ArticleJournal of bacteriology2014
Towards an informative mutant phenotype for every bacterial gene.
Article in Journal of bacteriology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- High-throughput dilution-based growth method enables time-resolved exo-metabolomics of Pseudomonas putida and Pseudomonas aeruginosa.Microbial biotechnology · 2021Article
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- A simplified strategy for titrating gene expression reveals new relationships between genotype, environment, and bacterial growth.Nucleic acids research · 2021Article
- A decade of advances in transposon-insertion sequencing.Nature reviews. Genetics · 2020Review
- Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4.PLoS computational biology · 2020Article
- A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding GeneFrontiers in microbiology · 2020Article
- Cell Aggregation and Aerobic Respiration Are Important forApplied and environmental microbiology · 2019Article
- A Markerless Method for Genome Engineering inFrontiers in microbiology · 2019Article
- Prediction and characterization of promoters and ribosomal binding sites ofBiotechnology for biofuels · 2019Article
- Nitro Sulfonyl Fluorides are a new pharmacophore for the development of antibiotics.Molecular systems design & engineering · 2018Article
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- Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions.Current biology : CB · 2018Article
- Complete genome sequence and the expression pattern of plasmids of the model ethanologenBiotechnology for biofuels · 2018Article
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- Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State inFrontiers in microbiology · 2018Article
- Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data.Bioinformatics (Oxford, England) · 2017Article
- Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacteriumThe Journal of biological chemistry · 2017Article
- Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri.Applied and environmental microbiology · 2016Article
Corrections and comments
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Authors and funding
9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, in Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.
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