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

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

PTMs are diverse Lipids Carbohydrates Degradation Protein/peptide processing Wang (2014) Cell Res 24: 143-160

? 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

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

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

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

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

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

PTMs increase proteome complexity

What do PTMs do? Charge Structure Localization Interaction Information processing Jensen (2006) Nature Rev Mol Cell Biol 7: 391-403

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

What do PTMs do? Jensen (2006) Nature Rev Mol Cell Biol 7: 391-403

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: 395-420

PTMs for cellular ‚information processing‘ Prakakaran et al. (2012) WIREs Syst Biol Med doi: 10.1002/wsbm.1185

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: 395-420

How to detect PTMs?

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

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

Antibodies for detecting a PTM acceptor protein PARP PARG NAD + ADP-ribose Poly (ADP-ribose) n Vainonen et al. 2016. Manuscript in preparation

Proteomic detection of PTMs Ytterberg & Jensen (2010) J Proteomics 73: 2249-2266

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

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

Summary: there are many PTMs

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

Summary: PTMs have many roles Jensen (2006) Nature Rev Mol Cell Biol 7: 391-403