Eugene Savenkov

Molecular Plant-Virus Interactions 

Viral infections cause substantial losses in crop yield and quality. These losses arise from virus-induced changes in host development, metabolism, and defence, which are manifested as disease symptoms. Our research aims to understand the molecular and cellular mechanisms by which plant RNA viruses manipulate host processes to promote infection and cause disease.

We focus on how viruses interfere with host gene expression, development, and immunity through nuclear-imported viral proteins (NVPs), virus-derived small RNAs, and noncanonical RNA species. By combining molecular genetics, cell biology, transcriptomics, and functional assays, we seek to identify host pathways that can be exploited for durable resistance and to define general principles of infection biology.

Current research themes

•    Viral control of host transcription and development
We study nuclear-imported viral proteins encoded by RNA viruses that act as transcriptional regulators and reprogram host gene expression. 

•    Organelle communication and stress responses
We investigate how viruses interact with mitochondria, chloroplasts, and the nucleolus to promote infection. This work examines mitochondrial function, retrograde signalling to the nucleus, and the intersection of organelle biology with antiviral defence.

•    RNA structure, stability, and noncanonical RNA species
We study exoribonuclease-resistant RNAs (xrRNAs), viral chimeric RNAs, and other structured RNA elements that influence viral RNA stability, processing, and function. This research connects RNA architecture to infection outcome, RNA metabolism, and viral evolution.

•    RNA silencing and its suppression
We analyse viral suppressors of RNA silencing, their sequence variability, and their interactions with host defence factors. This work addresses how viruses balance replication, movement, and defence evasion, and how suppressor function evolves under natural selection.

•    Virus cell-to-cell and long-distance movement
We examine viral movement proteins, host factors required for cell-to-cell and systemic infection, and the role of intracellular trafficking, microtubules, and phloem transport in virus spread.

To advance these studies, we integrate cell and molecular biology with bioinformatics, confocal microscopy, transcriptomics, ChIP-seq, promoter analysis, protein-interaction assays, and reverse genetics. Although rooted in plant virology, our work has broader implications for infection biology, gene regulation, organelle communication, and stress responses in eukaryotes. 

TEACHING IN HIGHER EDUCATION

2022-2026    Immunology and allergy in a food perspective, 7.5 HP, course administrator, lecturing, group discussions, examination
2022-2024    Genetics, 7.5 HP, lecturing
2017-2021    Immunology and Genetics at the organismal and molecular levels, 15 HP, course administrator, lecturing, group discussions, examination
2013-2016    Immunology, 5 HP, course administrator, lecturing, group discussions, examination
2011-2016    Genetics I, 10 HP, course administrator, lecturing, group discussions, examination
2008-2016    Virology, 15 HP, lecturing
2007-2016    Genetic Engineering, 15 HP, lecturing
2007             Biotechnology, lecturing
2002-2005    The Basic course in plant breading, lecturing and practicum
2002-2005    Gene Expression and regulation in animal, fungal and plant cells, lecturing 
2004-2005    RNA-interference and short regulatory RNAs Uppsala Graduate School in Biomedical Research (UGSBR), Uppsala BMC
2002-2004    The molecular defence of plants, 10 HP, lecturing

Original articles in refereed scientific journals

1.     Roy, S., Nemes, K., Saripella, G. V., Vetukuri, R. R., Siddique, A. B., & Savenkov, E. I. (2026). Comparative transcriptome profiling of Nicotiana benthamiana plants infected with potato mop-top virus and its mutant lacking a gene for the 8K protein underlines the role of chloroplasts during infection. Molecular Plant-Microbe Interactions, 39: 351-366.

2.    Nemes K., Gil J.F., Liebe S., Mansi M., Poimenopoulou E., Lennefors B-L., Mark Varrelmann M., Savenkov E.I. (2024) Intermolecular base-pairing interactions, a unique topology and exoribonuclease-resistant noncoding RNAs drive formation of viral chimeric RNAs in plants. New Phytologist, 241: 861-877.

3.    Muellender M., Savenkov E.I., Reichelt M., Varrelmann M., Liebe S. (2022) The Virulence Factor p25 of Beet Necrotic Yellow Vein Virus Interacts With Multiple Aux/IAA Proteins From Beta vulgaris: Implications for Rhizomania Development. Frontiers in Microbiology, 12: 809690. 

4.    Müllender M., Varrelmann M., Savenkov E.I., Liebe S. (2021) Manipulation of auxin signalling by plant viruses. Molecular Plant Pathology, 22: 1449-1458.  

5.    Vetukuri R.R., Kalyandurg P.B., Saripella G.V., Sen D., Gil J.F., Lukhovitskaya N.I., Grenville-Briggs L.J., Savenkov E.I. (2020) Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species. Archives of Virology, 165: 2953-2959.  

6.    Gil J.F., Wibberg D., Eini O., Savenkov E.I., Varrelmann M., Liebe S. (2020) Comparative Transcriptome Analysis Provides Molecular Insights into the Interaction of Beet necrotic yellow vein virus and Beet soil-borne mosaic virus with Their Host Sugar Beet. Viruses, 12, 76; doi:10.3390/v12010076 

7.    Kalyandurg P.B., Tahmasebi A., Vetukuri R.R., Kushwaha S.K., Lezzhov A.A., Solovyev A.G., Grenville-Briggs L.J., Savenkov E.I. (2019) Efficient RNA silencing suppression activity of Potato Mop-Top Virus 8K protein is driven by variability and positive selection. Virology, 535: 111-121. 

8.    Gil J.F., Liebe S., Thiel H., Lennfors B-L., Kraft T., Gilmer D., Maiss E., Varrelmann M., Savenkov E.I. (2018) Massive up-regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease. Molecular Plant Pathology, 19: 2333-2348

9.    Cowan G.H., Roberts A.G., Jones S., Kumar P., Kalyandurg P.B., Gil J.F., Savenkov E.I., Hemsley P.A., Torrance L. (2018) Potato mop-top virus co-opts the stress sensor HIPP26 for long-distance movement. Plant Physiology, 176: 2052-2070.

10.    Kalyandurg P., Gil J. F., Lukhovitskaya N.I., Flores B., Müller G., Chuquillanqui C., Palomino L., Monjane A., Barker I., Kreuze J., Savenkov E.I. (2017) Molecular and pathobiological characterization of 61 Potato mop-top virus full-length cDNAs reveals great variability of the virus in the centre of potato domestication, novel genotypes and evidence for recombination. Molecular Plant Pathology, 18: 864-877. 

11.    Moschou P.N., Savenkov E.I., Minina E.A., Fukada K., Reza S.H., Gutierrez-Beltran E., Sanchez-Vera V., Suarez M.F., Hussey P.J., Smertenko A.P., Bozhkov P.V. (2016) EXTRA SPINDLE POLES (Separase) controls anisotropic cell expansion in Norway spruce (Picea abies) embryos independently of its role in anaphase progression. New Phytologist, 212: 232-243. 

12.    Lukhovitskaya N.I., Cowan G.H., Vitukuri R. R., Tilsner J., Torrance L., Savenkov E.I. (2015) Importin-α mediated nucleolar localisation of potato mop-top virus TRIPLE GENE BLOCK1 (TGB1) protein facilitates virus systemic movement, whereas TGB1 self-interaction is required for cell-to-cell movement in Nicotiana benthamiana. Plant Physiology, 167: 738-752.

13.    Lukhovitskaya N. I., Vitukuri R. R., Sama I., Thaduri S., Solovyev A. G., Savenkov E.I. (2014) A viral transcription factor exhibits antiviral RNA silencing suppression activity independent of its nuclear localization. Journal of General Virology, 95: 2831-2837. 

14.     Lukhovitskaya N.I., Leshchiner A.D., Boddeti S.K., Thaduri S., Solovyev A.G., Savenkov E.I. (2013) An RNA virus-encoded zinc-finger protein acts as a plant transcription factor and induces a regulator of cell size and proliferation in two tobacco species. The Plant Cell, 25: 960-973.

15.    Lukhovitskaya N.I., Thaduri S., Garushyants S.K., Torrance L., Savenkov E.I. (2013) Deciphering the mechanism of defective interfering RNA (DI RNA) biogenesis reveals that a viral protein and the DI RNA act antagonistically in virus infection. Journal of Virology, 87: 6091-6103. 

•    Savenkov E.I. (2021) Pomoviruses (Virgaviridae). In: Encyclopedia of Virology, 4th edition, Vol. 3: 603-611. Elsevier. [Invited contribution]
•    Savenkov E.I. (2021) Virgaviruses (Virgaviridae). In: Encyclopedia of Virology, 4th edition, Vol. 3: 839-851. Elsevier. [Invited contribution]