Prof. Magda Konarska

Group Leader

Laboratory of RNA Biology
ORCID ID: 0000-0001-9235-1702

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Research interests

We use the yeast S. cerevisiae spliceosome as a model of a complex molecular machine; we want to understand the details of its architecture and function.

Our goal is to understand the complex set of substrate – spliceosome interactions during assembly and catalysis, which affect the positioning of reactive groups at the active site.

Our mechanistic studies in yeast will help us to understand the molecular interactions that influence splicing fidelity and alternative splicing in metazoan systems. The spliceosomal catalytic center undergoes dynamic changes during the catalytic phase of splicing; changes of relative stabilities of competing conformations at the catalytic center affect splicing catalysis, altering splicing fidelity and thus affecting the selection of splice site sequences for catalysis. These findings have implications for alternative splicing, common to most Eukaryotes.

We test new models of snRNA:snRNA interactions at the catalytic center implicated in the function of the catalytic triplex and positioning of the branch site.

We also study spliceosomal factors involved in the substrate positioning for catalysis, in particular, those containing disordered protein domains penetrating the catalytic center.

Another project investigates exon sequences that compensate for the defects of the intron 5’SS. Isolated yeast exon motifs are similar to metazoan exon enhancers; this striking sequence similarity suggests common underlying mechanisms of action. We hypothesize that yeast exon motifs represent substrate binding sites recognized by the spliceosome; we study the molecular mechanisms underlying their function.

Members of the group

NameSurnameDegreeE-mail
BogdanCichockiPhDb.cichocki@imol.institute
MajaCieplak-RotowskaPhDm.cieplak-rotowska@imol.institute
MagdaKonarskaProf.m.konarska@imol.institute
JadwigaMeissnerj.meissner@imol.institute
IshaniSenguptai.sengupta@imol.institute

Publications

2024
  • Meissner, J., Eysmont, K., Matylla-Kulińska, K., & Konarska, M. M. (2024). Characterization of Cwc2, U6 snRNA, and Prp8 interactions destabilized by Prp16 ATPase at the transition between the first and second steps of splicing.RNA (New York, N.Y.), 30(9), 1199–1212. https://doi.org/10.1261/rna.079886.123
2023
  • Chojnowski, G., Zaborowski, R., Magnus, M., Mukherjee, S., & Bujnicki, J. M. (2023). RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints. Bioinformatics (Oxford, England), 39(9), btad527. https://doi.org/10.1093/bioinformatics/btad527
2022
  • Magnus, M. (2022). rna-tools.online: A Swiss army knife for RNA 3D structure modeling workflow. Nucleic Acids Research, 50(W1), W657–W662. https://doi.org/10.1093/nar/gkac372
2019

  • Eysmont K, Matylla-Kulińska K, Jaskulska A, Magnus M, and Konarska MM. Rearrangements within the U6 snRNA core during the transition between the two catalytic steps of splicing. Mol Cell. 75(3):538-548 (2019). https://doi.org/10.1016/j.molcel.2019.05.018

2014

  • Kurtovic-Kozaric A, Przychodzen B, Singh J, Konarska M, Clemente M, Otrock Z, Nakashima M, His E, Yoshida K, Ogawa S, Boultwood J, Padgett R, Maciejewski J, and Makishima H. PRPF8 Defects Cause Missplicing in Myeloid Malignancies. Leukemia 29, 126-136 (2014). PMID: 24781015; DOI: 10.1038/leu.2014.144

2013

  • Query CC, Konarska MM. Structural biology: Spliceosome’s core exposed. News&Views. Nature. 493(7434):615-6 (2013). Epub 2013 Jan 23. PMID: 23354053; DOI: 0.1038/nature11857.

2012

  • Query CC, Konarska MM. CEF1/CDC5 alleles modulate transitions between catalytic conformations of the spliceosome. RNA 18, 1001-1013 (2012). PMID: 22408182; DOI: 10.1261/rna.029421.111

2009

  • Smith, D.J. and Konarska, M.M. A critical assessment of the utility of protein-free splicing systems. RNA. (1);1-3 (2009). Perspective. PMID: 19029306.

  • Smith, D.J. and Konarska, M.M. Identification and characterization of a short 2’-3’ bond-forming ribozyme. RNA. (1); 8-13 (2009). Report. PMID: 19029304; DOI: 10.1261/rna.1321909.

  • Smith, D.J., Konarska, M.M., and Query, C.C. Insights into branch nucleophile positioning and activation from an orthogonal pre-mRNA splicing system in yeast. Mol Cell. 34(3):333-43 (2009). PMID: 19450531; DOI: 10.1016/j.molcel.2009.03.012

2008

  • Konarska, M.M. A purified catalytically competent spliceosome. News&Views. Nature Struct. Mol. Biol. 15(3):222-4 (2008). PMID 18319737.

  • Smith, D.J., Query, C.C., and Konarska, M.M. “Nought may endure but mutability”: Spliceosome dynamics and the regulation of splicing. Mol Cell 30(6):657-66 (2008). Review. PMID 18570869.

  • Simoes-Barbosa, A., Meloni, D., Wohlschlegel, J.A., Konarska, M.M., and Johnson, P.J. Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 5’ cap structure. RNA 14(8), 1617-31 (2008). Epub 2008 Jul2. PMCID PMC2491460.

  • Smith, D.J. and Konarska, M.M. Mechanistic insights from reversible splicing catalysis. RNA. (10):1975-8 (2008). Epub 2008 Aug 28. Perspective. PMCID PMC2553733.

2007

  • Gendra E, Colgan DF, Meany B, Konarska MM. A sequence motif in the SV40 early core promoter affects alternative splicing of transcribed mRNA. J Biol Chem. 2007 Apr20;282(16):11648-57. Epub 2007 Mar1.

  • Liu, L., Query, C.C. and Konarska, M.M. Opposing classes of prp8 alleles modulate the transition between the catalytic steps of pre-mRNA splicing. Nature Struct. Mol. Biol. 14(6):519-26 (2007). Epub 2007 May 7.

  • Smith, D.J., Query, C.C., and Konarska, M.M. trans-Splicing to Spliceosomal U2 snRNA Suggests Disruption of Branch Site-U2 Pairing during Pre-mRNA Splicing. Mol Cell;26(6):883-90 (2007).

2006
2005

  • Konarska, M.M. and Query, C.C. Insights into the mechanisms of splicing: more lessons from the ribosome. Genes Dev. 2005 Oct 1;19(19):2255-60.

2004

  • Xu, Y-Z., Newnham, C.M., Kameoka, S., Huang, T., Konarska, M.M., and Query, C.C. Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA. EMBO J. 23, 376-385 (2004).

  • Kameoka, S., Duque, P., and Konarska, M.M. p54nrb associates with the 5’ splice site within large transcription/splicing complexes. EMBO J. 23, 1782-1791 (2004).

  • Query, C.C. and Konarska, M.M. Suppression of multiple substrate mutations by spliceosomal prp8 alleles suggests functional correlations with ribosomal ambiguity mutants. Molecular Cell 14, 343-354 (2004).

2001

  • Ismaili, N., Sha, M., Gustafson, H., and Konarska, M.M. The 100 kD U5 snRNP protein (hPrp28) contacts the 5’ splice site through its ATPase site. RNA 7, 182-193 (2001).

  • Yamaguchi, Y., Filipovska, J., Yano, K., Furuya, A., Inukai, N., Narita, T., Wada, T., Sugimoto, S., Konarska, M.M., Handa, H. Stimulation of RNA Polymerase II Elongation by Hepatitis Delta Antigen. Science 293:124-127 (2001). Published online 31 May 2001; 10.1126/science.1057925.

2000

  • Filipovska, J., and Konarska, M.M. Specific HDV RNA-templated transcription by pol II in vitro. RNA 6, 41-54 (2000).

1999

  • Reyes, J.L., Gustafson, E.H., Luo, H.R., Moore, M.J., and Konarska, M.M. The C-terminal region of hPrp8 interacts with the conserved GU dinucleotide at the 5’ splice site, RNA 5, 167-179 (1999).

  • Konarska, M.M. Site-specific derivatization of RNA with photocrosslinkable groups. Methods: A Companion to Methods in Enzymology 18, 22-28 (1999).

  • Konarska, M.M., Kois, P., Sha, M., Ismaîli, N., Gustafson, E.H. and McCloskey, J. Probing of ribonucleoprotein complexes with site-specifically derivatized RNAs, in NATO Advanced Research Workshops, J. Barciszewski and B.F.C. Clark (eds.), RNA Biochemistry and Biotechnology, 229-240. Kluwer Academic Publishers, Dordrecht, The Netherlands, 1999.

  • Siatecka, M., Reyes, J.L., and Konarska, M.M., Functional interactions of Prp8 with both splice sites at the spliceosomal catalytic center. Genes & Dev. 13:1983-1993 (1999).

1998

  • Sha, M., Kois, P., and Konarska, M.M. Probing of the spliceosome with site-specifically derivatized 5′ splice site RNA oligonucleotides. RNA 4, 1069-1082 (1998).

  • Konarska, M.M. (1999) Recognition of the 5’ splice site by the spliceosome. Acta Bioch.Pol. 45, 869-881 (1998).

1996

  • Reyes, J.L., Kois, P., Konforti, B.B. and Konarska, M.M. The canonical GU dinucleotide at the 5′ splice site is recognized by p220 of the U5 snRNP within the spliceosome. RNA 2, 213-225 (1996).

1995

  • Konforti, B.B. and Konarska, M.M. A short 5′ splice site RNA oligo can participate in both steps of splicing in mammalian extracts. RNA 1, 815-827 (1995).

1994

  • Konforti, B.B. and Konarska, M.M. U4/U5/U6 snRNP recognizes the 5′ splice site in the absence of U2 snRNP. Genes and Dev. 8, 1962-1973 (1994).

1993

  • Konforti, B.B., Koziolkiewicz, M.J. and Konarska, M.M. Disruption of base pairing between the 5′ splice site and the 5′ end of U1 snRNA is required for spliceosome assembly. Cell 75, 863-873 (1993).

1992

  • Hall, K.B. and Konarska, M.M. The 5′ splice site consensus RNA oligonucleotide induces assembly of spliceosome-type complexes. Proc. Natl. Acad. Sci. USA 89, 10969-10973 (1992).

1990

  • Konarska, M.M. and Sharp, P.A. Structure of RNAs replicated by the DNA-dependent T7 RNA polymerase. Cell 63, 609-618 (1990).

1989

  • Sharp, P.A. and Konarska, M.M. The biology of splicing of precursors to mRNAs. Bristol-Myers Symposia (1989).

  • Konarska, M.M. Analysis of splicing complexes and snRNP particles by native gel electrophoresis. Methods in Enzymology, vol.180, chapter 30, p.442-453 (1989).

  • Konarska, M.M. and Sharp, P.A. Replication of RNA by the DNA-dependent RNA polymerase of phage T7. Cell 57, 423-437 (1989).

1988

  • Konarska, M.M. and Sharp, P.A. Association of U2, U4, U5 and U6 snRNPs in a spliceosome-type complex in absence of precursor RNA. Proc. Natl. Acad. Sci. USA 85, 5459-5462 (1988).

  • Lamond, A.I., Konarska, M.M., Grabowski, P.J. and Sharp, P.A. Spliceosome assembly involves the binding and release of U4 snRNP. Proc. Natl. Acad. Sci. USA 85, 411-415 (1988).

1987

  • Konarska, M.M. and Sharp, P.A. Interactions between small nuclear ribonucleoprotein particles in formation of spliceosomes. Cell 49, 763-774 (1987).

  • Lamond, A.I., Konarska, M.M. and Sharp, P.A. A mutational analysis of spliceosome assembly: Evidence for splice site collaboration during spliceosome formation. Genes & Devel. 1, 532-543 (1987).

  • Sharp, P.A., Konarska, M.M., Grabowski, P.J., Lamond, A.I., Marciniak, R. and Seiler, S.R. Splicing of messenger RNA precursors. Cold Spring Harbor Symposia on Quantitative Biology, vol 52, #71, pp 277-285 (1987).

1986

  • Konarska, M.M. and Sharp, P.A. Does Trans-splicing in vitro require base-pairing between RNAs – Reply. Cell 44, 211-211 (1986).

  • Padgett, R.A., Grabowski, P.J., Konarska, M.M., Seiler, S. and Sharp, P.A. Splicing of messenger RNA precursors. Annual Reviews of Biochem., Vol. 55, Chapter 37, pp. 1119-1150 (1986).

  • Konarska, M.M. and Sharp, P.A. Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell 46, 845-855 (1986).

1985

  • Konarska, M.M., Grabowski, P.J., Padgett, R.A. and Sharp, P.A. Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature 313, 552-557 (1985).

  • Filipowicz, W., Strugala, K., Konarska, M.M. and Shatkin, A.J. Cyclization of RNA 3′- terminal phosphate by cyclase from HeLa cells proceeds via formation of N(3′)pp(5′)A activated intermediate. Proc. Natl. Acad. Sci. USA 82, 1316-1320 (1985).

  • Padgett, R.A., Grabowski, P.J., Konarska, M.M. and Sharp, P.A. Splicing of messenger RNA precursors: Branch sites and lariat RNAs. TIBS 10, 154-157 (1985).

  • Sharp, P.A., Kingston, R.E., Baldwin, A.S., Padgett, R.A., Konarska, M.M. and Grabowski, P.J. Expression of mRNA in eukaryotic cells. In: Molecular Biology of Muscle Development, UCLA Symp. on Molecular and Cellular Biol., New Series, Vol. 29 (C. Emerson, D.A. Fischman, B. Nadal-Ginard and M.A.Q. Siddiqui, eds.), Alan R. Liss, Inc., New York, NY (1985).

  • Padgett, R.A., Konarska, M.M., Grabowski, Aebi, M., Weissmann, C. and Sharp, P.A. Studies on the mechanism of mRNA splicing in vitro. In: Sequence Specificity in Transcription and Translation , UCLA Symp. on Molecular and Cellular Biol., New Series, Vol. 30 (C. Emerson, D.A. Fischman, B. Nadal-Ginard and M.A.Q. Siddiqui, eds.), Alan R. Liss, Inc., New York, NY (1985).

  • Konarska, M.M., Padgett, R.A. and Sharp, P.A. Trans-splicing of mRNA precursors in vitro. Cell 42, 165-171 (1985).

  • Padgett, R.A., Konarska, M.M., Aebi, M., Hornig, H., Weissmann, C. and Sharp, P.A. Nonconsensus branch-site sequences in the in vitro splicing of transcripts of mutant rabbit beta-globin genes. Proc. Natl. Acad. Sci. USA 82, 8349-8353 (1985).

1984

  • Tyc, K., Konarska, M.M., Gross, H.J., and Filipowicz, W. Multiple ribosome binding to the 5′- terminal leader sequence of Tobacco Mosaic Virus RNA. Assembly of an 80S ribosome-mRNA complex at the AUU codon. Eur. J. Biochem. 140, 503-511 (1984).

  • Padgett, R.A., Konarska, M.M., Grabowski, P.J., Hardy, S.F. and Sharp, P.A. Lariat RNAs as intermediates and products in the splicing of mRNA precursors. Science 225, 898-903 (1984).

  • Konarska, M.M., Padgett, R.A. and Sharp, P.A. Recognition of cap structure in splicing in vitro of mRNA precursors. Cell 38, 731-736 (1984).

1983

  • Filipowicz, W., Konarska, M.M., Gross, H.J., and Shatkin, A.J. RNA 3′-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract. Nucleic Acids Res. 11, 1405-1418 (1983).

  • Tyc, K., Kikuchi, Y., Konarska, M.M., Filipowicz, W. and Gross, H.J. Ligation of endogenous tRNA 3′-half molecules to their corresponding 5′-halves via 2′- phosphomonoester, 3′,5′- phosphodiester bonds in extracts of Chlamydomonas. EMBO J. 2, 605-610 (1983).

1982

  • Konarska, M.M., Filipowicz, W. and Gross, H.J. RNA ligation via 2′ phosphomonoester, 3′,5′- phosphodiester linkage: Requirement of 2′,3′-cyclic phosphate termini and involvement of a 5′-hydroxyl polynucleotide kinase. Proc. Natl. Acad. Sci. USA 79, 1474-1478 (1982).

1981

  • Konarska, M.M., Filipowicz, W., Domdey, H., and Gross, H.J. Binding of ribosomes to linear and circular forms of the 5′-terminal leader fragment of Tobacco Mosaic Virus RNA. Eur.J.Biochem. 114, 221-227 (1981).

  • Konarska, M.M., Filipowicz, W., Domdey, H. and Gross, H.J. Formation of a 2′-phosphomonoester, 3′,5′-phosphodiester linkage by a novel RNA ligase in wheat germ. Nature (London) 293, 112-116 (1981).

About Group Leader

Prof. Magda Konarska is deputy director of ReMedy IRAP and deputy director for science of the International Institute of Molecular Mechanisms and Machines PAS, IMol. Following PhD at the Institute of Biochemistry and Biophysics PAS with prof. Witold Filipowicz and post-doctoral training with prof. Phillip A. Sharp at MIT, for over 25 years she led a Laboratory of Molecular Biology and Biochemistry at the Rockefeller University in New York. In 2015 she formed a Laboratory of RNA Biology at CeNT UW, later on transferred to IMol. She is a corresponding member of PAS and a member of EMBO and Academia Europaea.

Memberships and awards

2020
  • The Jakub Karol Parnas Award of the Polish Biochemical Society Member of the Academia Europaea,
2017
  • Member of the European Molecular Biology Organization
2016
  • Corresponding Member of the Polish Academy of Science
1992-1997
  • The Monique Weill-Caulier Career Scientist Award
1987-1994
  • The Lucille P. Markey Scholar Award
1983-1986
  • The Jane Coffin Childs Memorial Fund Postdoctoral Fellowship,
1985
  • The Jakub Karol Parnas Award of the Polish Biochemical Society.

Funding

2021-2025
  • National Science Centre, OPUS 20: “Structure-function analysis of the catalytic center of the spliceosome”, (01.09.2021– 31.08.2025), Leader: Magda Konarska
2017-2022
  • Foundation for Polish Science, ReMedy, “Regenerative Mechanisms for Health”, International Research Agenda Unit, (01.11.2017. – 31.10.2022), leader: Agnieszka Chacińska, deputy leader: Magda Konarska

Express interview

0.1 Dream profession of your childhood?

I was always curious about the world, mostly plants, wanting to know how they work. For example, how and why do Drosera plants (sundews) eat flies? In my early childhood I did not know who could answer such questions, so I did not have any particular dream profession in mind.

0.2 Your dream profession – now?

Now I know that I found my dream profession and I do not plan to change it. But now, rather than enjoying doing science for my own benefit, I emphasize helping others to realize how wonderful it can be!

0.3 What melody do you hum when working in the lab?

I prefer to listen to music than to make it – it is safer for my immediate environment! When writing papers or grants, there is nothing better than listening to J.S. Bach. To stimulate my brain to produce creative new ideas, I turn to modernist masters.

0.4 Your favourite joke about scientists?

A physicist, a biologist, and a chemist went to the ocean. The physicist became fascinated by the waves. He said he wanted to study the fluid dynamics of the waves and walked into the ocean. He drowned and never returned.

The biologist wanted to study the ocean’s fauna and flora and also walked into the ocean. He, too, never returned.

After a long while, the chemist concluded: “The physicist and the biologist are soluble in ocean water.”