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

Abstract

Genomic analyses have proliferated without being tied to tangible phenotypes. For example, although coordination of both gene expression and genetic linkage have been offered as genetic mechanisms for the frequently observed clustering of genes participating in fungal metabolic pathways, elucidation of the phenotype(s) favored by selection, resulting in cluster formation and maintenance, has not been forthcoming. We noted that the cause of certain well-studied human metabolic disorders is the accumulation of toxic intermediate compounds (ICs), which occurs when the product of an enzyme is not used as a substrate by a downstream neighbor in the metabolic network. This raises the hypothesis that the phenotype favored by selection to drive gene clustering is the mitigation of IC toxicity. To test this, we examined 100 diverse fungal genomes for the simplest type of cluster, gene pairs that are both metabolic neighbors and chromosomal neighbors immediately adjacent to each other, which we refer to as "double neighbor gene pairs" (DNGPs). Examination of the toxicity of their corresponding ICs shows that, compared with chromosomally nonadjacent metabolic neighbors, DNGPs are enriched for ICs that have acutely toxic LD 50 doses or reactive functional groups. Furthermore, DNGPs are significantly more likely to be divergently oriented on the chromosome; remarkably, ∼40% of these DNGPs have ICs known to be toxic. We submit that the structure of synteny in metabolic pathways of fungi is a signature of selection for protection against the accumulation of toxic metabolic intermediates.gene cluster | gene orientation | inborn error of metabolism | secondary metabolism | specialized metabolism T here is a critical distinction between selection for a trait, which occurs at the phenotypic level, and selection of the underlying molecular genetic mechanisms that generate the trait (1). For example, some butterfly species avoid predation by mimicking the wing-pattern morphs of other butterflies that are toxic to birds (2, 3). In this case, predation avoidance selects for specific wing-pattern morphs, resulting in the selection of specific allelic combinations of genes in a supergene locus (4).The rise of molecular biology and subsequent abundance of genomic data have shifted the focus from phenotypes to genotypes, blurring the distinction between selection for and selection of. For example, many studies indicate that selection has sculpted the order and orientation of genes in eukaryotic genomes (5-13); although these analyses convincingly argue that specific genetic mechanisms are important in fine-tuning the structure of synteny on chromosomes, they implicitly assume that it is the genetic mechanisms themselves, rather than organismal phenotypes, that selection targets.One of the most conspicuous characteristics of fungal genomes is that the genes participating in a metabolic pathway are often physically linked, or clustered. Although both coordination of gene expression (5,6,(11)(12)(13)(14)(15)(16) and genetic linkage (7, 17) h...

The biosynthetic gene cluster for the cyanogenic glucoside dhurrin in Sorghum bicolor contains its co-expressed vacuolar MATE transporter

“…Its inclusion in the dhurrin biosynthetic gene cluster is consistent with ideas that selection for reduced recombination between beneficially interacting alleles leads to gene cluster formation151641. Such selection is proposed to result from antagonistic selection pressures, such as the benefits maintaining a functional pathway provides in specific ecological context, e.g.…”

“…One of the negative cost associated with the production of chemical defence metabolites is the possibility of self-toxicity. Co-inheritance of a co-adapted gene set is thought to provide protection against the self-toxic biochemical nature of many chemical defence compounds or their pathway intermediates1516. In the case of dhurrin the transport of this pH-dependent unstable cyanogenic glucoside from its cytoplasmic site of production to the acidic vacuole likely contributes to reducing self-toxicity.…”

“…These clusters are proposed to promote the co-inheritance of beneficially interacting alleles and to additionally facilitate the co-expression of the biosynthetic genes by regulation at the chromatin level1115. An important driver for gene cluster formation and maintenance, via selection for reduced recombination between the interacting genes, is thought to be the fact that incompletely inherited biosynthetic pathways may result in the release of toxic intermediates causing self-toxicity1516.…”

Variability of chromosome structure in pathogenic fungi—of ‘ends and odds’

“…Strict coordination of gene expression may be particularly important during the biosynthesis of secondary metabolites as intermediate compounds are potentially toxic. Indeed, a recent analysis of the simplest possible gene clusters, gene pairs, uncovered a strong bias for the pairing of enzymes that share a toxic intermediate [25]. Moreover, many of these gene pairs are divergently oriented around a single promoter, an arrangement that favors tight co-regulation.…”

Fungal genomes tell a story of ecological adaptations

“…Such pathways are sometimes conserved among distant evolutionary groups. Interestingly homologs of gene clusters with toxic intermediates which co-localize in fungi are often co-regulated in distant organisms, even in humans (McGary et al 2013). It seems that clustering genes involved in a common pathway with toxic intermediates is selected for protection against the accumulation of such intermediates.…”