Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi

Abstract

A notable characteristic of fungal genomes is that genes involved in successive steps of a metabolic pathway are often physically linked or clustered. To investigate how such clusters of functionally related genes are assembled and maintained, we examined the evolution of gene sequences and order in the galactose utilization (GAL) pathway in whole-genome data from 80 diverse fungi. We found that GAL gene clusters originated independently and by different mechanisms in three unrelated yeast lineages. Specifically, the GAL cluster found in Saccharomyces and Candida yeasts originated through the relocation of native unclustered genes, whereas the GAL cluster of Schizosaccharomyces yeasts was acquired through horizontal gene transfer from a Candida yeast. In contrast, the GAL cluster of Cryptococcus yeasts was assembled independently from the Saccharomyces/Candida and Schizosaccharomyces GAL clusters and coexists in the Cryptococcus genome with unclustered GAL paralogs. These independently evolved GAL clusters represent a striking example of analogy at the genomic level. We also found that species with GAL clusters exhibited significantly higher rates of GAL pathway loss than species with unclustered GAL genes. These results suggest that clustering of metabolic genes might facilitate fungal adaptation to changing environments both through the acquisition and loss of metabolic capacities. F ungal genes involved in successive steps of a pathway are frequently physically clustered (1-12). Evolutionary analysis of several different fungal gene clusters has shown that they have originated through different mechanisms (13-16). For example, the DAL cluster for allantoin utilization in Saccharomyces cerevisiae and close relatives originated through adaptive gene relocation (13), whereas a nitrate assimilation cluster in Trichoderma originated through horizontal gene transfer (14). However, it is unclear how these mechanisms shape the assembly of gene clusters, or how the evolutionary trajectories differ between species containing clusters and species in which the genes in a pathway are scattered across the genome.To better understand the origins and maintenance of gene clusters over a large evolutionary timescale and a range of ecological conditions, we investigated the evolution of the Leloir galactose utilization (GAL) pathway in fungi. The detailed knowledge on GAL pathway function in S. cerevisiae (15, 16), and the abundance of genomic data from a wide diversity of fungal species (17), make it an excellent model pathway to address these questions. Furthermore, the relative galactose content varies substantially among different plant substrata (from hundreds of mg/g legume seeds and algal mats to less than 1 mg/g in some fruits) (18-21), suggesting that the natural substrates of fungi have likely provided ample opportunity for populations to evolve niche-dependent adaptations for galactose utilization.The protein products of three GAL genes (GAL1, GAL7, and GAL10) are involved in four enzymatic steps (22). In the first s...

Identification of GIG1 , a GlcNAc-Induced Gene in Candida albicans Needed for Normal Sensitivity to the Chitin Synthase Inhibitor Nikkomycin Z

“…The GIG1 gene and GlcNAc catabolic genes were also missing from Batrachochytrium dendrobatidis in the phylum Chytridiomycotina. This overall pattern of gene conservation in different organisms is analogous to observations for the galactose genes, which have been lost in various fungal species (9,31).…”

Gene transfer into the fungi

“…This theory is analogous to the Selfish Operon Theory (Lawrence and Roth, 1996) and has also been invoked for acquisition of pathogenic functions in the fungi, where transfer of gene clusters has been suggested to be important for the evolution of virulence (van der Does and Rep, 2007). Considerable support for this hypothesis has emerged recently, with key examples of HGT of gene clusters generally (Slot and Hibbett, 2007;Slot and Rokas, 2010) and specific examples of transfer of gene clusters which function in secondary metabolism and toxin production Patron et al, 2007;Slot and Rokas, 2011). An alternative hypothesis for clustering of secondary metabolic pathways concerns the potential toxicity of biosynthetic intermediates, providing selective pressure for all steps of a given biosynthetic pathway to be maintained together over evolutionary time (Slot and Rokas, 2011).…”

Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds

“…Indeed, the evolution of many mycotoxins is likely to have involved the stepwise modification of toxic compounds to modulate their toxicity; for example, sterigmatocystin, a highly toxic secondary metabolic compound, is the penultimate step in the production of aflatoxin, a potent natural carcinogen (29). With the distinction between selection for a phenotype versus selection of a specific molecular mechanism, we can begin to understand how inherent biochemical "pain points" in metabolic networks, such as toxic ICs, necessitate lineage (30-39) and environment-specific (20,40) adaptations. To this end, preliminary analysis of one metazoan (Homo sapiens) and one plant (Arabidopsis lyrata) genome identified eight and four DNGPs, respectively, including two human DNGPs that match fungal DNGPs (Dataset S1, Table S4).…”

“…The most severe type of galactosemia results from the loss of galactose-1-phosphate uridyl transferase (encoded by Galt in human; Gal7 in yeast), which leads to accumulation of galactose-1-phosphate (18), a potent competitive inhibitor of phosphoglucomutase (19), which disrupts the glycolytic pathway. Intriguingly, the genes of the Gal pathway are clustered in several different yeast lineages (20) (Fig. 1A).…”