[Vierstra, 2003 TIPS ]

1. [Vierstra, 2003 TIPS]

2. [Vierstra, 2003 TIPS]

3. Ubiquitin/26S proteasome pathway Simplified Ubiquitination Proteolysis + ATP Ub E1 E2 E3 Ub Ub Ub Ub Target Target + ATP 26S proteasome

4. Loss of 26S proteasome function WT rpn10-1 Smalle et al., 2003 Loss of proteasome function in the rpn10-1 mutant, leads to growth inhibition and the accumulation of polyubiquitinated target proteins.

5. Diversity in Ubiquitination Machinery is largely provided by the many E3s Single E1 Few E2’s Many E3’s

6. Ub Ub E2 E2 E3 structure/function Target protein E3 (Ubiquitin ligase) Target binding E2 binding Target protein E3 (Ubiquitin ligase) Target binding E2 binding

7. Ub Ub Ub Ub Ub Ub Ub Ub Ub Ub Ub Ub E3 structure/function Target protein 26S proteasome Target protein E3 Target binding E2 binding

8. Number of E3s per genome Saccharomyces cereviseae Caenorhabditis elegans Drosophila melanogaster Homo sapiens Arabidopsis thaliana 68 657 189 527 1156

9. Advantages of proteolysis control in signal transduction Fast response to a change in signal intensity: direct control of protein activities in contrast to transcriptional regulation that involves transcription, transcript processing and translation steps before protein abundance is increased. 2) Proteolysis control can rapidly increase as well as decrease a proteins activity(only an increase is possible with transcriptional regulation). 3) Accurate reflection of signal intensity in response output: secundary modifications such as phosporylation/dephosphorylation can also directly change a proteins activity. However since such controls tend to be leaky, i.e. are the result of modification/demodification equilibria, their outcome depends on the initial abundance of the target protein.

10. Why more E3s in plants? • * More E3s means more proteolysis control of signaling. • * Energetically wasteful? • * Animals can side-step adverse environmental conditions. • The sessile plant must endure. • Plants need to be more sensitive to environmental changes. • * Proteolysis control of signaling allows for quick responses to changes in signal intensities (changes in environmental conditions). • * Proteolysis control also allows for an accurate response-strength to signal-intensity ratio. • * Allows for a constant state of readiness. • * Plants are less energy-limited. From Kepinski and Leyser, 2003

11. Proteolysis control of signaling Signal transduction leads to destabilization of a repressor of the response or stabilization of a response activator. This is accomplished via secundary modification (phosphorylation or dephosphorylation) of the target protein that leads to or prevents its detection by a Ubiquitin ligase (E3). Alternatively, signaling directly controls E3 affinity for the target protein. Controllingthe activity of a protein via its degradation rate allows for faster and more accurate responses to changing concentrations/intensities of the signal (changing environment).

12. The Ub/26SP pathway and signaling Describe two mechanisms that can be used to transform a signal into a response via the regulated degradation of a repressor of this response. Show how increased signal intensity leads to an increased response output.

13. The Ub/26SP pathway and signaling Describe two mechanisms that can be used to transform a signal into a response via the regulated degradation of an activator of this response. Show how increased signal intensity leads to an increased response output.

14. o r s e r s n e e p s p s e r o R Control of gene expression via conditional proteolysis EXAMPLE 1: Signal (variable) * DNA RNA Response repressor Response repressor Constitutive expression E3 Response (variable)

15. E3 a o Response (variable) r s i t v n e c p s e o R Control of gene expression via conditional proteolysis EXAMPLE 2: Signal (variable) * DNA RNA Response activator Response activator Constitutive expression

16. ABA response (Vierstra, 2009)

17. a o r s i t v n e c p s e o R Control of gene expression via conditional proteolysis EXAMPLE 3: Signal (variable) E3 DNA RNA Response activator Constitutive expression Response (variable)

18. a o r s i t v n e c p s e o R Control of gene expression via conditional proteolysis EXAMPLE 3: Photomorphogenesis Light(variable) COP1 DNA RNA HY5 Constitutive expression Light responses(variable)

19. RING Coil WD-40 repeats Ub Ub Ub Ub Ub Ub Ub COP1 acts as an E3 to target HY5 for degradation COP1 COP1 E2* bZIP HY5 HY5 E2 Degradation via 26S Proteasome Degradation by the 26S proteasome E1 (Osterlund et al.,2000)

20. Photomorphogenesis • LIGHT Light intensity COP1 HY5 LIGHT RESPONSES HY5 (Osterlund et al., 2000)

21. o r s e r s n e e p s p s e r o R Control of gene expression via conditional proteolysis EXAMPLE 4: Signal (variable) E3 DNA RNA Response repressor Constitutive expression Response (variable)

22. o r s e r s n e e p s p s e r o R Control of gene expression via conditional proteolysis EXAMPLE 4: Auxin response pathway Auxin(variable) TIR1 DNA RNA AUX/IAA factors Constitutive expression Auxin Response(variable)

23. Auxin response (Vierstra, 2009)

24. Jasmonate response (Vierstra, 2009)

25. Summary: important to remember How does a target protein become polyubiquitinated through the sequential action of E1, E2 and E3 enzymes? 26S Proteasome: structure/function. How does the proteasome detect and then degrade target proteins? Where in the cell does the Ubiquitin/26S Proteasome pathway act? ATP requiring steps in the pathway? Energy is needed to establish specific proteolysis (as opposite to non-specific). Predict the effects of loss of function of different components of the pathway (proteasome --- pleiotropic; E3 --- highly specific phenotype). Why proteolysis control of signal transduction (what are the advantages)? Possible mechanisms of conditional protein degradation to control signal/response ratios (see examples 1-4).

26. 2011

27. 2009

28. 2008