Analysis of gene essentiality in Escherichia coli across strains and growth conditions

Ida Bonde, Rebecca Lennen, Joao Cardoso, Anna Koza, Markus Herrgard

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Abstract

Different types of knock-out studies have for years been applied in addressing the question of gene essentiality in various organisms. The development within the field of next generation sequencing has paved the way for more extensive studies due to the high throughput. One of these fairly resent methods is transposon insertion sequencing (Tn-Seq), in which a mutant library is constructed by randomly inserting transposons into the genome, the position of which is determined by sequencing. By knowing the number of inserts in each gene in the initial library it is possible to determine if genes are either essential or detrimental for growth in the test condition in question. In this study the TN-Seq method was used to investigate the differences in gene essentiality between four laboratory strains of E.coli subjected to four different growth conditions to investigate the reason for the differences in osmotic and chemical stress tolerance that exists between the strains as well as to assess the commonalities. Based on the sequencing data we identified genes that were essential for growth under the different conditions, some of which are essential in all conditions across strains and others that are specifically essential under certain growth conditions and/or in certain strains. This knowledge is important in the effort to engineer more stress tolerant strains, which are highly relevant for industrial purposes. Here is presented the bioinformatics analysis of the data, which includes one to one comparisons for each strain in each condition to the control condition and a multivariate analysis including all strains across conditions.
Original languageEnglish
Publication date2015
Number of pages1
Publication statusPublished - 2015
EventFirst Annual Danish Bioinformatics Conference - Odense, Denmark
Duration: 27 Aug 201527 Nov 2015

Conference

ConferenceFirst Annual Danish Bioinformatics Conference
CountryDenmark
CityOdense
Period27/08/201527/11/2015

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