Aleksandra Skirycz

Professor
Lab Number: 210
Office number: 205
Research Overview

Small-molecule regulatory networks – from interactions to function

Small-molecule Regulatory Network

The Small-molecule Regulatory Networks group aims to uncover the function of small molecules. We are especially interested in identifying and characterizing the functionality of metabolites acting at the nexus of metabolism and growth under control (health) and stress (disease) conditions. The group works primarily with Arabidopsis and yeast, but we don’t shy away from other model and non-model organisms. The long-term goal of our research is to apply our findings to improve plant and animal health.

Living organisms are outstanding organic chemists, producing diverse small-molecule compounds that cover vast structural and functional diversity. These compounds – called metabolites – are central to all biological processes, from structural elements and energy sources, to regulators and signals. Not surprisingly, natural compounds constitute an essential source of drugs and agrochemicals. Yet, the metabolome remains largely terra incognita.

Why the mystery? First of all, we do not understand the full chemical complexity of even well-studied model organisms. Secondly, we often do not understand the function of the metabolites we do know, while new roles are constantly being assigned to central compounds such as amino acids and sugars.

How do you identify the function of a metabolite? Small molecules rarely work on their own but rather via interactions with proteins. Thus, following the proverbial “tell me who your friends are, and I will tell you who you are,” identification of protein interactors can be used to unravel the function of a metabolite.

How do you identify metabolite–protein interactions? To gain insight into the function of small molecules, the Small-molecule Regulatory Networks group uses a unique experimental toolbox, which enables metabolite–protein–protein interaction studies on a cell-wide scale and in near-in vivo conditions. We combine classical biochemistry with state-of-the-art mass spectrometry metabolomic and proteomic methods, and use computational tools to generate and mine metabolite–protein interaction networks.

The group originated at the Max-Planck-Institute of Molecular Plant Physiology, Golm, Germany, where it will continue as a partner guest group until March 2022. https://www.mpimp-golm.mpg.de/2218806/skirycz

The diversity of quinoa morphological traits and seed metabolic composition
2022.
Tabatabaei, I., Alseekh, S., Shahid, M., Leniak, E., Wagner, M., Mahmoudi, H., Thushar, S., Fernie, A.R., Murphy, K.M., Schmöckel, S.M., Tester, M., Mueller-Roeber, B., Skirycz, Aleksandra, Balazadeh, S.
Sci Data.
9
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Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae.
2022.
Palos, K., Nelson Dittrich, A.C., Yu, L., Brock, J.R., Railey, C.E., Wu, H.L., Sokolowska, E., Skirycz, Aleksandra, Hsu, P.Y., Gregory, B.D., Lyons, E., Beilstein, M.A., Nelson, Andrew D.L.
Plant Cell..
:
Past accomplishments and future challenges of the multi-omics characterization of leaf growth.
2022.
Skirycz, Aleksandra, Fernie, A.R.
Plant Physiol..
:
Regulation of Plant Primary Metabolism–How Results From Novel Technologies Are Extending Our Understanding From Classical Targeted Approaches
2022.
Skirycz, Aleksandra, Caldana, C., Fernie, A.R.
Critical Reviews in Plant Sciences.
:
A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato
2022.
Mi, J., Vallarino, J.G., Petřík, I., Novák, O., Correa, S.M., Chodasiewicz, M., Havaux, M., Rodriguez-Concepcion, M., Al-Babili, S., Fernie, A.R., Skirycz, Aleksandra, Moreno, J.C.
Metab Eng..
70
:
166–180
2′,3′-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana
2022.
Chodasiewicz, M., Kerber, O., Gorka, M., Moreno, J.C., Maruri-Lopez, I., Minen, R.I., Sampathkumar, A., Nelson, Andrew D.L., Skirycz, Aleksandra
Plant Physiol..
:
The AtMYB60 transcription factor regulates stomatal opening by modulating oxylipin synthesis in guard cells
2022.
Simeoni, F., Skirycz, Aleksandra, Simoni, L., Castorina, G., de Souza, L.P., Fernie, A.R., Alseekh, S., Giavalisco, P., Conti, L., Tonelli, C., Galbiati, M.
Sci Rep.
12
:
533
The Role of Triacylglycerol in the Protection of Cells Against Lipotoxicity Under Drought in Lolium multiflorum/Festuca arundinacea Introgression Forms.
2022.
Perlikowski, D., Lechowicz, K., Skirycz, Aleksandra, Michaelis, Ä., Pawłowicz, I., Kosmala, A.
Plant Cell Physiol..
pcac003
:
Combination of network and molecule structure accurately predicts competitive inhibitory interactions
2021.
Razaghi-Moghadam, Z., Sokolowska, E.M., Sowa, M.A., Skirycz, Aleksandra, Nikoloski, Z.
Comput Struct Biotechnol J..
19
:
2170–2178
Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana
2021.
Calderan-Rodrigues, M.J. Luzarowski, M., Monte-Bello, C.C., Minen, R.I., Zühlke, B.M., Nikoloski, Z., Skirycz, Aleksandra, Caldana, C.
Front Plant Sci..
12
:
758933
PROMISed: A novel web-based tool to facilitate analysis and visualization of the molecular interaction networks from co-fractionation mass spectrometry (CF-MS) experiments.
2021.
Schlossarek, D., Luzarowski, M., Sokołowska, E., Górka, M., Willmitzer, L., Skirycz, Aleksandra
Comput Struct Biotechnol J..
:
Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins.
2021.
Ginsawaeng, O., Gorka, M., Erban, A., Heise, C., Brueckner, F., Hoefgen, R., Kopka, J., Skirycz, Aleksandra, Hincha, D.K., Zuther, E.
Int J Mol Sci..
22
:
8172
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
2021.
Alseekh, S., Aharoni, A., Brotman, Y., Contrepois, K., D'Auria, J., Ewald, J., C Ewald, J., Fraser, PD., Giavalisco, P., Hall, RD., Heinemann, M., Link, H., Luo, J., Neumann. S., Nielsen, J., Perez de Souza, L., Saito, K., Sauer, U., Schroeder, Frank, Schuster, S., Siuzdak, G., Skirycz, Aleksandra, Sumner, LW., Snyder, MP., Tang, H., Tohge, T., Wang, Y., Wen, W., Wu, S., Xu, G., Zamboni, N., Fernie, AR.
Nature Methods.
18
:
747–756
Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism
2021.
Camilo Moreno, J., Rojas, B.E., Vicente, R., Gorka, M., Matz, T., Chodasiewicz, M., Peralta-Ariza, J.S., Zhang, Y., Alseekh, S., Childs, D., Luzarowski, M., Nikoloski, Z., Zarivach, R., Walther, D., Hartman, M.D., Figueroa, C.M., Iglesias, A.A., Fernie AR, Skirycz, Aleksandra
EMBO J..
40
:
e106800
Functional characterization of proton antiport regulation in the thylakoid membrane
2021.
Uflewski, M., Mielke, S., Galvis, V.C., von Bismarck, T., Chen, X., Tietz, E., Ruß, J., Luzarowski, M., Sokolowska, E., Skirycz, Aleksandra, Eirich, J., Finkemeier, I., Schöttler, M.A., Armbruster, U.
Plant Physiol..
:
A Multi-OMICs Approach Sheds Light on the Higher Yield Phenotype and Enhanced Abiotic Stress Tolerance in Tobacco Lines Expressing the Carrot lycopene β-cyclase1 Gene
2021.
Moreno, J.C., Martinez-Jaime, S., Kosmacz, M., Sokolowska, E.M., Schulz, P., Fischer, A., Luzarowska, U., Havaux, M., Skirycz, Aleksandra
Front Plant Sci.
12
:
Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity
2021.
Luzarowski, M., Vicente, R., Kiselev, A., Wagner, M., Schlossarek, D., Erban, A., de Souza, L.P., Childs, D., Wojciechowska, I., Luzarowska, U., Górka, M., Sokołowska, E.M., Kosmacz, M., Moreno, J.C., Brzezińska, A., Vegesna, B., Kopka, J., Fernie, A.R., Willmitzer, L., Ewald, J.C., Skirycz, Aleksandra
Communications Biology.
4
:
Adjustment of Photosynthetic and Antioxidant Activities to Water Deficit Is Crucial in the Drought Tolerance of Lolium multiflorum/Festuca arundinacea Introgression Forms
2020.
Lechowicz, K., Pawlowicz, I., Perlikowski, D., Arasimowicz-Jelonek, M., Blicharz, S., Skirycz, Aleksandra, Augustyniak, A., Malinowski, R., Rapacz, M., Kosmala, A.
Int J Mol Sci.
:
Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90 and ROF1
2020.
Tirumalaikumar, V.P., Gorka, M., Schulz, K., Maxclaux-Daubresse, C., Sampathkumar, A., Skirycz, Aleksandra, Vierstra, R.D., Balazadeh, S.
Authphagy.
:
Identification and Characterization of the Heat-Induced Plastidial Stress Granules Reveal New Insight Into Arabidopsis Stress Response
2020.
Chodasiewicz, M., Sokolowska, E.M., Nelson-Dittrich, Anna C., Masiuk, A., Beltran, J.C.M., Nelson, Andrew D.L., Skirycz, Aleksandra
Front Plant Sci..
11
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