Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases
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PROVIDER: PRJNA1037143 | ENA |
REPOSITORIES: ENA
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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
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
Project description:Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [Bisulfite-seq]
| PRJNA1037147 | ENA
Project description:Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases [RNA-seq]
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Project description:This SuperSeries is composed of the SubSeries listed below.
2024-11-08 | GSE247354 | GEO
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
Project description:Substrate Specificity of the TRAMP Nuclear Surveillance Complexes
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Project description:Plasticity in AAA+ proteases reveals substrate specificity niches
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Project description:Cytochrome P450s (CYPs) are a family of enzymes responsible for metabolizing nearly 80% of small molecule drugs. Variants in CYPs can substantially alter drug metabolism, which may result in improper dosing and severe adverse drug reactions. CYPs have low sequence conservation, making it difficult to anticipate whether variant effects measured in one CYP may extend to others based on sequence alone. Even closely related CYPs, like CYP2C9 and its closest homolog CYP2C19, have distinct phenotypic properties despite sharing 92% of their sequences. Thus, we used Variant Abundance by Massively Parallel sequencing (VAMP-seq) to measure the protein abundance of 7,660 missense variants in CYP2C19 expressed in cultured human cells. Our results confirmed positions and structural features critical for CYP function and revealed how variants at positions conserved across all eukaryotic CYPs influence abundance. We jointly analyzed 4,670 variants whose abundance was measured in both CYP2C19 and CYP2C9, finding that the homologs have different variant abundances in substrate recognition sites within the hydrophobic core, and that substitutions in some regions reduced abundance in CYP2C19 but not CYP2C9. We also measured the abundance of all single and some multiple WT amino acid exchanges between CYP2C19 and CYP2C9. While most exchanges had no effect, substitutions in substrate recognition site 4 (SRS4) reduced abundance in CYP2C19. When nearby amino acids were exchanged in double and triple mutants, we found distinct interactions between the sites in CYP2C19 and CYP2C9, revealing a region that is partially responsible for the difference in thermodynamic stability between the two homologs. Since these positions are also important for determining substrate specificity, there may be an evolutionary tradeoff between stability and altered enzymatic function. Finally, we used our data to analyze 368 previously unannotated human variants, finding that 43% had decreased abundance. Thus, by comparing variant effects between two closely related, important human genes, we have uncovered regions underlying their functional differences and paved the way for a more complete understanding of one of the most versatile families of enzymes.
2024-10-02 | GSE244489 | GEO
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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