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Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability.
Wanzek K, Schwindt E, Capra JA, Paeschke K
(2017) Nucleic Acids Res 45: 7796-7806
MeSH Terms: Binding Sites, Cell Cycle, Cullin Proteins, DNA Helicases, DNA Replication, DNA, Fungal, Endodeoxyribonucleases, Exodeoxyribonucleases, G-Quadruplexes, GC Rich Sequence, Genomic Instability, Models, Biological, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins
Show Abstract · Added March 14, 2018
The regulation of replication is essential to preserve genome integrity. Mms1 is part of the E3 ubiquitin ligase complex that is linked to replication fork progression. By identifying Mms1 binding sites genome-wide in Saccharomyces cerevisiae we connected Mms1 function to genome integrity and replication fork progression at particular G-rich motifs. This motif can form G-quadruplex (G4) structures in vitro. G4 are stable DNA structures that are known to impede replication fork progression. In the absence of Mms1, genome stability is at risk at these G-rich/G4 regions as demonstrated by gross chromosomal rearrangement assays. Mms1 binds throughout the cell cycle to these G-rich/G4 regions and supports the binding of Pif1 DNA helicase. Based on these data we propose a mechanistic model in which Mms1 binds to specific G-rich/G4 motif located on the lagging strand template for DNA replication and supports Pif1 function, DNA replication and genome integrity.
© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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14 MeSH Terms
Endogenous Hot Spots of De Novo Telomere Addition in the Yeast Genome Contain Proximal Enhancers That Bind Cdc13.
Obodo UC, Epum EA, Platts MH, Seloff J, Dahlson NA, Velkovsky SM, Paul SR, Friedman KL
(2016) Mol Cell Biol 36: 1750-63
MeSH Terms: Binding Sites, DNA Breaks, Double-Stranded, DNA Repair, DNA, Fungal, Enhancer Elements, Genetic, Genome, Fungal, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Telomerase, Telomere, Telomere-Binding Proteins
Show Abstract · Added April 8, 2019
DNA double-strand breaks (DSBs) pose a threat to genome stability and are repaired through multiple mechanisms. Rarely, telomerase, the enzyme that maintains telomeres, acts upon a DSB in a mutagenic process termed telomere healing. The probability of telomere addition is increased at specific genomic sequences termed sites of repair-associated telomere addition (SiRTAs). By monitoring repair of an induced DSB, we show that SiRTAs on chromosomes V and IX share a bipartite structure in which a core sequence (Core) is directly targeted by telomerase, while a proximal sequence (Stim) enhances the probability of de novo telomere formation. The Stim and Core sequences are sufficient to confer a high frequency of telomere addition to an ectopic site. Cdc13, a single-stranded DNA binding protein that recruits telomerase to endogenous telomeres, is known to stimulate de novo telomere addition when artificially recruited to an induced DSB. Here we show that the ability of the Stim sequence to enhance de novo telomere addition correlates with its ability to bind Cdc13, indicating that natural sites at which telomere addition occurs at high frequency require binding by Cdc13 to a sequence 20 to 100 bp internal from the site at which telomerase acts to initiate de novo telomere addition.
Copyright © 2016, American Society for Microbiology. All Rights Reserved.
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MeSH Terms
Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe.
Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF
(2013) DNA Repair (Amst) 12: 196-204
MeSH Terms: Amino Acid Sequence, Apurinic Acid, Catalytic Domain, Crystallography, X-Ray, DNA Damage, DNA Glycosylases, DNA, Fungal, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, Protein Binding, Protein Structure, Secondary, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Surface Properties
Show Abstract · Added March 7, 2014
Schizosaccharomyces pombe contains two paralogous proteins, Mag1 and Mag2, related to the helix-hairpin-helix (HhH) superfamily of alkylpurine DNA glycosylases from yeast and bacteria. Phylogenetic analysis of related proteins from four Schizosaccharomyces and other fungal species shows that the Mag1/Mag2 duplication is unique to the genus Schizosaccharomyces and most likely occurred in its ancestor. Mag1 excises N3- and N7-alkylguanines and 1,N(6)-ethenoadenine from DNA, whereas Mag2 has been reported to have no detectible alkylpurine base excision activity despite high sequence and active site similarity to Mag1. To understand this discrepancy we determined the crystal structure of Mag2 bound to abasic DNA and compared it to our previously determined Mag1-DNA structure. In contrast to Mag1, Mag2 does not flip the abasic moiety into the active site or stabilize the DNA strand 5' to the lesion, suggesting that it is incapable of forming a catalytically competent protein-DNA complex. Subtle differences in Mag1 and Mag2 interactions with the DNA duplex illustrate how Mag2 can stall at damage sites without fully engaging the lesion. We tested our structural predictions by mutational analysis of base excision and found a single amino acid responsible at least in part for Mag2's lack of activity. Substitution of Mag2 Asp56, which caps the helix at the base of the DNA intercalation loop, with the corresponding serine residue in Mag1 endows Mag2 with ɛA excision activity comparable to Mag1. This work provides novel insight into the chemical and physical determinants by which the HhH glycosylases engage DNA in a catalytically productive manner.
Copyright © 2012 Elsevier B.V. All rights reserved.
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16 MeSH Terms
Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.
Adhikary S, Eichman BF
(2011) EMBO Rep 12: 1286-92
MeSH Terms: Adenine, Alkylation, Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, DNA Glycosylases, DNA Repair, DNA, Fungal, Molecular Sequence Data, Nucleic Acid Conformation, Purines, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Substrate Specificity
Show Abstract · Added March 7, 2014
DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N(6)-ethenoadenine (ɛA) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their ɛA activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.
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14 MeSH Terms
Peripheral blood eosinophilia as a clue to the diagnosis of an occult Coccidioides infection.
Simons CM, Stratton CW, Kim AS
(2011) Hum Pathol 42: 449-53
MeSH Terms: Aged, Antifungal Agents, Antigens, Fungal, Coccidioides, Coccidioidomycosis, DNA, Fungal, Eosinophilia, Fluconazole, Humans, Lung Diseases, Fungal, Male, Radiography, Thoracic, Treatment Outcome
Show Abstract · Added May 28, 2014
A marked peripheral blood eosinophilia is an uncommon finding in a complete blood count (CBC). According to Wardlaw and Kay (Eosinophils and Their Disorders. In: Beutler E, Lichtman MA, Coller BS, Kipps TJ, Seligsohn U, editors. Williams Hematology. 6(th) ed. New York: McGraw-Hill, 2001. p. 790-93), the most common causes are infection by helminthic parasites, atopic disease, and, less commonly, primary hypereosinophilic syndromes. Therefore, when eosinophilia is seen in a CBC, it can provide an important clue to the correct diagnosis. We present a case of a patient with a finding of pulmonary nodules in the setting of cancer and a CBC finding of profound peripheral blood eosinophilia. As a result of the high level of clinical suspicion for Coccidioides infection due in part to the eosinophilia, adequate steps were taken in the clinical laboratory not only to correctly diagnosis the patient, but also to protect the laboratory staff from work-related exposure to this easily aerosolizable infectious agent.
Copyright © 2011 Elsevier Inc. All rights reserved.
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13 MeSH Terms
Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi.
Slot JC, Rokas A
(2011) Curr Biol 21: 134-9
MeSH Terms: Aspergillus nidulans, DNA, Fungal, Expressed Sequence Tags, Gene Transfer, Horizontal, Multigene Family, Phylogeny, Podospora, Sterigmatocystin
Show Abstract · Added May 30, 2014
Genes involved in intermediary and secondary metabolism in fungi are frequently physically linked or clustered. For example, in Aspergillus nidulans the entire pathway for the production of sterigmatocystin (ST), a highly toxic secondary metabolite and a precursor to the aflatoxins (AF), is located in a ∼54 kb, 23 gene cluster. We discovered that a complete ST gene cluster in Podospora anserina was horizontally transferred from Aspergillus. Phylogenetic analysis shows that most Podospora cluster genes are adjacent to or nested within Aspergillus cluster genes, although the two genera belong to different taxonomic classes. Furthermore, the Podospora cluster is highly conserved in content, sequence, and microsynteny with the Aspergillus ST/AF clusters and its intergenic regions contain 14 putative binding sites for AflR, the transcription factor required for activation of the ST/AF biosynthetic genes. Examination of ∼52,000 Podospora expressed sequence tags identified transcripts for 14 genes in the cluster, with several expressed at multiple life cycle stages. The presence of putative AflR-binding sites and the expression evidence for several cluster genes, coupled with the recent independent discovery of ST production in Podospora [1], suggest that this HGT event probably resulted in a functional cluster. Given the abundance of metabolic gene clusters in fungi, our finding that one of the largest known metabolic gene clusters moved intact between species suggests that such transfers might have significantly contributed to fungal metabolic diversity. PAPERFLICK:
Copyright © 2011 Elsevier Ltd. All rights reserved.
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8 MeSH Terms
G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.
Capra JA, Paeschke K, Singh M, Zakian VA
(2010) PLoS Comput Biol 6: e1000861
MeSH Terms: Base Sequence, Conserved Sequence, DNA Breaks, Double-Stranded, DNA, Fungal, G-Quadruplexes, Genome, Fungal, Markov Chains, Models, Genetic, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, Saccharomyces cerevisiae, Sequence Analysis, DNA, Yeasts
Show Abstract · Added April 18, 2017
G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs) across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs). Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.
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14 MeSH Terms
Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi.
Slot JC, Rokas A
(2010) Proc Natl Acad Sci U S A 107: 10136-41
MeSH Terms: Ascomycota, Base Sequence, Biological Evolution, Candida, Cryptococcus, DNA, Fungal, Evolution, Molecular, Fungi, Galactose, Gene Transfer, Horizontal, Genes, Fungal, Models, Genetic, Multigene Family, Phylogeny, Saccharomyces, Schizosaccharomyces
Show Abstract · Added May 30, 2014
A notable characteristic of fungal genomes is that genes involved in successive steps of a metabolic pathway are often physically linked or clustered. To investigate how such clusters of functionally related genes are assembled and maintained, we examined the evolution of gene sequences and order in the galactose utilization (GAL) pathway in whole-genome data from 80 diverse fungi. We found that GAL gene clusters originated independently and by different mechanisms in three unrelated yeast lineages. Specifically, the GAL cluster found in Saccharomyces and Candida yeasts originated through the relocation of native unclustered genes, whereas the GAL cluster of Schizosaccharomyces yeasts was acquired through horizontal gene transfer from a Candida yeast. In contrast, the GAL cluster of Cryptococcus yeasts was assembled independently from the Saccharomyces/Candida and Schizosaccharomyces GAL clusters and coexists in the Cryptococcus genome with unclustered GAL paralogs. These independently evolved GAL clusters represent a striking example of analogy at the genomic level. We also found that species with GAL clusters exhibited significantly higher rates of GAL pathway loss than species with unclustered GAL genes. These results suggest that clustering of metabolic genes might facilitate fungal adaptation to changing environments both through the acquisition and loss of metabolic capacities.
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16 MeSH Terms
The diversity and evolution of circadian clock proteins in fungi.
Salichos L, Rokas A
(2010) Mycologia 102: 269-78
MeSH Terms: Amino Acid Sequence, Base Sequence, CLOCK Proteins, Circadian Rhythm, Conserved Sequence, DNA, Fungal, Evolution, Molecular, Genetic Variation, Genome, Fungal, Molecular Sequence Data, Neurospora, Phylogeny, Sequence Alignment
Show Abstract · Added May 30, 2014
Circadian rhythms are endogenous cellular patterns that associate multiple physiological and molecular functions with time. The Neurospora circadian system contains at least three oscillators: the FRQ/WC-dependent circadian oscillator (FWO), whose core components are the FRQ, WC-1, WC-2, FRH, and FWD-1 proteins; the WC-dependent circadian oscillator (WC-FLO); and one or more FRQ/ WC-independent oscillators (FLO). Little is known about the distribution of homologs of the Neurospora clock proteins or about the molecular foundations of circadian rhythms across fungi. Here, we examined 64 diverse fungal proteomes for homologs of all five Neurospora clock proteins and retraced their evolutionary history. The FRH and FWD-1 proteins were likely present in the fungal ancestor. WC-1 and WC-2 homologs are absent from the early diverging chytrids and Microsporidia but are present in all other major clades. In contrast to the deep origins of these four clock proteins FRQ homologs are taxonomically restricted within Sordariomycetes, Leotiomycetes and Dothideomycetes. The large number of FRH and FWD-1 homologs identified and their lack of concordance with the fungal species phylogeny indicate that they likely underwent multiple rounds of duplications and losses. In contrast, the FRQ, WC-1 and WC-2 proteins exhibit relatively few duplications and losses. A notable exception is the 10 FRQ-like proteins in Fusarium oxysporum, which resulted from nine duplication events. Our results suggest that the machinery required for FWO oscillator function is taxonomically restricted within Ascomycetes. Although the WC proteins are widely distributed, the functional diversity of the few non-Neurospora circadian oscillators suggests that a WC-FLO oscillator is unlikely to fully explain the observed rhythms. The contrast between the diversity of circadian oscillators and the conservation of most of their machinery is likely best explained by considering the centrality of noncircadian functions in which RNA helicase (FRH), F-box (FWD-1), WC-1 and WC-2 (light-sensing) proteins participate in fungi and eukaryotes.
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13 MeSH Terms
Ty3 nuclear entry is initiated by viruslike particle docking on GLFG nucleoporins.
Beliakova-Bethell N, Terry LJ, Bilanchone V, DaSilva R, Nagashima K, Wente SR, Sandmeyer S
(2009) J Virol 83: 11914-25
MeSH Terms: Adaptor Proteins, Signal Transducing, DNA, Fungal, Long Interspersed Nucleotide Elements, Nuclear Pore, Nuclear Pore Complex Proteins, PDZ Domains, RNA-Directed DNA Polymerase, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins
Show Abstract · Added March 21, 2014
Yeast retrotransposons form intracellular particles within which replication occurs. Because fungal nuclear membranes do not break down during mitosis, similar to retroviruses infecting nondividing cells, the cDNA produced must be translocated through nuclear pore complexes. The Saccharomyces cerevisiae long terminal repeat retrotransposon Ty3 assembles its Gag3 and Gag3-Pol3 precursor polyproteins into viruslike particles in association with perinuclear P-body foci. These perinuclear clusters of Ty3 viruslike particles localized to sites of clustered nuclear pore complexes (NPCs) in a nup120Delta mutant, indicating that Ty3 particles and NPCs interact physically. The NPC channels are lined with nucleoporins (Nups) with extended FG (Phe-Gly) motif repeat domains, further classified as FG, FxFG, or GLFG repeat types. These domains mediate partitioning of proteins between the cytoplasm and the nucleus. Here we have systematically examined the requirements for FG repeat domains in Ty3 nuclear transport. The GLFG domains interacted in vitro with virus-like particle Gag3, and this interaction was disrupted by mutations in the amino-terminal domain of Gag3, which is predicted to lie on the external surface of the particles. Accordingly, Ty3 transposition was decreased in strains with the GLFG repeats deleted. The spacer-nucleocapsid domain of Gag3, which is predicted to be internal to the particle, interacted with GLFG repeats and nucleocapsid localized to the nucleus. We conclude that Ty3 particle docking on nuclear pores is facilitated by interactions between Gag3 and GLFG Nups and that nuclear entry of the preintegration complex is further promoted by nuclear localization signals within the nucleocapsid and integrase.
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9 MeSH Terms