Similar Datasets
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
| PRJNA1037143 | ENA
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]
| PRJNA1037150 | ENA
Project description:We present a general probabilistic framework for predicting the substrate specificity of enzymes. We designed this approach to be easily applicable to different organisms and enzymes. Therefore, our predictive models do not rely on species-specific properties and use mostly sequence-derived data. Maximum Likelihood optimization is used to fine-tune model parameters and the Akaike Information Criterion is employed to overcome the issue of correlated variables. As a proof-of-principle, we apply our approach to predicting general substrate specificity of yeast methyltransferases (MTases). As input, we use several physico-chemical and biological properties of MTases: structural fold, isoelectric point, expression pattern and cellular localization. Our method accurately predicts whether a yeast MTase methylates a protein, RNA or another molecule. Among our experimentally tested predictions, 89% were confirmed, including the surprising prediction that YOR021C is the first known MTase with a SPOUT fold that methylates a substrate other than RNA (protein). Our approach not only allows for highly accurate prediction of functional specificity of MTases, but also provides insight into general rules governing MTase substrate specificity.
| S-EPMC3961171 | biostudies-literature
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:DNA methylation is an important epigenetic mark conserved in eukaryotes from fungi to animals and plants, where it plays a crucial role in regulating gene expression and transposon silencing. Once the methylation mark is established by de novo DNA methyltransferases, specific regulatory mechanisms are required to maintain the methylation state during chromatin replication, both during meiosis and mitosis. Plant DNA methylation is found in three contexts; CG, CHG, and CHH (H = A, T, C), which are established and maintained by a unique set of DNA methyltransferases and are regulated by plant-specific pathways. DNA methylation in plants is often associated with other epigenetic modifications, such as noncoding RNA and histone modifications. This chapter focuses on the structure, function, and regulatory mechanism of plant DNA methyltransferases and their crosstalk with other epigenetic pathways.
| S-EPMC10112988 | biostudies-literature
Project description:The mom gene of bacteriophage Mu encodes an enzyme that converts adenine to N(6)-(1-acetamido)-adenine in the phage DNA and thereby protects the viral genome from cleavage by a wide variety of restriction endonucleases. Mu-like prophage sequences present in Haemophilus influenzae Rd (FluMu), Neisseria meningitidis type A strain Z2491 (Pnme1) and H. influenzae biotype aegyptius ATCC 11116 do not possess a Mom-encoding gene. Instead, at the position occupied by mom in Mu they carry an unrelated gene that encodes a protein with homology to DNA adenine N(6)-methyltransferases (hin1523, nma1821, hia5, respectively). Products of the hin1523, hia5 and nma1821 genes modify adenine residues to N(6)-methyladenine, both in vitro and in vivo. All of these enzymes catalyzed extensive DNA methylation; most notably the Hia5 protein caused the methylation of 61% of the adenines in λ DNA. Kinetic analysis of oligonucleotide methylation suggests that all adenine residues in DNA, with the possible exception of poly(A)-tracts, constitute substrates for the Hia5 and Hin1523 enzymes. Their potential 'sequence specificity' could be summarized as AB or BA (where B = C, G or T). Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine methylation.
| S-EPMC3299994 | biostudies-literature
Project description:DNA methylation is now seen as a primary signal in the cell for mediating transcriptional repression through chromatin formation. The construction and evaluation of enzymes capable of influencing this process in vivo is therefore of significant interest. We have fused the C5-cytosine DNA methyltransferases, M.HhaI and M.HpaII, which both methylate 4 bp sequences containing a CpG dinucleotide, to a three zinc finger protein recognising a 9 bp DNA sequence. DNA methylation analyses demonstrate specific DNA methylation by both enzymes at target sites comprising adjacent methyltransferase and zinc finger subsites, targeted M.HpaII being the most specific. Binding analysis of the targeted M.HpaII enzyme reveals an 8-fold preference for binding to its target site, compared to binding to a zinc finger site alone, and an 18-fold preference over binding to a methyltransferase site alone, thereby demonstrating enhanced binding by the fusion protein, compared to its component proteins. Both DNA binding and methylation are specific for the target site up to separations of approximately 40 bp between the zinc finger and methyltransferase subsites. Ex vivo plasmid methylation experiments are also described that demonstrate targeted methylation. These targeted enzymes, however, are shown to be not fully mono-functional, retaining a significant non-targeted activity most evident at elevated protein concentrations.
| S-EPMC137423 | biostudies-literature