@article{MTMT:34832088,
	title = {Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region},
	url = {https://m2.mtmt.hu/api/publication/34832088},
	author = {Gálné Remenyik, Judit and Csige, László and Dávid, Péter and Fauszt, Péter and Szilágyi-Rácz, Anna Anita and Szőllősi, Erzsébet and Bacsó, Zsófia Réka and Szepsy Jnr, István and Molnár, Krisztina and Rácz, Csaba and Fidler, Gábor and Kállai, Zoltán and Stündl, László and Dobos, Attila Csaba and Paholcsek, Melinda},
	doi = {10.1371/journal.pone.0300563},
	journal-iso = {PLOS ONE},
	journal = {PLOS ONE},
	volume = {19},
	unique-id = {34832088},
	issn = {1932-6203},
	abstract = {A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia , Bacteroidetes , Chloroflexi , and Rokubacteria , the classes Acidobacteria , Deltaproteobacteria , Gemmatimonadetes , and Betaproteobacteria , the order Sphingomonadales , Hypomicrobiales , as well as the family Sphingomonadaceae and the genus Sphingomonas . Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium , known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae , the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.},
	year = {2024},
	eissn = {1932-6203},
	orcid-numbers = {Szilágyi-Rácz, Anna Anita/0000-0003-3612-3574; Molnár, Krisztina/0000-0001-6203-6154; Rácz, Csaba/0000-0002-0307-6508; Dobos, Attila Csaba/0000-0001-7904-2155}
}

@article{MTMT:34802432,
	title = {Aspergillus nidulans gfdB, Encoding the Hyperosmotic Stress Protein Glycerol-3-phosphate Dehydrogenase, Disrupts Osmoadaptation in Aspergillus wentii},
	url = {https://m2.mtmt.hu/api/publication/34802432},
	author = {Bodnár , Veronika and Antal, Károly and de Vries, Ronald P. and Pócsi, István and Emri, Tamás},
	doi = {10.3390/jof10040291},
	journal-iso = {J FUNGI},
	journal = {JOURNAL OF FUNGI},
	volume = {10},
	unique-id = {34802432},
	abstract = {The genome of the osmophilic Aspergillus wentii, unlike that of the osmotolerant Aspergillus nidulans, contains only the gfdA, but not the gfdB, glycerol 3-phosphate dehydrogenase gene. Here, we studied transcriptomic changes of A. nidulans (reference strain and ΔgfdB gene deletion mutant) and A. wentii (reference strain and An-gfdB expressing mutant) elicited by high osmolarity. A. nidulans showed a canonic hyperosmotic stress response characterized by the upregulation of the trehalose and glycerol metabolism genes (including gfdB), as well as the genes of the high-osmolarity glycerol (HOG) map kinase pathway. The deletion of gfdB caused only negligible alterations in the transcriptome, suggesting that the glycerol metabolism was flexible enough to compensate for the missing GfdB activity in this species. A. wentii responded differently to increased osmolarity than did A. nidulans, e.g., the bulk upregulation of the glycerol and trehalose metabolism genes, along with the HOG pathway genes, was not detected. The expression of An-gfdB in A. wentii did not abolish osmophily, but it reduced growth and caused much bigger alterations in the transcriptome than did the missing gfdB gene in A. nidulans. Flexible glycerol metabolism and hence, two differently regulated gfd genes, may be more beneficial for osmotolerant (living under changing osmolarity) than for osmophilic (living under constantly high osmolarity) species.},
	keywords = {hyperosmotic stress; Aspergillus nidulans; RNA sequencing; Aspergillus wentii; glycerol-3-phosphate dehydrogenase},
	year = {2024},
	eissn = {2309-608X},
	orcid-numbers = {Antal, Károly/0000-0001-8993-3314; de Vries, Ronald P./0000-0002-4363-1123}
}

@CONFERENCE{MTMT:34753304,
	title = {Specific high effect mutations in clinical and experimentally evolved Saccharomyces ‘boulardii’ isolates show that genes involved in chemical response might have a role during the adaptation to the human host},
	url = {https://m2.mtmt.hu/api/publication/34753304},
	author = {Imre, Alexandra and Kovács, Renátó and Ibrahim, Al’ Abri and Nathan, Crook and Pfliegler, Valter Péter},
	booktitle = {The Allied Genetics Conference 2024 Abstract Book},
	unique-id = {34753304},
	year = {2024},
	orcid-numbers = {Pfliegler, Valter Péter/0000-0001-6723-4416}
}

@CONFERENCE{MTMT:34751176,
	title = {Second Alternative Oxidase Genes in Aspergillaceae: Genesis, Loss and Mutations},
	url = {https://m2.mtmt.hu/api/publication/34751176},
	author = {Karaffa, Levente and Flipphi, Michel Johannes Anthonie and Márton, Alexandra and Bíró, Vivien and Bakondi-Kovács, István and Ág-Rácz, Viktória and Ág, Norbert and Fekete, Erzsébet},
	booktitle = {The 20th International Aspergillus Meeting,Asperfest20 Program and Abstract Book},
	unique-id = {34751176},
	abstract = {Alternative oxidase (Aox) is a terminal oxidase in branched mitochondrial electron transport that provides a non-electrogenic alternative to canonical cytochrome-mediated electron flow, bypassing the proton- pumping complexes III and IV. The consequence of the direct transfer of electrons from ubiquinol to oxygen without concomitant build up of proton motive force is the uncoupling of ATP synthesis via oxidative phosporylation from NADH reoxidation, to allow carbon catabolism to continue unabated even when ATP demand is low or when non-carbon nutrients become limiting. Thus, Aox plays an important role in the energetics of overflow metabolism-based bioprocesses such as Aspergillus niger citric acid fermentation and Aspergillus terreus itaconate production.
		Aox (aoxA gene) is near ubiquitous in the fungal kingdom, but coexistence of multiple aox genes is rare. However, a second aox gene (aoxB) is present in some taxa of Aspergillaceae. Paralogous genes generally originate from duplication and inherit vertically; we provide evidence for four independent duplication events at different points in evolution that resulted in aoxB paralogs in contemporary Aspergilli and Penicillia. The paralog in A. niger has a different origin than the paralog in A. terreus, while a third independently formed paralog is found in A. wentii. All paralogous clades arise from original aoxA parent genes but never replace them. Few species have accumulated three co-expressed aox genes. Therefore, loss of once acquired paralogs co-determines contemporary aox gene content in individual species. For instance, section Fumigati has lost all its transient paralogs. In the subgenus Nidulantes, we identified seven independent occasions of aoxB gene loss and two gains. In A. calidoustus, both more ancient aoxB paralogs present in the last common ancestor of the subgenus have been substituted by two other aoxB genes of completely distinct origins.
		We found that the paralogous aoxB gene in some 75 genome-sequenced A. niger strains features variation at a level not detected for the ubiquitous aoxA gene. Five mutations were identified that plausibly affect transcription, function, or terminally modify the gene product. A full-length AoxB is encoded in the acid producer ATCC 1015. Hence, the A. niger sensu stricto complex can be subdivided into six taxa according to the resident aoxB allele. To date, confident separation could only be accomplished after comparative analyses of whole genome sequences.},
	year = {2024},
	pages = {26-27}
}

@misc{MTMT:34751163,
	title = {Second Alternative Oxidase Genes in Aspergillaceae: Genesis, Loss and Mutations},
	url = {https://m2.mtmt.hu/api/publication/34751163},
	author = {Karaffa, Levente and Flipphi, Michel Johannes Anthonie and Márton, Alexandra and Bíró, Vivien and Bakondi-Kovács, István and Ág-Rácz, Viktória and Ág, Norbert and Fekete, Erzsébet},
	unique-id = {34751163},
	abstract = {Alternative oxidase (Aox) is a terminal oxidase in branched mitochondrial electron transport that provides a non-electrogenic alternative to canonical cytochrome-mediated electron flow, bypassing the proton- pumping complexes III and IV. The consequence of the direct transfer of electrons from ubiquinol to oxygen without concomitant build up of proton motive force is the uncoupling of ATP synthesis via oxidative phosporylation from NADH reoxidation, to allow carbon catabolism to continue unabated even when ATP demand is low or when non-carbon nutrients become limiting. Thus, Aox plays an important role in the energetics of overflow metabolism-based bioprocesses such as Aspergillus niger citric acid fermentation and Aspergillus terreus itaconate production.
		Aox (aoxA gene) is near ubiquitous in the fungal kingdom, but coexistence of multiple aox genes is rare. However, a second aox gene (aoxB) is present in some taxa of Aspergillaceae. Paralogous genes generally originate from duplication and inherit vertically; we provide evidence for four independent duplication events at different points in evolution that resulted in aoxB paralogs in contemporary Aspergilli and Penicillia. The paralog in A. niger has a different origin than the paralog in A. terreus, while a third independently formed paralog is found in A. wentii. All paralogous clades arise from original aoxA parent genes but never replace them. Few species have accumulated three co-expressed aox genes. Therefore, loss of once acquired paralogs co-determines contemporary aox gene content in individual species. For instance, section Fumigati has lost all its transient paralogs. In the subgenus Nidulantes, we identified seven independent occasions of aoxB gene loss and two gains. In A. calidoustus, both more ancient aoxB paralogs present in the last common ancestor of the subgenus have been substituted by two other aoxB genes of completely distinct origins.
		We found that the paralogous aoxB gene in some 75 genome-sequenced A. niger strains features variation at a level not detected for the ubiquitous aoxA gene. Five mutations were identified that plausibly affect transcription, function, or terminally modify the gene product. A full-length AoxB is encoded in the acid producer ATCC 1015. Hence, the A. niger sensu stricto complex can be subdivided into six taxa according to the resident aoxB allele. To date, confident separation could only be accomplished after comparative analyses of whole genome sequences.},
	year = {2024}
}

@CONFERENCE{MTMT:34751135,
	title = {Transcriptome analysis of manganese(II) ion depletion during high-yield citric acid fermentation in Aspergillus niger},
	url = {https://m2.mtmt.hu/api/publication/34751135},
	author = {Karaffa, Levente and Bíró, Vivien and Márton, Alexandra and Bakondi-Kovács, István and Nicholas, Geoffrion and Adrian, Tsang and Christian, P. Kubicek and Fekete, Erzsébet},
	booktitle = {The 20th International Aspergillus Meeting,Asperfest20 Program and Abstract Book},
	unique-id = {34751135},
	abstract = {Structural and Functional Genomics, Concordia University, Montreal, QC, Canada, 3Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria Citric acid (citrate) is amongst the most important bulk products of industrial biotechnology. The discovery of its accumulation by the filamentous fungus Aspergillus niger led to the development of a large-scale submerged fermentation process employing stirred tank reactors, which today accounts for 95% of the world’s production. High-yield citric acid production requires a combination of unusual nutritional conditions, of which establishing a low (<5 ppb) manganese(II) ion concentration at the onset of the fermentation is a key feature.
		Changes in the metabolism of A. niger prompted by Mn(II)-deficiency has not been investigated on a functional genomics level so far. In order to get an insight into how Mn(II) deficiency triggers citric acid accumulation, we compared the transcriptome of the citric acid hyperproducer A. niger NRRL 2270 strain at three time points (24-hour, 48-hour, and 72-hour) at Mn(II)-deficient (=5 ppb) and Mn(II)-sufficient (=100 ppb) fermentation conditions. This experimental design emanates from our previous observation that the effect of Mn(II) ions on citric acid accumulation is dependent on the cultivation time: it has the strongest effect at the onset of the cultivation and then gradually decreases (Fekete et al., 2022).
		Comparison of the transcriptomes of Mn(II)-deficient and Mn(II)-sufficient fermentation conditions revealed that 1436 transcripts are differentially regulated (log2> 2 at p <0.05). Of these, 629 transcripts are upregulated and 807 transcripts are downregulated under Mn(II)-deficient condition. Of the transcripts that displayed differential regulation only at the 24-hour timepoint, 101 transcripts were upregulated and 101 were downregulated. Among the 133 transcripts that were upregulated at all three timepoints under Mn(II)-deficient condition, the majority (= 97) transcripts are predicted to encode secreted or membrane-bound proteins. Notably, cexA, encoding the major citrate exporter in A. niger (Reinfurt et al., 2023), was upregulated 75-, 15- and 2-fold at the three respective timepoints of cultivation under Mn(II)-deficient condition.},
	year = {2024},
	pages = {27-27}
}

@CONFERENCE{MTMT:34750649,
	title = {Second Alternative Oxidase Genes in Aspergillaceae: Genesis, Loss and Mutations},
	url = {https://m2.mtmt.hu/api/publication/34750649},
	author = {Karaffa, Levente and Flipphi, Michel Johannes Anthonie and Márton, Alexandra and Bíró, Vivien and Bakondi-Kovács, István and Ág-Rácz, Viktória and Ág, Norbert and Fekete, Erzsébet},
	booktitle = {32nd Fugal Genetics Conference Abstract Book},
	unique-id = {34750649},
	abstract = {Alternative oxidase (Aox) is a terminal oxidase in branched mitochondrial electron transport that provides a non-electrogenic alternative to canonical cytochrome-mediated electron flow, bypassing the proton-pumping complexes III and IV. The consequence of the direct transfer of electrons from ubiquinol to oxygen without concomitant build up of proton motive force is the uncoupling of ATP synthesis via oxidative phosporylation from NADH reoxidation, to allow carbon catabolism to continue unabated even when ATP demand is low or when non-carbon nutrients become limiting. Thus, Aox plays an important role in the energetics of overflow metabolism-based bioprocesses such as Aspergillus niger citric acid fermentation and Aspergillus terreus itaconate production.
		Aox (aoxA gene) is near ubiquitous in the fungal kingdom, but coexistence of multiple aox genes is rare. However, a second aox gene (aoxB) is present in some taxa of Aspergillaceae. Paralogous genes generally originate from duplication and inherit vertically; we provide evidence for four independent duplication events at different points in evolution that resulted in aoxB paralogs in contemporary Aspergilli and Penicillia. The paralog in A. niger has a different origin than the paralog in A. terreus, while a third independently formed paralog is found in A. wentii. All paralogous clades arise from original aoxA parent genes but never replace them. Few species have accumulated three co-expressed aox genes. Therefore, loss of once acquired paralogs co-determines contemporary aox gene content in individual species. For instance, section Fumigati has lost all its transient paralogs. In the subgenus Nidulantes, we identified seven independent occasions of aoxB gene loss and two gains. In A. calidoustus, both more ancient aoxB paralogs present in the last common ancestor of the subgenus have been substituted by two other aoxB genes of completely distinct origins.
		We found that the paralogous aoxB gene in some 75 genome-sequenced A. niger strains features variation at a level not detected for the ubiquitous aoxA gene. Five mutations were identified that plausibly affect transcription, function, or terminally modify the gene product. A full-length AoxB is encoded in the acid producer ATCC 1015. Hence, the A. niger sensu stricto complex can be subdivided into six taxa according to the resident aoxB allele. To date, confident separation could only be accomplished after comparative analyses of whole genome sequences.},
	year = {2024},
	pages = {300-301}
}

@CONFERENCE{MTMT:34750608,
	title = {Continual propagation of [D1,2] stwintrons in divergent Xylariales},
	url = {https://m2.mtmt.hu/api/publication/34750608},
	author = {Fekete, Erzsébet and Ág, Norbert and Ág-Rácz, Viktória and Márton, Alexandra and Bíró, Vivien and Flipphi, Michel Johannes Anthonie and Karaffa, Levente},
	booktitle = {32nd Fugal Genetics Conference Abstract Book},
	unique-id = {34750608},
	abstract = {Spliceosomal twin introns consist of two nested U2 introns excised consecutively. In a [D1,2] stwintron, an internal intron interrupts the 5’-donor of an external intron between the 1st and 2nd nucleotide (nt) (5’-G 1|U 2). For Hypoxylon sp. CO27-5, one can classify [D1,2]’s in two groups. Of these, sequence-similar “sister” stwintrons cross-identify by blastn, and occur at new intron positions in narrow taxa (species, variants). When reciprocal blastn screens were performed in genomes of other Xylariales species–using proven CO27-5 sister stwintrons as primary queries–258 new sequence-similar stwintrons were revealed in 12 species. Some species contain > 50 sister stwintrons, others < 10. All of them are integrated seamlessly in seemingly random exonic sequences, excluding transposon-driven mechanisms or splice-site co-option for their propagation. One observes essentially species-specific clades of sister stwintrons in maximum likelihood trees, implying vertical transmission of sequence-diverging duplication- competent [D1,2]’s. Xylaria sp. MSU SB201401 and X. striata RK1-1 are intimately related–like strains of the same species–albeit isolated from very different plant species, growing on different continents. 4 stwintrons unique to MSU SB201401 are phylogenetically clustered and the 3 most similar ones are >99 % identical, while the genes harboring them are completely unrelated in sequence, intron-exon structure and function. This lineage involves consecutive strain-specific stwintron duplication events, arguably the most recent duplications in our set. Although the continuous 11-nt near-terminal inverted repeat in these 4 MSU SB201401 stwintrons is not as long as those in prototypical CO27-5 sisters, the near-terminal stem structure is the stand-out common feature. We propose that this stem structure can bring the donor G1 of the internal- and the acceptor G3 of the external intron in close proximity, necessary for the rare duplication of [D1,2] stwintrons into double-stranded DNA breaks, including those with smaller or less perfect terminal inverted repeats. We also identified one potential lateral transfer: one MSU SB201401 stwintron is >93 % sequence-identical with two different [D1,2]’s in Xylariaceae sp. FL1651. The 3 genes harboring them are completely unrelated. This may imply that duplication-competent stwintrons can be (re)acquired by lateral transfer. Such rare events could contibute to the periodicity of overall (stw)intron gain and loss.},
	year = {2024},
	pages = {158-158}
}

@CONFERENCE{MTMT:34750415,
	title = {Continual propagation of [D1,2] stwintrons in divergent Xylariales},
	url = {https://m2.mtmt.hu/api/publication/34750415},
	author = {Fekete, Erzsébet and Ág, Norbert and Ág-Rácz, Viktória and Márton, Alexandra and Bíró, Vivien and Flipphi, Michel Johannes Anthonie and Karaffa, Levente},
	booktitle = {32nd Fugal Genetics Conference Abstract Book},
	unique-id = {34750415},
	abstract = {Spliceosomal twin introns consist of two nested U2 introns excised consecutively. In a [D1,2] stwintron, an internal intron interrupts the 5’-donor of an external intron between the 1st and 2nd nucleotide (nt) (5’-G 1|U 2). For Hypoxylon sp. CO27-5, one can classify [D1,2]’s in two groups. Of these, sequence-similar “sister” stwintrons cross-identify by blastn, and occur at new intron positions in narrow taxa (species, variants). When reciprocal blastn screens were performed in genomes of other Xylariales species–using proven CO27-5 sister stwintrons as primary queries–258 new sequence-similar stwintrons were revealed in 12 species. Some species contain > 50 sister stwintrons, others < 10. All of them are integrated seamlessly in seemingly random exonic sequences, excluding transposon-driven mechanisms or splice-site co-option for their propagation. One observes essentially species-specific clades of sister stwintrons in maximum likelihood trees, implying vertical transmission of sequence-diverging duplication- competent [D1,2]’s. Xylaria sp. MSU SB201401 and X. striata RK1-1 are intimately related–like strains of the same species–albeit isolated from very different plant species, growing on different continents. 4 stwintrons unique to MSU SB201401 are phylogenetically clustered and the 3 most similar ones are >99 % identical, while the genes harboring them are completely unrelated in sequence, intron-exon structure and function. This lineage involves consecutive strain-specific stwintron duplication events, arguably the most recent duplications in our set. Although the continuous 11-nt near-terminal inverted repeat in these 4 MSU SB201401 stwintrons is not as long as those in prototypical CO27-5 sisters, the near-terminal stem structure is the stand-out common feature. We propose that this stem structure can bring the donor G1 of the internal- and the acceptor G3 of the external intron in close proximity, necessary for the rare duplication of [D1,2] stwintrons into double-stranded DNA breaks, including those with smaller or less perfect terminal inverted repeats. We also identified one potential lateral transfer: one MSU SB201401 stwintron is >93 % sequence-identical with two different [D1,2]’s in Xylariaceae sp. FL1651. The 3 genes harboring them are completely unrelated. This may imply that duplication-competent stwintrons can be (re)acquired by lateral transfer. Such rare events could contibute to the periodicity of overall (stw)intron gain and loss.},
	year = {2024},
	pages = {24-24}
}

@article{MTMT:34750126,
	title = {The Oxidative Stress Response Highly Depends on Glucose and Iron Availability in Aspergillus fumigatus},
	url = {https://m2.mtmt.hu/api/publication/34750126},
	author = {Emri, Tamás and Antal, Károly and Varga, Kinga and Gila, Csaba Barnabás and Pócsi, István},
	doi = {10.3390/jof10030221},
	journal-iso = {J FUNGI},
	journal = {JOURNAL OF FUNGI},
	volume = {10},
	unique-id = {34750126},
	abstract = {Pathogens have to cope with oxidative, iron- and carbon(glucose)-limitation stresses in the human body. To understand how combined iron–carbon limitation alters oxidative stress responses, Aspergillus fumigatus was cultured in glucose–peptone or peptone containing media supplemented or not with deferiprone as an iron chelator. Changes in the transcriptome in these cultures were recorded after H2O2 treatment. Responses to oxidative stress were highly dependent on the availability of glucose and iron. Out of the 16 stress responsive antioxidative enzyme genes, only the cat2 catalase–peroxidase gene was upregulated in more than two culturing conditions. The transcriptional responses observed in iron metabolism also varied substantially in these cultures. Only extracellular siderophore production appeared important regardless of culturing conditions in oxidative stress protection, while the enhanced synthesis of Fe-S cluster proteins seemed to be crucial for oxidative stress treated iron-limited and fast growing (glucose rich) cultures. Although pathogens and host cells live together in the same place, their culturing conditions (e.g., iron availability or occurrence of oxidative stress) can be different. Therefore, inhibition of a universally important biochemical process, like Fe-S cluster assembly, may selectively inhibit the pathogen growth in vivo and represent a potential target for antifungal therapy.},
	keywords = {DEFERIPRONE; Aspergillus fumigatus; carbon limitation},
	year = {2024},
	eissn = {2309-608X},
	orcid-numbers = {Antal, Károly/0000-0001-8993-3314; Gila, Csaba Barnabás/0000-0001-9609-2795}
}