PatternLab for proteomics: a tool for differential shotgun proteomics

Carvalho, Paulo C.; Fischer, Juliana de Saldanha da Gama; Chen, Emily I.; Yates, John R.; Barbosa, Valmir C.

doi:10.1186/1471-2105-9-316

Cited by 133 publications

(130 citation statements)

References 30 publications

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“…Statistical comparison between nanoLC-MS/MS detected proteins in different conditions was carried out with the PatternLab program (42). Data were normalized by the total number of spectral counts per replicate and analyzed using the ACFold method with a p value below 0.01 and a minimum fold of 2.…”

Section: Bacteria Andmentioning

confidence: 99%

Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria

Christie-Oleza

Piña-Villalonga

Bosch

et al. 2012

Molecular & Cellular Proteomics

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Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the encoded proteome of these microorganisms could be exported. The ratio of the different protein categories varied in accordance to the ecological distinctness of each strain, a trait reinforced by quantitative proteomics data. Despite the interspecies variations found, the most abundantly detected proteins by shotgun proteomics were from transporter, adhesion, motility, and toxin-like protein categories, defining four different plausible adaptive strategies within the Roseobacter group. In some strains the toxin-secretion strategy was over-represented with repeats-in-toxin-like proteins. Our results show that exoproteomes strongly depend on bacterial trophic strategy and can slightly change because of culture conditions. Simulated natural conditions and the effect of the indigenous microbial community on the exoproteome of Ruegeria pomeroyi DSS-3 were also assayed. Interestingly, we observed a significant depletion of the toxin-like proteins usually secreted by R. pomeroyi DSS-3 when grown in presence of a natural community sampled from a Mediterranean Sea port.

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Section: Bacteria Andmentioning

confidence: 99%

Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria

Christie-Oleza

Piña-Villalonga

Bosch

et al. 2012

Molecular & Cellular Proteomics

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“…Significant variations were assessed using Patternlab software (37), as previously described (12). Supplemental Table S3 reports log 2 (fold change) and p values obtained with the T-fold statistical method adapted for high throughput hypothesis tests (37). A BH-FDR statistical test was calculated to evaluate the global false discovery rate for each comparison.…”

Section: Nanolc-ms/ms Analysis-nanolc-ms/msmentioning

confidence: 99%

Restricting Fermentative Potential by Proteome Remodeling

Clair¹,

Armengaud²,

Duport³

2012

Molecular & Cellular Proteomics

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Pathogenesis hinges on successful colonization of the gastrointestinal (GI) tract by pathogenic facultative anaerobes. The GI tract is a carbohydrate-limited environment with varying oxygen availability and oxidoreduction potential (ORP). How pathogenic bacteria are able to adapt and grow in these varying conditions remains a key fundamental question. Here, we designed a system biologyinspired approach to pinpoint the key regulators allowing Bacillus cereus to survive and grow efficiently under low ORP anoxic conditions mimicking those encountered in the intestinal lumen. We assessed the proteome components using high throughput nanoLC-MS/MS techniques, reconstituted the main metabolic circuits, constructed ⌬ohrA and ⌬ohrR mutants, and analyzed the impacts of ohrA and ohrR disruptions by a novel round of shotgun proteomics. Our study revealed that OhrR and OhrA are crucial to the successful adaptation of B. cereus to the GI tract environment. Specifically, we showed that B. cereus restricts its fermentative growth under low ORP anaerobiosis and sustains efficient aerobic respiratory metabolism, motility, and stress response via OhrRA-dependent proteome remodeling. Finally, our results introduced a new adaptive strategy where facultative anaerobes prefer to restrict their fermentative potential for a long term benefit. Molecular & Cellular Proteomics 11: 10.1074/ mcp.M111.013102, 1-13, 2012.Facultative anaerobes encompass all the major pathogens of the human gastrointestinal (GI) 1 tract. The GI tract poses several challenges for pathogens because it is sliced into distinct niches with different oxygen concentrations and different oxidoreduction potentials (ORP) (1-3). Although much is known about gene expression and metabolism under fully aerobic and high ORP anaerobic condition (4, 5), our knowledge about the physiological impact of low ORP anoxic conditions and the underlying molecular mechanisms is scarce (6).Bacillus cereus is a notorious food-borne pathogenic bacterium. Like the closely related Bacillus anthracis (7,8), it is a recognized agent of GI tract infections (9 -11). The critical step of infection takes place in the small intestine, where B. cereus has to grow and produce virulence factors to induce diarrheal disease (11, 12). Thus, how B. cereus adapts its catabolism and regulates its proteome across the range of physiologically relevant ORP and oxygen availabilities is important for its survival and growth. In B. cereus, anaerobic and aerobic catabolism work through different pathways. In the presence of oxygen, reducing equivalents generated by glycolysis and the TCA cycle (NADH and FADH) are reoxidized by the respiratory chain, resulting in the buildup of a proton motive force and the subsequent synthesis of ATP. Acetate excretion can occur aerobically when carbon flux into the cells exceeds TCA cycle capacity. In the absence of oxygen or other external electron acceptors (such as nitrate), NADH is reoxidized in terminal step fermentative reactions from pyruvate. When grown in pH-controlled ana...

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“…Proteins identified by at least two fully tryptic unique peptides, each with a false positive rate of less than 5%, were considered to be present in the sample. Differential protein expression analysis was performed using the ACfold algorithm as implemented in the PatternLab software suite (37). Spectral counts were normalized using the Row Sigma method of PatternLab (37).…”

Section: Preparation Of Membrane Fractions and Purification Of Biotinmentioning

confidence: 99%

“…Differential protein expression analysis was performed using the ACfold algorithm as implemented in the PatternLab software suite (37). Spectral counts were normalized using the Row Sigma method of PatternLab (37). Proteins were considered differentially expressed if they met the following criteria: 1) a -fold change cutoff of 2.5, 2) an estimated -fold change false discovery rate of less than 0.1, and 3) an ACtest p value of less than 0.01.…”

Section: Preparation Of Membrane Fractions and Purification Of Biotinmentioning

confidence: 99%

“…To search for proteins that are over-represented in highly adherent relative to less adherent strains, spectral counts were normalized to minimize run to run variation and compared between strains using the ACfold algorithm (37). Proteins that exhibited changes in normalized spectral counts that were greater than 2.5-fold and possessed p values from the ACtest of less than 0.01 were considered differentially expressed.…”

Section: Identification Of Membrane Proteins That Are Differentially mentioning

confidence: 99%

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NGALR Is Overexpressed and Regulated by Hypomethylation in Esophageal Squamous Cell Carcinoma

Cui¹,

Shen

et al. 2008

Clinical Cancer Research

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The identification of surface proteins on the plasma membrane of pathogens is of fundamental importance in understanding host-pathogen interactions. Surface proteins of the extracellular parasite Trichomonas are implicated in the initial adherence to mucosal tissue and are likely to play a critical role in the long term survival of this pathogen in the urogenital tract. In this study, we used cell surface biotinylation and multidimensional protein identification technology to identify the surface proteome of six strains of Trichomonas vaginalis with differing adherence capacities to vaginal epithelial cells. A combined total of 411 proteins were identified, and of these, 11 were found to be more abundant in adherent strains relative to less adherent parasites. The mRNA levels of five differentially expressed proteins selected for quantitative RT-PCR analysis mirrored their observed protein levels, confirming their up-regulation in highly adherent strains. As proof of principle and to investigate a possible role in pathogenesis for differentially expressed proteins, gain of function experiments were performed using two novel proteins that were among the most highly expressed surface proteins in adherent strains. Overexpression of either of these proteins, TVAG_244130 or TVAG_166850, in a relatively non-adherent strain increased attachment of transfected parasites to vaginal epithelial cells ϳ2.2-fold. These data support a role in adhesion for these abundant surface proteins. Our analyses demonstrate that comprehensive profiling of the cell surface proteome of different parasite strains is an effective approach to identify potential new adhesion factors as well as other surface molecules that may participate in establishing and maintaining infection by this extracellular pathogen. Molecular & Cellular Proteomics 9:1554 -1566, 2010.

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PatternLab for proteomics: a tool for differential shotgun proteomics

Cited by 133 publications

References 30 publications

Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria

Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria

Restricting Fermentative Potential by Proteome Remodeling

NGALR Is Overexpressed and Regulated by Hypomethylation in Esophageal Squamous Cell Carcinoma

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