Giant GAL gene clusters for the melibiose‐galactose pathway in Torulaspora

Abstract

In many yeast species, the three genes at the centre of the galactose catabolism pathway, GAL1, GAL10 and GAL7, are neighbours in the genome and form a metabolic gene cluster. We report here that some yeast strains in the genus Torulaspora have much larger GAL clusters that include genes for melibiase (MEL1), galactose permease (GAL2), glucose transporter (HGT1), phosphoglucomutase (PGM1) and the transcription factor GAL4, in addition to GAL1, GAL10, and GAL7. Together, these eight genes encode almost all the steps in the pathway for catabolism of extracellular melibiose (a disaccharide of galactose and glucose). We show that a progenitor 5‐gene cluster containing GAL 7‐1‐10‐4‐2 was likely present in the common ancestor of Torulaspora and Zygotorulaspora. It added PGM1 and MEL1 in the ancestor of most Torulaspora species. It underwent further expansion in the T. pretoriensis clade, involving the fusion of three progenitor clusters in tandem and the gain of HGT1. These giant GAL clusters are highly polymorphic in structure, and subject to horizontal transfers, pseudogenization and gene losses. We identify recent horizontal transfers of complete GAL clusters from T. franciscae into one strain of T. delbrueckii, and from a relative of T. maleeae into one strain of T. globosa. The variability and dynamic evolution of GAL clusters in Torulaspora indicates that there is strong natural selection on the GAL pathway in this genus.

A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast

“…Given previous indications gathered in earlier stages of this study, we analysed in more detail the genes implicated in galactose and maltose metabolism. It was recently reported that species of Torulaspora have large clusters of genes necessary for galactose metabolization (Venkatesh et al, 2020). These clusters have the GAL 7 ‐ 1 ‐ 10 ‐ 4 and the GAL 7 ‐ 1 ‐ 10 ‐ 2 configuration (other genes, such as HGT1 , MEL1 and PGM1 , are also part of the GAL cluster).…”

Molecular Response of Meyerozyma guilliermondii to Patulin: Transcriptomic-Based Analysis

“…A series of genes related to growth and reproduction were also up-regulated in PATinduced M. guilliermondii. The gene mel1 is a metabolism-associated gene that encodes α-galactosidase, a key enzyme in the catabolic pathway of galactose and glucose disaccharide [30], and the gene ETR1 that encodes enoyl reductase is associated with yeast fatty acid synthesis (fatty acid synthesis type II) and respiratory metabolism [31]. The flavodoxin-like genes YCP4 regulate the expression of several metabolism-related genes during the late growth stage of yeast [32].…”

A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family

“…As in other eukaryotes, the chromosomal location of most genes in budding yeasts seems to be arbitrary and unrelated to their function or other properties [ 76 ]. Only a few examples of non-random gene locations are known, such as the metabolic clusters of GAL and DAL genes [ 77 , 78 ]. A few gene families such as the MAL and COS genes are specific to subtelomeric regions [ 79 , 80 ].…”