How Bacterial Enzymes Change Tomato DNA on a Large Scale

Jenn Hoskins
20th May, 2024

How Bacterial Enzymes Change Tomato DNA on a Large Scale

Schematic representation of the different plants produced in the study. Yellow sphere, expression of the M.SssI enzyme. Red asterisk, plant methylomes sequenced in the study.

Image adapted from: Kumar et al. / CC BY (Source)

Key Findings

  • The study by the Agricultural Research Organization, Volcani Center, explored altering the tomato genome's methylation using a bacterial enzyme
  • Researchers found that this enzyme caused specific hypermethylation in gene-rich regions, affecting some genes' expression
  • These induced methylation changes were stable and inheritable, suggesting potential for long-term epigenetic modifications in tomatoes
Epigenetic variation, specifically DNA methylation, is a critical mechanism in gene expression regulation and chromatin stability in plants. DNA methylation involves the addition of methyl groups to DNA, affecting gene expression without altering the DNA sequence. This process is essential for development and stress responses, as well as maintaining chromatin stability[2]. Recent research from the Agricultural Research Organization, Volcani Center, has explored the potential to stably alter the tomato genome methylome using a bacterial CG-specific M.SssI methyltransferase expressed through the LhG4/pOP transactivation system[1]. The study aimed to investigate whether the heterologous expression of M.SssI could create new, inheritable epigenetic variations in tomatoes. The researchers focused on CG methylation, which is crucial for silencing transposable elements and regulating gene expression. Typically, the establishment of CG methylation in plants occurs via the RNA-directed DNA methylation pathway, with maintenance relying on METHYLTRANSFERASE1, analogous to the mammalian DNMT1. The research team conducted a methylome analysis on M.SssI-expressing tomato plants. The results revealed that euchromatic regions of the genome were specifically hypermethylated in the CG context, including most genes. However, changes in gene expression were only observed in a subset of genes that showed greater susceptibility to CG hypermethylation near their transcription start sites. Interestingly, heterochromatic regions exhibited slight hypomethylation at CG sites, contrasting with the hypermethylation seen in euchromatic regions. These findings align with earlier studies indicating that DNA methylation can dynamically change in response to environmental factors and stress conditions, influencing gene expression and stress responses[2]. The current study builds on this understanding by demonstrating that targeted methylation using M.SssI can induce stable, inheritable changes in the tomato genome's methylation profile. Moreover, the study's observation that some M.SssI-induced hypermethylation persisted even without the presence of the methylase or transgenes suggests a potential for long-term epigenetic modifications. This persistence implies that the induced epigenetic changes could be inherited over generations, contributing to transgenerational epigenetic inheritance. This concept was previously highlighted in studies where DNA methylation changes were stably inherited across multiple generations, affecting trait variations without altering the DNA sequence[3]. The ability to create new inherited epigenetic variations opens up exciting possibilities for plant breeding. By generating epigenetic recombinant inbred line populations, researchers can potentially uncover agriculturally valuable epialleles in tomatoes. This approach could complement traditional breeding methods, offering a novel tool for selecting desirable traits based on epigenetic markers[2]. In summary, the study conducted by the Agricultural Research Organization, Volcani Center, demonstrates the potential of using a bacterial CG-specific M.SssI methyltransferase to induce stable and inheritable epigenetic changes in the tomato genome. This research not only expands our understanding of DNA methylation's role in gene regulation but also offers new avenues for developing epigenetic-based breeding strategies in agriculture.

GeneticsBiochemPlant Science

References

Main Study

1) Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase.

Published 20th May, 2024

https://doi.org/10.1007/s00018-024-05255-7

Related Studies

2) DNA methylation dynamics in response to abiotic and pathogen stress in plants.

https://doi.org/10.1007/s00299-022-02901-x

3) The epiallelic potential of transposable elements and its evolutionary significance in plants.

https://doi.org/10.1098/rstb.2020.0123


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