1. Signal transduction in plants b Post-translational modifications (PTMS)
Michael Wrzaczek
Dept of Biosciences, Plant Biology
Viikki Plant Science Centre (ViPS)
University of Helsinki, Finland
Helsinki, August 18th, 2016

2. Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis.
(source:

3. PTMs are diverse Lipids Carbohydrates Degradation Protein/peptide
processing
Wang (2014) Cell Res 24:

4. ? Plants possess more than 300 PTMs
Phosphorylation is arguably the most widely studied PTM
Phosphoserine (pS)
Serine (S)
Lecture by Julia Krasensky, Friday August 19

5. PTMs can be reversible or irreversible
e.g.
Phosphorylation
PARylation
Ubiquitination
Acetylation
Degradation
Cleavage
Some forms of protein methylation

6. Friso & van Wijk (2016) Plant Physiol 169: 1469-1487

8. are attached enzymatically
Many – but not all – PTMs
are attached enzymatically
Enzyme
Substrate protein
Substrate protein
Mod
’Reverse enzyme’

9. Friso & van Wijk (2016) Plant Physiol 169: 1469-1487

10. What do PTMs do?
Increase proteome diversity
Increase functionality
Allow for rapid responses
Relatively low cost for the cell

11. PTMs increase proteome complexity

12. What do PTMs do? Charge Structure Localization Interaction
Information processing
Jensen (2006) Nature Rev Mol Cell Biol 7:

13. What do PTMs do? Hydrophobic groups for membrane localization
myristoylation
palmitoylation
isoprenylation or prenylation (farnesylation, geranylgeranylation)
GPI anchor formation

14. What do PTMs do?
Jensen (2006) Nature Rev Mol Cell Biol 7:

15. Eraser: an enzyme that removes a
Writer: an enzyme that is responsible for adding a posttranslational modification(s) into a given protein (e.g., HKMT)
Reader: a protein or protein complex that recognizes and binds specifically to a particular posttranslationally modified substrate
Eraser: an enzyme that removes a
Posttranslational modification(s) from a given protein (e.g., HDM)
Schematic representation of the processes of writing, reading, and erasing the histone posttranslational modifications.Writer enzymes add marks to histones and these marks are removed by eraser enzymes. To produce a biological readout, reader proteins specifically bind to the histone modification. The round shape in grey represents histones. The peanutlike shaped mark in blue represents the specific histone modifications.
Liu et al. (2010) Annu Rev Plant Biol 61:

16. PTMs for cellular ‚information processing‘
Prakakaran et al. (2012) WIREs Syst Biol Med doi: /wsbm.1185

17. Model for vernalization-mediated histone modifications of FLC chromatin in winter-annual accessions. Before vernalization, H3K4me3 created by ATX1 and histone acetylation promote FLC transcription despite the presence of the low level of repressive mark H3K27me3 catalyzed by the VRN2-PRC2 complex. Vernalization induces VIN3 expression; VRN5 and VEL1 are recruited to FLC chromatin to form a larger VRN2-containing PRC2 complex together with PRC2 core members to mediate H3K27me3 and histone deacetylation; and the silencing state is established and maintained. Furthermore, one or multiple unknown H3K9 methyltransferase(s) (denoted by an X) is required for catalyzing H3K9 methylation. Subsequently, LHP1 and VRN1 are recruited to stably maintain the repressed state of FLC.
Liu et al. (2010) Annu Rev Plant Biol 61:

18. How to detect PTMs?

19. protein is carrying a PTM?
How do you know your
protein is carrying a PTM?
Buehl et al. (2014) BioTechniques 57: 72-80

20. Goldknopf & Busch (1977) PNAS 74: 864-868

21. Antibodies for detecting a PTM
acceptor
protein
PARP
PARG
NAD +
ADP-ribose
Poly (ADP-ribose) n
Vainonen et al Manuscript in preparation

22. Proteomic detection of PTMs
Ytterberg & Jensen (2010) J Proteomics 73:

23. Ytterberg & Jensen (2010) J Proteomics 73: 2249-2266

24. Ytterberg & Jensen (2010) J Proteomics 73: 2249-2266

25. Summary: there are many PTMs

26. Summary: PTMs have many roles
PTMs add complexity to proteomes
and allow fast responses
Charge
Structure
Localization
Interaction
Information processing

27. Summary: PTMs have many roles
Jensen (2006) Nature Rev Mol Cell Biol 7: