Dataset Information

Chemical cross-linking enables drafting ClpXP proximity maps and taking snapshots of in vivo interaction networks

ABSTRACT: Protein-protein interactions within complexes and networks are often dynamic and their elucidation remains a challenging task. Here, we show on the example of the proteolytic ClpXP complex the power of combined chemical cross-linking and mass-spectrometry to capture transient binding interactions within ClpP and ClpX as well as across the enigmatic ClpX hexamer – ClpP heptamer interface. Our data suggests that a few hot spot lysine residues located in signature loops in ClpX mediate the ClpX-ClpP interaction. This study further confirms that Listeria monocytogenes ClpX solely interacts with the heterooligomeric ClpP1/2 complex via the ClpP2 apical site. Moreover, the cellular interaction network of human and bacterial proteases was elucidated via in situ chemical cross-linking followed by an antibody-based pull-down against ClpP from genetically unmodified cells. A subsequent gel-free, quantitative mass spectrometric analysis demonstrated an up to 3-fold higher coverage compared to conventional co-immunoprecipitation without cross-linker revealing unprecedented insight into intracellular ClpXP networks.

INSTRUMENT(S): Orbitrap Fusion ETD, Q Exactive

ORGANISM(S): Homo Sapiens (human) Escherichia Coli Staphylococcus Aureus

SUBMITTER: Anja Fux

LAB HEAD: Stephan A. Sieber

PROVIDER: PXD009224 | Pride | 2018-11-21

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	10_eP_BS3.zip	Other
	20170818_10mikro_eP_BS3.raw	Raw
	20170818_5mikro_eP_BS3.raw	Raw
	20171123_IG1_in_vivo_MS2.raw	Raw
	20171123_Ig2_in_vivo_MS2.raw	Raw

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Publications

Chemical Cross-Linking Enables Drafting ClpXP Proximity Maps and Taking Snapshots of In Situ Interaction Networks.

Fux Anja A Korotkov Vadim S VS Schneider Markus M Antes Iris I Sieber Stephan A SA

Cell chemical biology 20181108 1

Detection of dynamic protein-protein interactions within complexes and networks remains a challenging task. Here, we show by the example of the proteolytic ClpXP complex the utility of combined chemical cross-linking and mass spectrometry (XL-MS) to map interactions within ClpP and ClpX as well as across the enigmatic ClpX hexamer-ClpP heptamer interface. A few hot-spot lysines located in signature loops in ClpX were shown to be in proximity to several structural regions of ClpP providing an ini ...[more]

PMID: 30415967

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Project description:The peptidase ClpP is conserved from bacteria to human. In the mitochondrial matrix, it multimerizes and forms a macromolecular proteasome-like cylinder. Because of its known relevance for the mitochondrial unfolded protein response during cell stress, we characterized two ClpP knock-out mouse founder lines and documented similar phenotypes. Ubiquitously, ClpP absence led to accumulation of its interactor protein ClpX without transcript upregulation. Interestingly, most wild-type tissues with substantial ClpP amounts had no detectable ClpX. This inverse correlation suggests that ClpX levels and degradation are regulated by ClpP. The expectation of similar protein levels, in view of a reported association of heptameric ClpP rings with hexameric ClpX rings, was confirmed only in testis of wild-type animals. Germline tissue was exceptional also in its vulnerability to ClpP deletion, with both founder lines showing complete infertility for males and females. Otherwise, ubiquitous mitochondrial dysfunction was apparent from severe growth retardation and reduced spontaneous motor activity of the animals, and from a pronounced decrease in pre-/postnatal survival. Spermatogenesis was found aborted at the spermatid stage, acrosomes and axonemes were not formed. Overall, tissue-specific roles of ClpP were evident by this massive effect for germ cells, mild bioenergetic deficits in muscle and liver tissues, and excellent compensation in brain. ClpX was previously reported to chaperone unfolded proteins and also DNA condensation in mitochondria, so it is likely that this pathway is particularly susceptible in germ cells. In conclusion, our study indicates that the role of ClpP in quality control is indispensable during development for cells with rapid changes of mitochondrial numbers, and is relevant during aging for growth and survival of the organism. Factorial design comparing ClpP knock-out mice with wild type littermates in five different tissues (brain, testis, liver, skeletal and heart muscle)