The energy-demand and metabolic requirements of plant cells differ under changing environmental conditions. Mitochondria and chloroplasts, which are both organelles of endosymbiotic origin, are central hubs in the conversion of energy and redox homeostasis in plant cells. They are connected to metabolic pathways from different subcellular compartments. Hence, both organelles are ideally placed to act as sensors of the energetic and metabolic status of the plant cell. Perturbations of the cellular energy status can lead to a reconfiguration of organellar activities, which in turn have profound effects on other cellular compartments, including major changes in nuclear gene expression. Changes in nuclear gene expression triggered by signals derived from metabolic perturbations in organelles are termed retrograde responses and are critical to allow adaptation of the bioenergetic state of the organelles. Nearly nothing is known about the signaling processes transducing the retrograde responses. We are interested in deciphering the role of post-translational modifications (PTMs) in this process. PTMs provide a powerful mechanism to rapidly and temporarily alter protein functions and locations in the cell, and they are also capable of providing information to regulatory proteins by creating docking sites for PTM-recognition domains. Intriguingly, the substrates of several major PTM-modifying enzymes are either central metabolites or redox-active compounds, as for example ATP, acetyl-CoA, NAD+, and glutathione, which suggests that the activity of these enzymes could be directly coupled to the energy status or redox status of the of the organelle (Hartl and Finkemeier, 2012). The main goal of our research is to unravel the regulatory processes that coordinate organellar functions in dependence on environmental and metabolic cues.

Current research projects:

1. Exploring the role of lysine acetylation in the regulation of cellular functions

Reversible acetylation of the ε-amino group of lysine has recently emerged as a major post-translational modification of proteins controlling many important cellular functions beyond histone modification. Acetylation of lysine residues of proteins is regulated by the activities of acetyltransferases and deacetylases. Both our own recent results in Arabidopsis and research in animal systems showed that lysine acetylation acts as an on/off switch for enzyme activities as well as a signal for cargo transport in several cellular processes regulating energy metabolism, signaling cascades and cytoskeleton dynamics. The aim of our research is to reveal the function and importance of lysine acetylation in the regulating of plant metabolic pathways and signaling processes involved in the plant stress response. Recently, we mapped the Arabidopsis acetylome and identified lysine-acetylated sites on organellar and cytosolic proteins of diverse functional classes in Arabidopsis thaliana. We have now also developed a new isotope-labeling and immunoenrichment-based method for relative quantification of lysine acetylation sites on plant proteins.

Fig 1 Finkemeier

Fig. 1. Work-flow for identification of lysine-acetylated proteins in Arabidopsis.

Fig 2 Finkemeier

Fig. 2. Lysine acetylation is a reversible post-translational modification of proteins catalysed by lysine acetyltransferases (KATs) and deacetylases (KDACs). Proteins of diverse cellular compartments and functions have been identified as lysine acetylated in plants and other organisms (from Finkemeier and Schwarzer, Biospektrum, 2013, modified).

2. Sensing and signaling of metabolic states in plants

One of the most important mechanisms to coordinate adjustments of the metabolic network is by regulation via internal signals generated from specific metabolites to regulate gene expression in the nucleus. A large number of metabolic genes is already known whose expression is regulated by altered concentrations of key nutrient metabolites such as sugars and nitrate. Furthermore, evidence is emerging that metabolite signaling of gene expression may be mediated through many additional metabolites, such as tricarboxylic acids (Finkemeier et al., 2013). The aim of our research is to identify novel metabolite binding proteins that could act as sensors for changes in metabolite abundances. Since nearly nothing is known about the interacting proteins that link metabolites and signaling pathways together, it will be of great importance to identify new sensor proteins and to define their functions in plants.

Fig 3 Finkemeier

Fig. 3: Mitochondrial metabolism and central metabolites potentially involved in retrograde signaling.