A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression

Liu, Gang; Jiang, Youxing; Liu, Yongcheng; Liang, Han; Hong, Feng

doi:10.1007/s00253-020-10475-5

Cited by 8 publications

(6 citation statements)

References 70 publications

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“…These modifications in the methylome profile are probably responsible in the large change in gene expression. A similar phenomenon was previously demonstrated in Bacillus pumilus when the type I RM-encoding genes were deleted [55]. This study highlighted the metabolic/genetic adaptation of the E. limosum B2 strain growing on methanol-defined medium and showed the importance of improving our knowledge of cell adaptation mechanisms in a constrained environment.…”

Section: Discussionsupporting

confidence: 84%

Genome Sequence of Eubacterium limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO2 as Sole Carbon Sources

2022

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Eubacterium limosum is an acetogen that can produce butyrate along with acetate as the main fermentation end-product from methanol, a promising C1 feedstock. Although physiological characterization of E. limosum B2 during methylotrophy was previously performed, the strain was cultured in a semi-defined medium, limiting the scope for further metabolic insights. Here, we sequenced the complete genome of the native strain and performed adaptive laboratory evolution to sustain growth on methanol mineral medium. The evolved population significantly improved its maximal growth rate by 3.45-fold. Furthermore, three clones from the evolved population were isolated on methanol mineral medium without cysteine by the addition of sodium thiosulfate. To identify mutations related to growth improvement, the whole genomes of wild-type E. limosum B2, the 10th, 25th, 50th, and 75th generations, and the three clones were sequenced. We explored the total proteomes of the native and the best evolved clone (n°2) and noticed significant differences in proteins involved in gluconeogenesis, anaplerotic reactions, and sulphate metabolism. Furthermore, a homologous recombination was found in subunit S of the type I restriction-modification system between both strains, changing the structure of the subunit, its sequence recognition and the methylome of the evolved clone. Taken together, the genomic, proteomic and methylomic data suggest a possible epigenetic mechanism of metabolic regulation.

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Section: Discussionsupporting

confidence: 84%

Genome Sequence of Eubacterium limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO2 as Sole Carbon Sources

2022

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“…The differences of methylation type become more dramatic when making crossspecies comparisons in Bacillus species (Reva et al, 2020). As previously reported, B. pumilus SAFR-032 has an increased survival phenotype for non-ionizing radiation exposure compared to B. subtilis (Gioia et al, 2007), which may be due to differences in methylation (Liu et al, 2020;Reva et al, 2020) and genetic features (Gioia et al, 2007).…”

Section: Mapping and Quality Of Long-readsmentioning

confidence: 74%

“…Because both of these programs were trained using E. coli sequences with GATC m6A modifications, these results were not surprising. It has been reported that Gramnegative bacterial genomes have a relatively consistent methylation pattern of m6A for GATC positions through various growth phases and after exposure to antibiotics (Shaiwale et al, 2015;Cohen et al, 2016;Westphal et al, 2016;Liu et al, 2020). Additionally, not all GATC positions are methylated, with some being heritably nonmethylated (Blyn et al, 1990;Casadesús and Low, 2006).…”

Section: Mapping and Quality Of Long-readsmentioning

confidence: 99%

“…It is clear that for high-throughput Nanopore MinION identification of methylation modifications, programs need to be more robustly trained on different (i) methylation sequence motifs and (ii) bacterial sequences outside of E. coli. A literature review shows that genome-wide methylation modification research is dominated by the use of PacBio's SMRT platform (Flusberg et al, 2010;Fang et al, 2012;Lluch-Senar et al, 2013;Krebes et al, 2014;Beaulaurier et al, 2015;Zautner et al, 2015;Cohen et al, 2016;Westphal et al, 2016;Couturier and Lindås, 2018;Hagemann et al, 2018;Nicholson et al, 2018;Payelleville et al, 2018;Zhao et al, 2018;Forde et al, 2019;Chhotaray et al, 2020;Coy et al, 2020;Estibariz et al, 2020;Liu et al, 2020;Nye et al, 2019Nye et al, , 2020Reva et al, 2020) compared to Nanopore's Minion (Rand et al, 2017;Jain et al, 2018;Giesselmann et al, 2019;Gigante et al, 2019;Miga et al, 2019;Zhang et al, 2021); of particular note, the organisms that have been studied using Nanopore's Minion tend to be eukaryotic. And with a few exceptions, bacterial methylomes are dominated by reads from the SMRT platform.…”

Section: Mapping and Quality Of Long-readsmentioning

confidence: 99%

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Long-read sequencing reveals increased occurrence of genomic variants and adenosine methylation in Bacillus pumilus SAFR-032 after long-duration flight exposure onboard the International Space Station

Waters

Ledford

Wacker

et al. 2021

International Journal of Astrobiology

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Bacillus pumilus SAFR-032, an endospore-forming bacterial strain, was investigated to determine its methylation pattern (methylome) change, compared to ground control, after direct exposure to space conditions onboard the International Space Station (ISS) for 1.5 years. The resulting ISS-flown and non-flown strains were sequenced using the Nanopore MinION and an in-house method and pipeline to identify methylated positions in the genome. Our analysis indicated genomic variants and m6A methylation increased in the ISS-flown SAFR-032. To complement the broader omics investigation and explore phenotypic changes, ISS-flown and non-flown strains were compared in a series of laboratory-based chamber experiments using an X-ray irradiation source (doses applied at 250, 500, 750, 1000 and 1250 Gy); results show a potentially higher survival fraction of ISS-flown DS2 at the two highest exposures. Taken together, results from this study document lasting changes to the genome by methylation, potentially triggered by conditions in spaceflight, with functional consequences for the resistance of bacteria to stressors expected on long-duration missions beyond low Earth orbit.

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“…vesca , sorted data (41-bp fragments with different modQV scores) were downloaded from the MDR database. 39 Selecting the optimal modQV threshold was challenging, as thresholds of 20 61 and 30, 62 corresponding to p values of 0.01 and 0.001, respectively, are recommended in different studies. The existing methods utilized positive samples with a modQV greater than 30.…”

Section: Methodsmentioning

confidence: 99%

Empirical Comparison and Analysis of Web-Based DNA N4-Methylcytosine Site Prediction Tools

Manavalan

Hasan

Basith

et al. 2020

Molecular Therapy - Nucleic Acids

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DNA N 4 -methylcytosine (4mC) is a crucial epigenetic modification involved in various biological processes. Accurate genome-wide identification of these sites is critical for improving our understanding of their biological functions and mechanisms. As experimental methods for 4mC identification are tedious, expensive, and labor-intensive, several machine learning-based approaches have been developed for genome-wide detection of such sites in multiple species. However, the predictions projected by these tools are difficult to quantify and compare. To date, no systematic performance comparison of 4mC tools has been reported. The aim of this study was to compare and critically evaluate 12 publicly available 4mC site prediction tools according to species specificity, based on a huge independent validation dataset. The tools 4mCCNN ( Escherichia coli ), DNA4mC-LIP ( Arabidopsis thaliana ), iDNA-MS ( Fragaria vesca ), DNA4mC-LIP and 4mCCNN ( Drosophila melanogaster ), and four tools for Caenorhabditis elegans achieved excellent overall performance compared with their counterparts. However, none of the existing methods was suitable for Geoalkalibacter subterraneus , Geobacter pickeringii , and Mus musculus , thereby limiting their practical applicability. Model transferability to five species and non-transferability to three species are also discussed. The presented evaluation will assist researchers in selecting appropriate prediction tools that best suit their purpose and provide useful guidelines for the development of improved 4mC predictors in the future.

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A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression

Cited by 8 publications

References 70 publications

Genome Sequence of Eubacterium limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO2 as Sole Carbon Sources

Genome Sequence of Eubacterium limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO2 as Sole Carbon Sources

Long-read sequencing reveals increased occurrence of genomic variants and adenosine methylation in Bacillus pumilus SAFR-032 after long-duration flight exposure onboard the International Space Station

Empirical Comparison and Analysis of Web-Based DNA N4-Methylcytosine Site Prediction Tools

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