Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities

The restriction-modification systems use epigenetic modification to distinguish between self and nonself DNA. A modification enzyme transfers a methyl group to a base in a specific DNA sequence while its cognate restriction enzyme introduces breaks in DNA lacking this methyl group. So far, all the restriction enzymes hydrolyze phosphodiester bonds linking the monomer units of DNA. We recently reported that a restriction enzyme (R.PabI) of the PabI superfamily with half-pipe fold has DNA glycosylase activity that excises an adenine base in the recognition sequence (5′-GTAC). We now found a second activity in this enzyme: at the resulting apurinic/apyrimidinic (AP) (abasic) site (5′-GT#C, # = AP), its AP lyase activity generates an atypical strand break. Although the lyase activity is weak and lacks sequence specificity, its covalent DNA–R.PabI reaction intermediates can be trapped by NaBH[subscript 4] reduction. The base excision is not coupled with the strand breakage and yet causes restriction because the restriction enzyme action can impair transformation ability of unmethylated DNA even in the absence of strand breaks in vitro. The base excision of R.PabI is inhibited by methylation of the target adenine base. These findings expand our understanding of genetic and epigenetic processes linking those in prokaryotes and eukaryotes

Parental satisfaction and seizure outcome after corpus callosotomy in patients with infantile or early childhood onset epilepsy

AbstractPurposeTo elucidate the benefit of corpus callosotmy in terms of parental satisfaction and seizure outcome.MethodThis study included 16 consecutive patients with infantile or early childhood onset epilepsy who underwent total corpus callosotomy for alleviation of seizures. Questionnaires were sent anonymously to the parents asking about relative changes in seizures and about parental satisfaction for the post-operative outcome.ResultsThe improvements in frequency, intensity, and duration of seizures were correlated with the level of satisfaction (Spearman's rank-order correlation coefficient, ρ=0.87, 0.93, and 0.75, respectively). The highest level of satisfaction was only seen in patients who achieved freedom from all seizures or drop attacks.ConclusionComplete seizure freedom and freedom from drop attacks are important goals of corpus callosotomy for parental satisfaction. These factors should be considered in assessing post-operative outcome after corpus callosotomy

The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

なぜ感染で死ぬのか?感染の集団生物学の「実験+数理」解析系の創出

Why do some organisms succumb and die easily when infected? Microbial infection often leads to expression of virulence and host death when symbiosis seems more beneficial for the infecting microbe\u27s maintenance. Previously proposed explanations have focused on the pathogen\u27s side. In this work, I tested a hypothesis focused on the host strategy. If a member of a host population dies immediately upon infection with a pathogen, thereby ending its reproduction, then its death could protect the host population from secondary and further infections. I tested this "Suicidal Defense Against Infection" (SDAI) hypothesis by developing an experimental infection system that involves a huge number of bacterial cells as host and their virus as pathogen and is linked to mathematical modeling. I prepared two host strains, one with the SDAI strategy (type A) and the other without (type S), mixed them at varying ratios, challenged them with the pathogen and monitored any change in the ratio during infection. I used two conditions for infection: standing solid agar providing spatial structure, thereby ensuring that individuals preferentially interact with their neighbors, and well-mixed liquid lacking spatial structure. I found that the SDAI strategy has great advantage in the presence of spatial structure: Pathogen increase was accompanied by a large increase in the A:S ratio. In contrast, there was a decrease in the A:S ratio in the absence of spatial structure. My simulation reproduced the essential features of the experimental results. These results provide a new perspective for understanding host-pathogen interaction.University of Tokyo (東京大学

Higher methylation subtype of malignant melanoma and its correlation with thicker progression and worse prognosis

Abstract Malignant melanoma (MM) is the most life‐threatening disease among all skin malignancies, and recent genome‐wide studies reported BRAF, RAS, and NF1 as the most frequently mutated driver genes. While epigenetic aberrations are known to contribute to the oncogenic activity seen in various cancers, their role in MM has not been fully investigated. To investigate the role of epigenetic aberrations in MM, we performed genome‐wide DNA methylation analysis of 51 clinical MM samples using Infinium 450k beadarray. Hierarchical clustering analysis stratified MM into two DNA methylation epigenotypes: high‐ and low‐methylation subgroups. Tumor thickness was significantly greater in case of high‐methylation tumors than low‐methylation tumors (8.3 ± 5.3 mm vs 4.5 ± 2.9 mm, P = .003). Moreover, prognosis was significantly worse in high‐methylation cases (P = .03). Twenty‐seven genes were found to undergo significant and frequent hypermethylation in high‐methylation subgroup, where TFPI2 was identified as the most frequently hypermethylated gene. MM cases with lower expression levels of TFPI2 showed significantly worse prognosis (P = .001). Knockdown of TFPI2 in two MM cell lines, CHL‐1 and G361, resulted in significant increases of cell proliferation and invasion. These indicate that MM can be stratified into at least two different epigenetic subgroups, that the MM subgroup with higher DNA methylation shows a more progressive phenotype, and that methylation of TFPI2 may contribute to the tumor progression of MM

A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands.

Genomes of a given bacterial species can show great variation in gene content and thus systematic analysis of the entire gene repertoire, termed the pan-genome, is important for understanding bacterial intra-species diversity, population genetics, and evolution. Here, we analyzed the pan-genome from 30 completely sequenced strains of the human gastric pathogen Helicobacter pylori belonging to various phylogeographic groups, focusing on 991 accessory (not fully conserved) orthologous groups (OGs). We developed a method to evaluate the mobility of genes within a genome, using the gene order in the syntenically conserved regions as a reference, and classified the 991 accessory OGs into five classes: Core, Stable, Intermediate, Mobile, and Unique. Phylogenetic networks based on the gene content of Core and Stable classes are highly congruent with that created from the concatenated alignment of fully conserved core genes, in contrast to those of Intermediate and Mobile classes, which show quite different topologies. By clustering the accessory OGs on the basis of phylogenetic pattern similarity and chromosomal proximity, we identified 60 co-occurring gene clusters (CGCs). In addition to known genomic islands, including cag pathogenicity island, bacteriophages, and integrating conjugative elements, we identified some novel ones. One island encodes TerY-phosphorylation triad, which includes the eukaryote-type protein kinase/phosphatase gene pair, and components of type VII secretion system. Another one contains a reverse-transcriptase homolog, which may be involved in the defense against phage infection through altruistic suicide. Many of the CGCs contained restriction-modification (RM) genes. Different RM systems sometimes occupied the same (orthologous) locus in the strains. We anticipate that our method will facilitate pan-genome studies in general and help identify novel genomic islands in various bacterial species

Pan-genome and core genome among <i>Helicobacter pylori</i>.

<p>(A) Histogram showing the distribution of the number of strains in each OG among the 30 strains. Sets of OGs corresponding to pan-genome, universal core, accessory, and unique OGs are indicated. (B) Sizes of the syntenic core, universal core, and pan-genome as functions of the number of strains. An ordered lists of the 30 strains was randomly generated and the sets of <i>n</i> strains (<i>n</i> = 2,4,…,30) generated from this list was subject to core- and pan-genome analysis. The test was repeated 20 times and the average numbers of core- and pan-genome sizes were plotted with error bars that represent standard deviations. Syntenic core between two genomes is not well defined and thus is not plotted. (C) The number of new OGs added to the pan-genome as a function of the number of strains. The number of new OG in <i>n</i> strains (<i>n</i> = 4,6,…,30) was calculated as the difference between the pan-genome size in <i>n</i> strains and that in <i>n–</i> 2 strains.</p

Co-occurring gene clusters (CGCs).

<p>(A) The 60 CGCs ordered according to the cluster size (the number of OGs included). An occurrence pattern represents presence/absence of CGC in each strain where a large box indicates that the strain contains all OGs in the CGC and a small box indicates that the strain contains only part of the OGs. In the occurrence pattern, strains are ordered in the same way as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159419#pone.0159419.s006" target="_blank">S1 Table</a> and colors are assigned according to the phylogeographical groups in the same way as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159419#pone.0159419.g004" target="_blank">Fig 4</a>. (B-F) The five largest CGCs displayed on the RECOG system. (B) CGC-1 corresponding to <i>cag</i> pathogenicity island; (C) CGC-2 corresponding to a part of bacteriophage 1961P; (D) CGC-3 containing protein kinase C and protein phosphatase C2 homologs; (E) CGC-4 corresponding to a part of ICE containing type IV secretion system; (F) CGC-5 corresponding to a part of bacteriophage 1961P. The left part shows a hierarchical clustering tree based on the occurrence pattern similarity. The central part shows occurrence patterns, where the order of strains is same as in (A), and the colors are assigned according to the neighboring clustering, i.e., the cells filled in the same color in each column contain genes that are closely located on the chromosome (here, we used 8000 bp window for the neighborhood criterion). Enlarged figures B-F are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159419#pone.0159419.s001" target="_blank">S1 Fig</a>.</p