-GlcNAc is a regulatory post-translational modification of nucleocytoplasmic proteins that has been implicated in multiple biological processes, including transcription. In humans, single genes encode enzymes for its attachment (-GlcNAc transferase (OGT)) and removal (-GlcNAcase (OGA)). An X-chromosome exome screen identified a missense mutation, which encodes an amino acid in the tetratricopeptide repeat, in (759G>T (p.L254F)) that segregates with X-linked intellectual disability (XLID) in an affected family. A decrease in steady-state OGT protein levels was observed in isolated lymphoblastoid cell lines from affected individuals, consistent with molecular modeling experiments. Recombinant expression of L254F-OGT demonstrated that the enzyme is active as both a glycosyltransferase and an HCF-1 protease. Despite the reduction in OGT levels seen in the L254F-OGT individual cells, we observed that steady-state global-GlcNAc levels remained grossly unaltered. Surprisingly, lymphoblastoids from affected individuals displayed a marked decrease in steady-state OGA protein and mRNA levels. We observed an enrichment of the OGT-containing transcriptional repressor complex mSin3A-HDAC1 at the proximal promoter region of and correspondingly decreased promoter activity in affected cells. Global transcriptome analysis of L254F-OGT lymphoblastoids compared with controls revealed a small subset of genes that are differentially expressed. Thus, we have begun to unravel the molecular consequences of the 759G>T (p.L254F) mutation in that uncovered a compensation mechanism, albeit imperfect, given the phenotype of affected individuals, to maintain steady-state-GlcNAc levels. Thus, a single amino acid substitution in the regulatory domain (the tetratricopeptide repeat domain) of OGT, which catalyzes the -GlcNAc post-translational modification of nuclear and cytosolic proteins, appears causal for XLID.

Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility and its recognition by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full nucleosome, totaling 65 microseconds of molecular dynamics simulations. We observe rapid conformational transitions between tail bound and unbound states, and characterize kinetic and thermodynamic properties of histone tail-DNA interactions. Different histone types exhibit distinct binding modes to specific DNA regions. Using a comprehensive set of experimental nucleosome complexes, we find that the majority of them target mutually exclusive regions with histone tails on nucleosomal/linker DNA around the super-helical locations ± 1, ± 2, and ± 7, and histone tails H3 and H4 contribute most to this process. These findings are explained within competitive binding and tail displacement models. Finally, we demonstrate the crosstalk between different histone tail post-translational modifications and mutations; those which change charge, suppress tail-DNA interactions and enhance histone tail dynamics and DNA accessibility.

Supplementary data are available at Bioinformatics online.

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A method based on capillary electrophoresis with electrochemical detection has been developed to analyze flavonoids and phenolic acids in Perilla frutescens L. for the first time. Catechin, ferulic acid, apigenin, luteolin, rosmarinic acid, and caffeic acid are major important active ingredients in the plant. Operated in a wall-jet configuration, a 300 microm diameter carbon-disk electrode was used as the working electrode, which exhibits a good response at 0.90 V (versus saturated calomel electrode) for the analytes. Under the optimum conditions, the analytes were baseline separated within 20 min in a 100 mmol/L borax buffer (pH 8.7). Notably, excellent linearity was obtained over 3 orders of magnitude with detection limits (S/N = 3) ranging from 2 x 10(-7) to 1 x 10(-6) g/mL for all analytes. This proposed method has been successfully applied to monitor the flavonoids and phenolic acids contents in the leaves and seeds of P. frutescens L. at different growth stages with relatively simple extraction procedures, and the assay results were satisfactory.

Single amino acid variations (SAV) occurring in human population result in natural differences between individuals or cause diseases. It is well understood that the molecular effect of SAV can be manifested as changes of the wild type characteristics of the corresponding protein, among which are the protein stability and protein interactions. Typically the effect of SAV on protein stability and interactions is assessed via the changes of the wild type folding and binding free energies. However, in terms of SAV affecting protein functionally and disease susceptibility, one wants to know to what extend the wild type function is perturbed by the SAV. Here we demonstrate that relative, rather than the absolute, change of the folding and binding free energy serves as a good indicator for SAV association with disease. Using HumVar as a source for disease-causing SAV and experimentally determined free energy changes from ProTherm and SKEMPI databases, we achieved correlation coefficients (CC) between the disease index (Pd) and relative folding ( Ppr,f and binding ( Ppr,b) probability indexes, respectively. The obtained CCs demonstrate the applicability of the proposed approach and serves as good indicators for SAV association with disease.

No abstract

Supplementary data are available at Bioinformatics online.