TY - JOUR
T1 - Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes
AU - Ghiaci, Payam
AU - Jouhten, Paula
AU - Martyushenko, Nikolay
AU - Roca-Mesa, Helena
AU - Vázquez, Jennifer
AU - Konstantinidis, Dimitrios
AU - Stenberg, Simon
AU - Andrejev, Sergej
AU - Grkovska, Kristina
AU - Mas, Albert
AU - Beltran, Gemma
AU - Almaas, Eivind
AU - Patil, Kiran R.
AU - Warringer, Jonas
N1 - Publisher Copyright:
© The Author(s) 2024.
PY - 2024/10/3
Y1 - 2024/10/3
N2 - Adaptive Laboratory Evolution (ALE) of microorganisms can improve the efficiency of sustainable industrial processes important to the global economy. However, stochasticity and genetic background effects often lead to suboptimal outcomes during laboratory evolution. Here we report an ALE platform to circumvent these shortcomings through parallelized clonal evolution at an unprecedented scale. Using this platform, we evolved 104 yeast populations in parallel from many strains for eight desired wine fermentation-related traits. Expansions of both ALE replicates and lineage numbers broadened the evolutionary search spectrum leading to improved wine yeasts unencumbered by unwanted side effects. At the genomic level, evolutionary gains in metabolic characteristics often coincided with distinct chromosome amplifications and the emergence of side-effect syndromes that were characteristic of each selection niche. Several high-performing ALE strains exhibited desired wine fermentation kinetics when tested in larger liquid cultures, supporting their suitability for application. More broadly, our high-throughput ALE platform opens opportunities for rapid optimization of microbes which otherwise could take many years to accomplish.
AB - Adaptive Laboratory Evolution (ALE) of microorganisms can improve the efficiency of sustainable industrial processes important to the global economy. However, stochasticity and genetic background effects often lead to suboptimal outcomes during laboratory evolution. Here we report an ALE platform to circumvent these shortcomings through parallelized clonal evolution at an unprecedented scale. Using this platform, we evolved 104 yeast populations in parallel from many strains for eight desired wine fermentation-related traits. Expansions of both ALE replicates and lineage numbers broadened the evolutionary search spectrum leading to improved wine yeasts unencumbered by unwanted side effects. At the genomic level, evolutionary gains in metabolic characteristics often coincided with distinct chromosome amplifications and the emergence of side-effect syndromes that were characteristic of each selection niche. Several high-performing ALE strains exhibited desired wine fermentation kinetics when tested in larger liquid cultures, supporting their suitability for application. More broadly, our high-throughput ALE platform opens opportunities for rapid optimization of microbes which otherwise could take many years to accomplish.
KW - Evolutionary Engineering
KW - Experimental Evolution
KW - Fermentation
KW - Metabolism
KW - Yeast
UR - http://www.scopus.com/inward/record.url?scp=85201823222&partnerID=8YFLogxK
U2 - 10.1038/s44320-024-00059-0
DO - 10.1038/s44320-024-00059-0
M3 - Article
AN - SCOPUS:85201823222
SN - 1744-4292
VL - 20
SP - 1109
EP - 1133
JO - MOLECULAR SYSTEMS BIOLOGY
JF - MOLECULAR SYSTEMS BIOLOGY
IS - 10
ER -