Cytosine methylation changes in the ice plant Ppc1 promoter during transition from C3 to Crassulacean acid metabolism

Huang, Nu-Chuan; Li, Changhua; Lee, Jun-Yi; Yen, Hungchen Emilie

doi:10.1016/j.plantsci.2009.10.005

Cited by 15 publications

(8 citation statements)

References 35 publications

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“…The salt-tolerant mechanism of ice plant is regulated at the chromatin, transcriptional, post-transcriptional, translational, and post-translational levels. For example, gene coding for the key CAM cycle enzyme phosphoenolpyruvate carboxylase was found to be regulated at the level of DNA methylation (Huang et al, 2010 ), transcription activation, post-transcriptional regulation (Cushman et al, 1989 ), and protein phosphorylation (Nimmo, 2000 ). Although the genome of ice plant has not yet been completely resolved, large-scale gene expression profiling studies have shown salt-induced changes of thousands of genes using the conventional expressed sequence tag analysis (Kore-eda et al, 2004 ), an oligonucleotide microarray (Cushman et al, 2008 ), and next-generation sequencing (NGS; Oh et al, 2015 ; Tsukagoshi et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings

et al. 2016

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The halophyte Mesembryanthemum crystallinum (common or crystalline ice plant) is a useful model for studying molecular mechanisms of salt tolerance. The morphology, physiology, metabolism, and gene expression of ice plant have been studied and large-scale analyses of gene expression profiling have drawn an outline of salt tolerance in ice plant. A rapid root growth to a sudden increase in salinity was observed in ice plant seedlings. Using a fluorescent dye to detect Na+, we found that ice plant roots respond to an increased flux of Na+ by either secreting or storing Na+ in specialized cells. High-throughput sequencing was used to identify small RNA profiles in 3-day-old seedlings treated with or without 200 mM NaCl. In total, 135 conserved miRNAs belonging to 21 families were found. The hairpin precursor of 19 conserved mcr-miRNAs and 12 novel mcr-miRNAs were identified. After 6 h of salt stress, the expression of most mcr-miRNAs showed decreased relative abundance, whereas the expression of their corresponding target genes showed increased mRNA relative abundance. The cognate target genes are involved in a broad range of biological processes: transcription factors that regulate growth and development, enzymes that catalyze miRNA biogenesis for the most conserved mcr-miRNA, and proteins that are involved in ion homeostasis and drought-stress responses for some novel mcr-miRNAs. Analyses of the functions of target genes revealed that cellular processes, including growth and development, metabolism, and ion transport activity are likely to be enhanced in roots under salt stress. The expression of eleven conserved miRNAs and two novel miRNAs were correlated reciprocally with predicted targets within hours after salt stress exposure. Several conserved miRNAs have been known to regulate root elongation, root apical meristem activity, and lateral root formation. Based upon the expression pattern of miRNA and target genes in combination with the observation of Na+ distribution, ice plant likely responds to increased salinity by using Na+ as an osmoticum for cell expansion and guard cell opening. Excessive Na+ could either be secreted through the root epidermis or stored in specialized leaf epidermal cells. These responses are regulated in part at the miRNA-mediated post-transcriptional level.

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Section: Introductionmentioning

confidence: 99%

Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings

et al. 2016

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“…The level of DNA methylation can also change in response to environmental stress and in correlation with the activation of stress-responsive genes (Wada et al 2004). In the context of stress responses, methylation has been gaining increasing interest because it can regulate the expression of genes that play a key role in acclimation responses (Boyko et al 2007;Choi and Sano 2007;Huang et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Involvement of DNA methylation in the control of cell growth during heat stress in tobacco BY-2 cells

et al. 2015

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The alteration of growth patterns, through the adjustment of cell division and expansion, is a characteristic response of plants to environmental stress. In order to study this response in more depth, the effect of heat stress on growth was investigated in tobacco BY-2 cells. The results indicate that heat stress inhibited cell division, by slowing cell cycle progression. Cells were stopped in the pre-mitotic phases, as shown by the increased expression of CycD3-1 and by the decrease in the NtCycA13, NtCyc29 and CDKB1-1 transcripts. The decrease in cell length and the reduced expression of Nt-EXPA5 indicated that cell expansion was also inhibited. Since DNA methylation plays a key role in controlling gene expression, the possibility that the altered expression of genes involved in the control of cell growth, observed during heat stress, could be due to changes in the methylation state of their promoters was investigated. The results show that the altered expression of CycD3-1 and Nt-EXPA5 was consistent with changes in the methylation state of the upstream region of these genes. These results suggest that DNA methylation, controlling the expression of genes involved in plant development, contributes to growth alteration occurring in response to environmental changes.

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“…Indeed, previous work has linked DNA methylation with the expression of PEPC in plants. For example, methylation of four cytosines located in the promoter region and de-methylation of four cytosines in the 5' UTR of the McPPC1 gene from the facultative Crassulacean Acid Metabolism (CAM) plant Mesembryanthemum crystallinum is co-incident with an increase in expression associated with the switch from C 3 to CAM metabolism ( Huang et al , 2010 ). Furthermore, differential methylation of a Pvu II restriction site 3.1 kb upstream from the maize PEPC transcription start site in response to illumination was correlated with changes to PEPC expression ( Langdale et al , 1991 ).…”

Section: Introductionmentioning

confidence: 99%

Light-regulated and cell-specific methylation of the maize PEPC promoter

Tolley

Woodfield

Wanchana

et al. 2011

Journal of Experimental Botany

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The molecular mechanisms governing PEPC expression in maize remain to be fully defined. Differential methylation of a region in the PEPC promoter has been shown to correlate with transcript accumulation, however, to date, investigations into the role of DNA methylation in maize PEPC expression have relied on the use of methylation-sensitive restriction enzymes. Bisulphite sequencing was used here to provide a single-base resolution methylation map of the maize PEPC promoter. It is shown that four cytosine residues in the PEPC promoter are heavily methylated in maize root tissue. In leaves, de-methylation of these cytosines is dependent on illumination and is coincident with elevated PEPC expression. Furthermore, light-regulated de-methylation of these cytosines occurs only in mesophyll cells. No methylation was discovered in the 0.6 kb promoter required for mesophyll-specific expression indicating that cytosine methylation is not required to direct the cell-specificity of PEPC expression. This raises interesting questions regarding the function of the cell-specific cytosine de-methylation observed in the upstream region of the PEPC promoter.

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Cytosine methylation changes in the ice plant Ppc1 promoter during transition from C3 to Crassulacean acid metabolism

Cited by 15 publications

References 35 publications

Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings

Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings

Involvement of DNA methylation in the control of cell growth during heat stress in tobacco BY-2 cells

Light-regulated and cell-specific methylation of the maize PEPC promoter

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