The bRPS6-Family Protein RFC3 Prevents Interference by the Splicing Factor CFM3b during Plastid rRNA Biogenesis in Arabidopsis thaliana

Nagashima, Yumi; Ohshiro, Katsutomo; Iwase, Akiyasu; Nakata, Miyuki T; Maekawa, Shugo; Horiguchi, Gorou

doi:10.3390/plants9030328

Cited by 4 publications

(5 citation statements)

References 97 publications

(160 reference statements)

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“…Down-regulated DAPs produced GO annotations such as “biosynthetic processes” (GO:0009058), “RNA binding” (GO:0003729), “translation” (GO:0006412) and “post-embryonic development” (GO:0009791) ( Fig 11A ). Among down-regulated proteins detected in indPRPS1 samples, we found the regulator of fatty-acid composition 3 (RFC3; AT3G17170), which plays an important role in the plastid rRNA processing [ 77 ]. Many of these down-regulated proteins were located in chloroplast and nucleus ( Fig 11B ).…”

Section: Resultsmentioning

confidence: 99%

Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling

et al. 2023

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The chloroplast proteome is a dynamic mosaic of plastid- and nuclear-encoded proteins. Plastid protein homeostasis is maintained through the balance between de novo synthesis and proteolysis. Intracellular communication pathways, including the plastid-to-nucleus signalling and the protein homeostasis machinery, made of stromal chaperones and proteases, shape chloroplast proteome based on developmental and physiological needs. However, the maintenance of fully functional chloroplasts is costly and under specific stress conditions the degradation of damaged chloroplasts is essential to the maintenance of a healthy population of photosynthesising organelles while promoting nutrient redistribution to sink tissues. In this work, we have addressed this complex regulatory chloroplast-quality-control pathway by modulating the expression of two nuclear genes encoding plastid ribosomal proteins PRPS1 and PRPL4. By transcriptomics, proteomics and transmission electron microscopy analyses, we show that the increased expression of PRPS1 gene leads to chloroplast degradation and early flowering, as an escape strategy from stress. On the contrary, the overaccumulation of PRPL4 protein is kept under control by increasing the amount of plastid chaperones and components of the unfolded protein response (cpUPR) regulatory mechanism. This study advances our understanding of molecular mechanisms underlying chloroplast retrograde communication and provides new insight into cellular responses to impaired plastid protein homeostasis.

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Section: Resultsmentioning

confidence: 99%

Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling

et al. 2023

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“…11 A). Among down-regulated proteins detected in indPRPS1 samples we found the regulator of fatty-acid composition 3 (RFC3; AT3G17170) which plays an important role in the plastid rRNA processing (Nagashima et al ., 2020). Many of these down-regulated proteins were located in chloroplast and nucleus (Fig.…”

Section: Resultsmentioning

confidence: 99%

Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling

Tadini

Jeran

Domingo

et al. 2022

Preprint

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The chloroplast proteome is a dynamic mosaic of plastid- and nuclear-encoded proteins. Plastid protein homeostasis is maintained through the balance between de novo synthesis and proteolysis. Intracellular communication pathways, including the plastid-to-nucleus signalling and the protein homeostasis machinery, made of stromal chaperones and proteases, shape chloroplast proteome based on developmental and physiological needs. However, the maintenance of fully functional chloroplasts is costly and under specific stress conditions the degradation of damaged chloroplasts is essential to the maintenance of a healthy population of photosynthesising organelles while promoting nutrient redistribution to sink tissues. In this work, we have addressed this complex regulatory chloroplast- quality-control pathway by modulating the expression of two nuclear genes encoding plastid ribosomal proteins PRPS1 and PRPL4. By transcriptomics, proteomics and transmission electron microscopy analyses, we show that the increased expression of PRPS1 gene leads to chloroplast degradation and early flowering, as an escape strategy from stress. On the contrary, the overaccumulation of PRPL4 protein is kept under control by increasing the amount of plastid chaperones and components of the unfolded protein response (cpUPR) regulatory mechanism. This study advances our understanding of molecular mechanisms underlying chloroplast retrograde communication and provides new insight into cellular responses to impaired plastid protein homeostasis.

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“…B-like (CBL)-interacting protein kinase 9 ( CIPK9 ) of Brassica napus was reported to regulate seed oil content, and both rapeseed knock-out lines and gene-silenced lines showed decreased levels of polyunsaturated fatty acids [ 52 ]. SGK2 is responsible for encoding a ribosomal protein S6-like protein that is localized in the plastids, and by map-based cloning, it was revealed that the Arabidopsis rfc (regulator of fatty acid composition) 3 gene can alter the fatty acid composition of membrane lipids, resulting in an increase in oleic acid (18:1) levels and a decrease in α-linolenic acid (18:3) levels among total fatty acids [ 53 – 55 ]. In our integration analysis, we found that SlCAKM was down-regulated and SlSGK2 was up-regulated under nitrogen-limited treatment.…”

Section: Discussionmentioning

confidence: 99%

Integration analysis of ATAC-seq and RNA-seq provides insight into fatty acid biosynthesis in Schizochytrium limacinum under nitrogen limitation stress

Chen,

Dai

et al. 2024

BMC Genomics

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Background Schizochytrium limacinum holds significant value utilized in the industrial-scale synthesis of natural DHA. Nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. The objective of this research was to delve into the workings of fatty acid production in S. limacinum by examining the accessibility of promoters and profiling gene expressions. Results Results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, signal transduction mechanisms, and energy production. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlCAS1, SlNSDHL, and SlDGKI, are directly related to the biosynthesis of fatty acids, meanwhile, SlRPS6KA, SlCAMK1, SlMYB3R1, and SlMYB3R5 serve as transcription factors that could potentially influence the regulation of fatty acid production. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. Conclusions SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These insights enhance our comprehension of the processes underlying fatty acid and DHA production in S. limacinum. They also supply a foundational theoretical framework and practical assistance for the development of strains rich in fatty acids and DHA.

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The bRPS6-Family Protein RFC3 Prevents Interference by the Splicing Factor CFM3b during Plastid rRNA Biogenesis in Arabidopsis thaliana

Cited by 4 publications

References 97 publications

Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling

Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling

Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling

Integration analysis of ATAC-seq and RNA-seq provides insight into fatty acid biosynthesis in Schizochytrium limacinum under nitrogen limitation stress

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