Experimental Evolution Expands the Breadth of Adaptation to an Environmental Gradient Correlated With Genome Reduction.

Whether and how adaptive evolution adjusts the breadth of adaptation in coordination with the genome are essential issues for connecting evolution with ecology. To address these questions, experimental evolution in five Escherichia coli strains carrying either the wild-type genome or a reduced genome was performed in a defined minimal medium (C0). The ancestral and evolved populations were subsequently subjected to fitness and chemical niche analyses across an environmental gradient with 29 combinations of eight chemical components of the minimal medium. The results showed that adaptation was achieved not only specific to the evolutionary condition (C0), but also generally, to the environmental gradient; that is, the breadth of adaptation to the eight chemical niches was expanded. The magnitudes of the adaptive improvement and the breadth increase were both correlated with genome reduction and were highly significant in two out of eight niches (i.e., glucose and sulfate). The direct adaptation-induced correlated adaptation to the environmental gradient was determined by only a few genome mutations. An additive increase in fitness associated with the stepwise fixation of mutations was consistently observed in the reduced genomes. In summary, this preliminary survey demonstrated that evolution finely tuned the breadth of adaptation correlated with genome reduction.

Synthesis of thiophene-fused porphyrin dimers as effective π-extended helical chromophores.

We synthesized thiophene-fused porphyrin dimers as effective π-extended helical chromophores. The porphyrin dimers exhibit a red-shifted absorption with the edge extending up to 1100 nm, implying strong electronic communication over the two porphyrin moieties through the thiophene-fused structure. Importantly, their racemic inversion barriers can be modulated by the central metal ions.

Unique Role of Heterole-Fused Structures in Aromaticity and Physicochemical Properties of 7,8-Dehydropurpurins.

Porphyrins with a fused five-membered ring, such as 7,8-dehydropurpurins, have appeared as an emerging class of unique porphyrinoids. Their altered absorption spectra, relatively short lifetimes of excited states, and small HOMO-LUMO gaps arise from the harmony of the antiaromatic 20π-circuit and the aromatic 18π-circuit. In this regard, the electronic properties of 7,8-dehydropurpurins are expected to be controlled by modulating the contribution of the antiaromatic π-circuit to the whole aromaticity. Here the comparison of pyrrole- and phosphole-fused 7,8-dehydropurpurins is reported in terms of their aromaticity and physicochemical properties. The spectroscopic investigation revealed the larger contribution of the antiaromatic 24π-circuit in pyrrole-fused 7,8-dehyrdopurpurins than in phosphole-fused 7,8-dehydropurpurins. The DFT calculations also supported the feasibility of tuning the aromaticity of 7,8-dehydropurpurins by heterole-fused structures. Thus, the introduction of heterole-fused structures into porphyrinoids is a universal strategy to get new insight into aromaticity and their intrinsic properties in cyclic π-conjugated molecules.

Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction.

Genome size is determined during evolution, but it can also be altered by genetic engineering in laboratories. The systematic characterization of reduced genomes provides valuable insights into the cellular properties that are quantitatively described by the global parameters related to the dynamics of growth and mutation. In the present study, we analyzed a small collection of W3110 Escherichia coli derivatives containing either the wild-type genome or reduced genomes of various lengths to examine whether the mutation rate, a global parameter representing genomic plasticity, was affected by genome reduction. We found that the mutation rates of these cells increased with genome reduction. The correlation between genome length and mutation rate, which has been reported for the evolution of bacteria, was also identified, intriguingly, for genome reduction. Gene function enrichment analysis indicated that the deletion of many of the genes encoding membrane and transport proteins play a role in the mutation rate changes mediated by genome reduction. Furthermore, the increase in the mutation rate with genome reduction was highly associated with a decrease in the growth rate in a nutrition-dependent manner; thus, poorer media showed a larger change that was of higher significance. This negative correlation was strongly supported by experimental evidence that the serial transfer of the reduced genome improved the growth rate and reduced the mutation rate to a large extent. Taken together, the global parameters corresponding to the genome, growth, and mutation showed a coordinated relationship, which might be an essential working principle for balancing the cellular dynamics appropriate to the environment.IMPORTANCE Genome reduction is a powerful approach for investigating the fundamental rules for living systems. Whether genetically disturbed genomes have any specific properties that are different from or similar to those of natively evolved genomes has been under investigation. In the present study, we found that Escherichia coli cells with reduced genomes showed accelerated nucleotide substitution errors (mutation rates), although these cells retained the normal DNA mismatch repair systems. Intriguingly, this finding of correlation between reduced genome size and a higher mutation rate was consistent with the reported evolution of mutation rates. Furthermore, the increased mutation rate was quantitatively associated with a decreased growth rate, indicating that the global parameters related to the genome, growth, and mutation, which represent the amount of genetic information, the efficiency of propagation, and the fidelity of replication, respectively, are dynamically coordinated.