Department of Structure and Function of Retrotransposons


Head:


Katarzyna Pachulska-Wieczorek,

PhD

 


 

 Staff:

Katarzyna J. Purzycka, PhD

 

 


PhD Students:

Marcin Biesiada, MSc;

Julita Gumna, MSc;

Małgorzata Zawadzka, MSc;

Angelika Andrzejewska, MSc Eng.;

 


   

 

 

 

 

 

 

Affiliated professors:

Prof. Ryszard W. Adamiak

 

 
 

 

Key words:

retrotransposons, retroviruses, RNA structure, RNA function, nucleic acid chaperones, Gag, Ty1, HIV, HERV

 

Current research activity:

  • RNA structural elements and transitions on both 2D and 3D structure levels that specify RNA function at different stages of retroelements replication
  • RNA / protein interactions
  • Functions of Gag and Gag-derived proteins
  • Nucleic acid chaperones
  • Evolution of RNA structure

 

Actual research projects:

  • RNA structures and interactions with Gag protein that specify Ty1 RNA functions during retrotransposon replication, (2017-2021, National Since Center (Sonata Bis), Principal Investigator: Katarzyna Pachulska-Wieczorek
  • Effectors of retrotransposon movement, National Institutes of Health (2018-2022), Principal Investigator: Professor David J. Garfinkel, Collaboration: To understand how the retrotransposon restriction factor affects RNA dynamics and structure.
  • Impact of dimerization on RNA stability in the cel and Ty1 retrotransposition, (2018), Ministry of Science and Higher Education research grant for young scientists, Principal Investigator: Julita Gumna

 

Selected publications:

  1. Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R.(2018) Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition., Nat Commun. ;9(1):1549.
  2. Lepeta K, Purzycka KJ, Pachulska-Wieczorek K, Mitjans M, Begemann M, Vafadari B, Bijata K, Adamiak RW, Ehrenreich H, Dziembowska M, Kaczmarek L (2017), A normal genetic variation modulates synaptic MMP-9 protein levels and the severity of schizophrenia symptoms, EMBO Molecular Medicine, 9(8):1100-1116
  3. Z. Miao, R.W. Adamiak, M. Antczak, R.T. Batey, A.J. Becka, M. Biesiada, M.J. Boniecki, J. Bujnicki, S.J. Chen, C.Y. Cheng, F.C. Chou, A.R. Ferré-D'Amaré, R. Das, W.K. Dawson, D. Feng, N.V. Dokholyan, S. Dunin-Horkawicz, C. Geniesse, K. Kappel, W. Kladwang, A. Krokhotin, G.E. Łach, F. Major, T.H. Mann, M. Magnus, K. Pachulska-Wieczorek, D.J. Patel, J.A. Piccirilli, M. Popenda, K.J. Purzycka, A. Ren, G.M. Rice, J.J. Santalucia, J. Sarzynska, M. Szachniuk, M. Tandon, J.J. Trausch, S.Tian, J. Wang, K.M. Weeks, B. Williams, Y. Xiao, X. Xu, D. Zhang, T. Zok, E. Westhof (2017) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA, 23(5):655-672
  4. Gómez Ramos LM, Degtyareva NN, Kovacs NA, Holguin SY, Jiang L, Petrov AS, Biesiada M, Hu MY, Purzycka KJ, Arya DP, Williams LD. (2017), Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets., Biochemistry, 56(40):5288-5299.
  5. Błaszczyk L, Biesiada M, Saha A, Garfinkel DJ, Purzycka KJ. (2017), Structure of Ty1 Internally Initiated RNA Influences Restriction Factor Expression, Viruses, 9(4). pii: E74.
  6. K. Pachulska-Wieczorek, S.F. Le Grice, K.J. Purzycka (2016) Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3. Viruses, 8(7)
  7. M. Biesiada, K. Pachulska-Wieczorek, R.W. Adamiak, K.J. Purzycka (2016) RNAComposer and RNA 3D structure prediction for nanotechnology. Methods, 103:120-7
  8. D.J. Garfinkel, J.M. Tucker, A. Saha, Y. Nishida, K. Pachulska-Wieczorek, L. Błaszczyk, K.J. Purzycka (2016) A self-encoded capsid derivative restricts Ty1 retrotransposition in Saccharomyces. Curr Genet., 62(2):321-9
  9. K. Pachulska-Wieczorek, L. Błaszczyk, M. Biesiada, R.W. Adamiak, K.J. Purzycka (2016) The matrix domain contributes to the nucleic acid chaperone activity of HIV-2 Gag. Retrovirology, 13:18
  10. K. Pachulska-Wieczorek, L. Błaszczyk, J. Gumna, Y. Nishida, A. Saha, M. Biesiada, D.J. Garfinkel, K.J. Purzycka (2016) Characterizing the functions of Ty1 Gag and the Gag-derived restriction factor p22/p18. Mob Genet Elements, 6(2):e1154637
  11. Biesiada M, Purzycka KJ, Szachniuk M, Blazewicz J, Adamiak RW, (2016) Automated RNA 3D Structure Prediction with RNAComposer, Methods Mol Biol.;1490:199-215
  12. Y. Nishida, K. Pachulska-Wieczorek, L. Błaszczyk, A. Saha, J. Gumna, D.J. Garfinkel, K.J. Purzycka (2015) Ty1 retrovirus-like element Gag contains overlapping restriction factor and nucleic acid chaperone functions. Nucleic Acids Res., 3;43(15):7414-31
  13. K. Pachulska-Wieczorek, A.K. Stefaniak, K.J. Purzycka (2014) Similarities and differences in the nucleic acid chaperone activity of HIV-2 and HIV-1 nucleocapsid proteins in vitro. Retrovirology, 11:54