Characterization of the SET DOMAIN GROUP gene family members in Camellia sinensis and functional analysis of the SDG43 gene in abiotic stresses

Chen, Qinghua; Hu, Shuangling; Guo, Fei; Zhao, Hua; Wang, Mingle; Ni, Dejiang; Wang, Yu; Wang, Pu

doi:10.1016/j.envexpbot.2020.104306

Cited by 8 publications

(15 citation statements)

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“…Moreover, it is reported that plants respond to environmental stress through DNA methylation and histone methylation modifications. More recently, DNA methylation and histone methylation-related regulatory genes have been investigated and found to play pivotal functions in stress response ( Zhu et al, 2020 ; Chen et al, 2021 ). However, the roles of RNA methylation and related regulatory genes in tea plants against various stresses during preharvest and postharvest processing are still far from clear to date.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process

et al. 2021

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N6-methyladenosine (m6A), one of the internal modifications of RNA molecules, can directly influence RNA abundance and function without altering the nucleotide sequence, and plays a pivotal role in response to diverse environmental stresses. The precise m6A regulatory mechanism comprises three types of components, namely, m6A writers, erasers, and readers. To date, the research focusing on m6A regulatory genes in plant kingdom is still in its infancy. Here, a total of 34 m6A regulatory genes were identified from the chromosome-scale genome of tea plants. The expansion of m6A regulatory genes was driven mainly by whole-genome duplication (WGD) and segmental duplication, and the duplicated gene pairs evolved through purifying selection. Gene structure analysis revealed that the sequence variation contributed to the functional diversification of m6A regulatory genes. Expression pattern analysis showed that most m6A regulatory genes were differentially expressed under environmental stresses and tea-withering stage. These observations indicated that m6A regulatory genes play essential roles in response to environmental stresses and tea-withering stage. We also found that RNA methylation and DNA methylation formed a negative feedback by interacting with each other’s methylation regulatory genes. This study provided a foundation for understanding the m6A-mediated regulatory mechanism in tea plants under environmental stresses and tea-withering stage.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process

et al. 2021

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“…According to the data of the SDG gene family in our previous study, the full-length SDS sequence of CsSDG36 was cloned from tea cultivar ‘Fuding Dabaicha’ [ 37 ]. The amino acid sequence of the CsSDG36 gene was analyzed by multiple comparisons with highly similar proteins in the NCBI database, which is highly similar to ATX4 proteins of different species containing the amino acid of PWWP, PHD, SET and PostSET domains ( Figure 2 ).…”

Section: Resultsmentioning

confidence: 99%

“…Based on the CsSDG36 gene sequence obtained from the CsSDG family in our previous study [ 37 ], the complete CDS of CsSDG36 was amplified with primers, listed in Table 1 , followed by cloning the sequence into the pCAMBIA1300s vector and transforming the recombinant vector by agrobacterium-mediated inflorescence infection [ 50 ]. Positive screening was performed by hygromycin and PCR.…”

Section: Methodsmentioning

confidence: 99%

“…Under hyperosmotic stress, miR159 is significantly upregulated, which activates ABI3 expression through an ABA-dependent pathway, thus enhancing its osmotic tolerance [ 35 , 36 ]. In our previous study, the SDG genes were identified and CsSDG36 was clustered into the TRX subfamily, which catalyze H3K4me2 and H3K4me3 in vivo [ 37 ]. However, the function of CsSDG36 remains unclear.…”

Section: Introductionmentioning

confidence: 99%

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Ectopic Overexpression of Histone H3K4 Methyltransferase CsSDG36 from Tea Plant Decreases Hyperosmotic Stress Tolerance in Arabidopsis thaliana

Chen

Guo

Yuan

et al. 2021

IJMS

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Histone methylation plays an important regulatory role in the drought response of many plants, but its regulatory mechanism in the drought response of the tea plant remains poorly understood. Here, drought stress was shown to induce lower relative water content and significantly downregulate the methylations of histone H3K4 in the tea plant. Based on our previous analysis of the SET Domain Group (SDG) gene family, the full-length coding sequence (CDS) of CsSDG36 was cloned from the tea cultivar ‘Fuding Dabaicha’. Bioinformatics analysis showed that the open reading frame (ORF) of the CsSDG36 gene was 3138 bp, encoding 1045 amino acids and containing the conserved structural domains of PWWP, PHD, SET and PostSET. The CsSDG36 protein showed a close relationship to AtATX4 of the TRX subfamily, with a molecular weight of 118,249.89 Da, and a theoretical isoelectric point of 8.87, belonging to a hydrophilic protein without a transmembrane domain, probably located on the nucleus. The expression of CsSDG36 was not detected in the wild type, while it was clearly detected in the over-expression lines of Arabidopsis. Compared with the wild type, the over-expression lines exhibited lower hyperosmotic resistance by accelerating plant water loss, increasing reactive oxygen species (ROS) pressure, and increasing leaf stomatal density. RNA-seq analysis suggested that the CsSDG36 overexpression caused the differential expression of genes related to chromatin assembly, microtubule assembly, and leaf stomatal development pathways. qRT-PCR analysis revealed the significant down-regulation of stomatal development-related genes (BASL, SBT1.2(SDD1), EPF2, TCX3, CHAL, TMM, SPCH, ERL1, and EPFL9) in the overexpression lines. This study provides a novel sight on the function of histone methyltransferase CsSDG36 under drought stress.

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“…The SET domain-containing genes have been identified and functionally characterised for their roles in growth, development, and stress responses in several plant species, including Arabidopsis thaliana [21], Camellia sinensis [22], Gossypium raimondii [23], Malus domestica [24], Oryza sativa [25], Populus trichocarpa [26], Setaria italica [27], Solanum lycopersicum [28], and Triticum aestivum [29]. These studies comprehensively characterised the SET domain-containing genes, including the inference of phylogenetic relationships, investigation of the role of gene duplications on the expansion of this gene family, protein domain organisation, tissue-specific expression analysis and expression responses upon abiotic stresses.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.)

Suppiyar,

Bonthala,

Shrestha

et al. 2024

BMC Genomics

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Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.

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Characterization of the SET DOMAIN GROUP gene family members in Camellia sinensis and functional analysis of the SDG43 gene in abiotic stresses

Cited by 8 publications

References 36 publications

Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process

Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process

Ectopic Overexpression of Histone H3K4 Methyltransferase CsSDG36 from Tea Plant Decreases Hyperosmotic Stress Tolerance in Arabidopsis thaliana

Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.)

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