Experimental Determination and System Level Analysis of Essential Genes in &lt;i&gt;Escherichia coli&lt;/i&gt; MG1655

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Journal of Bacteriology, 185(19), 5673-5684

Abstract

Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.

Related collections

Most cited references 25

Record: found
Abstract: found
Article: not found

Global transposon mutagenesis and a minimal Mycoplasma genome.

C. Hutchison, S N Peterson, S. Gill … (1999)

Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently replicating cell so far identified. Global transposon mutagenesis was used to identify nonessential genes in an effort to learn whether the naturally occurring gene complement is a true minimal genome under laboratory growth conditions. The positions of 2209 transposon insertions in the completely sequenced genomes of M. genitalium and its close relative M. pneumoniae were determined by sequencing across the junction of the transposon and the genomic DNA. These junctions defined 1354 distinct sites of insertion that were not lethal. The analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including about 100 genes of unknown function.

0 comments Cited 185 times – based on 0 reviews      Review now

Record: found
Abstract: found
Article: not found

Metabolic network structure determines key aspects of functionality and regulation.

Jörg Stelling, Steffen Klamt, Katja Bettenbrock … (2002)

The relationship between structure, function and regulation in complex cellular networks is a still largely open question. Systems biology aims to explain this relationship by combining experimental and theoretical approaches. Current theories have various strengths and shortcomings in providing an integrated, predictive description of cellular networks. Specifically, dynamic mathematical modelling of large-scale networks meets difficulties because the necessary mechanistic detail and kinetic parameters are rarely available. In contrast, structure-oriented analyses only require network topology, which is well known in many cases. Previous approaches of this type focus on network robustness or metabolic phenotype, but do not give predictions on cellular regulation. Here, we devise a theoretical method for simultaneously predicting key aspects of network functionality, robustness and gene regulation from network structure alone. This is achieved by determining and analysing the non-decomposable pathways able to operate coherently at steady state (elementary flux modes). We use the example of Escherichia coli central metabolism to illustrate the method.

0 comments Cited 182 times – based on 0 reviews      Review now

Record: found
Abstract: found
Article: not found

Comprehensive identification of conditionally essential genes in mycobacteria.

C M Sassetti, D. Boyd, E. J. Rubin (2001)

An increasing number of microbial genomes have been completely sequenced, and the identified genes are categorized based on their homology to genes of known function. However, the function of a large number of genes cannot be determined on this basis alone. Here, we describe a technique, transposon site hybridization (TraSH), which allows rapid functional characterization by identifying the complete set of genes required for growth under different conditions. TraSH combines high-density insertional mutagenesis with microarray mapping of pools of mutants. We have made large pools of independent transposon mutants in mycobacteria by using a mariner-based transposon and efficient phage transduction. By using TraSH, we have defined the set of genes required for growth of Mycobacterium bovis bacillus Calmette-Guérin on minimal but not rich medium. Genes of both known and unknown functions were identified. Of the genes with known functions, nearly all were involved in amino acid biosynthesis. TraSH is a powerful method for categorizing gene function that should be applicable to a variety of microorganisms.

0 comments Cited 162 times – based on 0 reviews      Review now

All references

Author and article information

Journal

Publisher: American Society for Microbiology

Publication date (Electronic): 2003

Publication date (Issued): 01 October 2003

Publication date Updated: 11 October 2017

Article

DOI: 10.1128/JB.185.19.5673-5684.2003

PMC ID: 193955

PubMed ID: 13129938

SO-VID: d76f74a5-5996-4191-8752-3ea6ee238669

History

Data availability:

Comments

Comment on this article

Cited by 212

See all cited by

Experimental Determination and System Level Analysis of Essential Genes in <i>Escherichia coli</i> MG1655

Read this article at

Abstract

Abstract

Related collections

Redox Experimental Medicine

Most cited references 25

Global transposon mutagenesis and a minimal Mycoplasma genome.

Metabolic network structure determines key aspects of functionality and regulation.

Comprehensive identification of conditionally essential genes in mycobacteria.

Author and article information

Journal

Article

History

Comments

Comment on this article

Similar content 419

Cited by 212