A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria

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.

Sterigmatocystin production is restricted to hyphae located in the proximity of hülle cells

“…Incubation of A. nidulans with traditionally used nitrogen sources (e.g., acetamide, urea, hypoxanthine, xanthine, allantoin, uric acid, nitrate, ammonium, or arginine) resulted in multiple layers of hyphae at the regions of interest, which made the microscopic analysis less feasible. In order to circumvent this problem, we applied nicotinic acid as sole nitrogen source that is utilized less efficiently than any other nitrogen sources . By growing the colonies on nicotinate, we were able to investigate separately running monolayer hyphae even after several days of incubation (Fig.…”

“…The stcO reporter cassette was constructed by the double‐joint PCR method . The cassette is composed of five components: i) the stcO (AN7811) promoter and its upstream region (component A, nested size 2436 bp) followed by ii) the nuclear localization signal (NLS) of the transcription factor prnA (component B/1, nested size 550 bp) from wild type A. nidulans (HZS.145) ; iii) the yCFP (Cyan Fluorescent Protein optimized for yeasts) coding gene (component B/2, 944 bp) amplified from plasmid pKT174 ; iv) the pyroA homologue (component B/3, nested size 2414 bp) of Aspergillus fumigatus (Afu5g08090 from A. fumigatus ); and v) the downstream flanking sequence of the stcO gene (component C, nested size 2421 bp). The double‐joint PCR was performed by using two consecutive assembly steps (assembly of B/1‐B/2‐B/3 and A‐B1/2/3‐C).…”

Reticulate evolution in eukaryotes: origin and evolution of the nitrate assimilation pathway

“…However, specific induction by nitrate cannot be excluded. In the nicotinate assimilation pathway of A. nidulans , we see both specific induction and high expression under nitrogen starvation conditions, mediated by the same transcription factor [62]. It is possible that in this latter instance the intracellular inducer is generated by degradation of intracellular metabolites.…”

Fungal adaptation to plant defences through convergent assembly of metabolic modules

“…Convergence is indicative of strong directional selection for optimal phenotypes in similar environments (Bittleston, Pierce, Ellison, & Pringle, ; Conant & Wagner, ). Several other examples of convergent evolution of particular combinations of clustered genes have previously been reported, notably galactose utilization clusters in divergent yeast lineages (Slot & Rokas, ), cyanate detoxification clusters in the Pezizomycotina (Elmore et al, ), nicotinate degradation clusters in fungi and bacteria (Amon et al, ), and triterpene biosynthesis clusters in plants (Field & Osbourn, ). While our analysis was limited to examining cluster assembly from the perspective of sco , the organizational histories of genes associated with sco are also marked by convergence.…”