ArticleNature communications2019
Environmental conditions shape the nature of a minimal bacterial genome.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Article
- Article
- Improving the Annotations of JCVI-Syn3a Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- KEGG orthology prediction of bacterial proteins using natural language processing.BMC bioinformatics · 2024Article
- Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome.BMC genomics · 2024Article
- Applications of Machine Learning (ML) and Mathematical Modeling (MM) in Healthcare with Special Focus on Cancer Prognosis and Anticancer Therapy: Current Status and Challenges.Pharmaceutics · 2024Review
- Evolution of a minimal cell.Nature · 2023Article
- Genomic analysis ofHeliyon · 2023Article
- Organizing the bacterial annotation space with amino acid sequence embeddings.BMC bioinformatics · 2022Article
- Toward the Complete Functional Characterization of a Minimal Bacterial Proteome.The journal of physical chemistry. B · 2022Article
- Article
- Article
- A synthetic 'essentialome' for axenic culturing of 'Candidatus Liberibacter asiaticus'.BMC research notes · 2022Article
- Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterized proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A guide to machine learning for biologists.Nature reviews. Molecular cell biology · 2022Review
- Adaptability of a Caproate-Producing Bacterium Contributes to Its Dominance in an Anaerobic Fermentation System.Applied and environmental microbiology · 2021Article
- Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem.Microbiology spectrum · 2021Article
- Genome-scale metabolic modeling reveals key features of a minimal gene set.Molecular systems biology · 2021Article
- Genome annotation of disease-causing microorganisms.Briefings in bioinformatics · 2021Review
- Tetracycline Resistance Mediated byAntimicrobial agents and chemotherapy · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Of the 473 genes in the genome of the bacterium with the smallest genome generated to date, 149 genes have unknown function, emphasising a universal problem; less than 1% of proteins have experimentally determined annotations. Here, we combine the results from state-of-the-art in silico methods for functional annotation and assign functions to 66 of the 149 proteins. Proteins that are still not annotated lack orthologues, lack protein domains, and/ or are membrane proteins. Twenty-four likely transporter proteins are identified indicating the importance of nutrient uptake into and waste disposal out of the minimal bacterial cell in a nutrient-rich environment after removal of metabolic enzymes. Hence, the environment shapes the nature of a minimal genome. Our findings also show that the combination of multiple different state-of-the-art in silico methods for annotating proteins is able to predict functions, even for difficult to characterise proteins and identify crucial gaps for further development.
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