Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway.

Galactose is a secondary fermentable sugar that requires specific regulatory and structural genes for its assimilation, which are under catabolite repression by glucose. When glucose is absent, the catabolic repression is attenuated, and the structural GAL genes are fully activated. In Saccharomyces cerevisiae, the GAL pathway is under selection in environments where galactose is present. However, it is unclear the adaptive strategies in response to long-term propagation in galactose as a sole carbon source in laboratory evolution experiments. Here, we performed a 4,000-generation evolution experiment using 48 diploid Saccharomyces cerevisiae populations to study adaptation in galactose. We show that fitness gains were greater in the galactose-evolved population than in identically evolved populations with glucose as a sole carbon source. Whole-genome sequencing of 96 evolved clones revealed recurrent de novo single nucleotide mutations in candidate targets of selection, copy number variations, and ploidy changes. We find that most mutations that improve fitness in galactose lie outside of the canonical GAL pathway. Reconstruction of specific evolved alleles in candidate target of selection, SEC23 and IRA1, showed a significant increase in fitness in galactose compared to glucose. In addition, most of our evolved populations (28/46; 61%) fixed aneuploidies on Chromosome VIII, suggesting a parallel adaptive amplification. Finally, we show greater loss of extrachromosomal elements in our glucose-evolved lineages compared with previous glucose evolution. Broadly, these data further our understanding of the evolutionary pressures that drive adaptation to less-preferred carbon sources.

Genome Sequence of Arthrobacter sp. Phage Scuttle.

Arthrobacter phage Scuttle was isolated by enrichment from a dry soil sample (collected in Upper Darby, Pennsylvania) on host Arthrobacter sp. ATCC 21022. The genome of this phage is 43,729 bp long, has a GC content of 61.1%, and has 61 annotated protein-coding genes.

Genome Sequences of Arthrobacter sp. Phages Inspire2, Ronnie, Hunnie, DeWayne, CGermain, Copper, Azathoth, and Arby.

Eight siphoviral phages isolated from various soil types and locations in southwestern Pennsylvania using Arthrobacter sp. strain ATCC 21022 were sequenced. The phages all have relatively small genomes, with each genome containing 15,556 bp. All 8 phages are closely related to previously described cluster AN Arthrobacter phages (K. K. Klyczek, J. A. Bonilla, D. Jacobs-Sera, T. L. Adair, et al., PLoS One 12:e0180517, 2017, https://doi.org/10.1371/journal.pone.0180517; J. Y. Lee-Soety, S. Bhatt, T. L. Adair, J. A. Bonilla, et al., Genome Announc 5:e01092-17, 2017, https://doi.org/10.1128/genomeA.01092-17).

Genome Sequence of Mycobacteriophage Cabrinians.

Mycobacteriophage Cabrinians is a newly isolated phage capable of infecting both Mycobacterium phlei and Mycobacterium smegmatis and was recovered from a soil sample in New York City, NY. Cabrinians has a genome length of 56,669 bp, encodes 101 predicted proteins, and is a member of mycobacteriophages in cluster F.