Most of the mitochondrial proteome originates from nuclear genes and is transported into the mitochondria after synthesis in the cytosol. Complex machineries which maintain the specificity of protein import and sorting include the TIM23 translocase responsible for the transfer of precursor proteins into the matrix, and the mitochondrial intermembrane space import and assembly (MIA) machinery required for the biogenesis of intermembrane space proteins. Dysfunction of mitochondrial protein sorting pathways results in diminishing specific substrate proteins, followed by systemic pathology of the organelle and organismal death1,2,3,4. The cellular responses caused by accumulation of mitochondrial precursor proteins in the cytosol are mainly unknown. Here we present a comprehensive picture of the changes in the cellular transcriptome and proteome in response to a mitochondrial import defect and precursor over-accumulation stress. Pathways were identified that protect the cell against mitochondrial biogenesis defects by inhibiting protein synthesis and by activation of the proteasome, a major machine for cellular protein clearance. Proteasomal activity is modulated in proportion to the quantity of mislocalized mitochondrial precursor proteins in the cytosol. We propose that this type of unfolded protein response activated by mistargeting of proteins (UPRam) is beneficial for the cells. UPRam provides a means for buffering the consequences of physiological slowdown in mitochondrial protein import and for counteracting pathologies that are caused or contributed by mitochondrial dysfunction.

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Data deposits

RNA-seq data have been submitted to the ArrayExpress database under accession number E-MTAB-3588. The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001495.


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We thank A. Fergin, B. Knapp, B. Guiard, W. Voos, M. Glickman, A. Gornicka, A. Loniewska-Lwowska, and T. Wegierski for materials, experimental assistance and discussions. Deposition of the data to the ProteomeXchange Consortium is supported by PRIDE Team, EBI. Research in the B.W. laboratory is supported by the Deutsche Forschungsgemeinschaft and the Excellence Initiative of the German Federal & State Governments (EXC 294 BIOSS). Research in the A.C. laboratory was supported by Foundation for Polish Science – Welcome Programme co-financed by the EU within the European Regional Development Fund (L.W., M.E.S. and E.J.), National Science Centre grants 2011/02/B/NZ2/01402 (L.W., U.T. and A.V.) and 2013/11/B/NZ3/00974 (P.C.) and Ministerial Ideas Plus schema 000263 (E.J.). L.W. and U.T. were also supported by National Science Centre grant 2013/08/T/NZ1/00770 and Swiss National Science Foundation postdoctoral fellowship (PP300P3-147899), respectively. P.B. was supported by the National Science Centre grant 2013/11/D/NZ1/02294.

Author information

Author notes

    • Sebastian Wiese

    Present address: Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, D-89081 Ulm, Germany.

    • Lidia Wrobel
    •  & Ulrike Topf

    These authors contributed equally to this work.


  1. International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland

    • Lidia Wrobel
    • , Ulrike Topf
    • , Piotr Bragoszewski
    • , Malgorzata E. Sztolsztener
    • , Aksana Varabyova
    • , Piotr Chroscicki
    • , Elzbieta Januszewicz
    •  & Agnieszka Chacinska
  2. Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany

    • Sebastian Wiese
    • , Silke Oeljeklaus
    •  & Bettina Warscheid
  3. ZBSA Centre for Biological Systems Analysis, University of Freiburg, D-79104 Freiburg, Germany

    • Sebastian Wiese
    •  & Bettina Warscheid
  4. Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland

    • Maciej Lirski
    • , Seweryn Mroczek
    • , Andrzej Dziembowski
    •  & Marta Koblowska
  5. Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland

    • Seweryn Mroczek
    •  & Andrzej Dziembowski
  6. Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland

    • Marta Koblowska


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P.B. and S.W. are joint second authors. L.W., U.T., P.B., M.E.S., A.V., P.C., S.M. and E.J. performed and analysed biochemical experiments. P.B. and M.L. performed RNA-seq and analyses. S.W. and S.O. performed the mass spectrometric measurements and analyses. A.C., B.W., M.K. and A.D. analysed and supervised the study. A.C and B.W. conceived the project. All authors interpreted the experiments. A.C. wrote the manuscript with the input of other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Bettina Warscheid or Agnieszka Chacinska.

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    Supplementary Information

    This file contains full legends for Supplementary Tables 1-3 and Supplementary images.

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    Supplementary Table 1

    This file contains RNA-Seq analysis of the mia40-4int mutant versus wild-type strain – see Supplementary Information file for full legend.

  2. 2.

    Supplementary Table 2

    This file contains SILAC-based proteomics analysis of mia40-4intS mutant versus wild-type - see Supplementary Information file for full legend.

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    Supplementary Table 3

    This file contains proteins quantified in SILAC-based proteomics in at least two biological replicates - see Supplementary Information file for full legend.

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