Rice cytosine DNA methyltransferases – gene expression profiling during reproductive development and abiotic stress

Abstract

DNA methylation affects important developmental processes in both plants and animals. The process of methylation of cytosines at C‐5 is catalysed by DNA methyltransferases (MTases), which are highly conserved, both structurally and functionally, in eukaryotes. In this study, we identified and characterized cytosine DNA MTase genes that are activated with the onset of reproductive development in rice. The rice genome (Oryza sativa L. subsp. japonica) encodes a total of 10 genes that contain the highly conserved MTase catalytic domain. These genes have been categorized into subfamilies on the basis of phylogenetic relationships. A microarray‐based gene expression profile of all 10 MTases during 22 stages/tissues that included 14 stages of reproductive development and five vegetative tissues together with three stresses, cold, salt and dehydration stress, revealed specific windows of MTase activity during panicle and seed development. The expression of six methylases was specifically/preferentially upregulated with the initiation of floral organs. Significantly, one of the MTases was also activated in young seedlings in response to cold and salt stress. The molecular studies presented here suggest a greater role for these proteins and the epigenetic process in affecting genome activity during reproductive development and stress than was previously anticipated.

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)

“…The 3 CMT genes (OsCMT1-3), used for their resemblance to the corresponding protein in Arabidopsis and other plant species. The OsCMT1-3 were characterized by the presence of a BAH domain in the N-terminal half and a preserved chromodomain inserted between motif I and motif IV (Sharma et al, 2009). OsCMT2 deviated from the other 2 proteins (Figure 1) by an additional stretch of 193 amino acids at the beginning of the BAH domain in the amino terminal region.…”

“…AK242475, AK112062, AK109728, AK111502, AK108034, AK111461, AK063482, AK065147, AK065147, and AK065147) were identified as reported previously (Sharma et al, 2009). Individually, each accession number was used to form a rice proteome database profile to confirm each gene.…”

“…In plants and especially in rice, 4 subfamilies of cytosine-5 MTases have been identified (Pavlopoulou and Kossida, 2009;Sharma et al, 2009): CMT, DNMT2, MET1, and DRM (Finnegan et al, 1996;Henikoff and Comai, 1998). After identifying and analyzing a complete set of 10 de novo and maintenance MTase genes in rice, we aligned the protein of these specific MTases with a set of proteins from Zea mays and Nicotiana tabacum using the CLUSTALX software (Thompson et al, 1997) and generated a bootstrapped tree (Figure 1).…”

“…The number of cytosine DNA MTases varies among different organisms. In fungi, protozoa, and insects, a single methylase performs the methylation, while more than 10 are involved in higher plants like rice (Sharma et al, 2009). To understand the mechanism of DNA methylation under environmental stresses in rice, we analyzed the activities of MTases under 2 major abiotic stresses (salt and osmotic) separately and by dividing the plant into root and shoot.…”

Epigenetic Chromatin Regulators as Mediators of Abiotic Stress Responses in Cereals

“…OsCMT2 was found to be induced by cold and high salinity but not by drought. Conversely, OsCMT3 showed approximately a six-and four-fold reduction in mRNA accumulation in rice seedlings subjected to high salt and dehydration conditions, respectively [ 84 Sharma et al, 2009]. In a recent study, the gene encoding the Arabidopsis DNA glycosylase ROS1 (REPRESSOR OF SILENCING 1)-now known as DML3 (DEMETER-LIKE protein 3) and involved in DNA demethylation-was indirectly implicated in the response to abiotic stress, as it was shown to be the target of the stress-responsive miRNA402 [ 85 ].…”