Abstract
Genome reduction, as a top-down approach to obtain the minimal genetic information essential for a living organism, has been conducted with bacterial cells for decades. The most popular and well-studied cell models for genome reduction are Escherichia coli strains. As the previous literature intensively introduced the genetic construction and application of the genome-reduced Escherichia coli strains, the present review focuses the design principles and compares the reduced genome collections from the specific viewpoint of growth, which represents a fundamental property of living cells and is an important feature for their biotechnological application. For the extended simplification of the genomic sequences, the approach of experimental evolution and concern for medium optimization are newly proposed. The combination of the current techniques of genomic construction and the newly proposed methodologies could allow us to acquire growing Escherichia coli cells carrying the extensively reduced genome and to address the question of what the minimal genome essential for life is.
Highlights
A comprehensive analysis of a total of 69 Multiple-Deletion Series (MDS) strains showed that the genome reduction had no advantage for growth fitness, because the growth rate of MDS69 was 17% lower than that of MG1655 [60]
The changes in growth seemed to be correlated with the genome reduction (Figure 2A, blue), which was similar to the result found in the Minimum Genome Factory (MGF) series
The results showed that the activation rate in MDS41 was only ~8% of that in MG1655, indicating that the insertion sequence (IS)-related mutation rate was significantly decreased due to genome reduction [59]
Summary
The experimental methods used for the genetic construction of the genome-reduced strains have been previously reviewed in detail [6]. We made an effort to review the relationship between the genome reduction and the growth rate of E. coli, because the growth rate was one of the most important global parameters, which quantitatively represents the activity of living cells. Our previous study showed that the accumulation of the genome reduction caused a correlated decrease in the growth rates of E. coli [7]. This finding indicated that the growth rate was a key factor in determining the importance of genome size and in understanding the size–survival relationship. We proposed experimental approaches of how to achieve genome reduction without a growth decrease
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