Genome-wide identification of the radiation sensitivity protein-23 (RAD23) family members in apple (Malus×domestica Borkh.) and expression analysis of their stress responsiveness

Wang, Na; Gong, Xiaoqing; Ma, Fengwang

doi:10.1016/s2095-3119(16)61517-4

Cited by 7 publications

(7 citation statements)

References 33 publications

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“…OsRAD23 is also responsive to salt stress (Nveawiah‐Yoho et al ., 2013; Li et al ., 2015; Lakra et al ., 2019). RAD23 proteins play a role in stress response and development through their delivery of ubiquitinated substrates to the 26S proteasome (Farmer et al ., 2010; Kang et al ., 2017; Wang et al ., 2017). Specifically, the UBA2 domain is important for ubiquitin binding and RAD23 stability in proteasomal degradation (Chen et al ., 2001; Heessen et al ., 2005; Jang et al ., 2012).…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide discovery of natural variation in pre‐mRNA splicing and prioritising causal alternative splicing to salt stress response in rice

Campbell

et al. 2021

New Phytologist

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Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VASP). VASP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions. In total, 764 significant GSS events were identified in salt stress conditions. GSS events were used as markers for a GWAS with the shoot Na + accumulation, which identified six GSS events in five genes significantly associated with the shoot Na + content. Two of these genes, OsNUC1 and OsRAD23 emerged as top candidate genes with splice variants that exhibited significant divergence between the variants for shoot growth under salt stress conditions. VASP is a versatile tool for alternative splicing analysis in plants and a powerful tool for prioritising candidate causal pre-mRNA splicing and corresponding genomic variations in GWAS.

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Section: Discussionmentioning

confidence: 99%

Genome‐wide discovery of natural variation in pre‐mRNA splicing and prioritising causal alternative splicing to salt stress response in rice

Campbell

et al. 2021

New Phytologist

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“…Sequencing of the apple genome has facilitated the identification and analysis of putative apple gene families genome-wide. The encoded proteins include members of the DREB [ 39 ], MYB [ 40 ], MADS-box [ 41 ], PHT [ 42 ], RAD23 [ 43 ], UGTs [ 44 ], SnRK2 [ 45 ] and WRKY families [ 46 , 47 ]. Although NPF s have been identified in other species, this family is not as well-understood in apple.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of Apple NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER Family (NPF) Genes Reveals MdNPF6.5 Confers High Capacity for Nitrogen Uptake under Low-Nitrogen Conditions

Wang

Liu

Dong

et al. 2018

IJMS

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The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins play important roles in moving substrates such as nitrate, peptides, amino acids, dicarboxylates, malate, glucosinolates, indole acetic acid (IAA), abscisic acid (ABA), and jasmonic acid. Although a unified nomenclature of NPF members in plants has been reported, this gene family has not been studied as thoroughly in apple (Malus × domestica Borkh.) as it has in other species. Our objective was to provide general information about apple MdNPFs and analyze the transcriptional responses of some members to different levels of nitrate supplies. We identified 73 of these genes from the apple genome and used phylogenetic analysis to organize them into eight major groups. These apple NPFs are structurally conserved, based on alignment of amino acid sequences and analyses of phylogenetics and conserved domains. Examination of their genomic structures indicated that these genes are highly conserved among other species. We monitored 14 cloned MdNPFs that showed varied expression patterns under different nitrate concentrations and in different tissues. Among them, NPF6.5 was significantly induced by both low and high levels of nitrate. When compared with the wild type, 35S:MdNPF6.5 transgenic apple calli were more tolerant to low-N stress, which demonstrated that this gene confers greater capacity for nitrogen uptake under those conditions. We also analyzed the expression patterns of those 73 genes in various tissues. Our findings benefit future research on this family of genes.

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“…MdRAD23D1, MdRAD23D2, and MdRAD23A were, respectively, collinear with AtRAD23C, AtRAD23D, and AtRAD23A (Figure S1c ). Among these three genes, the expression level of MdRAD23D1 was induced by both ABA treatment and drought stress (Wang et al ., 2017 , Figure 1a ). We also examined the MdRAD23D1 protein levels under drought using ‘Orin’ apple calli.…”

Section: Resultsmentioning

confidence: 98%

“…We previously identified MdRAD23 family members in the apple genome (Wang et al ., 2017 ), like Arabidopsis RAD23 proteins, MdRAD23s also contained the signature UBL domain at the N terminal and UBA domain at the C terminal (Figure S1a ). The evolutionary relationship between Arabidopsis and apples was analysed, and we found that C and D type RAD23s were close in the phylogenetic tree (Figure S1b ).…”

Section: Resultsmentioning

confidence: 99%

The ubiquitin‐binding protein MdRAD23D1 mediates drought response by regulating degradation of the proline‐rich protein MdPRP6 in apple (Malus domestica)

Zhang

Gong

et al. 2023

Plant Biotechnology Journal

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Summary RAD23 (RADIATION SENSITIVE23) proteins are a group of UBL‐UBA (ubiquitin‐like‐ubiquitin‐associated) proteins that shuttle ubiquitylated proteins to the 26S proteasome for breakdown. Drought stress is a major environmental constraint that limits plant growth and production, but whether RAD23 proteins are involved in this process is unclear. Here, we demonstrated that a shuttle protein, MdRAD23D1, mediated drought response in apple plants (Malus domestica). MdRAD23D1 levels increased under drought stress, and its suppression resulted in decreased stress tolerance in apple plants. Through in vitro and in vivo assays, we demonstrated that MdRAD23D1 interacted with a proline‐rich protein MdPRP6, resulting in the degradation of MdPRP6 by the 26S proteasome. And MdRAD23D1 accelerated the degradation of MdPRP6 under drought stress. Suppression of MdPRP6 resulted in enhanced drought tolerance in apple plants, mainly because the free proline accumulation is changed. And the free proline is also involved in MdRAD23D1‐mediated drought response. Taken together, these findings demonstrated that MdRAD23D1 and MdPRP6 oppositely regulated drought response. MdRAD23D1 levels increased under drought, accelerating the degradation of MdPRP6. MdPRP6 negatively regulated drought response, probably by regulating proline accumulation. Thus, “MdRAD23D1‐MdPRP6” conferred drought stress tolerance in apple plants.

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Genome-wide identification of the radiation sensitivity protein-23 (RAD23) family members in apple (Malus×domestica Borkh.) and expression analysis of their stress responsiveness

Cited by 7 publications

References 33 publications

Genome‐wide discovery of natural variation in pre‐mRNA splicing and prioritising causal alternative splicing to salt stress response in rice

Genome‐wide discovery of natural variation in pre‐mRNA splicing and prioritising causal alternative splicing to salt stress response in rice

Genome-Wide Identification and Analysis of Apple NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER Family (NPF) Genes Reveals MdNPF6.5 Confers High Capacity for Nitrogen Uptake under Low-Nitrogen Conditions

The ubiquitin‐binding protein MdRAD23D1 mediates drought response by regulating degradation of the proline‐rich protein MdPRP6 in apple (Malus domestica)

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