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Functional analysis of Rpn4-like proteins from Komagataella (Pichia) pastoris and Yarrowia lipolytica on a genetic background of Saccharomyces cerevisiae

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Abstract

Expression of the Saccharomyces cerevisiae proteasomal genes is regulated coordinately by ScRpn4 transcription factor and its binding site known as PACE. Genomic analysis demonstrates that only Saccharomycetes yeasts carry ScRpn4-orthologous genes and PACE-like elements in the promoters of proteasomal genes. This taxonomic group includes species of biotechnological importance such as Komagataella (Pichia) pastoris and Yarrowia lipolytica. A literature search has failed to identify studies focused on ScRpn4 orthologs of these yeast species. In the present work, using the genetic background of S. cerevisiae, we showed that ScRpn4 orthologs from K. pastoris and Y. lipolytica restore the mRNA levels of proteasomal genes and confer stress tolerance in a S. cerevisiae strain with knockout of the SCRPN4 gene. In other words, these proteins are functionally similar to ScRpn4 of S. cerevisiae.

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Abbreviations

a.a.:

amino acid

HMF:

5-hydroxymethylfurfural

A:

absorbance

PCR:

a polymerase chain reaction

ATP:

adenosine triphosphate

dT:

deoxythymidine

KpRpn4:

a Rpn4-like protein of Komagataella (Pichia) pastoris

MMS:

a methyl methane sulfonate

PACE:

proteasome-associated control element

ScRpn4:

the Rpn4 gene of Saccharomyces cerevisiae

YlRpn4:

a Rpn4-lijek protein of Yarrowia lipolytica

References

  1. Glickman, M.H. and Ciechanover, A., The ubiquitinproteasome proteolytic pathway: destruction for the sake of construction, Physiol. Rev., 2002, vol. 82, pp. 373–428.

    Article  CAS  PubMed  Google Scholar 

  2. Kapranov, A.B., Kuryatova, M.V., Preobrazhenskaya, O.V., Tyutyaeva, V.V., Shtucka, R., Feldmann, H., and Karpov, V.L., Isolation and identification of PACEbinding protein Rpn4, a new transcriptional activator regulating 26S-proteasomal and other genes, Mol. Biol. (Moscow), 2001, vol. 35, pp. 356–364.

    Article  CAS  Google Scholar 

  3. Mannhaupt, G., Schnall, R., Karpov, V., Vetter, I., and Feldmann, H., Rpn4 acts as a transcription factor by binding to pace, a nonamer box found upstream of 26A proteasomal and other genes in yeast, FEBS Lett., 1999, vol. 450, pp. 27–34.

    Article  CAS  PubMed  Google Scholar 

  4. Ju, D., Wang, L., Mao, X., and Xie, Y., Homeostatic regulation of the proteasome via an Rpn4-dependent feedback circuit, Biochem. Biophys. Res. Commun., 2004, vol. 321, pp. 51–57.

    Article  CAS  PubMed  Google Scholar 

  5. Xie, Y and Varshavsky, A., Rpn4 is a ligand, substrate and transcriptional regulator of the 26S proteasome: a negative feedback circuit, Proc. Natl. Acad. Sci. USA, 2001, vol. 98, pp. 3056–3061.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Owsianik, G., Balzil, L., and Ghislain, M., Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae, Mol. Microbiol., 2002, vol. 43, pp. 1295–1308.

    Article  CAS  PubMed  Google Scholar 

  7. Teixeira, M.C., Dias, P.J., Simoes, T., and Sa-Correia, I., Yeast adaptation to mancozeb involves the up-regulation of FLR1 under the coordinate control of Yap1, Rpn4, Pdr3, and Yrrl, Biochem. Biophys. Res. Commun., 2008, vol. 367, pp. 249–255.

    Article  CAS  PubMed  Google Scholar 

  8. London, M., Keck, B.I., Ramos, P.C., and Dohmen, R.J., Regulatory mechanisms controlling biogenesis of ubiquitin and the proteasome, FEBS Lett., 2004, vol. 567, pp. 259–264.

    Article  CAS  PubMed  Google Scholar 

  9. Mannhaupt, G. and Feldann, H., Genomic evolution of the proteasome system among hemiascomycetous yeasts, J. Mol. Evol., 2007, vol. 65, pp. 529–540.

    Article  CAS  PubMed  Google Scholar 

  10. Ahmad, M., Hirz, M., Pichler, H., and Schwab, H., Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production, Appl. Microbiol. Biotechnol., 2014, vol. 12, pp. 5301–5317.

    Article  Google Scholar 

  11. Goncalves, F.A., Colen, G., and Takahashi, J.A., Yarrowia lipolytica and its multiple applications in the biotechnological industry, Sci. World J., 2014, p. 476207.

    Google Scholar 

  12. Gietz, D., St.-Jean, A., Woods, R.A., and Schiestl, R.H., Improved method for high efficiency transformation of intact yeast cells, Nucleic Acids Res., 1992, vol. 20, p. 1425.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Karpov, D.S., Spasskaya, D.S., Tutyaeva, V.V., Mironov, A.S., and Karpov, V.L., Proteasome inhibition enhances resistance to DNA damage via upregulation of Rpn4-dependent DNA repair genes, FEBS Lett., 2013, vol. 587, pp. 3108–3114.

    Article  CAS  PubMed  Google Scholar 

  14. Spasskaya, D.S., Karpov, D.S., and Karpov, V.L., Escherichia coli Dam-methylase as a molecular tool for mapping binding sites of the yeast transcription factor Rpn4, Mol. Biol. (Moscow), 2011, vol. 45, pp. 591–599.

    Article  CAS  Google Scholar 

  15. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Smith, J.A., Seidman, J.G., and Struhl, K., Current Protocols in Molecular Biology, New York: John Wiley and Sons, 1998.

    Google Scholar 

  16. Schmitt, M.E., Brown, T.A., and Trumpower, B.L., A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae, Nucleic Acids Res., 1990, vol. 18, pp. 3091–3092.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Gasch, A.P., Moses, A.M., Chiang, D.Y., Fraser, H.B., Berardini, M., and Eisen, M.B., Conservation and evolution of cis-regulatory systems in ascomycete fungi, PLoS Biol., 2004, vol. 2, p. e398.

    Article  PubMed Central  PubMed  Google Scholar 

  18. Vermitsky, J.-P., Earhart, K.D., Smith, W.L., Homayouni, R., Edlind, T.D., and Rogers, P.D., Pdr1 regulates multidrug resistance in Candida glabrata: gene disruption and genome-wide expression studies, Mol. Microbiol., 2006, vol. 61, pp. 704–722.

    Article  CAS  PubMed  Google Scholar 

  19. Enjalbert, B., Smith, D.A., Cornell, M.J., Alam, I., Nicholls, S., Brown, A.J.P., and Quinn, J., Role of the hog1 stress-activated protein kinase in the global transcriptional response to stress in the fungal pathogen Candida albicans, Mol. Biol. Cell, 2006, vol. 17, pp. 1018–1032.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Ha, S.W., Ju, D., and Xie, Y., The N-terminal domain of Rpn4 serves as a portable ubiquitin-independent degron and is recognized by specific 19S RP subunits, Biochem. Biophys. Res. Commun., 2012, vol. 419, pp. 226–231.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. McWilliam, H., Li, W., Uludag, M., Squizzato, S., Park, Y.M., Buso, N., Cowley, A.P., and Lopez, R., Analysis tool web services from the EMBL-EBI, Nucleic Acids Res., 2013, vol. 41, pp. W597–W600.

    Article  PubMed Central  PubMed  Google Scholar 

  22. Karpov, D.S., Tutyaeva, V.V., and Karpov, V.L., Mapping of yeast Rpn4p transactivation domains, FEBS Lett., 2008, vol. 582, pp. 3459–3464.

    Article  PubMed  Google Scholar 

  23. Gonzalez-Ramos, D., van den Broek, M., van Maris, A.J., Pronk, J.T., and Daran, J.M., Genome-scale analyses of butanol tolerance in Saccharomyces cerevisiae reveal an essential role of protein degradation, Biotechnol. Biofuels, 2013, vol. 6, p. 48.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Zaki, A.M., Wimalasena, T.T., and Grretham, D., Phenotypic characterization of Saccharomyces spp. for tolerance to 1-butanol, J. Ind. Microbiol. Biotechnol., 2014, vol. 41, pp. 1627–1636.

    Article  CAS  PubMed  Google Scholar 

  25. Ma, M. and Liu, Z.L., Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae, BMC Genomics, vol. 11, p. 660.

  26. Larsson, S., Palmqvist, E., Hahn-Hagerdal, B., Tengborg, C., Stenberg, K., Zacchi, G., and Nilvebrant, N.O., The generation of inhibitors during dilute acid hydrolysis of softwood, Enz. Microb. Technol., 1999, vol. 24, pp. 151–159.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Engelhardt Institute for Molecular Biology, Moscow, 119991, Russia

    E. N. Grineva, A. T. Leinsoo, D. S. Spasskaya, D. S. Karpov & V. L. Karpov

  2. State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia

    D. S. Spasskaya

  3. Orekhovich Research Institute for Biomedical Chemistry, Moscow, 119121, Russia

    D. S. Karpov

Authors
  1. E. N. Grineva
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  2. A. T. Leinsoo
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  3. D. S. Spasskaya
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  4. D. S. Karpov
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  5. V. L. Karpov
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Correspondence to A. T. Leinsoo.

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Original Russian Text © E.N. Grineva, A.T. Leinsoo, D.S. Spasskaya, D.S. Karpov, V.L. Karpov, 2014, published in Biotekhnologiya, 2014, No. 6, pp. 8–17.

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Grineva, E.N., Leinsoo, A.T., Spasskaya, D.S. et al. Functional analysis of Rpn4-like proteins from Komagataella (Pichia) pastoris and Yarrowia lipolytica on a genetic background of Saccharomyces cerevisiae . Appl Biochem Microbiol 51, 757–765 (2015). https://doi.org/10.1134/S0003683815070029

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  • DOI: https://doi.org/10.1134/S0003683815070029

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