Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

@article{Steenwyk2019ExtensiveLO,
  title={Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts},
  author={J. Steenwyk and D. A. Opulente and Jacek Kominek and Xing-Xing Shen and Xiaofan Zhou and A. Labella and Noah P Bradley and B. F. Eichman and N. {\vC}ade{\vz} and D. Libkind and Jeremy DeVirgilio and A. B. Hulfachor and C. Kurtzman and C. T. Hittinger and A. Rokas},
  journal={bioRxiv},
  year={2019}
}
Cell cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low GC content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18 / 21 known species in the genus. Our phylogenomic… Expand
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References

SHOWING 1-10 OF 195 REFERENCES
Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi
TLDR
It is hypothesized that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes, and it is shown that SBF can regulate promoters with E1F binding sites in budding yeast. Expand
Evolution of networks and sequences in eukaryotic cell cycle control
TLDR
Forward genetics in non-opisthokonts, such as plants or their green algal relatives, will provide direct information on cell cycle control in these organisms, and may elucidate the potentially more complexcell cycle control network of the last common eukaryotic ancestor. Expand
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts.
TLDR
The results suggest that rapid and irreversible gene inactivation and pathway degeneration are associated with adaptation to new ecological niches in natural populations. Expand
Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair.
TLDR
It is concluded that the checkpoint in budding yeast consists of overlapping S-phase and G2-phase pathways that respond to incomplete DNA replication and/or DNA damage and cause arret of cells before mitosis. Expand
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
TLDR
It is argued that reductive evolution is a major mode of evolutionary diversification and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. Expand
Checkpoint Adaptation Precedes Spontaneous and Damage-Induced Genomic Instability in Yeast
TLDR
The spontaneous and X-ray-induced frequencies of chromosome loss, translocations, and a repair process called break-induced replication occur at significantly reduced rates in adaptation-defective mutants, which indicates that these events occur after a cell has first arrested at the checkpoint and then adapted to that arrest. Expand
Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast
TLDR
Genetic analysis revealed a complex network of newly found factors that govern critical cell size at Start, the most potent of which were Sfp1, Sch9, Cdh1, Prs3, and Whi5. Expand
Selection-Driven Gene Loss in Bacteria
TLDR
The hypothesis that gene loss is selected because carriage of superfluous genes confers a fitness cost to the bacterium is examined, suggesting that selection could be a significant driver of gene loss and reductive genome evolution. Expand
Mutational landscape of yeast mutator strains
TLDR
This comprehensive analytical approach of mutator defects provides a model to understand how genome variations might accumulate during clonal evolution of somatic cell populations, including tumor cells. Expand
Natural mismatch repair mutations mediate phenotypic diversity and drug resistance in Cryptococcus deuterogattii
TLDR
It is suggested that pathogenic eukaryotic microbes may experience similar selection pressures on mutation rate as bacterial pathogens, particularly during long periods of clonal growth or while expanding into new environments. Expand
...
1
2
3
4
5
...