Bacterial genes involved in the same process are often clustered together in the same location on the chromosome, where they are under the control of the same promoter. This ensures that all of the genes are expressed at the same time, and under the conditions in which they are all needed. The genes encoding the proteins needed for fermentation of citrate are all clustered together in the cit operon that is controlled by a promoter that is only active when no oxygen is present.
A Duplication Mutation and a New Arrangement
Whole-genome sequencing has shown that the cells in the Cit+ lineage from LTEE population #9 all have a duplication mutation that overlaps the cit operon. The duplicated segment is 2933 bp long, and extends from the 3’ end of the citG gene (in the purple arrow in the diagram) to the 5’ end of the rnk gene (the blue arrow).
The duplication contains citT as well as the upstream regulatory region and promoter of rnk. The duplication is tandem, meaning that the new copy is immediately adjacent, head-to-tail with the original copy. Because of this structure, the new copy of citT ends up being downstream and under the control of a copy of rnk’s promoter, rewiring these genetic elements and creating the new rnk-citT regulatory module. The rnk gene is normally expressed during aerobic growth, meaning that its promoter supports rnk transcription when oxygen is present. The rnk-citT module therefore leads to expression of CitT during aerobic growth, and provides access to the large citrate resource.