Mycoplasma agalactiae enrofloxacin spontaneous mutants
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ABSTRACT:
PROVIDER: PRJEB28036 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:During evolution, each bacterial strain shapes its metabolism in order to colonise a diversity of niches. Unraveling the biochemical reactions underlying bacteria metabolism is important for biotechnological purposes and for understanding relationships within a complex microbiome as well as the microbiome’s connection with its host. Here we propose a new approach to identifying active metabolic pathways, by integrating essentiality analysis and protein abundance. As an example, we used two bacterial species (Mycoplasma pneumoniae and Mycoplasma agalactiae) that share a high gene similarity yet show significant metabolic differences. After integrating all available metabolic knowledge about their enzymes, metabolites and reactions, we built detailed metabolic maps of their carbon metabolism. We determined the carbon sources that allow growth in M. agalactiae (as known for M. pneumoniae) and introduced glucose-dependent growth in M. agalactiae. By analyzing gene essentiality and performing quantitative proteomics, we could predict the active metabolic pathways and directionalities for the sugar, phospholipids, DNA/RNA precursors, glycoproteins, and glycolipids metabolism of these two bacteria. Comparison between predicted and experimentally determined active pathways shows an excellent agreement. Thus, protein essentiality profiling using transposon sequencing analysis combined with quantitative proteomics and metabolic maps could be used to determine and engineer metabolic fluxes.
2020-06-08 | PXD015800 | Pride
Project description:We used RNA-seq to investigate gene expression changes in sheep mammary gland and spleen tissue after experimental infection with Mycoplasma agalactiae (strain PG2). Sheep (3 per each group) were given an intra-mammary infection with 10^9 cfu infectious organisms or PBS as control. The animals were euthanized 15 days post infection to obtain the samples. Two replicates of mammary gland and spleen tissue per animal were used for Illumina RNA-sequencing.
2016-11-14 | E-MTAB-5216 | biostudies-arrayexpress
Project description:Mycoplasma agalactiae (Ma) is one of the main aetiological agents of intramammary infections in small ruminants, causing contagious agalactia. To better understand the underlying disease patterns a primary goat mammary epithelial cell (pgMEC) culture was established from the mammary tissue and it was challenged with Ma. High-throughput mRNA sequencing was performed to reveal differentially expressed genes (DEG) at different time-points (3 h, 12 h, and 24 h) post infection (PI). The pathway enrichment analysis of the DEG showed that infection significantly affected pathways associated with immune response, steroid metabolism, fatty acid metabolism, apoptosis signalling, transcription regulation, and cell cycle regulation. Based on the results we suggest that mammary epithelial cells in vivo contribute to the immune system by the induced expression of cytokines and other chemotactic agents, activation of the complement system and apoptosis pathways, and expression of genes coding for antimicrobial molecules and peptides. In our study we attempted to interpret the detected transcriptomic changes in a biological context and infer mammary infection resistance candidate genes, interesting for further validation. Additionally, the results represent comprehensive goat mammary transcriptome information and demonstrate the applicability of the comparative genomics approach for annotation of goat data, using transcriptome information of a closely related species (Bos taurus) as a reference.
2013-01-01 | GSE30379 | GEO
Project description:Transcriptional profiling of A. baumannii ATCC 17978 comparing two spontaneous rpoB mutants (Rif5 and Rif 8) with the wild-type parental strain
2017-06-12 | GSE73193 | GEO
Project description:Mycoplasma gallisepticum is a convenient model object for studying the regulation of transcription because it has a reduced genome, lack of cell wall and many metabolic pathways, and also easy to culture and non-pathogenic to humans. For rapid investigation of gene expression we developed microarray design including 3 366 probes for 678 genes. They included 665 protein coding sequences and 13 antisense RNAs from 816 genes and 17 ncRNAs present in Mycoplasma gallisepticum. This work was carried out transcriptomic profiling for different types of effects on the expression of genes of Mycoplasma gallisepticum: 1) genetic knock-out mutants; 2) cell culture exposed to sublethal concentrations of antibiotics; and 3) well-characterized heat stress effect. The study was performed on Agilent one-color microarray with custom design and random-T7 polymerase primer for cDNA synthesis. Using set of different probes for each gene or ncRNA allows to increase accuracy of gene expression quality.
2016-08-18 | GSE85777 | GEO
Project description:The immune response associated with mastitis caused by Mycoplasma bovis is a very complicated biological process in several type of cells, including immune cells, mammary epithelial cells and, endothelial cells. Thus, revealing of the microRNAs in the Mycoplasma bovis infected mammary gland tissues is particularly important for the immune response mechanism to Mycoplasma bovis. Firstly, mammary gland tissue samples were collected from Holstein cows and screened for Mycoplasma bovis. Then, total RNA was isolated from mycoplasma bovis infected tissues and RNA sequencing was performed. After bioinformatics analysis, GO and KEGG analysis of target genes of identified microRNAs were conducted. Our results revaled that 24 of the known microRNAs were expressed differently and 13 of the novel microRNAs were expressed differently in Mycoplasma bovis positive tissues. The target genes of these microRNAs were found to be associated with especially inflammation pathways. In conclusion, this study demonstrated that identified miRNAs may be involved in the signaling pathways during mastitis case caused by Mycoplasma bovis.
2021-05-25 | GSE152865 | GEO
Project description:Genomic and epigenomic of Mycoplasma agalactiae
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Project description:This dataset was used to assess the random insertion by tranposases of lox sites in Mycoplasma pneumoniae. This is part of the protocol LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of Lox sites by transposon mutagenesis, and the generation of mutants via cre recombinase, catalogued via deep-sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from >50 bp to 28 Kb, which represent 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other similar regions that could not, providing a guide for future genome reductions.
2021-08-18 | E-MTAB-9590 | biostudies-arrayexpress
Project description:We used a combination of genetic and proteomic approaches to characterize tmRNA (ssrA) activity in the genome-reduced bacterium Mycoplasma pneumoniae. For this, we generated tmRNA mutants encoding a tag resistant to proteolysis. Endogenous protein tagging by the mutant tmRNA gene (ssrAmk) was then examined by immunoprecipitation (IP) enrichment followed by LC-MS/MS analysis. Additionally, RNA-seq differential expression analysis of the mutants compared to the wild-type strain was assessed.
2021-08-09 | E-MTAB-10111 | biostudies-arrayexpress
Project description:Whole-transcriptome sequencing of luminal epithelial cells was performed in order to profile the transcriptomic response to infection and to elucidate the immune response signaling capability of milk producing epithelial cells. Primary goat mammary epithelial cell (pgMEC) culture model, mimicking the function of luminal cells in vivo, was established and infected with Mycoplasma agalactiae (Ma). After infection total RNA was extracted from the cells at different time-points post infection (PI) and sequenced using Illumina Gene Analyzer IIx. Four datasets were generated including controls and pgMECs challenged for 3 h, 12 h, and 24 h. The obtained 50 bp sequences were mapped against the bovine reference transcriptome. In addition to analysing individual genes for differential expression (DEG), we performed functional annotation of regulated genes to assess kinetics of the immune response on a more global scale. The DEGs were analysed for representative gene ontology (GO) enrichement terms, and biological processes as well as pathways regulated in response to Ma infection using different bioinformatic tools. The results show that in response to infection pgMECs are capable to induce genes involved in proinflammatory-cytokine signaling, activation of complement system, and can produce several bactericidal molecules of innate immune response. The pathway analyses revealed that in addition to immune response, the most regulated pathways were associated with lipid metabolism, apoptosis, transcription regulation, and cell cycle regulation. The obtained data is important for assessing the dynamics of the immune response signaling in MECs and opens new possibilities to idenitfy promising candidate genes, which could be beneficial for development of new therapeutic methods and introduction of a marker assisted selection towards enhanced mastitis resistance in breeding schemes. Transcriptome analysis of 12 samples; 3 replicated samples from control cells, and from cells 3 h, 12 h, and 24 h post infection.
2013-01-01 | E-GEOD-30379 | biostudies-arrayexpress