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1.
Mol Cell Oncol ; 11(1): 2369388, 2024.
Article in English | MEDLINE | ID: mdl-38919375

ABSTRACT

Aneuploidy, the presence of an aberrant number of chromosomes, has been associated with tumorigenesis for over a century. More recently, advances in karyotyping techniques have revealed its high prevalence in cancer: About 90% of solid tumors and 50-70% of hematopoietic cancers exhibit chromosome gains or losses. When analyzed at the level of specific chromosomes, there are strong patterns that are observed in cancer karyotypes both pan-cancer and for specific cancer types. These specific aneuploidy patterns correlate strongly with outcomes for tumor initiation, progression, metastasis formation, immune evasion and resistance to therapeutic treatment. Despite their prominence, understanding the basis underlying aneuploidy patterns in cancer has been challenging. Advances in genetic engineering and bioinformatic analyses now offer insights into the genetic determinants of aneuploidy pattern selection. Overall, there is substantial evidence that expression changes of particular genes can act as the positive selective forces for adaptation through aneuploidy. Recent findings suggest that multiple genes contribute to the selection of specific aneuploid chromosomes in cancer; however, further research is necessary to identify the most impactful driver genes. Determining the genetic basis and accompanying vulnerabilities of specific aneuploidy patterns is an essential step in selectively targeting these hallmarks of tumors.

2.
Sci Rep ; 14(1): 14715, 2024 06 26.
Article in English | MEDLINE | ID: mdl-38926482

ABSTRACT

Opioids are the gold standard for the treatment of chronic pain but are limited by adverse side effects. In our earlier work, we showed that Heat shock protein 90 (Hsp90) has a crucial role in regulating opioid signaling in spinal cord; Hsp90 inhibition in spinal cord enhances opioid anti-nociception. Building on these findings, we injected the non-selective Hsp90 inhibitor KU-32 by the intrathecal route into male and female CD-1 mice, showing that morphine anti-nociceptive potency was boosted by 1.9-3.5-fold in acute and chronic pain models. At the same time, tolerance was reduced from 21-fold to 2.9 fold and established tolerance was rescued, while the potency of constipation and reward was unchanged. These results demonstrate that spinal Hsp90 inhibition can improve the therapeutic index of morphine. However, we also found that systemic non-selective Hsp90 inhibition blocked opioid pain relief. To avoid this effect, we used selective small molecule inhibitors and CRISPR gene editing to identify 3 Hsp90 isoforms active in spinal cord (Hsp90α, Hsp90ß, and Grp94) while only Hsp90α was active in brain. We thus hypothesized that a systemically delivered selective inhibitor to Hsp90ß or Grp94 could selectively inhibit spinal cord Hsp90 activity, resulting in enhanced opioid therapy. We tested this hypothesis using intravenous delivery of KUNB106 (Hsp90ß) and KUNG65 (Grp94), showing that both drugs enhanced morphine anti-nociceptive potency while rescuing tolerance. Together, these results suggest that selective inhibition of spinal cord Hsp90 isoforms is a novel, translationally feasible strategy to improve the therapeutic index of opioids.


Subject(s)
Analgesics, Opioid , HSP90 Heat-Shock Proteins , Morphine , Spinal Cord , Animals , HSP90 Heat-Shock Proteins/antagonists & inhibitors , HSP90 Heat-Shock Proteins/metabolism , Spinal Cord/metabolism , Spinal Cord/drug effects , Mice , Analgesics, Opioid/pharmacology , Male , Female , Morphine/pharmacology , Protein Isoforms/metabolism , Drug Tolerance , Chronic Pain/drug therapy , Chronic Pain/metabolism , Disease Models, Animal , Injections, Spinal
3.
Genes Dev ; 37(5-6): 171-190, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36859339

ABSTRACT

Both the presence of an abnormal complement of chromosomes (aneuploidy) and an increased frequency of chromosome missegregation (chromosomal instability) are hallmarks of cancer. Analyses of cancer genome data have identified certain aneuploidy patterns in tumors; however, the bases behind their selection are largely unexplored. By establishing time-resolved long-term adaptation protocols, we found that human cells adapt to persistent spindle assembly checkpoint (SAC) inhibition by acquiring specific chromosome arm gains and losses. Independently adapted populations converge on complex karyotypes, which over time are refined to contain ever smaller chromosomal changes. Of note, the frequencies of chromosome arm gains in adapted cells correlate with those detected in cancers, suggesting that our cellular adaptation approach recapitulates selective traits that dictate the selection of aneuploidies frequently observed across many cancer types. We further engineered specific aneuploidies to determine the genetic basis behind the observed karyotype patterns. These experiments demonstrated that the adapted and engineered aneuploid cell lines limit CIN by extending mitotic duration. Heterozygous deletions of key SAC and APC/C genes recapitulated the rescue phenotypes of the monosomic chromosomes. We conclude that aneuploidy-induced gene dosage imbalances of individual mitotic regulators are sufficient for altering mitotic timing to reduce CIN.


Subject(s)
M Phase Cell Cycle Checkpoints , Neoplasms , Humans , M Phase Cell Cycle Checkpoints/genetics , Aneuploidy , Neoplasms/genetics , Chromosomal Instability/genetics , Karyotype , Spindle Apparatus/genetics , Mitosis
4.
EMBO J ; 42(8): e111500, 2023 04 17.
Article in English | MEDLINE | ID: mdl-36530167

ABSTRACT

Both an increased frequency of chromosome missegregation (chromosomal instability, CIN) and the presence of an abnormal complement of chromosomes (aneuploidy) are hallmarks of cancer. To better understand how cells are able to adapt to high levels of chromosomal instability, we previously examined yeast cells that were deleted of the gene BIR1, a member of the chromosomal passenger complex (CPC). We found bir1Δ cells quickly adapted by acquiring specific combinations of beneficial aneuploidies. In this study, we monitored these yeast strains for longer periods of time to determine how cells adapt to high levels of both CIN and aneuploidy in the long term. We identify suppressor mutations that mitigate the chromosome missegregation phenotype. The mutated proteins fall into four main categories: outer kinetochore subunits, the SCFCdc4 ubiquitin ligase complex, the mitotic kinase Mps1, and the CPC itself. The identified suppressor mutations functioned by reducing chromosomal instability rather than alleviating the negative effects of aneuploidy. Following the accumulation of suppressor point mutations, the number of beneficial aneuploidies decreased. These experiments demonstrate a time line of adaptation to high rates of CIN.


Subject(s)
F-Box Proteins , Neoplasms , Saccharomyces cerevisiae Proteins , Saccharomycetales , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomycetales/genetics , Saccharomycetales/metabolism , Aneuploidy , Chromosomal Instability/genetics , Kinetochores/metabolism , Neoplasms/genetics , Chromosome Segregation , Cell Cycle Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , F-Box Proteins/genetics
5.
Mol Biol Cell ; 33(9): ar85, 2022 08 01.
Article in English | MEDLINE | ID: mdl-35704464

ABSTRACT

Chromosome biorientation is promoted by the four-member chromosomal passenger complex (CPC) through phosphorylation of incorrect kinetochore-microtubule attachments. During chromosome alignment, the CPC localizes to the inner centromere, the inner kinetochore, and spindle microtubules. Here we show that a small domain of the CPC subunit INCENP/Sli15 is required to target the complex to all three of these locations in budding yeast. This domain, the single alpha helix (SAH), is essential for phosphorylation of outer kinetochore substrates, chromosome segregation, and viability. By restoring the CPC to each of its three locations through targeted mutations and fusion constructs, we determined their individual contributions to chromosome biorientation. We find that only the inner centromere localization is sufficient for cell viability on its own. However, when combined, the inner kinetochore and microtubule binding activities are also sufficient to promote accurate chromosome segregation. Furthermore, we find that the two pathways target the CPC to different kinetochore attachment states, as the inner centromere-targeting pathway is primarily responsible for bringing the complex to unattached kinetochores. We have therefore discovered that two parallel localization pathways are each sufficient to promote CPC activity in chromosome biorientation, both depending on the SAH domain of INCENP/Sli15.


Subject(s)
Saccharomyces cerevisiae Proteins , Saccharomycetales , Aurora Kinase B/metabolism , Centromere/metabolism , Chromosome Segregation , Kinetochores/metabolism , Microtubules/metabolism , Phosphorylation , Saccharomyces cerevisiae Proteins/metabolism , Saccharomycetales/metabolism
6.
eNeuro ; 9(3)2022.
Article in English | MEDLINE | ID: mdl-35508370

ABSTRACT

Because of their ex utero development, relatively simple nervous system, translucency, and availability of tools to investigate neural function, larval zebrafish are an exceptional model for understanding neurodevelopmental disorders and the consequences of environmental toxins. Furthermore, early in development, zebrafish larvae easily absorb chemicals from water, a significant advantage over methods required to expose developing organisms to chemical agents in utero Bisphenol A (BPA) and BPA analogs are ubiquitous environmental toxins with known molecular consequences. All humans have measurable quantities of BPA in their bodies. Most concerning, the level of BPA exposure is correlated with neurodevelopmental difficulties in people. Given the importance of understanding the health-related effects of this common toxin, we have exploited the experimental advantages of the larval zebrafish model system to investigate the behavioral and anatomic effects of BPA exposure. We discovered that BPA exposure early in development leads to deficits in the processing of sensory information, as indicated by BPA's effects on prepulse inhibition (PPI) and short-term habituation (STH) of the C-start reflex. We observed no changes in locomotion, thigmotaxis, and repetitive behaviors (circling). Despite changes in sensory processing, we detected no regional or whole-brain volume changes. Our results show that early BPA exposure can induce sensory processing deficits, as revealed by alterations in simple behaviors that are mediated by a well-defined neural circuit.


Subject(s)
Benzhydryl Compounds , Zebrafish , Animals , Benzhydryl Compounds/toxicity , Humans , Larva , Perception , Phenols
7.
Mol Phylogenet Evol ; 147: 106784, 2020 06.
Article in English | MEDLINE | ID: mdl-32135308

ABSTRACT

The Amelanchier-Malacomeles-Peraphyllum (AMP) clade consists of ca. 26 species distributed in North and Central America, Europe, Asia, and northwestern Africa. While molecular and morphological data strongly support this clade, relationships of its genera are uncertain. Support for the monophyly of Amelanchier and for the phylogenetic positions of Malacomeles and Peraphyllum has varied between studies. Our goals were to reconstruct a robust phylogeny of the AMP clade in the framework of Maleae and clarify the phylogenetic placements of Malacomeles and Peraphyllum. This study employs sequences of the whole plastome and nuclear ribosomal DNA (nrDNA) repeats assembled using genome skimming with 131 samples representing 115 species in 31 genera of Rosaceae, especially Maleae. Maximum likelihood (ML) and Bayesian analysis (BI) of whole plastome datasets strongly supported Amelanchier as not monophyletic, with Peraphyllum sister to eastern North American Amelanchier and Malacomeles sister to the western North American-Eurasian Amelanchier. In contrast, nrDNA recovered the monophyly of Amelanchier, with Peraphyllum sister to Amelanchier and Malacomeles sister to the Amelanchier-Peraphyllum clade. The strong topological conflicts between plastome and nrDNA phylogenies of Peraphyllum and of Malacomeles are best explained by ancient chloroplast capture that occurred in SW North America.


Subject(s)
Cell Nucleus/genetics , Chloroplasts/genetics , DNA, Ribosomal/genetics , Genome, Chloroplast , Genomics/methods , Phylogeny , Rosaceae/classification , Rosaceae/genetics , Bayes Theorem , Chromosome Mapping , Evolution, Molecular , Geography , Rosaceae/anatomy & histology , Sequence Analysis, DNA
8.
Genes Dev ; 32(23-24): 1485-1498, 2018 12 01.
Article in English | MEDLINE | ID: mdl-30463904

ABSTRACT

Cells that contain an abnormal number of chromosomes are called aneuploid. High rates of aneuploidy in cancer are correlated with an increased frequency of chromosome missegregation, termed chromosomal instability (CIN). Both high levels of aneuploidy and CIN are associated with cancers that are resistant to treatment. Although aneuploidy and CIN are typically detrimental to cell growth, they can aid in adaptation to selective pressures. Here, we induced extremely high rates of chromosome missegregation in yeast to determine how cells adapt to CIN over time. We found that adaptation to CIN occurs initially through many different individual chromosomal aneuploidies. Interestingly, the adapted yeast strains acquire complex karyotypes with specific subsets of the beneficial aneuploid chromosomes. These complex aneuploidy patterns are governed by synthetic genetic interactions between individual chromosomal abnormalities, which we refer to as chromosome copy number interactions (CCNIs). Given enough time, distinct karyotypic patterns in separate yeast populations converge on a refined complex aneuploid state. Surprisingly, some chromosomal aneuploidies that provided an advantage early on in adaptation are eventually lost due to negative CCNIs with even more beneficial aneuploid chromosome combinations. Together, our results show how cells adapt by obtaining specific complex aneuploid karyotypes in the presence of CIN.


Subject(s)
Aneuploidy , Chromosome Segregation/genetics , Chromosomes, Fungal/genetics , Saccharomyces cerevisiae/genetics , Chromosomal Instability , Chromosome Aberrations , DNA Copy Number Variations/genetics , Evolution, Molecular , Karyotype
9.
Am J Bot ; 105(9): 1531-1544, 2018 09.
Article in English | MEDLINE | ID: mdl-30157290

ABSTRACT

PREMISE OF THE STUDY: Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record. METHODS: We surveyed the current state of knowledge in conifer phylogenetics to present a new time-calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species-rich and well known from fossils. KEY RESULTS: Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging. CONCLUSIONS: Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.


Subject(s)
Fossils , Tracheophyta , Biodiversity , Biological Evolution , Fossils/anatomy & histology , Phylogeny , Tracheophyta/anatomy & histology , Tracheophyta/genetics , Tracheophyta/physiology
10.
PLoS Genet ; 14(1): e1007170, 2018 01.
Article in English | MEDLINE | ID: mdl-29320491

ABSTRACT

Defects in the genes encoding the Paf1 complex can cause increased genome instability. Loss of Paf1, Cdc73, and Ctr9, but not Rtf1 or Leo1, caused increased accumulation of gross chromosomal rearrangements (GCRs). Combining the cdc73Δ mutation with individual deletions of 43 other genes, including TEL1 and YKU80, which are involved in telomere maintenance, resulted in synergistic increases in GCR rates. Whole genome sequence analysis of GCRs indicated that there were reduced relative rates of GCRs mediated by de novo telomere additions and increased rates of translocations and inverted duplications in cdc73Δ single and double mutants. Analysis of telomere lengths and telomeric gene silencing in strains containing different combinations of cdc73Δ, tel1Δ and yku80Δ mutations suggested that combinations of these mutations caused increased defects in telomere maintenance. A deletion analysis of Cdc73 revealed that a central 105 amino acid region was necessary and sufficient for suppressing the defects observed in cdc73Δ strains; this region was required for the binding of Cdc73 to the Paf1 complex through Ctr9 and for nuclear localization of Cdc73. Taken together, these data suggest that the increased GCR rate of cdc73Δ single and double mutants is due to partial telomere dysfunction and that Ctr9 and Paf1 play a central role in the Paf1 complex potentially by scaffolding the Paf1 complex subunits or by mediating recruitment of the Paf1 complex to the different processes it functions in.


Subject(s)
Genomic Instability/genetics , Nuclear Proteins/physiology , Saccharomyces cerevisiae Proteins/physiology , Telomere Homeostasis/genetics , Cell Cycle Proteins/genetics , DNA-Binding Proteins/physiology , Intracellular Signaling Peptides and Proteins/physiology , Nuclear Proteins/genetics , Organisms, Genetically Modified , Phenotype , Protein Binding , Protein Serine-Threonine Kinases/physiology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Telomere/metabolism , Transcriptional Elongation Factors/genetics
11.
J Cell Biol ; 216(4): 911-923, 2017 04 03.
Article in English | MEDLINE | ID: mdl-28314741

ABSTRACT

The four-subunit chromosomal passenger complex (CPC), whose enzymatic subunit is Aurora B kinase, promotes chromosome biorientation by detaching incorrect kinetochore-microtubule attachments. In this study, we use a combination of truncations and artificial dimerization in budding yeast to define the minimal CPC elements essential for its biorientation function. We engineered a minimal CPC comprised of the dimerized last third of the kinase-activating Sli15/INCENP scaffold and the catalytic subunit Ipl1/Aurora B. Although native Sli15 is not oligomeric, artificial dimerization suppressed the biorientation defect and lethality associated with deletion of a majority of its microtubule-binding domain. Dimerization did not act through a physical clustering-based kinase activation mechanism but instead promoted spindle association, likely via a putative helical domain in Sli15 that is essential even when dimerized and is required to target kinetochore substrates. Based on the engineering and characterization of a minimal CPC, we suggest that spindle association is important for active Ipl1/Aurora B complexes to preferentially destabilize misattached kinetochores.


Subject(s)
Chromosome Positioning/physiology , Chromosomes/physiology , Fungal Proteins/metabolism , Microtubule-Associated Proteins/metabolism , Saccharomycetales/physiology , Spindle Apparatus/metabolism , Spindle Apparatus/physiology , Aurora Kinase B/metabolism , Aurora Kinases/metabolism , Chromosomal Proteins, Non-Histone/metabolism , Chromosome Segregation/physiology , Chromosomes/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Kinetochores/metabolism , Kinetochores/physiology , Microtubules/metabolism , Protein Serine-Threonine Kinases/metabolism , Saccharomycetales/metabolism
12.
J Biomater Appl ; 30(8): 1142-53, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26620223

ABSTRACT

Intraperitoneal cisplatin delivery has recently been shown to benefit ovarian cancer patients. Cisplatin-containing poly(lactide-co-glycolide) (PLGA) microspheres have been proposed for cisplatin delivery. The drug loading of cisplatin containing microspheres produced elsewhere is 3-10%w. Similar microspheres are reported here with a mean diameter of 38.8 µm, and a drug loading of 11.7%w, but using ethyl acetate as a safer solvent. In addition, novel formulations of cisplatin-containing solid and hollow PLGA 65:35 (lactide:glycolide) fibres were prepared and are reported here for the first time. PLGA hollow fibres were produced by phase inversion with a high drug loading of 27%w. Mechanistic mathematical models were applied to the cisplatin release profiles to allow quantitative comparison of microsphere, solid fibre and hollow fibre formulations. The diffusion coefficient of cisplatin eluting from a typical batch of PLGA microspheres was 4.8 × 10(-13) cm(2) s(-1); this low diffusivity of cisplatin in microspheres was caused by the low porosity of the polymer matrix. The diffusion coefficients of cisplatin eluting from a batch of PLGA solid fibres and hollow fibres were 6.1 × 10(-10) and 3.3 × 10(-10) cm(2) s(-1), respectively. These fibres allowed the controlled release of high doses of cisplatin over four days and may represent an improvement in slow release technology for treatment of ovarian cancer.


Subject(s)
Antineoplastic Agents/administration & dosage , Cisplatin/administration & dosage , Delayed-Action Preparations/chemistry , Polyglactin 910/chemistry , Antineoplastic Agents/chemistry , Cisplatin/chemistry , Diffusion , Drug Liberation , Microspheres
13.
Am J Bot ; 102(12): 2041-57, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26643889

ABSTRACT

PREMISE OF THE STUDY: Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity. METHODS: We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM. KEY RESULTS: Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B. CONCLUSIONS: Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.


Subject(s)
Apomixis , Biological Evolution , Diploidy , Genetic Variation , Rosaceae/physiology , Chloroplast Proteins/genetics , DNA, Intergenic/genetics , Introns , Phylogeny , Plant Proteins/genetics , Rosaceae/genetics
14.
Curr Biol ; 25(3): 348-356, 2015 Feb 02.
Article in English | MEDLINE | ID: mdl-25619765

ABSTRACT

In most eukaryotes, centromeres are defined epigenetically by presence of the histone H3 variant CENP-A [1-3]. CENP-A-containing chromatin recruits the constitutive centromere-associated network (CCAN) of proteins, which in turn directs assembly of the outer kinetochore to form microtubule attachments and ensure chromosome segregation fidelity [4-6]. Whereas the mechanisms that load CENP-A at centromeres are being elucidated, the functions of its divergent N-terminal tail remain enigmatic [7-12]. Here, we employ the well-studied fission yeast centromere [13-16] to investigate the function of the CENP-A (Cnp1) N-tail. We show that alteration of the N-tail does not affect Cnp1 loading at centromeres, outer kinetochore formation, or spindle checkpoint signaling but nevertheless elevates chromosome loss. N-tail mutants exhibited synthetic lethality with an altered centromeric DNA sequence, with rare survivors harboring chromosomal fusions in which the altered centromere was epigenetically inactivated. Elevated centromere inactivation was also observed for N-tail mutants with unaltered centromeric DNA sequences. N-tail mutants specifically reduced localization of the CCAN proteins Cnp20/CENP-T and Mis6/CENP-I, but not Cnp3/CENP-C. Overexpression of Cnp20/CENP-T suppressed defects in an N-tail mutant, suggesting a link between reduced CENP-T recruitment and the observed centromere inactivation phenotype. Thus, the Cnp1 N-tail promotes epigenetic stability of centromeres in fission yeast, at least in part via recruitment of the CENP-T branch of the CCAN.


Subject(s)
Centromere/physiology , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , Epigenesis, Genetic/physiology , Schizosaccharomyces pombe Proteins/metabolism , Centromere/metabolism , Chromatin Immunoprecipitation , DNA Primers/genetics , Electrophoresis, Gel, Pulsed-Field , Fluorescence , Histones/metabolism , Immunoblotting , Mutation/genetics , Polymerase Chain Reaction , Schizosaccharomyces , Schizosaccharomyces pombe Proteins/genetics
15.
Am J Bot ; 101(8): 1375-87, 2014 Aug.
Article in English | MEDLINE | ID: mdl-25156985

ABSTRACT

UNLABELLED: • PREMISE OF THE STUDY: Amelanchier polyploid apomicts differ from sexual diploids in their more complex diversification, greater species problems, and geographic distribution. To understand these differences, we investigated the occurrence of polyploidy and frequency of apomixis. This research helps clarify species delimitation in an evolutionarily complex genus.• METHODS: We used flow cytometry to estimate genome size of 1355 plants. We estimated the frequency of apomixis from flow-cytometrically determined ploidy levels of embryo and endosperm and from a progeny study using RAPD markers. We explored relationships of triploids to other ploidy levels and of ploidy levels to latitude plus elevation.• KEY RESULTS: Diploids (32% of sample) and tetraploids (62%) were widespread. Triploids (6%) mostly occurred in small numbers with diploids from two or more species or with diploids and tetraploids. Seeds from diploids were 2% apomictic, the first report of apomixis in Amelanchier diploids. Seeds from triploids were 75% apomictic. We documented potential triploid bridge and triploid block from unbalanced endosperm and low pollen viability. Seeds from tetraploids were 97% apomictic, and tetraploids often formed microspecies. We did not find strong evidence for geographical parthenogenesis in North American Amelanchier. Most currently recognized species contained multiple ploidy levels that were morphologically semicryptic.• CONCLUSIONS: Documentation of numerous transitions from diploidy to polyploidy helps clarify diversification, geographic distribution, and the species problem in Amelanchier. Despite the infrequent occurrence of triploids, their retention of 25% sexuality and capacity for triploid bridge may be important steps between sexual diploids and predominantly apomictic tetraploids.


Subject(s)
Apomixis , Biodiversity , Genetic Speciation , Plant Dispersal , Ploidies , Rosaceae/physiology , Chromosomes, Plant , Ecosystem , Endosperm , Genome, Plant , North America , Pollen , Polyploidy , Reproduction/genetics , Rosaceae/genetics , Seeds , Species Specificity
16.
Mol Cell ; 55(2): 291-304, 2014 Jul 17.
Article in English | MEDLINE | ID: mdl-24981171

ABSTRACT

Genetic evidence has implicated multiple pathways in eukaryotic DNA mismatch repair (MMR) downstream of mispair recognition and Mlh1-Pms1 recruitment, including Exonuclease 1 (Exo1)-dependent and -independent pathways. We identified 14 mutations in POL30, which encodes PCNA in Saccharomyces cerevisiae, specific to Exo1-independent MMR. The mutations identified affected amino acids at three distinct sites on the PCNA structure. Multiple mutant PCNA proteins had defects either in trimerization and Msh2-Msh6 binding or in activation of the Mlh1-Pms1 endonuclease that initiates excision during MMR. The latter class of mutations led to hyperaccumulation of repair intermediate Mlh1-Pms1 foci and were enhanced by an msh6 mutation that disrupted the Msh2-Msh6 interaction with PCNA. These results reveal a central role for PCNA in the Exo1-independent MMR pathway and suggest that Msh2-Msh6 localizes PCNA to repair sites after mispair recognition to activate the Mlh1-Pms1 endonuclease for initiating Exo1-dependent repair or for driving progressive excision in Exo1-independent repair.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Carrier Proteins/metabolism , DNA-Binding Proteins/metabolism , Exodeoxyribonucleases/metabolism , MutS Homolog 2 Protein/metabolism , Proliferating Cell Nuclear Antigen/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , DNA Mismatch Repair , DNA, Fungal/genetics , Enzyme Activation , Models, Molecular , MutL Protein Homolog 1 , MutL Proteins , Mutation, Missense , Proliferating Cell Nuclear Antigen/chemistry , Proliferating Cell Nuclear Antigen/metabolism , Protein Binding , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Stability , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/chemistry , Signal Transduction
17.
PLoS Genet ; 10(5): e1004327, 2014 May.
Article in English | MEDLINE | ID: mdl-24811092

ABSTRACT

In Saccharomyces cerevisiae, the essential mismatch repair (MMR) endonuclease Mlh1-Pms1 forms foci promoted by Msh2-Msh6 or Msh2-Msh3 in response to mispaired bases. Here we analyzed the Mlh1-Mlh2 complex, whose role in MMR has been unclear. Mlh1-Mlh2 formed foci that often colocalized with and had a longer lifetime than Mlh1-Pms1 foci. Mlh1-Mlh2 foci were similar to Mlh1-Pms1 foci: they required mispair recognition by Msh2-Msh6, increased in response to increased mispairs or downstream defects in MMR, and formed after induction of DNA damage by phleomycin but not double-stranded breaks by I-SceI. Mlh1-Mlh2 could be recruited to mispair-containing DNA in vitro by either Msh2-Msh6 or Msh2-Msh3. Deletion of MLH2 caused a synergistic increase in mutation rate in combination with deletion of MSH6 or reduced expression of Pms1. Phylogenetic analysis demonstrated that the S. cerevisiae Mlh2 protein and the mammalian PMS1 protein are homologs. These results support a hypothesis that Mlh1-Mlh2 is a non-essential accessory factor that acts to enhance the activity of Mlh1-Pms1.


Subject(s)
Base Pair Mismatch , DNA, Fungal/genetics , Nuclear Proteins/physiology , Saccharomyces cerevisiae Proteins/physiology , Saccharomyces cerevisiae/genetics , Carrier Proteins/physiology , DNA Damage , Frameshift Mutation , MutL Proteins
18.
PLoS Genet ; 9(10): e1003869, 2013 Oct.
Article in English | MEDLINE | ID: mdl-24204293

ABSTRACT

Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Carrier Proteins/genetics , DNA Mismatch Repair/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Adaptor Proteins, Signal Transducing/metabolism , Carrier Proteins/metabolism , Catalytic Domain/genetics , Colorectal Neoplasms, Hereditary Nonpolyposis/genetics , Colorectal Neoplasms, Hereditary Nonpolyposis/pathology , DNA-Binding Proteins/genetics , Exodeoxyribonucleases/metabolism , Humans , MutL Protein Homolog 1 , MutL Proteins , Mutation , Protein Structure, Tertiary , Saccharomyces cerevisiae/growth & development , Saccharomyces cerevisiae Proteins/metabolism , Signal Transduction
19.
Nature ; 497(7447): 118-21, 2013 May 02.
Article in English | MEDLINE | ID: mdl-23604256

ABSTRACT

Accurate segregation of the replicated genome requires chromosome biorientation on the spindle. Biorientation is ensured by Aurora B kinase (Ipl1), a member of the four-subunit chromosomal passenger complex (CPC). Localization of the CPC to the inner centromere is central to the current model for how tension ensures chromosome biorientation: kinetochore-spindle attachments that are not under tension remain close to the inner centromere and are destabilized by Aurora B phosphorylation, whereas kinetochores under tension are pulled away from the influence of Aurora B, stabilizing their microtubule attachments. Here we show that an engineered truncation of the Sli15 (known as INCENP in humans) subunit of budding yeast CPC that eliminates association with the inner centromere nevertheless supports proper chromosome segregation during both mitosis and meiosis. Truncated Sli15 suppresses the deletion phenotypes of the inner-centromere-targeting proteins survivin (Bir1), borealin (Nbl1), Bub1 and Sgo1 (ref. 6). Unlike wild-type Sli15, truncated Sli15 localizes to pre-anaphase spindle microtubules. Premature targeting of full-length Sli15 to microtubules by preventing Cdk1 (also known as Cdc28) phosphorylation also suppresses the inviability of Bir1 deletion. These results suggest that activation of Aurora B kinase by clustering either on chromatin or on microtubules is sufficient for chromosome biorientation.


Subject(s)
Centromere/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Microtubule-Associated Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/metabolism , Aurora Kinase B , Aurora Kinases , CDC2 Protein Kinase/antagonists & inhibitors , CDC2 Protein Kinase/metabolism , Carrier Proteins/genetics , Carrier Proteins/metabolism , Chromatin/metabolism , Chromosome Segregation , Kinetochores/metabolism , Meiosis , Microbial Viability , Microtubule-Associated Proteins/deficiency , Microtubule-Associated Proteins/genetics , Microtubules/metabolism , Mitosis , Models, Biological , Movement , Nuclear Proteins/metabolism , Phosphorylation , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae Proteins/genetics , Sequence Deletion/genetics
20.
Dev Cell ; 25(1): 3-4, 2013 Apr 15.
Article in English | MEDLINE | ID: mdl-23597481

ABSTRACT

In this issue of Developmental Cell, Gui and Homer (2013) report that the proper execution of meiosis I in mouse oocytes requires the stabilization of cyclin B2 by the kinetochore protein Hec1, revealing unanticipated functions for both proteins.

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