Ontology highlight
ABSTRACT:
PROVIDER: PRJNA506132 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8236350_1.fastq.gz | Fastqsanger.gz | |||
| SRR8236350_2.fastq.gz | Fastqsanger.gz | |||
| SRR8236360_1.fastq.gz | Fastqsanger.gz | |||
| SRR8236360_2.fastq.gz | Fastqsanger.gz | |||
| SRR8236370_1.fastq.gz | Fastqsanger.gz |
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Project description:To understand nontuberculous mycobacterial (NTM) pathogenesis, we evaluated immune responses to Mycobacterium avium (Mav) in asymptomatic individuals with a previous history of M. avium complex lung disease (MACDZ). We analyzed global gene expression in paired Mav-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls.
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Project description:Mycobacterium avium is one of the prominent disease causing bacteria in humans. It causes lymphadenitis, chronic pulmonary and extrapulmonary and disseminated infections in adults, children and immunocompromised humans. M. avium has ~4,500 predicted gene models, out of which not all are identified at proteomic level. Proteomic database search followed by proteogenomic analysis helps in the correction of gene models, identification of novel exons/genes, variant proteins. As part of this study, we performed proteomic analysis of M. avium cultures by data-dependent acquisition (DDA) and data-independent acquisition (DIA) method followed by proteogenomic analysis of M. avium proteomic data. M. avium culture was subjected to proteomic sample preparation. The resulting peptides were acquired in 120min DDA (12 bRPLC) and DIA method using EASY nLC 1200 liquid chromatogram system coupled to Orbitrap Fusion Tribrid mass spectrometer. The resulting DDA raw files were searched sequentially against the M. avium proteome database, Mycobacterium tuberculosis H37Rv and Ra proteome database (Mtb), M. avium genome six-frame translated proteome and variant proteins database, respectively. The database search result was converted into a spectral library and used for DIA data search for the validation of GSSPs and variant peptides. The database search of M. avium DDA has resulted in the identification of 2,954 M. avium proteins, 128 Mtb proteins, 174 GSSPs (M. avium genome six-frame translated proteome) and 795 SNPs corresponding to 612 proteins (variant proteins database), respectively. The M. avium proteome database search has covered 62.09% of the proteome with the identification of 2,954 proteins out of 4,757 proteins in the database. From the manual categorization of 174 GSSPs, we observed 23 N-terminal extensions, 142 pseudogene coding peptides and one each novel exon and short peptide, respectively.
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Project description:Mycobacterium avium complex (MAC), including Mycobacterium avium and Mycobacterium intracellulare (MI), accounts for a significant portion of nontuberculous mycobacterial lung disease affecting immunocompromised and lung structural disease patients. Adapting pathogens to a host-induced hostile environment is critical to establishing infection and persistence within the host. However, the cellular and molecular mechanisms of stress response for MAC still need to be elucidated. In this study, we analyzed the transcriptional profile of MI under acidic and oxidative stress conditions using RNA-seq. At the transcriptome level, 80 genes were shown [FC] ≥2.0 and p <0.05 under oxidative stress with 10 mM hydrogen peroxide. In detail, 77 genes were upregulated, while 3 genes were downregulated. Also, 878 genes were shown [FC] ≥2.0 and p <0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis revealed the activation of several pathways, including nitrogen and sulfur metabolism, under acidic stress conditions. On the contrary, oxidative stress conditions activated DNA replication and repair pathways. Our data demonstrate the activation of nitrogen and sulfur metabolism in MAC infection, which could be crucial for persistence and survival under stress conditions encountered within the host during infection. In conclusion, this study suggests the importance of stress responses in MAC pathogenesis and identifies potential therapeutic target pathways.
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Project description:Lower airway microbiota in patients with clinically suspected Mycobacterium avium complex lung disease
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Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization Each isolate was competitively hybridized against Map K10 with a minimum of 2 dye flip hybridizations per isolate.
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