RESUMO
Two-dimensional gel electrophoresis (2D-GE) is an indispensable technique for the study of proteomes of biological systems, providing an assessment of changes in protein abundance under various experimental conditions. However, due to the complexity of 2D-GE gels, there is no systematic, automatic, and reproducible protocol for image analysis and specific implementations are required for each context. In addition, practically all available solutions are commercial, which implies high cost and little flexibility to modulate the parameters of the algorithms. Using the bacterial strain, Pseudomonas aeruginosaAG1 as a model, we obtained images from 2D-GE of periplasmic protein profiles when the strain was exposed to multiple conditions, including antibiotics. Then, we proceeded to implement and evaluate an image analysis protocol with open-source software, CellProfiler. First, a preprocessing step included a bUnwarpJ-Image pipeline for aligning 2D-GE images. Then, using CellProfiler, we standardized two pipelines for spots identification. Total spots recognition was achieved using segmentation by intensity, whose performance was evaluated when compared with a reference protocol. In a second pipeline with the same program, differential identification of spots was addressed when comparing pairs of protein profiles. Due to the characteristics of the programs used, our workflow can automatically analyze a large number of images and it is parallelizable, which is an advantage with respect to other implementations. Finally, we compared six experimental conditions of bacterial strain in the presence or absence of antibiotics, determining protein profiles relationships by applying clustering algorithms PCA (Principal Components Analysis) and HC (Hierarchical Clustering).
Assuntos
Eletroforese em Gel Bidimensional/métodos , Processamento de Imagem Assistida por Computador/métodos , Proteômica/métodos , Pseudomonas aeruginosa/citologia , Humanos , Proteômica/instrumentaçãoRESUMO
C. difficile induces antibiotic-associated diarrhea due to the action of two secreted toxins, TcdA and TcdB. A considerable range of virulence among C. difficile strains has been widely reported. During a hospital outbreak, 46 isolates were collected that belonged to different genotypes. Of those, the majority corresponded to two virulent strains, the globally distributed Sequence Type 1 (ST1)_North American Pulsotype 1 (NAP1) and the endemic ST54_NAPCR1 genotypes, respectively. Whereas the virulence of the latter has been attributed to increased secretion of toxins and production of a highly cytotoxic TcdB, these characteristics do not explain the increased lethality of the former. We undertook a proteomic comparative approach of the isolates participating in the outbreak to look for proteins present in the exoproteome of the ST1_NAP1and ST54_NAPCR1 strains. We used a low virulent ST2_NAP4 strain isolated also in the outbreak as control. Dendrograms constructed using the exoproteomes of the strains were very similar to those created using genomic information, suggesting an association between secreted proteins and relative virulence of the strains. By 2D electrophoresis and mass spectrometry it was found that approximately half of the proteins are shared among strains of different genotypes. From the identified proteins, the surface-located SlpA draw our attention due to its detection in ST54_NAPCR1 exoproteomes. Biochemical analysis indicated that the processing of SlpA is different in the ST54_NAPCR1 strain and confirmed that this strain secretes more SlpA than its counterparts. Furthermore, SlpA from the ST54_NAPCR1 strain exerted an increased proinflammatory activity. Altogether, these results indicate that the exoproteome composition correlates with the C. difficile genotype and suggest that particular proteins secreted by some strains could synergize with the effects of TcdA and TcdB increasing their virulence.
Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Clostridioides difficile/genética , Clostridioides difficile/metabolismo , Infecções por Clostridium/microbiologia , Filogenia , Proteômica , Clostridioides difficile/classificação , Enterotoxinas/genética , Genoma Bacteriano , Genômica/métodos , Genótipo , Humanos , Tipagem de Sequências Multilocus , Proteômica/métodos , VirulênciaRESUMO
Clostridium difficile strains within the hypervirulent clade 2 are responsible for nosocomial outbreaks worldwide. The increased pathogenic potential of these strains has been attributed to several factors but is still poorly understood. During a C. difficile outbreak, a strain from this clade was found to induce a variant cytopathic effect (CPE), different from the canonical arborizing CPE. This strain (NAP1V) belongs to the NAP1 genotype but to a ribotype different from the epidemic NAP1/RT027 strain. NAP1V and NAP1 share some properties, including the overproduction of toxins, the binary toxin, and mutations in tcdC. NAP1V is not resistant to fluoroquinolones, however. A comparative analysis of TcdB proteins from NAP1/RT027 and NAP1V strains indicated that both target Rac, Cdc42, Rap, and R-Ras but only the former glucosylates RhoA. Thus, TcdB from hypervirulent clade 2 strains possesses an extended substrate profile, and RhoA is crucial for the type of CPE induced. Sequence comparison and structural modeling revealed that TcdBNAP1 and TcdBNAP1V share the receptor-binding and autoprocessing activities but vary in the glucosyltransferase domain, consistent with the different substrate profile. Whereas the two toxins displayed identical cytotoxic potencies, TcdBNAP1 induced a stronger proinflammatory response than TcdBNAP1V as determined in ex vivo experiments and animal models. Since immune activation at the level of intestinal mucosa is a hallmark of C. difficile-induced infections, we propose that the panel of substrates targeted by TcdB is a determining factor in the pathogenesis of this pathogen and in the differential virulence potential seen among C. difficile strains.