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)

GRYGANSKYI A.P., GOLAN J., DOLATABADI S., MONDO S., ROBB S., IDNURM A., MUSZEWSKA A., STECZKIEWICZ K., MASONJONES S., LIAO H-J., GAJDECZKA M.T., ANIKE F., VUEK A., ANISHCHENKO I.M., VOIGT K., DE HOOG G.S., SMITH M.E., HEITMAN J., VILGALYS R., STAJICH J.E., Phylogenetic and phylogenomic definition of Rhizopus species. G3-Genes Genomes Genetics (2018) 8(6): 2007-2018 DOI: 10.1534/g3.118.200235 IF 2.630 (2018)
CIACH M.A., MUSZEWSKA A., GÓRECKI P., Locus-aware decomposition of gene trees with respect to polytomous species trees. Algorithms for Molecular Biology (2018) 13: 11 (18 p.) DOI: 10.1186/s13015-018-0128-1 IF 1.585 (2018)
SCHOVILLE S.D., CHEN Y. H., ANDERSSON M.N., BENOIT J.B., GRYNBERG M., MUSZEWSKA A., ET AL. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Scientific Reports (2018) 8: 1931 (18 p.) DOI: 10.1038/s41598-018-20154-1 IF 4.011 (2018)
KIRKLAND T.N., MUSZEWSKA A., STAJICH J.E., Analysis of transposable elements in Coccidioides species. Journal of Fungi (2018) 4(1): 13 (13 p.) DOI: 10.3390/jof4010013 IF - (2018)
MUSZEWSKA A., PIŁSYK S., PERLIŃSKA-LENART U., KRUSZEWSKA J.S., Diversity of cell wall related proteins in human pathogenic fungi. Journal of Fungi (2018) 4(1): 6 (19 p.) DOI: 10.3390/jof4010006 IF - (2018)
MUSZEWSKA A., STECZKIEWICZ K., STĘPNIEWSKA-DZIUBIŃSKA M.M., GINALSKI K., Cut-and-paste transposons in fungi with diverse lifestyles. Genome Biology and Evolution (2017) 9(12): 3463–3477 DOI: 10.1093/gbe/evx261 IF 3.940 (2017)
MUSZEWSKA A., STĘPNIEWSKA-DZIUBIŃSKA M.M., STECZKIEWICZ K., PAWŁOWSKA J., DZIEDZIC A., GINALSKI K., Fungal lifestyle reflected in serine protease repertoire. Scientific Reports (2017) 7: 9147 (12 p.) DOI: 10.1038/s41598-017-09644-w IF 4.122 (2017)
KOTLIŃSKI M., KNIŻEWSKI Ł., MUSZEWSKA A., RUTOWICZ K., LIRSKI M., SCHMIDT A., BAROUX C., GINALSKI K., JERZMANOWSKI A., Phylogeny-based systematization of Arabidopsis proteins with histone H1 globular domain. Plant Physiology (2017) 174(1): 27-34 DOI: 10.1104/pp.16.00214 IF 5.949 (2017)
TEIXEIRA M.M.,MORENO L.F., STIELOW B.J., MUSZEWSKA A., HAINAUT M., GONZAGA L., ABOUELLEIL A., PATANÉ J.S.L., PRIEST M., SOUZA R., YOUNG S., FERREIRA K.S., ZENG Q., DA CUNHA M.M.L., GŁADKI A., ET AL. Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota). Studies in Mycology (2017) 86: 1-28 DOI: 10.1016/j.simyco.2017.01.001 IF 11.633 (2017)
NGUYEN KIM B., SREELATHA A., DURRANT E.S., LOPEZ-GARRIDO J., MUSZEWSKA A., DUDKIEWICZ M., GRYNBERG M., YEE S., POGLIANO K., TOMCHICK D.R., PAWŁOWSKI K., DIXON J.E., TAGLIABRACCI V.S., Phosphorylation of spore coat proteins by a family of atypical protein kinases. Proceedings of the National Academy of Sciences USA (2016) 113(25): E3482-E3491 DOI: 10.1073/pnas.1605917113 IF 9.423
KUCHTA K., MUSZEWSKA A., KNIŻEWSKI Ł., STECZKIEWICZ K., WYRWICZ L.S., PAWŁOWSKI K., RYCHLEWSKI L., GINALSKI K., FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. Nucleic Acids Research (2016) 44(8): 3534-3548 DOI: 10.1093/nar/gkw222 IF 9.202
PAWŁOWSKA J., ALEKSANDRZAK-PIEKARCZYK T., BANACH A., KIERSZTYN B., MUSZEWSKA A., SEREWA L., SZATRAJ K., WRZOSEK M., Preliminary studies on the evolution of carbon assimilation abilities within Mucorales. Fungal Biology (2016) 120(5): 752-763 DOI: 10.1016/j.funbio.2016.02.004 IF 2.244
MUSZEWSKA A., GINALSKI K., Phylogenetic analysis especially in relation to fungi. Chapter 3 in: Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi. Food Microbiology. Ed. Russel R. Paterson M., Lima N., CRC Press; ISBN 978-1-4665-5986-8 [620 p.] 2015, p. 15-36 IF-
RUTOWICZ K., PUZIO M., HALIBART-PUZIO J., LIRSKI M., KOTLIŃSKI M., KROTEŃ M.A., KNIŻEWSKI Ł., LANGE B., MUSZEWSKA A., ŚNIEGOWSKA-ŚWIERK K., KOŚCIELNIAK J., IWANICKA-NOWICKA R., BUZA K., JANOWIAK F., ŻMUDA K., JÕESAAR I., LASKOWSKA-KASZUB K., FOGTMAN A., KOLLIST H., ZIELENKIEWICZ P., TIURYN J., SIEDLECKI P., ŚWIEŻEWSKI S.S., GINALSKI K., KOBLOWSKA M., ARCHACKI R., WILCZYŃSKI B., RAPACZ M., JERZMANOWSKI A., A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis. Plant Physiology (2015) 169(3): 2080-2101 DOI: 10.1104/pp.15.00493 IF 6.841
GRYGANSKYI A.P., MUSZEWSKA A., Whole genome sequencing and the Zygomycota. Fungal Genomics & Biology (2014) 4(1): e116. doi:10.4172/2165- 8056.1000e116 (3 p.) IF-
MUSZEWSKA A., Fungal genomes tell a story of ecological adaptations. Acta Universitatis Lodziensis, Folia Biologica et Oecologica (2014) 10: 9-17 IF -
MUSZEWSKA A., GRYNBERG M., Odkrywanie i wykrywanie transpozytorów w sekwencji genomu. Rozdział w: Inżynieria biomedyczna: podstawy i zastosowania. T. 10: Bioinformatyka. Red. P.Pawłowski, A. Świerniak, A. Polański, P. Zielenkiewicz, EXIT; ISBN 978-83-7837-039-0 [414 s.] 2014, s. 213-223
MAJOREK K.A., DUNIN-HORKAWICZ S., STECZKIEWICZ K., MUSZEWSKA A., NOWOTNY M., GINALSKI K., BUJNICKI J.M., The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. Nucleic Acids Research (2014) 42(7): 4160-4179 IF 8.808
MUSZEWSKA A., PAWŁOWSKA J., KRZYŚCIAK P., Biology, systematics, and clinical manifestations of Zygomycota infections. European Journal of Clinical Microbiology & Infectious Diseases (2014) 33(8): 1273–1287 IF 2.544
SZCZĘSNY R.J., HEJNOWICZ M.S., STECZKIEWICZ K., MUSZEWSKA A., BOROWSKI Ł.S., GINALSKI K., DZIEMBOWSKI A., Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels. Nucleic Acids Research (2013) 41(5): 3144-3161 IF 8.278

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.