Functional analysis of the <i>Arabidopsis thaliana <scp>CHLOROPLAST BIOGENESIS</scp> 19</i> pentatricopeptide repeat editing protein

Ramos‐Vega, Maricela; Guevara-García, Ángel Arturo; Llamas, Ernesto; Sánchez-León, Nidia; Olmedo-Monfil, Vianey; Vielle‐Calzada, Jean‐Philippe; León, Patricia

doi:10.1111/nph.13468

Cited by 35 publications

(30 citation statements)

References 60 publications

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“…Recent reports suggested that PPR proteins interact with MORF proteins for RNA editing (Bentolila et al ., ; Zhang et al ., ; Ramos‐Vega et al ., ). To identify proteins associated with AtECB2 for RNA editing, we performed a protein co‐immunoprecipitation (Co‐IP) experiment with MYC antibody using the AtECB2–4xMYC transgenic plants.…”

Section: Resultsmentioning

confidence: 97%

“…The E domain of PPR proteins is believed to be a protein–protein interaction motif (Shikanai, ; Okuda et al ., ). Recently, the PPR‐protein CLB19 was confirmed to interact with MORF2 through its E domain (Ramos‐Vega et al ., ). AtECB2 contains 17 PPR motifs and an E/E + and a DYW domain.…”

Section: Resultsmentioning

confidence: 97%

“…Crystal structure analysis has shown that the PPR motif configures as two anti‐parallel alpha‐helices, with successive PPR domains forming an extended superhelix surrounding a central groove that functions in RNA binding (Ban et al ., ; Ke et al ., ; Yin et al ., ; Gully et al ., ). The E region has been suggested to be a protein–protein interaction motif (Shikanai, ; Okuda et al ., ; Ramos‐Vega et al ., ). The DYW domain includes a highly conserved zinc binding motif (HxE(x) n PCxxC) that shares residue similarities with cytidine deaminases (Salone et al ., ), which suggests that it may have certain catalytic activity.…”

Section: Introductionmentioning

confidence: 97%

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Porphobilinogen deaminase HEMC interacts with the PPR‐protein AtECB2 for chloroplast RNA editing

Huang

et al. 2017

The Plant Journal

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The pentatricopeptide repeat-DYW protein AtECB2 affects plastid RNA editing at seven sites, including accD-794, accD-1568, ndhF-290, ndhG-50, petL-5, rpoA-200 and rpoC1-488. To understand the mechanism of its involvement in RNA editing, a transgenic line was constructed with AtECB2 fused to a 4xMYC tag that could complement the atecb2 phenotype. RNA immunoprecipitation analysis indicated that AtECB2 is associated with the transcripts of accD, ndhF, ndhG and petL. Co-immunoprecipitation and mass spectrometry experiments showed that multiple organelle RNA editing factor 2 (MORF2) and porphobilinogen deaminase HEMC are associated with AtECB2. Biochemical analysis showed that AtECB2 directly interacts with HEMC through its E domain, while HEMC interacts with MORF8/RIP1. Deletion analysis showed that the E domain is essential for RNA editing. The hemc-1 mutant showed an albino and seedling-lethal phenotype. Of the seven editing sites affected in atecb2, the editing of accD-794 and ndhF-290 was also reduced in hemc-1. RNA immunoprecipitation analysis suggested that HEMC is associated with the editing sites of ndhF transcripts. These results showed that both HEMC and multiple organellar RNA editing factor (MORF) proteins are associated with AtECB2 for RNA editing in plastids.

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Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

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Porphobilinogen deaminase HEMC interacts with the PPR‐protein AtECB2 for chloroplast RNA editing

Huang

et al. 2017

The Plant Journal

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“…Chloroplast development is associated with a shift in the primary RNA polymerase from NEP to PEP. Furthermore, compensatory responses can be observed between the two RNA polymerases, as depletion of PEP activity increases the expression of NEP-dependent transcripts (Myouga et al, 2008; Pfalz et al, 2006; Ramos-Vega et al, 2015; Zhou et al, 2009). This process was designated as the “Δ- rpo phenotype” (Allison et al, 1996; Hajdukiewicz et al, 1997; De Santis-Maciossek et al, 1999), but the underlying mechanisms are still unknown.…”

Section: Introductionmentioning

confidence: 99%

GUN1 influences the accumulation of NEP-dependent transcripts and chloroplast protein import in Arabidopsis cotyledons upon perturbation of chloroplast protein homeostasis

Tadini

Peracchio

Trotta

et al. 2019

Preprint

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Correct chloroplast development and function require coordinated expression of chloroplast and nuclear genes. This is achieved through chloroplast signals that modulate nuclear gene expression in accordance with the chloroplast's needs. Genetic evidence indicates that GUN1, a chloroplast-localized pentatricopeptide-repeat (PPR) protein with a C-terminal Small MutS-Related (SMR) domain, is involved in integrating multiple developmental and stress-related signals in both young seedlings and adult leaves. Recently, GUN1 was found to interact physically with factors involved in chloroplast protein homeostasis, and with enzymes of tetrapyrrole biosynthesis in adult leaves that function in various retrograde signaling pathways. Here we show that, following perturbation of chloroplast protein homeostasis i) by growth in lincomycin-containing medium, or ii) in mutants defective in either the FtsH protease complex (ftsh), plastid ribosome activity (prps21-1 and prpl11-1) or plastid protein import and folding (cphsp70-1), GUN1 influences NEP-dependent transcript accumulation during cotyledon greening and also intervenes in chloroplast protein import. import Chloroplast biogenesis is achieved through a cascade of events that include cytosolic synthesis of chloroplasttargeted proteins, followed by their import, assembly and folding, while unfolded/misfolded proteins and damaged or malformed chloroplasts are degraded (Sakamoto et al., 2008; Jarvi and López-Jauez, 2013; Izumi and Nakamura, 2018; Otegui, 2018). Most chloroplast-targeted proteins enter the chloroplasts via the protein complexes TOC ('translocon at outer envelope of chloroplast') and TIC ('translocon at inner envelope of chloroplast'). On the cytosolic side, precursor proteins are directed to the Toc34 and Toc159 receptors through the interaction of their chloroplast-targeting peptides with the chaperone heat shock protein 90 (Hsp90) and the guidance complex formed by Hsp70 and a 14-3-3 protein. Active transport through the chloroplast envelope is then mediated by an ATP-dependent import motor, consisting of Hsp70, Hsp90 and the stromal Hsp93 (ClpC2) proteins (Kessler and Schnell, 2009; Sjuts et al., 2017).On the stromal side, transcription of the plastid-encoded genes in higher plants requires two different RNA polymerases: the nuclear-encoded RNA polymerase (NEP), also termed RpoTp (located specifically in the chloroplasts and encoded by the RPOT3 gene) or RpoTmp (located both in mitochondria and plastids and encoded by the RPOT2 gene) and the plastid-encoded RNA polymerase (PEP) (Yu et al., 2014; Börner et al., 2015). NEP is a monomeric T3-T7 bacteriophage-type RNA polymerase that is mainly responsible for transcribing housekeeping genes, whereas PEP is a bacterial-type multisubunit enzyme largely tasked with transcribing photosynthesis-related genes. Chloroplast development is associated with a shift in the primary RNA polymerase from NEP to PEP. Furthermore, compensatory responses can be observed between the two RNA polymerases, as depletion of PEP activ...

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“…These two amino acids are generally positively charged (Small and Peeters, 2000; Ban et al, 2013). The binding between these amino acids and the target nucleotide has been experimentally proven in the case of the PPR10 (Barkan et al, 2012), the THA8 (Ke et al, 2013), the CLB19 (Kindgren et al, 2015; Ramos-Vega et al, 2015) and the AEF1/MPR25 (Yap et al, 2015) PPR proteins. In the context of CMS, where Rf proteins process unusual transcripts, nucleic acid specificity is essential to specifically target the CMS-conferring transcript.…”

Section: Introductionmentioning

confidence: 99%

The Propensity of Pentatricopeptide Repeat Genes to Evolve into Restorers of Cytoplasmic Male Sterility

2016

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Cytoplasmic male sterility (CMS) is a widespread phenotype in plants, which present a defect in the production of functional pollen. The male sterilizing factors usually consist of unusual genes or open reading frames encoded by the mitochondrial genome. CMS can be suppressed by specific nuclear genes called restorers of fertility (Rfs). In the majority of cases, Rf genes produce proteins that act directly on the CMS conferring mitochondrial transcripts by binding them specifically and promoting processing events. In this review, we explore the wide array of mechanisms guiding fertility restoration. PPR proteins represent the most frequent protein class among identified Rfs and they exhibit ideal characteristics to evolve into restorer of fertility when the mechanism of restoration implies a post-transcriptional action. Here, we review the literature that highlights those characteristics and help explain why PPR proteins are ideal for the roles they play as restorers of fertility.

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Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

Cited by 35 publications

References 60 publications

Porphobilinogen deaminase HEMC interacts with the PPR‐protein AtECB2 for chloroplast RNA editing

Porphobilinogen deaminase HEMC interacts with the PPR‐protein AtECB2 for chloroplast RNA editing

GUN1 influences the accumulation of NEP-dependent transcripts and chloroplast protein import in Arabidopsis cotyledons upon perturbation of chloroplast protein homeostasis

The Propensity of Pentatricopeptide Repeat Genes to Evolve into Restorers of Cytoplasmic Male Sterility

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