title: Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis.
abstract: BACKGROUND
  In the yeast Saccharomyces cerevisiae, interactions between galactose, Gal3p, Gal80p, and Gal4p determine the transcriptional status of the genes required for the galactose utilization. Increase in the cellular galactose concentration causes the galactose molecules to bind onto Gal3p which, via Gal80p, activates Gal4p, which induces the GAL3 and GAL80 gene transcription. Recently, a linear time-invariant multi-input multi-output (MIMO) model of this GAL regulatory network has been proposed; the inputs being galactose and Gal4p, and the outputs being the active Gal4p and galactose utilization. Unfortunately, this model assumes the cell culture to be homogeneous, although it is not so in practice. We overcome this drawback by including more biochemical reactions, and derive a quadratic ordinary differential equation (ODE) based model.
  
  
  RESULTS
  We show that the model, referred to above, does not exhibit bistability. We establish sufficiency conditions for the domain of attraction of an equilibrium point of our ODE model for the special case of full-state feedback controller. We observe that the GAL regulatory system of Kluyveromyces lactis exhibits an aberration of monotone nonlinearity and apply the Rantzer multipliers to establish a class of stabilizing controllers for this system.
  
  
  CONCLUSIONS
  Feedback in a GAL regulatory system can be used to enhance the cellular memory. We show that the system can be modeled as a quadratic nonlinear system for which the effect of feedback on the domain of attraction of the equilibrium point can be characterized using linear matrix inequality (LMI) conditions that are easily implementable in software. The benefit of this result is that a mathematically sound approach to the synthesis of full-state and partial-state feedback controllers to regulate the cellular memory is now possible, irrespective of the number of state-variables or parameters of interest.
authors.affiliation: Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400 076, India. vishwesh@ee.iitb.ac.in
authors.forename: Vishwesh V
authors.initials: VV
authors.lastname: Kulkarni
authors.forename: Venkatesh
authors.initials: V
authors.lastname: Kareenhalli
authors.forename: Pushkar
authors.initials: P
authors.lastname: Malakar
authors.forename: Lucy Y
authors.initials: LY
authors.lastname: Pao
authors.forename: Michael G
authors.initials: MG
authors.lastname: Safonov
authors.forename: Ganesh A
authors.initials: GA
authors.lastname: Viswanathan
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D005690:Galactose / Q000378:metabolism*; D007716:Kluyveromyces / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; D005690:Galactose