High resolution RNA‐seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in <i>Arabidopsis thaliana</i>

Xiong, Wei; Zhang, Jiancong; Lan, Ting; Kong, Wenwen; Wang, Xiaoyan; Liu, Lin; Mo, Beixin

doi:10.1002/pld3.320

Cited by 5 publications

(4 citation statements)

References 72 publications

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“…In Arabidopsis , ribosomes are highly heterogenous, and each organ might need a different association of non-paralogous ribosomal proteins. It was reported that the expression of ribosomal protein genes varied dramatically in different organs [ 33 ]. In Brassica napus , it was also reported that the number of paralogues expressed for each ribosomal protein gene varied extensively with tissue types [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

Insights into Adaptive Regulation of the Leaf-Petiole System: Strategies for Survival of Water Lily Plants under Salt Stress

Liu

Chen

et al. 2023

IJMS

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The water lily (Nymphaea tetragona) is an ancient angiosperm that belongs to the Nymphaeaceae family. As a rooted floating-leaf plant, water lilies are generally cultivated in fresh water, therefore, little is known about their survival strategies under salt stress. Long-term salt stress causes morphological changes, such as the rapid regeneration of floating leaves and a significant decrease in leaf number and surface area. We demonstrate that salt stress induces toxicity soon after treatment, but plants can adapt by regenerating floating leaves that are photosynthetically active. Transcriptome profiling revealed that ion binding was one of the most-enriched GO terms in leaf-petiole systems under salt stress. Sodium-transporter-related genes were downregulated, whereas K+ transporter genes were both up- and downregulated. These results suggest that restricting intracellular Na+ importing while maintaining balanced K+ homeostasis is an adaptive strategy for tolerating long-term salt stress. ICP-MS analysis identified the petioles and leaves as Na-hyperaccumulators, with a maximum content of over 80 g kg−1 DW under salt stress. Mapping of the Na-hyperaccumulation trait onto the phylogenetic relationships revealed that water lily plants might have a long evolutionary history from ancient marine plants, or may have undergone historical ecological events from salt to fresh water. Ammonium transporter genes involved in nitrogen metabolism were downregulated, whereas NO3−-related transporters were upregulated in both the leaves and petioles, suggesting a selective bias toward NO3− uptake under salt stress. The morphological changes we observed may be due to the reduced expression of genes related to auxin signal transduction. In conclusion, the floating leaves and submerged petioles of the water lily use a series of adaptive strategies to survive salt stress. These include the absorption and transport of ions and nutrients from the surrounding environments, and the ability to hyperaccumulate Na+. These adaptations may serve as the physiological basis for salt tolerance in water lily plants.

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Section: Discussionmentioning

confidence: 99%

Insights into Adaptive Regulation of the Leaf-Petiole System: Strategies for Survival of Water Lily Plants under Salt Stress

Liu

Chen

et al. 2023

IJMS

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“…In other cases, their levels of expression and contributions to the ribosome are equivalent [reviewed in Petibon et al (2021)]. Loss of function of either gene of a pair produces a similar mutant phenotype, indicating that both paralogs are required for normal development (Savada and Bonham-Smith, 2014;Salih et al, 2020;Xiong et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Cross-kingdom conservation of Arabidopsis RPS24 function in 18S rRNA maturation

Cabezas-Fuster

Micol-Ponce

Sarmiento-Mañús

et al. 2023

Preprint

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All 81 ribosomal proteins (RPs) that form the Arabidopsis (Arabidopsis thaliana) 80S ribosome are encoded by several paralogous genes. For example, the nearly identical RPS24A and RPS24B proteins are encoded by RPS24A and RPS24B, respectively. Here we explored the functions of RPS24A and RPS24B in Arabidopsis. Their encoding genes exhibit combined haploinsufficiency, as at least two wild-type copies of either RPS24A or RPS24B are required for plant viability and at least three are required for normal plant development. Loss-of-function of either gene caused a pointed-leaf phenotype, a typical phenotype of null or hypomorphic recessive alleles of genes encoding ribosome biogenesis factors (RBFs) or RPs. We also found that RPS24A and RPS24B act as RBFs during early stages of 18S ribosomal RNA (rRNA) maturation, as loss of RPS24A or RPS24B function reduced the 18S/25S rRNA ratio. An RPS24B-GFP fusion protein predominantly localized to the nucleolus, as expected. The rps24b-2 mutation strengthened the phenotypes of the RBF mutants mRNA transporter4-2 and small organ4-3, which are defective in 5.8S rRNA maturation. This synergistic interaction might be an effect of increased 45S rDNA transcription, which we also observed in the rps24 mutants. Therefore, the Arabidopsis RPS24 proteins act as RBFs during 18S rRNA maturation, like their human and yeast putative orthologs. Only two plant RPs were previously shown to act not only as structural components of the ribosome but also as RBFs. We provide evidence that RPS24 proteins also regulate 45S rDNA transcription, which has not been described for their yeast or human orthologs.

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“…A clear reduced dosage was observed for Arabidopsis uS7 ( AtRPS5A and AtRPS5B ), uL23 ( RPL23aA and RPL23aB ), uL4 ( RPL4A and RPL4D ), uL18 ( RPL5A and RPL5B ), eL42 ( RPL36aA and RPL36aB ) and eS6 ( RPS6A and RPS6B ) paralogs (Casanova‐Sáez et al., 2014; Creff et al., 2010; Fujikura et al., 2009; Rosado et al., 2010; Weijers et al., 2001; Xiong et al., 2020). Several studies have also revealed divergent abundance or subcellular localization patterns of the CRP paralogs (Savada & Bonham‐Smith, 2014; Whittle & Krochko, 2009; Xiong et al., 2021) or CRPs with extra‐ribosomal functions (Table S10), indicating that they may undergo neofunctionalization and/or subfunctionalization. In general, we infer that constraints imposed by dosage balance are relaxed in plants, providing ample time for continuous degeneration over the course of evolution, and thus increasing the probability of ribosome heterogeneity and non‐canonical functions.…”

Section: Discussionmentioning

confidence: 99%

Plant cytoplasmic ribosomal proteins: an update on classification, nomenclature, evolution and resources

Lan

Xiong

et al. 2022

The Plant Journal

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Standardized naming systems are essential to integrate and unify distinct research fields, and to link multispecies data within and across kingdoms. We conducted a comprehensive survey of cytoplasmic ribosomal proteins (CRPs) in the dicot model Arabidopsis thaliana and the monocot model rice, noting that the standardized naming system has not been widely adopted in the plant community. We generated a database linking the old classical names to their updated and compliant names. We also explored the sequences, molecular evolution, and structural and functional characteristics of all plant CRP families, emphasizing evolutionarily conserved and plant-specific features through cross-kingdom comparisons. Unlike fungal CRP paralogs that were mainly created by whole-genome duplication (WGD) or retroposition under a concerted evolution mode, plant CRP genes evolved primarily through both WGD and tandem duplications in a rapid birth-and-death process. We also provide a web-based resource (http://www.plantcrp.cn/) with the aim of sharing the latest knowledge on plant CRPs and facilitating the continued development of a standardized framework across the entire community.

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High resolution RNA‐seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 5 publications

References 72 publications

Insights into Adaptive Regulation of the Leaf-Petiole System: Strategies for Survival of Water Lily Plants under Salt Stress

Insights into Adaptive Regulation of the Leaf-Petiole System: Strategies for Survival of Water Lily Plants under Salt Stress

Cross-kingdom conservation of Arabidopsis RPS24 function in 18S rRNA maturation

Plant cytoplasmic ribosomal proteins: an update on classification, nomenclature, evolution and resources

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