Systematic changes in gene expression patterns following adaptive evolution in yeast.

T L Ferea; D Botstein; P O Brown; R F Rosenzweig

doi:10.1073/pnas.96.17.9721

Home/Archive/PubMed

PubMed · 10449761

Systematic changes in gene expression patterns following adaptive evolution in yeast.

T L Ferea·D Botstein·P O Brown·R F Rosenzweig

View original source ↗Export metadata ↓

Abstract

Culturing a population of Saccharomyces cerevisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design provides a tractable model of adaptive evolution under natural selection. Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after continuous aerobic growth in glucose-limited chemostats for more than 250 generations. DNA microarrays were used to compare genome-wide patterns of gene expression in the evolved strains and the parental strain. Several hundred genes were found to have significantly altered expression in the evolved strains. Many of these genes showed similar alterations in their expression in all three evolved strains. Genes with altered expression in the three evolved strains included genes involved in glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolite transport. These results are consistent with physiological observations and indicate that increased fitness is acquired by altering regulation of central metabolism such that less glucose is fermented and more glucose is completely oxidized.

Explore related subjects

Adaptation, Physiological Citric Acid Cycle Gene Expression Regulation, Fungal Gene Library Genetic Variation Glucose Internet Microscopy Saccharomyces cerevisiae Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

T L Ferea, D Botstein, P O Brown, R F Rosenzweig. 1999-08-17. Systematic changes in gene expression patterns following adaptive evolution in yeast.. https://doi.org/10.1073/pnas.96.17.9721

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2025

Genome sequencing and population genetics provide insights into local adaptation of Opisthopappus species on cliff environments of Taihang Mountains.

Local adaptation represents a pivotal theme in evolutionary biology. The Opisthopappus genus, comprising Opisthopappus longilobus and O. taihangensis, thrives on the cliffs of the Taihang Mountains. During their evolutionary history, two species are hypothesized to have locally adapted to their cliff habitats. In the present study, we employed a combined approach of whole-genome sequencing of O. taihangensis and population genomic analysis from both species to gain deeper insights into their patterns of local adaptation. Our results revealed that the expansive genome of O. taihangensis (3010.18 Mb), a consequence of a whole-genome duplication (WGD) event, coupled with a high proportion of repetitive sequences (82.70%), was postulated as one of its adaptive strategies. A clear differentiation between O. taihangensis and O. longilobus was observed, with the two species diverging approximately 17.57 million years ago (Mya), with O. longilobus serving as the ancestor. Since their divergence, limited gene flow was observed between the two species. Post-divergence, the effective population sizes of both species expanded, yet underwent a dramatic reduction at approximately 0.07 Mya. Furthermore, a total of 798 adaptive genes were identified, of which 207 overlapped with expanded genes, and eight genes were found to be under positive selection. These genes primarily regulated the growth and development of both species via pathways such as oxidation-reduction and ubiquitin-proteasome, enabling them to withstand climate changes. These findings provide profound insights into the local adaptation of Opisthopappus species to the cliff environments and offer valuable clues for further exploring the local adaptation among various cliff-dwelling organisms.

Adaptation, Physiological↗

PubMed2015

Variation in Drosophila melanogaster central metabolic genes appears driven by natural selection both within and between populations.

In this report, we examine the hypothesis that the drivers of latitudinal selection observed in the eastern US Drosophila melanogaster populations are reiterated within seasons in a temperate orchard population in Pennsylvania, USA. Specifically, we ask whether alleles that are apparently favoured in northern populations are also favoured early in the spring, and decrease in frequency from the spring to autumn with the population expansion. We use SNP data collected for 46 metabolic genes and 128 SNPs representing the central metabolic pathway and examine for the aggregate SNP allele frequencies whether the association of allele change with latitude and that with increasing days of spring-autumn season are reversed. Testing by random permutation, we observe a highly significant negative correlation between these associations that is consistent with this expectation. This correlation is stronger when we confine our analysis to only those alleles that show significant latitudinal changes. This pattern is not caused by association with chromosomal inversions. When data are resampled using SNPs for amino acid change the relationship is not significant but is supported when SNPs associated with cis-expression are only considered. Our results suggest that climate factors driving latitudinal molecular variation in a metabolic pathway are related to those operating on a seasonal level within populations.

Adaptation, Physiological↗

PubMed2002

Acute effects of intramuscular aponeurotomy and tenotomy on multitendoned rat EDL: indications for local adaptation of intramuscular connective tissue.

Intervention with the continuity of the tendon and part of the muscle fibers allows investigation of myofascial force transmission. The present study investigates the effects of proximal aponeurotomy on length-force characteristics and the geometry of the extensor digitorum longus (EDL) muscle, and compares those effects with the effects of both distal tenotomy (TT) and intramuscular fasciotomy (IF) of the EDL. After proximal aponeurotomy, the intramuscular connective tissue ruptured spontaneously below the location of intervention. Due to this rupturing, a gap developed within the proximal aponeurosis. The fibers that were continuous with the tendon at only one end were substantially shorter than before the intervention. Optimum muscle force was reduced by 29%. After distal TT (of heads II-IV) a gap developed within the muscle belly. This gap increased at higher muscle lengths. However, the length of the gap was much smaller than after aponeurotomy. Despite the TT-related gap, there was no rupturing of intramuscular connective tissue at the interface between heads IV and V, as there was after proximal aponeurotomy. The effects of TT on length-force characteristics and on lengths of fibers continuous with the tendon at only one end were much less compared to the effects of aponeurotomy. Subsequent IF for two-thirds the length of the interface between heads IV and V resulted in changes similar to the effects of proximal aponeurotomy plus rupture. The contrast regarding the occurrence of intramuscular connective tissue rupture indicates increased failure strength of the intramuscular connective tissue at distal locations. It is hypothesized that for multitendoned muscles in vivo, local shear and stress deformations will initiate local adaptation of the intramuscular connective tissue.

Adaptation, Physiological↗