High-throughput Functional Genomic Screening using Saturating Transposon Mutant Libraries and Next Generation Sequencing in Rhizobium leguminosarum

Date
2015-04
Authors
Perry, Benjamin John
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Faculty of Graduate Studies and Research, University of Regina
Abstract

To increase the rate of scientific discovery in the Rhizobiaceae family of bacteria there is a need to adapt high-throughput genetic screens like insertion sequencing. Here we describe the adaptation of a Rhizobiaceae-compatible MmeI-adapted mariner transposon, from a previous vector pSAM_Bt, that can be used with insertion sequencing for highthroughput forward genetic screening. The newly constructed mariner transposon pSAM_Rl mutagenized R. leguminosarum, S. meliloti, and A. tumefaciens at a high frequency. In R. leguminosarum, two high-throughput forward genetic screens were performed with the vector to identify genes involved in proper cell growth on complex and minimal media. Mutant pools of R. leguminosarum 3841 were generated that saturated 83% and 80% of potential mariner insertions sites in the genome, on complex and minimal media, respectively. Analysis of the R. leguminosarum transposon insertion sequencing data with a previously described HMMbased method resulted in assignment of the contribution of the majority of the genes in the R. leguminosarum 3841 genome for growth under both growth conditions. By cross referencing these two data sets a subset of genes was found to belong to a core functional genome which contained genes required for proper growth under both conditions. Based on this analysis it is estimated that 72 and 176 genes, when interrupted by a transposon insertion, uniquely result in an impaired ability to grow on complex and minimal media, respectively; and 516 genes belonged to the core functional genome of R. leguminosarum 3841. Good concordance was observed between genes observed to be required for growth on the complex medium, but not minimal media, as described in previous studies. Growth impaired genes were annotated with their Riley functional classifications for comparison and discussion of the possible mechanisms behind the growth impaired phenotypes. Also, an overview of the functional diversity of the core functional genome is presented and discussed. Adaptation of this high-throughput forward genetic screening methodology to R. leguminosarum has been shown to be an effective method for hypothesis generation, by providing large data sets of candidate genes that require further genetic testing and characterization for there impact on cellular physiology. While the method has minor limitations and considerations that must be taken into account, it will provide a technique for future investigation of the functional genomics of R. leguminosarum in a variety of testable conditions.

Description
A Thesis Submitted to the Faculty of Graduate Studies and Research In Partial Fulfillment of the Requirements for the Degree of Master of Science in Biology, University of Regina. xi, 82 p.
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