cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12117291
title: Table S3. RNA-seq results for Doxycycline treatment in Col-0 and for the <i>mrpl</i> mutant. from The transcription factor ANAC017 is a key regulator of mitochondrial proteotoxic stress responses in plants

description: Impaired mitochondrial translation or reduced mitochondrial protein import can lead to imbalances in mitochondrial protein composition. Such mitochondrial proteotoxic stresses can trigger a nuclear transcriptional response commonly described as the mitochondrial unfolded protein response (UPR<sup>mt</sup>). Despite extensive studies of UPR<sup>mt</sup> pathways in animal and fungal systems, very little is known about how the UPR<sup>mt</sup> is regulated in plants. Through comparison of <i>Arabidopsis thaliana</i> whole-genome transcriptome data, it was found that most genes induced by mitochondrial ribosome inhibitor doxycycline are also induced by Complex III inhibitor antimycin A. We demonstrate that transcriptional responses to a wide range of mitochondrial proteotoxic stress-triggers are regulated by the transcription factor ANAC017, which was shown to reside in the endoplasmic reticulum (ER). By contrast, no consistent evidence was found for genes that are specifically induced by doxycycline but not antimycin A. Furthermore, ANAC017 gain- and loss-of-function mutants showed marked resistance or susceptibility, respectively, to mitochondrial stress-inducing treatments, demonstrating the physiological importance of ANAC017 during mitochondrial proteotoxic stress. Finally, it was shown that ethylene signalling promotes mitochondria-to-nucleus signalling, most likely independently of ANAC017. Overall, this study shows that in plants, the UPR<sup>mt</sup> is largely overlapping with, and perhaps identical to, ‘classical’ mitochondrial retrograde signalling, and is mediated by ER-anchored transcription factor ANAC017.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117291.v1
title: Table S3. RNA-seq results for Doxycycline treatment in Col-0 and for the <i>mrpl</i> mutant. from The transcription factor ANAC017 is a key regulator of mitochondrial proteotoxic stress responses in plants

description: Impaired mitochondrial translation or reduced mitochondrial protein import can lead to imbalances in mitochondrial protein composition. Such mitochondrial proteotoxic stresses can trigger a nuclear transcriptional response commonly described as the mitochondrial unfolded protein response (UPR<sup>mt</sup>). Despite extensive studies of UPR<sup>mt</sup> pathways in animal and fungal systems, very little is known about how the UPR<sup>mt</sup> is regulated in plants. Through comparison of <i>Arabidopsis thaliana</i> whole-genome transcriptome data, it was found that most genes induced by mitochondrial ribosome inhibitor doxycycline are also induced by Complex III inhibitor antimycin A. We demonstrate that transcriptional responses to a wide range of mitochondrial proteotoxic stress-triggers are regulated by the transcription factor ANAC017, which was shown to reside in the endoplasmic reticulum (ER). By contrast, no consistent evidence was found for genes that are specifically induced by doxycycline but not antimycin A. Furthermore, ANAC017 gain- and loss-of-function mutants showed marked resistance or susceptibility, respectively, to mitochondrial stress-inducing treatments, demonstrating the physiological importance of ANAC017 during mitochondrial proteotoxic stress. Finally, it was shown that ethylene signalling promotes mitochondria-to-nucleus signalling, most likely independently of ANAC017. Overall, this study shows that in plants, the UPR<sup>mt</sup> is largely overlapping with, and perhaps identical to, ‘classical’ mitochondrial retrograde signalling, and is mediated by ER-anchored transcription factor ANAC017.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117213
title: Table SIII Primer from The <i>genomes uncoupled</i>-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

description: In recent years, it became evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of <i>PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES</i>. Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in <i>gun</i> mutants. We propose that regulation of <i>PHANGs</i> and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117213.v1
title: Table SIII Primer from The <i>genomes uncoupled</i>-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

description: In recent years, it became evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of <i>PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES</i>. Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in <i>gun</i> mutants. We propose that regulation of <i>PHANGs</i> and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117198
title: Table SII genotypes used from The <i>genomes uncoupled</i>-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

description: In recent years, it became evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of <i>PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES</i>. Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in <i>gun</i> mutants. We propose that regulation of <i>PHANGs</i> and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117201
title: Table SI - RNAseq from The <i>genomes uncoupled</i>-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

description: In recent years, it became evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of <i>PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES</i>. Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in <i>gun</i> mutants. We propose that regulation of <i>PHANGs</i> and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117198.v1
title: Table SII genotypes used from The <i>genomes uncoupled</i>-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

description: In recent years, it became evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of <i>PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES</i>. Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in <i>gun</i> mutants. We propose that regulation of <i>PHANGs</i> and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117186
title: Supplementary Table S5 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117201.v1
title: Table SI - RNAseq from The <i>genomes uncoupled</i>-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

description: In recent years, it became evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of <i>PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES</i>. Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in <i>gun</i> mutants. We propose that regulation of <i>PHANGs</i> and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117180
title: Supplementary Table S1 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117183
title: Supplementary Table S3 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117186.v1
title: Supplementary Table S5 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117174
title: Supplementary Table S6 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.