scholarly journals The evolutionary plasticity of chromosome metabolism allows adaptation to DNA replication stress

2019 ◽  
Author(s):  
Marco Fumasoni ◽  
Andrew W. Murray
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Natural Populations ◽  
Replication Stress ◽  
Dna Damage Checkpoint ◽  
Whole Genome ◽  
Replication Forks ◽  
Evolutionary Trajectory ◽  
Chromatid Cohesion ◽  
Dna Replication Stress

AbstractChromosome metabolism is defined by the pathways that collectively maintain the genome, including chromosome replication, repair and segregation. Because aspects of these pathways are conserved, chromosome metabolism is considered resistant to evolutionary change. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, successive mutations. Whole-genome sequencing and testing candidate mutations revealed adaptive changes in three aspects of chromosome metabolism: DNA replication, DNA damage checkpoint and sister chromatid cohesion. Although no gene was mutated in every population, the same pathways were sequentially altered, defining a functionally reproducible evolutionary trajectory. We propose that this evolutionary plasticity of chromosome metabolism has important implications for genome evolution in natural populations and cancer.

scholarly journals The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Marco Fumasoni ◽  
Andrew W Murray
Keyword(s):  
Dna Replication ◽  
Natural Populations ◽  
Replication Stress ◽  
Replication Forks ◽  
Yeast Saccharomyces Cerevisiae ◽  
Evolutionary Trajectory ◽  
Biological Features ◽  
Chromatid Cohesion ◽  
Conserved Genes ◽  
Dna Replication Stress

Many biological features are conserved and thus considered to be resistant to evolutionary change. While rapid genetic adaptation following the removal of conserved genes has been observed, we often lack a mechanistic understanding of how adaptation happens. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism, a network of evolutionary conserved modules. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the enzymatic activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, concerted mutations. These mutations altered conserved features of two chromosome metabolism modules, DNA replication and sister chromatid cohesion, and inactivated a third, the DNA damage checkpoint. The selected mutations define a functionally reproducible evolutionary trajectory. We suggest that the evolutionary plasticity of chromosome metabolism has implications for genome evolution in natural populations and cancer.

scholarly journals Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009875
Author(s):  
Marco Fumasoni ◽  
Andrew W. Murray
Keyword(s):  
Dna Replication ◽  
Replication Stress ◽  
Dna Damage Checkpoint ◽  
Functional Modules ◽  
Evolutionary Adaptation ◽  
Genome Maintenance ◽  
Genomic Features ◽  
Evolutionary Response ◽  
Chromatid Cohesion ◽  
Dna Replication Stress

In haploid budding yeast, evolutionary adaptation to constitutive DNA replication stress alters three genome maintenance modules: DNA replication, the DNA damage checkpoint, and sister chromatid cohesion. We asked how these trajectories depend on genomic features by comparing the adaptation in three strains: haploids, diploids, and recombination deficient haploids. In all three, adaptation happens within 1000 generations at rates that are correlated with the initial fitness defect of the ancestors. Mutations in individual genes are selected at different frequencies in populations with different genomic features, but the benefits these mutations confer are similar in the three strains, and combinations of these mutations reproduce the fitness gains of evolved populations. Despite the differences in the selected mutations, adaptation targets the same three functional modules despite differences in genomic features, revealing a common evolutionary response to constitutive DNA replication stress.

scholarly journals Tolerance of DNA Replication Stress Is Promoted by Fumarate Through Modulation of Histone Demethylation and Enhancement of Replicative Intermediate Processing in Saccharomyces cerevisiae

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 631-654 ◽  
Author(s):  
Faeze Saatchi ◽  
Ann L. Kirchmaier
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Mammalian Cells ◽  
Cell Cancer ◽  
Replication Stress ◽  
Histone Demethylase ◽  
Loss Of Function ◽  
Cycle Enzyme ◽  
Link Type ◽  
Dna Replication Stress

Fumarase is a well-characterized TCA cycle enzyme that catalyzes the reversible conversion of fumarate to malate. In mammals, fumarase acts as a tumor suppressor, and loss-of-function mutations in the FH gene in hereditary leiomyomatosis and renal cell cancer result in the accumulation of intracellular fumarate—an inhibitor of α-ketoglutarate-dependent dioxygenases. Fumarase promotes DNA repair by nonhomologous end joining in mammalian cells through interaction with the histone variant H2A.Z, and inhibition of KDM2B, a H3 K36-specific histone demethylase. Here, we report that Saccharomyces cerevisiae fumarase, Fum1p, acts as a response factor during DNA replication stress, and fumarate enhances survival of yeast lacking Htz1p (H2A.Z in mammals). We observed that exposure to DNA replication stress led to upregulation as well as nuclear enrichment of Fum1p, and raising levels of fumarate in cells via deletion of FUM1 or addition of exogenous fumarate suppressed the sensitivity to DNA replication stress of htz1Δ mutants. This suppression was independent of modulating nucleotide pool levels. Rather, our results are consistent with fumarate conferring resistance to DNA replication stress in htz1Δ mutants by inhibiting the H3 K4-specific histone demethylase Jhd2p, and increasing H3 K4 methylation. Although the timing of checkpoint activation and deactivation remained largely unaffected by fumarate, sensors and mediators of the DNA replication checkpoint were required for fumarate-dependent resistance to replication stress in the htz1Δ mutants. Together, our findings imply metabolic enzymes and metabolites aid in processing replicative intermediates by affecting chromatin modification states, thereby promoting genome integrity.

scholarly journals Break-Induced Replication Repair of Damaged Forks Induces Genomic Duplications in Human Cells

Science ◽  
2013 ◽  
Vol 343 (6166) ◽  
pp. 88-91 ◽  
Author(s):  
Lorenzo Costantino ◽  
Sotirios K. Sotiriou ◽  
Juha K. Rantala ◽  
Simon Magin ◽  
Emil Mladenov ◽  
...  
Keyword(s):  
Dna Replication ◽  
Cell Cycle Progression ◽  
Cyclin E ◽  
Replication Stress ◽  
Replication Forks ◽  
Dna Polymerase Delta ◽  
Dna Double Strand Breaks ◽  
Dna Replication Stress ◽  
Recombination Pathway ◽  
Break Induced Replication

In budding yeast, one-ended DNA double-strand breaks (DSBs) and damaged replication forks are repaired by break-induced replication (BIR), a homologous recombination pathway that requires the Pol32 subunit of DNA polymerase delta. DNA replication stress is prevalent in cancer, but BIR has not been characterized in mammals. In a cyclin E overexpression model of DNA replication stress, POLD3, the human ortholog of POL32, was required for cell cycle progression and processive DNA synthesis. Segmental genomic duplications induced by cyclin E overexpression were also dependent on POLD3, as were BIR-mediated recombination events captured with a specialized DSB repair assay. We propose that BIR repairs damaged replication forks in mammals, accounting for the high frequency of genomic duplications in human cancers.

scholarly journals The activation loop residue serine 173 of S.pombe Chk1 kinase is critical for the response to DNA replication stress

2017 ◽  
Author(s):  
Naomi Coulton ◽  
Thomas Caspari
Keyword(s):  
Dna Damage ◽  
Dna Replication ◽  
Replication Stress ◽  
Genetic Alterations ◽  
Activation Loop ◽  
Replication Forks ◽  
Dna Polymerase Delta ◽  
Dna Replication Stress ◽  
Summary Statement ◽  
Chk1 Kinase

AbstractWhy the DNA damage checkpoint kinase Chk1 protects the genome of lower and higher eukaryotic cells differentially is still unclear. Mammalian Chk1 regulates replication origins, safeguards DNA replication forks and promotes fork progression. Conversely, yeast Chk1 acts only in G1 and G2. We report here that the mutation of serine 173 (S173A) in the activation loop of fission yeast Chk1 abolishes the G1-M and S-M checkpoints without affecting the G2-M arrest. Although Chk1-S173A is fully phosphorylated at serine 345 by the DNA damage sensor Rad3 (ATR) when DNA replication forks break, cells fail to stop the cell cycle. Mutant cells are uniquely sensitive to the DNA alkylation agent methyl- methanesulfate (MMS). This MMS sensitivity is genetically linked with the lagging strand DNA polymerase delta. Chk1-S173A is also unable to block mitosis when the G1 transcription factor Cdc10 is impaired. Serine 173 is equivalent to lysine 166 in human Chk1, an amino acid important for substrate specificity. We conclude that the removal of serine 173 impairs the phosphorylation of a Chk1 target that is important to protect cells from DNA replication stress.Summary statementMutation of serine-173 in the activation loop of Chk1 kinase may promote cancer as it abolishes the response to genetic alterations that arise while chromosomes are being copied.

scholarly journals Centrosome impairment causes DNA replication stress through MLK3/MK2 signaling and R-loop formation

2020 ◽  
Author(s):  
Zainab Tayeh ◽  
Kim Stegmann ◽  
Antonia Kleeberg ◽  
Mascha Friedrich ◽  
Josephine Ann Mun Yee Choo ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Replication Stress ◽  
List Type ◽  
Replication Forks ◽  
Loop Formation ◽  
Animal Cells ◽  
Replication Fork Progression ◽  
Primordial Dwarfism ◽  
Dna Replication Stress

AbstractCentrosomes function as organizing centers of microtubules and support accurate mitosis in many animal cells. However, it remains to be explored whether and how centrosomes also facilitate the progression through different phases of the cell cycle. Here we show that impairing the composition of centrosomes, by depletion of centrosomal components or by inhibition of polo-like kinase 4 (PLK4), reduces the progression of DNA replication forks. This occurs even when the cell cycle is arrested before damaging the centrosomes, thus excluding mitotic failure as the source of replication stress. Mechanistically, the kinase MLK3 associates with centrosomes. When centrosomes are disintegrated, MLK3 activates the kinases p38 and MK2/MAPKAPK2. Transcription-dependent RNA:DNA hybrids (R-loops) are then causing DNA replication stress. Fibroblasts from patients with microcephalic primordial dwarfism (Seckel syndrome) harbouring defective centrosomes showed replication stress and diminished proliferation, which were each alleviated by inhibition of MK2. Thus, centrosomes not only facilitate mitosis, but their integrity is also supportive in DNA replication.HighlightsCentrosome defects cause replication stress independent of mitosis.MLK3, p38 and MK2 (alias MAPKAPK2) are signalling between centrosome defects and DNA replication stress through R-loop formation.Patient-derived cells with defective centrosomes display replication stress, whereas inhibition of MK2 restores their DNA replication fork progression and proliferation.Graphical abstract

scholarly journals Smarcal1 and Zranb3 Protect Replication Forks from Myc-Induced DNA Replication Stress

2019 ◽  
Vol 79 (7) ◽  
pp. 1612-1623 ◽  
Author(s):  
Matthew V. Puccetti ◽  
Clare M. Adams ◽  
Saul Kushinsky ◽  
Christine M. Eischen
Keyword(s):  
Dna Replication ◽  
Replication Stress ◽  
Replication Forks ◽  
Dna Replication Stress

scholarly journals Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae

2006 ◽  
Vol 175 (5) ◽  
pp. 729-741 ◽  
Author(s):  
Jorrit M. Enserink ◽  
Marcus B. Smolka ◽  
Huilin Zhou ◽  
Richard D. Kolodner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Cell Morphology ◽  
Replication Fork ◽  
Replication Stress ◽  
Replication Checkpoint ◽  
Checkpoint Proteins ◽  
Checkpoint Kinases ◽  
Dna Replication Checkpoint ◽  
Dna Replication Stress

In response to DNA replication stress in Saccharomyces cerevisiae, the DNA replication checkpoint maintains replication fork stability, prevents precocious chromosome segregation, and causes cells to arrest as large-budded cells. The checkpoint kinases Mec1 and Rad53 act in this checkpoint. Treatment of mec1 or rad53Δ mutants with replication inhibitors results in replication fork collapse and inappropriate partitioning of partially replicated chromosomes, leading to cell death. We describe a previously unappreciated function of various replication stress checkpoint proteins, including Rad53, in the control of cell morphology. Checkpoint mutants have aberrant cell morphology and cell walls, and show defective bud site selection. Rad53 shows genetic interactions with septin ring pathway components, and, along with other checkpoint proteins, controls the timely degradation of Swe1 during replication stress, thereby facilitating proper bud growth. Thus, checkpoint proteins play an important role in coordinating morphogenetic events with DNA replication during replication stress.

scholarly journals Genome architecture shapes evolutionary adaptation to DNA replication stress

2020 ◽  
Author(s):  
Marco Fumasoni ◽  
Andrew W. Murray
Keyword(s):  
Dna Damage ◽  
Dna Replication ◽  
Replication Stress ◽  
Selective Advantage ◽  
Genome Architecture ◽  
Dna Damage Checkpoint ◽  
Evolutionary Adaptation ◽  
Loss Of Function ◽  
Genome Maintenance ◽  
Dna Replication Stress

ABSTRACTEvolutionary adaptation to perturbations in DNA replication follows reproducible trajectories that lead to changes in three important aspects of genome maintenance: DNA replication, the DNA damage checkpoint, and sister chromatid cohesion. We asked how these trajectories depend on a population’s genome architecture by testing whether ploidy or the ability to perform homologous recombination influence the evolutionary fate of the budding yeast, Saccharomyces cerevisiae, as it adapts to constitutive DNA replication stress, a condition that characterizes many cancer cells. In all three genome architectures, adaptation happens within 1000 generations at rates that are linearly correlated with the initial fitness defect of the ancestors. Which genes are mutated depends on the frequency at which mutations occur and the selective advantage they confer. The recombination-deficient strain amplifies adaptive chromosomal regions less often, whereas the selective advantage of loss-of-function mutations, such as those that inactivate the DNA damage checkpoint, is reduced in diploids because of the presence of a second, wild-type copy of the gene. Despite these differences, selection targets the same three functional modules in all three architectures, suggesting that genome architecture controls which genes are mutated but not which modules are modified.

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