Comparative Methylation Analysis of Caldimonas thermodepolymerans Using Third-Generation Sequencing

Comparative Methylation Analysis of Caldimonas thermodepolymerans Using Third-Generation Sequencing

Stať ve sborníku mimo WoS a Scopus

DNA methylation in the bacterial genome plays an important role in epigenetic modification, which affects gene expression, regulation and environmental adaptation, etc. In this study, we conducted a comparative analysis of methylation patterns in the Gram-Negative bacteria Caldimonas thermopolymerans DSM 15344T. The type strain was initially isolated from activated sludge in Germany and then deposited in Leibniz Institute DSMZ in Germany (CT-DSMZ) and later in the Czech Collection of Microorganisms in Czechia (CT-CCM). Our aim was to assess whether a change in cultivation conditions and phenotype characteristics of the cultures deposited in various public collections coincides with methylation patterns. We used Oxford Nanopore Technology (ONT) sequencing with R10.4.1 flow cells and V14 chemistry for more accurate analysis. Despite being the same strain, we observed a significant difference in methylation counts between these two samples. The sample CT-CCM showed 7,350 6mA modifications, 2,764 5mC modifications, and 732 4mC modifications, while the sample CT-DSMZ showed slightly lower modification counts, with 6,884 6mA, 2,681 5mC, and 643 4mC modifications. We also analysed the distribution of methylation across different genomic annotation features, such as coding sequences (CDS), rRNA, and tRNA regions. The analysis also revealed significant differences between the two samples. In the Coding sequences (CDS), CT-CCM showed 7,153 6mA modifications, 2,339 5mC modifications, and 708 4mC modifications, while CT-DSMZ showed slightly lower counts with 6,680 6mA, 2,290 5mC, and 620 4mC modifications. To enhance our detection of methylated bases, we employed the Pacific Biosciences (PacBio) Sequel IIe platform. We integrated the methylation data from both sequencing platforms while comparing the epigenomes of specific sample cultivation. The differences in methylation levels between these two cultures suggest the role of cultivation conditions like temperature and nutrient availability that may lead to unique epigenetic changes. Given the role played by methylation in gene regulation, our finding contributes to knowledge of the potential impact of cultivation conditions on bacterial physiology. Our research will help in enhancing our understanding of bacterial epigenetics and how the DNA methylation landscape is affected by the cultivation environment

DNA methylation in the bacterial genome plays an important role in epigenetic modification, which affects gene expression, regulation and environmental adaptation, etc. In this study, we conducted a comparative analysis of methylation patterns in the Gram-Negative bacteria Caldimonas thermopolymerans DSM 15344T. The type strain was initially isolated from activated sludge in Germany and then deposited in Leibniz Institute DSMZ in Germany (CT-DSMZ) and later in the Czech Collection of Microorganisms in Czechia (CT-CCM). Our aim was to assess whether a change in cultivation conditions and phenotype characteristics of the cultures deposited in various public collections coincides with methylation patterns. We used Oxford Nanopore Technology (ONT) sequencing with R10.4.1 flow cells and V14 chemistry for more accurate analysis. Despite being the same strain, we observed a significant difference in methylation counts between these two samples. The sample CT-CCM showed 7,350 6mA modifications, 2,764 5mC modifications, and 732 4mC modifications, while the sample CT-DSMZ showed slightly lower modification counts, with 6,884 6mA, 2,681 5mC, and 643 4mC modifications. We also analysed the distribution of methylation across different genomic annotation features, such as coding sequences (CDS), rRNA, and tRNA regions. The analysis also revealed significant differences between the two samples. In the Coding sequences (CDS), CT-CCM showed 7,153 6mA modifications, 2,339 5mC modifications, and 708 4mC modifications, while CT-DSMZ showed slightly lower counts with 6,680 6mA, 2,290 5mC, and 620 4mC modifications. To enhance our detection of methylated bases, we employed the Pacific Biosciences (PacBio) Sequel IIe platform. We integrated the methylation data from both sequencing platforms while comparing the epigenomes of specific sample cultivation. The differences in methylation levels between these two cultures suggest the role of cultivation conditions like temperature and nutrient availability that may lead to unique epigenetic changes. Given the role played by methylation in gene regulation, our finding contributes to knowledge of the potential impact of cultivation conditions on bacterial physiology. Our research will help in enhancing our understanding of bacterial epigenetics and how the DNA methylation landscape is affected by the cultivation environment

Caldimonas thermodepolymerans , Methylation, Oxford Nanopore

Caldimonas thermodepolymerans , Methylation, Oxford Nanopore

UMAIR, M.; SEDLÁŘ, K.; VÍTKOVÁ, H.; JAKUBÍČKOVÁ, M.; BUCHTÍKOVÁ, I.; BEZDÍČEK, M.; OBRUČA, S.

01.10.2025

Czech chemical society

Prague, Czechia

978-80-88307-24-2

Proceedings of the 12th International Conference on Chemical Technology

13

18

6

https://webadmin.icct.cz/Amca-ICCT/media/content/2025/Program/Book_of_abstracts_-ICCT2025.pdf

Proceedings_ICCT-2025