Nitrogen Metabolism of Saccharomyce cervisiae

A Matlab numerical simulation based on the research of ter Schure published in the Journal of Bacteriology and Microbiology

Sarah Carratt

BIOL 398/MATH 388Loyola Marymount University

February 24, 2011

OverviewContext and purpose for modelState variablesParametersTerms for Equations How do they fit context?Differential EquationsSimulation graphs (D=.05, .29)TrendsBrief comparison with ter Schure studies

Context and PurposeThe System = The Cell

•Model shows change over time as related to state variables.

•By changing the parameters, starting concentrations, ect., my model allows observation of consequent changes in cell

State Variables factors to watch/model as they change over time

Ammonium → nitrogen α-ketoglutarate Glutamate Glutamine

Parameters V#= indirect measure of enzyme level (ke)

GDA, GS, NAD-GDH, NADPH-GDH k# = rate constant for each enzyme Du = source, inflow (dilution rate*feed concentration)

u = nitrogen + carbon D = 1/time

Understanding the Math

V4, k4V2, k2

V3, k3 V1, k1

V5, k5 V5, k5

V5, k5V5, k5

•Adding/subtracting these terms in differential equation can show production/consumption of product

Differential Equations

dxdt(keto) = V3(mate/(k3+mate))-V4(keto/(k4+keto))dxdt(mine) = V2(mate/(k2+mate))-V1(mine/(k1+mine))dxdt(mate) =

V1(mine/(k1+mine))-V2(mate*NH4/(k2+mate*NH4))+V3(keto*NH4/(k3+keto*NH4))-V4(mate/(k4+mate))+V5(keto*mine/(k5+keto*mine))

dxdt(NH4) = D*u+V1(mine/(k1+mine))+V3(mate/(k3+mate))-V2(NH4/(k2+NH4))-V4(NH4/(k4+NH4))

Simulation at Microbiology Dilution Rates

K values= 2V values = 5u = 10t = 0-10x0 = 10 or 20

FUTURE: Expand model to provide better comparison between dilution rates and alter other variables/parameters in equations

Overview of Model“Ends” of process were mostly constant (-ketoglutarate

and glutamine)Glutamate is positive and linear

Place in metabolism/Pathways that produce glutamate in cycle

Ammonium is mostly constant Slight loss initially followed by low growth in .29 (positive trend) Steeper loss initially followed by low loss in .05 (negative trend)

FUTURE Expand model to provide better comparison between dilution

rates Alter other variables/parameters in equations

Comparision with ter Schure Papers

Microbiology Bacteriology My ModelCONSTANTS Ammonium and

glucoseAmmonium flux Ammonium and

feed concentrationCHANGES Dilution rate Ammonium

concentrationDilution rate

GOALS Determine what is the regulating factor in nitrogen metabolism.

Study transcription and effect of changing carbon and nitrogen fluxes and dilution rates.

Produce a model to illustrate interaction of the four substrates of nitrogen metabolism

•Microbiology paper helped to clarify methods of Bacteriology paper•My model shows interaction of substrates ter Schure measured

Review Model shows how state variables/substrates change over time. State variables:

Ammonium → nitrogen, α-ketoglutarate, Glutamate, Glutamine Parameters:

V, k, D, u Assigned constants to reactions and +/- in equation shows

production/consumption Simulation graphs (D=.05, .29) Trends:

Middle vs. Ends The goal was to examine the interaction of substrates in nitrogen

metabolism proposed by ter Schure studies accomplished?

References

Nitrogen-regulated transcription and enzyme activities in continuous cultures of Saccharomyces cerevisia (Microbiology, 1995, 141, pp1101-1108)

The Concentration of Ammonia Regulates Nitrogen Metabolism in Saccharomyces cerevisiae (Bacteriology, 1995, 177, no. 22, pp6672-6675)

Images from class presentations by Dr. Dahlquist and Dr. Fitzpatrick