Pracownie badawcze

Dr hab. Anna Muszewska, Prof. IBB PAN

Pracownia Bioinformatyki Grzybów

ORCID: 0000-0002-4578-844X

E-mail:

Web of Science: JFS-3455-2023

ResearchGate: Link

Zakres badań

We trace genomic changes across branches of the fungal tree of life. We also study the relationship between the genome composition and the ecology of the organism.

Badania

Najważniejsze osiągnięcia badawcze

  • We confirmed several peculiarities of Mucoromycotina including lipid production, carbon utilization profiles, cell wall sugar composition which make them distinct from Ascomycota and support the idea of independent ways of infection treatment.
  • We discovered the utilization of cobalamin in basal fungal lineages.
  • We have found tendencies for transposon accumulation in plant-associated fungi and symbiotic fungi.
  • We confirmed that HGT favours short, low LCR sequences and occur more often in symbiotic fungi.
  • We found that lipids are essential in diverse fungal interactions with other organisms.

Opis badań

  • Summary of research

The life strategies of known fungi are very diverse; they can be saprotrophs, pathogens and symbionts. The ability to enter into various interactions with the environment and to adapt flexibly to environmental conditions is determined genetically. Our bioinformatic research carried out on a large scale, covering hundreds of genomes and predicted proteomes, uncovered many correlations between the set of genes/transposons in the genome and the ecology of the fungus. The obtained results showed that adaptation to a given lifestyle may result from the presence of as little as a small subset of enzymes/regions encoded in fungal genomes. In the future, these findings could lead to predictions of ecological properties, including infectiousness potential directly from genomic data. Moreover, they can contribute to the possibility of obtaining novel engineered fungi equipped with a tailored gene set towards a new ecological niche or industrial application.

  • Research topics

We work on the synthesis of currently fragmented knowledge on diverse traits in Mucoromycota. One of the lasting scientific interests is genome content, organization changes across the tree of life and protein-coding sequence evolution. In collaboration with Dr Julia Pawłowska (University of Warsaw) we study bacteria-fungi interactions.

Metodologia

We use Pfam protein domain definitions as the golden standard and starting point in describing a protein domain/non-domain characters. We benefit from the FungalTraits database (Põlme et al. 2020) describing the ecological and morphological features of Fungi as well as expert knowledge. We provide distant mappings for protein domains using FFAS03 and HH-suite3 fold recognition methods. We integrate annotations from functional databases like SGD, MetaCyc, KEGG, STRING, SEED, InterPro, CaZy, MEROPS, MiBig.

Wybrane publikacje

  • Utilization of cobalamin is ubiquitous in early-branching fungal phyla. Orłowska M, Steczkiewicz K, Muszewska A. Genome Biology and Evol. 2021. doi: 10.1093/gbe/evab043.
  • Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina. Muszewska A, Okrasińska A, Steczkiewicz K, Drgas O, Orłowska M, Perlińska-Lenart U, Aleksandrzak-Piekarczyk T, Szatraj K, Zielenkiewicz U, Piłsyk S, Malc E, Mieczkowski P, Kruszewska JS, Bernat P, Pawłowska J. Front Microbiol. 2021. doi: 10.3389/fmicb.2021.636986.
  • Transposable elements contribute to fungal genes and impact fungal lifestyle. Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K. Sci Rep. 2019. doi: 10.1038/s41598-019-40965-0.
  • Cut and paste transposons in fungi with diverse lifestyles. Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K. Genome Biol Evol. 2017. doi: 10.1093/gbe/evx261.
  • Fungal lifestyle reflected in serine protease repertoire. Muszewska A, Stepniewska-Dziubinska MM, Steczkiewicz K, Pawlowska J,Dziedzic A, Ginalski K. Sci Rep. 2017. doi: 10.1038/s41598-017-09644-w.

Współpraca

  • Julia Pawłowska, Department of Biology, University of Warsaw
  • Paweł Górecki, MIM, Univestity of Warsaw
  • Przemysław Bernat, Department of Biology, University of Łódź
  • Krzysztof Pawłowski, University of Texas Southwestern Medical Center
  • Grzegorz Koczyk, IGR PAS
  • Kerstin Voigt, HKI Jena
  • Andrii Gryganskyi, UES, Inc. USA
  • Ekaterina Shelest, University of Portsmouth
  • Bridget Barker, Northern Arizona University
  • Marcus Teixeira, University of Brasília

Nagrody i wyróżnienia

  • Anna Muszewska. Habilitation Fellowship of L’Oréal Poland for Women in Science. 2018. L’Oréal Polska, Poland.
  • Anna Muszewska. Scholarship for Outstanding Young Scientists. 2014. Minister of Science and Higher Education, Poland.

Publikacje (z afiliacją IBB PAN)

CIACH M.A., PAWŁOWSKA J., GÓRECKI P., MUSZEWSKA A., The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities. Evolution Letters (2024) 8(4): 526–538 DOI: 10.1093/evlett/qrae009 IF 3.8 (2023)
LAX C., MONDO S.J., OSORIO-CONCEPCIÓN M., MUSZEWSKA A., CORROCHANO-LUQUE M., GUTIÉRREZ G., RILEY R., LIPZEN A., GUO J., HUNDLEY H., AMIREBRAHIMI M., NG V., LORENZO-GUTIÉRREZ D., BINDER U., YANG J., SONG Y., CÁNOVAS D., NAVARRO E., FREITAG M., GABALDÓN T., GRIGORIEV I.V., CORROCHANO L.M., NICOLÁS F.E., GARRE V., Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales. Nature Communications (2024) 15(1): 6066 (21 p.) DOI: 10.1038/s41467-024-50365-2 IF 14.7 (2023)
BARUA D., PŁECHA M., MUSZEWSKA A., A minimal Fanconi Anemia complex in early diverging fungi. Scientific Reports (2024) 14(1): 9922 ( 15 p.) DOI: 10.1038/s41598-024-60318-w IF 3.8 (2023)
BREVIK K., SCHOVILLE S.D., MUSZEWSKA A., PÉLISSIÉ B., COHEN Z., IZZO V., CHEN Y. H., Transposable elements differ between geographic populations of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Environmental Entomology (2023) 52(6): 1162-1171 DOI: 10.1093/ee/nvad105 IF 1.8 (2023)
SOKOŁOWSKA B., ORŁOWSKA M., OKRASIŃSKA A., PIŁSYK S., PAWŁOWSKA J., MUSZEWSKA A., What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota. IMA Fungus (2023) 14(1): 22 (21 p.) DOI: 10.1186/s43008-023-00127-4 IF 5.2 (2023)
ORŁOWSKA M., BARUA D., PIŁSYK S., MUSZEWSKA A., Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages. IMA Fungus (2023) 14: 17 (17 p.) DOI: 10.1186/s43008-023-00123-8 IF 5.2 (2023)
GRYGANSKYI A.P., GOLAN J., MUSZEWSKA A., IDNURM A., DOLATABADI S., MONDO S.J., KUTOVENKO V.B., KUTOVENKO V.O., GAJDECZKA M.T., ANISHCHENKO I.M., PAWŁOWSKA J., TRAN N.V., EBERSBERGER I., VOIGT K., WANG Y., CHANG Y., PAWLOWSKA T.E., HEITMAN J., VILGALYS R., BONITO G., BENNY G.L., SMITH M.E., REYNOLDS N., JAMES T.Y., GRIGORIEV I.V., SPATAFORA J.W., STAJICH J.E., Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms (2023) 11(7): 1830 (24 p.) DOI: 10.3390/microorganisms11071830 IF 4.1 (2023)
OKRASIŃSKA A., DECEWICZ P., MAJCHROWSKA M., DZIEWIT Ł., MUSZEWSKA A., DOLATABADI S., KRUSZEWSKI Ł., BŁOCKA Z., PAWŁOWSKA J., Marginal lands and fungi - linking the type of soil contamination with fungal community composition. Environmental Microbiology (2022) 24(8): 3809–3825 DOI: 10.1111/1462-2920.16007 IF 5.1 (2022)
OPPERT B., MUSZEWSKA A., STECZKIEWICZ K., ET AL. The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes (2022) 13(3): 446 (43 p.) DOI: 10.3390/genes13030446 IF 3.5 (2022)
ORŁOWSKA M., MUSZEWSKA A., In silico predictions of ecological plasticity mediated by protein family expansions in early-diverging fungi. Journal of Fungi (2022) 8(1): 67 (26 p.) DOI: 10.3390/jof8010067 IF 4.7 (2022)
ORŁOWSKA M., STECZKIEWICZ K., MUSZEWSKA A., Utilization of cobalamin is ubiquitous in early-branching fungal phyla. Genome Biology and Evolution (2021) 13(4): evab043 DOI: 10.1093/gbe/evab043 IF 4.065 (2021)
KOCZYK G., PAWŁOWSKA J., MUSZEWSKA A., Terpenoid biosynthesis dominates among secondary metabolite clusters in Mucoromycotina genomes. Journal of Fungi (2021) 7(4): 285 DOI: 10.3390/jof7040285 IF 5.724 (2021)
MUSZEWSKA A., OKRASIŃSKA A., STECZKIEWICZ K., DRGAS O., ORŁOWSKA M., PERLIŃSKA-LENART U., ALEKSANDRZAK-PIEKARCZYK T., SZATRAJ K., ZIELENKIEWICZ U., PIŁSYK S., MALC E.P., MIECZKOWSKI P., KRUSZEWSKA J.S., BERNAT P., PAWŁOWSKA J., Metabolic potential, ecology and presence of associated bacteria is reflected in genomic diversity of Mucoromycotina. Frontiers in Microbiology (2021) 12: 636986 (21 p.) DOI: 10.3389/fmicb.2021.636986 IF 6.064 (2021)
GOLAN M.P., PIŁSYK S., MUSZEWSKA A., WAWRZYNIAK A., Ferritins in Chordata: potential evolutionary trajectory marked by discrete selective pressures. Bioessays (2021) 43(1): e2000207 (10 p.) DOI: 10.1002/bies.202000207 IF 4.653 (2021)
TEIXEIRA M.M.,MUSZEWSKA A., TRAVIS J., MORENO L.F., AHMED S., ROE CH., MEAD H., STECZKIEWICZ K., LEMMER D., DE HOOG G.S., KEIM P., WIEDERHOLD N., BARKER B.M., Genomic characterization of Parengyodontium americanum sp. nov. Fungal Genetics and Biology (2020) 138: 103351 (9 p.) DOI:10.1016/j.fgb.2020.103351 IF 3.495 (2020)
PAWŁOWSKA J., OKRASIŃSKA A., KISŁO K., ALEKSANDRZAK-PIEKARCZYK T., SZATRAJ K., DOLATABADI S., MUSZEWSKA A., Carbon assimilation profiles of mucoralean fungi show their metabolic versatility. Scientific Reports (2019) 9(1): 11864 (8 p.) DOI: 10.1038/s41598-019-48296-w IF 3.998 (2019)
GRYZ E., PERLIŃSKA-LENART U., GAWARECKA K., JÓŹWIAK A., PIŁSYK S., LIPKO A., JEMIOŁA-RZEMIŃSKA M., BERNAT P., MUSZEWSKA A., STECZKIEWICZ K., GINALSKI K., DŁUGOŃSKI J., STRZAŁKA K., ŚWIEŻEWSKA E., KRUSZEWSKA J.S., Poly-saturated dolichols from filamentous fungi modulate activity of dolichol-dependent glycosyltransferase and physical properties of membranes. International Journal of Molecular Sciences (2019) 20(12): 3043 (24 p.) DOI: 10.3390/ijms20123043 IF 4.556 (2019)
MUSZEWSKA A., STECZKIEWICZ K., STĘPNIEWSKA-DZIUBIŃSKA M., GINALSKI K., Transposable elements contribute to fungal genes and impact fungal lifestyle. Scientific Reports (2019) 9(1): 4307(10 p.) DOI: 10.1038/s41598-019-40965-0 IF 3.998 (2019)
POZNAŃSKI J., TOPIŃSKI J., MUSZEWSKA A., DĘBSKI K.J., HOFFMAN-SOMMER M., PAWŁOWSKI K., GRYNBERG M., Global pentapeptide statistics are far away from expected distributions. Scientific Reports (2018) 8(1): 15178 (18 p.) DOI: 10.1038/s41598-018-33433-8 IF 4.011 (2018)
WIJAYAWARDENE N.N., PAWŁOWSKA J., LETCHER P.M., KIRK P.M., HUMBER R.A., SCHÜßLER A., WRZOSEK M., MUSZEWSKA A., OKRASIŃSKA A., ISTEL Ł., GĘSIORSKA A., MUNGAI P., LATEEF A.A., RAJESHKUMAR K.C., SINGH R.V., RADEK R., WALTHER G., WAGNER L., WALKER CH., WIJESUNDARA D.S.A., PAPIZADEH M., DOLATABADI S., SHENOY B.D., TOKAREV Y.S., LUMYONG S., HYDE K.D., Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). Fungal Diversity (2018) 92(1): 43-129 DOI: 10.1007/s13225-018-0409-5 IF 15.596 (2018)

Zespół

  • Anna Muszewska, PhD, DSc, Kierownik Pracowni, ORCID: 0000-0002-4578-844X
  • Magdalena Płecha, PhD, Pracownik
  • Drishtee Barua, Doktorant
  • Aleksander Kossakowski, Doktorant

Granty

  • Ancestral traits and genomic innovations in early diverging fungi - implications for mucormycosis. Anna Muszewska. OPUS 21, National Science Center, 2022-2026.