Two pivotal <scp>RNA</scp> editing sites in the mitochondrial <i>atp1</i><scp>mRNA</scp> are required for <scp>ATP</scp> synthase to produce sufficient <scp>ATP</scp> for cotton fiber cell elongation

He, Peng; Xiao, Gao; Líu, Hao; Zhang, Lihua; Zhao, Li; Tang, Meiju; Huang, Sheng; An, Yingjie; Yu, Jianing

doi:10.1111/nph.14999

Cited by 48 publications

(17 citation statements)

References 74 publications

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“…Mitochondrial RNA editing in higher plants is related to potentially molecular functions and physiological processes (Yang et al. 2017; He et al. 2018).…”

Section: Discussionmentioning

confidence: 99%

Evolution and Diversification of Kiwifruit Mitogenomes through Extensive Whole-Genome Rearrangement and Mosaic Loss of Intergenic Sequences in a Highly Variable Region

Wang

Yao

et al. 2019

Genome Biology and Evolution

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Angiosperm mitochondrial genomes (mitogenomes) are notable for their extreme diversity in both size and structure. However, our current understanding of this diversity is limited, and the underlying mechanism contributing to this diversity remains unclear. Here, we completely assembled and compared the mitogenomes of three kiwifruit ( Actinidia ) species, which represent an early divergent lineage in asterids. We found conserved gene content and fewer genomic repeats, particularly large repeats (>1 kb), in the three mitogenomes. However, sequence transfers such as intracellular events are variable and dynamic, in which both ancestral shared and recently species-specific events as well as complicated transfers of two plastid-derived sequences into the nucleus through the mitogenomic bridge were detected. We identified extensive whole-genome rearrangements among kiwifruit mitogenomes and found a highly variable V region in which fragmentation and frequent mosaic loss of intergenic sequences occurred, resulting in greatly interspecific variations. One example is the fragmentation of the V region into two regions, V1 and V2, giving rise to the two mitochondrial chromosomes of Actinidia chinensis . Finally, we compared the kiwifruit mitogenomes with those of other asterids to characterize their overall mitogenomic diversity, which identified frequent gain/loss of genes/introns across lineages. In addition to repeat-mediated recombination and import-driven hypothesis of genome size expansion reported in previous studies, our results highlight a pattern of dynamic structural variation in plant mitogenomes through global genomic rearrangements and species-specific fragmentation and mosaic loss of intergenic sequences in highly variable regions on the basis of a relatively large ancestral mitogenome.

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“…Mitochondrial RNA editing in higher plants is related to potentially molecular functions and physiological processes (Yang et al. 2017; He et al. 2018).…”

Section: Discussionmentioning

confidence: 99%

Evolution and Diversification of Kiwifruit Mitogenomes through Extensive Whole-Genome Rearrangement and Mosaic Loss of Intergenic Sequences in a Highly Variable Region

Wang

Yao

et al. 2019

Genome Biology and Evolution

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“…Of the 552 mitochondrial editing sites we identified, 392 (72%) were distributed in coding regions. Similar surveys of mitochondrial editing sites in cotton and tobacco showed 422 (61% of 692 total) (He et al ., 2018) and 582 (92% of 635 total) editing sites (Grimes et al ., 2014), respectively, to be in mitochondrial coding regions. RNA editing in coding regions can prematurely terminate protein synthesis, create a new peptide and/or alter the amino acid sequence.…”

Section: Discussionmentioning

confidence: 99%

Molecular and functional diversity of organelle RNA editing mediated by RNA recognition motif‐containing protein ORRM4 in tomato

et al. 2020

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Plant organellar RNA editing is a distinct type of post-transcriptional RNA modification that is critical for plant development. We showed previously that the RNA editing factor SlORRM4 is required for mitochondrial function and fruit ripening in tomato (Solanum lycopersicum). However, a comprehensive atlas of the RNA editing mediated by SlORRM4 is lacking. We observed that SlORRM4 is targeted to both chloroplasts and mitochondria, and its knockout results in pale-green leaves and delayed fruit ripening. Using high-throughput sequencing, we identified 12 chloroplast editing sites and 336 mitochondrial editing sites controlled by SlORRM4, accounting for 23% of chloroplast sites in leaves and 61% of mitochondrial sites in fruits, respectively. Analysis of native RNA immunoprecipitation sequencing revealed that SlORRM4 binds to 31 RNA targets; 19 of these targets contain SlORRM4-dependent editing sites. Large-scale analysis of putative SlORRM4-interacting proteins identified SlRIP1b, a RIP/MORF protein. Moreover, functional characterization demonstrated that SlRIP1b is involved in tomato fruit ripening. Our results indicate that SlORRM4 binds to RNA targets and interacts with SlRIP1b to broadly affect RNA editing in tomato organelles. These results provide insights into the molecular and functional diversity of RNA editing factors in higher plants.

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“…For cotton samples, the plant material was frozen in liquid nitrogen and then ground to a fine powder with a mortar and pestle using a modified method (He et al ., 2018). For Arabidopsis samples, total RNA was isolated from rosette leaves and seedlings at 0, 2, 4, 8, 12 and 20 days after germination.…”

Section: Methodsmentioning

confidence: 99%

GhARF16‐1 modulates leaf development by transcriptionally regulating the GhKNOX2‐1 gene in cotton

Xiao

Zhang

et al. 2020

Plant Biotechnology Journal

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Summary The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16‐1 and GhKNOX2‐1 genes might be potential regulators of leaf shape. We functionally characterized the auxin‐responsive factor ARF16‐1 acting upstream of GhKNOX2‐1 to determine leaf morphology in cotton. The transcription of GhARF16‐1 was significantly higher in lobed‐leaved cotton than in smooth‐leaved cotton. Furthermore, the overexpression of GhARF16‐1 led to the up‐regulation of GhKNOX2‐1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2‐1. We found that GhARF16‐1 specifically bound to the promoter of GhKNOX2‐1 to induce its expression. The heterologous expression of GhARF16‐1 and GhKNOX2‐1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2‐1 is epistatic to GhARF16‐1 in Arabidopsis, suggesting that the GhARF16‐1 and GhKNOX2‐1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16‐1 and its downstream‐activated gene KNOX2‐1, determines leaf morphology in eudicots.

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Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation

Cited by 48 publications

References 74 publications

Evolution and Diversification of Kiwifruit Mitogenomes through Extensive Whole-Genome Rearrangement and Mosaic Loss of Intergenic Sequences in a Highly Variable Region

Evolution and Diversification of Kiwifruit Mitogenomes through Extensive Whole-Genome Rearrangement and Mosaic Loss of Intergenic Sequences in a Highly Variable Region

Molecular and functional diversity of organelle RNA editing mediated by RNA recognition motif‐containing protein ORRM4 in tomato

GhARF16‐1 modulates leaf development by transcriptionally regulating the GhKNOX2‐1 gene in cotton

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