Structural assembly of the bacterial essential interactome
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Abstract
The study of protein interactions in living organisms is fundamental for understanding biological processes and central metabolic pathways. Yet, our knowledge of the bacterial interactome remains limited. Here, we combined gene deletion mutant analysis with deep-learning protein folding using AlphaFold2 to predict the core bacterial essential interactome. We predicted and modeled 1402 interactions between essential proteins in bacteria and generated 146 high-accuracy models. Our analysis reveals previously unknown details about the assembly mechanisms of these complexes, highlighting the importance of specific structural features in their stability and function. Our work provides a framework for predicting the essential interactomes of bacteria and highlight the potential of deep-learning algorithms in advancing our understanding of the complex biology of living organisms. Also, the results presented here offer a promising approach to identify novel antibiotic targets.
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Steudle, A., Spann, D., Pross, E. K., Shanmugam, S. K., Dalbey, R., & Kühn, A. (2021) · Scientific Reports · doi:10.1038/s41598-021-83224-x · Cited by 10 · see citing works
HPIPred: Host–pathogen interactome prediction with phenotypic scoring
Rendón, J. M., Rios, R. R., & Torrent, M. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.11.026 · Cited by 10 · see citing works
A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks
Zhao, B., Hu, S., Liu, X., Xiong, H., Han, X., Zhang, Z., Li, X., & Wang, L. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00343 · Cited by 10 · see citing works
Launay, R., Teppa, E., Martins, C., Abby, S. S., Pierrel, F., André, I., & Esque, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231810323 · Cited by 9 · see citing works
Craven, S. J., Condon, S. G. F., & Senes, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.30.514410 · Cited by 9 · see citing works
van Teeseling, M. C. F. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.732031 · Cited by 8 · see citing works
Mslar: Microbial synthetic lethal and rescue database
Zhu, S.-B., Jiang, Q.-H., Chen, Z., Zhou, X. Y., Jin, Y.-T., Deng, Z., & Guo, F. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011218 · Cited by 2 · see citing works
Flagged first, then by citations
2 of the 108 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Borrego, J. G., & Torrent, M. (2025) · Journal of Cheminformatics · doi:10.1186/s13321-025-01067-4 · Cited by 20 · see citing works
Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target
Yoon, Y., & Song, S. (2024) · The Journal of Microbiology · doi:10.1007/s12275-024-00137-w · Cited by 15 · see citing works
The ubiquitin ligase SINA3 and the transcription factor WOX14 regulate tomato growth and development
Yuan, Y., Li, H., Lu, H., Xia, C., Ramirez, C., Gao, M., Zhang, C., & Xiao, F. (2025) · The Plant Cell · doi:10.1093/plcell/koaf096 · Cited by 10 · see citing works
Mitochondrial Sorting and Assembly Machinery: Chaperoning a Moonlighting Role?
Ravi, R., Routray, D., & Mahalakshmi, R. (2025) · Biochemistry · doi:10.1021/acs.biochem.4c00727 · Cited by 7 · see citing works
Sakaguchi, T., Irifune, Y., Kamada, R., & Sakaguchi, K. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26199326 · Cited by 3 · see citing works
Rapid Proteome‐Wide Discovery of Protein–Protein Interactions With ppIRIS
Piochi, L. F., Tang, D., Malmström, J. A., Karami, Y., & Khakzad, H. (2026) · Advanced Science · doi:10.1002/advs.202521310 · Cited by 3 · see citing works
Liu, C., Duan, B., Chen, P., Jiang, Q., Wang, Y., Lu, L., Chen, Y., Hu, C., Zhang, L., & Guo, A. (2026) · eLife · doi:10.7554/elife.107677.4 · Cited by 3 · see citing works
Zhang, R., Zhu, X., Dong, L., Guo, C., & Shu, Y. (2026) · Plant Cell & Environment · doi:10.1111/pce.70408 · Cited by 2 · see citing works
Chen, L., Duan, B., Chen, P., Jiang, Q., Wang, Y., Lu, L., Chen, Y., Hu, C., Zhang, L., & Guo, A. (2025) · eLife · doi:10.7554/elife.107677 · Cited by 2 · see citing works
Chen, L., Duan, B., Chen, P., Jiang, Q., Wang, Y., Lu, L., Chen, Y., Hu, C., Zhang, L., & Guo, A. (2025) · eLife · doi:10.7554/elife.107677.1 · Cited by 2 · see citing works
Chen, L., Duan, B., Chen, P., Jiang, Q., Wang, Y., Lu, L., Chen, Y., Hu, C., Zhang, L., & Guo, A. (2026) · eLife · doi:10.7554/elife.107677.2 · Cited by 1 · see citing works
Saha, C. K., Roghanian, M., Häußler, S., & Guy, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.23.634437
Chen, L., Duan, B., Chen, P., Jiang, Q., Wang, Y., Lu, L., Chen, Y., Hu, C., Zhang, L., & Guo, A. (2026) · eLife · doi:10.7554/elife.107677.2.sa0
Chen, L., Duan, B., Chen, P., Jiang, Q., Wang, Y., Lu, L., Chen, Y., Hu, C., Zhang, L., & Guo, A. (2026) · eLife · doi:10.7554/elife.107677.3.sa0
Chen, L., Duan, B., Chen, P., Jiang, Q., Wang, Y., Lu, L., Chen, Y., Hu, C., Zhang, L., & Guo, A. (2026) · eLife · doi:10.7554/elife.107677.3
Zhang, R., Zhu, X., Xue, Y. J., Tang, X., Yao, Y., Cao, D., He, W., Guo, C., Liu, X. Y., & Shu, Y. (2026) · Journal of Agriculture and Food Research · doi:10.1016/j.jafr.2026.103139
Oka, G. U., Adan, W. C. D. S., Calomeno, C. V. A. Q., & de Souza, R. F. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.23.746524
- Authors
- Gómez Borrego, J., & Torrent Burgas, M.
- Affiliations
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2024-01-16
- Volume
- 13
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC10863985
- OpenAlex
- W4390909534
- Cited by
- 16
- References
- 108
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 2
- FWCI
- 2.17
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Ministerio de Ciencia e Innovación (PDC2021-121544-I00, PID2020-114627RB-I00)
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID2022)
- Generalitat de Catalunya (Joan Oró Fellowship 2023 FI-100278)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- essential proteins, protein-protein interaction, protein complex formation, deletion mutants, AlphaFold2, protein structure prediction, antibiotic targets, protein stability
- MeSH terms
- Bacteria, Proteins, Computational Biology, Protein Interaction Mapping, Metabolic Networks and Pathways
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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