The Deponte lab compares enzymes and protein machineries from baker's yeast (Saccharomyces cerevisiae), the kinetoplastid parasite Leishmania tarentolae and the apicomplexan human malaria parasite Plasmodium falciparum. These unicellular organisms are excellent study objects for comparative biochemistry because they belong to three independent eukaryotic lineages and have a completely different lifestyle and biology.

The objective of our organismic triangulation is to decipher:

1) Principles in biochemistry that are common to all eukaryotes

2) Parasite-specific properties and anomalies that could be exploited for intervention

Methods

We perform in-depth analyses of enzyme mechanisms and protein structure-function relationships using a variety of methods that range from:

1) Molecular modeling and other bioinformatic analyses in order to develop hypotheses.

2) Purification and in vitro charcaterization of recombinant wild-type and mutant proteins including redox titrations, UV-Vis spectroscopy, CD spectroscopy as well as steady-state and stopped-flow enzyme kinetic measurements and inhibition studies.

3) Heterologous complementation assays, plasmid shuffling and/or SLI and CRISPR-Cas9 genetics in S. cerevisiae, L. tarentolae and/or P. falciparum.

Current projects

The research concept on comparative biochemistry is currently applied to two major topics: thiol-dependent redox metabolism and mitochondrial protein import. 

1) For example, we assess the catalytic mechanisms of peroxiredoxins and glutaredoxins in living cells using redox-sensitive green fluorescent protein (shown above) in collaboration with Bruce Morgan (Saarbrücken), Jan Riemer (Cologne) and Ana Tomás (Porto).

2) The enzyme kinetics and redox properties of diverse wild-type and mutant glutaredoxins, peroxiredoxins, flavoenzymes and the artemisinin-susceptibility factor kelch13 from P. falciparum are also compared in vitro to identify structure-function relationships and mechanistic principles (DFG grants DE 1431/19-1 and DE 1431/20-1 since 2023).

3) Protein-protein interactions within mitochondrial protein import machineries are studied by quantitative mass spectrometry in collaboration with Michael Schroda and Timo Mühlhaus (BioComp since 2022).

4) The relevance of redox processes for parasite development and the mode of action of antimalarial drugs are analyzed in collaboration with Michael Lanzer and the Parasitology Unit in Heidelberg as well as the DFG-funded graduate school RTG 2737 (Stressistance since 2022).

For further information, please have a look at the publications and/or contact Marcel Deponte.

Complete list of publications

ORCID (external summary)   &   Google scholar (external summary)

Enzymology selection

• Lang L, Reinert P, Diaz C, and Deponte M. (2024) The dithiol mechanism of class I glutaredoxins promotes specificity for glutathione as a reducing agent. Redox Biol. 78:103410.

• Geissel F*, Lang L*, Husemann B, Morgan B, and Deponte M. (2024) Deciphering the mechanism of glutaredoxin-catalyzed roGFP2 redox sensing reveals a ternary complex with glutathione for protein disulfide reduction. Nature Commun. 15:1733.

• Lang L, Wolf AC, Riedel M, Thibol L, Geissel F, Feld K, Zimmermann J, Morgan B, Manolikakes G, and Deponte M. (2023) Substrate promiscuity and hyperoxidation susceptibility as potential driving forces for the co-evolution of Prx5-type and Prx6-type 1-Cys peroxiredoxin mechanisms. ACS Catalysis 13:3627-43.

• Zimmermann J, Oestreicher J, Hess S, Herrmann JM, Deponte M*, and Morgan B*. (2020) One cysteine is enough: A monothiol Grx can functionally replace all cytosolic Trx and dithiol Grx. Redox Biol. 36:101598.

• Liedgens L*, Zimmermann J*, Wäschenbach L*, Geissel F, Laporte H, Gohlke H*, Morgan B*, and Deponte M*. (2020) Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins. Nature Commun. 11:1725.

• Staudacher V, Trujillo M, Diederichs T, Dick TP, Radi R*, Morgan B*, and Deponte M*. (2018) Redox-sensitive GFP fusions for monitoring the catalytic mechanism and inactivation of peroxiredoxins in living cells. Redox Biol. 14:549-56.

• Begas P*, Liedgens L*, Moseler A, Meyer AJ, and Deponte M. (2017) Glutaredoxin catalysis requires two distinct glutathione interaction sites. Nature Commun. 8:14835.

Molecular parasitology selection

• Hieronimus K, Donauer T, Klein J, Hinkel B, Spänle JV, Probst A, Niemeyer J, Kibrom S, Kiefer AM, Schneider L, Husemann B, Bischoff E, Möhring S, Bayer N, Klein D, Engels A, Ziehmer BG, Stieß J, Moroka P, Schroda M* , and Deponte M*. (2024) A modular cloning toolkit for the production of recombinant proteins in Leishmania tarentolae. Microbial Cell 11:128-42.

• Haag M, Kehrer J, Sanchez C, Deponte M*, and Lanzer M*. (2022) Physiological jump in erythrocyte redox potential during Plasmodium falciparum development occurs independent of the sickle cell trait. Redox Biol. 58:102536.

• Schumann R, Bischoff E, Klaus S, Möhring S, Flock J, Keller S, Remans K, Ganter M, and Deponte M. (2021) Protein abundance and folding rather than the redox state of Kelch13 determine the artemisinin susceptibility of Plasmodium falciparum. Redox Biol. 48:102177.

• Turra GL, Liedgens L, Sommer F, Schneider L, Zimmer D, Vilurbina Perez J, Koncarevic S, Schroda M, Mühlhaus T, and Deponte M. (2021) In vivo structure-function analysis and redox interactomes of Leishmania tarentolae Erv. Microbiol. Spec. e00809-21.

• Turra GL, Schneider L, Liedgens L, and Deponte M. (2021) Testing the CRISPR-Cas9 and glmS ribozyme systems in Leishmania tarentolae. Mol. Biochem. Parasitol. 241:111336.

• Specht S, Liedgens L, Duarte M, Stiegler A, Wirth U, Eberhardt M, Tomás AM, Hell K*, and Deponte M*. (2018) A single-cysteine mutant and chimeras of essential Leishmania Erv can complement the loss of Erv1 but not of Mia40 in yeast. Redox Biol. 15:363-74.

• Wezena CA, Alisch R, Golzmann A, Liedgens L, Staudacher V, Pradel G, and Deponte M. (2017) The cytosolic glyoxalases of Plasmodium falciparum are dispensable during asexual blood-stage development. Microbial Cell 5:32-41.

• Eckers E, Cyrklaff M, Simpson L, and Deponte M. (2012) Mitochondrial protein import pathways are functionally conserved among eukaryotes despite compositional diversity of the import machineries. Biol. Chem. 393:513-24.

Review selection

• Deponte M. (2022) Glutathione and glutathione-dependent enzymes. In Redox Chem. Biol. Thiols 241-275.

• Deponte M. (2017) The incomplete glutathione puzzle: Just guessing at numbers and figures? Antioxid. Redox Signal. 27:1130-61.

• Deponte M. (2013) Glutathione catalysis and the reaction mechanisms of glutathione-dependent enzymes. Biochim. Biophys. Acta 1830:3217-66.

• Deponte M*, Hoppe HC*, Lee M*, Maier AG*, Richard D*, Rug M*, Spielmann T*, and Przyborski JM*. (2012) Wherever I may roam: Protein and membrane trafficking in P. falciparum-infected red blood cells. Mol. Biochem. Parasitol. 186:95-116.