Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BP001-002-pub:The genomic landscape of compensatory evolution

ABSTRACT: This hybset contains the expression profiles of several yeast deletion mutants, grown after normal and evolution conditions

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Marian Groot Koerkamp

PROVIDER: E-MTAB-2352 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The genomic landscape of compensatory evolution.

Szamecz Béla B Boross Gábor G Kalapis Dorottya D Kovács Károly K Fekete Gergely G Farkas Zoltán Z Lázár Viktória V Hrtyan Mónika M Kemmeren Patrick P Groot Koerkamp Marian J A MJ Rutkai Edit E Holstege Frank C P FC Papp Balázs B Pál Csaba C

PLoS biology 20140826 8

Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, as deleterious mutations are common in natural populations, they generate a strong selection pressure to mitigate their detrimental effects through compensatory genetic changes. This process can potentially influence directions of adaptive evolution by enabling evolutionary routes that are otherwise inaccessible. Therefore, the extent to which compensatory mutations shape genomic evolut ...[more]

PMID: 25157590

Similar Datasets

BP001-002: The genomic landscape of compensatory evolution

Project description:Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, deleterious mutations may also have an important role by promoting adaptive genetic changes that are otherwise inaccessible. Here we study the capacity of the bakerM-bM-^@M-^Ys yeast genome to compensate the complete loss of genes during evolution, and explore the long-term consequences of this process. We initiated laboratory evolutionary experiments with over 180 haploid yeast genotypes, all of which initially displayed slow growth due to the deletion of a single gene. Compensatory adaptation was rapid and pervasive, and it promoted the genomic divergence of parallel evolving populations. The accumulated mutations did not restore wild type genomic expression states and generated diverse growth phenotypes across environments. Taken together, gene loss initiates genomic changes that can influence evolutionary potential upon environmental change. Evolved yeast-lines were generated by growing strains for 400 doublings during 104 days on YPD medium in 96 wells plates, 8 evolved lines were selected for microarray analysis. Two independent colonies of the wild type control, evolved and corresponding ancestor knock-out strains were grown to early midlog and used for transcription profiling by dual channel array against a common reference.

2014-08-27 | E-GEOD-55373 | biostudies-arrayexpress

Integrative genomic and proteomic analysis of response of Lactobacillus casei str. Zhang to glucose limitation

Project description:Nutrient starvation is an important survival challenge for bacteria during industrial production of functional foods. Lactobacilli are increasingly being used as probiotics in functional foods. As next-generation sequencing technology has greatly advanced, we performed integrative proteomic and genomic analysis to investigate the response of Lactobacillus casei Zhang to a glucose-restricted environment. L. casei Zhang strains were permitted to evolve in glucose-limited or normal medium from a common ancestor over a 3-year period, and they were sampled after 1000, 2000, 3000, 4000, 5000, 6000, 7000, and 8000 generations and subjected to proteomic and genomic analyses. Genomic resequencing data revealed different point mutations and other mutational events in each generation of L. casei Zhang under glucose limitation stress. The proteins expressed differentially under glucose limitation were found to be significantly related to fructose and mannose metabolism, carbohydrate metabolic processes, lyase activity, and amino acid-transporting ATPase activity. The integrative proteomic and genomic analysis revealed that the mutations protected L. casei Zhang against glucose starvation by regulating other cellular carbohydrate, fatty acid, and amino acid catabolism; phosphoenolpyruvate system pathway activation; glycogen synthesis; ATP consumption; pyruvate metabolism; and general stress response protein expression. The results help reveal the mechanisms of adapting to glucose starvation and provide new strategies for enhancing the industrial utility of L. casei Zhang.

2018-02-08 | PXD006643 | Pride

Multiple means to the same end: The genetic basis of acquired stress resistance in yeast

Project description:A series of experiments comparing the gene expression response before and after 30 min 0.7M NaCl exposure in WT and mutant yeast strains. Mutant strains were identified as having a defect in acquiring resistance to H2O2 following mild NaCl pretreatment. The mutants in this study were taken from the Yeast Knock-Out Collection, mat a. Unstressed cells vs cells exposed to 0.7M NaCl for 30 min; 5 replicates for WT, 3 replicates for hog1∆, msn2∆, mck1∆, pde2∆, rim101∆, and 2 replicates for the remaining mutants.

2014-03-06 | E-GEOD-27819 | biostudies-arrayexpress

Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor

Project description:The Crabtree effect, in which fermentative metabolism is preferred at the expense of respiration, is a hallmark of budding yeast’s glucose response and a model for the Warburg effect in human tumors. While the glucose-responsive transcriptional repressors Mig1p and Mig2p play well-characterized roles in the Crabtree effect, little function for the related Mig3p transcription factor has been uncovered despite numerous investigations of laboratory yeast strains. Here we studied a wild isolate of Saccharomyces cerevisiae to uncover a critical role for Mig3p that has been lost in S288c-derived laboratory strains. We found that Mig3p affects the expression of hundreds of glucose-responsive genes in the oak strain YPS163, both during growth under standard conditions and upon ethanol treatment. Our results suggest that Mig3p may act as a multifunctional activator/repressor that plays separate roles under standard versus stress conditions, but this function has been largely lost in the lab strains. Population analysis suggests that the lab strain, and several wild strains, harbor mutations that diminish Mig3p function. Thus, by expanding our attention to multiple genetic backgrounds, we have uncovered an important missing link in a key metabolic response. We performed a series of microarray experiments comparing the gene expression response of unstressed or EtOH stressed wild-type or mig3∆ strains in either the BY4741 or YPS163 background (biological triplicates). We also compared gene expression for in reciprocal hemizygous strains (YPS163/BY4741mig3∆ and YPS163mig3∆/BY4742; biological duplicates). Lastly, we measured the gene expression of BY4741 over-expressing BY_MIG3 via galactose induction (biological triplicates).

2012-11-01 | E-GEOD-40153 | biostudies-arrayexpress

Comparative transcriptomics of Escherichia coli growing in complex environments

Project description:Long-term experiment (150 days) of Escherichia coli MC1000 with daily transfers into fresh LB medium and under three different oxygen regimes. An overnight culture of E coli (ancestor culture) was propagated in LB media with three different oxygen regimes during 150 days. One regime involved transfers under constant shaking (200rpm): Treatment A-Replica populations 1 and 2 , second regime consisted in a daily shift between shaking and static (no shaking) conditions: Treatment B-replica populations 3,4 and 5. The third regime involved transfers in constant static conditions: Treatment C-Populations 6 and 7. After 150 days and plating, 3 different colony types were selected by population (populations 6 and 7 only had 2 different morphologies). Morpholigies were marked as a, b, c in each population. cDNA was obtainned from each morphology after growing separately in LB medium, under they correspondant evolving condition until late logaritmic phase (0,6-0,7 in OD600). A total of 19 evolved forms were analyzed plus one ancestor. Each morphology was labeled in a dye-swap design and hybridized to the ancestor into genome-wide multi-strain E. coli (8x15K) microarrays.

2013-03-01 | E-GEOD-44614 | biostudies-arrayexpress

Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-11-28 | E-GEOD-52787 | biostudies-arrayexpress

Cryptococcus neoformans Hsf3 LC-MS/MS

Project description:Mitochondrial quality control is essential in modulating intramitochondrial ROS (mtROS) homeostasis that is a critical determinant for many human disorders. Here we identified an atypical function of a heat shock factor, Hsf3, as an important mtROS regulator. Despite HSFs are nuclear proteins and master regulators of protein unfolded response (UPR) across taxa, we demonstrate that Hsf3 is a both nuclei and mitochondria targeting transcription factor that plays an irrelevant function in controlling UPR process. Instead, Hsf3 represses TCA cycle genes and simultaneously regulates electron transfer chain genes encoded from both nuclei and mitochondria. Moreover, both nuclear and mitochondrial targeting signal are required for promising Hsf3 function. Hsf3 regulation responds to multiple intramitochondrial stresses, which activates and ameliorates Hsf3 DNA binding via oxidation of the cysteine residue on DNA binding domain of Hsf3. Collectively, our findings reveal a previously unknown role of HSF family in modulation of mitochondrial function and damage.

2022-09-01 | PXD033799 | Pride

Evolution of gene expression during long term coexistence in a bacterial evolution experiment

Project description:We used microarrays to study the evolution of gene expression in two bacterial ecotypes that coexisted for more than 35000 generations of experimental evolution in an extremely simple environment We sampled four clones from each of two lineages at generations 6,500, 17,000 and 40,000 from the polymorphic Ara-2 population of the E. coli long-term evolution experiment. The four clones from each lineage and generation were mixed equally and used for global expression profiling, growth assays and competition experiments. Global expression profiles and growth assays were also performed on the ancestral strain. RNA extractions were done using cells in mid-exponential growth in the same glucose-limited minimal medium used in the evolution experiment. Global expression profiles were obtained by using Affymetrix arrays, with 5 or 6 biological replicates for each lineage-generation sample.

2012-01-01 | E-GEOD-30639 | biostudies-arrayexpress

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (CGH)

Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium. Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)

2010-06-19 | E-GEOD-10267 | biostudies-arrayexpress

Analysing of Chromosome VIII of EC9-7 after experimental evolution (S. cerevisiae)

Project description:The genomic DNA of wild-type chromosome VIII of evolved EC9-7 cells was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify its chromosomal composition Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit. After PFGE, The ChrVIII DNA was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit.

2011-11-13 | E-GEOD-33652 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data