A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes

Abstract

Functional environmental genomics has the potential to identify novel biological functions that the systematic sequencing of microbial genomes or environmental DNA may fail to uncover. We targeted the functions expressed by soil eukaryotes using a metatranscriptomic approach based on the use of soil-extracted polyadenylated messenger RNA to construct environmental complementary DNA expression libraries. Functional complementation of a yeast mutant defective in di/tripeptide uptake identified a novel family of oligopeptide transporters expressed by fungi. This family has a patchy distribution in the Basidiomycota and Ascomycota and is present in the genome of a Saccharomyces cerevisiae wine strain. High throughput phenotyping of yeast mutants expressing two environmental transporters showed that they both displayed broad substrate specificity and could transport more than 60-80 dipeptides. When expressed in Xenopus oocytes one environmental transporter induced currents upon dipeptide addition, suggesting protoncoupled co-transport of dipeptides. This transporter was also able to transport specifically cysteine. Deletion of the two copies of the corresponding gene family members in the genome of the wine yeast strain severely reduced the number of dipeptides that it could assimilate. These results demonstrate that these genes are functional and can be used by fungi to efficiently scavenge the numerous, low concentration, oligopeptides continuously generated in soils by proteolysis.

Assessing the Mechanisms Responsible for Differences between Nitrogen Requirements of Saccharomyces cerevisiae Wine Yeasts in Alcoholic Fermentation

“…The fermentation capacities of yeast strains in medium with a low nitrogen content differ (12,14,38). We screened 23 strains of different origins for their nitrogen requirements and confirmed here the variability of this character.…”

“…S7 in the supplemental material). These are the genes FOT1 and FOT2, corresponding to two fungal oligopeptide transporters (38), and the SEO1 gene, corresponding by sequence homology to a putative permease, a member of the allantoate transporter subfamily (28). Although the expression of these three genes in all LNR strains might suggest a role in the nitrogen requirement, a similar behavior in HNR strain K1M contradicts this hypothesis.…”

Geographic Origin and Diversity of Wine Strains ofSaccharomyces

“…This transporter has a high affinity for fructose in contrast to the native HXT hexose transporter genes and is thought to be responsible for the elevated use of fructose late in fermentation seen in EC1118. EC1118 also carries a gene encoding a protein similar to the peptide transporters found in fungi and can therefore perhaps transport a wider array of peptides to be broken down internally and used as nitrogen source (Damon et al 2011). The source of this introgression is unknown.…”

“…Perhaps the most surprising conclusion from the analysis of wine strain diversity is the existence of interspecies hybrids (Belloch et al 2009, González et al 2006, 2008, Lopandic et al 2007, Masneuf et al 1998, 2002 and introgressions from non-Saccharomyces genera (Damon et al 2011, Galeote et al 2010, Novo et al 2009). These variants have arisen naturally in native populations and demonstrate the potential for development of novel reproductively isolated organisms.…”

Toward genome-enabled mycology

“…A rich taxonomic catalog alone, however, does not provide an understanding of the functions of Fungi in their habitats. As more robustly annotated genomes become available, backed by functional and biochemical analyses, it will become easier to incorporate metatranscriptomic and metaproteomic approaches in environmental surveys (Damon et al 2012, Seifert et al 2013), which will provide insights into the ecological services provided by individual species as well as entire communities (Damon et al 2011, Aylward et al 2013, Takasaki et al 2013.…”