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 proton-coupled 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.
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Acknowledgements
We would like to thank the Lindquist's laboratory for the gift of the yeast strains deleted of either PTR2 or DAL5; Laurence Loiseau for the use of the Omnilog reader on the PARMIC platform; Jacques Ranger for access to the Breuil forest, and Daniel Wipf for helpful discussions on oligopeptide transporters. This work was funded by the ECCO programme AO 2005 (project Microger) and the Agence Nationale de la Recherche Biodiversity program (project ANR-06-443 BDIV-006 Fundiv). MZ Haider was financially supported by a scholarship from the Higher Education Commission of Pakistan.
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Damon, C., Vallon, L., Zimmermann, S. et al. A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J 5, 1871–1880 (2011). https://doi.org/10.1038/ismej.2011.67
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DOI: https://doi.org/10.1038/ismej.2011.67
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