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COG-imposed Golgi functional integrity determines the onset of dark-induced senescence

Nature Plants volume 9, pages 1890–1901 (2023)Cite this article

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Abstract

Plant survival depends on dynamic stress-response pathways in changing environments. To uncover pathway components, we screened an ethyl methanesulfonate-mutagenized transgenic line containing a stress-inducible luciferase construct and isolated a constitutive expression mutant. The mutant is the result of an amino acid substitution in the seventh subunit of the hetero-octameric conserved oligomeric Golgi (COG) complex of Arabidopsis thaliana. Complementation studies verified the Golgi localization of cog7, and stress tests established accelerated dark-induced carbon deprivation/senescence of the mutant compared with wild-type plants. Multiomics and biochemical analyses revealed accelerated induction of protein ubiquitination and autophagy, and a counterintuitive increased protein N-glycosylation in senescencing cog7 relative to wild-type. A revertant screen using the overexpressor (FOX)-hunting system established partial, but notable rescue of cog7 phenotypes by COG5 overexpression, and conversely premature senescence in reduced COG5 expressing lines. These findings identify COG-imposed Golgi functional integrity as a main player in ensuring cellular survival under energy-limiting conditions.

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Fig. 1: The cog7 mutant displays constitutively induced RSRE and accelerated dark-induced senescence.
Fig. 2: The cog7 mutant display accelerated dark-induced ubiquitination and autophagy.
Fig. 3: Sucrose reverts the dark-induced accelerated senescence phenotypes of the cog7 mutant.
Fig. 4: Dark-induced senescence is accompanied by enhanced protein N-glycosylation.
Fig. 5: COG subunits differently compensate the cog7 phenotypes.
Fig. 6: Simplified schematic model of the link between Golgi’s functional integrity and reconfiguration of hypometabolic response network.

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Data availability

All processed data are contained either in the manuscript, Extended Data or Supplementary Information. RNA sequencing reads were aligned to the TAIR10 genome and counts were assigned to genes in the Araport11 annotation. Global transcriptome data are available via NCBI-BioProject (SubmissionID: SUB12956374, BioProject ID:PRJNA945907). Peptide raw data are available via ProteomeXchange with identifier PXD040920. Agreement number is CE258GM6H1. Source data underlying Figs. 1b, 2f,h, 3b,c, 4c and 5g–i, and Extended Data Figs. 1f and 4 are provided with this paper.

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Acknowledgements

This work was supported by J. W. Leibacher and K. Cookson endowed chair funds, and by grants from the National Institutes of Health (grant no. R01GM107311-8) and the National Science Foundation (grant no. 2104365) to K.D.

Author information

Authors and Affiliations

  1. Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA

    Hee-Seung Choi, Jiubo Liang, Jinzheng Wang, Haiyan Ke, Manhoi Hur, Amancio De Souza & Katayoon Dehesh

  2. Department of Plant Sciences, University of California, Davis, CA, USA

    Marta Bjornson

  3. Lawrence Berkeley National Lab, Joint BioEnergy Institute, Emeryville, CA, USA

    Kavitha Satish Kumar & Jenny C. Mortimer

  4. School of Agriculture Food and Wine & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia

    Jenny C. Mortimer

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Contributions

K.D. conceived and designed the experiments and wrote the manuscript. H.-S.C. and M.B. performed experiments and analysed the data. J.L., J.W., H.K., A.D.S., K.S.K. and J.C.M. performed the experiments. M.H. analysed the data.

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Correspondence to Katayoon Dehesh.

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Extended data

Extended Data Fig. 1 High susceptibility of cog7 plants to reduced light intensity.

(a-b) Bacterial growth in mature leaves of 3-4 weeks old WT, cog7, and cog7/COG7 plants at 0 and 3 days post-inoculation (dpi) with (a) Pseudomonas syringae (P. Syringea) DC3000 (n = 14, 30, 15, 30, 15, and 30 independent experiments, respectively), and (b) P. Syringea HrcC (n = 18, 26, 20, 29, 19, and 29 independent experiments, respectively). (c) Disease symptoms in mature leaves of 3-4 weeks old WT, cog7, and cog7/COG7 plants at 0 and 4 dpi with Botrytis cinerea. (d) Fresh weight of 2-week-old WT, cog7, and cog7/COG7 seedlings grown on a medium containing 0 mM or 100 mM NaCl (n = 18 biological replicates for each condition). (e) Representative images and the respective (f) seedling size of 2-week-old WT and cog7 grown under three different white light intensities (20, 60, and 100 μmol/m2/s). There were two independent experiments with varying number of biological replicates (n = 10, 11, 11, 14, 19, and 15 biological replicates for each condition respectively). The means were compared using a two-tailed Student t-test *P = 0.02673 or **P = 0.00389. In a-b, d, and f, the lower and upper bounds of the box plot represent the 25th and 75th percentile respectively; the midline bar represents the median. The lower and upper ends of the whiskers represent minimum and maximum values respectively.

Source data

Extended Data Fig. 2 Quantification of ATG8/ATG8-PE abundance.

(a-b) The densitograms of ATG8-PE relative to the respective Ponceau S-stained band from (a) Fig. 2h, and (b) Fig. 3c.

Extended Data Fig. 3 Abundance of glycosyltransferase proteins.

MaxQuant-based quantification of protein abundance of glycosyltransferases of not treated and dark-treated WT and cog7 seedlings using the respective proteomic data.

Extended Data Fig. 4 DEX-induced reduced transcript levels COG5 and 7.

Transcript level of COG5 and COG7 in 2-week old seedlings of three genotypes (WT, COG5i and COG7i) grown in 16-hour light/8-hour dark at 4 days post water (Mock) or dexamethasone (DEX) induction. Error bars represent the SEM of three biological replicates, and the centers of the error bars represent the mean values. Two-tailed Student’s t-tests confirms significant differences of COG5 or COG7 expressions between Mock and DEX induction (*P = 0.00395 for COG5i or 0.00298 for COG7i).

Source data

Extended Data Fig. 5 Quantification of ATG8/ATG8-PE abundance.

The densitograms of ATG8-PE relative to the respective Ponceau S-stained band from Fig. 5h.

Supplementary information

Source data

Source Data Fig. 1

Statistical source data.

Source Data Fig. 2

Unprocessed Ponceau stained membrane.

Source Data Fig. 3

Unprocessed Ponceau stained membrane.

Source Data Fig. 4

Unprocessed Ponceau stained membrane.

Source Data Fig. 5

Unprocessed Ponceau stained membrane.

Source Data Extended Data Fig. 1

Statistical source data.

Source Data Extended Data Fig. 4

Statistical source data.

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Choi, HS., Bjornson, M., Liang, J. et al. COG-imposed Golgi functional integrity determines the onset of dark-induced senescence. Nat. Plants 9, 1890–1901 (2023). https://doi.org/10.1038/s41477-023-01545-3

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