Epigenomic landscape of Lyme disease spirochetes reveals novel motifs
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA716641 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14049000_1.fastq.gz | Fastqsanger.gz | |||
| SRR14049000_2.fastq.gz | Fastqsanger.gz | |||
| SRR14049001_1.fastq.gz | Fastqsanger.gz | |||
| SRR14049001_2.fastq.gz | Fastqsanger.gz | |||
| SRR14049002_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 96 |
Similar Datasets
Project description:Borrelia burgdorferi, the etiological agent of Lyme disease, persists in nature through an enzootic cycle consisting of a vertebrate host and an Ixodes tick vector. The sequence motifs modified by two well-characterized restriction/modification loci of B. burgdorferi type strain B31 were recently described, but the methylation profiles of other Lyme disease Borrelia have not been characterized. Herein, the methylomes of B. burgdorferi type strain B31 and 7 clonal derivatives, along with B. burgdorferi N40, B. burgdorferi 297, B. burgdorferi CA-11, B. afzelii PKo, B. afzelii BO23, and B. garinii PBr, were defined through PacBio SMRT sequencing. This analysis revealed 9 novel sequence motifs methylated by the plasmid-encoded restriction/modification enzymes of these Borrelia strains. Furthermore, while a previous analysis of B. burgdorferi B31 revealed an epigenetic impact of methylation on the global transcriptome, the current data contradict those findings; our analyses of wild-type B. burgdorferi B31 revealed no consistent differences in gene expression among isogenic derivatives lacking one or more restriction/modification enzyme(s).
2021-03-24 | GSE169460 | GEO
Project description:Borrelia burgdorferi, the etiological agent of Lyme disease, persists in nature through an enzootic cycle consisting of a vertebrate host and an Ixodes tick vector. The sequence motifs modified by two well-characterized restriction/modification (R/M) loci of B. burgdorferi type strain B31 were recently described, but the methylation profiles of other Lyme disease Borrelia bacteria have not been characterized. Here, the methylomes of B. burgdorferi type strain B31 and 7 clonal derivatives, along with B. burgdorferi N40, B. burgdorferi 297, B. burgdorferi CA-11, B. afzelii PKo, B. afzelii BO23, and B. garinii PBr, were defined through PacBio single-molecule real-time (SMRT) sequencing. This analysis revealed 9 novel sequence motifs methylated by the plasmid-encoded restriction/modification enzymes of these Borrelia strains. Furthermore, while a previous analysis of B. burgdorferi B31 revealed an epigenetic impact of methylation on the global transcriptome, the current data contradict those findings; our analyses of wild-type B. burgdorferi B31 revealed no consistent differences in gene expression among isogenic derivatives lacking one or more restriction/modification enzymes. IMPORTANCE The principal causative agent of Lyme disease in humans in the United States is Borrelia burgdorferi, while B. burgdorferi, B. afzelii, and B. garinii, collectively members of the Borrelia burgdorferi sensu lato species complex, cause Lyme disease in Europe and Asia. Two plasmid-encoded restriction/modification systems have been shown to limit the genetic transformation of B. burgdorferi type strain B31 with foreign DNA, but little is known about the restriction/modification systems of other Lyme disease Borrelia bacteria. This paper describes the methylation motifs present on genomic DNAs of multiple B. burgdorferi, B. afzelii, and B. garinii strains. Contrary to a previous report, we did not find evidence for an epigenetic impact on gene expression by methylation. Knowledge of the motifs recognized and methylated by the restriction/modification enzymes of Lyme disease Borrelia will facilitate molecular genetic investigations of these important human pathogens. Additionally, the similar motifs methylated by orthologous restriction/modification systems of Lyme disease Borrelia bacteria and the presence of these motifs within recombinogenic loci suggest a biological role for these ubiquitous restriction/modification systems in horizontal gene transfer.
| S-EPMC8262957 | biostudies-literature
Project description:Lyme disease spirochetes must induce RpoS-dependent genes during tick feeding to prepare for host infection. Previous work in our lab identified bbd18 as a negative regulator of RpoS, but inactivation of bbd18 in wild-type spirochetes was never achieved. In the current study we generated an inducible bbd18 gene at the endogenous plasmid locus and demonstrated the essential nature of BBD18 for viability of wild-type spirochetes in vitro and at a unique point in vivo. Transcriptomic analyses demonstrated global induction of RpoS and RpoS-dependent genes following BBD18 depletion, culminating in spirochete lysis. Plasmid prophage genes were also induced and phage particles were detected in lysed culture supernatants, suggesting that RpoS regulates phage lysis-lysogeny decisions. The absolute requirement for BBD18 persisted following displacement of the entire set of cp32 plasmid prophages but could be circumvented by deletion of rpoS. This is the first report of a mechanistic link between endogenous transducing prophages and the RpoS-dependent adaptive response of the Lyme disease spirochete.
2022-12-12 | GSE207123 | GEO
Project description:The Epigenomic Landscape of Prokaryotes
| PRJNA287040 | ENA
Project description:Lyme neuroborreliosis (LNB) is a nervous system infection caused by tick-borne spirochetes of the Borrelia burgdorferi sensu lato complex and is one of the most frequent bacterial infections of the nervous system in Europe. Early diagnosis remains challenging due to limited sensitivity and specificity of current tests and the need for invasive lumbar punctures, highlighting the need for improved and potentially less invasive diagnostic tools. In this study, we used bottom-up proteomics to analyze 308 cerebrospinal fluid (CSF) samples and 207 plasma samples from well-characterized cohorts, including patients with LNB, viral meningitis, other manifestations of Lyme borreliosis without central nervous system involvement, and controls with normal CSF findings. We identified diagnostic panels of regulated proteins and evaluated their performance using machine learning–based classifiers. The resulting models distinguished LNB from viral meningitis and controls in CSF with areas under the ROC curve (AUC) of 0.92 and 0.90, respectively. In plasma, LNB was distinguished from controls with an AUC of 0.80. These findings suggest a potential diagnostic role for proteomics-based biomarker panels in LNB and provide a large-scale, publicly available proteomic resource for further biomarker discovery and validation studies. NOTE the CSF search and raw files can be found in PXD067474.
2025-09-30 | PXD067583 | Pride
Project description:Lyme neuroborreliosis (LNB) is a nervous system infection caused by tick-borne spirochetes of the Borrelia burgdorferi sensu lato complex and is one of the most frequent bacterial infections of the nervous system in Europe. Early diagnosis remains challenging due to limited sensitivity and specificity of current tests and the need for invasive lumbar punctures, highlighting the need for improved and potentially less invasive diagnostic tools. In this study, we used bottom-up proteomics to analyze 308 cerebrospinal fluid (CSF) samples and 207 plasma samples from well-characterized cohorts, including patients with LNB, viral meningitis, other manifestations of Lyme borreliosis without central nervous system involvement, and controls with normal CSF findings. We identified diagnostic panels of regulated proteins and evaluated their performance using machine learning–based classifiers. The resulting models distinguished LNB from viral meningitis and controls in CSF with areas under the ROC curve (AUC) of 0.92 and 0.90, respectively. In plasma, LNB was distinguished from controls with an AUC of 0.80. These findings suggest a potential diagnostic role for proteomics-based biomarker panels in LNB and provide a large-scale, publicly available proteomic resource for further biomarker discovery and validation studies. NB: the plasma submission is seperate to this CSF submission
2025-09-30 | PXD067474 | Pride
Project description:The alternative sigma factor RpoS plays a central role in the critical host-adaptive response of the Lyme disease spirochete, Borrelia burgdorferi. We previously identified bbd18 as a negative regulator of RpoS but could not inactivate bbd18 in wild-type spirochetes. In the current study we employed an inducible bbd18 gene to demonstrate the essential nature of BBD18 for viability of wild-type spirochete viability in vitro and at a unique point in vivo. Transcriptomic analyses of BBD18 depleted cells demonstrated global induction of RpoS-dependent genes prior to lysis, with the absolute requirement for BBD18, both in vitro and in vivo, circumvented by deletion of rpoS. The increased expression of plasmid prophage genes and the presence of phage particles in the supernatants of lysing cultures indicate that RpoS regulates phage lysis-lysogeny decisions. Through this work we identify a mechanistic link between endogenous transducing prophages and the RpoS-dependent adaptive response of the Lyme disease spirochete. The alternative sigma factor RpoS plays a central role in the critical host-adaptive response of the Lyme disease spirochete, Borrelia burgdorferi. We previously identified bbd18 as a negative regulator of RpoS but could not inactivate bbd18 in wild-type spirochetes. In the current study we employed an inducible bbd18 gene to demonstrate the essential nature of BBD18 for viability of wild-type spirochete viability in vitro and at a unique point in vivo. Transcriptomic analyses of BBD18 depleted cells demonstrated global induction of RpoS-dependent genes prior to lysis, with the absolute requirement for BBD18, both in vitro and in vivo, circumvented by deletion of rpoS. The increased expression of plasmid prophage genes and the presence of phage particles in the supernatants of lysing cultures indicate that RpoS regulates phage lysis-lysogeny decisions. Through this work we identify a mechanistic link between endogenous transducing prophages and the RpoS-dependent adaptive response of the Lyme disease spirochete.
2022-12-12 | PXD037736 | Pride
Project description:A Unique Epigenomic Landscape Defines Human Erythropoiesis
| PRJNA526914 | ENA
Project description:Establish the male meiocyte-specific epigenomic landscape
| PRJNA903804 | ENA
Project description:Lyme disease is a result from an infection by the spirochete Borrelia burgdorferi, and is the leading vector-borne disease in North America. Due to the genomic and proteomic variability of different B. burgdorferi isolates, the study and further comparison of their proteome is key to understand the biology and infectivity of these spirochetes. Mass spectrometry-based proteomics was used to assemble peptide datasets of laboratory isolates B31, MM1, B31-ML23, and the infective isolates B31-5A4, B31-A3, and 297, as well as other public datasets, and is publicly available as the Borrelia PeptideAtlas (http://www.peptideatlas.org/builds/borrelia/). These datasets include information on total proteome, secretome, and membrane proteome of the B. burgdorferi.
2024-09-03 | PXD046281 | Pride