Research interests

RNA processing represents an important, highly intricate and relatively underexplored layer of gene expression in plants. Plant hormonal pathways have been relatively well elucidated (Hrtyan et al., 2015). We are a small team that utilizes the excellent lab expertise on hormonal pathways in plants to explore the relevance of key steps of mRNA processing, particularly alternative splicing (AS) and m⁶A mRNA methylation, connecting these two seemingly unrelated fields.

We have previously identified the Arabidopsis factors (writers) required for the m⁶A methylation of mRNA (Ruzicka et al., 2017). Later, we proposed the possible molecular mechanism(s) underlying the role of m⁶A in auxin-dependent processes (Zemlyanskaya et al., 2023). We are currently studying the importance of subcellular compartmentalization of another RNA modification, t⁶A on tRNA (Zemlyanskaya et al., unpublished).  Additionally, we uncovered earlier how AS interferes with the function of the major auxin transporter PIN7 (Kashkan et al., 2020, 2022b). We are currently seeking the upstream (possibly m⁶A-related) cues regulating this process (Viveka et al., unpublished). We are also currently exploring selected examples of how AS can impact auxin signaling (Sun et al., unpublished) and auxin synthesis (Yamoune et al., unpublished).

We have also developed some tools. First, we designed a box where the temporal dynamics of seedling morphology can be monitored under various light conditions (Kashkan et al., 2022a). Second, we made available a machine-learning algorithm for determining evolutionary conservation of protein splice isoforms (plant and animal) (Timofeyenko et al., 2023), including a user-friendly interface (catsnap.cesnet.cz).

Team

Kamil Růžička

Supervisor

Elena Zemlyanskaya

Postdoc

Amel Yamoune

Postdoc

Viveka

PhD student

Feijian Sun

PhD student

Anastasiia Holoborodko

Master student

Collaborators (recent and ongoing)

Maria Kalyna (BOKU Vienna, AT), Jozef Mravec (Slovak Academy of Sciences, SK), Dorothee Staiger (Bielefeld University, DE), Mary O’Connell, Miloslava Fojtová (CEITEC Masaryk University, Brno, CZ), Dior Kelley (Iowa State University, Ames, US), Alper Akay (University of East Anglia, Norwich, UK), Ari Pekka Mähönen (University of Helsinki, FI)

Main publications

Zemlyanskaya EA, Zemlianski V, Pěnčík A, Kelley D, Helariutta Y, Novák O, Růžička K. 2023. N6-adenosine methylation of mRNA integrates multilevel auxin response and ground tissue development in Arabidopsis. Development, 150 (19): dev201775. DOI: 10.1242/dev.201775

Timofeyenko K, Kanavalau D, Alexiou P, Kalyna M, Růžička K. 2023. Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. New Phytologist 238(4):1722-1732. DOI: 10.1111/nph.18799

Kashkan I, García-González J, Lacek J, Müller K, Růžička K, Retzer K, Weckwerth W. 2022a. RaPiD-chamber: Easy to self-assemble live-imaging chamber with adjustable LEDs allows to track small differences in dynamic plant movement adaptation on tissue level. bioRxiv: 2022.08.13.503848. DOI: 10.1101/2022.08.13.503848

Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, et al. 2022b. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist 233: 329–343. DOI: 10.1111/nph.17792

Ruzicka K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El-Showk S, Li H, Zhong S, et al. 2017. Identification of Factors Required for m6A mRNA Methylation in Arabidopsis Reveals a Role for the Conserved E3 Ubiquitin Ligase HAKAI. New Phytologist 215: 157–172. DOI: 10.1111/nph.14586

Ruzicka K, Strader LC, Bailly A, Yang H, Blakeslee J, Langowski L, Nejedlá E, Fujita H, Itoh H, Syono K, et al. 2010. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole-3-butyric acid. Proceedings of the National Academy of Sciences of the United States of America 107: 10749–10753. DOI: 10.1073/pnas.1005878107

Ruzicka K, Simásková M, Duclercq J, Petrásek J, Zazímalová E, Simon S, Friml J, Van Montagu MCE, Benková E. 2009. Cytokinin regulates root meristem activity via modulation of the polar auxin transport. Proceedings of the National Academy of Sciences of the United States of America 106: 4284–4289. DOI: 10.1073/pnas.0900060106

Ruzicka K, Ljung K, Vanneste S, Podhorská R, Beeckman T, Friml J, Benková E. 2007. Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution. The Plant Cell 19: 2197–2212. DOI: 10.1105/tpc.107.052126

Kashkan I, Timofeyenko K, Růžička K. 2022c. How alternative splicing changes the properties of plant proteins. Quantitative Plant Biology 3. DOI: 10.1017/qpb.2022.9

Hrtyan M, Šliková E, Hejátko J, Růžička K. 2015. RNA processing in auxin and cytokinin pathways. Journal of Experimental Botany 66: 4897–4912. DOI: 10.1093/jxb/erv189

Růžička K, Ursache R, Hejátko J, Helariutta Y. Xylem development – from the cradle to the grave. New Phytologist. 2015. DOI: 10.1111/nph.13383

Notable alumni

• Ksenia Timofeyenko, PhD student
• Ivan Kashkan, PhD student
• Gabriela Hristova, bachelor student
• Viktor Dressler, master student
• Dominika Honusová, master student
• Viktoria Mironova, bachelor student
• Mária Saleh, master student

Old memories