Identification of SET Domain-Containing Proteins in Gossypium raimondii and Their Response to High Temperature Stress

Huang, Yong; Mo, Yijia; Chen, Pengyun; Yuan, Xiaoling; Meng, Funing; Zhu, Shengwei; Li, Zhi

doi:10.1038/srep32729

Cited by 34 publications

(38 citation statements)

References 60 publications

(90 reference statements)

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“…Moreover, many SDGs were involved in high temperature responses. It can then be inferred that upon exposure to high temperature, up‐or‐downregulation of these genes might affect the status of methylation and further regulate the activity of target genes in response to high temperature …”

Section: Sdgs In Response To Stressmentioning

confidence: 99%

The function of histone lysine methylation related SET domain group proteins in plants

et al. 2020

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Histone methylation, which is mediated by the histone lysine (K) methyltransferases (HKMTases), is a mechanism associated with many pathways in eukaryotes. Most HKMTases have a conserved SET (Su(var) 3-9,E(z), Trithorax) domain, while the HKMTases with SET domains are called the SET domain group (SDG) proteins. In plants, only SDG proteins can work as HKMTases. In this review, we introduced the classification of SDG family proteins in plants and the structural characteristics of each subfamily, surmise the functions of SDG family members in plant growth and development processes, including pollen and female gametophyte development, flowering, plant morphology and the responses to stresses. This review will help researchers better understand the SDG proteins and histone methylation in plants and lay a basic foundation for further studies on SDG proteins. K E Y W O R D Shistone lysine (K) methyltransferase, histone methylation, HKMTases, SDG protein, SET domain group

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Section: Sdgs In Response To Stressmentioning

confidence: 99%

The function of histone lysine methylation related SET domain group proteins in plants

et al. 2020

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“…This suggests that Lys methylation of histones and non-histone substrates could be part of the diverging adaptation strategies of metallicolous populations. The expression of KMT genes coding enzymes of the SDG family has been previously analyzed in cotton plants stressed with high temperature (Huang et al, 2016) and in foxtail millet under different abiotic stresses (Yadav et al, 2016). In these studies, the expression pattern of some KMT genes was significantly changed in stress conditions.…”

Section: Discussionmentioning

confidence: 99%

Protein lysine methylation is involved in modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress

Serre¹,

Sarthou²,

Gigarel³

et al. 2019

Preprint

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The mechanisms underlying the response and adaptation of plants to excess of trace elements are not fully described. Here, we analyzed the importance of protein lysine methylation for plants to cope with cadmium. We analyzed the effect of cadmium on lysine-methylated proteins and protein lysine methyltransferases (KMTs) in three Arabidopsis species. Arabidopsis thaliana and A. lyrata were used as cadmium-sensitive models and compared with three populations of A. halleri with different properties of accumulation and tolerance to cadmium.Immunoblotting, protein mass spectrometry, and gene expression analysis showed that the expression of some lysine-methylated proteins and genes coding KMTs is regulated by cadmium. Using a genetic screening, we showed that nine A. thaliana mutants interrupted in KMT genes have a tolerance to cadmium that is significantly different from that of wild-type seedlings. We further characterized two of these mutants, one was knocked-out in the calmodulin lysine methyltransferase gene and displayed increased tolerance to cadmium, the other was interrupted in a KMT gene of unknown function and showed a decreased capacity to cope with cadmium. Together, our results showed that the fine-tuned regulation of nonhistone proteins by lysine methylation has a role in the response of Arabidopsis plants to cadmium stress. KEYWORDSArabidopsis halleri, Arabidopsis thaliana, cadmium, metal stress, methyltransferase, posttranslational modification, protein methylation, response, tolerance.(KMTs), the SET domain-containing group (SDG) and the seven-beta-strand (SBS) superfamily, which are able to add one to three methyl groups to specific Lys residues in proteins (Serre et al., 2018). In plants, these enzymes have been shown to methylate histones and non-histone proteins involved in all aspects of cell biology (transcription, protein synthesis, metabolism…). Protein Lys methylation can be reversible by the action of demethylases.However, demethylases acting on non-histone Lys-methylated proteins have never been reported in plants (Serre et al., 2018).Despite recent progress, the role of non-histone protein Lys methylation in regulating plant cellular functions is still limited (Serre et al., 2018). In particular, no information is available about the role of protein methylation in the response and adaptation of plants to metal stress. MATERIALS AND METHODS Plant material and growth conditionsArabidopsis thaliana ecotype Columbia (Col-0), Arabidopsis lyrata ssp. petraea (Linnaeus) O'Kane & Al-Shehbaz, and the Arabidopsis halleri spp. halleri (Linnaeus) O'Kane & Al-Shehbaz populations from the metallicolous soils located in Auby (North of France, AU population), Val del Riso (North of Italy, I16 population), and Bukowno (South of Poland, PL22 population) (Meyer et al., 2015) were grown in hydroponic conditions. The standard control medium (CM) was composed of 0.88 mM K 2 SO 4 , 2 mM Ca(NO 3 ) 2 , 1 mM MgSO 4 , 0.25 mM 6 KH 2 PO 4 , 10 µM H 3 BO 3 , 0.1 µM CuSO 4 , 0.6 µM MnSO 4 , 0.01 µM (NH 4 ) 6 Mo 7 O 24...

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“…Gene duplication, as a critical driving force, provides an extra copy of genetic material to tolerate random mutations to survive the natural selection and create new species during evolution. Gene duplication, including tandem duplication and polyploidy (whole genome duplication, WGD), considerably contributes to the formation of gene families [24], such as the SDG family in D.…”

Section: Evolution and Function Divergence Of Sdg Proteinsmentioning

confidence: 99%

“…It will be intriguing to further investigate their direct targets by highthroughput ChIP-seq method combined with excellent commercial antibodies against various histone methylation marks. Recently, Huang et al [24] thoroughly identified cotton SDG genes and noted that the expressions of most of these genes decreased under high-temperature conditions. In this study, 61% of DcSDG genes showed response to heat shock, but the number of upregulated genes was considerably higher than that of downregulated ones.…”

Section: Catenatum D Catenatum Has Undergone At Least Four Rounds Omentioning

confidence: 99%

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

Chen

Qiu

Huang

et al. 2020

Preprint

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Background: Dendrobium catenatum used as a precious Chinese herbal medicine is a kind of epiphytic orchid plant which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown. Results: In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris . We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su(var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually have wide but distinguished expression in different tissues and organs. Finally, environmental stresses examination showed the expression of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 is closely associated with drought-recovery treatment, the expression of DcSUVH5a , DcATXR5a and DcSUVR14a is significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock. Conclusions: This study systematically identifies and classifies SDG genes in orchid plant D. catenatum , indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchid.

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Identification of SET Domain-Containing Proteins in Gossypium raimondii and Their Response to High Temperature Stress

Cited by 34 publications

References 60 publications

The function of histone lysine methylation related SET domain group proteins in plants

The function of histone lysine methylation related SET domain group proteins in plants

Protein lysine methylation is involved in modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

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