ABSTRACT
Lactose assimilation is a relatively rare trait in yeasts, and
Kluyveromyces
yeast species have long served as model organisms for studying lactose metabolism. Meanwhile, the metabolic strategies of most other lactose-assimilating yeasts remain unknown. In this work, we have elucidated the genetic determinants of the superior lactose-growing yeast
Candida intermedia
. Through genomic and transcriptomic analyses, we identified three interdependent gene clusters responsible for the metabolism of lactose and its hydrolysis product galactose: the conserved
LAC
cluster (
LAC12
,
LAC4
) for lactose uptake and hydrolysis, the conserved
GAL
cluster (
GAL1
,
GAL7
, and
GAL10
) for galactose catabolism through the Leloir pathway, and a “
GALLAC
” cluster containing the transcriptional activator gene
LAC9
, second copies of
GAL1
and
GAL10
, and a
XYL1
gene encoding an aldose reductase involved in carbon overflow metabolism. Bioinformatic analysis suggests that the
GALLAC
cluster is unique to
C. intermedia
and has evolved through gene duplication and divergence, and deletion mutant phenotyping proved that the cluster is indispensable for
C. intermedia’s
growth on lactose and galactose. We also show that the regulatory network in
C. intermedia
, governed by Lac9 and Gal1 from the
GALLAC
cluster, differs significantly from the galactose and lactose regulons in
Saccharomyces cerevisiae
,
Kluyveromyces lactis
, and
Candida albicans
. Moreover, although lactose and galactose metabolism are closely linked in
C. intermedia
, our results also point to important regulatory differences.
IMPORTANCE
This study paves the way to a better understanding of lactose and galactose metabolism in the non-conventional yeast
C. intermedia
. Notably, the unique
GALLAC
cluster represents a new, interesting example of metabolic network rewiring and likely helps to explain how
C. intermedia
has evolved into an efficient lactose-assimilating yeast. With the Leloir pathway of budding yeasts acting like a model system for understanding the function, evolution, and regulation of eukaryotic metabolism, this work provides new evolutionary insights into yeast metabolic pathways and regulatory networks. In extension, the results will facilitate future development and use of
C. intermedia
as a cell-factory for conversion of lactose-rich whey into value-added products.