ArticlePLoS genetics2015
Rapid evolution of recombinant Saccharomyces cerevisiae for Xylose fermentation through formation of extra-chromosomal circular DNA.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 72 citations in OpenAlex.
- Resurrection and characterization of ancestral xylose transporters enhance the capability of xylose uptake in the mixed sugar co-fermentation of Recombinant Saccharomyces cerevisiae.Bioresources and bioprocessing · 2026Article
- Yeast EndoG prevents genome instability by degrading extranuclear DNA species.Nature communications · 2024Article
- Transcription as source of genetic heterogeneity in budding yeast.Yeast (Chichester, England) · 2024Review
- Enhancing xylose-fermentation capacity of engineered Saccharomyces cerevisiae by multistep evolutionary engineering in inhibitor-rich lignocellulose hydrolysate.FEMS yeast research · 2024Article
- Yeast EndoG prevents genome instability by degrading cytoplasmic DNA.Research square · 2024Article
- Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics.Cell genomics · 2023Article
- Extrachromosomal circular DNA as a vehicle to gene transfer in plants.Plant physiology · 2023Article
- PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae.PLoS genetics · 2023Article
- A Quick Method to Synthesize Extrachromosomal Circular DNA In Vitro.Molecules (Basel, Switzerland) · 2023Article
- Antigenic diversity in malaria parasites is maintained on extrachromosomal DNA.bioRxiv : the preprint server for biology · 2023Article
- Microevolutionary dynamics of eccDNA in Chinese hamster ovary cells grown in fed-batch cultures under control and lactate-stressed conditions.Scientific reports · 2023Article
- An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae.Nature communications · 2022Article
- Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate.Biotechnology for biofuels and bioproducts · 2022Article
- Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer.International journal of biological sciences · 2021Review
- The adaptive potential of circular DNA accumulation in ageing cells.Current genetics · 2020Review
- Review
- Near-Random Distribution of Chromosome-Derived Circular DNA in the Condensed Genome of Pigeons and the Larger, More Repeat-Rich Human Genome.Genome biology and evolution · 2020Article
- Improved simultaneous co-fermentation of glucose and xylose byBiotechnology for biofuels · 2020Article
- Transcription-induced formation of extrachromosomal DNA during yeast ageing.PLoS biology · 2019Article
- Extrachromosomal circular DNAs: an extra piece of evidence to depict tumor heterogeneity.Future science OA · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circular DNA elements are involved in genome plasticity, particularly of tandem repeats. However, amplifications of DNA segments in Saccharomyces cerevisiae reported so far involve pre-existing repetitive sequences such as ribosomal DNA, Ty elements and Long Terminal Repeats (LTRs). Here, we report the generation of an eccDNA, (extrachromosomal circular DNA element) in a region without any repetitive sequences during an adaptive evolution experiment. We performed whole genome sequence comparison between an efficient D-xylose fermenting yeast strain developed by metabolic and evolutionary engineering, and its parent industrial strain. We found that the heterologous gene XylA that had been inserted close to an ARS sequence in the parent strain has been amplified about 9 fold in both alleles of the chromosomal locus of the evolved strain compared to its parent. Analysis of the amplification process during the adaptive evolution revealed formation of a XylA-carrying eccDNA, pXI2-6, followed by chromosomal integration in tandem arrays over the course of the evolutionary adaptation. Formation of the eccDNA occurred in the absence of any repetitive DNA elements, probably using a micro-homology sequence of 8 nucleotides flanking the amplified sequence. We isolated the pXI2-6 eccDNA from an intermediate strain of the evolutionary adaptation process, sequenced it completely and showed that it confers high xylose fermentation capacity when it is transferred to a new strain. In this way, we have provided clear evidence that gene amplification can occur through generation of eccDNA without the presence of flanking repetitive sequences and can serve as a rapid means of adaptation to selection pressure.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.