title: Adaptation with transcriptional regulation.
abstract: Biochemical adaptation is one of the basic functions that are widely implemented in biological systems for a variety of purposes such as signal sensing, stress response and homeostasis. The adaptation time scales span from milliseconds to days, involving different regulatory machineries in different processes. The adaptive networks with enzymatic regulation (ERNs) have been investigated in detail. But it remains unclear if and how other forms of regulation will impact the network topology and other features of the function. Here, we systematically studied three-node transcriptional regulatory networks (TRNs), with three different types of gene regulation logics. We found that the topologies of adaptive gene regulatory networks can still be grouped into two general classes: negative feedback loop (NFBL) and incoherent feed-forward loop (IFFL), but with some distinct topological features comparing to the enzymatic networks. Specifically, an auto-activation loop on the buffer node is necessary for the NFBL class. For IFFL class, the control node can be either a proportional node or an inversely-proportional node. Furthermore, the tunability of adaptive behavior differs between TRNs and ERNs. Our findings highlight the role of regulation forms in network topology, implementation and dynamics.
authors.affiliation: Center for Quantitative Biology, Peking University, Beijing 100871, China.
authors.forename: Wenjia
authors.initials: W
authors.lastname: Shi
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Wenzhe
authors.initials: W
authors.lastname: Ma
authors.affiliation: Center for Quantitative Biology, Peking University, Beijing 100871, China.|School of Physics, Peking University, Beijing 100871, China.
authors.forename: Liyang
authors.initials: L
authors.lastname: Xiong
authors.affiliation: Center for Quantitative Biology, Peking University, Beijing 100871, China.|School of Physics, Peking University, Beijing 100871, China.
authors.forename: Mingyue
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Center for Quantitative Biology, Peking University, Beijing 100871, China.|School of Physics, Peking University, Beijing 100871, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Tang
mesh_terms: D000220:Adaptation, Biological; D000465:Algorithms; D025461:Feedback, Physiological; D005786:Gene Expression Regulation; D015971:Gene Expression Regulation, Enzymologic; D053263:Gene Regulatory Networks; D008954:Models, Biological; D014158:Transcription, Genetic