Overlapping Roles of Yeast Transporters Aqr1, Qdr2, and Qdr3 in Amino Acid Excretion and Cross-Feeding of Lactic Acid Bacteria

Abstract

Microbial species occupying the same ecological niche or codeveloping during a fermentation process can exchange metabolites and mutualistically influence each other’s metabolic states. For instance, yeast can excrete amino acids, thereby cross-feeding lactic acid bacteria unable to grow without an external amino acid supply. The yeast membrane transporters involved in amino acid excretion remain poorly known. Using a yeast mutant overproducing and excreting threonine (Thr) and its precursor homoserine (Hom), we show that excretion of both amino acids involves the Aqr1, Qdr2, and Qdr3 proteins of the Drug H+-Antiporter Family (DHA1) family. We further investigated Aqr1 as a representative of these closely related amino acid exporters. In particular, structural modeling and molecular docking coupled to mutagenesis experiments and excretion assays enabled us to identify residues in the Aqr1 substrate-binding pocket that are crucial for Thr and/or Hom export. We then co-cultivated yeast and Lactobacillus fermentum in an amino-acid-free medium and found a yeast mutant lacking Aqr1, Qdr2, and Qdr3 to display a reduced ability to sustain the growth of this lactic acid bacterium, a phenotype not observed with strains lacking only one of these transporters. This study highlights the importance of yeast DHA1 transporters in amino acid excretion and mutualistic interaction with lactic acid bacteria.

Deletion of QDR genes in a bioethanol-producing yeast strain reduces propagation of contaminating lactic acid bacteria

“…This cross-feeding can be visualized in experiments where the two microorganisms are co-cultivated in an appropriate amino-acid-free medium. For instance, we have previously reported that L. fermentum can grow in a MES-buffered glucose minimal medium (code number 169) containing NH 4 + as sole nitrogen source, and thus in the absence of any external amino acid supply, when it is co-cultivated with a laboratory yeast strain 16 . We sought to determine whether an industrial yeast strain selected for high-efficiency ethanol production could also cross-feed L. fermentum .…”

“…Hence, an important and still open question is whether such cross-feeding contributes to propagation of contaminating LAB in bioethanol production systems. In yeast, excretion of amino acids is mediated by proteins of Drug:H + Antiporter family 1 (DHA1), such as Aqr1, Qdr2, and Qdr3 15 , 16 . Importantly, we have recently demonstrated that deleting these three genes in a laboratory strain reduces the yeast’s ability to cross-feed Lactobacillus fermentum 16 , a LAB commonly found among contaminating bacteria in bioethanol production facilities.…”

“…In yeast, excretion of amino acids is mediated by proteins of Drug:H + Antiporter family 1 (DHA1), such as Aqr1, Qdr2, and Qdr3 15 , 16 . Importantly, we have recently demonstrated that deleting these three genes in a laboratory strain reduces the yeast’s ability to cross-feed Lactobacillus fermentum 16 , a LAB commonly found among contaminating bacteria in bioethanol production facilities. This observation suggests that cultivation of a bioethanol-producing yeast strain lacking specific DHA1-family transporters might be a way to reduce LAB contamination.…”

Interação entre leveduras e bactérias láticas no contexto da fermentação alcoólica brasileira: fisiologia, proteômica e metabolômica

“…O processo chamado de croos-feeding consiste na interação nutricional a partir da produção e transporte de metabólitos essenciais entre microrganismos que ocupam o mesmo nicho (KAPETANAKIS et al, 2021). A espécie S. cerevisiae foi relatada como sendo capaz de produzir e excretar glutamina, glutamato, arginina, histidina, triptofano, metionina e prolina e que…”

“…Glicose Frutose foram assimilados pela espécie L. hordei em substrato deficiente de nitrogênio e ácidos graxos (XU et al, 2019), como também em meios ricos nutricionalmente . A presença de aminoácidos no exometaboloma foi relatada como responsável por suprir a demanda de bactérias láticas durante a fermentação (KAPETANAKIS et al, 2021;.…”