RESUMO
Complex gene-regulation networks are made of simple recurring gene circuits called network motifs. The functions of several network motifs have recently been studied experimentally, including the coherent feed-forward loop (FFL) with an AND input function that acts as a sign-sensitive delay element. Here, we study the function of the coherent FFL with a sum input function (SUM-FFL). We analyze the dynamics of this motif by means of high-resolution expression measurements in the flagella gene-regulation network, the system that allows Escherichia coli to swim. In this system, the master regulator FlhDC activates a second regulator, FliA, and both activate in an additive fashion the operons that produce the flagella motor. We find that this motif prolongs flagella expression following deactivation of the master regulator, protecting flagella production from transient loss of input signal. Thus, in contrast to the AND-FFL that shows a delay following signal activation, the SUM-FFL shows delays after signal deactivation. The SUM-FFL in this system works as theoretically predicted despite being embedded in at least two additional feedback loops. The present function might be carried out by the SUM-FFL in systems found across organisms.
Assuntos
Proteínas de Bactérias/fisiologia , Proteínas de Ligação a DNA/fisiologia , Proteínas de Escherichia coli/fisiologia , Escherichia coli/fisiologia , Retroalimentação Fisiológica , Flagelos/fisiologia , Regulação Bacteriana da Expressão Gênica , Proteínas de Membrana/fisiologia , Modelos Genéticos , Fator sigma/fisiologia , Transativadores/fisiologia , Arabinose/farmacologia , Proteínas de Bactérias/biossíntese , Proteínas de Bactérias/genética , Proteínas de Ligação a DNA/biossíntese , Proteínas de Ligação a DNA/genética , Escherichia coli/genética , Proteínas de Escherichia coli/biossíntese , Proteínas de Escherichia coli/genética , Fucose/farmacologia , Regulação Bacteriana da Expressão Gênica/efeitos dos fármacos , Genes Reporter , Proteínas de Membrana/biossíntese , Proteínas de Membrana/genética , Óperon/genética , Proteínas Recombinantes de Fusão/biossíntese , Proteínas Recombinantes de Fusão/genética , Fator sigma/biossíntese , Fator sigma/deficiência , Fator sigma/genética , Fatores de Tempo , Transativadores/biossíntese , Transativadores/genéticaRESUMO
Detailed understanding and control of biological networks will require a level of description similar to that of electronic engineering blueprints. Currently, however, even the best-studied systems are usually described using qualitative arrow diagrams. A quantitative blueprint requires in vivo measurements of (1) the relative strength of the interactions (numbers on the arrows) and (2) the functions that integrate multiple inputs. Here, we address this using a well-studied system, the flagella biosynthesis transcription network in Escherichia coli. We use theory and high-resolution experiments to obtain a quantitative blueprint with (1) numbers on the arrows, finding different hierarchies of activation coefficients for the two regulators, FlhDC and FliA; and (2) cis-regulatory input functions, which summate the input from the two regulators (SUM gates). We then demonstrate experimentally how this blueprint can be used to reprogram temporal expression patterns in this system, using controlled expression of the regulators or point mutations in their binding sites. The present approach can be used to define blueprints of other gene networks and to quantitatively reprogram their dynamics.