Abstract
Cells generally adapt to environmental changes by first exhibiting an immediate response and then gradually returning to their original state to achieve homeostasis. Although simple network motifs consisting of a few genes have been shown to exhibit such adaptive dynamics, they do not reflect the complexity of real cells, where the expression of a large number of genes activates or represses other genes, permitting adaptive behaviors. Here, we investigated the responses of gene regulatory networks containing many genes that have undergone numerical evolution to achieve high fitness due to the adaptive response of only a single target gene; this single target gene responds to changes in external inputs and later returns to basal levels. Despite setting a single target, most genes showed adaptive responses after evolution. Such adaptive dynamics were not due to common motifs within a few genes; even without such motifs, almost all genes showed adaptation, albeit sometimes partial adaptation, in the sense that expression levels did not always return to original levels. The genes split into two groups: genes in the first group exhibited an initial increase in expression and then returned to basal levels, while genes in the second group exhibited the opposite changes in expression. From this model, genes in the first group received positive input from other genes within the first group, but negative input from genes in the second group, and vice versa. Thus, the adaptation dynamics of genes from both groups were consolidated. This cooperative adaptive behavior was commonly observed if the number of genes involved was larger than the order of ten. These results have implications in the collective responses of gene expression networks in microarray measurements of yeast Saccharomyces cerevisiae and the significance to the biological homeostasis of systems with many components.
Highlights
Adaptive responses to environmental changes are fundamental to all living organisms
Homeostasis is an inherent property of biological systems, which have a general tendency to adapt, i.e., to recover their original state following environmental changes
Cells respond to environmental changes by altered gene/protein expression; subsequently, the expression of most genes returns to basal levels, albeit not completely, as shown by recent experimental analyses of yeast
Summary
Adaptive responses to environmental changes are fundamental to all living organisms. When environmental conditions change, the cellular concentrations of some chemicals change immediately in response; the degree of change is later reduced, returning closer to the basal state. In general, some variables within a biological system first change in response to environmental changes, but slowly revert back to pre-stimulus values by adjusting the expression levels of proteins or mediating cellular activity for adaptation to the new conditions. In such an adaptive response, some internal variables change according to the external conditions, while other variables return to the original values, realizing both responsiveness and homeostasis. They found that only two major core topologies can show an adaptive response: a negative feedback loop with a buffering node and an incoherent feed-forward loop with a proportioned node
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
