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

A Conserved Glutamate Residue in the C-terminal Deaminase Domain of Pentatricopeptide Repeat Proteins Is Required for RNA Editing Activity

(2015) Michael L. Hayes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA

(2015) Benjamin S. Gully et al.   NUCLEIC ACIDS RESEARCH

Predictable Alteration of Sequence Recognition by RNA Editing Factors from Arabidopsis

(2015) Peter Kindgren et al.   PLANT CELL

AEF1/MPR25 is implicated in RNA editing of plastidatpFand mitochondrialnad5, and also promotesatpFsplicing in Arabidopsis and rice

(2015) Aaron Yap et al.   PLANT JOURNAL

The design and structural characterization of a synthetic pentatricopeptide repeat protein

(2015) Benjamin S. Gully et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Pentatricopeptide Repeat Proteins in Plants

(2014) Alice Barkan et al.   Annual Review of Plant Biology

Identification of a pentatricopeptide repeat RNA editing factor inPhyscomitrella patenschloroplasts

(2014) Mizuho Ichinose et al.   FEBS LETTERS

Massive Gene Transfer and Extensive RNA Editing of a Symbiotic Dinoflagellate Plastid Genome

(2014) Sutada Mungpakdee et al.   Genome Biology and Evolution

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

(2014) Quanxiu Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cytidine Deaminase Motifs within the DYW Domain of Two Pentatricopeptide Repeat-containing Proteins Are Required for Site-specific Chloroplast RNA Editing

(2014) Jessica A. Wagoner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing ofndhD-1

(2014) Clément Boussardon et al.   NEW PHYTOLOGIST

Quantitative analysis of motifs contributing to the interaction between PLS-subfamily members and their target RNA sequences in plastid RNA editing

(2014) Kenji Okuda et al.   PLANT JOURNAL

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyteSelaginella uncinata

(2014) Bastian Oldenkott et al.   RNA

An artificial PPR scaffold for programmable RNA recognition

(2014) Sandrine Coquille et al.   Nature Communications

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

(2014) Marcin J. Skwark et al.   PLoS Computational Biology

Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNA

(2014) Zhanar Abil et al.   Journal of Biological Engineering

RNA Editing in Plants and Its Evolution

(2013) Mizuki Takenaka et al.   Annual Review of Genetics

Helical repeats modular proteins are major players for organelle gene expression

(2013) Kamel Hammani et al.   BIOCHIMIE

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

(2013) Ting Ban et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of Two Pentatricopeptide Repeat Genes Required for RNA Editing and Zinc Binding by C-terminal Cytidine Deaminase-like Domains

(2013) Michael L. Hayes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Structural basis for the modular recognition of single-stranded RNA by PPR proteins

(2013) Ping Yin et al.   NATURE

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

(2013) Jiyuan Ke et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Two DYW Subclass PPR Proteins are Involved in RNA Editing of ccmFc and atp9 Transcripts in the Moss Physcomitrella patens: First Complete Set of PPR Editing Factors in Plant Mitochondria

(2013) Mizuho Ichinose et al.   PLANT AND CELL PHYSIOLOGY

The E domains of pentatricopeptide repeat proteins from different organelles are not functionally equivalent for RNA editing

(2013) Anne-Laure Chateigner-Boutin et al.   PLANT JOURNAL

A DYW-protein knockout inPhyscomitrellaaffects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype

(2013) Mareike Schallenberg-Rüdinger et al.   PLANT JOURNAL

Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants

(2013) Yusuke Yagi et al.   PLoS One

Improved Computational Target Site Prediction for Pentatricopeptide Repeat RNA Editing Factors

(2013) Mizuki Takenaka et al.   PLoS One

Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles

(2013) Jean Colcombet et al.   RNA Biology

Pentatricopeptide repeats

(2013) Aleksandra Filipovska et al.   RNA Biology

Mechanistic Insight into Pentatricopeptide Repeat Proteins as Sequence-Specific RNA-Binding Proteins for Organellar RNAs in Plants

(2012) T. Nakamura et al.   PLANT AND CELL PHYSIOLOGY

Two Interacting Proteins Are Necessary for the Editing of the NdhD-1 Site in Arabidopsis Plastids

(2012) C. Boussardon et al.   PLANT CELL

SLO2, a mitochondrial pentatricopeptide repeat protein affecting several RNA editing sites, is required for energy metabolism

(2012) Qiang Zhu et al.   PLANT JOURNAL

Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing

(2012) M. J. Howard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

(2012) Alice Barkan et al.   PLoS Genetics

Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes

(2011) Julia Hecht et al.   Genome Biology and Evolution

Revisiting the Yeast PPR Proteins—Application of an Iterative Hidden Markov Model Algorithm Reveals New Members of the Rapidly Evolving Family

(2011) Kamil A. Lipinski et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure of human mitochondrial RNA polymerase

(2011) Rieke Ringel et al.   NATURE

Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution

(2011) S. Fujii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant-type mitochondrial RNA editing in the protist Naegleria gruberi

(2011) M. Rudinger et al.   RNA

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

RNA editing competence oftrans-factor MEF1 is modulated by ecotype-specific differences but requires the DYW domain

(2010) Anja Zehrmann et al.   FEBS LETTERS

OTP70 is a pentatricopeptide repeat protein of the E subgroup involved in splicing of the plastid transcript rpoC1

(2010) Anne-Laure Chateigner-Boutin et al.   PLANT JOURNAL

Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts

(2009) K. Okuda et al.   PLANT CELL

MEF9, an E-Subclass Pentatricopeptide Repeat Protein, Is Required for an RNA Editing Event in the nad7 Transcript in Mitochondria of Arabidopsis

(2009) M. Takenaka   PLANT PHYSIOLOGY

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

The remarkable chloroplast genome of dinoflagellates

(2008) C. J. Howe et al.   JOURNAL OF EXPERIMENTAL BOTANY

On the Expansion of the Pentatricopeptide Repeat Gene Family in Plants

(2008) N. O'Toole et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pentatricopeptide repeat proteins: a socket set for organelle gene expression

(2008) C SCHMITZLINNEWEBER et al.   TRENDS IN PLANT SCIENCE