1. http://creativecommons.org/licenses/by-sa/2.0/

2. Generic and specific constraints shaping adaptive gene expression profiles in yeast Prof:Rui Alves ralves@cmb.udl.es 973702406 Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007 / Course: http://10.100.14.36/Student_Server/

3. Introduction  Environmental conditions change. Cells living in those environments need to adapt to those changes in order to survive environmental stresses (heat shock, osmotic...). Stress  To survive yeast changes its gene expression profile  This allows adaptation of fluxes and concentrations

4. Introduction  In principle different quantitative and qualitative gene expression profiles (GEP) could produce the same physiological adaptation  However, what has been observed is that GEPs are specific for each type of stress

5. Constraints to the changes in gene expression  Adaptation is multiobjective.  Gene expression profiles (GEPs) must induce expression of genes whose proteins are needed for the response SPECIFIC CONSTRAINTS  There may be constraints that are common to most stress conditions? GENERAL CONTRAINTS?

6. Goals  Can we identify general and specific constraints that shape an adaptive gene expression profile (GEP) of yeast under stress conditions?  If so, can we use them to characterize the quantitative changes (design principles) required for a given response?

7. Outline  Identification of a general type of constraints to GEP design  Identification of specific constraints for heat shock & Quantitative design of GEPs in heat shock response

8. What is common to all stress responses?  To adapt quickly cells need to synthesize proteins quickly and using as few resources as possible.  Globally, changes in gene expression correlate well with changes in protein levels.  Proteins are the most expensive of macromolecules.  Synthesis of new metabolites is expensive but stress specific.  Therefore a general selective pressure in stress response to adapt quickly and at low cost could shape the regulation of expression for the different genes in the GEP

9. How to save resources in protein synthesis?  H1: If proteins are abundant in the basal state, the cell is spending energy synthesizing them and keeping them at high level. Because their activity is already abundant, to save energy cells could inhibit expression of abundant proteins. Basal protein abundance Change in gene expression after stress Correlation

10. Abundant proteins are inhibited Protein abundance/10 3 1/changefold

11.  H2: Low abundance proteins have almost no total activity. To achieve larger relative increases in activity, cell could express proteins of low abundance Basal protein abundance Change in gene expression after stress Correlation How to achieve a fast increase in activity?

12. Proteins of low abundance are overexpressed Protein abundance/10 3 changefold

13.  H3: If in addition to downregulation of abundant proteins, the cell downregulates genes that code for large proteins, it will save more energy. Are there other ways to design GEP that use resources efficiently?

14.  H4: Upregulation of genes that code for small proteins. This will produce new proteins quicker and at lower cost than if upregulated proteins where larger. Protein size (MW or length) Change in gene expression after stress Correlation Are there other ways to design GEP that respond fast and use resources efficiently?

15. Size matters in modulation of gene expression? Protein size (MW) changefold Repressed genes Overexpressed genes Protein size (MW) 1/changefold Size matters in modulation of gene expression H3 H4

16. Resource usage and quickness of response general constraints for adaptive GEP?  H1: To save energy cells should inhibit proteins that are abundant  H2: To achieve larger relative increases in activity, cell should express proteins of low abundance  H3: Downregulation of genes that code for large proteins.  H4: Upregulation of genes that code for small proteins. Resource usage and quickness of response general constraints for many adaptive GEP The hypotheses are consistent with these selective pressures in the design of adaptive GEPs

17. Outline  Identification of a general constraint to GEP  Identification of specific constraints for heat shock & Quantitative design of GEPs in heat shock response

18. Heat shock response  Well characterized physiologically  Previous work ( Voit & Radivovevitch )  Enough information to identify contraints  Enough information for mathematical modelling of the relevant reactions

19. Metabolic network & physiological constraints Glycogen Trehalose NADPH HIGH ENERGY DEMAND C1 STRUCTURAL INTEGRITY -Avoids aggregation of denatured proteins -Membrane -Acts in synergism with chaperones C2 REDUCING POWER New synthesis of sphingolipids in order to change the membrane fluidity C3  Curto, Sorribas, Cascante (1995) Math. Biosci. 130, 25-50  Voit, Radivovevitch (2000) Bioinformatics 16: 1023-1037

20. Glycogen Trehalose Methodology ×5×5 ×5×5 ×5×5 5 × HXTGLKPFKTDHPYKTPSG6PDH hip 1 5 1 11 5 1 5 HXTGLKPFKTDHPYKTPSG6PDH hip 1 5 1 11 5 5 5 hip 2 3 3 33 3 3 3 HXTGLKPFKTDHPYKTPSG6PDH hip 1 5 1 11 5 5 5 hip 2 3 3 33 3 3 3 hip 3 2 1 11 2 7 7 ×2×2 ×7×7 ×2×2 7 × SIMULATIONS To explain why expression of particular genes is changed, we scanned the gene expression space and translated that procedure into different gene expression profiles (GEP) Consider a set of possible values for each enzyme. Explore all possible combinations. Total: 4.637.360 hypothetical GEPs GLK, TPS  [ 1, 2.5, 4,..., 14.5, 16, 17.5, 19] HXT  [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10] G6PDH  [1, 2, 3, 4, 5, 6, 7, 8] PFK, TDH, PYK  [ 0.25, 0.33, 0.5, 1, 2, 3, 4] HXTGLKPFKTDHPYKTPSG6PDH hip 1 5 1 11 5 5 5 hip 2 3 3 33 3 3 3 hip 3 2 1 11 2 7 7... hip 4637360 ×3×3 ×3×3 ×3×3 3 × ×3×3 ×3×3 ×3×3 NADPH

21. Implementation of stress responses Metabolic network Mathematical model Power Law form Biochemical System Theory (Savageau, 1969) Each GEP has associated a new steady state → functional changes → HS index of performance Reproduce basal conditions (25ºC) Generalised Mass Action Gene expression changes Evaluate HS performance

22. Criteria of performance  C1- Synthesis of ATP  C2- Synthesis of trehalose  C3- Synthesis of NADPH “Well-known” and studied by experimentalist

23. C1-C3 Production of trehalose, ATP, and NADPH  If we only consider the criteria concerning an increase of fluxes selects a wide set of possible GEPs (27.8 %, 1.290.454 )  The enzymes involved directly in the synthesis should be over- expressed.  In many cases, flux increase involve large metabolite accumulation, which is an undesirable situation in terms of appropriate response ■ % of the change-folds before any selection ■ % of the change-folds after selecting by C1-C3 Fold change in gene expression % of total GEPs HXT: Hexose transporters GLK: Glucokinase PFK: Phosphofructokinase TDH: Glyceraldhyde 3P dehydrogenase PYK: Pyruvate kinase TPS: Trehalose phosphate syntase G6PDH: Glucose-6-P dehydrogenase

24. Criteria of performance  C4- Accumulation of intermediates: High fluxes with high metabolite concentrations are considered a sub-optimal adaptation Reactivity Cell solubility Metabolic waste  C5- Cost of changing gene expression: GEPs that allow adaptation with minimal changes in gene expression are favoured Adaptation should be economic Minimize protein burden “Well-known” and studied by experimentalist Well-studied within a system biology perspective  C1- Synthesis of ATP  C2- Synthesis of trehalose  C3- Synthesis of NADPH cost 50 % No experimental measures are available, so we have chosen as a threshold the value that includes de 50% of all the cases

25. Criteria of performance  C1- Synthesis of ATP  C2- Synthesis of trehalose  C3- Synthesis of NADPH  C4- Accumulation of intermediates  C5- Cost of changing gene expression  C6- Glycerol production  C7- TPS and PFK over-expression  C8- F16P levels should be maintained “Well-known” and studied by experimentalist Well-studied within a system biology perspective

26. C6- Glycerol production  Glycerol production helps in producing NADPH from NADH  New synthesis of glycerolipids required  Genes are over-expressed Glicerol rate 50% Selecting GEPs with the highest glycerol production is synonymous of selecting GEPs with low PYK over- expression

27. C7- TPS and PFK  TPS is directly related with v trehalose  PFK is inversely related with v trehalose  If PFK is over-expressed, then TPS should also be over-expressed, which compromises C5 (cost)  Sensitivity analysis shows that the system is highly sensible to change PFK  50% Glycogen Trehalose

28.  F16P is required for glycerol synthesis  F16P feed-forward effect to the lower part of the glycolysis PYK velocity is increased in vitro by as much as 20 by F16P and hexose phosphates in their physiological concentration ranges This enzyme modulation facilitates the flow of material and avoids accumulation of intermediates C8- F16P levels should be maintained

29. Results based on all previous criteria C1 C2 C3 C4 C5 C6 C7 C8

30. Selected profiles HXT: Hexose transporters GLK: Glucokinase PFK: Phosphofructokinase TDH: Glyceraldhyde 3P dehydrogenase PYK: Piruvate kinase TPS: Trehalose phosphate syntase G6PDH: Glucose-6-P dehydrogenase ■ % of the change-folds before any selection ■ % of the change-folds after selecting by ALL criteria Fold change in gene expression % of total GEPs Fulfill all criteria of HS performance: SIMULATION: 0.06% of GEPs (4238 ) All experimental databases

31. Are the eight criteria of performance specific for heat shock? We analyzed 294 GEPs from microarray experiments under different environmental conditions C1C2C3C4C5C6C7C8 Alkali   H202H202   Diamide  ... HeatShock  Only heat shock conditions are selected

32. What happens under other conditions? (Principal Component Analysis) Stationary HeatS H2O2H2O2 Diamide Stationary HeatS H2O2H2O2 Diamide Sporulation factor1factor2factor3factor4 factor1 factor2factor3factor4 factor2 factor1 factor3

33. Summary  Identification of general constraints in GEP  Identification of a set of constraints that are specific for heat shock  Identification of the quantitative design of the heat shock GEP  Support by experimental evidence  Specificity of the set of constraints

34. Acknowledgments  FCT  Ramon y Cajal Program MCyT  FUP program MCyT