Transposomes: a system for identifying genes involved in bacterial pathogenesis

Application of Transposon Insertion Sequencing to Agricultural Science

Many plant-associated bacteria have the ability to positively affect plant growth and there is growing interest in utilizing such bacteria in agricultural settings to reduce reliance on pesticides and fertilizers. However, our capacity to utilize microbes in this way is currently limited due to patchy understanding of bacterial-plant interactions at a molecular level. Traditional methods of studying molecular interactions have sought to characterize the function of one gene at a time, but the slow pace of this work means the functions of the vast majority of bacterial genes remain unknown or poorly understood. New approaches to improve and speed up investigations into the functions of bacterial genes in agricultural systems will facilitate efforts to optimize microbial communities and develop microbe-based products. Techniques enabling high-throughput gene functional analysis, such as transposon insertion sequencing analyses, have great potential to be widely applied to determine key aspects of plant-bacterial interactions. Transposon insertion sequencing combines saturation transposon mutagenesis and high-throughput sequencing to simultaneously investigate the function of all the non-essential genes in a bacterial genome. This technique can be used for both in vitro and in vivo studies to identify genes involved in microbe-plant interactions, stress tolerance and pathogen virulence. The information provided by such investigations will rapidly accelerate the rate of bacterial gene functional determination and provide insights into the genes and pathways that underlie biotic interactions, metabolism, and survival of agriculturally relevant bacteria. This knowledge could be used to select the most appropriate plant growth promoting bacteria for a specific set of conditions, formulating crop inoculants, or developing crop protection products. This review provides an overview of transposon insertion sequencing, outlines how this approach has been applied to study plant-associated bacteria, and proposes new applications of these techniques for the benefit of agriculture.

Random chromosomal gene disruption in vivo using transposomes

Strain engineering of bacteria has been accomplished by many methods where mobile DNA elements (transposons) are inserted into the genomic DNA of a host organism. This chapter addresses engineering with transposable elements complexed with transposase enzyme. In traditional techniques, transposon and transposase are introduced as distinct entities. The method of mobilization into cells is often unique for each class of DNA element, and for each organism. The discovery of pre-formed transposon/transposase complexes (transposomes) that can be electroporated into living cells opens a new gateway to strain mutagenesis. Described are the preparation of electrocompetent bacterial cells and their transformation with transposomes. Once within the cell, the transposome is equipped to randomly insert its DNA into chromosomes without needing additional components. Ocr, a T7 phage protein that inhibits the host restriction of electroporated DNAs, will also be discussed as an adjunct reagent that can widen the applicability of transposomes. The transposomes used in most of the applications are commercially available, but also described is the process of making custom transposon DNAs and transposomes. The techniques are not limited to bacterial strain engineering per se and may be adapted for single-cell eukaryotes as well.