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Control of retrograde signalling by protein import and cytosolic folding stress

Abstract

Communication between organelles and the nucleus is essential for fitness and survival. Retrograde signals are cues emitted from the organelles to regulate nuclear gene expression. GENOMES UNCOUPLED1 (GUN1), a protein of unknown function, has emerged as a central integrator, participating in multiple retrograde signalling pathways that collectively regulate the nuclear transcriptome. Here, we show that GUN1 regulates chloroplast protein import through interaction with the import-related chaperone cpHSC70-1. We demonstrated that overaccumulation of unimported precursor proteins (preproteins) in the cytosol causes a GUN phenotype in the wild-type background and enhances the GUN phenotype of the gun1 mutant. Furthermore, we identified the cytosolic HSP90 chaperone complex, induced by overaccumulated preproteins, as a central regulator of photosynthetic gene expression that determines the expression of the GUN phenotype. Taken together, our results suggest a model in which protein import capacity, folding stress and the cytosolic HSP90 complex control retrograde communication.

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Fig. 1: GUN1 physically interacts with the ClpC1 and cpHSC70-1 chaperones.
Fig. 2: GUN1 regulates protein import under conditions that interfere with retrograde signalling.
Fig. 3: Unimported preproteins accumulate in the cytosol of gun1 mutants upon Lin or NF treatment.
Fig. 4: Precursors accumulating in the cytosol function in retrograde regulation of PhANG expression.
Fig. 5: The HSP90 chaperone complex functions as a component of retrograde signalling.
Fig. 6: Control of the import of TPB enzymes by GUN1 and a working model of the GUN1/GUN5–HSP90 retrograde signalling pathway.

Data availability

Mass spectrometry-based proteomic data have been deposited in the PRIDE partner repository of the ProteomeXchange Consortium with the data set identifiers PXD010730 and PXD013005. All other data are available in the main text or the Supplementary Information.

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Acknowledgements

We thank the MPI-MP GreenTeam for help with plant transformation. We are grateful to D. Leister (Ludwig-Maximilians-University Munich) for providing the gun1-102 seeds, Å. Strand (Umeå University, Umeå, Sweden) for providing seeds of the HSP90 RNAi lines, A. Clarke (Gothenburg University) for providing antibodies against Clp proteins and M. Gorka from MPI-MP for running the mass spectrometry samples to quantify the TOC–TIC subunits. This research was financed by the Max Planck Society, grants from the Deutsche Forschungsgemeinschaft to R.B. (FOR 804; SFB-TRR 175 A04), R.Z. (ZO 302/4-1; SFB-TRR 175 A04) and B.G. (SFB-TRR 175 C04), and grants from the Biotechnology and Biological Sciences Research Council (BBSRC) to R.P.J. (research grant numbers BB/N006372/1 and BB/R009333/1).

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Contributions

R.B. and G.-Z.W. conceived and designed the research. G.-Z.W. performed most of the experiments. E.H.M. performed the mass spectrometry-based proteomics. A.R. and B.G. investigated the import of the TPB enzymes. M.S. performed the ribosome profiling experiments, analysed and discussed the results with G.-Z.W. and R.Z. Q.L. and G.-Z.W. conducted the protein import assays and analysed the results with R.P.J. M.A.S. performed the photosynthesis measurements. D.W. mapped peptides to the transit peptide regions of chloroplast proteins. R.B. and G.-Z.W. wrote the manuscript, with input from the co-authors.

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Correspondence to Ralph Bock.

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Journal peer review information: Nature Plants thanks Chanhong Kim, Thomas Pfannschmidt and Jin-Zheng Wang for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figures 1–29 and Supplementary Tables 1–5.

Reporting Summary

Supplementary Data 1

Data from array-based ribosome profiling experiments.

Supplementary Data 2

Mass spectrometry data from co-IP experiments.

Supplementary Data 3

Mass spectrometry data of proteomic analyses of the wild type, the gun1 and clpc1 single mutants and the gun1clpc1 double mutant.

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Wu, GZ., Meyer, E.H., Richter, A.S. et al. Control of retrograde signalling by protein import and cytosolic folding stress. Nat. Plants 5, 525–538 (2019). https://doi.org/10.1038/s41477-019-0415-y

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