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Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome

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Abstract

Biological pathways are frequently identified via a genetic loss-of-function approach. While this approach has proven to be powerful, it is imperfect as illustrated by well-studied pathways continuing to have missing steps. One potential limiting factor is the masking of phenotypes through genetic redundancy. The prevalence of genetic redundancy in bacterial species has received little attention, although isolated examples of functionally redundant gene pairs exist. Here, we made use of a strain of Sinorhizobium meliloti whose genome was reduced by 45 % through the complete removal of a megaplasmid and a chromid (3 Mb of the 6.7 Mb genome was removed) to begin quantifying the level of genetic redundancy within a large bacterial genome. A mutagenesis of the strain with the reduced genome identified a set of transposon insertions precluding growth of this strain on minimal medium. Transfer of these mutations to the wild-type background revealed that 10–15 % of these chromosomal mutations were located within duplicated genes, as they did not prevent growth of cells with the full genome. The functionally redundant genes were involved in a variety of metabolic pathways, including central carbon metabolism, transport, and amino acid biosynthesis. These results indicate that genetic redundancy may be prevalent within large bacterial genomes. Failing to account for redundantly encoded functions in loss-of-function studies will impair our understanding of a broad range of biological processes and limit our ability to use synthetic biology in the construction of designer cell factories.

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Acknowledgments

Special thanks to Arlene Sutherland and the students in the Molecular Biology 3V03 course at McMaster University, who isolated many of the mutants used in this study. This work was supported by the Natural Sciences and Engineering Research Council of Canada through grants to T. M. F and an NSERC CGS scholarship to G. C. D.

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  1. Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada

    George C. diCenzo & Turlough M. Finan

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  1. George C. diCenzo
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Correspondence to Turlough M. Finan.

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diCenzo, G.C., Finan, T.M. Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome. Mol Genet Genomics 290, 1345–1356 (2015). https://doi.org/10.1007/s00438-015-0998-6

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