Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant

Tseng, Ching-Chih; Sung, Tzu-Ying; Li, Yi-Chiou; Hsu, Shih-Jui; Lin, Chien-Li; Hsieh, Ming‐Hsiun

doi:10.1007/s11103-010-9616-5

Cited by 68 publications

(52 citation statements)

References 76 publications

(98 reference statements)

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“…RNA editing increases the complexity of the plastid transcriptome, can influence the protein activity, and be affected by pigment deficiency (18,19). Sequencing of cloned cDNA-derived .…”

Section: Resultsmentioning

confidence: 99%

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

Babiychuk

Vandepoele²,

Wissing³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

135

274

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Plastids are DNA-containing organelles unique to plant cells. In Arabidopsis, one-third of the genes required for embryo development encode plastid-localized proteins. To help understand the role of plastids in embryogenesis and postembryonic development, we characterized proteins of the mitochondrial transcription termination factor (mTERF) family, which in animal models, comprises DNA-binding regulators of mitochondrial transcription. Of 35 Arabidopsis mTERF proteins, 11 are plastid-localized. Genetic complementation shows that at least one plastidic mTERF, BELAYA SMERT' (BSM), is required for embryogenesis. The main postembryonic phenotypes of genetic mosaics with the bsm mutation are severe abnormalities in leaf development. Mutant bsm cells are albino, are compromised in growth, and suffer defects in global plastidic gene expression. The bsm phenotype could be phenocopied by inhibition of plastid translation with spectinomycin. Plastid translation is essential for cell viability in dicotyledonous species such as tobacco but not in monocotyledonous maize. Here, genetic interactions between BSM and the gene encoding plastid homomeric acetyl-CoA carboxylase ACC2 suggest that there is a functional redundancy in malonyl-CoA biosynthesis that permits bsm cell survival in Arabidopsis. Overall, our results indicate that biosynthesis of malonyl-CoA and plastid-derived systemic growth-promoting compounds are the processes that link plant development and plastid gene expression. organellar gene expression | splicing | ClpPR protease | myrosinase | digitonin

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“…RNA editing increases the complexity of the plastid transcriptome, can influence the protein activity, and be affected by pigment deficiency (18,19). Sequencing of cloned cDNA-derived .…”

Section: Resultsmentioning

confidence: 99%

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

Babiychuk

Vandepoele²,

Wissing³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

135

274

View full text Add to dashboard Cite

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“…The function of these proteins, particularly PPR proteins, has been well characterized (Schmitz-Linneweber and Small, 2008;Stern et al, 2010;Shikanai and Fujii, 2013). PPR proteins in chloroplast have been implicated as being involved in regulating RNA splicing (Schmitz-Linneweber et al, 2006;de Longevialle et al, 2007;Ichinose et al, 2012), RNA editing (Kotera et al, 2005;Okuda et al, 2007;Chateigner-Boutin et al, 2008;Cai et al, 2009;Yu et al, 2009;Zhou et al, 2009;Tseng et al, 2010;Sosso et al, 2012), RNA cleavage (Meierhoff et al, 2003;Hattori et al, 2007), and translation (Williams and Barkan, 2003;Tavares-Carreón et al, 2008) during plant development. The disruption of tetratricopeptide repeat or PPR proteins generally causes defects in the development of chloroplast, eventually leading to the albino or chlorotic leaf phenotype in plants (Chi et al, 2008(Chi et al, , 2010Cao et al, 2011;Su et al, 2012;Gong et al, 2014).…”

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confidence: 99%

Albino Leaf 1 that Encodes the Sole Octotricopeptide Repeat Protein Is Responsible for Chloroplast Development in Rice

et al. 2016

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Chloroplast, the photosynthetic organelle in plants, plays a crucial role in plant development and growth through manipulating the capacity of photosynthesis. However, the regulatory mechanism of chloroplast development still remains elusive. Here, we characterized a mutant with defective chloroplasts in rice (Oryza sativa), termed albino leaf1 (al1), which exhibits a distinct albino phenotype in leaves, eventually leading to al1 seedling lethality. Electronic microscopy observation demonstrated that the number of thylakoids was reduced and the structure of thylakoids was disrupted in the al1 mutant during rice development, which eventually led to the breakdown of chloroplast. Molecular cloning revealed that AL1 encodes the sole octotricopeptide repeat protein (RAP) in rice. Genetic complementation of Arabidopsis (Arabidopsis thaliana) rap mutants indicated that the AL1 protein is a functional RAP. Further analysis illustrated that three transcript variants were present in the AL1 gene, and the altered splices occurred at the 39 untranslated region of the AL1 transcript. In addition, our results also indicate that disruption of the AL1 gene results in an altered expression of chloroplast-associated genes. Consistently, proteomic analysis demonstrated that the abundance of photosynthesis-associated proteins is altered significantly, as is that of a group of metabolism-associated proteins. More specifically, we found that the loss of AL1 resulted in altered abundances of ribosomal proteins, suggesting that RAP likely also regulates the homeostasis of ribosomal proteins in rice in addition to the ribosomal RNA. Taken together, we propose that AL1, particularly the AL1a and AL1c isoforms, plays an essential role in chloroplast development in rice.

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“…Editing of the psbZ and ndhF sites was highly reduced in the presence of the OTP84trcDYW transgene, although the ndhF site may have been somewhat higher than gene knock-out levels. The ndhF C290 editing site is also affected by disruption of the PPR gene, VAC1, which results in a partial loss of editing of the ndhF site (48). The DYW deami-FIGURE 2.…”

Section: Discussionmentioning

confidence: 99%

“…CREF7 appears to function as both a specificity factor and a deaminase in the editing of its cognate site, but also contributes to rpoA editing with the CLB19 as a specificity factor. VAC1 is a PPR protein with a DYW domain, and the gene knock-out results in a strong lethal phenotype and partial editing of ndhF C290 (a cognate site of OTP84) and accD C794 (a cognate site of RARE1) (48). Because the VAC1 knock-out exhibits partial editing, VAC1 is not essential for each site.…”

Section: Discussionmentioning

confidence: 99%

A Conserved Glutamate Residue in the C-terminal Deaminase Domain of Pentatricopeptide Repeat Proteins Is Required for RNA Editing Activity

Hayes

Dang

Diaz

et al. 2015

Journal of Biological Chemistry

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Background: Pentatricopeptide repeat (PPR) proteins that are required for RNA editing frequently include a C-terminal DYW deaminase domain. Results: Mutagenesis of a glutamate residue in the conserved deaminase HXE motif results in loss of editing activity. Conclusion:The glutamate residue is required for editing. Significance: The DYW deaminase domain of PPR proteins has the molecular characteristics of a deaminase.Many transcripts expressed from plant organelle genomes are modified by C-to-U RNA editing. Nuclear encoded pentatricopeptide repeat (PPR) proteins include an RNA binding domain that provides site specificity. In addition, many PPR proteins include a C-terminal DYW deaminase domain with characteristic zinc binding motifs (CXXC, HXE) and has recently been shown to bind zinc ions. The glutamate residue of the HXE motif is catalytically required in the reaction catalyzed by cytidine deaminase. In this work, we examine the activity of the DYW deaminase domain through truncation or mutagenesis of the HXE motif. OTP84 is required for editing three chloroplast sites, and transgenes expressing OTP84 with C-terminal truncations were capable of editing only one of the three cognate sites at high efficiency. These results suggest that the deaminase domain of OTP84 is required for editing two of the sites, but another deaminase is able to supply the deamination activity for the third site. OTP84 and CREF7 transgenes were mutagenized to replace the glutamate residue of the HXE motif, and transgenic plants expressing OTP84-E824A and CREF7-E554A were unable to efficiently edit the cognate editing sites for these genes. In addition, plants expressing CREF7-E554A exhibited substantially reduced capacity to edit a non-cognate site, rpoA C200. These results indicate that the DYW deaminase domains of PPR proteins are involved in editing their cognate editing sites, and in some cases may participate in editing additional sites in the chloroplast.RNA editing takes place in most land plant chloroplasts and mitochondria (1, 2). In flowering plants, the transcripts of chloroplasts and mitochondria are modified post-transcriptionally by C-to-U editing with about 35 C-to-U editing events in chloroplasts and hundreds of editing sites in the mitochondria (3).Editing in higher plants and in Physcomitrella patens is known to require nuclear proteins (4 -8).Pentatricopeptide repeat (PPR) 2 genes have been shown to be required for RNA editing (9), and form a large family of protein-coding genes in higher plants with over 400 members in Arabidopsis (10). The known editing factors are members of the PLS subfamily of PPR proteins, which are composed of characteristic P, L (long), and S (short) repeats (11). Amino acid residues located in specific locations within the repeats have been shown to specify the base recognized in the cis-element (12)(13)(14), and the PLS repeat domain interacts with specific nucleotides within the cis-element to provide site specificity for RNA editing (12,15).The PLS subfamily of PPR proteins also includes ...

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Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant

Cited by 68 publications

References 76 publications

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

Albino Leaf 1 that Encodes the Sole Octotricopeptide Repeat Protein Is Responsible for Chloroplast Development in Rice

A Conserved Glutamate Residue in the C-terminal Deaminase Domain of Pentatricopeptide Repeat Proteins Is Required for RNA Editing Activity

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