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

Kiwifruit (Actinidia chinensis) is well known for its high vitamin C content and good taste. Various diseases, especially bacterial canker, are a serious threat to the yield of kiwifruit. Multiple organellar RNA editing factor (MORF) genes are pivotal factors in the RNA editosome that mediates Cytosine-to-Uracil RNA editing, and they are also indispensable for the regulation of chloroplast development, plant growth, and response to stresses. Although the kiwifruit genome has been released, little is known about MORF genes in kiwifruit at the genome-wide level, especially those involved in the response to pathogens stress. In this study, we identified ten MORF genes in the kiwifruit genome. The genomic structures and chromosomal locations analysis indicated that all the MORF genes consisted of three conserved motifs, and they were distributed widely across the seven linkage groups and one contig of the kiwifruit genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the kiwifruit MORF gene family members were classified into six groups (Groups A–F). A synteny analysis indicated that two pairs of MORF genes were tandemly duplicated and five pairs of MORF genes were segmentally duplicated. Moreover, based on analysis of RNA-seq data from five tissues of kiwifruit, we found that both expressions of MORF genes and chloroplast RNA editing exhibited tissue-specific patterns. MORF2 and MORF9 were highly expressed in leaf and shoot, and may be responsible for chloroplast RNA editing, especially the ndhB genes. We also observed different MORF expression and chloroplast RNA editing profiles between resistant and susceptible kiwifruits after pathogen infection, indicating the roles of MORF genes in stress response by modulating the editing extend of mRNA. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes, in particular, for clarifying the resistance mechanisms in kiwifruits and breeding new cultivars with high resistance.

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

International Journal of Molecular Sciences ◽

10.3390/ijms20061425 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1425 ◽

Cited By ~ 1

Author(s):

Dongli Wang ◽

Sen Meng ◽

Wanlong Su ◽

Yu Bao ◽

Yingying Lu ◽

...

Keyword(s):

Drought Stress ◽

Rna Editing ◽

Functional Divergence ◽

Expression Patterns ◽

Purifying Selection ◽

Structural Features ◽

Specific Expression ◽

Poplar Genome ◽

Physiological Processes ◽

Genome Wide

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes—pivotal factors in the RNA editosome in Arabidopsis thaliana—are indispensable for the regulation of various physiological processes, including organelle C-to-U RNA editing and plasmid development, as well as in the response to stresses. Although the poplar genome sequence has been released, little is known about MORF genes in poplar, especially those involved in the response to drought stress at the genome-wide level. In this study, we identified nine MORF genes in the Populus genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the P. trichocarpa (Ptr) MORF family members were classified into six groups (Groups I–VI). A microsynteny analysis indicated that two (22.2%) PtrMORF genes were tandemly duplicated and seven genes (77.8%) were segmentally duplicated. Based on the dN/dS ratios, purifying selection likely played a major role in the evolution of this family and contributed to functional divergence among PtrMORF genes. Moreover, analysis of qRT-PCR data revealed that PtrMORFs exhibited tissue- and treatment-specific expression patterns. PtrMORF genes in all group were involved in the stress response. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes in poplar, and, in particular, for improving the drought resistance of poplar by genetics manipulation.

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PPR647 Protein Is Required for Chloroplast RNA Editing, Splicing and Chloroplast Development in Maize

International Journal of Molecular Sciences ◽

10.3390/ijms222011162 ◽

2021 ◽

Vol 22 (20) ◽

pp. 11162

Author(s):

Yan Zhao ◽

Wei Xu ◽

Yongzhong Zhang ◽

Shilei Sun ◽

Lijing Wang ◽

...

Keyword(s):

Plant Growth ◽

Rna Editing ◽

Rna Splicing ◽

Essential Role ◽

Chloroplast Development ◽

Rna Seq ◽

Chloroplast Genes ◽

Factors Affecting ◽

Transmission Electron ◽

Albino Phenotype

Chloroplasts play an essential role in plant growth and development. Any factors affecting chloroplast development will lead to abnormal plant growth. Here, we characterized a new maize mutant, albino seedling mutant 81647 (as-81647), which exhibits an entirely albino phenotype in leaves and eventually died before the three-leaf stage. Transmission electron microscopy (TEM) demonstrated that the chloroplast thylakoid membrane was impaired and the granum lamellae significantly decreased in as-81647. Map-based cloning and transgenic analysis confirmed that PPR647 encodes a new chloroplast protein consisting of 11 pentratricopeptide repeat domains. Quantitative real-time PCR (qRT-PCR) assays and transcriptome analysis (RNA-seq) showed that the PPR647 mutation significantly disrupted the expression of PEP-dependent plastid genes. In addition, RNA splicing and RNA editing of multiple chloroplast genes showed severe defects in as-81647. These results indicated that PPR647 is crucial for RNA editing, RNA splicing of chloroplast genes, and plays an essential role in chloroplast development.

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Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables

10.1101/254045 ◽

2018 ◽

Cited By ~ 1

Author(s):

Edoardo Giacopuzzi ◽

Massimo Gennarelli ◽

Chiara Sacco ◽

Alice Filippini ◽

Jessica Mingardi ◽

...

Keyword(s):

Rna Editing ◽

Human Blood ◽

Cell Types ◽

Small Region ◽

Rna Seq ◽

Biological Variables ◽

Genome Wide ◽

Genes Encoding ◽

Editing Process ◽

Detailed Picture

AbstractBackgroundA-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing contributes to generate transcriptomic diversity and it is found altered in cancer, autoimmune and neurological disorders. Emerging evidences indicate that editing process could be influenced by genetic variations, biological and environmental variables.ResultsWe analyzed RNA editing levels in human blood using RNA-seq data from 459 healthy individuals and identified 2,079 sites consistently edited in this tissue. As expected, analysis of gene expression revealed thatADARis the major contributor to editing on these sites, explaining ∼13% of observed variability. After removingADAReffect, we found significant associations for 1,122 genes, mainly involved in RNA processing. These genes were significantly enriched in genes encoding proteins interacting with ADARs, including 276 potential ADARs interactors and 9 ADARs direct partners. In addition, our analysis revealed several factors potentially influencing RNA editing in blood, including cell composition, age, Body Mass Index, smoke and alcohol consumption. Finally, we identified genetic loci associated with editing levels, including knownADAReQTLs and a small region on chromosome 7, containingLOC730338,a lincRNA gene that appears to modulate ADARs mRNA expression.ConclusionsOur data provides a detailed picture of the most relevant RNA editing events and their variability in human blood, giving interesting insights on potential mechanisms behind this post-transcriptional modification and its regulation in this tissue.

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Plastid caseinolytic protease OsClpR1 regulates chloroplast development and chloroplast RNA editing in rice

Rice ◽

10.1186/s12284-021-00489-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Xi Liu ◽

Ziyi Xu ◽

Yanrong Yang ◽

Penghui Cao ◽

Hang Cheng ◽

...

Keyword(s):

Rna Editing ◽

Chloroplast Development ◽

Chlorophyll Biosynthesis ◽

Wild Type ◽

Yeast Two Hybrid ◽

Lethal Mutant ◽

Caseinolytic Protease ◽

Young Leaves ◽

Chloroplast Rna ◽

Two Hybrid

Abstract Background Plant plastidic caseinolytic protease (Clp) is a central part of the plastid protease network and consists of multiple subunits. The molecular functions of many Clps in plants, especially in crops, are not well known. Results In this study, we identified an albino lethal mutant al3 in rice, which produces albino leaves and dies at the seedling stage. Molecular cloning revealed that AL3 encodes a plastid caseinolytic protease, OsClpR1, homologous to Arabidopsis ClpR1 and is targeted to the chloroplast. Compared with the wild type, chloroplast structure in the al3 mutant was poorly developed. OsClpR1 was constitutively expressed in all rice tissues, especially in young leaves. The OsClpR1 mutation affected the transcript levels of chlorophyll biosynthesis and chloroplast development-related genes. The RNA editing efficiency of three chloroplast genes (rpl2, ndhB, ndhA) was remarkably reduced in al3. Using a yeast two-hybrid screen, we found that OsClpR1 interacted with OsClpP4, OsClpP5, OsClpP2, and OsClpS1. Conclusions Collectively, our results provide novel insights into the function of Clps in rice.

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Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana

Cells ◽

10.3390/cells10030635 ◽

2021 ◽

Vol 10 (3) ◽

pp. 635

Author(s):

Ruchika ◽

Chisato Okudaira ◽

Matomo Sakari ◽

Toshifumi Tsukahara

Keyword(s):

Rna Editing ◽

Sanger Sequencing ◽

Developmental Stages ◽

Nuclear Genes ◽

Rna Seq ◽

Pentatricopeptide Repeat ◽

Stages Of Growth ◽

Genome Wide ◽

Ppr Genes ◽

Plant Organelles

Cytosine-to-Uridine (C-to-U) RNA editing involves the deamination phenomenon, which is observed in animal nucleus and plant organelles; however, it has been considered the U-to-C is confined to the organelles of limited non-angiosperm plant species. Although previous RNA-seq-based analysis implied U-to-C RNA editing events in plant nuclear genes, it has not been broadly accepted due to inadequate confirmatory analyses. Here we examined the U-to-C RNA editing in Arabidopsis tissues at different developmental stages of growth. In this study, the high-throughput RNA sequencing (RNA-seq) of 12-day-old and 20-day-old Arabidopsis seedlings was performed, which enabled transcriptome-wide identification of RNA editing sites to analyze differentially expressed genes (DEGs) and nucleotide base conversions. The results showed that DEGs were expressed to higher levels in 12-day-old seedlings than in 20-day-old seedlings. Additionally, pentatricopeptide repeat (PPR) genes were also expressed at higher levels, as indicated by the log2FC values. RNA-seq analysis of 12-day- and 20-day-old Arabidopsis seedlings revealed candidates of U-to-C RNA editing events. Sanger sequencing of both DNA and cDNA for all candidate nucleotide conversions confirmed the seven U-to-C RNA editing sites. This work clearly demonstrated presence of U-to-C RNA editing for nuclear genes in Arabidopsis, which provides the basis to study the mechanism as well as the functions of the unique post-transcriptional modification.

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SWEET Gene Family in Medicago truncatula: Genome-Wide Identification, Expression and Substrate Specificity Analysis

Plants ◽

10.3390/plants8090338 ◽

2019 ◽

Vol 8 (9) ◽

pp. 338 ◽

Cited By ~ 3

Author(s):

Bin Hu ◽

Hao Wu ◽

Weifeng Huang ◽

Jianbo Song ◽

Yong Zhou ◽

...

Keyword(s):

Medicago Truncatula ◽

Stress Responses ◽

Active Sites ◽

Developmental Stages ◽

Rna Seq ◽

Transmembrane Helices ◽

Functional Roles ◽

Genome Wide ◽

Solid Foundation ◽

As Stress

SWEET (Sugars Will Eventually be Exported Transporter) proteins mediate the translocation of sugars across cell membranes and play crucial roles in plant growth and development as well as stress responses. In this study, a total of 25 SWEET genes were identified from the Medicago truncatula genome and were divided into four clades based on the phylogenetic analysis. The MtSWEET genes are distributed unevenly on the M. truncatula chromosomes, and eight and 12 MtSWEET genes are segmentally and tandemly duplicated, respectively. Most MtSWEET genes contain five introns and encode proteins with seven transmembrane helices (TMHs). Besides, nearly all MtSWEET proteins have relatively conserved membrane domains, and contain conserved active sites. Analysis of microarray data showed that some MtSWEET genes are specifically expressed in disparate developmental stages or tissues, such as flowers, developing seeds and nodules. RNA-seq and qRT-PCR expression analysis indicated that many MtSWEET genes are responsive to various abiotic stresses such as cold, drought, and salt treatments. Functional analysis of six selected MtSWEETs in yeast revealed that they possess diverse transport activities for sucrose, fructose, glucose, galactose, and mannose. These results provide new insights into the characteristics of the MtSWEET genes, which lay a solid foundation for further investigating their functional roles in the developmental processes and stress responses of M. truncatula.

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HPC-REDItools: a Novel HPC-aware Tool for Improved Large Scale RNA-editing Analysis

10.1101/2020.04.30.069732 ◽

2020 ◽

Cited By ~ 2

Author(s):

Tiziano Flati ◽

Silvia Gioiosa ◽

Nicola Spallanzani ◽

Ilario Tagliaferri ◽

Maria Angela Diroma ◽

...

Keyword(s):

Rna Editing ◽

Large Scale ◽

Big Data Analysis ◽

Small Data ◽

Data Sets ◽

Rna Seq ◽

Large Dataset ◽

Rna Sequences ◽

Genome Wide ◽

Small Data Sets

AbstractBackgroundRNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process.ResultsIn this work we introduce HPC-REDItools, an upgraded tool for accurate RNA-editing events discovery from large dataset repositories. Availability: https://github.com/BioinfoUNIBA/REDItools2.ConclusionsHPC-REDItools is dramatically faster than the previous version, REDItools, enabling big-data analysis by means of a MPI-based implementation and scaling almost linearly with the number of available cores.

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