Non-canonical Features of Pentatricopeptide Repeat Protein-Facilitated RNA Editing in Arabidopsis Chloroplasts

AbstractCytosine (C) to uracil (U) RNA editing in plant mitochondria and chloroplasts is facilitated by site-specific pentatricopeptide repeat (PPR) editing factors. PPR editing factors contain multiple types of PPR motifs, and PPR motifs of the same type also show sequence variations. Therefore, no PPR motifs are invariant within a PPR protein or between different PPR proteins. This work evaluates the functional diversity of PPR motifs in CHLOROPLAST RNA EDITING FACTOR 3 (CREF3). The results indicate that previously overlooked features of PPR editing factors could also contribute to RNA editing activity. In particular, the N-terminal degenerated PPR motifs and the two L1-type PPR motifs in CREF3 are functionally indispensable. Furthermore, PPR motifs of the same type in CREF3 are not interchangeable. These non-canonical features of CREF3 have important implications on the understanding of PPR-facilitated RNA editing in plant organelles.

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The DYW-subgroup pentatricopeptide repeat protein PPR27 interacts with ZmMORF1 to facilitate mitochondrial RNA editing and seed development in maize

Journal of Experimental Botany ◽

10.1093/jxb/eraa273 ◽

2020 ◽

Vol 71 (18) ◽

pp. 5495-5505 ◽

Cited By ~ 1

Author(s):

Rui Liu ◽

Shi-Kai Cao ◽

Aqib Sayyed ◽

Huan-Huan Yang ◽

Jiao Zhao ◽

...

Keyword(s):

Rna Editing ◽

Seed Development ◽

Plant Mitochondria ◽

Endosperm Development ◽

Complex Iii ◽

Mitochondrial Rna ◽

Mitochondrial Complex ◽

Pentatricopeptide Repeat ◽

Ppr Protein ◽

Ppr Proteins

Abstract C-to-U RNA editing in plant mitochondria requires the participation of many nucleus-encoded factors, most of which are pentatricopeptide repeat (PPR) proteins. There is a large number of PPR proteins and the functions many of them are unknown. Here, we report a mitochondrion-localized DYW-subgroup PPR protein, PPR27, which functions in the editing of multiple mitochondrial transcripts in maize. The ppr27 mutant is completely deficient in C-to-U editing at the ccmFN-1357 and rps3-707 sites, and editing at six other sites is substantially reduced. The lack of editing at ccmFN-1357 causes a deficiency of CcmFN protein. As CcmFN functions in the maturation pathway of cytochrome proteins that are subunits of mitochondrial complex III, its deficiency results in an absence of cytochrome c1 and cytochrome c proteins. Consequently, the assembly of mitochondrial complex III and super-complex I+III2 is decreased, which impairs the electron transport chain and respiration, leading to arrests in embryogenesis and endosperm development in ppr27. In addition, PPR27 was found to physically interact with ZmMORF1, which interacts with ZmMORF8, suggesting that these three proteins may facilitate C-to-U RNA editing via the formation of a complex in maize mitochondria. This RNA editing is essential for complex III assembly and seed development in maize.

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The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize

BMC Plant Biology ◽

10.1186/s12870-020-02765-x ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Ru Chang Ren ◽

Xu Wei Yan ◽

Ya Jie Zhao ◽

Yi Ming Wei ◽

Xiaoduo Lu ◽

...

Keyword(s):

Rna Editing ◽

Rna Processing ◽

Mitochondrial Gene ◽

Endosperm Development ◽

Molecular Evidence ◽

Pentatricopeptide Repeat ◽

Reading Frame ◽

Maize Kernel ◽

Ppr Protein ◽

Ppr Proteins

Abstract Background Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown. Results In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of nad1 and nad4 introns. Mutation in the DEK55 gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291). Conclusions Our results demonstrated that a mutation in the DEK55 gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing.

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Maize pentatricopeptide repeat protein DEK53 is required for mitochondrial RNA editing at multiple sites and seed development

Journal of Experimental Botany ◽

10.1093/jxb/eraa348 ◽

2020 ◽

Vol 71 (20) ◽

pp. 6246-6261 ◽

Cited By ~ 2

Author(s):

Dawei Dai ◽

Lifang Jin ◽

Zhenzhen Huo ◽

Shumei Yan ◽

Zeyang Ma ◽

...

Keyword(s):

Rna Editing ◽

Protein Complexes ◽

Plant Mitochondria ◽

Mitochondrial Protein ◽

Electron Microscopic Examination ◽

Complex Iii ◽

Mitochondrial Rna ◽

Pentatricopeptide Repeat ◽

Electron Microscopic ◽

Ppr Protein

Abstract Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.

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The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity

Genome Biology and Evolution ◽

10.1093/gbe/evz232 ◽

2019 ◽

Vol 11 (11) ◽

pp. 3233-3239 ◽

Cited By ~ 3

Author(s):

Shanshan Dong ◽

Chaoxian Zhao ◽

Shouzhou Zhang ◽

Hong Wu ◽

Weixue Mu ◽

...

Keyword(s):

Rna Editing ◽

Phylogenetic Diversity ◽

Gc Content ◽

Pentatricopeptide Repeat ◽

Protein Coding ◽

Protein Diversity ◽

Ppr Protein ◽

Ppr Proteins ◽

Codon Positions ◽

Positive Correlations

Abstract RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.

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PPR proteins network as site-specific RNA editing factors in plant organelles

RNA Biology ◽

10.4161/rna.8.1.14298 ◽

2011 ◽

Vol 8 (1) ◽

pp. 67-70 ◽

Cited By ~ 30

Author(s):

Anja Zehrmann ◽

Daniil Verbitskiy ◽

Barbara Härtel ◽

Axel Brennicke ◽

Mizuki Takenaka

Keyword(s):

Rna Editing ◽

Site Specific ◽

Ppr Proteins ◽

Plant Organelles

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A synthetic RNA editing factor edits its target site in chloroplasts and bacteria

Communications Biology ◽

10.1038/s42003-021-02062-9 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Santana Royan ◽

Bernard Gutmann ◽

Catherine Colas des Francs-Small ◽

Suvi Honkanen ◽

Jason Schmidberger ◽

...

Keyword(s):

Rna Editing ◽

Rna Binding ◽

Rna Binding Proteins ◽

Target Sequence ◽

Pentatricopeptide Repeat ◽

Binding Assays ◽

E Coli ◽

Ppr Protein ◽

Ppr Proteins

AbstractMembers of the pentatricopeptide repeat (PPR) protein family act as specificity factors in C-to-U RNA editing. The expansion of the PPR superfamily in plants provides the sequence variation required for design of consensus-based RNA-binding proteins. We used this approach to design a synthetic RNA editing factor to target one of the sites in the Arabidopsis chloroplast transcriptome recognised by the natural editing factor CHLOROPLAST BIOGENESIS 19 (CLB19). We show that our synthetic editing factor specifically recognises the target sequence in in vitro binding assays. The designed factor is equally specific for the target rpoA site when expressed in chloroplasts and in the bacterium E. coli. This study serves as a successful pilot into the design and application of programmable RNA editing factors based on plant PPR proteins.

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GmPGL2, Encoding a Pentatricopeptide Repeat Protein, Is Essential for Chloroplast RNA Editing and Biogenesis in Soybean

Frontiers in Plant Science ◽

10.3389/fpls.2021.690973 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xingxing Feng ◽

Suxin Yang ◽

Yaohua Zhang ◽

Cheng Zhiyuan ◽

Kuanqiang Tang ◽

...

Keyword(s):

Rna Editing ◽

Pentatricopeptide Repeat ◽

Mobility Shift ◽

Single Nucleotide ◽

Chlorophyll Contents ◽

Complex Processes ◽

Ppr Protein ◽

Ppr Proteins ◽

Mobility Shift Assay

Chloroplast biogenesis and development are highly complex processes requiring interactions between plastids and nuclear genomic products. Pentatricopeptide repeat (PPR) proteins play an essential role in the development of chloroplasts; however, it remains unclear how RNA editing factors influence soybean development. In this study, a Glycine max pale green leaf 2 mutant (Gmpgl2) was identified with decreased chlorophyll contents. Genetic mapping revealed that a single-nucleotide deletion at position 1949 bp in the Glyma.05g132700 gene in the Gmpgl2 mutant, resulting in a truncated GmPGL2 protein. The nuclear-encoded GmPGL2 is a PLS-type PPR protein that localizes to the chloroplasts. The C-to-U editing efficiencies of rps16, rps18, ndhB, ndhD, ndhE, and ndhF were reduced in the Gmpgl2 mutant. RNA electrophoresis mobility shift assay (REMSA) analysis further revealed that GmPGL2 binds to the immediate upstream sequences at RNA editing sites of rps16 and ndhB in vitro, respectively. In addition, GmPGL2 was found to interact with GmMORF8, GmMORF9, and GmORRM6. These results suggest that GmPGL2 participates in C-to-U RNA editing via the formation of a complex RNA editosome in soybean chloroplasts.

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A novel E-Subgroup Pentatricopeptide Repeat Protein DEK55 is Responsible for RNA Editing at 15 Sites and Splicing of nad1 and nad4 in Maize

10.21203/rs.3.rs-26875/v1 ◽

2020 ◽

Author(s):

Ru Chang Ren ◽

Xu Wei Yan ◽

Ya Jie Zhao ◽

Yi Ming Wei ◽

Xiaoduo Lu ◽

...

Keyword(s):

Rna Editing ◽

Endosperm Development ◽

Pentatricopeptide Repeat ◽

Reading Frame ◽

Maize Kernel ◽

Ppr Protein ◽

Ppr Proteins ◽

Large Protein Family ◽

Underlying Mechanisms ◽

Mutant Phenotypes

Abstract Background Pentatricopeptide repeat (PPR) proteins is a large protein family, which participate in RNA processing in organelles and plant growth. Previous reports have generally considered E-subgroup PPR proteins as an editing factors for RNA editing. However, the underlying mechanisms and effects of E-subgroup PPR proteins remain to be investigated.Results In this study, we recognized and identified a new maize kernel mutant with arrested embryo and endosperm development, defective kernel 55 (dek55). Genetic and molecular evidences suggest that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 in the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within mitochondria. Molecular analyses suggest that DEK55 plays crucial roles in RNA editing at multiple sites of ribosomal protein S13, ATP synthase subunit1, NADH dehydrogenase-6 (nad6), and nad9 transcripts as well as in splicing of nad1 and nad4. The mutation of DEK55 lead to the dysfunction of mitochondrial complex I.Conclusions Our results demonstrate that the DEK55 mutation is responsible for the dek55 mutant phenotypes, as it affects mitochondrial function that is essential for maize kernel development. This study also provides novel insight into the molecular function of E-subgroup PPR proteins in plant organellar RNA metabolism.

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The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize

10.21203/rs.3.rs-26875/v3 ◽

2020 ◽

Author(s):

Ru Chang Ren ◽

Xu Wei Yan ◽

Ya Jie Zhao ◽

Yi Ming Wei ◽

Xiaoduo Lu ◽

...

Keyword(s):

Rna Editing ◽

Rna Processing ◽

Mitochondrial Gene ◽

Endosperm Development ◽

Molecular Evidence ◽

Pentatricopeptide Repeat ◽

Reading Frame ◽

Maize Kernel ◽

Ppr Protein ◽

Ppr Proteins

Abstract Background: Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown. Results: In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at +449 bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of nad1 and nad4 introns. Mutation in the DEK55 gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291).Conclusions: Our results demonstrated that a mutation in the DEK55 gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing.

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ZmPPR26, a DYW-type pentatricopeptide repeat protein, is required for C-to-U RNA editing at atpA-1148 in maize chloroplasts

Journal of Experimental Botany ◽

10.1093/jxb/erab185 ◽

2021 ◽

Author(s):

Xin-Yuan Liu ◽

Rui-Cheng Jiang ◽

Yong Wang ◽

Jiao-Jiao Tang ◽

Feng Sun ◽

...

Keyword(s):

Rna Editing ◽

Atp Synthase ◽

Protein Accumulation ◽

Chloroplast Biogenesis ◽

Pentatricopeptide Repeat ◽

Lethal Phenotype ◽

Ppr Protein ◽

Ppr Proteins ◽

Photosynthetic Complexes ◽

Maize Chloroplast

Abstract Pentatricopeptide repeat (PPR) proteins are involved in the C-to-U RNA editing of organellar transcripts. Maize genome contains over 600 PPR proteins and few have been found to function in the C-to-U RNA editing in chloroplasts. Here, we report the function of ZmPPR26 in the C-to-U RNA editing and chloroplast biogenesis in maize. ZmPPR26 encodes a DYW-type PPR protein targeted to chloroplasts. The zmppr26 mutant exhibits albino seedling-lethal phenotype. Loss-function of ZmPPR26 abolishes the editing at atpA-1148 site, and decreases the editing at ndhF-62, rpl20-308, rpl2-2, rpoC2-2774, petB-668, rps8-182, and ndhA-50 sites. Over-expression of ZmPPR26 in zmppr26 restores the editing efficiency and rescues the albino seedling-lethal phenotype. Abolished editing at atpA-1148 causes a Leu to Ser change at AtpA-383 that leads to a reduction in the abundance of chloroplast ATP synthase in zmppr26. The protein accumulation and content of photosynthetic complexes are also markedly reduced in zmppr26, providing an explanation for the albino seedling-lethal phenotype. These results indicate that ZmPPR26 is required for the editing at atpA-1148 and important for the editing at the other seven sites in maize chloroplast. The editing at atpA-1148 is critical to the AtpA function, assembly of ATP synthase complex, and chloroplast biogenesis in maize.

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