What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota

Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.

Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages

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 Mucoromycotina. The constitution of 25% and 12% of this sugar in the carbohydrates of cell wall in the respective Umbelopsis and Mucorales 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 in-silico approach to construct the fucose metabolic map in Fungi. We analyzed the taxonomic distribution of 85 protein families in Fungi 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 Metazoa suggesting an ancestral origin in Opisthokonta. However, the overall complexity of fucose metabolism is greater in Metazoa than in Fungi. 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 Dikarya and the early diverging lineages. We speculate that, while Dikarya 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.

In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi

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.

Utilization of cobalamin is ubiquitous in early-branching fungal phyla

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.

Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

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 Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). 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. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus 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.

[Acute gastroenteritis in Isolation Ward III Voivodeship Hospital in Warsaw 2001-2005]

Study was done to evaluate changes of serotypes of Salmonella, clinical pattern, methods of treatment of patients who were hospitalized in our ward between 2001-2005. Among 129 patients with microbiologicaly confirmed Salmonella serotype S. enteritidis is prevalent. No changes of etiology were detected. Signs and treatment was not significantly changed. The most common source of infection were poultry products.

[Adrenal incidentaloma as essential clinical problem in modern endocrinology]

Adrenal mass discovered during imaging for non-adrenal related causes is called incidentaloma. Adrenal masses can be asymptomatic or can have clinical manifestations related to hormone overproduction. The increasing number of discovered adrenal mass is by no doubt due to quick development of radiology procedures. The aim of study was determination of statistical frequency of different types of adrenal tumours and related clinical symptoms based on retrospective analysis of patients diagnosed in the Department of Endocrinology, Collegium Medicum, Jagiellonian University. There were 271 patients (184 female, 87 male) with incidentaloma confirmed in CT scan from January 2000 to June 2005. Mean patients' age was 56.8 +/- 12.7 years. The most common localisation was right adrenal gland (135 cases), bilaterally in 29 patients. Tumours less than 3 cm in diameter were observed in 58.5% of diagnosed persons, tumours from 3 to 6 cm in 33.3% of cases and tumours bigger than 6 cm in 8.2% patients. Hormone excess associated with adrenal mass was detected in 37 (13.6%) patients. Pheochromocytoma was diagnosed in 20 patients (7.4%). Subclinical hypercortisolism was found in 13 patients (4.8%). Primary hyperaldosteronism was diagnosed in 4 cases (1,4%). In patients with adrenal mass incidentaloma hormone tests should be performed before making therapeutic decisions despite no clinical symptoms.

Hyphomycetes in the snow from gymnosperm trees

The presence of 26 hyphomycete species was noted in snow water collected from coniferous trees. Camposporium pellucidum, Monodictys peruviana, Polystratorictus fusarioideus, Sporidesmium moniliforme, Tripospermum acerinum and Veronaea botryosa were recorded for the first time to Poland. Among the 26 species found in snow water from coniferous trees predominance of the socalled aero-aquatic hyphomycetes and only a few species belong to the group of aquatic hyphomycetes.

Hyphomycetes in the ice of water reservoirs

The presence of 111 Hyphomycetes species was noted in the water obtained from melting ice from four water bodies. The following fungi were recorded for the first time from Poland: Acrodictys martinii, A. peruamazonensis, Beltraniella peruamazonica, Blodgettia borneti, Cylindrocarpon aequatoriale, Diplocladiella appendiculata, Clavariopsis azlanii, Fusariella candida, Fusticeps laevisporus, Helicoma vaccinii, Heliscus submersus, Helminthosporium bigenum, Isthmolongispora geniculata, Lateriramulosa uniinflata, Lemonniera centrosphaera, Menispora amazonensis, Microstella pluvioriens, Nectria flavo-lanata, Paraarthrocladium amazonense, Paradactylella peruviana, Phaeodactylium acutisporum, Phialogeniculata multiseptata, Pseudohansfordia dimorpha, Pseudospiropes subliferus, P. lotorus, Pyricularia peruamasonica, Scolecobasidium fusarioideum, Scolecosporiella amazonensis, Stemphyliomma tambopataense, S. terricola, Taeniolina deightonii, Triscelophorus magnificus and Veronaea botryosa.

Hyphomycetes in the water of peatmoss (Sphagnum)

The authors investigated hyphomycetes in the water of peatmoss (Sphagnum) collected from forest peatbogs in the Augustowska and Knyszyńska Forests in northeastern Poland. The presence of 28 hyphomycete species was noted. Cordana musae, Helicoon macrosporum, Sporidesmiella aspera, Stemphyliomma tambopataënse and Tripospermum pes-gallinae were recorded for the first time from Poland.

Hyphomycetes in morning dew of meadows

Hyphomycetes in morning dew of meadows in northeastern Poland. The authors investigated of the Hyphomycetes in morning dew of meadows grass in the morning hours of sunny days in May and September 1994. The presence 23 Hyphomycetes species was noted. The following fungi were recorded for the first time from Poland: Blodgettia borneti, Canalisporium elegans, C. pulchrum, Paraepicoccum amazonense and Sporidesmium basiacutum.

Fungi in water reservoirs of the Western Suwałki Lake District and in some adjacent water basins

In the years 1991-1995 the authors investigated the mycoflora and the effect of environmental factors of 36 lakes and 4 rivers in the Western Suwałki Lake District. In addition the effect of environment factors on the occurrence of various aquatic fungi was analysed. Altogether of 109 fungi species were recorded. Twenty two species new the mycoflora of Poland were noted. The presence of Tripospermum myrti in Lake Oleckie Wielkie is noteworthy.

Hyphomycetes in rain water draining from intact trees

The authors investigated Hyphomycetes in rain water flowing down from leaves of 10 gymnospermous and 10 angiospermous tree species in northeastern Poland. The presence of 57 Hyphomycetes species was noted. Only 17 species were found to develop both on gymnospermous and angiospermous tree species out of 57 found in rain water flowing down the trees. 16 Hyphomycetes species were observed in rain water flowing down the angiospermous trees, while 24 species in the water from the gymnospermous trees. 13 Hyphomycetes species were recorded for the first time from Poland.