SMK6 mediates the C-to-U editing at multiple sites in maize mitochondria

Ding, Shuo; Liu, Xinyuan; Wang, Hongchun; Wang, Yong; Tang, Jiao-Jiao; Yang, Yan‐Zhuo; Tan, Bin

doi:10.1016/j.jplph.2019.152992

Cited by 12 publications

(5 citation statements)

References 47 publications

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“…Consistently, abolishment of editing at nad2-26 and nad5-1916 (also identified in this study) affects PCD and maize endosperm development [26]. Moreover, CDS-recoding editing events in nad4L (nad4L-110 and nad4L-179) encoding a subunit of complex I and atp9 (atp9-191 and atp9-212) encoding a subunit of complex V (also identified in this study), are closely associated with mutant maize endosperm [29,43]. In addition, abolishment of editing at nad7-836 affects the structural stability and activity of NAD7 (a subunit of complex I) and further influences respiration rate, starch biosynthesis, and maize endosperm development [35].…”

Section: Discussionsupporting

confidence: 88%

“…Consequently, over the past decades, valuable efforts have been devoted to investigating RNA editing during plant endosperm development. Evidence has been accumulated that RNA editing in mitochondrial transcripts plays a key role in endosperm development [26][27][28][29][30][31][32][33][34] by affecting functions of complexes comprising mETC, Cyt c biogenesis proteins, ribosomal proteins and MatR. Specifically, RNA editing in mitochondrial genes regulated by PPR proteins is related to rice endosperm development, as nad7 mediated by SMK1 [35], atp6, cob, cox3, nad1, nad9, rpl16 and rps12 by EMP5 [36], cox2, cox3, ccmC, nad2 and nad4 by OGR1 [37], and multiple mitochondrial genes (such as nad9) by cooperation of P-class FLO22 and PLS-class DYW3 [38].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Characterization of RNA editing profiles in rice endosperm development

Chen,

Xia,

Tan

et al. 2024

Preprint

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Rice (Oryza sativa L.) endosperm provides nutrients for seed germination and determines grain yield. RNA editing, a post-transcriptional modification essential for plant development, unfortunately, is not fully characterized during rice endosperm development. Here, we conduct genome re-sequencing and RNA sequencing for rice endosperms across five successive developmental stages and perform systematic analyses to characterize RNA editing profiles during rice endosperm development. We find that the majority of their editing sites are C-to-U CDS-recoding in mitochondria, leading to increased hydrophobic amino acids, and affecting structures and functions of mitochondrial proteins. Comparative analysis of RNA editing profiles across the five developmental stages reveals that CDS-recoding sites present higher editing frequencies with lower variabilities, and recoded amino acids, particularly caused by these sites with higher editing frequencies, tend to exhibit stronger evolutionary conservation across many land plants. Based on these results, we further classify mitochondrial genes into three groups that present distinct patterns in terms of editing frequency and variability of CDS-recoding sites. Besides, we identify a series of P- and PLS-class pentatricopeptide repeat (PPR) proteins with editing potential and construct PPR-RNA binding profiles, yielding candidate PPR editing factors related to rice endosperm development. Taken together, our findings provide valuable insights for deciphering fundamental mechanisms of rice endosperm development underlying RNA editing machinery.

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Section: Discussionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Characterization of RNA editing profiles in rice endosperm development

Chen,

Xia,

Tan

et al. 2024

Preprint

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“…The loss of function of DEK504 resulted in the dek phenotype of the kernel. Although all five known E+-type PPR proteins exhibit C-to-U RNA editing of mitochondrial transcripts, they differ in terms of the editing genes and sites: Dek36 at atp4 -59, ccmFN -302, and nad7 -383; Dek40 at nad5-1916 , nad2-26 , and cox3-314 ; E mp9 at ccmB-43 and rps4-335 ; Smk6 at nad1-740 , nad4L-110 , nad7-739 , mttB-138 , and mttB-139 ; and Dek504 at nad3 -44 and nad3 -317 [ 37 , 41 , 48 , 49 ]. Therefore, the present study unveiled a novel mitochondrion-localized E+-type PPR protein ( Figure 4 c) involved in C-to-U RNA editing at two novel sites, namely nad3 -44 and nad3 -317 ( Figure 5 a).…”

Section: Discussionmentioning

confidence: 99%

Dek504 Encodes a Mitochondrion-Targeted E+-Type Pentatricopeptide Repeat Protein Essential for RNA Editing and Seed Development in Maize

Wang

Chen

Zhang

et al. 2022

IJMS

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In flowering plants, RNA editing is a post-transcriptional process that selectively deaminates cytidines (C) to uridines (U) in organellar transcripts. Pentatricopeptide repeat (PPR) proteins have been identified as site-specific recognition factors for RNA editing. Here, we report the map-based cloning and molecular characterization of the defective kernel mutant dek504 in maize. Loss of Dek504 function leads to delayed embryogenesis and endosperm development, which produce small and collapsed kernels. Dek504 encodes an E+-type PPR protein targeted to the mitochondria, which is required for RNA editing of mitochondrial NADH dehydrogenase 3 at the nad3-317 and nad3-44 sites. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the mitochondrial NADH dehydrogenase complex I activity, indicating that the alteration of the amino acid sequence at nad3-44 and nad3-317 through RNA editing is essential for NAD3 function. Moreover, the amino acids are highly conserved in monocots and eudicots, whereas the events of C-to-U editing are not conserved in flowering plants. Thus, our results indicate that Dek504 is essential for RNA editing of nad3, which is critical for NAD3 function, mitochondrial complex I stability, and seed development in maize.

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“…For mitochondrion-targeted PPR proteins, their disruptions mostly cause diverse seed development mutants, including smk, dek, and emp, with different degrees of defects in embryo and endosperm. The loss-of-function of SMK1 [65], SMK4 [66], SMK6 [67], ZmSMK9 [68], PPR2263 [69], and MPPR6 [70] in maize and PPR19 [97] in Arabidopsis arrests both embryo and endosperm development, resulting in smk phenotypes. Some characterized mitochondrion-targeted PPR proteins, such as DEK2 [52], DEK10 [53], DEK35 [54], DEK36 [55], DEK37 [56], DEK39 [57], DEK40 [58], DEK41/43 [59,60], DEK46 [61], and DEK53 [62] in maize, are necessary for seed development, and their disruptions result in dek mutants with arrested development of both the embryo and endosperm at an early stage.…”

Section: Functions Of Ppr Proteins In Seed Developmentmentioning

confidence: 99%

Functions of PPR Proteins in Plant Growth and Development

Sun

Liu

et al. 2021

IJMS

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Pentatricopeptide repeat (PPR) proteins form a large protein family in land plants, with hundreds of different members in angiosperms. In the last decade, a number of studies have shown that PPR proteins are sequence-specific RNA-binding proteins involved in multiple aspects of plant organellar RNA processing, and perform numerous functions in plants throughout their life cycle. Recently, computational and structural studies have provided new insights into the working mechanisms of PPR proteins in RNA recognition and cytidine deamination. In this review, we summarized the research progress on the functions of PPR proteins in plant growth and development, with a particular focus on their effects on cytoplasmic male sterility, stress responses, and seed development. We also documented the molecular mechanisms of PPR proteins in mediating RNA processing in plant mitochondria and chloroplasts.

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SMK6 mediates the C-to-U editing at multiple sites in maize mitochondria

Cited by 12 publications

References 47 publications

Characterization of RNA editing profiles in rice endosperm development

Characterization of RNA editing profiles in rice endosperm development

Dek504 Encodes a Mitochondrion-Targeted E+-Type Pentatricopeptide Repeat Protein Essential for RNA Editing and Seed Development in Maize

Functions of PPR Proteins in Plant Growth and Development

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