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Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [RNA-seq]

ABSTRACT: Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [RNA-seq]

PROVIDER: PRJNA1037150 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26729560.fastq.gz	Fastqsanger.gz
	SRR26729561.fastq.gz	Fastqsanger.gz
	SRR26729562.fastq.gz	Fastqsanger.gz
	SRR26729563.fastq.gz	Fastqsanger.gz
	SRR26729564.fastq.gz	Fastqsanger.gz

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Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

Project description:Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

| PRJNA1037143 | ENA

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [RNA-seq]

Project description:DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, Chromomethylase3 (CMT3) and CMT2 are the major DNA methyltransferases mediating DNA methylation on CHG and CHH (H = A, C or T), respectively, but the underlying mechanisms of how CMT3 and CMT2 methylate different contexts during evolution is poorly known. Here we reveal the mechanisms of CMT3 and CMT2 divergence in flowering plants. CMT2 originates from a duplication of the evolutionarily more ancient CMT3 and change of a key arginine residue recognizing CHG in CMT2 makes it lose CHG methylation activity in most flowering plants. Mutation of the residue to arginine in Arabidopsis (V1200R) greatly increases its methylation activity on CHG DNA. Besides different substrate specificity, CMT2 contains a long and disordered N-terminus compared with a short one in CMT3. The long N-terminus reduces protein stability, especially under high temperature. Moreover, CMT2 N-terminus is plastic to various natural mutations. Together, our study reveals the mechanisms of chromomethylase divergence for methylating different DNA contexts in plants and sheds light on understanding of plant evolution.

2024-11-08 | GSE247353 | GEO

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [Bisulfite-seq]

2024-11-08 | GSE247352 | GEO

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [Bisulfite-seq]

Project description:Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [Bisulfite-seq]

| PRJNA1037147 | ENA

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases.

Project description:DNA methylation is an important epigenetic mechanism essential for transposon silencing and genome integrity. Across evolution, the substrates of DNA methylation have diversified between kingdoms. In plants, chromomethylase3 (CMT3) and CMT2 mediate CHG and CHH methylation, respectively. However, how these two methyltransferases diverge on substrate specificities during evolution remains unknown. Here, we reveal that CMT2 originates from a duplication of an evolutionarily ancient CMT3 in flowering plants. Lacking a key arginine residue recognizing CHG in CMT2 impairs its CHG methylation activity in most flowering plants. An engineered V1200R mutation empowers CMT2 to restore CHG and CHH methylations in Arabidopsis cmt2cmt3 mutant, testifying a loss-of-function effect for CMT2 during evolution. CMT2 has evolved a long and unstructured amino terminus critical for protein stability, especially under heat stress, and is plastic to tolerate various natural mutations. Together, this study reveals the mechanism of chromomethylase divergence for context-specific DNA methylation in plants and sheds important lights on DNA methylation evolution and function.

| S-EPMC11540031 | biostudies-literature

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-11-08 | GSE247354 | GEO

Project description:Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

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Substrate specificity divergence of granzyme tryptases.

Project description:Elucidating the true physiological functions of granzymes has been challenging since the origin of the granzyme studied, the use of non-physiological granzyme concentrations and the interspecies use of granzymes, with extrapolation of all these data to orthologous granzymes has led to inconsistencies. This is highly relevant for granzymes A and K where a debate is ongoing concerning their involvement in either cytotoxic or inflammatory processes, or in both. In order to tackle such contradictions, detailed knowledge of the substrate repertoires and substrate specificities of granzymes as well as their cleavage efficiencies may add in unraveling the primary signaling pathways these granzymes are involved in. Therefore, a degradome analysis using N-terminal COFRADIC was performed to unravel the substrate repertoires and subsite determinants for the closely related homologous human tryptases. We furthermore also profiled the uncharacterized mouse granzyme K in a comparative analysis with its human ortholog. Despite the subtle differences observed in the primary specificity profiles of these granzymes, for each granzyme distinguishing substrate subsite features could be elucidated.

2015-09-30 | PXD000570 | Pride

Plasticity in AAA+ proteases reveals substrate specificity niches

Project description:Plasticity in AAA+ proteases reveals substrate specificity niches

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Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

Project description:Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

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