1887

Abstract

RHA1 is able to degrade toxic compounds and accumulate high amounts of triacylglycerols (TAG) upon nitrogen starvation. These NADPH-dependent processes are essential for the adaptation of rhodococci to fluctuating environmental conditions. In this study, we used an MS-based, label-free and quantitative proteomic approach to better understand the integral response of RHA1 to the presence of methyl viologen (MV) in relation to the synthesis and accumulation of TAG. The addition of MV promoted a decrease of TAG accumulation in comparison to cells cultivated under nitrogen-limiting conditions in the absence of this pro-oxidant. Proteomic analyses revealed that the abundance of key proteins of fatty acid biosynthesis, the Kennedy pathway, glyceroneogenesis and methylmalonyl-CoA pathway, among others, decreased in the presence of MV. In contrast, some proteins involved in lipolysis and β-oxidation of fatty acids were upregulated. Some metabolic pathways linked to the synthesis of NADPH remained activated during oxidative stress as well as under nitrogen starvation conditions. Additionally, exposure to MV resulted in the activation of complete antioxidant machinery comprising superoxide dismutases, catalases, mycothiol biosynthesis, mycothione reductase and alkyl hydroperoxide reductases, among others. Our study suggests that oxidative stress response affects TAG accumulation under nitrogen-limiting conditions through programmed molecular mechanisms when both stresses occur simultaneously.

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2017-03-01
2019-12-11
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References

  1. Hand S, Wang B, Chu KH. Biodegradation of 1,4-dioxane: effects of enzyme inducers and trichloroethylene. Sci Total Environ 2015;520:154–159 [CrossRef][PubMed]
    [Google Scholar]
  2. Sainsbury PD, Hardiman EM, Ahmad M, Otani H, Seghezzi N et al. Breaking down lignin to high-value chemicals: the conversion of lignocellulose to vanillin in a gene deletion mutant of Rhodococcus jostii RHA1. ACS Chem Biol 2013;8:2151–2156 [CrossRef][PubMed]
    [Google Scholar]
  3. Takeda H, Shimodaira J, Yukawa K, Hara N, Kasai D et al. Dual two-component regulatory systems are involved in aromatic compound degradation in a polychlorinated-biphenyl degrader, Rhodococcus jostii RHA1. J Bacteriol 2010;192:4741–4751 [CrossRef][PubMed]
    [Google Scholar]
  4. Hernández MA, Mohn WW, Martínez E, Rost E, Alvarez AF et al. Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism. BMC Genomics 2008;9:600 [CrossRef][PubMed]
    [Google Scholar]
  5. Alvarez HM. Triacylglycerol and wax ester-accumulating machinery in prokaryotes. Biochimie 2016;120:28–39 [CrossRef][PubMed]
    [Google Scholar]
  6. Urbano SB, di Capua C, Cortez N, Farías ME, Alvarez HM. Triacylglycerol accumulation and oxidative stress in Rhodococcus species: differential effects of pro-oxidants on lipid metabolism. Extremophiles 2014;18:375–384 [CrossRef][PubMed]
    [Google Scholar]
  7. Dávila Costa JS, Herrero OM, Alvarez HM, Leichert L. Label-free and redox proteomic analyses of the triacylglycerol-accumulating Rhodococcus jostii RHA1. Microbiology 2015;161:593–610 [CrossRef][PubMed]
    [Google Scholar]
  8. Dávila Costa JS, Kothe E, Abate CM, Amoroso MJ. Unraveling the Amycolatopsis tucumanensis copper-resistome. Biometals 2012;25:905–917 [CrossRef][PubMed]
    [Google Scholar]
  9. El Shafey HM, Ghanem S. Regulation of expression of sodA and msrA genes of Corynebacterium glutamicum in response to oxidative and radiative stress. Genet Mol Res 2015;14:2104–2117 [CrossRef][PubMed]
    [Google Scholar]
  10. Nakajima S, Satoh Y, Yanashima K, Matsui T, Dairi T. Ergothioneine protects Streptomyces coelicolor A3(2) from oxidative stresses. J Biosci Bioeng 2015;120:294–298 [CrossRef]
    [Google Scholar]
  11. Sharp JD, Singh AK, Park ST, Lyubetskaya A, Peterson MW et al. Comprehensive definition of the SigH regulon of Mycobacterium tuberculosis reveals transcriptional control of diverse stress responses. PLoS One 2016;11:e0152145 [CrossRef][PubMed]
    [Google Scholar]
  12. Alvarez HM, Silva RA, Cesari AC, Zamit AL, Peressutti SR et al. Physiological and morphological responses of the soil bacterium Rhodococcus opacus strain PD630 to water stress. FEMS Microbiol Ecol 2004;50:75–86 [CrossRef][PubMed]
    [Google Scholar]
  13. Goordial J, Raymond-Bouchard I, Zolotarov Y, de Bethencourt L, Ronholm J et al. Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica. FEMS Microbiol Ecol 2016;92: [CrossRef][PubMed]
    [Google Scholar]
  14. Leblanc JC, Gonçalves ER, Mohn WW. Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 2008;74:2627–2636 [CrossRef][PubMed]
    [Google Scholar]
  15. Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014;14:547–565 [CrossRef][PubMed]
    [Google Scholar]
  16. Liu X, Hu Y, Pai PJ, Chen D, Lam H. Label-free quantitative proteomics analysis of antibiotic response in Staphylococcus aureus to oxacillin. J Proteome Res 2014;13:1223–1233 [CrossRef][PubMed]
    [Google Scholar]
  17. Müller JE, Litsanov B, Bortfeld-Miller M, Trachsel C, Grossmann J et al. Proteomic analysis of the thermophilic methylotroph Bacillus methanolicus MGA3. Proteomics 2014;14:725–737 [CrossRef][PubMed]
    [Google Scholar]
  18. Schlegel HG, Kaltwasser H, Gottschalk G. [A submersion method for culture of hydrogen-oxidizing bacteria: growth physiological studies]. Arch Mikrobiol 1961;38:209–222[PubMed][CrossRef]
    [Google Scholar]
  19. Alvarez HM, Kalscheuer R, Steinbüchel A. Accumulation and mobilization of storage lipids by Rhodococcus opacus PD630 and Rhodococcus ruber NCIMB 40126. Appl Microbiol Biotechnol 2000;54:218–223 [CrossRef][PubMed]
    [Google Scholar]
  20. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008;26:1367–1372 [CrossRef][PubMed]
    [Google Scholar]
  21. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 2011;10:1794–1805 [CrossRef][PubMed]
    [Google Scholar]
  22. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000;302:205–217 [CrossRef][PubMed]
    [Google Scholar]
  23. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195–202 [CrossRef][PubMed]
    [Google Scholar]
  24. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008;9:40 [CrossRef][PubMed]
    [Google Scholar]
  25. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 2015;10:845–858 [CrossRef][PubMed]
    [Google Scholar]
  26. Amara S, Seghezzi N, Otani H, Diaz-Salazar C, Liu J et al. Characterization of key triacylglycerol biosynthesis processes in rhodococci. Sci Rep 2016;6:24985 [CrossRef][PubMed]
    [Google Scholar]
  27. Hernández MA, Arabolaza A, Rodríguez E, Gramajo H, Alvarez HM. The atf2 gene is involved in triacylglycerol biosynthesis and accumulation in the oleaginous Rhodococcus opacus PD630. Appl Microbiol Biotechnol 2013;97:2119–2130 [CrossRef][PubMed]
    [Google Scholar]
  28. Bidaud P, Hébert L, Barbey C, Appourchaux AC, Torelli R et al. Rhodococcus equi's extreme resistance to hydrogen peroxide is mainly conferred by one of its four catalase genes. PLoS One 2012;7:e42396 [CrossRef][PubMed]
    [Google Scholar]
  29. Newton GL, Buchmeier N, Fahey RC. Biosynthesis and functions of mycothiol, the unique protective thiol of Actinobacteria. Microbiol Mol Biol Rev 2008;72:471–494 [CrossRef][PubMed]
    [Google Scholar]
  30. Rawat M, Av-Gay Y. Mycothiol-dependent proteins in actinomycetes. FEMS Microbiol Rev 2007;31:278–292 [CrossRef][PubMed]
    [Google Scholar]
  31. Ung KSE, Av-Gay Y. Mycothiol-dependent mycobacterial response to oxidative stress. FEBS Lett 2006;580:2712–2716 [CrossRef]
    [Google Scholar]
  32. Dosanjh M, Newton GL, Davies J. Characterization of a mycothiol ligase mutant of Rhodococcus jostii RHA1. Res Microbiol 2008;159:643–650 [CrossRef][PubMed]
    [Google Scholar]
  33. Patel MP, Blanchard JS. Expression, purification, and characterization of Mycobacterium tuberculosis mycothione reductase. Biochemistry 1999;38:11827–11833 [CrossRef][PubMed]
    [Google Scholar]
  34. Patel MP, Blanchard JS. Mycobacterium tuberculosis mycothione reductase: pH dependence of the kinetic parameters and kinetic isotope effects. Biochemistry 2001;40:5119–5126 [CrossRef][PubMed]
    [Google Scholar]
  35. Argyrou A, Blanchard JS. Flavoprotein disulfide reductases: advances in chemistry and function. Prog Nucleic Acid Res Mol Biol 2004;78:89–142 [CrossRef][PubMed]
    [Google Scholar]
  36. Bryk R, Lima CD, Erdjument-Bromage H, Tempst P, Nathan C. Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein. Science 2002;295:1073–1077 [CrossRef][PubMed]
    [Google Scholar]
  37. Dietz K-J. Peroxiredoxins in plants and cyanobacteria. Antioxidants & Redox Signaling 2011;15:1129–1159 [CrossRef]
    [Google Scholar]
  38. Guimarães BG, Souchon H, Honoré N, Saint-Joanis B, Brosch R et al. Structure and mechanism of the alkyl hydroperoxidase AhpC, a key element of the Mycobacterium tuberculosis defense system against oxidative stress. J Biol Chem 2005;280:25735–25742 [CrossRef][PubMed]
    [Google Scholar]
  39. Ermolenko DN, Makhatadze GI. Bacterial cold-shock proteins. Cell Mol Life Sci 2002;59:1902–1913 [CrossRef][PubMed]
    [Google Scholar]
  40. Kitagawa M, Matsumura Y, Tsuchido T. Small heat shock proteins, IbpA and IbpB, are involved in resistances to heat and superoxide stresses in Escherichia coli. FEMS Microbiol Lett 2000;184:165–171 [CrossRef][PubMed]
    [Google Scholar]
  41. Kvint K, Nachin L, Diez A, Nyström T. The bacterial universal stress protein: function and regulation. Curr Opin Microbiol 2003;6:140–145 [CrossRef][PubMed]
    [Google Scholar]
  42. Alix JH, Guérin MF. Mutant DnaK chaperones cause ribosome assembly defects in Escherichia coli. Proc Natl Acad Sci USA 1993;90:9725–9729 [CrossRef][PubMed]
    [Google Scholar]
  43. Gragerov A, Nudler E, Komissarova N, Gaitanaris GA, Gottesman ME et al. Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia coli. Proc Natl Acad Sci USA 1992;89:10341–10344 [CrossRef][PubMed]
    [Google Scholar]
  44. Liberek K, Galitski TP, Zylicz M, Georgopoulos C. The DnaK chaperone modulates the heat shock response of Escherichia coli by binding to the Sigma 32 transcription factor. Proc Natl Acad Sci USA 1992;89:3516–3520[PubMed][CrossRef]
    [Google Scholar]
  45. Fisher SH. Regulation of nitrogen metabolism in Bacillus Subtilis: vive la différence! Mol Microbiol. 1999;32223–232
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