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Department of Protein Biosynthesis

Head: Professor Włodzimierz Zagórski-Ostoja

 

During the last few years, the Department of Protein Biosynthesis has continued studies proteins and the genomesof RNA viruses.

The studies on the PVY VPg (Potato Virus Y), carried out by the Prof. W. Zagórski and Prof. Jadwiga Chroboczek’s team, concerned the interaction of this protein with the eIF4E factor and the impact of this interaction on the inhibition of cell proliferation.

The Anna Boguszewska-Chachulska team till March 2009 continued search for inhibitors of HCV (Hepatitis Virus C) replication. This activity is continued by Professor Anna Boguszewska in her new laboratory in Warsaw Polytechnics.

Studies on regulatory elements of PRLV genome carried out under leadership of Dr. A. Pałucha were ended in the beginning on 2009, team members joined the other groups at the Institute.

One of the main interest of Department stays in genomic studies. This is reflected in participation of several Institute groups in the international Potato Genome Sequencing Consortium (PGSC). This intra-institute effort is coordinated by W. Zagórski. In October 2009 first draft of potato genome sequence was submitted by PGSG to public domain.

Research has also been continued on PSTVd RNA aimed at achieving better understanding of viroid infection (ADr. nna Góra-Sochacka’s team).

On-going research at the Department also covers studies on Adenovirus dodecahedron perceived as a possible vector anticancer drugs and as a delivery platform for influenza virus antigens (Dr. Ewa Szołajska’s team).

A novel field of studies focuses on the development of electrochemical sensors allowing for the detection of biologically active proteins and their structural dynamics (Assoc. Prof. Krystyna Grzelak’s team in cooperation with Institute of Animal Reproduction and Food Research, Prof. J. and Hanna Radeccy, Olsztyn).

The teams of Prof. A. Jerzmanowski and Dr. M. Prymakowska-Bosak deal with chromatin-based mechanisms underlying development and epigenetic memory in vascular plants.


Regulation of gene expression, synthesis and proteins structures

Group leader: Assoc. Prof. Krystyna Grzelak

The potato virus Y terminal protein (Vpg)

Group leader: Prof. Włodzimierz Zagórski-Ostoja
Staff: Assoc. Prof. Jadwiga Chroboczek, Dr. Ewa Szołajska, M.Sc. Izabela Wojtal (Ph.D student)

 

Potyviruses belong to the picornavirus superfamily of RNA plus-stranded viruses. Potato virus Y (PVY) is a common potyvirus of agricultural importance. Plant viruses belonging to the Potyviridae family have VPg protein covalently attached to the 5` end of their linear RNA genomes. VPg is the virulence factor of potyviruses since its removal abolishes viral RNA infectivity. However, its precise role in the virus life cycle is not well understood. It has been implicated in protein translation, long-distance movement in plant tissue, and replication. It has been shown that it interacts with viral RNA polymerase, suggesting a role in viral RNA synthesis. In the infected cells as well as in vitro, through interaction with the host initiation factor eIF4E, potyviruses VPg proteins are implicated in modulating plant resistance to virus infection. Natural plant resistance to potyvirus infection has been shown to stem from the inability of VPg to interact with eIF4E, as a result of amino acid mutations either in VPg or in eIF4E.

 

Current projects:
Current project on plant virus VPg protein has two major goals. The first is identification of the site on VPg responsible for the interaction with eIF4E in the infected host. The second goal is identification of other components of the host cell interacting with VPg protein. This approach might pinpoint novel mechanism, through which the virus insures the success of its life cycle.

 

Research grant:
2009-2010 "Viral protein VPg, structural and functional studies", (Ministry of Sciences and Higher Education)
2007-2009 "Interaction of viral genom-linked protein VPg with host cell factors", (Ministry of Sciences and Higher Education)

 

Selected publications:

  1. Grzela R., Szołajska E., Ebel C., Madern D., Favier A., Wojtal I., Zagórski W., Chroboczek J. Virulence Factor of Potato Virus Y, Genome-attached Terminal Protein VPg, Is a Highly Disordered Protein. J. Biol. Chem. (2008) 283: 213-221
  2. Strokovskaia L.I., Grzela R., Chroboczek J., Kikhno I.M., Chashchina L.I., Solomko A.P. Complex formation between recombinant protein VPg of potato virus Y and heterologous eukaryotic translation initiation factors eIF4E. Ukr. Biokhim. Zh. (2007) 79(1): 85-93
  3. Grzela R., Strokovska L., Andrieu J.P., Dublet B., Zagorski W., Chroboczek J. Potyvirus terminal protein VPg, effector of host eukaryotic initiation factor eIF4E. Biochimie. (2006) 88(7): 887-96

Patent:

Chroboczek J. , Grzela R. , Ostoja-Zagórski W.  Cell-proliferation inhibiting VPg proteins, fragments or analogs thereof and their applications, WO2008/152527


Regulation of gene expression, synthesis and proteins structures: the study on structure and function of insect proteins. The synthesis of biologically active proteins in heterologous expression systems

Group leader: Assoc. Prof. Krystyna Grzelak

Staff: Dr. Edyta Kopera, Dr. Andżeła Dwornyk, Dr. Małgorzata Milner, MM.Sc. Marcin Mielecki(Ph.D. student)

 

In our laboratory the studies on structure and function of selected recombinant proteins, which might be promising in biotechnology (silk proteinase inhibitor, SPI), agriculture (juvenile hormone binding protein, JHBP) or be important for medicine (Jak and RIO kinases), are conducted.

Recombinant SPI-His6 expressed in yeast (Pichia pastoris) is a highly active against bacterial and fungal serine proteinases. We demonstrated that rSPI when fused to a target protein could protect the target against proteinases degradation. The structure of rSPI-His6 was resolved in NMR studies.

The research on rJHBP-His8 expressed in P. pastoris focused on characterization of glycan associated with protein using electrospray mass spectrometry. The studies on the identification of the site(s) of the ligand(s) binding to rJHBP-His8 are in progress.

Both rSPI-His6 and rJHBP-His8 were used as model proteins for studying of protein-antybody and protein-hormone interactions by electro-chemical sensors (collaboration with the Institute of Animal Reproduction and Food Research, Prof. H. and J. Radeccy). We developed two sensors. The first one, based on anti-His antibody, for the detection of his-tagged protein (rSPI-His6) in the culture medium. The limit of detection of rSPI-His6 was 50fg/ml. The second sensor enables research on interaction of rJHBP-His8 with juvenile hormones (JHs) and methoprene. The obtained results indicated that JHBP undergoes conformation changes upon JHs or methoprene binding. The analytical system proposed might be applied to the monitoring in the environment of methoprene, which is a widely used insecticide.

We were also interested in obtaining the recombinant Janus Kinase 2 (Jak2) in baculovirus system and RIO1/RIO3 kinases in E.coli cells and purification of the proteins to homogeneity. The expressed recombinant Jak2 kinase domain was purified in a two step chromatography, first on glutathione-agarose and further on Ni-NTA agarose resin. The activity of purified rJak2 kinase domain as well as rRIO1/rRIO3 kinases were verified by in vitro autocatalytic kinase assay with [γ32P]ATP and by luminescence test. The studies on interaction of the enzymes with commercial and new-synthesized inhibitors are in progress. The inhibitors of Jak and RIO kinase families are potential anticancer drugs.

 

Current projects:

  1. Fabricating an immunosensor based on Fab fragments of anti-His antibody for the detection of histidine tagged proteins. With this approach we are expecting increased stability and reusability of the system.
  2. Investigation a novel inhibitors of oncogenic Jak2 tyrosine kinases by screening of low molecular compounds library in Center for Bio-Active Molecules Screening (CMBA, Grenoble).

Research projects:
2009-2012 "Macromolecules participating in the transport of juvenile hormone binding protein and the expression
                   of its gene", (Ministry of Sciences and Higher Education)
2005-2008 "Application of Biosensors in Molecular Biology", (Ministry of Sciences and Higher Education)
2005-2008 "The protein kinase inhibitors as potential anticancer and antiviral agents", (Ministry of Sciences
                   and Higher Education)
2005-2008 "The Juvenile hormone binding protein structure; its gene, regulatory elements and expression",
                   (Ministry of Sciences and Higher Education)
2003-2005 "The novel method of removing of affinity tag during protein purification", (Ministry of Sciences
                   and Higher Education)
2002-2004 "Natural and recombinant protease inhibitors", (NATO Czech-Polish Linkage Grant)

 

Selected publications:

  1. Wasowicz M., Viswanathan S., Dvornyk A., Grzelak K., Kłudkiewicz B., Radecka H. Comparison of electrochemical immunosensors based on gold nano materials and immunoblot techniques for detection of histidine-tagged proteins in culture medium. Biosens. Bioelectron. (2008) 24: 284-289
  2. Grzelak K., Radecka H. Elektrochemiczna biosonda molekularna w badaniach oddziaływań białko-hormon. Na pograniczu chemii i biologii, Henryk Koroniak, Jan Barciszewski (red), Wydawnictwo Naukowe UAM w Poznaniu (2008) XX: 541-559
  3. Stobiecka A., Dvornyk A., Grzelak K., Radecka H. Electrochemical impedance spectroscopy for the study of juvenile hormones-recombinant protein interactions. Front. Biosci. (2008) 13: 2866-74
  4. Milner M., Grzelak K., Zhukov I., Zagórski-Ostoja W. Niestandardowe inhibitory proteaz – peptydy rodziny Kazala. Na pograniczu Chemii i Biologii, Wydawnictwo Naukowe Uniwersytetu A. Mickiewicza w Poznaniu (2008) XVII: 347-63
  5. Milner M., Chroboczek J., Zagorski-Ostoja W. Engineered resistance against proteinases. Acta Biochim. Pol. (2007) 54: 523-36
  6. Kłudkiewicz B., Kodrik D., Grzelak K., Nirmala X., Sehnal F. Structurally unique recombinant Kazal-type proteinase inhibitor retains activity when terminally extended and glycosylated. Protein Expr. Purif. (2005) 43: 94-102
  7. Dębski J., Wysłouch-Cieszyńska A., Dadlez M., Grzelak K., Kłudkiewicz B., Kołodziejczyk R., Lalik A., Ożyhar A., Kochman M. Positions of disulfide bonds and N-glycosylation site in juvenile hormone binding protein. Arch. Biochem. Biophys. (2004) 421: 260-266
  8. Grzelak K., Kłudkiewicz B., Kolomiets L.I., Dębski J., Dadlez M., Lalik A., Ożyhar A., Kochman M. Overexpression of juvenile hormone binding protein in bacteria and Pichia pastoris. Protein Expr. Purif. (2003) 31: 173-180

Patent:
Sehnal, F., Kodrik, D., Zurovec, M., Grzelak, K., Kludkiewicz, B., Milner, M., Zagorski-Ostoja, W. Design and use of Kazal-type proteinase inhibitors, WO2005/007693


Adenovirus dodecahedron - vector of intracellular transfer. Adenovirus dodecahedron as a delivery platform for vaccine

Group leader: Dr. Ewa Szołajska
Staff: Prof. Włodzimierz Zagórski-Ostoja, Assoc. Prof. Jadwiga Chroboczek, Dr. Antonina Naskalska , M.Sc. Monika Żochowska (Ph.D. student), M.Sc. Inga Szurgot (Ph.D. Student), M.Sc. Małgorzata Białoskórska

 

Dodecahedron (Dd) is a smaller-than-virion virus like particle (VLP) formed by self-assembly of adenovirus penton base protein, responsible for virus intracellular penetration. Thanks to its remarkable efficiency of penetration, Dd constitutes an attractive tool for delivery of therapeutic agents.

Two applications of Dd are studied. The first one is the use of VLP as a delivery platform for antigens in a novel approach to influenza vaccine production. In our vaccine design the antigens are attached to the surface of purified Dds, through so called WW domains. As antigens, a genetically unstable external influenza protein, hemagglutinin, and a less variable internal matrix protein M1, are used. Dodecahedric VLP platform should act as adjuvant, and together with multivalently displayed antigens will induce an effective protection against heterologous influenza strains.

We have already shown that the noncovalent complex of Dd with M1 is efficiently internalized by human myeloid dendritic cells (MDC), induces their maturation and is efficiently presented by MDC to antigen-specific CD8+ T lymphocytes. In the next steps we plan to construct the vaccine combining both antigens and investigate the potential of our new vaccine to protect against influenza challenge in an animal model.

In the second application Dd is used as a vector for delivery of therapeutic factors to tumors. As a model drug we have used anticancer antibiotic bleomycin (BLM), which is an extremely cytotoxic agent once inside the cell nucleus, where it cleaves DNA. However BLM cytotoxicity is limited by its inability to freely diffuse through membranes, which results in the use of high antibiotic doses, inducing severe side-effects. BLM was chemically attached to Dd. The Dd-BLM conjugate upon penetration induced death of transformed cells. Significantly, efficient cytotoxic concentration of BLM delivered with Dd was 100 times lower than that of the free antibiotic. Our studies are the first example of successful use of a recombinant, easily obtainable VLP for increasing the bioavailability of the drug. The experiments on activity of the Dd-BLM conjugate in an animal mice cancer model are in progress.

 

Current projects:

  1. Adenovirus dodecahedron as a vector for direct delivery of therapeutic factors to tumors.
  2. Development of a novel influenza vaccine.

Research grants:

2010-2012 "Nasal influenza vaccine for animals", (Ministry of Sciences and Higher Education)

2006-2009 "Development of novel influenza vaccine for poultry", (NATO Collaborative Linkage Grant)
2005-2008 "Adenovirus dodecahedron as a vector for direct delivery of therapeutic factors to tumors",
                   (Ministry of Sciences and Higher Education)
2005-2008 "The protein kinase inhibitors as potential antitumor and antiviral drugs", (Ministry of Sciences
                   and Higher Education)

 

Selected publications:

  1. Naskalska A., Szolajska E., Chaperot L., Angel J., Plumas J., Chroboczek J. Influenza recombinant vaccine: Matrix protein M1 on the platform of the adenovirus dodecahedron. Vaccine. 2009 Sep 18. [Epub ahead of print]
  2. Zochowska M., Paca A., Schoehn G., Andrieu J-P., Chroboczek J., Dublet B., Szolajska E. Adenovirus Dodecahedron, as a drug delivery vector. 2009 PLoS ONE 2009 4(5):e5569
  3. Hong S.S., Szołajska E., Schoehn G., Franqueville L., Myhre S., Lindholm L., Ruigrok R.W., Boulanger P., Chroboczek J.  The 100K-chaperone protein from adenovirus serotype 2 (Subgroup C) assists in trimerization and nuclear localization of hexons from subgroups C and B adenoviruses. J Mol Biol. 2005 352:125-38

Patents:

  1. Naskalska A., Szolajska E., Chaperot L., Angel J., Plumas J., Chroboczek J. Influenza recombinant vaccine: Matrix protein M1 on the platform of the adenovirus dodecahedron. Vaccine (2009) Sep 18. [Epub ahead of print]
  2. Zochowska M., Paca A., Schoehn G., Andrieu J.-P., Chroboczek J., Dublet B., Szolajska E. Adenovirus Dodecahedron, as a drug delivery vector. PLoS ONE (2009) 4(5): e5569
  3. Hong S.S., Szołajska E., Schoehn G., Franqueville L., Myhre S., Lindholm L., Ruigrok R.W., Boulanger P., Chroboczek J. The 100K-chaperone protein from adenovirus serotype 2 (Subgroup C) assists in trimerization and nuclear localization of hexons from subgroups C and B adenoviruses. J. Mol. Biol. (2005) 352:125-38

Sequencing of genomes of selected viroid and plant viruses strains and their detection

Group leader: Dr. Anna Góra-Sochacka
Staff: M.Sc. Aneta Więsyk (Ph.D. student)

 

Our research project is aimed towards understanding the pathogenesis of the potato spindle tuber viroid (PSTVd). Viroid genome does not code for proteins and thus must interact directly with host components to accomplish various functions required for infection.

To better understand the process of viroid infection a comparative study of nuclear proteome of PSTVd infected and non-infected plants was initiated. For this purpose two isolates, PSTVd-M (mild) and PSTVd-S23 (severe), causing clearly different disease symptoms were chosen.

So far, most of our effort was focused on the first steps of the task, namely, optimization of the method of nuclei isolation from tomato leaf tissue. The isolation of pure nuclei from plants is difficult due to rigidity of plant cell walls and large quantities of secondary compounds in the vacuoles which upon tissue disruption can lead to protein precipitation. We tested sucrose and Percoll density gradient centrifugation technique to obtain purified nuclei. The purity of the isolated nuclei was analyzed by DAPI staining and visualizing by confocal microscopy. Comparison of proteomes will be performed after successful accomplishment of the nuclei isolation step.

We also continued a study on thirteen previously selected sequence variants of PSTVd carrying mutations in the P (pathogenicity) and the TL (left terminal) domain. All of them are genetically stable and induced typical disease symptoms. They seem to be very interesting because mutations in the TL and P domains are observed very rarely. In the future we plan to use these mutants to study protein profiles in infected plants.

The analyses of altered protein profiles elicited by PSTVd infection may help to identify molecular host defense response mechanisms against this pathogen, to recognize cell proteins which are important for pathogen infection and to elucidate mechanisms of pathogenicity.

 

Current projects:

  1. Comparative proteome analysis of molecular PSTVd infection.
  2. Identification and characterization of tomato nuclear proteins involved in PSTVd infection.

Chromatin in regulation of gene expression

Group leader: Prof. Andrzej Jerzmanowski
Staff:

 

Current projects:

Research grants:

Publications:


Dynamics of the plant transcriptome in normal and stress conditions

Group leader: Dr. Marta Prymakowska-Bosak
Staff:

Current projects:

Research grants:

Publications: 

 


The role of chromatin in the control of basic regulatory processes in Eucaryota

Group leader: Dr. Tomasz Sarnowski 

 

Postdcotoral Fellows:
Anna Maassen, PhD
Szymon Kubala, PhD

PhD Students:
Sebastian Sacharowski, MSc
Dorota Zugaj, MSc
Paweł Ćwiek, MSc Eng.
Paulina Kondrak, MSc Eng. (Lab Manager)
Jaroslaw Steciuk. MSc Eng.

Undergraduate students:
Pawel Kowalewski, Eng.
Piotr Bartosz

Trainee:
Marcin Leszczyński, MSc
Joanna Szarkowska, MSc, Eng.
Iga Jancewicz, MSc, Eng.

Former Members:
Anna Rolicka, PhD
Ernest Bucior, PhD
Dominika Gratkowska, PhD
Klaudia Kogut, MSc Eng.
Monika Cieśla, MSc Eng.

Awards:

Szymon Kubala - Scholarship of Polish Ministry of Science and Higher Education for young talented scientists (2016-2019)
Sebastian Sacharowski - START fellowship by Foundation for Polish Science (2016-2017)
Dorota Zugaj and Sebastian Sacharowski - ETIUDA fellowships by Polish National Science Center (2016-2017)

Selected publications:

  1. Sarnowska, E., Gratkowska, D.M., Sacharowski, S.P., Cwiek P., Tohge T., Fernie, A.R., Siedlecki, J.A., Koncz, C., Sarnowski, T.J. (2016) The Role of SWI/SNF Chromatin Remodeling Complexes in Hormone Crosstalk. Trends Plant Sci. doi: 10.1016/j.tplants.2016.01.017 5-year IF: 14,67
  2. Sacharowski, S., Gratkowska, D.M., Sarnowska, E.A., Kondrak, P., Jancewicz, I., Porri, A., Bucior, E., Rolicka, A.T., Franzen, R., Kowalczyk, J., Pawlikowska, K., Huettel, B., Torti, S., Schmelzer, E., Coupland, G., Jerzmanowski, A., Koncz, C., Sarnowski, T.J. (2015) SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development, Plant Cell, 27(7):1889-906; 5-year IF: 10,529
  3. Sarnowska, E., Rolicka, A., Bucior, E., Cwiek, P., Tohge, T., Fernie, A.R., Jikumaru, Y., Kamiya, Y., Franzen, R., Schmelzer, E., Porri, A., Sacharowski, S., Gratkowska, D., Zugaj D., Taff, Zalewska, A., Archacki, R., Davis, S.J., Coupland, G., Koncz, C., Jerzmanowski, A., Sarnowski, T.J. (2013). DELLA-interacting SWI3C core subunit of SWI/SNF chromatin remodeling complex modulates gibberellin responses and hormonal crosstalk in Arabidopsis, Plant Physiol. 163:305-317; 5-year IF: 8,03
  4. Sarnowska E., Balcerak A., Olszyna-Serementa M., Sarnowski T. J. *, Siedlecki J. A.* (2013) The AMP dependent AMPK kinase. Postepy Hig Med Dosw 67:750-60 * corresponding author, shared last authorship

Patents:

  1. Patent No. 220415 Sarnowski T.J., Rolicka A., Bucior E., Jerzmanowski A. (2015) Sposób określania wpływu substancji chemicznych na działanie szlaku kinazy AMPK i/lub bezpośrednio na kompleks SWI/SNF.

Selected projects:

  1. (2016-2019) Functional characteristics of Arabidopsis SWI/SNF chromatin remodeling complex containing SWP73A and SWP73B - National Science Centre 2015/17/N/NZ2/01919 Preludium for S. Sacharowski
  2. (2015-2018) Analiza zależności funkcjonalnej pomiędzy kompleksami remodelującymi chromatynę typu SWI/SNF i splicingiem pre-mRNA u Arabidopsis - National Science Centre 2015/16/S/NZ2/00042 Fuga for S. Kubala
  3. (2015-2019) Analiza funkcji kompleksów remodelujących chromatynę typu SWI/SNF w kontroli struktur chromatynowych wyższego rzędu - Ministry of Science and Higher Education DI2014 007044 Diamond Grant for P. Kondrak
  4. (2015-2018) Comparison of functional interdependence between AMPK pathway controlling energy homeostasis and SWI/SNF-type chromatin remodeling complex, in Arabidopsis and humans - National Science Centre 2014/13/B/NZ2/01187 Opus for T. Sarnowski
  5. (2014-2017) The function of SWI/SNF - type chromatin remodeling complexes in control of metabolic processes - National Science Centre 2013/11/B/NZ1/02101 Opus for T. Sarnowski
  6. (2013-2017) Identyfikacja nowych mechanizmów sygnałowych regulujących aktywność kompleksów remodelujących chromatynę typu SWI/SNF u Arabidopsis thaliana - Ministry of Science and Higher Education DI2012 021842 Diamond Grant for P. Cwiek
  7. (2012-2016) Identyfikacja molekularnych mechanizmów odpowiedzi na stres chłodu z wykorzystaniem mutantów w genach kodujących rdzeniowe podjednostki kompleksu SWI/SNF u Arabidopsis thaliana - Ministry of Science and Higher Education DI2011 026941 Diamond Grant for D. Gratkowska
  8. (2011-2014) The analysis of function of RCF-family proteins - potential gibberellin pathway membrane receptors in Arabidopsis with focus on regulation at the chromatin level - National Science Centre 2011/01/B/NZ1/00053 Opus for T. Sarnowski
  9. (2011-2014) The functional analysis of SWI/SNF complexes in flowering time control in Arabidopsis - Ministry of Science and Higher Education N N301 645040 for T. Sarnowski
  10. (2010-2013) The analysis of SWI/SNF chromatin remodeling complexes function in the response to environmental stress - Ministry of Science and Higher Education N N302 142739 for T. Sarnowski
  11. (2010-2013) Characterization of regulatory roles of SWI/SNF-type chromatin remodeling complexes in the control of development and hormonal, biotic and abiotic stress responses in Arabidopsis - Marie Curie European Re-Integration Grant FP7-PEOPLE-2010-RG 268313 for T. Sarnowski
  12. Characterization of regulatory roles of SWI/SNF-type chromatin remodeling complexes in the control of development and hormonal, biotic and abiotic stress responses in Arabidopsis - Ministry of Science and Higher Education 2061/7.PR/2011/2 -Supplementation from MNiSW (SPUB) for Marie Curie FP7-PEOPLE-2010-RG 268313 project for T. Sarnowski

Description of Current Research

Our laboratory focuses on functional studies of chromatin and ATP- dependent chromatin remodeling complexes (CRCs) in the control of basic regulatory processes in Eukaryota.

Chromatin remodeling complexes regulate the structure, activity and organization of chromatin, and play critical roles in the maintenance, transmission and expression of eukaryotic genomes. Regulatory properties of CRCs are determined by their canonical SNF2-type ATPase subunits, as well as the composition of other core subunits, including auxiliary proteins. The SWI/SNF class of ATP-dependent chromatin remodeling complexes, a prototype of which was first described in Saccharomyces cerevisiae, is conserved from fungi to mammals. The central catalytic subunit of SWI/SNF CRCs is a bromodomain-containing SWI2/SNF2 ATPase, which is associated with a small set of conserved ‘core’ subunits that together are capable of reconstituting the full SWI/SNF remodeling activity in vitro. In all eukaryotes, the ‘core’ of SWI/SNF CRCs consists of homologues of yeast SWI3 and SNF5 proteins that form a complex with dimers of two SWI3-type subunits. In multicellular eukaryotes, the lack or aberrant stoichiometry of individual core subunits causes severe defects in development, often leading to carcinogenesis. Many known mutation in the core subunits of human SWI/SNF complexes correlate with various pathological genetic syndromes, such as the Nicolaides- Baraitser (NBS) and Coffin - Siris (CSS) syndromes.
Recent studies of human SWI/SNFs have identified the existence of several novel subunits, including BCL7A, BCL7B, BCL7C, BCL11A, BCL11B, BRD9 and SS18 (Fig.1.). These non-canonical subunits are missing from yeast and Drosophila CRCs but they are present in Arabidopsis CRCs. This suggests that they are specific for higher eukaryotes. The multiplication of subunits in human and plants, as well as the existence of new auxiliary subunits suggest that SWI/SNF CRCs in higher eukaryotes are structurally more diverse compared to their counterparts in such less developed organisms as yeast and flies.

 


Fig. 1. SWI/SNF complexes are involved in the control of basic regulatory processes in Eucaryota. The impairment of SWI/SNF complexes causes either developmental alterations or genetic disorders. The viability of Arabidopsis swi/snf mutants provides attractive opportunity to study SWI/SNF - dependent evolutionarily conserved processes in eukaryotic cells.

While there is no data about the effect of complete loss of SWI/SNF complex on functioning of human body, a large set of available data indicates that the human CRCs act analogously in hormone signal transduction, and are involved in the control of hormonal crosstalk (Sarnowska et al., 2016). Moreover, our studies show that in both plants and mammals the SWI/SNF complexes control basic regulatory processes via both direct effects on target genes (i.e. transcriptional control by nucleosome remodeling) and physical interactions with key regulatory factors involved in the control of regulatory pathways (Sarnowska et al., 2013; Sacharowski et al., 2015 and our recent unpublished study).
It has been shown that even small aberrations affecting the functions of SWI/SNF complexes cause dosage-dependent genetic defects in human development. No patients carrying homozygous mutations in genes of SWI/SNF subunits have been described so far, most likely due to lethal effects of such mutations at early stages of development as seen also in mice.
We observed similar effects for some (e.g. SWI3A or SWI3B) but not all mutations affecting core components of Arabidopsis SWI/SNF complexes. A dosage-dependent genomic imprinting effect along with early embryonic lethality was thus observed in a heterozygous mutant line carrying a knockout mutation in the Arabidopsis SWI3B gene. Other SWI/SNF subunit mutations (swi3c, swi3d and the swp73b) are viable but display characteristic and dramatic developmental defects (Sarnowski et al., 2005, Sacharowski et al., 2015).
We found that loss of the SWI/SNF activity affects the expression of a large cluster of genes involved in the control of basic regulatory processes including cell cycle control, hormonal response, metabolic homeostasis and amino acid, and lipid biosynthesis (Sacharowski et al., 2015 and our recent unpublished data). Furthermore, we found a direct link between the SWI/SNF complex and components of pathways involved in the control of basic regulatory processes. Using human HeLa cell line, we showed that these interactions are strongly conserved in evolution. Furthermore, we observed that Arabidopsis mutants impaired in the function of SWI3C core subunit of SWI/SNF show dramatic developmental alterations in roots (shortened, branching roots) when grown on medium containing sucrose or glucose and this effect can be reverted by metformin, a known drug used for many years in treatment of type II diabetes. This suggests that loss of SWI/SNF activity in this mutant line may cause metabolic reprogramming and the swi3c mutant line may serve as a perfect tool to searching for new metformin- like compounds which may be used for treatment of human diseases (Patent No. 220415).
Our combined results obtained from parallel studies using mutants of the model plant Arabidopsis thaliana along with suitably modified human cell lines (study in the direction ‘from plants to humans’) show that loss of SWI/SNF complex strongly affects the regulatory pathways controlling basic, evolutionarily conserved processes in Eucaryota. As the use of human mutants is ethically unacceptable, we propose to complement the currently used human cell and mice models by a novel platform based on Arabidopsis mutant plants. Supported by exhaustive bioinformatics analyses, we posit that this can help to better understanding evolutionarily conserved function of SWI/SNF complexes in the control of basic signalling pathways.

International collaboration:

2003 - present Prof. Csaba Koncz, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
2007 - present Dr. hab Seth Davis, University of York, York, England
2007 - present Prof. George Coupland, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
2011 - present Dr. hab Alisdair Fernie, Max-Planck Institute for Plant Molecular Physiology, Potsdam-Golm, Germany
2015 - present Prof. Mien- Chie Hung, University of Texas M. D. Anderson Cancer Center, Houston, USA
2017 - present Prof. Louis Staudt, National Cancer Institute, NIH, Bethesda, USA
2017 - present Dr. Laszlo Szabados, Biological Research Centre HAS, Szeged, Hungary
2017 - present Dr. Zoltan Magyar, Biological Research Centre HAS, Szeged, Hungary

Domestic collaboration:

2003- present Prof. Janusz Siedlecki, Department of Molecular and Translational Oncology, Marie Curie Memorial Cancer Center, Warsaw, Poland