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Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

ABSTRACT: BACKGROUND:Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development. METHODOLOGY/PRINCIPAL FINDINGS:Working from the premise that essential genes differ in absolute requirement for growth, we describe silencing of putative essential genes in E. coli to obtain a titration of declining growth rates and transcript levels by using antisense peptide nucleic acids (PNA) and expressed antisense RNA. The relationship between mRNA decline and growth rate decline reflects the degree of essentiality, or stringency, of an essential gene, which is here defined by the minimum transcript level for a 50% reduction in growth rate (MTL(50)). When applied to four growth essential genes, both RNA silencing methods resulted in MTL(50) values that reveal acpP as the most stringently required of the four genes examined, with ftsZ the next most stringently required. The established antibacterial targets murA and fabI were less stringently required. CONCLUSIONS:RNA silencing can reveal stringent requirements for gene expression with respect to growth. This method may be used to validate existing essential genes and to quantify drug target requirement.

SUBMITTER: Goh S

PROVIDER: S-EPMC2698124 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

Goh Shan S Boberek Jaroslaw M JM Nakashima Nobutaka N Stach Jem J Good Liam L

PloS one 20090626 6

<h4>Background</h4>Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development.<h4>Methodology/principal findings</h4>Working from the premise that essential genes differ in absolute requirement for growth, we des ...[more]

PMID: 19557168

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Project description:BackgroundBacterial growth is an important topic in microbiology and of crucial importance to better understand living cells. Bacterial growth dynamics are quantitatively examined using various methods to determine the physical, chemical or biological features of growing populations. Due to methodological differences, the exponential growth rate, which is a parameter that is representative of growth dynamics, should be differentiated. Ignoring such differentiation in the growth analysis might overlook somehow slight but significant changes in cellular features of the growing population. Both experimental and theoretical investigations are required to address these issues.ResultsThis study experimentally verified the differentiation in growth rates attributed to different methodologies, and demonstrated that the most popular method, optical turbidity, led to the determination of a lower growth rate in comparison to the methods based on colony formation and cellular adenosine triphosphate, due to a decay effect of reading OD600 during a population increase. Accordingly, the logistic model, which is commonly applied to the high-throughput growth data reading the OD600, was revised by introducing a new parameter: the decay rate, to compensate for the lowered estimation in growth rates. An improved goodness of fit in comparison to the original model was acquired due to this revision. Applying the modified logistic model to hundreds of growth data acquired from an assortment of Escherichia coli strains carrying the reduced genomes led to an intriguing finding of a correlation between the decay rate and the genome size. The decay effect seemed to be partially attributed to the decrease in cell size accompanied by a population increase and was medium dependent.ConclusionsThe present study provides not only an improved theoretical tool for the high-throughput studies on bacterial growth dynamics linking with optical turbidity to biological meaning, but also a novel insight of the genome reduction correlated decay effect, which potentially reflects the changing cellular features during population increase. It is valuable for understanding the genome evolution and the fitness increase in microbial life.

Dataset Information

Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

Publications

Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

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