4.7 Article

A Genome-Wide Analysis of the Pentatricopeptide Repeat Protein Gene Family in Two Kiwifruit Species with an Emphasis on the Role of RNA Editing in Pathogen Stress

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Plant Sciences

A Phage Therapy Model for the Prevention of Pseudomonas syringae pv. actinidiae Infection of Kiwifruit Plants

Anna Fiorillo et al.

Summary: The study found that the phage phi PSA2 can effectively control the occurrence and spread of kiwifruit canker, providing a possibility for the development of phage therapy based on this phage.

PLANT DISEASE (2023)

Article Biochemistry & Molecular Biology

The PPR protein RARE1-mediated editing of chloroplast accD transcripts is required for fatty acid biosynthesis and heat tolerance in Arabidopsis

Chao Huang et al.

Summary: It has been found that loss of accD-C794 RNA editing under heat stress leads to a yellow and dwarf phenotype with decreased chloroplast gene expression. Artificial enhancement of C794-edited accD gene expression improves heat tolerance in Arabidopsis. The defective accD-C794 editing may result in reduced ACCase activity and membrane structural disruption under heat stress.

PLANT COMMUNICATIONS (2023)

Article Biochemistry & Molecular Biology

Maize PPR-E proteins mediate RNA C-to-U editing in mitochondria by recruiting the trans deaminase PCW1

Yong Wang et al.

Summary: The PPR-E proteins recruit the trans deaminase PCW1 and bCCP1 to carry out RNA C-to-U editing, with assistance from the MORF1/8 proteins through protein-protein interactions. This process is essential for plant growth and development.

PLANT CELL (2023)

Article Plant Sciences

MSP1 encodes an essential RNA-binding pentatricopeptide repeat factor required for nad1 maturation and complex I biogenesis in Arabidopsis mitochondria

Corinne Best et al.

Summary: Mitochondrial biogenesis relies on nuclearly encoded factors, which regulate the expression of the organellar-encoded genes. Pentatricopeptide repeat (PPR) proteins constitute a major gene family in angiosperms that are pivotal in many aspects of mitochondrial (mt)RNA metabolism (e.g. trimming, splicing, or stability). The loss-of-function allele of the MSP1 gene leads to seed abortion.

NEW PHYTOLOGIST (2023)

Editorial Material Plant Sciences

Engineering of pentatricopeptide repeat proteins in organellar gene regulation

Kwanuk Lee et al.

FRONTIERS IN PLANT SCIENCE (2023)

Article Biochemical Research Methods

Cytoscape.js 2023 update: a graph theory library for visualization and analysis

Max Franz et al.

Summary: Cytoscape.js is an open-source graph library implemented in JavaScript. It can be used as a visualization software component to render interactive graphs in web browsers, or in a headless manner for server-side graph operations with Node.js.

BIOINFORMATICS (2023)

Article Plant Sciences

Genome-Wide Analysis of Multiple Organellar RNA Editing Factor (MORF) Family in Kiwifruit (Actinidia chinensis) Reveals Its Roles in Chloroplast RNA Editing and Pathogens Stress

Yuhong Xiong et al.

Summary: In this study, ten MORF genes were identified in the kiwifruit genome, and their genomic structures and chromosomal locations were analyzed. Based on RNA-seq data, tissue-specific patterns of MORF gene expression and chloroplast RNA editing were found. Differential expression and editing profiles were observed between resistant and susceptible kiwifruits after pathogen infection.

PLANTS-BASEL (2022)

Article Virology

Genomic characterization of two nickie-like bacteriophages that infect the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae

Hairong Zhang et al.

Summary: Here, we report the genomic characterization of two siphophages, named hairong and ZY21, that infect the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. Comparative genomic analysis revealed some common features shared by the four nickie-like phages.

ARCHIVES OF VIROLOGY (2022)

Article Plant Sciences

Integrative analyses of metabolome and genome-wide transcriptome reveal the regulatory network governing flavor formation in kiwifruit (Actinidia chinensis)

Ruochen Wang et al.

Summary: This study integrated metabolome and transcriptome data from 12 fruit developmental and ripening stages of Actinidia chinensis cv Hongyang, revealing key genes and transcription factors regulating flavor metabolism in kiwifruit. The research provides new insights into the metabolic regulation of flavor during fruit development and ripening, establishing a foundation for flavor improvement in kiwifruit.

NEW PHYTOLOGIST (2022)

Article Plant Sciences

A cytosolic pentatricopeptide repeat protein is essential for tapetal plastid development by regulating OsGLK1 transcript levels in rice

Shaoyan Zheng et al.

Summary: This study reveals the important regulatory role of the cytosolic PPR protein OsCPPR1 in pollen development in rice. OsCPPR1 inhibits the transcription factor OsGLK1 to regulate plastid development and programmed cell death. The findings highlight the novel functions of cytosolic PPRs and identify a new regulatory mechanism for pollen development in rice.

NEW PHYTOLOGIST (2022)

Review Virology

Advancements in the Use of Bacteriophages to Combat the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae

Jinyan Luo et al.

Summary: Kiwifruit production has been severely damaged by the bacterial plant pathogen Pseudomonas syringae pv. actinidiae (Psa) in recent decades, leading to significant economic losses worldwide. The use of antibiotics for control is becoming ineffective, making the development of phage-based biocontrol strategies crucial.

VIRUSES-BASEL (2022)

Article Agronomy

The PPR-Domain Protein SOAR1 Regulates Salt Tolerance in Rice

Kai Lu et al.

Summary: This study demonstrates that the expression of SOAR1 in rice enhances salt tolerance and promotes productivity, possibly through increased ABA sensitivity and altered transcription and splicing of salt stress-related genes. Additionally, other salt-induced SOAR1-like proteins were identified.
Article Biochemistry & Molecular Biology

Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein

F. Vanessa Loiacono et al.

Summary: RNA editing is an important process in converting cytidines to uridines in plant organellar transcripts. This study investigates the evolution and recognition of a recently gained editing site, demonstrating that changes in RNA recognition motifs allow an ancient PPR protein, QED1, to specifically target this site. The study also finds that the target specificity of PPR proteins depends on the RNA:protein ratio and the low expression levels of PPR proteins are necessary to ensure editing site selection specificity.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

Article Multidisciplinary Sciences

GRP23 plays a core role in E-type editosomes via interacting with MORFs and atypical PPR-DYWs in Arabidopsis mitochondria

Yan-Zhuo Yang et al.

Summary: The GLUTAMINE-RICH PROTEIN23 (GRP23) plays an essential role in mitochondrial RNA editing by interacting with MORF proteins and atypical DYW-type PPR proteins. GRP23 is targeted to mitochondria, plastids, and nuclei. The interactions between GRP23, MORF proteins, and PPR-DYW proteins increase the stability of the editing complex and facilitate the formation of the editosome.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Plant Sciences

Genome-wide identification and expression analysis of peach multiple organellar RNA editing factors reveals the roles of RNA editing in plant immunity

Aidi Zhang et al.

Summary: MORF genes play important roles in regulating plant immunity, especially against biotic and abiotic stresses. By studying the genome-wide analysis of peach MORF genes and the regulatory role of RNA editing in plant immunity, this research provides a foundation for further analysis of MORF gene functions and breeding new cultivars with high resistance.

BMC PLANT BIOLOGY (2022)

Review Genetics & Heredity

Research Progress of PPR Proteins in RNA Editing, Stress Response, Plant Growth and Development

Tengfei Qin et al.

Summary: RNA editing is a posttranscriptional phenomenon that primarily occurs in the genomes of mitochondria and chloroplasts in higher plants. Pentatricopeptide repeat (PPR) proteins, identified as potential trans-acting factors of RNA editing, have attracted attention in molecular biology research in recent years. The molecular functions and physiological roles of PPR proteins throughout plant growth and development are extensively studied.

FRONTIERS IN GENETICS (2021)

Article Genetics & Heredity

Dynamic response of RNA editing to temperature in grape by RNA deep sequencing

Aidi Zhang et al.

FUNCTIONAL & INTEGRATIVE GENOMICS (2020)

Article Biochemistry & Molecular Biology

The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants

Bernard Gutmann et al.

MOLECULAR PLANT (2020)

Article Biochemistry & Molecular Biology

Salinity effects on nad3 gene RNA editing of wild barley mitochondria

Ahmed M. Ramadan

MOLECULAR BIOLOGY REPORTS (2020)

Article Biochemistry & Molecular Biology

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

Chengjie Chen et al.

MOLECULAR PLANT (2020)

Article Biochemistry & Molecular Biology

Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

Dongli Wang et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biochemistry & Molecular Biology

HMMER web server: 2018 update

Simon C. Potter et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results

Shuangyang Wu et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2018)

Article Biochemical Research Methods

BCFtools/csq: haplotype-aware variant consequences

Petr Danecek et al.

BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Review Plant Sciences

The Unexpected Diversity of Plant Organelle RNA Editosomes

Tao Sun et al.

TRENDS IN PLANT SCIENCE (2016)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Review Plant Sciences

Pentatricopeptide Repeat Proteins in Plants

Alice Barkan et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 65 (2014)

Article Multidisciplinary Sciences

Tetrapyrrole biosynthetic enzyme protoporphyrinogen IX oxidase 1 is required for plastid RNA editing

Fan Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Microbiology

Mediated Plastid RNA Editing in Plant Immunity

Javier Garcia-Andrade et al.

PLOS PATHOGENS (2013)

Article Biochemistry & Molecular Biology

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants

Mizuki Takenaka et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Review Biochemistry & Molecular Biology

Plant RNA editing

Anne-Laure Chateigner-Boutin et al.

RNA BIOLOGY (2010)

Article Biochemical Research Methods

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder et al.

BMC BIOINFORMATICS (2008)

Review Plant Sciences

The role of the mitochondrion in plant responses to biotic stress

Sasan Amirsadeghi et al.

PHYSIOLOGIA PLANTARUM (2007)

Article Multidisciplinary Sciences

A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts

E Kotera et al.

NATURE (2005)

Article Biochemical Research Methods

Predotar:: A tool for rapidly screening proteomes for N-terminal targeting sequences

I Small et al.

PROTEOMICS (2004)