dr Małgorzata Orłowska

@article{https://doi.org/10.1002/pro.4846,

title = {AlphaFold2 captures the conformational landscape of the HAMP signaling domain},

author = {Aleksander Winski and Jan Ludwiczak and Malgorzata Orlowska and Rafal Madaj and Kamil Kaminski and Stanislaw Dunin-Horkawicz},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4846},

doi = {https://doi.org/10.1002/pro.4846},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Protein Science},

volume = {33},

number = {1},

pages = {e4846},

abstract = {Abstract In this study, we present a conformational landscape of 5000 AlphaFold2 models of the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) domain, a short helical bundle that transduces signals from sensors to effectors in two-component signaling proteins such as sensory histidine kinases and chemoreceptors. The landscape reveals the conformational variability of the HAMP domain, including rotations, shifts, displacements, and tilts of helices, many combinations of which have not been observed in experimental structures. HAMP domains belonging to a single family tend to occupy a defined region of the landscape, even when their sequence similarity is low, suggesting that individual HAMP families have evolved to operate in a specific conformational range. The functional importance of this structural conservation is illustrated by poly-HAMP arrays, in which HAMP domains from families with opposite conformational preferences alternate, consistent with the rotational model of signal transduction. The only poly-HAMP arrays that violate this rule are predicted to be of recent evolutionary origin and structurally unstable. Finally, we identify a family of HAMP domains that are likely to be dynamic due to the presence of a conserved pi-helical bulge. All code associated with this work, including a tool for rapid sequence-based prediction of the rotational state in HAMP domains, is deposited at https://github.com/labstructbioinf/HAMPpred.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sokolowska23,

title = {What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota},

author = {Blanka Sokołowska and Małgorzata Orłowska and Alicja Okrasińska and Sebastian Piłsyk and Julia Pawłowska and Anna Muszewska},

doi = {https://doi.org/10.1186/s43008-023-00127-4},

year  = {2023},

date = {2023-11-06},

journal = {IMA Fungus},

volume = {14},

issue = {22},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Orłowska2023,

title = {Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages},

author = {Małgorzata Orłowska and Drishtee Barua and Sebastian Piłsyk and Anna Muszewska},

doi = {10.1186/s43008-023-00123-8},

issn = {2210-6359},

year  = {2023},

date = {2023-09-05},

urldate = {2023-12-00},

journal = {IMA Fungus},

volume = {14},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:sec>

                <jats:title>Abstract</jats:title>

                <jats:p>Fucose is a deoxyhexose sugar present and studied in mammals. The process of fucosylation has been the primary focus in studies relating to fucose in animals due to the presence of fucose in Lewis antigens. Very few studies have reported its presence in Fungi, mostly in <jats:italic>Mucoromycotina</jats:italic>. The constitution of 25% and 12% of this sugar in the carbohydrates of cell wall in the respective <jats:italic>Umbelopsis</jats:italic> and <jats:italic>Mucorales</jats:italic> strains boosts the need to bridge the gap of knowledge on fucose metabolism across the fungal tree of life. In the absence of a network map involving fucose proteins, we carried out an <jats:italic>in-silico</jats:italic> approach to construct the fucose metabolic map in <jats:italic>Fungi</jats:italic>. We analyzed the taxonomic distribution of 85 protein families in <jats:italic>Fungi</jats:italic> including diverse early diverging fungal lineages. The expression of fucose-related protein-coding genes proteins was validated with the help of transcriptomic data originating from representatives of early diverging fungi. We found proteins involved in several metabolic activities apart from fucosylation such as synthesis, transport and binding. Most of the identified protein families are shared with <jats:italic>Metazoa</jats:italic> suggesting an ancestral origin in <jats:italic>Opisthokonta</jats:italic>. However, the overall complexity of fucose metabolism is greater in Metazoa than in <jats:italic>Fungi</jats:italic>. Massive gene loss has shaped the evolutionary history of these metabolic pathways, leading to a repeated reduction of these pathways in most yeast-forming lineages. Our results point to a distinctive mode of utilization of fucose among fungi belonging to <jats:italic>Dikarya</jats:italic> and the early diverging lineages. We speculate that, while <jats:italic>Dikarya</jats:italic> used fucose as a source of nutrients for metabolism, the early diverging group of fungi depended on fucose as a building block and signaling compound.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Graphical abstract</jats:title>

                

              </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35050007,

title = {In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi},

author = {Małgorzata Orłowska and Anna Muszewska},

doi = {10.3390/jof8010067},

issn = {2309-608X},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {J Fungi (Basel)},

volume = {8},

number = {1},

abstract = {Early-diverging fungi (EDF) are ubiquitous and versatile. Their diversity is reflected in their genome sizes and complexity. For instance, multiple protein families have been reported to expand or disappear either in particular genomes or even whole lineages. The most commonly mentioned are CAZymes (carbohydrate-active enzymes), peptidases and transporters that serve multiple biological roles connected to, e.g., metabolism and nutrients intake. In order to study the link between ecology and its genomic underpinnings in a more comprehensive manner, we carried out a systematic in silico survey of protein family expansions and losses among EDF with diverse lifestyles. We found that 86 protein families are represented differently according to EDF ecological features (assessed by median count differences). Among these there are 19 families of proteases, 43 CAZymes and 24 transporters. Some of these protein families have been recognized before as serine and metallopeptidases, cellulases and other nutrition-related enzymes. Other clearly pronounced differences refer to cell wall remodelling and glycosylation. We hypothesize that these protein families altogether define the preliminary fungal adaptasome. However, our findings need experimental validation. Many of the protein families have never been characterized in fungi and are discussed in the light of fungal ecology for the first time.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid33682003,

title = {Utilization of cobalamin is ubiquitous in early-branching fungal phyla},

author = {Małgorzata Orłowska and Kamil Steczkiewicz and Anna Muszewska},

doi = {10.1093/gbe/evab043},

issn = {1759-6653},

year  = {2021},

date = {2021-04-01},

urldate = {2021-04-01},

journal = {Genome Biol Evol},

volume = {13},

number = {4},

abstract = {Cobalamin is a cofactor present in essential metabolic pathways in animals and one of the water-soluble vitamins. It is a complex compound synthesized solely by prokaryotes. Cobalamin dependence is scattered across the tree of life. In particular, fungi and plants were deemed devoid of cobalamin. We demonstrate that cobalamin is utilized by all non-Dikarya fungi lineages. This observation is supported by the genomic presence of both B12-dependent enzymes and cobalamin modifying enzymes. Fungal cobalamin-dependent enzymes are highly similar to their animal homologs. Phylogenetic analyses support a scenario of vertical inheritance of the cobalamin usage with several losses. Cobalamin usage was probably lost in Mucorinae and at the base of Dikarya which groups most of the model organisms and which hindered B12-dependent metabolism discovery in fungi. Our results indicate that cobalamin dependence was a widely distributed trait at least in Opisthokonta, across diverse microbial eukaryotes and was likely present in the LECA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid33679672,

title = {Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina},

author = {Anna Muszewska and Alicja Okrasińska and Kamil Steczkiewicz and Olga Drgas and Małgorzata Orłowska and Urszula Perlińska-Lenart and Tamara Aleksandrzak-Piekarczyk and Katarzyna Szatraj and Urszula Zielenkiewicz and Sebastian Piłsyk and Ewa Malc and Piotr Mieczkowski and Joanna S Kruszewska and Przemysław Bernat and Julia Pawłowska},

doi = {10.3389/fmicb.2021.636986},

issn = {1664-302X},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Front Microbiol},

volume = {12},

pages = {636986},

abstract = {Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two  isolates from soil (i.e., ), two soil-derived  isolates (i.e., ), and two Mucorales representatives with extended proteolytic activity (i.e.,  and . We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics.  harbors an additional, complete genome of an associated bacterium classified to  sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}