Comprehensive proteomic analysis of <i>Penicillium verrucosum</i>

Long-term exposures to environmental toxicants and endogenous electrophiles are causative factors for human diseases including cancer. DNA adducts reflect the internal exposure to genotoxicants and can serve as biomarkers for risk assessment. Liquid chromatography-multistage mass spectrometry (LC-MSn) is the most common method for biomonitoring DNA adducts, generally targeting single exposures and measuring up to several adducts. However, the data often provide limited evidence for a role of a chemical in the etiology of cancer. An “untargeted” method is required that captures global exposures to chemicals, by simultaneously detecting their DNA adducts in the genome; some of which may induce cancer-causing mutations. We established a wide selected ion monitoring tandem mass spectrometry (Wide-SIM/MS2) screening method utilizing ultra-performance-LC nanoelectrospray ionization Orbitrap MSn with on-line trapping to enrich bulky, non-polar adducts. Wide-SIM scan events are followed by MS2 scans to screen for modified nucleosides by co-eluting peaks containing precursor and fragment ions differing by -116.0473 Da, attributed to the neutral loss of deoxyribose. Wide-SIM/MS2 was shown to be superior in sensitivity, specificity, and breadth of adduct coverage to other tested adductomic methods with detection possible at adduct levels as low as 4 per 109 nucleotides. Wide-SIM/MS2 data can be analyzed in a “targeted” fashion by generation of extracted ion chromatograms or in an “untargeted” fashion where a chromatographic peak-picking algorithm can be used to detect putative DNA adducts. Wide-SIM/MS2 successfully detected DNA adducts, derived from chemicals in the diet and traditional medicines and from lipid peroxidation products, in human prostate and renal specimens.

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“…SWATH has been successfully applied to qualitative and quantitative analyses of proteomics. 35,36 and metabolomics. 37,38 …”

Section: Introductionmentioning

confidence: 99%

Data-Independent Mass Spectrometry Approach for Screening and Identification of DNA Adducts

2017

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“…The use of proteomics as a novel tool in aflatoxin research has been reviewed [ 159 ]. There are many factors that influence mycotoxin biosynthesis such as fungal species, host plants, nutritional and environmental signals [ 160 ]. Nöbauer and co-authors were able to provide a comprehensive protein identification for P. verrucosum by using shotgun proteomics [ 160 ].…”

Section: Proteomics Approachmentioning

confidence: 99%

“…There are many factors that influence mycotoxin biosynthesis such as fungal species, host plants, nutritional and environmental signals [ 160 ]. Nöbauer and co-authors were able to provide a comprehensive protein identification for P. verrucosum by using shotgun proteomics [ 160 ]. They were able to get further information about the role of adaptive changes on fungal physiology that effects secondary metabolite production [ 160 ].…”

Section: Proteomics Approachmentioning

confidence: 99%

“…Nöbauer and co-authors were able to provide a comprehensive protein identification for P. verrucosum by using shotgun proteomics [ 160 ]. They were able to get further information about the role of adaptive changes on fungal physiology that effects secondary metabolite production [ 160 ]. Additionally, drought stress and preharvest aflatoxin contamination on the groundnuts ( Arachis hypogaea L.) also has been reviewed recently concluding that more research is required to investigate the genes that related to resistance associated proteins [ 161 ].…”

Section: Proteomics Approachmentioning

confidence: 99%

“…Additionally, it would enable the identification and characterisation of plant and fungal factors that can impact mycotoxin contamination. Recognition of this important aspect has been highlighted by the research, education and economics information system (United States Department of Agriculture, USDA), which has started a project using genomic and metabolomics approaches for the detection and control of mycotoxins on corn [ 160 ]. The project is funded until 2020 and aims to develop a strategy to control mycotoxin contamination by using omics tools.…”

Section: The Current Status Of Omics Studies and Future Opportunitmentioning

confidence: 99%

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Current Status and Future Opportunities of Omics Tools in Mycotoxin Research

Eshelli

Qader

Jambi

et al. 2018

Toxins

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Mycotoxins are toxic secondary metabolites of low molecular weight produced by filamentous fungi, such as Aspergillus, Fusarium, and Penicillium spp. Mycotoxins are natural contaminants of agricultural commodities and their prevalence may increase due to global warming. Dangerous mycotoxins cause a variety of health problems not only for humans, but also for animals. For instance, they possess carcinogenic, immunosuppressive, hepatotoxic, nephrotoxic, and neurotoxic effects. Hence, various approaches have been used to assess and control mycotoxin contamination. Significant challenges still exist because of the complex heterogeneous nature of food composition. The potential of combined omics approaches such as metabolomics, genomics, transcriptomics, and proteomics would contribute to our understanding about pathogen fungal crosstalk as well as strengthen our ability to identify, isolate, and characterise mycotoxins pre and post-harvest. Multi-omics approaches along with advanced analytical tools and chemometrics provide a complete annotation of such metabolites produced before/during the contamination of crops. We have assessed the merits of these individual and combined omics approaches and their promising applications to mitigate the issue of mycotoxin contamination. The data included in this review focus on aflatoxin, ochratoxin, and patulin and would be useful as benchmark information for future research.

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