Unraveling proteomic chaos by independent component analysis - ClpX proficiency promotes the iron and oxygen limitation responses of Staphylococcus aureus and affects the intracellular bacterial behavior Article Swipe
Larissa M. Busch
,
Hannes Wolfgramm
,
Supradipta De
,
Christian Hentschker
,
Manuela Gesell Salazar
,
Magdalena Kröber
,
Celina Hopp
,
Marie-Sofie Illenseher
,
Alexander Ganske
,
Stephan Michalik
,
Alexander Reder
,
Sven Hammerschmidt
,
Dorte Frees
,
Ulf Gerth
,
Kristin Surmann
,
Ulrike Mäder
,
Uwe Völker
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.09.04.674172
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.09.04.674172
In the opportunistic pathogen Staphylococcus aureus , protein homeostasis is largely mediated by the Caseinolytic protease (Clp) system. The proteases ClpXP and ClpCP are crucial for general and targeted proteolysis, which rely on the unfoldases ClpX and ClpC interacting with specific targets. However, the global effect on the proteome especially under infection-relevant stresses is not well-understood. To assess the effect of ClpX deficiency during infection-related processes, mass spectrometry-based global proteome profiles of S. aureus HG001 wild-type, an isogenic Δ clpX mutant, and a clpX complemented strain were recorded under control conditions as well as iron and oxygen limitation. The proteomic profiles revealed specific ClpX- and stress-dependent changes. A set of 24 robust stress-independent ClpX modulated proteins was identified and the stress-dependent influences were unraveled by independent component analysis (using the iModulon approach). These analyses revealed a role of ClpX in e.g., cell division, cell envelope homeostasis, the quinone stress response and prophage activation. Moreover, ClpX-dependent stress-specific effects were observed in the Δ clpX mutant, e.g. reduced induction of the heme uptake system under iron limitation and a dampened Rex-controlled oxygen limitation response. This revealed in particular that ClpX is central for heme homeostasis in S. aureus . Furthermore, in a Galleria infection model, the S. aureus Δ clpX mutant was attenuated compared to the wild-type HG001. This is consistent with a drastically reduced intracellular replication of the Δ clpX -mutant in cell culture-based infection experiments, however, high intracellular persistence of the Δ clpX mutant was also observed. This highlights the relevance of ClpX for bacterial fitness and virulence. Importance During infection processes, pathogens cope with host-mediated stressors. In response to those stressors, bacteria adapt their gene expression as well as their proteome profile. In the pathogen Staphylococcus aureus , protein homeostasis is mainly controlled by the Clp system. In particular, ClpX is the most conserved Clp unfoldase and is involved in overall regulation of virulence and bacterial fitness. However, the majority of ClpX targets remains elusive in S. aureus . With our proteomics approach and in depth data analysis, we provide a resource for global insight into ClpX-dependent adaptation of S. aureus physiology under infection-relevant conditions. Based on this, we uncover ClpX’s role as a central player in the iron and oxygen limitation response. In addition, we demonstrate the importance of ClpX in S. aureus bacterial fitness in infection processes. However, reduced levels of ClpX lead to high intracellular persistence, which questions ClpX’s suitability as a therapeutical target.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.09.04.674172
- https://www.biorxiv.org/content/biorxiv/early/2025/09/10/2025.09.04.674172.full.pdf
- OA Status
- green
- Cited By
- 1
- References
- 154
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4414098632
All OpenAlex metadata
Raw OpenAlex JSON
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- Title
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Unraveling proteomic chaos by independent component analysis - ClpX proficiency promotes the iron and oxygen limitation responses of Staphylococcus aureus and affects the intracellular bacterial behaviorWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-09-10Full publication date if available
- Authors
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Larissa M. Busch, Hannes Wolfgramm, Supradipta De, Christian Hentschker, Manuela Gesell Salazar, Magdalena Kröber, Celina Hopp, Marie-Sofie Illenseher, Alexander Ganske, Stephan Michalik, Alexander Reder, Sven Hammerschmidt, Dorte Frees, Ulf Gerth, Kristin Surmann, Ulrike Mäder, Uwe VölkerList of authors in order
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https://doi.org/10.1101/2025.09.04.674172Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2025/09/10/2025.09.04.674172.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2025/09/10/2025.09.04.674172.full.pdfDirect OA link when available
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1Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.controlled | 294 |
| abstract_inverted_index.deficiency | 63 |
| abstract_inverted_index.especially | 50 |
| abstract_inverted_index.expression | 277 |
| abstract_inverted_index.highlights | 249 |
| abstract_inverted_index.identified | 118 |
| abstract_inverted_index.importance | 380 |
| abstract_inverted_index.influences | 122 |
| abstract_inverted_index.limitation | 175, 181, 373 |
| abstract_inverted_index.particular | 186 |
| abstract_inverted_index.physiology | 353 |
| abstract_inverted_index.processes, | 66, 262 |
| abstract_inverted_index.processes. | 390 |
| abstract_inverted_index.proteomics | 333 |
| abstract_inverted_index.regulation | 313 |
| abstract_inverted_index.stressors, | 272 |
| abstract_inverted_index.stressors. | 267 |
| abstract_inverted_index.unfoldases | 35 |
| abstract_inverted_index.virulence. | 258 |
| abstract_inverted_index.wild-type, | 76 |
| abstract_inverted_index.activation. | 153 |
| abstract_inverted_index.conditions. | 356 |
| abstract_inverted_index.demonstrate | 378 |
| abstract_inverted_index.drastically | 222 |
| abstract_inverted_index.homeostasis | 9, 193, 291 |
| abstract_inverted_index.independent | 126 |
| abstract_inverted_index.interacting | 39 |
| abstract_inverted_index.limitation. | 98 |
| abstract_inverted_index.particular, | 300 |
| abstract_inverted_index.persistence | 239 |
| abstract_inverted_index.replication | 225 |
| abstract_inverted_index.suitability | 404 |
| abstract_inverted_index.Caseinolytic | 15 |
| abstract_inverted_index.Furthermore, | 198 |
| abstract_inverted_index.complemented | 85 |
| abstract_inverted_index.experiments, | 235 |
| abstract_inverted_index.homeostasis, | 146 |
| abstract_inverted_index.persistence, | 400 |
| abstract_inverted_index.proteolysis, | 30 |
| abstract_inverted_index.culture-based | 233 |
| abstract_inverted_index.host-mediated | 266 |
| abstract_inverted_index.intracellular | 224, 238, 399 |
| abstract_inverted_index.opportunistic | 3 |
| abstract_inverted_index.therapeutical | 407 |
| abstract_inverted_index.ClpX-dependent | 155, 348 |
| abstract_inverted_index.Rex-controlled | 179 |
| abstract_inverted_index.Staphylococcus | 5, 287 |
| abstract_inverted_index.stress-specific | 156 |
| abstract_inverted_index.stress-dependent | 106, 121 |
| abstract_inverted_index.well-understood. | 56 |
| abstract_inverted_index.infection-related | 65 |
| abstract_inverted_index.infection-relevant | 52, 355 |
| abstract_inverted_index.spectrometry-based | 68 |
| abstract_inverted_index.stress-independent | 113 |
| cited_by_percentile_year.max | 95 |
| cited_by_percentile_year.min | 91 |
| corresponding_author_ids | https://openalex.org/A5049855503, https://openalex.org/A5085667735 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 17 |
| corresponding_institution_ids | https://openalex.org/I2799318839 |
| citation_normalized_percentile.value | 0.90405529 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |