Method for the isolation of Escherichia coli K-12 mutants deficient in essential genes.

Investigation of essential genes, besides contributing to understanding the fundamental principles of life, has numerous practical applications. Essential genes can be exploited as building blocks of a tightly controlled cell ‘chassis’. Bacillus subtilis and Escherichia coli K-12 are both well-characterized model bacteria used as hosts for a plethora of biotechnological applications. Determination of the essential genes that constitute the B. subtilis and E. coli minimal genomes is therefore of the highest importance. Recent advances have led to the modification of the original B. subtilis and E. coli essential gene sets identified 10 years ago. Furthermore, significant progress has been made in the area of genome minimization of both model bacteria. This review provides an update, with particular emphasis on the current essential gene sets and their comparison with the original gene sets identified 10 years ago. Special attention is focused on the genome reduction analyses in B. subtilis and E. coli and the construction of minimal cell factories for industrial applications.

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Development of a system for discovery of genetic interactions for essential genes in Escherichia coli K-12

Genes & Genetic Systems ◽

10.1266/ggs.88.233 ◽

2013 ◽

Vol 88 (4) ◽

pp. 233-240 ◽

Cited By ~ 5

Author(s):

Han Tek Yong ◽

Natsuko Yamamoto ◽

Rikiya Takeuchi ◽

Yi-Ju Hsieh ◽

Tom M. Conrad ◽

...

Keyword(s):

Escherichia Coli ◽

Essential Genes ◽

Genetic Interactions ◽

K 12

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An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features

Molecular BioSystems ◽

10.1039/c7mb00234c ◽

2017 ◽

Vol 13 (8) ◽

pp. 1584-1596 ◽

Cited By ~ 13

Author(s):

Sutanu Nandi ◽

Abhishek Subramanian ◽

Ram Rup Sarkar

Keyword(s):

Machine Learning ◽

Escherichia Coli ◽

Learning Process ◽

Learning Strategy ◽

Essential Genes ◽

Gene Essentiality ◽

K 12

We propose an integrated machine learning process to predict gene essentiality in Escherichia coli K-12 MG1655 metabolism that outperforms known methods.

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The essential genome ofEscherichia coliK-12

10.1101/237842 ◽

2017 ◽

Author(s):

Emily C. A. Goodall ◽

Ashley Robinson ◽

Iain G. Johnston ◽

Sara Jabbari ◽

Keith A. Turner ◽

...

Keyword(s):

Escherichia Coli ◽

Statistical Analysis ◽

Essential Gene ◽

Automated Analysis ◽

Transposon Mutagenesis ◽

Essential Genes ◽

High Density ◽

Bacterial Physiology ◽

E Coli ◽

K 12

ABSTRACTTransposon-Directed Insertion-site Sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries and therefore it remains unclear whether the two methodologies are comparable. To address this, a high density transposon library was constructed inEscherichia coliK-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false positive identification of essential gene candidates, statistical data analysis included corrections for both gene length and genome length. Through this analysis new essential genes and genes previously incorrectly designated as essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects and fine resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis datasets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry.IMPORTANCEIncentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes inE. coli, we constructed a very high density transposon mutant library. Initial automated analysis of the resulting data revealed many discrepancies when compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high density TraDIS sequencing data for each putative essential gene for the model laboratory organism,Escherichia coli. This paper is important because it provides a better understanding of the essential genes ofE. coli, reveals the limitations of relying on automated analysis alone and a provides new standard for the analysis of TraDIS data.

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Essential genes in the metB-malB region of Escherichia coli K-12.

Journal of Bacteriology ◽

10.1128/jb.126.1.48-55.1976 ◽

1976 ◽

Vol 126 (1) ◽

pp. 48-55 ◽

Cited By ~ 3

Author(s):

K A Armstrong ◽

D P Fan

Keyword(s):

Escherichia Coli ◽

Essential Genes ◽

K 12

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The Essential Genome of Escherichia coli K-12

mBio ◽

10.1128/mbio.02096-17 ◽

2018 ◽

Vol 9 (1) ◽

Cited By ~ 73

Author(s):

Emily C. A. Goodall ◽

Ashley Robinson ◽

Iain G. Johnston ◽

Sara Jabbari ◽

Keith A. Turner ◽

...

Keyword(s):

Escherichia Coli ◽

Statistical Analysis ◽

Essential Gene ◽

Automated Analysis ◽

Transposon Mutagenesis ◽

Essential Genes ◽

High Density ◽

Bacterial Physiology ◽

E Coli ◽

K 12

ABSTRACTTransposon-directed insertion site sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries, and therefore, it remains unclear whether the two methodologies are comparable. To address this, a high-density transposon library was constructed inEscherichia coliK-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false-positive identification of essential genes, statistical data analysis included corrections for both gene length and genome length. Through this analysis, new essential genes and genes previously incorrectly designated essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects, and fine-resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis data sets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry.IMPORTANCEIncentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes inEscherichia coli, we constructed a transposon mutant library of unprecedented density. Initial automated analysis of the resulting data revealed many discrepancies compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high-density TraDIS sequencing data for each putative essential gene for theE. colimodel laboratory organism. This paper is important because it provides a better understanding of the essential genes ofE. coli, reveals the limitations of relying on automated analysis alone, and provides a new standard for the analysis of TraDIS data.

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