ArticleBMC microbiology2016
Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions.
Article in BMC microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it, 62 citations in OpenAlex.
- Pooled it
- Core Proteome Subtractive Genomics Reveals Potential Therapeutic Targets in Bacillus anthracis.Current microbiology · 2026Article
- Targeting Fusobacterium nucleatum in colorectal cancer: therapeutic strategies and future directions.Infectious agents and cancer · 2025Review
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- Core-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii.Scientific reports · 2025Article
- Computational Strategies in Drug Discovery: Leveraging Subtractive Genomic Analysis for Target Identification.Current pharmaceutical biotechnology · 2025Review
- Article
- Diversification of the Rho transcription termination factor in bacteria.Nucleic acids research · 2024Article
- Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila.Scientific reports · 2024Article
- Screening of Novel Drug Targets and Drug Design forCurrent research in microbial sciences · 2024Article
- Oral microbiota-host interaction: the chief culprit of alveolar bone resorption.Frontiers in immunology · 2024Review
- Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors.Genomics & informatics · 2023Article
- Review
- Mining bacterial NGS data vastly expands the complete genomes of temperate phages.NAR genomics and bioinformatics · 2022Article
- Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS fromMolecules (Basel, Switzerland) · 2022Article
- In Silico Core Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors againstInternational journal of environmental research and public health · 2021Article
- RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum.Nature microbiology · 2021Article
- Resolving the Contradictory Functions of Lysine Decarboxylase and Butyrate in Periodontal and Intestinal Diseases.Journal of clinical medicine · 2021Review
- Interconnections Between the Oral and Gut Microbiomes: Reversal of Microbial Dysbiosis and the Balance Between Systemic Health and Disease.Microorganisms · 2021Review
- Leptin Gene Protects Against Cold Stress in Antarctic Toothfish.Frontiers in physiology · 2021Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFusobacterium 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.
resultsIn 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.
conclusionSubtractive 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.
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