Enhancement of K-strategy evolution in histidine utilization using a container with compartments.

Evolutionary strategies in growth improvement can be classified into r- or K-strategies. The former strategy corresponds to an evolutionary increase in growth rate, whereas the latter corresponds to an increase in the maximum amount of organisms or carrying capacity. What determines the strategies to be adopted during evolution? Spatial structures that compartmentalize the population into small patches are key to inducing the K-strategy. Interestingly, previous evolution experiments using Escherichia coli in a glucose-limited batch culture showed that carrying capacity could improve evolutionally even in the absence of spatial structures. However, it is unclear if the lack of spatial structures can direct evolution toward high carrying capacity for utilization of other resources. To address this question, we established a simplified evolution experiment using histidine-requiring E. coli grown under histidine limitation in a container with compartments. We confirmed the importance of spatial structures in K-strategy evolution in histidine utilization. Whole genome sequencing of the K-adapted strains showed functional variety of the mutated genes during the fitness-increasing period. These results validate the importance of spatial structures and imply that restriction of K-strategy evolution on a sort of nutrients is attributable to a paucity of appropriate selection rather than a paucity of causal mutation.

A reduced genome decreases the host carrying capacity for foreign DNA.

BACKGROUND: Host-plasmid interactions have been discussed largely in terms of the influences of plasmids, whereas the contributions of variations in host genomes to host interactions with foreign DNA remain unclear. A strain with a so-called "clean genome" (i.e., MDS42) of reduced genome size has recently been generated from the wild-type strain MG1655, a commonly used host strain. A quantitative evaluation of the influence of plasmid burdens in these two Escherichia coli strains can not only provide an understanding of how a reduced genome responds to foreign DNA but also offer insights into the proper application of these strains. RESULTS: The decreases in growth caused by the cost of carrying foreign DNA were similar for the wild-type and clean-genome strains. A negative correlation between the growth rate and the total amount of exogenous DNA was observed in both strains, but a better theoretical fit with a higher statistical significance was found for the strain with the clean genome. Compared to the wild-type strain, the clean-genome strain exhibited a reduced carrying capacity for exogenous DNA, which was largely attributed to its ability to restrict the replication of foreign DNA. A tendency to allocate energy and resources toward gene expression, but not DNA replication, was observed in the strain with the clean genome. CONCLUSIONS: The possession of a clean genome constrained the plasmid copy number to a wild-type-equivalent load. The results indicate that the wild-type strain possesses a greater tolerance for foreign DNA, as in endosymbiosis, and that the use of strains with clean genomes will be favorable in the applications that require precise control and theoretical prediction.

Construction of synthetic gene circuits in the Escherichia coli genome.

The construction of stable and functional synthetic circuits in bacteria is necessary in the areas of systems and synthetic biology. The common approach using plasmids to carry foreign genetic circuits offers convenience in genetic construction but is poor in genetic stability (e.g., variation in copy number). Genome recombination provides the stable genetic maintenance of synthetic circuits, but is often labor intensive and time consuming when the genetic circuits are complex and the DNA fragments become larger. The method introduced here is modified from that reported by Wanner's group and is available for integration of complex genetic circuits into the Escherichia coli chromosome.