Proteomics, phylogenetics, and coexpression analyses indicate novel interactions in the plastid CLP chaperone-protease system

• Published in: The Journal of biological chemistry Vol. 298; no. 3; p. 101609
• Main Authors: Rei Liao, Jui-Yun, Friso, Giulia, Forsythe, Evan S., Michel, Elena J.S., Williams, Alissa M., Boguraev, Sasha S., Ponnala, Lalit, Sloan, Daniel B., van Wijk, Klaas J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.03.2022; American Society for Biochemistry and Molecular Biology
• Subjects: AAA+ chaperone; adaptors; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; chloroplast; Chloroplast Proteins - genetics; Chloroplast Proteins - metabolism; Chloroplasts - genetics; Chloroplasts - metabolism; CLP serine protease; domain of unknown function (DUF) proteins; Endopeptidase Clp - metabolism; Heat-Shock Proteins - genetics; Heat-Shock Proteins - metabolism; Molecular Chaperones - metabolism; Phylogeny; Plastids - genetics; Plastids - metabolism; proteolysis; Proteomics; proteostasis; substrate trapping; LS; SPC; substrate trapping; adaptors; domain of unknown function (DUF) proteins; proteostasis; MS/MS; CLP serine protease; Arabidopsis thaliana; SPP; chloroplast; DUF; GBP; GluTR; AAA+ chaperone; ERC; PPDB; ARM; proteolysis
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1016/j.jbc.2022.101609

The chloroplast chaperone CLPC1 unfolds and delivers substrates to the stromal CLPPRT protease complex for degradation. We previously used an in vivo trapping approach to identify interactors with CLPC1 in Arabidopsis thaliana by expressing a STREPII-tagged copy of CLPC1 mutated in its Walker B domains (CLPC1-TRAP) followed by affinity purification and mass spectrometry. To create a larger pool of candidate substrates, adaptors, or regulators, we carried out a far more sensitive and comprehensive in vivo protein trapping analysis. We identified 59 highly enriched CLPC1 protein interactors, in particular proteins belonging to families of unknown functions (DUF760, DUF179, DUF3143, UVR-DUF151, HugZ/DUF2470), as well as the UVR domain proteins EXE1 and EXE2 implicated in singlet oxygen damage and signaling. Phylogenetic and functional domain analyses identified other members of these families that appear to localize (nearly) exclusively to plastids. In addition, several of these DUF proteins are of very low abundance as determined through the Arabidopsis PeptideAtlas http://www.peptideatlas.org/builds/arabidopsis/ showing that enrichment in the CLPC1-TRAP was extremely selective. Evolutionary rate covariation indicated that the HugZ/DUF2470 family coevolved with the plastid CLP machinery suggesting functional and/or physical interactions. Finally, mRNA-based coexpression networks showed that all 12 CLP protease subunits tightly coexpressed as a single cluster with deep connections to DUF760-3. Coexpression modules for other trapped proteins suggested specific functions in biological processes, e.g., UVR2 and UVR3 were associated with extraplastidic degradation, whereas DUF760-6 is likely involved in senescence. This study provides a strong foundation for discovery of substrate selection by the chloroplast CLP protease system.