parallel α-helices that form a right-handed superhelical structure. The two helices in a PPR motif are referred to as helix A and helix B, with all odd-numbered helices A in a superhelical PPR arrangement forming an inner concave surface while all even-numbered helices B are facing outwards and form the convex surface.…”

Section: Resultsmentioning

confidence: 99%

Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5′ End Processing Enzymes

Karasik

Shanmuganathan

Howard

et al. 2016

Journal of Molecular Biology

View full text Add to dashboard Cite

Protein-only RNase Ps (PRORPs) are a recently discovered class of RNA processing enzymes that catalyze maturation of the 5′ end of precursor tRNAs (pre-tRNAs) in Eukaryotes. PRORPs are found in the nucleus and/or organelles of most eukaryotic organisms. Arabidopsis thaliana is a representative organism that contains PRORP enzymes (PRORP1, PRORP2, PRORP3) in both its nucleus and organelles; PRORP2 and 3 localize to the nucleus, PRORP1 to the chloroplast and the mitochondria. Apart from their identification, almost nothing is known about the structure and function of PRORPs that act in the nucleus. Here we use a combination of biochemical assays and X-ray crystallography to characterize A. thaliana PRORP2. We solved the crystal structure of PRORP2 (3.2 Å) revealing an overall V-shaped protein and conserved metallonuclease active site structure. Our biochemical studies indicate that PRORP2 requires Mg2+ for catalysis and catalyzes the maturation of nuclear encoded substrates up to 10-fold faster than mitochondrial encoded precursor nad6 t-element under single turnover conditions. We also demonstrate that PRORP2 preferentially binds pre-tRNAs containing short 5′ leaders and 3′ trailers; however, leader and trailer length do not significantly alter the observed rate constants of PRORP2 in single turnover cleavage assays. Our data provide a biochemical and structural framework to begin understanding how nuclear localized PRORPs recognize and cleave their substrates.

show abstract

“…The PPR protein crystal and solution structures reveal tandem repeats of a-hairpin motifs which assemble to form a righthanded a-solenoid, where the RNA-binding residues are located on the inside surface of the superhelix (Yin et al, 2013). Although dimerisation of PPR proteins has been observed in crystal structures of PPR10 (Yin et al, 2013), further studies suggest that the protein-RNA complex is monomeric in solution, and that the overall superhelical form is preserved (Li et al, 2014;Gully et al, 2015a). There are currently no experimental structures of PLS-class proteins, although the structure of THA8L is a salutary example of the confusion caused by misannotation of PPR motifs.…”

Section: Introductionmentioning

confidence: 99%

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

et al. 2016

View full text Add to dashboard Cite

These authors contributed equally to the manuscript. SUMMARYThe pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterised by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence-specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria, where they play important roles in post-transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide-binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA-editing factors. We show that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes. We report a high error rate in PPR gene models in many public plant proteomes, due to gene fusions and insertions of spurious introns. These consistently annotated datasets across a wide range of species are valuable resources for future comparative genomics studies, and an essential pre-requisite for accurate large-scale computational predictions of PPR targets. We have created a web portal (http://www.-plantppr.com) that provides open access to these resources for the community.

show abstract

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

Cited by 16 publications

References 43 publications

RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10

RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10

Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5′ End Processing Enzymes

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

Contact Info

Product

Resources

About