Network Dynamics and Cell Physiology John J. Tyson Dept. Biological Sciences Virginia Tech

Budapest Univ. Techn. & Econ. Bela Novak Attila Csikasz-Nagy Andrea Ciliberto Virginia Tech Kathy Chen Dorjsuren Battogtokh Collaborators Funding James S. McDonnell Foundation DARPA

Computational Molecular Biology DNA mRNA Protein Enzyme Reaction Network Cell Physiology …TACCCGATGGCGAAATGC... …AUGGGCUACCGCUUUACG... …Met -Gly -Tyr -Arg -Phe -Thr... ATP ADP -P XYZ E1E1 E2E2 E3E3 E4E4 Last Step

S G1 DNA replication G2 M mitosis cell division The cell cycle is the sequence of events whereby a growing cell replicates all its components and divides them more-or-less evenly between two daughter cells...

Cdk1 S G1 DNA replication G2 M mitosis cell division CycB P P Cyclin-dependent kinase Cyclin B

P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD Coupled Intra-cellular Networks !

R S response (R) signal (S) linear S=1 R rate (dR/dt) rate of degradation rate of synthesis S=2 S=3 Gene Expression Signal-Response Curve

R Kinase RP ATP ADP H2OH2O PiPi Protein Phosphorylation RP rate (dRP/dt) Phosphatase response (RP) Signal (Kinase) “Buzzer” Goldbeter & Koshland, R 0

R S EP E R rate (dR/dt) S=0 S=8 S=16 response (R) signal (S) Protein Synthesis: Positive Feedback “Fuse” Bistability Closed Open Griffith, 1968

Example: Fuse response (R) signal (S) dying Apoptosis (Programmed Cell Death) living

R S EP E R rate (dR/dt) response (R) signal (S) S=0.6 S=1.2 S=1.8 SN Protein Degradation: Mutual Inhibition “Toggle”Bistability

R S EP E X X R Positive Feedback & Substrate Depletion positive substrate signal (S) Hopf response (R) “Blinker” Glycolytic Oscillations Oscillation sss uss Higgins, 1965; Selkov, 1968

S X Y YP R RP time X YP RP response (RP) signal (S) Hopf Negative Feedback Loop Goodwin, 1965

Example: Bacterial Chemotaxis Barkai & Leibler, 1997 Goldbeter & Segel, 1986 Bray, Bourret & Simon, 1993

R S X R rate (dR/dt) S=1 S=3 S=2 S X R time Sniffer Response is independent of Signal (Levchenko & Iglesias, 2002)

primed RC fired RC primed MEN fired MEN Cdk1 CycB high MPF low MPF high SPF low SPF Cdk2 CycA Example 2: Cell Cycle (Csikasz-Nagy & Novak, 2005)

LALA Response = F L Signal = CDK Cock-and-Fire LALA L + Cdk2 CycA F +

Signal = MPF Response = B A TATA T TATA BABA B + + Cdk1 CycB Cock-and-Fire-2

P Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD bistable switch oscillator Cdc25

P Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD G1 M S/G2 M mass/nucleus M Fission Yeast

mass/nucleus Cdk1:CycB G1 S/G2 M Wild type SNIPER

Genetic control of cell size at cell division in yeast Paul Nurse Department of Zoology, West Mains Road, Edinburgh EH9 3JT, UK Nature, Vol, 256, No. 5518, pp , August 14, 1975 wild-type wee1 

P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD

wee1  mass/nucleus Cdk1:CycB G1 S/G2 M wee1  cells are about one-half the size of wild type

cell mass (au.) Wee1 activity wild-type wee period (min) PHYSIOLOGY GENETICS Two-parameter Bifurcation Diagram SNIPER

P Cdc25 Wee1 P CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD Cdc25

mass/nucleus Cdk1:CycB G1 S/G2 M cki  The Start module is not required during mitotic cycles

P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD CycB

G1 S/G2 M cki  wee1 ts 1 st 2 nd 3 rd 4 th mass/nucleus Cdk1:CycB Cells become progressively smaller without size control

P Cdc25 Wee1 P Cdc25 CycB P Cdc20 Cdh1 CKI CycB CKI CycA APC-P APC TFB I TFB A CycE CycD TFE A TFE I Cyc E,A,B CycE TFI A TFI I Cdc20 CKI CycE Cdc14 CycA CycB CycD Cdh1 CycD

endoreplication Act CycA cdc13  Fission yeast 2 param bifn diag for Cdc13 mitotic cycles endoreplication S G2 G1 M mitotic cycle mass Production of Cdc13 X No production of cyclin B (Cdc13) Wild type cdc13  cdc13 +/  ??

The Dynamical Perspective Molecular Mechanism ? ? ? Physiological Properties

The Dynamical Perspective Molecular Mechanism Kinetic Equations Vector Field Stable Attractors Physiological Properties

References Tyson, Chen & Novak, “Network dynamics and cell physiology,” Nature Rev. Molec. Cell Biol. 2:908 (2001). Tyson, Csikasz-Nagy & Novak, “The dynamics of cell cycle regulation,” BioEssays 24:1095 (2002). Tyson, Chen & Novak, “Sniffers, buzzers, toggles and blinkers,” Curr. Opin. Cell Biol. 15:221 (2003).