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FEMS Yeast Res. 2017 Sep 1;17(6). doi: 10.1093/femsyr/fox060.

Yeast-bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri.

Author information

1
Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
2
Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, P Bag 16, 00267 Palapye, Botswana.
3
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
4
Carlsberg Laboratories, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark.
5
Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS UMR7156, 67083 Strasbourg, France.
6
Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
7
Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
8
Department of Food, Environmental and Nutritional Sciences, University of Milan, Via Giovanni Celoria 2, 20133 Milan, Italy.

Abstract

Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations. We described a long-term cross-kingdom competition experiment between Lachancea kluyveri and five species of bacteria. Now, we report how we further subjected the same yeast to a sixth species of bacteria, Pseudomonas fluorescens, resulting in the appearance of a fixed and stably inherited large-scale genomic rearrangement in two out of three parallel evolution lines. The 'extra-banded' karyotype, characterized by a higher fitness and an elevated fermentative capacity, conferred the emergence of new metabolic traits in most carbon sources and osmolytes. We tracked down the event to a duplication and translocation event involving a 261-kb segment. Such an experimental setup described here is an attractive method for developing industrial strains without genetic engineering strategies.

KEYWORDS:

experimental evolution; genome evolution; large-scale genomic rearrangements; strain development; yeast–bacteria co-evolution

PMID:
28910985
DOI:
10.1093/femsyr/fox060
[Indexed for MEDLINE]

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