Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T

Murphy, Trevor R; Xiao, R.; Hamilton-Brehm, Scott D.

doi:10.1186/s12864-021-07535-z

Cited by 3 publications

(3 citation statements)

References 93 publications

(107 reference statements)

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“…In this scenario, highly conserved DNA methyltransferases (MTases) are potential targets for epigenetic inhibitors to fight infections [139]. Besides, they may have potential biotechnological applications [146]. Additionally, they represent a valuable tool for aligning metagenomic contigs and scaffolds, preventing errors, as well as assigning mobile genetic elements (MGE), such as transposable elements (TE), to their host genomes [135].…”

Section: Epigenomicsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

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Section: Epigenomicsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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“…Recent development in single-molecule sequencing technologies, for example, Nanopore sequencing, allows for the detection of these multiple DNA methylation base modifications. Using this approach, bacterial DNA methylation signatures have recently been shown to impact gene expression profiles and genome stability ( 19 , 20 ).…”

Section: Introductionmentioning

confidence: 99%

Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis

et al. 2023

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Periodontal disease is a chronic inflammatory disease in which the oral pathogen Porphyromonas gingivalis plays an important role. Porphyromonas gingivalis expresses virulence determinants in response to higher hemin concentrations, but the underlying regulatory processes remain unclear. Bacterial DNA methylation has the potential to fulfil this mechanistic role. We characterized the methylome of P. gingivalis , and compared its variation to transcriptome changes in response to hemin availability. Porphyromonas gingivalis W50 was grown in chemostat continuous culture with excess or limited hemin, prior to whole-methylome and transcriptome profiling using Nanopore and Illumina RNA-Seq. DNA methylation was quantified for Dam/Dcm motifs and all-context N6-methyladenine (6mA) and 5-methylcytosine (5mC). Of all 1,992 genes analyzed, 161 and 268 were respectively over- and under-expressed with excess hemin. Notably, we detected differential DNA methylation signatures for the Dam “GATC” motif and both all-context 6mA and 5mC in response to hemin availability. Joint analyses identified a subset of coordinated changes in gene expression, 6mA, and 5mC methylation that target genes involved in lactate utilization and ABC transporters. The results identify altered methylation and expression responses to hemin availability in P. gingivalis , with insights into mechanisms regulating its virulence in periodontal disease. IMPORTANCE DNA methylation has important roles in bacteria, including in the regulation of transcription. Porphyromonas gingivalis , an oral pathogen in periodontitis, exhibits well-established gene expression changes in response to hemin availability. However, the regulatory processes underlying these effects remain unknown. We profiled the novel P. gingivalis epigenome, and assessed epigenetic and transcriptome variation under limited and excess hemin conditions. As expected, multiple gene expression changes were detected in response to limited and excess hemin that reflect health and disease, respectively. Notably, we also detected differential DNA methylation signatures for the Dam “GATC” motif and both all-context 6mA and 5mC in response to hemin. Joint analyses identified coordinated changes in gene expression, 6mA, and 5mC methylation that target genes involved in lactate utilization and ABC transporters. The results identify novel regulatory processes underlying the mechanism of hemin regulated gene expression in P. gingivalis, with phenotypic impacts on its virulence in periodontal disease.

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“…Recent development in single molecule sequencing technologies, for example Nanopore sequencing, allow for the detection of these multiple DNA methylation base modifications. Using this approach, bacterial DNA methylation signatures have recently been shown to impact gene expression profiles and genome stability (16, 17).…”

Section: Introductionmentioning

confidence: 99%

Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis

Costeira

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Vernon

et al. 2022

Preprint

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Periodontal disease is a common chronic inflammatory disease driven by the sub-gingival microbiota. Porphyromonas gingivalis is an important bacterium in the development of the disease that expresses a variety of virulence determinants. The environmental concentration of hemin, an essential nutrient of this organism, is a global regulator of virulence in P. gingivalis: high levels of hemin lead to increased expression of several virulence determinants. However, the mechanism through which hemin influences bacterial gene expression is poorly understood. Bacterial epigenetic processes, primarily DNA methylation, have the potential to fulfil this mechanistic role. Here, we characterised the methylome of P. gingivalis, and compared its variation to transcriptomic changes in response to changes in hemin concentration. Gene expression and DNA methylation profiling of P. gingivalis W50 was performed, following continuous culture in chemostats with excess or limited hemin, using Illumina RNA-Seq and Nanopore DNA sequencing. DNA methylation quantification was carried out for N6-methyladenine (6mA) and 5-methylcytosine (5mC) base pair modifications. Differential expression and differential methylation in response to excess hemin availability are presented after multiple testing correction (FDR 5%). In excess hemin there were 161 over- and 268 under-expressed genes, compared to limited hemin culture. Genes under-expressed in excess hemin were involved in iron recruitment (the hemophore HmuY) and transport (TonB-dependent receptors), and those over-expressed were involved in Fe-S and 4FE-4S cluster binding, and metal cluster binding. Hemin-dependent differentially methylated signals were observed for both 6mA and 5mC, with 49 and 47 signals, respectively. Coordinated genome-wide differential expression and methylation effects were observed in 6 genes, a Ppx/GppA family phosphatase, a lactate utilization protein, 4-alpha-glucanotransferase, two ABC transporter proteins, and a hypothetical protein HMPREF1322_RS00730. The findings indicate that altered genome methylation occurs in response to the availability of hemin and give insights into the molecular mechanisms of regulation of virulence in this bacterium.

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Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T

Cited by 3 publications

References 93 publications

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis

Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis

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