Bhave, D. | Search bioRxiv

bioRxiv2021

Effects of the expression of random sequence clones on growth and transcriptome regulation in Escherichia coli

Comparative genomic analyses have provided evidence that new genetic functions can emerge out of random nucleotide sequences. Here, we apply a direct experimental approach to study the effects of plasmids harbouring random sequence inserts under the control of an inducible promoter. Based on data from previously described experiments dealing with the growth of clones within whole libraries, we extracted specific clones that had shown either negative or positive effects on relative cell growth. We analysed these individually with respect to growth characteristics and impact on the transcriptome. We find that candidate clones for negative peptides lead to growth arrest by eliciting a general stress response. Overexpression of positive clones, on the other hand, does not change the exponential growth rates of hosts, but they show a growth advantage over a neutral candidate clone when tested in direct competition experiments. Transcriptomic changes in positive clones are relatively moderate and specific to each clone. We conclude from our experiments that random sequence peptides are indeed a suitable source for the de novo evolution of genetic functions.

evolutionary biology↗

bioRxiv2017

Extent of adaptation is not limited by unpredictability of the environment in laboratory populations of Escherichia coli

Environmental variability is on the rise in different parts of the earth and the survival of many species depend on how well they cope with these fluctuations. Our current understanding of how organisms adapt to unpredictably fluctuating environments is almost entirely based on studies that investigate fluctuations among different values of a single environmental stressor like temperature or pH. However, in nature multiple stresses often exist simultaneously. How would unpredictability in environmental fluctuations affect adaptation under such a scenario? To answer this question, we subjected laboratory populations of Escherichia coli to selection over ~260 generations. The populations faced predictable and unpredictable environmental fluctuations across qualitatively different selection environments, namely, salt and acidic pH. We show that predictability of environmental fluctuations does not play a role in determining the extent of adaptation. Interestingly, the extent of ancestral adaptation, to the chosen selection environments, is of key importance. Integrating the insights from two previous studies, our results suggest that it is the simultaneous presence of multiple environmental factors that poses a bigger constraint on extent of adaptation, rather than unpredictability of the fluctuations.

evolutionary biology↗