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Transcriptional profiling of Mycobacterium tuberculosis exposed to antibiotic treatment in broth culture.

ABSTRACT: Transcriptional profiling of Mycobacterium tuberculosis exposed to antibiotic treatment in broth culture.

PROVIDER: PRJNA1238098 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32767200.fastq.gz	Fastqsanger.gz
	SRR32767201.fastq.gz	Fastqsanger.gz
	SRR32767202.fastq.gz	Fastqsanger.gz
	SRR32767203.fastq.gz	Fastqsanger.gz
	SRR32767204.fastq.gz	Fastqsanger.gz

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Transcriptional profiling of Mycobacterium tuberculosis exposed to antibiotic treatment in broth culture.

Project description:We profiled Mtb transcriptional response to a range of different antibiotic drug exposures in 7H9 broth culture by RNA-seq. Compound abbreviations: (AMK = amikacin, BDQ = bedaquiline, CPF = ciprofloxacin, LVF = levofloxacin, MXF = moxifloxacin, CFZ = clofazimine, PA824 = pretomanid, RPE = rifapentine, PZA = pyrazinamide). We also hypothesized that an improved Mycobacterium tuberculosis (Mtb) transcriptional regulatory network (TRN) could be inferred using a large, diverse compendium of RNA-seq data and therefore sought to supplement the existing repository of Mtb expression data available on SRA with additional conditions that could inform on Mtb's underlying regulatory programs. We went on to infer Mtb's TRN using a collection of inference methods in combination with this compendium, and employed it to build an interpretable machine learning model of Mtb fitness under stress.

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Transcriptional profiling of Mycobacterium tuberculosis exposed to proton pump inhibitor treatment in broth culture.

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Transcriptional profiling of Mycobacterium tuberculosis exposed to antibiotics and drug combinations in broth culture.

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Transcriptional profiling of Mycobacterium tuberculosis exposed to antibiotics and drug combinations in broth culture.

Project description:We profiled Mtb transcriptional response to a range of different antibiotic drug exposures in 7H9 broth culture by RNA-seq. Compound abbreviations: (EMB = ethambutol, BTZ = BTZ043, TYL = tyloxapol). We also hypothesized that an improved Mtb TRN could be inferred using a large, diverse compendium of RNA-seq data and therefore sought to supplement the existing repository of Mtb expression data available on SRA with additional conditions that could inform on Mtb's underlying regulatory programs. We went on to infer Mtb's TRN using a collection of inference methods in combination with this compendium, and employed it to build an interpretable machine learning model of Mtb fitness under stress.

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Project description:Streptococcus pneumoniae (‘pneumococcus’) is a leading cause of morbidity and mortality worldwide and a frequent coloniser of the nasopharynx. Competition among bacterial members of the nasopharynx is believed to be mediated by bacteriocins: antimicrobial toxins produced by bacteria to inhibit growth of other bacteria. We have identified 14 newly-discovered bacteriocin gene clusters among pneumococci. Here, RNA-seq analysis was performed to investigate whether bacteriocin genes are transcriptionally active when two different strains are competing in broth culture. Pneumococcal reference strains PMEN3 (Spain9V-3) and PMEN6 (Hungary19A-6) were grown together in broth culture. Samples were taken at sequential time points and RNA was extracted and sequenced. The controls were prepared by growing each strain individually in identical experiential conditions and combining the RNA sequencing reads from each individual strain in silico. Differential expression analyses were performed by comparing reads generated when strains were competing in broth culture to those from when strains were grown individually.

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Project description:The development of antibiotic tolerance is believed to be a major factor in the lengthy duration of current tuberculosis therapies. In the current study, we have modeled antibiotic tolerance in vitro by exposing Mycobacterium tuberculosis to two distinct stress conditions: progressive hypoxia and nutrient starvation [phosphate-buffered saline (PBS)]. We then studied the bacterial transcriptional response using RNA-seq and employed a bioinformatics approach to identify important transcriptional regulators, which was facilitated by a novel Regulon Enrichment Test (RET). A total of 17 transcription factor (TF) regulons were enriched in the hypoxia gene set and 16 regulons were enriched in the nutrient starvation, with 12 regulons enriched in both conditions. Using the same approach to analyze previously published gene expression datasets, we found that three M. tuberculosis regulons (Rv0023, SigH, and Crp) were commonly induced in both stress conditions and were also among the regulons enriched in our data. These regulators are worthy of further study to determine their potential role in the development and maintenance of antibiotic tolerance in M. tuberculosis following stress exposure.

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Culture filtrate of Mycobacterium tuberculosis clinical isolate S169

Project description:Phagosome acidification is one of the challenges faced by Mycobacterium tuberculosis during infection. This intracellular pathogen is known to adapt to its stressful environment though stress response pathways and by secreting proteins to modify the host immune response for survival and proliferation. However, M. tuberculosis also holds the potential to form viable but non-replicating (VBNR) and antibiotic tolerant persisters in response to environmental stress, including acid stress. In this study we used a in vitro acid stress model to stimulate the formation of a VBNR subpopulation in a M. tuberculosis clinical isolate with an increased propensity to form VBNR bacteria. Mass spectrometry-based proteomics was used to characterize the cellular proteome and culture filtrate proteome of actively replicating (pH 6,5) and VBNR enriched (pH 4,5) cultures. We show that in response to acid stress, M. tuberculosis S169 increases the expression of known stress response proteins, including the methyltransferase Rv1405c and the acid stress response two-component regulatory protein TcrX. Interestingly, we found that the dormancy response regulon components were less abundant in acid stressed M. tuberculosis S169. Our protein aggregation capture culture filtrate proteomic approach revealed that the culture filtrates of low pH stressed M. tuberculosis S169 contained less proteins than that of actively replicating cultures. We identified several proteins previously implicated in M. tuberculosis persistence, including toxin-antitoxin proteins (VapC51 and VapB10), the chorismate mutase (Rv1885c), and several uncharacterized proteins. The observed differences identified in the characterisation of this clinical isolate in comparison to published M. tuberculosis H37Rv highlights the need to investigate M. tuberculosis clinical isolates for a more representative understanding of the tuberculosis stress response.

2025-10-04 | PXD068720 | Pride

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