Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase

Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased k_cat and reduced K_m relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (K_m) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation. Figure Electrostatic isosurfaces of cod uracil DNA glycosylase in complex with double stranded DNA     

DNA Replication and Cell Cycle Progression Regulatedby Long Range Interaction between Protein Complexes bound to DNA

A nonstationary interaction that controlsDNA replication and the cell cycle isderived from many-body physics in achemically open T cell. The model predictsa long range force F() =– (/2) (1 – )(2 – )between thepre-replication complexes (pre-RCs) boundby the origins in DNA, = /N being the relativedisplacement of pre-RCs, the number of pre-RCs, Nthe number of replicons to be replicated,and the compressibilitymodulus in the lattice of pre-RCs whichbehaves dynamically like an elasticallybraced string. Initiation of DNAreplication is induced at the threshold = N by a switch ofsign of F'(), fromattraction (–) and assembly in the G ₁ phase (0<<N), to repulsion (+) and partialdisassembly in the S phase (N< < 2N), withrelease of licensing factors from pre-RCs,thus explaining prevention ofre-replication. Replication is terminatedby a switch of sign of force at = 2N, from repulsion inS phase back to attraction in G ₂, when all primed replicons havebeen duplicated once. F(0) = 0corresponds to a resting cell in theabsence of driving force at = 0. The model thus ensures that the DNAcontent in G ₂ cells is exactlytwice that of G ₁ cells. The switch of interaction at the R-point, at which N pre-RCs have been assembled, starts the release of Rb protein thus also explaining the shift in the Rb phosphorylation from mitogen-dependent cyclinD to mitogen-independent cyclin E.Shape,slope and scale of the response curvesderived agree well with experimental datafrom dividing T cells and polymerising MTs,the variable length of which is due to anonlinear dependence of the growthamplitude on the initial concentrations oftubulin dimers and guanosine-tri-phosphate(GTP). The model also explains the dynamic instabilityin growing MTs.     

Gene expression and DNA methylation analyses suggest that immune process-related ADCY6 is a prognostic factor of luminal-like breast cancer

Breast cancer is a malignant tumor that seriously threatens women's health, and luminal-like cancer subtypes account for the majority of the cases. The purpose of this study was to investigate the relationships among DNA methylation, gene expression profile, and the tumor-immune microenvironment of luminal-like breast cancer, and to identify the potential key genes that regulate immune cell infiltration in luminal-like breast cancer. The ESTIMATE algorithm was applied to calculate immune scores and stromal scores of patients with breast cancer. Kaplan-Meier curves were generated for survival analysis. The clusterProfile package was used for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Correlations between ADCY6 expression and immune cell infiltration-related pathways were analyzed by gene set variation analysis. R software was used for the statistical analysis and figure generation. Disease-free survival was higher in the immune score-high group than it was in the immune score-low group, while the stromal score had no correlation with prognosis. There were 515 genes that differed in both gene expression and DNA methylation levels, and these genes were mainly enriched in immune process-related pathways. ADCY6 was enriched in module A of the PPI network. Patients with downregulation and hypermethylation of ADCY6 associated with a better prognosis. ADCY6 expression was negatively correlated with the activation of immune process-related signaling pathways, immune checkpoint receptors, and ligands, except for CLEC4G. DNA methylation was found to be involved in the regulation of the key cellular pathways of luminal-like breast cancer immune cell infiltration. Additionally, ADCY6 was identified as a prognostic factor involved in the DNA methylation-regulated immune processes in luminal-like breast cancer.     

Restriction fragment length polymorphisms in mitochondrial DNA and ribosomal RNA gene complexes as an aid to the characterization of species and sub-species populations in the genus Verticillium

Abstract Genomic DNA was extracted from seven species of Verticillium and digested with the restriction endonucleases Eco RI or Hae III. Hybridization with an homologous V. albo-atrum ribosomal RNA gene probe revealed restriction fragment length polymorphisms (RFLPs) which could differentiate V. lateritium, V. lecanii, V. nigrescens, V. nubilum and V. tricorpus . Digestion with Eco RI did not provide RFLPs which could distinguish between V. albo-atrum and V. dahliae . Digestion of genomic and mitochondrial DNA with Hae III showed distinctive patterns on ethidium bromide gels which allowed each species to be distinguished. Some intra-species variation in patterns occurred and a combination of mitochondrial and ribosomal RNA gene complex RFLPs has potential as an aid for the characterization of species and sub-species populations in the genes Verticillium .     

Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies

Understanding the dynamics of biodiversity, including the spatial distribution of genetic diversity, is critical for predicting responses to environmental changes, as well as for effective conservation measures. This task requires tracking changes in biodiversity at large spatial scales and correlating with species functional traits. We provide three comprehensive resources to understand the determinants for mitochondrial DNA differentiation represented by (a) 15,609 COI sequences and (b) 14 traits belonging to 307 butterfly species occurring in Western‐Central Europe and (c) the first multi‐locus phylogenetic tree of all European butterfly species. By applying phylogenetic regressions we show that mitochondrial DNA spatial differentiation (as measured with G_ST, G′_ST, D and D_ST) is negatively correlated with species traits determining dispersal capability and colonization ability. Thanks to the high spatial resolution of the COI data, we also provide the first zoogeographic regionalization maps based on intraspecific genetic variation. The overall pattern obtained by averaging the spatial differentiation of all Western‐Central European butterflies shows that the paradigm of long‐term glacial isolation followed by rapid pulses of post‐glacial expansion has been a pervasive phenomenon in European butterflies. The results and the extensive data sets we provide here constitute the basis for genetically‐informed conservation plans for a charismatic group in a continent where flying insects are under alarming decline.     

Development of PCR-based chloroplast DNA markers that characterize domesticated cowpea (Vigna unguiculata ssp. unguiculata var. unguiculata) and highlight its crop-weed complex

In 1992, Vaillancourt and Weeden discovered a very important mutation for studying cowpea evolution and domestication. A loss of a BamHI restriction site in chloroplast DNA characterized all domesticated accessions and a few wild (Vigna unguiculata ssp. unguiculata var. spontanea) accessions. In order to screen a larger number of accessions, primers were designed to check this mutation using PCR RFLP or direct PCR methods. Using these new primers, 54 domesticated cowpea accessions and 130 accessions from the wild progenitor were screened. The absence of haplotype 0 was confirmed within domesticated accessions, including primitive landraces from cultivar-groups Biflora and Textilis, suggesting that this mutation occurred prior to domestication. However, 40 var. spontanea accessions distributed from Senegal to Tanzania and South Africa showed haplotype 1. Whereas this marker could not be used to identify a precise center of origin, it did highlight the widely distributed cowpea crop-weed complex. Its very high frequency in West Africa could be interpreted as a result of either genetic swamping of the wild/weedy gene pool by the domesticated cowpea gene pool or as the result of domestication by ethnic groups focusing primarily on cowpea as fodder.     

The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr

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