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Identification of new proteins related with cisplatin resistance in Saccharomyces cerevisiae

Abstract

The aim of this study is to select a cisplatin-resistant Saccharomyces cerevisiae strain to look for new molecular markers of resistance and the identification of mechanisms/interactions involved. A resistant strain was obtained after 80 days of cisplatin exposure. Then, total protein extraction, purification, and identification were carried out, in wild-type (wt) and resistant strains, by tandem mass spectrometry using a “nano HPLC-ESI-MS/MS” ion trap system. The increase in the exponentially modified protein abundance index (emPAI) (resistant vs wt strains) was calculated to study the increase in protein expression. “Genemania” software (http://www.Genemania.org/) was used to compare the effects, functions, and protein interactions. KEGG tool was used for metabolic pathway analysis. Data are available via ProteomeXchange with identifier PXD020665. The cisplatin-resistant strain showed 2.5 times more resistance than the wt strain for the inhibitory dose 50% (ID50) value (224 μg/ml vs 89.68 μg/ml) and 2.78 times more resistant for the inhibitory dose 90% (ID90) value (735.2 μg/ml vs 264.04 μg/ml). Multiple deregulated proteins were found in the glutathione and carbon metabolism, oxidative phosphorylation, proteasome, glycolysis and gluconeogenesis, glyoxylate metabolism, fatty acid degradation pathway, citric acid cycle, and ribosome. The most overexpressed proteins in the cisplatin-resistant strain were related to growth and metabolism (QCR2, QCR1, ALDH4, ATPB, ATPA, ATPG, and PCKA), cell structure (SCW10), and thermal shock (HSP26). The results suggest that these proteins could be involved in cisplatin resistance. The resistance acquisition process is complex and involves the activation of multiple mechanisms that interact together.

Key points

• Identification of new proteins/genes related to cisplatin resistance

• Increased expression of QCR2/QCR1/ALDH4/ATPB/ATPA/SCW10/HSP26/ATPG and PCKA proteins

• Multiple molecular mechanisms that interact together are involved in resistance

Graphical abstract

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Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al. 2019) partner repository with the dataset identifier PXD020665.

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Acknowledgements

We express our gratitude to Dr Anna A. Friedl (Department of Radiation Oncology, Ludwig-Maximilians-Universität München, Munich, Germany) for kindly providing the yeast strain. We thank Ms. L. Gil Carmona (University of Málaga, Spain) for her technical assistance in yeast culture. Thanks to Kanehisa Laboratories for permission to reproduce the images generated with KEGG pathway enrichment analysis tool.

Funding

This work was supported by the “Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI); Junta de Andalucía”, code CTS-181.

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Contributions

MJRG conceived, designed, and supervised the study. AMBM, SMS, CC, BLD, and FSP conducted the experiments. AMBM, SMS, CC, BLD, FSP, and MJRG analyzed the data. AMBM, CC, and MJRG designed and generated the figures. AMBM, CC, and MJRG wrote the manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to Miguel J. Ruiz-Gómez.

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Permission was obtained from Kanehisa Laboratories to reproduce the images generated with KEGG pathway enrichment analysis tool.

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Burgos-Molina, A.M., Mercado-Sáenz, S., Cárdenas, C. et al. Identification of new proteins related with cisplatin resistance in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 105, 1965–1977 (2021). https://doi.org/10.1007/s00253-021-11137-w

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  • DOI: https://doi.org/10.1007/s00253-021-11137-w

Keywords

  • Yeast
  • S. cerevisiae
  • Proteomics
  • Cisplatin
  • Resistance