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The Bacterial ClpXP-ClpB Family is Enriched with RNA-Binding Protein Complexes
Version 1
: Received: 5 July 2022 / Approved: 6 July 2022 / Online: 6 July 2022 (15:26:30 CEST)
A peer-reviewed article of this Preprint also exists.
Auburger, G.; Key, J.; Gispert, S. The Bacterial ClpXP-ClpB Family Is Enriched with RNA-Binding Protein Complexes. Cells 2022, 11, 2370. Auburger, G.; Key, J.; Gispert, S. The Bacterial ClpXP-ClpB Family Is Enriched with RNA-Binding Protein Complexes. Cells 2022, 11, 2370.
Abstract
In the matrix of bacteria/mitochondria/chloroplasts, Lon acts as the degradation machine for soluble proteins. In stress periods, however, proteostasis and survival depend on the strongly conserved Clp/Hsp100 family. Currently, the targets of ATP-powered unfoldases/disaggregases ClpB and ClpX, and of peptidase ClpP heptameric rings, are still unclear. Trapping experiments and proteome profiling in multiple organisms triggered confusion, so we analyzed the consistency of ClpP-trap targets in bacteria. We also provide meta-analyses of protein interactions in humans, to elucidate where Clp family members are enriched. Furthermore, meta-analyses of mouse complexomics are provided. Genotype-phenotype correlations confirmed our concept. Trapping, proteome, and complexome data retrieved consistent coaccumulation of ClpXP with GFM1 and TUFM orthologs. ClpX shows broad interaction selectivity encompassing mitochondrial translation elongation, RNA granule, and nucleoid; ClpB preferentially attaches to mitochondrial RNA granule and translation initiation components; ClpP is enriched with them all, and associates with release/recycling factors. Mutations in ClpP cause Perrault syndrome, with phenotypes similar to defects in mtDNA/mtRNA. Thus, we propose that ClpB and ClpXP are crucial to counteract misfolded insoluble protein assemblies that contain nucleotide-phosphates. This insight is relevant to improve ClpP-modulating drugs that block bacterial growth, and for the treatment of human infertility, deafness and neurodegeneration.
Keywords
mass spectrometry; substrate-trapping assay; BioID; POLDIP2; LRPPRC; GRSF1; PNPT1; MTIF2; ataxia
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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