@article{MTMT:35212141, title = {Transcriptomics identify the triggering of citrate export as the key event caused by manganese deficiency in Aspergillus niger}, url = {https://m2.mtmt.hu/api/publication/35212141}, author = {Fekete, Erzsébet and Bíró, Vivien and Márton, Alexandra and Bakondi-Kovács, István and Karaffa, Erzsébet Mónika and KOVÁCS, B and GEOFFRION, N and TSANG, A and KUBICEK, CP and Karaffa, Levente}, journal-iso = {MICROBIOL SPEC}, journal = {MICROBIOLOGY SPECTRUM}, volume = {&}, unique-id = {35212141}, issn = {2165-0497}, year = {2024}, eissn = {2165-0497} } @CONFERENCE{MTMT:35089557, title = {Fémionok szerepe gomba alapú szerves sav fermentációiban}, url = {https://m2.mtmt.hu/api/publication/35089557}, author = {Karaffa, Levente and Bíró, Vivien and Márton, Alexandra and Bakondi-Kovács, István and KUBICEK, Christian P. and Fekete, Erzsébet}, booktitle = {VII. Magyar Mikológiai Konferencia, 2024. június 5–7. Budapest}, unique-id = {35089557}, abstract = {Egyes fonalasgomba-fajokban meghatározott élettani–környezeti (ill. az ezeket reprodukáló technológiai) körülmények között a szénforrás lebontása a szerves savak szintjén megakadhat, amit jelentős mértékű felhalmozódás és kiválasztódás követhet. A „túltermelő anyagcsere” jelenségére egy komplett iparág épült: a fermentációs úton előállított egy-, illetve többértékű szerves savak (karbonsavak) az ipari biotechnológia legrégibb, mennyiségileg és gazdaságilag legjelentősebb tömegtermékei közé tartoznak. Magas termékhozam eléréséhez meghatározott összetételű fermentációs táptalajra van szükség, melyben négy átmenetifém-ion – a mangán (Mn2+), a vas (Fe2+), a réz (Cu2+) és a cink (Zn2+) – koncentrációja és egymáshoz viszonyított aránya kritikusan fontos. E fémionok szervessav-túltermelésben játszott biokémiai és élettani szerepét, a fermentációkhoz kapcsolódó technológiai és analitikai aspektusokat foglaljuk össze, kihang- súlyozva a piaci szempontból messze legjelentősebb szerves sav, a citromsav esetét.}, year = {2024}, pages = {23-23} } @misc{MTMT:35089529, title = {Fémionok szerepe gomba alapú szerves sav fermentációiban}, url = {https://m2.mtmt.hu/api/publication/35089529}, author = {Karaffa, Levente and Bíró, Vivien and Márton, Alexandra and Bakondi-Kovács, István and KUBICEK, Christian P. and Fekete, Erzsébet}, unique-id = {35089529}, year = {2024} } @CONFERENCE{MTMT:34847827, title = {MANGANESE EFFECT ON CITRIC ACID PRODUCTION BY ASPERGILLUS NIGER: UNLOCKING AN EFFICIENCY BOOSTING HIDDEN KEY}, url = {https://m2.mtmt.hu/api/publication/34847827}, author = {Bíró, Vivien and Márton, Alexandra and Fekete, Erzsébet and Karaffa, Levente}, booktitle = {FIBOK 2024 6th National Conference of Young Biotechnologists}, unique-id = {34847827}, abstract = {Achieving high yields of citric acid requires a unique combination of culture conditions, with the deficiency of manganese(II) ions in the growth medium being especially crucial. Concentrations exceeding 5 μg/L (= 5 ppb) result in a reduction of around 25% in the final citric acid yield. Because of its characteristics, this organic acid finds utility across a spectrum of industrial sectors, spanning from food and beverage to detergent and pharmaceutical industries. The predominant method for citric acid production involves large-scale industrial fermentations utilizing the filamentous fungus Aspergillus niger. When compared to alternative hosts, A. niger stands out for its ability to achieve remarkably high yields, with potential outputs reaching up to 95 kg of citric acid per 100 kg of sugar. Technical-scale production of citric acid predominantly uses stainless steel tank fermenters. However, glass bioreactors, commonly used for process development, also incorporate stainless steel components, where manganese serves as a crucial alloying element. Our study reveals that manganese(II) ions leach from these bioreactors into the growth medium during citric acid fermentation. This leaching phenomenon leads to alterations in fungal physiology and morphology, resulting in a significant decrease in citric acid yields. The extent of manganese(II) ion leaching depends on factors such as fermentation duration, the acidity of the culture broth, and the sterilization method employed. Moreover, CexA is the main citrate exporter of A. niger. The citric acid production was examined in overexpression mutant strains of cexA under manganese deficiency and sufficient conditions. This leads to citric acid accumulation even in the presence of high manganese(II) ion concentrations. Additionally, the impact of CexA on fungal morphology was elucidated through microscopic analysis.}, year = {2024} } @CONFERENCE{MTMT:34847686, title = {INSIGHTS INTO THE EVOLUTION AND MUTATIONS OF SECOND ALTERNATIVE OXIDASE GENES IN ASPERGILLACEAE}, url = {https://m2.mtmt.hu/api/publication/34847686}, author = {Márton, Alexandra and Bíró, Vivien and Flipphi, Michel Johannes Anthonie and Fekete, Erzsébet and Karaffa, Levente}, booktitle = {FIBOK 2024 6th National Conference of Young Biotechnologists}, unique-id = {34847686}, abstract = {Alternative oxidase (Aox) is a branched mitochondrial terminal oxidase, that bypasses Complex III and IV. Aox accepts electrons directly from ubiquinol and reduces oxygen to water without contributing to the proton gradient used for ATP synthesis. Aox is known to have various functions, including helping cells manage stress conditions, regulating cellular metabolism, and maintaining redox balance. In certain organisms, such as plants, it can play a role in preventing excessive reactive oxygen species production under stress conditions. Aox is nearly ubiquitous in fungi, yet the presence of multiple aox genes is uncommon. However, a second aox gene (aoxB) is present in some taxa of Aspergillaceae. Paralogous genes typically originate from duplication events and are passed down vertically. We offer evidence of four separate duplication events along the lineage that resulted in aox paralogues (aoxB) in contemporary Aspergillus and Penicillium taxa. In certain species, three aox genes are co-expressed, yet there are entire sections and series within Aspergillus that lose transient aoxB content. Within the subgenus Nidulantes, we have identified seven instances of independent aoxB gene loss and two instances of gain. The paralogous clades originate from widespread aoxA parent genes but never replace them, aoxA remains permanent across filamentous fungi. Within the database, Aspergillus niger strains possess six different alleles of the aoxB gene. Besides the wild type, we found five different mutations that caused errors in the gene product. A full-length AoxB is encoded in the acid producer ATCC 1015 strain. The investigation of alternative oxidase genes is crucial for a deeper understanding of citric acid production or clinical aspects. Fermentation occurs based on highly complex biochemical relationships, wherein the aox gene plays a crucial role. Understanding a gene well significantly contributes to strain development or possible clinical treatment.}, year = {2024} } @misc{MTMT:34847654, title = {INSIGHTS INTO THE EVOLUTION AND MUTATIONS OF SECOND ALTERNATIVE OXIDASE GENES IN ASPERGILLACEAE}, url = {https://m2.mtmt.hu/api/publication/34847654}, author = {Márton, Alexandra and Bíró, Vivien and Flipphi, Michel Johannes Anthonie and Fekete, Erzsébet and Karaffa, Levente}, unique-id = {34847654}, abstract = {Alternative oxidase (Aox) is a branched mitochondrial terminal oxidase, that bypasses Complex III and IV. Aox accepts electrons directly from ubiquinol and reduces oxygen to water without contributing to the proton gradient used for ATP synthesis. Aox is known to have various functions, including helping cells manage stress conditions, regulating cellular metabolism, and maintaining redox balance. In certain organisms, such as plants, it can play a role in preventing excessive reactive oxygen species production under stress conditions. Aox is nearly ubiquitous in fungi, yet the presence of multiple aox genes is uncommon. However, a second aox gene (aoxB) is present in some taxa of Aspergillaceae. Paralogous genes typically originate from duplication events and are passed down vertically. We offer evidence of four separate duplication events along the lineage that resulted in aox paralogues (aoxB) in contemporary Aspergillus and Penicillium taxa. In certain species, three aox genes are co-expressed, yet there are entire sections and series within Aspergillus that lose transient aoxB content. Within the subgenus Nidulantes, we have identified seven instances of independent aoxB gene loss and two instances of gain. The paralogous clades originate from widespread aoxA parent genes but never replace them, aoxA remains permanent across filamentous fungi. Within the database, Aspergillus niger strains possess six different alleles of the aoxB gene. Besides the wild type, we found five different mutations that caused errors in the gene product. A full-length AoxB is encoded in the acid producer ATCC 1015 strain. The investigation of alternative oxidase genes is crucial for a deeper understanding of citric acid production or clinical aspects. Fermentation occurs based on highly complex biochemical relationships, wherein the aox gene plays a crucial role. Understanding a gene well significantly contributes to strain development or possible clinical treatment.}, year = {2024} } @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} }