Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function. (December 2017)

• Record Type: Journal Article
• Authors: Rodrigo, Guillermo; Bajić, Djordje; Elola, Ignacio; Poyatos, Juan
• Is Part Of: Npj systems biology and applications. Volume 3(2017)
• Page Start: 1
• Page End: 9
• Publication Date: 2017-12
• Subjects: Systems biology -- Periodicals; 570.113
• DOI: 10.1038/s41540-017-0031-2
• Languages: English
• ISSNs: 2056-7189

Abstract

Abstract Many essential bacterial responses present complex transcriptional regulation of gene expression. To what extent can the study of these responses substantiate the logic of their regulation? Here, we show how the input function of the genes constituting the response, i.e., the information of how their transcription rates change as function of the signals acting on the regulators, can serve as a quantitative tool to deconstruct the corresponding regulatory logic. To demonstrate this approach, we consider the multiple antibiotic resistance (mar ) response inEscherichia coli . By characterizing the input function of its representative genes in wild-type and mutant bacteria, we recognize a dual autoregulation motif as main determinant of the response, which is further adjusted by the interplay with other regulators. We show that basic attributes, like its reaction to a wide range of stress or its moderate expression change, are associated with a strong negative autoregulation, while others, like the buffering of metabolic signals or the lack of memory to previous stress, are related to a weak positive autoregulation. With a mathematical model of the input functions, we identify some constraints fixing the molecular attributes of the regulators, and also notice the relevance of the bicystronic architecture harboring the dual autoregulation that is unique inE. coli . The input function emerges then as a tool to disentangle the rationale behind most of the attributes defining themar phenotype. Overall, the present study supports the value of characterizing input functions to deconstruct the complexity of regulatory architectures in prokaryotic and eukaryotic systems. Dissecting cellular "recipes": Reverse engineering the complex regulation of a bacterial response with the use of input functions Many cellular responses result from the integration of numerous regulatory signals. To deconstruct the regulation of one of these responses, which enables resistance to multiple antibiotics inEscherichia coli, a team led by Juan F. Poyatos at the National Center for Biotechnology in Madrid studied the response input function by combining theoretical models and experiments. This function quantifies the rate of transcription of the genes constituting the response with respect to the signals acting on its cognate regulators. By examining how the shape of the function changes in different situations, e.g., when a given regulator is mutated, the team identified the implications for the specificity and dynamics of the response of a dual autoregulation at the core of the control architecture. The use of input functions as quantitative tools allows us to reverse engineer the complex regulations that dictate essential physiological functions in both prokaryotic and eukaryotic cells.