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LC–MS/MS proteomic analysis of starved Bacillus subtilis cells overexpressing ribonucleotide reductase (nrdEF): implications in stress-associated mutagenesis

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Abstract

The non-appropriate conditions faced by nutritionally stressed bacteria propitiate error-prone repair events underlying stationary-phase- or stress-associated mutagenesis (SPM). The genetic and molecular mechanisms involved in SPM have been deeply studied but the biochemical aspects of this process have so far been less explored. Previous evidence showed that under conditions of nutritional stress, non-dividing cells of strain B. subtilis YB955 overexpressing ribonucleotide reductase (RNR) exhibited a strong propensity to generate true reversions in the hisC952 (amber), metB5 (ochre) and leuC425 (missense) mutant alleles. To further advance our knowledge on the metabolic conditions underlying this hypermutagenic phenotype, a high-throughput LC–MS/MS proteomic analysis was performed in non-dividing cells of an amino acid-starved strain, deficient for NrdR, the RNR repressor. Compared with the parental strain, the level of 57 proteins was found to increase and of 80 decreases in the NrdR-deficient strain. The proteomic analysis revealed an altered content in proteins associated with the stringent response, nucleotide metabolism, DNA repair, and cell signaling in amino acid-starved cells of the ∆nrdR strain. Overall, our results revealed that amino acid-starved cells of strain B. subtilis ∆nrdR that escape from growth-limiting conditions exhibit a complex proteomic pattern reminiscent of a disturbed metabolism. Future experiments aimed to understand the consequences of disrupting the cell signaling pathways unveiled in this study, will advance our knowledge on the genetic adaptations deployed by bacteria to escape from growth-limiting environments.

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Acknowledgements

This work was supported by the Consejo Nacional de Ciencia y Tecnología (CONACYT; Grants 205744 and 221231) of México and by the University of Guanajuato (Grants 936-2016 and 1090-2016) to M.P-R. Work at K. Wrobel and K. Wrobel laboratory was supported by Grant (CONACyT, 123732). KV. Castro-Cerritos was supported by a scholarship from CONACYT.

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  1. Karla Viridiana Castro-Cerritos and Adolfo Lopez-Torres contributed equally to this work.

Authors and Affiliations

  1. Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico

    Karla Viridiana Castro-Cerritos, Armando Obregón-Herrera & Mario Pedraza-Reyes

  2. Institute of Applied Chemistry, University of Papaloapan, Tuxtepec, Oaxaca, Mexico

    Adolfo Lopez-Torres

  3. Division of Natural and Exact Sciences, Chemistry Department, University of Guanajuato, Guanajuato, Mexico

    Katarzyna Wrobel & Kazimierz Wrobel

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  1. Karla Viridiana Castro-Cerritos
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  2. Adolfo Lopez-Torres
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  3. Armando Obregón-Herrera
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  4. Katarzyna Wrobel
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  5. Kazimierz Wrobel
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Correspondence to Mario Pedraza-Reyes.

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Communicated by M. Kupiec.

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Castro-Cerritos, K.V., Lopez-Torres, A., Obregón-Herrera, A. et al. LC–MS/MS proteomic analysis of starved Bacillus subtilis cells overexpressing ribonucleotide reductase (nrdEF): implications in stress-associated mutagenesis. Curr Genet 64, 215–222 (2018). https://doi.org/10.1007/s00294-017-0722-7

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