Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses

Parida, Adwaita Prasad; Raghuvanshi, Utkarsh; Pareek, Amit; Singh, Vijendra; Kumar, Rahul; Sharma, Arun Kumar

doi:10.1007/s11033-018-4435-x

Cited by 11 publications

(13 citation statements)

References 63 publications

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“…Interestingly, despite the genome size of petunia (1.4 GB) being almost 1.5 times greater than that of tomato (900 MB), 1.6 times greater than that of potato (844 MB), 3 times greater than that of rice (466 MB) and 11 times greater than that of Arabidopsis (125 MB), the number of C5-MTase members in petunia is very similar, ranging from 7 to 11, indicating that there is no strong correlation between the number of C5-MTase members and genome size. However, unlike the PhC5-MTases, the number of MBD genes in petunia was less than in tomato (18), potato (15), rice (17) and Arabidopsis (14), and the number of DNA methylation-related genes is associated with genome-wide duplication and gene loss events [10,25,53]. Consequently, we suspect that gene duplication and loss events during evolution may have contributed to the difference in the number of MBD genes, which is consistent with the research on maize [25].…”

Section: Discussionmentioning

confidence: 99%

“…The MBD protein family is divided into six subclasses in plants, and it exhibits two evolutionary branches, dicot and monocot, among which subclasses VI and IV are only present in the former, indicating dicot specificity [ 8 , 9 ]. Studies on the MBD family in plants have mainly focused on model plants, such as Arabidopsis , rice, maize and populous, which have between 13 and 18 MBD members [ 9 , 10 , 11 ]. In comparison, knowledge on MBD proteins in ornamental crops is still limited.…”

Section: Introductionmentioning

confidence: 99%

“…Particularly, GA is also involved in plant growth and differentiation, especially in anther development, which is closely related to male fertility and fertilization [ 20 , 21 ]. The C5-MTase and MBD proteins have been identified in Arabidopsis thaliana [ 11 , 27 ], Zea mays [ 25 , 28 ], Solanum lycopersicum [ 10 , 17 ] and Triticum aestivum [ 29 , 30 ]. However, to the best of our knowledge, no research has yet focused on the identification of C5-MTase and MBD proteins in Petunia.…”

Section: Introductionmentioning

confidence: 99%

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Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses

Shi

Shen

Liu

et al. 2022

Genes

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Cytosine-5 DNA methyltransferases (C5-MTases) and methyl-CpG-binding-domain (MBD) genes can be co-expressed. They directly control target gene expression by enhancing their DNA methylation levels in humans; however, the presence of this kind of cooperative relationship in plants has not been determined. A popular garden plant worldwide, petunia (Petunia hybrida) is also a model plant in molecular biology. In this study, 9 PhC5-MTase and 11 PhMBD proteins were identified in petunia, and they were categorized into four and six subgroups, respectively, on the basis of phylogenetic analyses. An expression correlation analysis was performed to explore the co-expression relationships between PhC5-MTases and PhMBDs using RNA-seq data, and 11 PhC5-MTase/PhMBD pairs preferentially expressed in anthers were identified as having the most significant correlations (Pearson’s correlation coefficients > 0.9). Remarkably, the stability levels of the PhC5-MTase and PhMBD pairs significantly decreased in different tissues and organs compared with that in anthers, and most of the selected PhC5-MTases and PhMBDs responded to the abiotic and hormonal stresses. However, highly correlated expression relationships between most pairs were not observed under different stress conditions, indicating that anther developmental processes are preferentially influenced by the co-expression of PhC5-MTases and PhMBDs. Interestingly, the nuclear localization genes PhDRM2 and PhMBD2 still had higher correlations under GA treatment conditions, implying that they play important roles in the GA-mediated development of petunia. Collectively, our study suggests a regulatory role for DNA methylation by C5-MTase and MBD genes in petunia anther maturation processes and multi-stress responses, and it provides a framework for the functional characterization of C5-MTases and MBDs in the future.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses

Shi

Shen

Liu

et al. 2022

Genes

View full text Add to dashboard Cite

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“…MBD family proteins have been functionally characterized in various plant species, including Arabidopsis [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23], wheat [24,25], maize [26], and tomato [27,28]. MBD proteins play pivotal roles in plant growth, development, and stress responses.…”

Section: Discussionmentioning

confidence: 99%

“…Overexpressing of the SlMBD5 gene leads to dark fruit color and dwarf phenotype in transgenic plants [27]. A number of MBD genes in four different solanaceae species have been observed to be differentially induced or suppressed during fruit development or abiotic stress responses, suggesting their roles involved in these processes [28].…”

Section: Introductionmentioning

confidence: 99%

Overexpression of a methyl-CpG-binding Protein Gene OsMBD707, Leads to Larger Tiller Angles and Reduced Photoperiod Sensitivity in Rice

Zhang

Liang

et al. 2020

Preprint

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Background: Methyl-CpG-binding domain (MBD) proteins play important roles in epigenetic gene regulation, and have diverse molecular, cellular, and biological functions in plants. MBD proteins have been functionally characterized in various plant species, including Arabidopsis, wheat, maize, and tomato. In rice, 17 sequences were bioinformatically predicted as putative MBD proteins. However, very little is known regarding the function of MBD proteins in rice.Results: We explored the expression patterns of the rice OsMBD family genes and identified 13 OsMBDs with active expression in various rice tissues. We further characterized the function of a rice class I MBD protein OsMBD707, and demonstrated that OsMBD707 is constitutively expressed and localized in the nucleus. Transgenic rice overexpressing OsMBD707 displayed larger tiller angles and reduced photoperiod sensitivity—delayed flowering under short day (SD) and early flowering under long day (LD). RNA-seq analysis revealed that overexpression of OsMBD707 led to reduced photoperiod sensitivity in rice through regulating expression of key flowering regulator genes in the Ehd1-Hd3a/RFT1 pathway.Conclusion: The results of this study demonstrated that OsMBD707 plays important roles in rice growth and development, and should lead to further studies on the functions of OsMBD proteins in growth, development, or other molecular, cellular, and biological processes in rice.

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AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes

Parida

Sharma

2019

J Biosci

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Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses

Cited by 11 publications

References 63 publications

Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses

Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses

Overexpression of a methyl-CpG-binding Protein Gene OsMBD707, Leads to Larger Tiller Angles and Reduced Photoperiod Sensitivity in Rice

AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes

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