MAL33 drives natural variation in maltose metabolism in Saccharomyces eubayanus

Journal Article · Thu Feb 05 00:00:00 UTC 2026 · Genetics (Online)

DOI: https://doi.org/10.1093/genetics/iyag032 · OSTI ID:3016212

Quintrel, Pablo ^[1]; Muñoz-Guzmán, Felipe  ^[2]; Villarreal, Pablo ^[3]; Peña, Tomas A. ^[1]; Garate, Natalia I. ^[4]; Muñoz-Tapia, Catalina ^[5]; Oporto, Christian I. ^[6]; Crandall, Johnathan G.  ^[7]; Larrondo, Luis F.  ^[8]; Hittinger, Chris Todd  ^[7]; Fischer, Gilles  ^[9]; Cubillos, Francisco A.  ^[10]

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1. Univ. de Santiago de Chile (Chile); Millennium Institute for Integrative Biology (iBio), Santiago (Chile)
2. Univ. de Santiago de Chile (Chile); Millennium Institute for Integrative Biology (iBio), Santiago (Chile); Fundación Ciencia & Vida, Santiago (Chile)
3. Millennium Institute for Integrative Biology (iBio), Santiago (Chile); Univ. Mayor, Santiago (Chile)
4. Univ. de Santiago de Chile (Chile)
5. Millennium Institute for Integrative Biology (iBio), Santiago (Chile); Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago (Chile); Pontificia Univ. Católica de Chile, Santiago (Chile)
6. Univ. de Santiago de Chile, Santiago (Chile); Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago (Chile)
7. Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States)
8. Pontificia Univ. Católica de Chile, Santiago (Chile)
9. Sorbonne Univ., Paris (France). Laboratory of Computational and Quantitative Biology (CQSB), Institut de Biologie Paris-Seine (IBPS); Centre National de la Recherche Scientifique (CNRS), Paris (France)
10. Univ. de Santiago de Chile (Chile); Millennium Institute for Integrative Biology (iBio), Santiago (Chile); Fundación Ciencia & Vida, Santiago (Chile); Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago (Chile)

Maltose is one of the most abundant sugars in brewer’s wort, and its efficient utilization is critical for successful fermentation. However, maltose consumption varies naturally among Saccharomyces eubayanus strains isolated from different host trees, such as Quercus and Nothofagus. To identify the genetic determinants underlying these phenotypic differences, we performed bulk segregant analysis (BSA) and quantitative trait loci (QTL) mapping using an F₂ offspring derived from QC18 (Quercus-associated) and CL467.1 (Nothofagus-associated) strains. QTL mapping identified two significant genomic regions on subtelomeric loci of chromosomes V-R and XVI-L, each containing complete MAL loci composed of MAL32 (encoding maltase), MAL31 (transporter), and MAL33 (transcriptional activator) genes. Comparative polymorphism analyses identified mutations in MAL32 and MAL33 of QC18, including frameshift mutations resulting in premature stop codons. Functional validation demonstrated that the heterologous expression of MAL33_ChrV from CL467.1 fully restored maltose utilization in QC18, indicating the functional presence of MAL33 cis-regulatory sequences and MAL32 and MAL31 genes in QC18. While structural protein predictions identified truncation and impaired functionality in the maltose-responsive activation domain of Mal33p from QC18, overexpression of QC18’s own MAL33_ChrV allele also improved maltose metabolism, suggesting dosage-dependent transcriptional limitations rather than complete functional loss. These results indicate that allelic variations in the maltose-responsive activation domain of Mal33p result in differences in maltose consumption between strains. Here, we hypothesized that reduced maltose metabolism in QC18 is an adaptive response to the distinct sugar composition in Quercus robur bark, contrasting with the starch-rich environment of Nothofagus pumilio. These findings highlight subtelomeric MAL gene diversity as a reservoir of genetic variation, representing a key evolutionary mechanism that influences maltose adaptation among natural Saccharomyces isolates.

• Research Organization: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: SC0018409
• OSTI ID: 3016212
• Journal Information: Genetics (Online), Journal Name: Genetics (Online); ISSN 1943-2631
• Publisher: Oxford University Press; Genetics Society of AmericaCopyright Statement
• Country of Publication: United States
• Language: English