Novel ovine polymorphisms and adaptive evolution in mammalian TLR2 suggest existence of multiple pathogen binding regions

Toll-like receptors initiate inflammatory responses following the recognition of a wide repertoire of pathogens including bacteria, fungi, protozoa and viruses. They are composed of an extracellular leucine-rich repeat domain responsible for detecting pathogen-associated molecular patterns, a membrane spanning region and an intracellular Toll/Interleukin 1 receptor domain which invokes signal transduction. Toll-like receptor 2 is the most diverse of these receptors as it recognises infectious agents from a range of pathogenic groups. Over 1400 breeds of sheep exist worldwide that inhabit a diverse range of environments, which leads to the potential contact with a wide variety of pathogens likely detected by Toll-like receptor 2. In this study, we evaluated the extent of both long term evolutionary changes, across the mammalian phylogeny of the TLR2 gene, and recent divergence of this same gene in sheep breeds. Evolutionary analyses identified positive selective pressure across the mammalian phylogeny, and differential selection pressure within the artiodactyl and primate lineage. Finally, we identified localised positively-selected sites within two regions of the extracellular domain which suggest that multiple binding regions in TLR2 may be involved in pathogen detection. These results are consistent with the hypothesis that competition between host and pathogen is driving adaptation of Toll-like receptor 2 genes.     

Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: Resolving the taxonomic affiliation of the Cicer canariense rhizobia

Cicer canariense is a wild chickpea that can be nodulated by Mesorhizobium strains belonging to nine different genomic groups or genospecies. In this study, multilocus sequence analysis (MLSA) of seven protein-coding genes, recA, glnII, dnaK, rpoB, gyrB, truA and thrA, was used to resolve the phylogenetic relationships and taxonomic affiliation of 27 representative strains from all the genotypes. Individual phylogenies were mostly congruent, although there were a few discrepancies. Some genes were more discriminative than others, but concatenation of the seven genes produced a robust phylogeny of the genus Mesorhizobium. MLSA gave good support for the taxonomic affiliations of most of the genomic groups to previously recognized species and delineated several potential new species. Five genospecies found in C. canariense nodules showed average nucleotide identity values for seven genes (ANIg7) of >96% and they could be assigned to previously described Mesorhizobium species. Two large closely related genomic groups had M. caraganae as the closest species and they shared ANIg7 values in the 94–95% range, suggesting that they could be different subspecies or sister species. The predominant genospecies represented a novel monophyletic lineage that was well resolved from all currently recognized species of Mesorhizobium, with the highest ANIg7 below 92%. Other single strains represented potential new species.     

Development of inhibitors of heterotrimeric Gαi subunits

Heterotrimeric G-proteins are the immediate downstream effectors of G-protein coupled receptors (GPCRs). Endogenous protein guanine nucleotide dissociation inhibitors (GDIs) like AGS3/4 and RGS12/14 function through GPR/Goloco GDI domains. Extensive characterization of GPR domain peptides indicate they function as selective GDIs for Gα_i by competing for the GPCR and Gβγ and preventing GDP release. We modified a GPR consensus peptide by testing FGF and TAT leader sequences to make the peptide cell permeable. FGF modification inhibited GDI activity while TAT preserved GDI activity. TAT-GPR suppresses G-protein coupling to the receptor and completely blocked α₂-adrenoceptor (α₂AR) mediated decreases in cAMP in HEK293 cells at 100 nM. We then sought to discover selective small molecule inhibitors for Gα_i. Molecular docking was used to identify potential molecules that bind to and stabilize the Gα_i–GDP complex by directly interacting with both Gα_i and GDP. Gα_i–GTP and Gα_q–GDP were used as a computational counter screen and Gα_q–GDP was used as a biological counter screen. Thirty-seven molecules were tested using nucleotide exchange. STD NMR assays with compound 0990, a quinazoline derivative, showed direct interaction with Gα_i. Several compounds showed Gα_i specific inhibition and were able to block α₂AR mediated regulation of cAMP. In addition to being a pharmacologic tool, GDI inhibition of Gα subunits has the advantage of circumventing the upstream component of GPCR-related signaling in cases of overstimulation by agonists, mutations, polymorphisms, and expression-related defects often seen in disease.     

亚甲基四氢叶酸还原酶(C677/T)基因的单核苷酸多态性

亚甲基四氢叶酸还原酶(methylene tetrahydrofolatucte redase,MTHFR)是叶酸代谢过程中的关键酶,对叶酸和同型半胱氨酸的代谢以及DNA的合成、修复与甲基化均有重要作用。MTHFR基因变异导致酶热稳定性及活性降低,引起相关代谢及DNA甲基化异常,进而发生相关疾病。MTHFR具有多种变异型,本文对其中常见的一种C677T的多态性及其与疾病的相关性的研究进展做一综述。     

LINE-1 methylation in granulocyte DNA and trihalomethane exposure is associated with bladder cancer risk

DNA methylation changes contribute to bladder carcinogenesis. Trihalomethanes (THM), a class of disinfection by-products, are associated with increased urothelial bladder cancer (UBC) risk. THM exposure in animal models produces DNA hypomethylation. We evaluated the relationship of LINE-1 5-methylcytosine levels (LINE-1%5mC) as outcome of long-term THM exposure among controls and as an effect modifier in the association between THM exposure and UBC risk. We used a case-control study of UBC conducted in Spain. We obtained personal lifetime residential THM levels and measured LINE-1%5mC by pyrosequencing in granulocyte DNA from blood samples in 548 incident cases and 559 hospital controls. Two LINE-1%5mC clusters (above and below 64%) were identified through unsupervised hierarchical cluster analysis. The association between THM levels and LINE-1%5mC was evaluated with β regression analyses and logistic regression was used to estimate odds ratios (OR) adjusting for covariables. LINE-1%5mC change between percentiles 75^th and 25^th of THM levels was 1.8% (95% confidence interval (CI): 0.1, 3.4%) among controls. THM levels above vs. below the median (26 μg/L) were associated with increased UBC risk, OR = 1.86 (95% CI: 1.25, 2.75), overall and among subjects with low levels of LINE-1%5mC (n = 975), OR = 2.14 (95% CI: 1.39, 3.30), but not associated with UBC risk among subjects’ high levels of LINE-1%5mC (n = 162), interaction P = 0.03. Results suggest a positive association between LINE-1%5mC and THM levels among controls, and LINE-1%5mC status may modify the association between UBC risk and THM exposure. Because reverse causation and chance cannot be ruled out, confirmation studies are warranted.     

Investigation of bacterial nucleotide excision repair using single-molecule techniques

Despite three decades of biochemical and structural analysis of the prokaryotic nucleotide excision repair (NER) system, many intriguing questions remain with regard to how the UvrA, UvrB, and UvrC proteins detect, verify and remove a wide range of DNA lesions. Single-molecule techniques have begun to allow more detailed understanding of the kinetics and action mechanism of this complex process. This article reviews how atomic force microscopy and fluorescence microscopy have captured new glimpses of how these proteins work together to mediate NER.     

The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation?

The first eukaryotic NER factor that recognizes NER substrates is the heterodimeric XPC-RAD23B protein. The currently accepted hypothesis is that this protein recognizes the distortions/destabilization caused by DNA lesions rather than the lesions themselves. The resulting XPC-RAD23B–DNA complexes serve as scaffolds for the recruitment of subsequent NER factors that lead to the excision of the oligonucleotide sequences containing the lesions. Based on several well-known examples of DNA lesions like the UV radiation-induced CPD and 6–4 photodimers, as well as cisplatin-derived intrastrand cross-linked lesions, it is generally believed that the differences in excision activities in human cell extracts is correlated with the binding affinities of XPC-RAD23B to these DNA lesions. However, using electrophoretic mobility shift assays, we have found that XPC-RAD23B binding affinities of certain bulky lesions derived from metabolically activated polycyclic aromatic hydrocarbon compounds such as benzo[a]pyrene and dibenzo[a,l]pyrene, are not directly, or necessarily correlated with NER excision activities observed in cell-free extracts. These findings point to features of XPC-RAD23B–bulky DNA adduct complexes that may involve the formation of NER-productive or unproductive forms of binding that depend on the structural and stereochemical properties of the DNA adducts studied. The pronounced differences in NER cleavage efficiencies observed in cell-free extracts may be due to differences in the successful recruitment of subsequent NER factors by the XPC-RAD23B–DNA adduct complexes, and/or in the verification step. These phenomena appear to depend on the structural and conformational properties of the class of bulky DNA adducts studied.     

A C. elegans homolog of the Cockayne syndrome complementation group A gene

Cockayne syndrome (CS) is a debilitating and complex disorder that results from inherited mutations in the CS complementation genes A and B, CSA and CSB. The links between the molecular functions of the CS genes and the complex pathophysiology of CS are as of yet poorly understood and are the subject of intense debate. While mouse models reflect the complexity of CS, studies on simpler genetic models might shed new light on the consequences of CS mutations. Here we describe a functional homolog of the human CSA gene in Caenorhabditis elegans. Similar to its human counterpart, mutations in the nematode csa-1 gene lead to developmental growth defects as a consequence of DNA lesions.     

Genetic risk variants for dyslexia on chromosome 18 in a German cohort

Dyslexia is characterized by impaired reading and spelling. The disorder has a prevalence of about 5% in Germany, and a strong hereditary component. Several loci are thought to be involved in the development of dyslexia. Scerri et al. identified eight potential dyslexia‐associated single nucleotide polymorphisms (SNPs) in seven genes on chromosome 18 in an English‐speaking population. Here, we present an association analysis that explores the relevance of these SNPs in a German population comprising 388 dyslexia cases and 364 control cases. In case–control analysis, three nominal SNP associations were replicated. The major alleles of NEDD4L‐rs12606138 and NEDD4L‐rs8094327 were risk associated [odds ratio (OR) = 1.35, 95% confidence interval (CI) = 1.0–1.7, P‐value = 0.017 and OR = 1.39, 95% CI = 1.1–1.7, P‐value = 0.007, respectively], and both SNPs were in strong linkage disequilibrium (r² = 0.95). For MYO5B‐rs555879, the minor allele was risk associated (OR = 1.31, 95% CI = 1.1–1.6, P‐value = 0.011). The combined analysis of SNP sets using set enrichment analysis revealed a study‐wide significant association for three SNPs with susceptibility for dyslexia. In summary, our results substantiate genetic markers in NEDD4L and MYO5B as risk factors for dyslexia and provide first evidence that the relevance of these markers is not restricted to the English language .     

Mining the 30UTR of Autism-implicated Genes for SNPs Perturbing MicroRNA Regulation

Autism spectrum disorder（ASD） refers to a group of childhood neurodevelopmental disorders with polygenic etiology. The expression of many genes implicated in ASD is tightly regulated by various factors including microRNAs（miRNAs）, a class of noncoding RNAs 22 nucleotides in length that function to suppress translation by pairing with ‘miRNA recognition elements’（MREs） present in the 30untranslated region（30UTR） of target mRNAs. This emphasizes the role played by miRNAs in regulating neurogenesis, brain development and differentiation and hence any perturbations in this regulatory mechanism might affect these processes as well. Recently, single nucleotide polymorphisms（SNPs） present within 30UTRs of mRNAs have been shown to modulate existing MREs or even create new MREs. Therefore, we hypothesized that SNPs perturbing miRNA-mediated gene regulation might lead to aberrant expression of autism-implicated genes, thus resulting in disease predisposition or pathogenesis in at least a subpopulation of ASD individuals. We developed a systematic computational pipeline that integrates data from well-established databases. By following a stringent selection criterion, we identified 9 MRE-modulating SNPs and another 12 MRE-creating SNPs in the 30UTR of autism-implicated genes. These high-confidence candidate SNPs may play roles in ASD and hence would be valuable for further functional validation.