Abstract:
:The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More recently, Stigler and Veliz-Cuba proposed a Boolean model that captures the bistability of the system and all of the biological steady states. In this paper, we model the well-known arabinose operon in E. coli with a Boolean network. This has several complex features not found in the lac operon, such as a protein that is both an activator and repressor, a DNA looping mechanism for gene repression, and the lack of inducer exclusion by glucose. For 11 out of 12 choices of initial conditions, we use computational algebra and Sage to verify that the state space contains a single fixed point that correctly matches the biology. The final initial condition, medium levels of arabinose and no glucose, successfully predicts the system's bistability. Finally, we compare the state space under synchronous and asynchronous update and see that the former has several artificial cycles that go away under a general asynchronous update.
journal_name
Bull Math Bioljournal_title
Bulletin of mathematical biologyauthors
Jenkins A,Macauley Mdoi
10.1007/s11538-017-0306-1subject
Has Abstractpub_date
2017-08-01 00:00:00pages
1778-1795issue
8eissn
0092-8240issn
1522-9602pii
10.1007/s11538-017-0306-1journal_volume
79pub_type
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