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Updated: Mar 21, 2026
Label-Free Quantitative Proteomics Workflow for Discovery-Driven Host-Pathogen Interactions
Published on: October 20, 2020
Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of
Amit Kumar1, Pragna Lakshmi Thotakura1, Basant Kumar Tiwary2
1Centre for Bioinformatics, Pondicherry University, Puducherry, 605014, India.
Background:
Fusobacterium nucleatum, a well studied bacterium in periodontal diseases, appendicitis, gingivitis, osteomyelitis and pregnancy complications has recently gained attention due to its association with colorectal cancer (CRC) progression. Treatment with berberine was shown to reverse F. nucleatum-induced CRC progression in mice by balancing the growth of opportunistic pathogens in tumor microenvironment. Intestinal microbiota imbalance and the infections caused by F. nucleatum might be regulated by therapeutic intervention. Hence, we aimed to predict drug target proteins in F. nucleatum, through subtractive genomics approach and host-pathogen protein-protein interactions (HP-PPIs). We also carried out enrichment analysis of host interacting partners to hypothesize the possible mechanisms involved in CRC progression due to F. nucleatum.
Results:
In subtractive genomics approach, the essential, virulence and resistance related proteins were retrieved from RefSeq proteome of F. nucleatum by searching against Database of Essential Genes (DEG), Virulence Factor Database (VFDB) and Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) tool respectively. A subsequent hierarchical screening to identify non-human homologous, metabolic pathway-independent/pathway-specific and druggable proteins resulted in eight pathway-independent and 27 pathway-specific druggable targets. Co-aggregation of F. nucleatum with host induces proinflammatory gene expression thereby potentiates tumorigenesis. Hence, proteins from IBDsite, a database for inflammatory bowel disease (IBD) research and those involved in colorectal adenocarcinoma as interpreted from The Cancer Genome Atlas (TCGA) were retrieved to predict drug targets based on HP-PPIs with F. nucleatum proteome. Prediction of HP-PPIs exhibited 186 interactions contributed by 103 host and 76 bacterial proteins. Bacterial interacting partners were accounted as putative targets. And enrichment analysis of host interacting partners showed statistically enriched terms that were in positive correlation with CRC, atherosclerosis, cardiovascular, osteoporosis, Alzheimer's and other diseases.
Conclusion:
Subtractive genomics analysis provided a set of target proteins suggested to be indispensable for survival and pathogenicity of F. nucleatum. These target proteins might be considered for designing potent inhibitors to abrogate F. nucleatum infections. From enrichment analysis, it was hypothesized that F. nucleatum infection might enhance CRC progression by simultaneously regulating multiple signaling cascades which could lead to up-regulation of proinflammatory responses, oncogenes, modulation of host immune defense mechanism and suppression of DNA repair system.
Insights
This study identifies potential drug targets in Fusobacterium nucleatum, a bacterium linked to colorectal cancer (CRC) progression. These targets could lead to new therapies for F. nucleatum infections and potentially impact CRC treatment.
Area of Science:
- Microbiology and Cancer Research
- Genomics and Bioinformatics
- Drug Discovery
Background:
- Fusobacterium nucleatum is implicated in colorectal cancer (CRC) progression.
- Intestinal microbiota imbalance and F. nucleatum infections may be therapeutically regulated.
- Berberine treatment has shown potential in reversing F. nucleatum-induced CRC in mice.
Purpose of the Study:
- To predict drug target proteins in F. nucleatum using subtractive genomics.
- To identify host-pathogen protein-protein interactions (HP-PPIs).
- To hypothesize mechanisms of F. nucleatum in CRC progression through enrichment analysis.
Main Methods:
- Subtractive genomics approach to identify essential, virulence, and resistance proteins.
- Screening for non-human homologous, druggable proteins.
- Host-pathogen protein-protein interaction (HP-PPI) prediction using IBDsite and TCGA data.
- Enrichment analysis of host interacting partners.
Main Results:
- Identified eight pathway-independent and 27 pathway-specific druggable protein targets in F. nucleatum.
- Predicted 186 HP-PPIs involving 103 host and 76 bacterial proteins.
- Enrichment analysis revealed host interactions correlated with CRC, atherosclerosis, and other diseases.
Conclusions:
- Subtractive genomics yielded target proteins crucial for F. nucleatum survival and pathogenicity.
- These targets are candidates for developing inhibitors against F. nucleatum infections.
- F. nucleatum may promote CRC by up-regulating inflammation, oncogenes, and modulating host immunity and DNA repair.
