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1.  Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California 
Genome Announcements  2014;2(6):e00977-14.
The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion Personal Genome Machine (PGM) platform, and showed a size of 2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These results will serve as a basis for further studies on the pathogenicity of C. pseudotuberculosis bv. equi.
doi:10.1128/genomeA.00977-14
PMCID: PMC4241654  PMID: 25395628
2.  Complete Genome Sequences of Corynebacterium pseudotuberculosis Strains 3/99-5 and 42/02-A, Isolated from Sheep in Scotland and Australia, Respectively 
Journal of Bacteriology  2012;194(17):4736-4737.
Here, we report the whole-genome sequences of two ovine-pathogenic Corynebacterium pseudotuberculosis isolates: strain 3/99-5, which represents the first C. pseudotuberculosis genome originating from the United Kingdom, and 42/02-A, the second from Australia. These genome sequences will contribute to the objective of determining the global pan-genome of this bacterium.
doi:10.1128/JB.00918-12
PMCID: PMC3415504  PMID: 22887652
3.  Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 1/06-A, Isolated from a Horse in North America 
Journal of Bacteriology  2012;194(16):4476.
Corynebacterium pseudotuberculosis causes disease in several animal species, although distinct biovars exist that appear to be restricted to specific hosts. In order to facilitate a better understanding of the differences between biovars, we report here the complete genome sequence of the equine pathogen Corynebacterium pseudotuberculosis strain 1/06-A.
doi:10.1128/JB.00922-12
PMCID: PMC3416248  PMID: 22843601
4.  Differential transcriptional profile of Corynebacterium pseudotuberculosis in response to abiotic stresses 
BMC Genomics  2014;15:14.
Background
The completion of whole-genome sequencing for Corynebacterium pseudotuberculosis strain 1002 has contributed to major advances in research aimed at understanding the biology of this microorganism. This bacterium causes significant loss to goat and sheep farmers because it is the causal agent of the infectious disease caseous lymphadenitis, which may lead to outcomes ranging from skin injury to animal death. In the current study, we simulated the conditions experienced by the bacteria during host infection. By sequencing transcripts using the SOLiDTM 3 Plus platform, we identified new targets expected to potentiate the survival and replication of the pathogen in adverse environments. These results may also identify possible candidates useful for the development of vaccines, diagnostic kits or therapies aimed at the reduction of losses in agribusiness.
Results
Under the 3 simulated conditions (acid, osmotic and thermal shock stresses), 474 differentially expressed genes exhibiting at least a 2-fold change in expression levels were identified. Important genes to the infection process were induced, such as those involved in virulence, defence against oxidative stress, adhesion and regulation, and many genes encoded hypothetical proteins, indicating that further investigation of the bacterium is necessary. The data will contribute to a better understanding of the biology of C. pseudotuberculosis and to studies investigating strategies to control the disease.
Conclusions
Despite the veterinary importance of C. pseudotuberculosis, the bacterium is poorly characterised; therefore, effective treatments for caseous lymphadenitis have been difficult to establish. Through the use of RNAseq, these results provide a better biological understanding of this bacterium, shed light on the most likely survival mechanisms used by this microorganism in adverse environments and identify candidates that may help reduce or even eradicate the problems caused by this disease.
doi:10.1186/1471-2164-15-14
PMCID: PMC3890534  PMID: 24405787
Differential gene expression; Transcripts; RNAseq; SOLID™; Stress; C. pseudotuberculosis
5.  Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method 
Microbial Biotechnology  2013;6(2):168-177.
Corynebacterium pseudotuberculosis equi is a Gram-positive pathogenic bacterium which affects a variety of hosts. Besides the great economic losses it causes to horse-breeders, this organism is also known to be an important infectious agent to cattle and buffaloes. As an outcome of the efforts in characterizing the molecular basis of its virulence, several complete genome sequences were made available in recent years, enabling the large-scale assessment of genes throughout distinct isolates. Meanwhile, the RNA-seq stood out as the technology of choice for comprehensive transcriptome studies, which may bring valuable information regarding active genomic regions, despite of the still impeditive associated costs. In an attempt to increase the use of generated reads per instrument run, by effectively eliminating unwanted rRNAs from total RNA samples without relying on any commercially available kits, we applied denaturing high-performance liquid chromatography (DHPLC) as an alternative method to assess the transcriptional profile of C. pseudotuberculosis. We have found that the DHPLC depletion method, allied to Ion Torrent sequencing, allows mapping of transcripts in a comprehensive way and identifying novel transcripts when a de novo approach is used. These data encourage us to use DHPLC in future transcriptional evaluations in C. pseudotuberculosis.
doi:10.1111/1751-7915.12020
PMCID: PMC3917459  PMID: 23316806
6.  The Pan-Genome of the Animal Pathogen Corynebacterium pseudotuberculosis Reveals Differences in Genome Plasticity between the Biovar ovis and equi Strains 
PLoS ONE  2013;8(1):e53818.
Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.
doi:10.1371/journal.pone.0053818
PMCID: PMC3544762  PMID: 23342011
7.  Proteomics Analysis of the Effects of Cyanate on Chromobacterium violaceum Metabolism 
Genes  2011;2(4):736-747.
Chromobacterium violaceum is a gram-negative betaproteobacterium that has been isolated from various Brazilian ecosystems. Its genome contains the cyn operon, which gives it the ability to metabolize highly toxic cyanate into ammonium and carbon dioxide. We used a proteomics approach to investigate the effects of cyanate on the metabolism of this bacterium. The proteome of cells grown with and without cyanate was compared on 2-D gels. Differential spots were digested and identified by mass spectrometry. The bacterium was able to grow at concentrations of up to 1 mM cyanate. Eighteen spots were differentially expressed in the presence of cyanate, of which 16 were downregulated and only two were upregulated. An additional 12 spots were detected only in extracts of cells unexposed to cyanate, and one was expressed only by the exposed cells. Fourteen spots were identified, corresponding to 13 different proteins. We conclude that cyanate promotes expression of enzymes that combat oxidative stress and represses enzymes of the citric acid cycle, strongly affecting the energetic metabolism of the cell. Other proteins that were under-expressed in bacteria exposed to cyanate are involved in amino-acid metabolism or are hypothetical proteins, demonstrating that cyanate also affects expression of genes that are not part of the cyn operon.
doi:10.3390/genes2040736
PMCID: PMC3927592  PMID: 24710289
2DE; bacteria; cyanate; mass spectrometry; proteomic
8.  Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae†  
Vasconcelos, Ana Tereza R. | Ferreira, Henrique B. | Bizarro, Cristiano V. | Bonatto, Sandro L. | Carvalho, Marcos O. | Pinto, Paulo M. | Almeida, Darcy F. | Almeida, Luiz G. P. | Almeida, Rosana | Alves-Filho, Leonardo | Assunção, Enedina N. | Azevedo, Vasco A. C. | Bogo, Maurício R. | Brigido, Marcelo M. | Brocchi, Marcelo | Burity, Helio A. | Camargo, Anamaria A. | Camargo, Sandro S. | Carepo, Marta S. | Carraro, Dirce M. | de Mattos Cascardo, Júlio C. | Castro, Luiza A. | Cavalcanti, Gisele | Chemale, Gustavo | Collevatti, Rosane G. | Cunha, Cristina W. | Dallagiovanna, Bruno | Dambrós, Bibiana P. | Dellagostin, Odir A. | Falcão, Clarissa | Fantinatti-Garboggini, Fabiana | Felipe, Maria S. S. | Fiorentin, Laurimar | Franco, Gloria R. | Freitas, Nara S. A. | Frías, Diego | Grangeiro, Thalles B. | Grisard, Edmundo C. | Guimarães, Claudia T. | Hungria, Mariangela | Jardim, Sílvia N. | Krieger, Marco A. | Laurino, Jomar P. | Lima, Lucymara F. A. | Lopes, Maryellen I. | Loreto, Élgion L. S. | Madeira, Humberto M. F. | Manfio, Gilson P. | Maranhão, Andrea Q. | Martinkovics, Christyanne T. | Medeiros, Sílvia R. B. | Moreira, Miguel A. M. | Neiva, Márcia | Ramalho-Neto, Cicero E. | Nicolás, Marisa F. | Oliveira, Sergio C. | Paixão, Roger F. C. | Pedrosa, Fábio O. | Pena, Sérgio D. J. | Pereira, Maristela | Pereira-Ferrari, Lilian | Piffer, Itamar | Pinto, Luciano S. | Potrich, Deise P. | Salim, Anna C. M. | Santos, Fabrício R. | Schmitt, Renata | Schneider, Maria P. C. | Schrank, Augusto | Schrank, Irene S. | Schuck, Adriana F. | Seuanez, Hector N. | Silva, Denise W. | Silva, Rosane | Silva, Sérgio C. | Soares, Célia M. A. | Souza, Kelly R. L. | Souza, Rangel C. | Staats, Charley C. | Steffens, Maria B. R. | Teixeira, Santuza M. R. | Urmenyi, Turan P. | Vainstein, Marilene H. | Zuccherato, Luciana W. | Simpson, Andrew J. G. | Zaha, Arnaldo
Journal of Bacteriology  2005;187(16):5568-5577.
This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.
doi:10.1128/JB.187.16.5568-5577.2005
PMCID: PMC1196056  PMID: 16077101

Results 1-8 (8)