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Bokor E, Ámon J, Varga M, Szekeres A, Hegedűs Z, Jakusch T, Szakonyi Z, Flipphi M, Vágvölgyi C, Gácser A, Scazzocchio C, Hamari Z. A complete nicotinate degradation pathway in the microbial eukaryote Aspergillus nidulans. Commun Biol 2022; 5:723. [PMID: 35864155 PMCID: PMC9304392 DOI: 10.1038/s42003-022-03684-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Several strikingly different aerobic and anaerobic pathways of nicotinate breakdown are extant in bacteria. Here, through reverse genetics and analytical techniques we elucidated in Aspergillus nidulans, a complete eukaryotic nicotinate utilization pathway. The pathway extant in this fungus and other ascomycetes, is quite different from bacterial ones. All intermediate metabolites were identified. The cognate proteins, encoded by eleven genes (hxn) mapping in three clusters are co-regulated by a specific transcription factor. Several enzymatic steps have no prokaryotic equivalent and two metabolites, 3-hydroxypiperidine-2,6-dione and 5,6-dihydroxypiperidine-2-one, have not been identified previously in any organism, the latter being a novel chemical compound. Hydrolytic ring opening results in α-hydroxyglutaramate, a compound not detected in analogous prokaryotic pathways. Our earlier phylogenetic analysis of Hxn proteins together with this complete biochemical pathway illustrates convergent evolution of catabolic pathways between fungi and bacteria.
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Affiliation(s)
- Eszter Bokor
- University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary
| | - Judit Ámon
- University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary
| | - Mónika Varga
- University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary
| | - András Szekeres
- University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary
| | - Zsófia Hegedűs
- University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary
| | - Tamás Jakusch
- University of Szeged Faculty of Science and Informatics, Department of Inorganic and Analytical Chemistry, Szeged, Hungary
| | - Zsolt Szakonyi
- University of Szeged Faculty of Pharmacy, Institute of Pharmaceutical Chemistry, Szeged, Hungary
| | - Michel Flipphi
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Csaba Vágvölgyi
- University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary
| | - Attila Gácser
- HCEMM-USZ Fungal Pathogens Research Group, University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary
- MTA-SZTE "Lendület" Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Claudio Scazzocchio
- Section of Microbiology, Department of Infectious Diseases, Imperial College, London, United Kingdom.
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Zsuzsanna Hamari
- University of Szeged Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary.
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Bokor E, Flipphi M, Kocsubé S, Ámon J, Vágvölgyi C, Scazzocchio C, Hamari Z. Genome organization and evolution of a eukaryotic nicotinate co-inducible pathway. Open Biol 2021; 11:210099. [PMID: 34582709 PMCID: PMC8478523 DOI: 10.1098/rsob.210099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In Aspergillus nidulans a regulon including 11 hxn genes (hxnS, T, R, P, Y, Z, X, W, V, M and N) is inducible by a nicotinate metabolic derivative, repressible by ammonium and under stringent control of the nitrogen-state-sensitive GATA factor AreA and the specific transcription factor HxnR. This is the first report in a eukaryote of the genomic organization of a possibly complete pathway of nicotinate utilization. In A. nidulans the regulon is organized in three distinct clusters, this organization is variable in the Ascomycota. In some Pezizomycotina species all 11 genes map in a single cluster; in others they map in two clusters. This variable organization sheds light on cluster evolution. Instances of gene duplication followed by or simultaneous with integration in the cluster, partial or total cluster loss, and horizontal gene transfer of several genes (including an example of whole cluster re-acquisition in Aspergillus of section Flavi) were detected, together with the incorporation in some clusters of genes not found in the A. nidulans co-regulated regulon, which underlie both the plasticity and the reticulate character of metabolic cluster evolution. This study provides a comprehensive phylogeny of six members of the cluster across representatives of all Ascomycota classes.
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Affiliation(s)
- Eszter Bokor
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Michel Flipphi
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Sándor Kocsubé
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Judit Ámon
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, UK,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Zsuzsanna Hamari
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
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Ámon J, Fernández-Martín R, Bokor E, Cultrone A, Kelly JM, Flipphi M, Scazzocchio C, Hamari Z. A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria. Open Biol 2018; 7:rsob.170199. [PMID: 29212709 PMCID: PMC5746545 DOI: 10.1098/rsob.170199] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/09/2017] [Indexed: 12/23/2022] Open
Abstract
Nicotinate degradation has hitherto been elucidated only in bacteria. In the ascomycete Aspergillus nidulans, six loci, hxnS/AN9178 encoding the molybdenum cofactor-containing nicotinate hydroxylase, AN11197 encoding a Cys2/His2 zinc finger regulator HxnR, together with AN11196/hxnZ, AN11188/hxnY, AN11189/hxnP and AN9177/hxnT, are clustered and stringently co-induced by a nicotinate derivative and subject to nitrogen metabolite repression mediated by the GATA factor AreA. These genes are strictly co-regulated by HxnR. Within the hxnR gene, constitutive mutations map in two discrete regions. Aspergillus nidulans is capable of using nicotinate and its oxidation products 6-hydroxynicotinic acid and 2,5-dihydroxypyridine as sole nitrogen sources in an HxnR-dependent way. HxnS is highly similar to HxA, the canonical xanthine dehydrogenase (XDH), and has originated by gene duplication, preceding the origin of the Pezizomycotina. This cluster is conserved with some variations throughout the Aspergillaceae. Our results imply that a fungal pathway has arisen independently from bacterial ones. Significantly, the neo-functionalization of XDH into nicotinate hydroxylase has occurred independently from analogous events in bacteria. This work describes for the first time a gene cluster involved in nicotinate catabolism in a eukaryote and has relevance for the formation and evolution of co-regulated primary metabolic gene clusters and the microbial degradation of N-heterocyclic compounds.
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Affiliation(s)
- Judit Ámon
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH)
| | | | - Eszter Bokor
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH)
| | - Antonietta Cultrone
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Joan M Kelly
- Department of Biology, University of Essex, Colchester, UK
| | - Michel Flipphi
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Claudio Scazzocchio
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France .,Department of Biology, University of Essex, Colchester, UK.,Department of Microbiology, Imperial College, London, UK (present address of CS).,Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France (present address of CS)
| | - Zsuzsanna Hamari
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH) .,Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
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Maia LB, Moura I, Moura JJ. EPR Spectroscopy on Mononuclear Molybdenum-Containing Enzymes. FUTURE DIRECTIONS IN METALLOPROTEIN AND METALLOENZYME RESEARCH 2017. [DOI: 10.1007/978-3-319-59100-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Completing the purine utilisation pathway of Aspergillus nidulans. Fungal Genet Biol 2011; 48:840-8. [DOI: 10.1016/j.fgb.2011.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/07/2011] [Accepted: 03/07/2011] [Indexed: 11/22/2022]
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Cultrone A, Scazzocchio C, Rochet M, Montero-Morán G, Drevet C, Fernández-Martín R. Convergent evolution of hydroxylation mechanisms in the fungal kingdom: molybdenum cofactor-independent hydroxylation of xanthine via α-ketoglutarate-dependent dioxygenases. Mol Microbiol 2005; 57:276-90. [PMID: 15948966 DOI: 10.1111/j.1365-2958.2005.04686.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xanthine oxidases and dehydrogenases are among the most conserved enzymes in all living kingdoms. They contain the molybdopterin cofactor Moco. We show here that in the fungi, in addition to xanthine dehydrogenase, a completely different enzyme is able to catalyse the oxidation of xanthine to uric acid. In Aspergillus nidulans this enzyme is coded by the xanA gene. We have cloned the xanA gene and determined its sequence. A deletion of the gene has the same phenotype as the previously known xanA1 miss-sense mutation. Homologues of xanA exist only in the fungal kingdom. We have inactivated the cognate gene of Schizosaccharomyces pombe and this results in strongly impaired xanthine utilization as a nitrogen source. We have shown that the Neurospora crassa homologue is functionally equivalent to xanA. The enzyme coded by xanA is an alpha-ketoglutarate- and Fe(II)-dependent dioxygenase which shares a number of properties with other enzymes of this group. This work shows that only in the fungal kingdom, an alternative mechanism of xanthine oxidation, not involving Moco, has evolved using the dioxygenase scaffold.
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Affiliation(s)
- Antonietta Cultrone
- Institut de Génétique et de Microbiologie, Université Paris-Sud, Bâtiment 409, UMR 8621 CNRS, 91405 Orsay Cedex, France
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Hesberg C, Hänsch R, Mendel RR, Bittner F. Tandem Orientation of Duplicated Xanthine Dehydrogenase Genes from Arabidopsis thaliana. J Biol Chem 2004; 279:13547-54. [PMID: 14726515 DOI: 10.1074/jbc.m312929200] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Xanthine dehydrogenase from the plant Arabidopsis thaliana was analyzed on molecular and biochemical levels. Whereas most other organisms appear to own only one gene for xanthine dehydrogenase A. thaliana possesses two genes in tandem orientation spaced by 704 base pairs. The cDNAs as well as the proteins AtXDH1 and AtXDH2 share an overall identity of 93% and show high homologies to xanthine dehydrogenases from other organisms. Whereas AtXDH2 mRNA is expressed constitutively, alterations of AtXDH1 transcript levels were observed at various stresses like drought, salinity, cold, and natural senescence, but also after abscisic acid treatment. Transcript alteration did not mandatorily result in changes of xanthine dehydrogenase activities. Whereas salt treatment had no effect on xanthine dehydrogenase activities, cold stress caused a decrease, but desiccation and senescence caused a strong increase of activities in leaves. Because AtXDH1 presumably is the more important isoenzyme in A. thaliana it was expressed in Pichia pastoris, purified, and used for biochemical studies. AtXDH1 protein is a homodimer of about 300 kDa consisting of identical subunits of 150 kDa. Like xanthine dehydrogenases from other organisms AtXDH1 uses hypoxanthine and xanthine as main substrates and is strongly inhibited by allopurinol. AtXDH1 could be activated by the purified molybdenum cofactor sulfurase ABA3 that converts inactive desulfo-into active sulfoenzymes. Finally it was found that AtXDH1 is a strict dehydrogenase and not an oxidase, but is able to produce superoxide radicals indicating that besides purine catabolism it might also be involved in response to various stresses that require reactive oxygen species.
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Affiliation(s)
- Christine Hesberg
- Department of Plant Biology, Technical University of Braunschweig, 38023 Braunschweig, Germany
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de Beyer A, Lingens F. Microbial metabolism of quinoline and related compounds. XVI. Quinaldine oxidoreductase from Arthrobacter spec. Rü 61a: a molybdenum-containing enzyme catalysing the hydroxylation at C-4 of the heterocycle. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1993; 374:101-9. [PMID: 8471177 DOI: 10.1515/bchm3.1993.374.1-6.101] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Quinaldine oxidoreductase from Arthrobacter spec. Rü 61a converts quinaldine to 1H-4-oxoquinaldine. The enzyme was purified 70-fold to apparent homogeneity in a 5-step procedure with a recovery of 4%. The molecular mass of the native enzyme was calculated to be 340,000 Da by gel filtration. SDS-polyacrylamide gel electrophoresis of the enzyme revealed 3 protein bands corresponding to 82,000 Da, 35,000 Da and 22,000 Da. The enzyme contained 1.6 atoms of molybdenum, 8 atoms of iron, 8 atoms of acid labile sulfur, 2 molecules of FAD and as part of the molybdenum cofactor, molybdopterin cytosine dinucleotide. Due to the composition of the cofactors the quinaldine oxidoreductase belongs to the class of molybdo-iron/sulfur-flavoproteins. Cyanide, arsenite and 4-hydroxymercuribenzoate were effective inhibitors whereas the enzyme was not affected by methanol.
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Affiliation(s)
- A de Beyer
- Institut für Mikrobiologie, Universität Hohenheim
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Turner N, Barata B, Bray RC, Deistung J, Le Gall J, Moura JJ. The molybdenum iron-sulphur protein from Desulfovibrio gigas as a form of aldehyde oxidase. Biochem J 1987; 243:755-61. [PMID: 2821990 PMCID: PMC1147922 DOI: 10.1042/bj2430755] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The molybdenum iron-sulphur protein originally isolated from Desulfovibrio gigas by Moura, Xavier, Bruschi, Le Gall, Hall & Cammack [(1976) Biochem. Biophys. Res. Commun. 72, 782-789] has been further investigated by e.p.r. spectroscopy of molybdenum(V). The signal obtained on extended reduction of the protein with sodium dithionite has been shown, by studies at 9 and 35 HGz in 1H2O and 2H2O and computer simulations, to have parameters corresponding to those of the Slow signal from the inactive desulpho form of various molybdenum-containing hydroxylases. Another signal obtained on brief reduction of the protein with small amounts of dithionite was shown by e.p.r. difference techniques to be a Rapid type 2 signal, like that from the active form of such enzymes. In confirmation that the protein is a molybdenum-containing hydroxylase, activity measurements revealed that it had aldehyde:2,6-dichlorophenol-indophenol oxidoreductase activity. No such activity towards xanthine or purine was observed. Salicylaldehyde was a particularly good substrate, and treatment of the protein with it also gave rise to the Rapid signal. Molybdenum cofactor liberated from the protein was active in the nit-1 Neurospora crassa nitrate reductase assay. It is concluded that the protein is a form of an aldehyde oxidase or dehydrogenase. From the intensity of the e.p.r. signals and from enzyme activity measurements, 10-30% of the protein in the sample examined appeared to be in the functional form. The evolutionary significance of the protein, which may represent a primitive form of the enzyme rather than a degradation product, is discussed briefly.
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Affiliation(s)
- N Turner
- School of Chemistry and Molecular Sciences, University of Sussex, Falmer, Brighton, U.K
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Coughlan MP, Mehra RK, Barber MJ, Siegel LM. Optical and electron paramagnetic resonance spectroscopic studies on purine hydroxylase II from Aspergillus nidulans. Arch Biochem Biophys 1984; 229:596-603. [PMID: 6322698 DOI: 10.1016/0003-9861(84)90192-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Purine hydroxylase II from Aspergillus nidulans contains a molybdenum cofactor very similar to that found in a number of other molybdenum-containing hydroxylases. (A. nidulans contains two purine hydroxylases, I and II, related to each other by possession of a common cofactor and overlapping substrate specificity.) Addition of reducing substrates effects bleaching of the visible absorption spectrum of the enzyme, the decrease in absorbance at 450 nm being linearly proportional to that at 550 nm. No increase in absorption at longer wavelengths was observed during such titrations. Electron paramagnetic resonance studies of reduced samples of native and modified enzyme species showed the presence of a number of Mo(V) signals (gav = 1.97), exhibiting H hyperfine coupling, comparable to those in the corresponding enzymes from other sources. The enzyme possesses two non-heme-iron-sulfur centers, one (Fe2S2)I with gav less than 2.0 and the other (Fe2S2)II with gav greater than 2.0. The flavin radical signal observed at pH 7.8 had a linewidth of 1.5 mT, indicating it to be the anionic form FAD- . In this respect purine hydroxylase II is unique among all molybdenum-containing hydroxylases studied to date.
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