40 research outputs found
A reduced genome decreases the host carrying capacity for foreign DNA
BackgroundHost-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.ResultsThe 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.ConclusionsThe 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
Mutation accumulation under UV radiation in Escherichia coli
Mutations are induced by not only intrinsic factors such as inherent molecular errors but also by extrinsic mutagenic factors such as UV radiation. Therefore, identifying the mutational properties for both factors is necessary to achieve a comprehensive understanding of evolutionary processes both in nature and in artificial situations. Although there have been extensive studies on intrinsic factors, the mutational profiles of extrinsic factors are poorly understood on a genomic scale. Here, we explored the mutation profiles of UV radiation, a ubiquitous mutagen, in Escherichia coli on the genomic scale. We performed an evolution experiment under periodic UV radiation for 28 days. The accumulation speed of the mutations was found to increase so that it exceeded that of a typical mutator strain with deficient mismatch repair processes. The huge contribution of the extrinsic factors to all mutations consequently increased the risk of the destruction of inherent error correction systems. The spectrum of the UV-induced mutations was broader than that of the spontaneous mutations in the mutator. The broad spectrum and high upper limit of the frequency of occurrence suggested ubiquitous roles for UV radiation in accelerating the evolutionary process
Global coordination in adaptation to gene rewiring
Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional changes. However, the probability of adaptation and the underlying common principles are not clear. We performed a systematic survey of an assortment of gene-rewired Escherichia coli strains to address these questions. Three different cell fates, designated good survivors, poor survivors and failures, were observed when the strains starved. Large fluctuations in the expression of the rewired gene were commonly observed with increasing cell size, but these changes were insufficient for adaptation. Cooperative reorganizations in the corresponding operon and genome-wide gene expression largely contributed to the final success. Transcriptome reorganizations that generally showed high-dimensional dynamic changes were restricted within a one-dimensional trajectory for adaptation to gene rewiring, indicating a general path directed toward cellular plasticity for a successful cell fate. This finding of global coordination supports a mechanism of stochastic adaptation and provides novel insights into the design and application of complex genetic or metabolic networks
Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli
Stochastic switching of a bistable genetic circuit represents a potential cost-saving strategy for adaptation to environmental challenges. This study reports that stochastic switching of a monostable circuit can be sufficient to mediate reversible adaptation in E. coli
Bacterial Cells Carrying Synthetic Dual-Function Operon Survived Starvation
A synthetic dual-function operon with a bistable structure was designed and successfully integrated into the bacterial genome. Bistability was generated by the mutual inhibitory structure comprised of the promoters P tet and P lac and the repressors LacI and TetR. Dual function essential for cell growth was introduced by replacing the genes (i.e., hisC and leuB) encoding proteins involved in the biosynthesis of histidine and leucine from their native chromosomal locations to the synthetic operon. Both colony formation and population dynamics of the cells carrying this operon showed that the cells survived starvation and the newly formed population transited between the two stable states, representing the induced hisC and leuB levels, in accordance with the nutritional status. The results strongly suggested that the synthetic design of proto-operons sensitive to external perturbations is practical and functional in native cells
Stochasticity in Gene Expression in a Cell-Sized Compartment
The gene expression in a clonal cell
population fluctuates significantly,
and its relevance to various cellular functions is under intensive
debate. A fundamental question is whether the fluctuation is a consequence
of the complexity and redundancy in living cells or an inevitable
attribute of the minute microreactor nature of cells. To answer this
question, we constructed an artificial cell, which consists of only
necessary components for the gene expression (<i>in vitro</i> transcription and translation system) and its boundary as a microreactor
(cell-sized lipid vesicle), and investigated the gene expression noise.
The variation in the expression of two fluorescent proteins was decomposed
into the components that were correlated and uncorrelated between
the two proteins using a method similar to the one used by Elowitz
and co-workers to analyze the expression noise in <i>E. coli</i>. The observed fluctuation was compared with a theoretical model
that expresses the amplitude of noise as a function of the average
number of intermediate molecules and products. With the assumption
that the transcripts are partly active, the theoretical model was
able to well describe the noise in the artificial system. Furthermore,
the same measurement for <i>E. coli</i> cells harboring
an identical plasmid revealed that the <i>E. coli</i> exhibited
a similar level of expression noise. Our results demonstrated that
the level of fluctuation found in bacterial cells is mostly an intrinsic
property that arises even in a primitive form of the cell