Entangled gene regulatory networks with cooperative expression endow robust adaptive responses to unforeseen environmental changes

Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, however, biological responses should also be robust to environmental or intracellular noise and mutations. Furthermore, cells must also respond to unforeseen environmental changes that have not previously been experienced, to avoid extinction prior to the evolutionary rewiring of their networks, which takes numerous generations. To address the question of how cells can make robust adaptation even to unforeseen challenges, we have investigated gene regulatory networks that mutually activate or inhibit, and we have demonstrated that complex entangled networks can make appropriate input-output relationships that satisfy such adaptive responses. Such entangled networks function when the expression of each gene shows sloppy and unreliable responses with low Hill coefficient reactions. To compensate for such sloppiness, several detours in the regulatory network exist. By taking advantage of the averaging over such detours, the network shows a higher robustness to environmental and intracellular noise as well as to mutations in the network, when compared to simple unidirectional circuits. Furthermore, it is demonstrated that the appropriate response to unforeseen environmental changes, allowing for functional outputs, is achieved as many genes exhibit similar dynamic expression responses, irrespective of inputs including unforeseen inputs. The similarity of the responses is statistically confirmed by applying dynamic time warping and dynamic mode decomposition methods. As complex entangled networks are commonly observed in the data in gene regulatory networks whereas global gene expression responses are measured in transcriptome analysis in microbial experiments, the present results give an answer to how cells make adaptive responses and also provide a different design principle for cellular networks.