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

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

PROVIDER: PRJNA1037147 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26729572.fastq.gz	Fastqsanger.gz
	SRR26729573.fastq.gz	Fastqsanger.gz
	SRR26729574.fastq.gz	Fastqsanger.gz
	SRR26729575.fastq.gz	Fastqsanger.gz
	SRR26729576.fastq.gz	Fastqsanger.gz

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Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [Bisulfite-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 | GSE247352 | GEO

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

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

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

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

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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

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.

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Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

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

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Plasticity in AAA+ proteases reveals substrate specificity niches

Project description:Purpose: The goal of this study is to compare RNA-seq libraries of wildtype Caulobacter crescentus with two lon deletion strains (delta lon and delta lon clpX*). Methods: See Methods section of "Plasticity in AAA+ proteases reveals substrate specificity niches" for information regarding methods or contact lead correspondence. Briefly, Samples for RNAseq were extracted from wt and lon deletion strains grown to stationary phase. Conclusions: Our study represents the first detailed analysis of lon deletions (delta lon and delta lon clpX*) comparison to wt caulobacter transcriptomes, with biologic replicates, generated by RNA-seq technology in stationary phas

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