Global Transcriptional Analysis of Mycoplasma hyopneumoniae Following Exposure to Norepinephrine
Ontology highlight
ABSTRACT:
ORGANISM(S): Mesomycoplasma hyopneumoniae
PROVIDER: GSE8494 | GEO | 2008/03/01
SECONDARY ACCESSION(S): PRJNA101593
REPOSITORIES: GEO
Similar Datasets
Project description:The goal of this study is to gain a better understanding of the transcriptional responses of M. hyopneumoniae under norepinephrine stress. Six independent RNA samples from norepinephrine-exposed cultures were paired with six independent RNA samples from control cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other three arrays to overcome dye bias. Keywords: stress response Six independent RNA samples from norepinephrine-exposed cultures were paired with six independent RNA samples from control cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other three arrays to overcome dye bias.
2010-05-26 | E-GEOD-8494 | biostudies-arrayexpress
Project description:Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia and a major factor in the porcine respiratory disease complex. A clear understanding of the mechanisms of pathogenesis does not exist although it is clear that M. hyopneumoniae adheres to porcine ciliated epithelium by action of a protein called P97. Previous studies have shown variation in the gene encoding the P97cilium adhesin within different strains of M. hyopneumoniae, but the extent of genetic variation among field strains across the genome is not known. Since M. hyopneumoniae is a worldwide problem, it is reasonable to expect that a wide range of genetic variability may exist given all of the different breed and housing conditions. This variation may impact the overall virulence of a single strain. Using microarray technology, this study examined potential variation of fourteen field strains in comparison to strain 232 on which the array was based. Genomic DNA was obtained, amplified with TempliPhiâ¢, and labeled indirectly with Alexa dyes. Post genomic hybridization, the arrays were scanned and data analyzed using a linear statistical model. Results indicate that genetic variation could be detected in all fourteen field strains but across different loci, suggesting that variation occurs throughout the genome. Fifty-nine percent of the variable loci were hypothetical genes. Twenty-two percent of the lipoprotein genes showed variation in at least one field strain. A permutation test identified a location in M. hyopneumoniae genome where spatial clustering of variability between the field strains and strain 232 exists. TempliPhi⢠amplified DNA samples from field isolates were compared to control strain 232 using a two-color experimental microarray design. Independent samples from one isolate labeled with one dye were paired with control samples labeled with the alternate dye; the samples were mixed and hybridized to the microarray. For nine of the fourteen isolates (95MP1501, 95MP1502, 95MP1503, 95MP1504, 95MP1508, 95MP1509, 97MP0001, 00MP1301, and 05MP2301), four independent field isolate DNA samples were paired with four independent DNA samples from control 232. In two of the four arrays, the control sample was labeled with Alexa 555 dye and compared to the field isolate sample labeled with Alexa 647 dye (Molecular Probes, Inc., Eugene, Ore.). The dye assignment to control and treated samples was reversed for the other two arrays (dye swap). The arrays were hybridized under identical conditions as described below. This procedure was repeated for isolates 95MP1510 for a total of four arrays, where the control sample was labeled with Alexa 647 dye in three of the arrays and Alexa 555 dye for the fourth array. For isolates 95MP1505, 95MP1506 and 95MP1507, a total of five arrays each, including two dye swaps, were done; and for isolate 00MP1502, a total of six arrays were done with the control labeled with Alexa 555 dye for four of the arrays and Alexa 647 for the other two arrays.
2010-05-27 | E-GEOD-8306 | biostudies-arrayexpress
Project description:Mycoplasma hyopneumoniae, the causative agent of swine enzootic pneumonia, colonizes the cilia of swine lungs, causing ciliostasis and cell death. Mycoplasma hyopneumoniae is a component of the porcine respiratory disease complex (PRDC) and is especially problematic for the finishing swine industry, causing the loss of hundreds of millions of dollars in farm revenues worldwide. For successful infection, M. hyopneumoniae must effectively resist oxidative stresses due to the release of oxidative compounds from neutrophils and macrophages during the host’s immune response. However, the mechanism M. hyopneumoniae uses to avert the host response is still unclear. To gain a better understanding of the transcriptional responses of M. hyopneumoniae under oxidative stress, cultures were grown to early exponential phase and exposed to 0.5% percent hydrogen peroxide for 15 minutes. RNA samples from these cultures were collected and compared to RNA samples from control cultures using two-color PCR-based M. hyopneumoniae microarrays. This study revealed significant down-regulation of important glycolytic pathway genes and gene transcription proteins, as well as a protein known to activate oxidative stressor cascades in neutrophils. This study has also contained significantly differentially expressed genes common to other environmental stress responses, and merits further study of universal stress response genes of M. hyopneumoniae. Keywords: Mycoplasma hyopneumoniae, RNA microarray
2007-11-01 | GSE8304 | GEO
Project description:Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia and a major factor in the porcine respiratory disease complex. A clear understanding of the mechanisms of pathogenesis does not exist although it is clear that M. hyopneumoniae adheres to porcine ciliated epithelium by action of a protein called P97. Previous studies have shown variation in the gene encoding the P97cilium adhesin within different strains of M. hyopneumoniae, but the extent of genetic variation among field strains across the genome is not known. Since M. hyopneumoniae is a worldwide problem, it is reasonable to expect that a wide range of genetic variability may exist given all of the different breed and housing conditions. This variation may impact the overall virulence of a single strain. Using microarray technology, this study examined potential variation of fourteen field strains in comparison to strain 232 on which the array was based. Genomic DNA was obtained, amplified with TempliPhi™, and labeled indirectly with Alexa dyes. Post genomic hybridization, the arrays were scanned and data analyzed using a linear statistical model. Results indicate that genetic variation could be detected in all fourteen field strains but across different loci, suggesting that variation occurs throughout the genome. Fifty-nine percent of the variable loci were hypothetical genes. Twenty-two percent of the lipoprotein genes showed variation in at least one field strain. A permutation test identified a location in M. hyopneumoniae genome where spatial clustering of variability between the field strains and strain 232 exists. Keywords: CGH, Mycoplasma Hyopneumoniae
2008-01-01 | GSE8306 | GEO
Project description:Mycoplasma hyopneumoniae causes swine pneumonia and contributes significantly to porcine respiratory disease complex. The mechanisms of pathogenesis are difficult to address since there is a lack of genetic tools, but microarrays can be used to study transcriptional changes that occur during colonization and disease in pigs. This approach has the potential to identify genes important to virulence. This study sought to identify genes that change transcript levels during infection. To accomplish this, organisms collected from bronchial alveolar lavages were compared to that of broth grown organisms. Bronchial alveolar lavage was performed on pigs 28 days post infection with M. hyopneumoniae, and organisms were isolated by differential centrifugation. Mycoplasma RNA enriched preparations were then obtained from total RNA by subtracting eucaryotic ribosomal and messenger RNAs. cDNA was generated with mycoplasma ORF-specific primers, fluorescently labeled with Cy3 and Cy5, and used to interrogate microarrays. Arrays were scanned and analyzed using a mixed linear statistical model. Nine biological replicates were analyzed in this fashion. Our analysis indicated that 33 Mhyo genes were up-regulated and 46 genes were down-regulated (p<0.01) during disease in the pig lung at a false discovery rate < 2.7%. Of the down-regulated genes, 27 of 46 (59%) lacked assigned function, and 20 of 33 (61%) of the up-regulated genes were hypothetical genes. Four down-regulated and two up-regulated genes were putative lipoproteins. secA (mhp295; p = 0.003), and two glycerol transport permeases (potA (mhp380); p = 0.006 and ugpA (mhp381); p = 0.003) were up-regulated in vivo. Elongation factor EF-G (fusA (mhp083); p = 0.002), rpoC (mhp635; p = 0.003), adenylate kinase (adk (mhp208); p = 0.001), prolyl aminoacyl tRNA synthetase (proS (mhp397); p = 0.009) and cysteinyl-tRNA synthetase (cysS (mhp661); p < 0.001) were down-regulated in vivo. Keywords: RNA, spotted DNA/cDNA
2008-01-01 | GSE9057 | GEO
Project description:Mycoplasma hyopneumoniae pathogenic strains, like 7448, are the causative agents of porcine enzootic pneumonia. Non-pathogenic strains, like M. hyopneumoniae J, does not cause disease, although shares the entire repertoire of known virulence-related genes with M. hyopneumoniae 7448. In this context, the differential expression of ortholog genes is likely responsible, at least in part, for differences in pathogenicity or virulence level between these strains. Moreover, in the porcine lung, M. hyopneumoniae faces a hostile environment, with both oxidative and heat stresses. The performed comparative proteomics analyses provided evidence of differential stress responses between a pathogenic and a non-pathogenic M. hyopneumoniae strain, involving tens of proteins, including some known virulence factors. The results suggest that stress conditions trigger the expression of potential virulence factors in the pathogenic M. hyopneumoniae 7448, but not in the non-pathogenic M. hyopneumoniae J.
2019-03-29 | PXD012742 | Pride
Project description:Combined transcriptome sequencing of Mycoplasma hyopneumoniae and infected pig lung tissue
| PRJNA593525 | ENA
Project description:Global Transcriptional Analysis of Mycoplasma hyopneumoniae Following Exposure to Norepinephrine
| PRJNA101593 | ENA
Project description:Kamminga2017 - Metabolic model of Mycoplasma hyopneumoniae growth
This model is described in the article:
Metabolic modeling of energy
balances in Mycoplasma hyopneumoniae shows that pyruvate
addition increases growth rate.
Kamminga T, Slagman SJ, Bijlsma JJE,
Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ.
Biotechnol. Bioeng. 2017 Jun; :
Abstract:
Mycoplasma hyopneumoniae is cultured on large-scale to
produce antigen for inactivated whole-cell vaccines against
respiratory disease in pigs. However, the fastidious nutrient
requirements of this minimal bacterium and the low growth rate
make it challenging to reach sufficient biomass yield for
antigen production. In this study, we sequenced the genome of
M. hyopneumoniae strain 11 and constructed a high quality
constraint-based genome-scale metabolic model of 284 chemical
reactions and 298 metabolites. We validated the model with
time-series data of duplicate fermentation cultures to aim for
an integrated model describing the dynamic profiles measured in
fermentations. The model predicted that 84% of cellular energy
in a standard M. hyopneumoniae cultivation was used for
non-growth associated maintenance and only 16% of cellular
energy was used for growth and growth associated maintenance.
Following a cycle of model-driven experimentation in dedicated
fermentation experiments, we were able to increase the fraction
of cellular energy used for growth through pyruvate addition to
the medium. This increase in turn led to an increase in growth
rate and a 2.3 times increase in the total biomass
concentration reached after 3-4 days of fermentation, enhancing
the productivity of the overall process. The model presented
provides a solid basis to understand and further improve M.
hyopneumoniae fermentation processes. Biotechnol. Bioeng.
2017;9999: 1-9. © 2017 Wiley Periodicals, Inc.
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2017-08-08 | MODEL1704250001 | BioModels
Project description:The experiment consists of M.hyp 232 cultures digests analyzed on two mass specs, LTQ Velos Pro and LTQ FT Ultra LTQ Velos Pro: Six cell culture replicates of M.hyo 232 were hydrophobically separated using tree detergents: Digitonin, Tween, and SDS. Each francion, including the insoluble pellet, was trypsin digested and then cleaned using an SCX trap follwed by a RP trap to remove detergents. Each fraction was sepated using a Dionex U3000 splitless nanoflow system operating at 333 nl per minute using a gradient of 2% ACN to 50% ACN in 4 hours. Eluate was analyzed using an LTQ Velos Pro mass spectrometer with 20 MS/MS scans of the 20 most intense peaks from each MS scan. Dynamic exclusion was enable for 3 minutes for each m/z with a repeat count of 1. LTQ FT Ultra: Two cell pellets for high resolution analysis were lysed and trypsin digested. Digested peptides were dried, resuspended in 20 mM KH2PO4, 20% ACN, pH 3 (Buffer A) in 2.5 µL and transferred to low retention vials in preparation for separation using an Ultimate 3000 configured for 2D-LC. Each sample was loaded at 15 µl/min onto an SCX microtrap for the first dimension of separation, involving SCX steps of Buffer A + 0, 5, 10, 15, 20, 25, 30, 40, 50, 100, 250, 500, and 1000 mM KCl. For the second dimension of separation, each eluted salt step was desalted with an inline peptide microtrap with 2% ACN, 0.1% FA at 5 µl/min. Once desalted, the microtrap was switched into line with a fritless nano column (75µm x ~10cm) containing C18 media (5µ, 200 Å Magic, Michrom). Peptides were eluted using a gradient of 2% to 36% ACN, 0.1% FA at 350 nl/min over 60 min and electrospray ionized for analysis using an LTQ FT Ultra mass spectrometer. A survey scan m/z 350-1750 was acquired in the FT ICR cell (Resolution = 100,000 at m/z 400, with an accumulation target value of 1,000,000 ions). Up to the 6 most abundant ions (>3,000 counts) with charge states > +2 were sequentially isolated and fragmented within the linear ion trap using collisionally induced dissociation with an activation q = 0.25 and activation time of 30 ms at a target value of 30,000 ions. M/z ratios selected for MS/ MS were dynamically excluded for 30 seconds. Analysis: X!tandem searches were performed using the Mycoplasma hyopneumoniae strain 232 reference protein set from NCBI. The only difference between the searches for the LTQ Velos and LTQ FT was the precursor mass tolenance being set to +-1500ppm and +-24ppm respectively. Decoy searches were performed and the data filtered at e-value <= 0.01 with single peptide proteins discarded. These results are included in the submission as two tab-delimited text files.
2018-01-10 | PXD000118 | Pride