Holocarboxylase synthetase (HCS) catalyzes the binding of the vitamin biotin to histones H3 and H4, thereby creating rare histone biotinylation marks in the epigenome. These marks co-localize with ...K9-methylated histone H3 (H3K9me), an abundant gene repression mark. The abundance of H3K9me marks in transcriptionally competent loci decreases when HCS is knocked down and when cells are depleted of biotin. Here we tested the hypothesis that the creation of H3K9me marks is at least partially explained by physical interactions between HCS and histone-lysine N-methyltransferases. Using a novel in silico protocol, we predicted that HCS-interacting proteins contain a GGGG(K/R)G(I/M)R motif. This motif, with minor variations, is present in the histone-lysine N-methyltransferase EHMT1. Physical interactions between HCS and the N-terminal, ankyrin and SET domains in EHMT1 were confirmed using yeast-two-hybrid assays, limited proteolysis assays and co-immunoprecipitation. The interactions were stronger between HCS and the N-terminus in EHMT1 compared with the ankyrin and SET domains, consistent with the localization of the HCS-binding motif in the EHMT1 N-terminus. HCS has the catalytic activity to biotinylate K161 within the binding motif in EHMT1. Mutation of K161 weakened the physical interaction between EHMT1 and HCS, but it is unknown whether this effect was caused by loss of biotinylation or loss of the motif. Importantly, HCS knockdown decreased the abundance of H3K9me marks in repeats, suggesting that HCS plays a role in creating histone methylation marks in these loci. We conclude that physical interactions between HCS and EHMT1 mediate epigenomic synergies between biotinylation and methylation events.
Agricultural soils constitute highly diverse ecosystems with very rich bacterial populations. Recent studies employing next-generation sequencing techniques have begun to explore the dynamics of ...bacterial species of such soils and utilized metagenomics approaches to understand how the diversity in soil microorganisms is affected or modified by agricultural practices. Understanding any microorganism's environmental adaptability in the genomic era starts by fully appreciating their encoding genome. Here, we report the draft genome sequences of three Devosia species based on three type strains that originated from soil samples: D. insulae strain DS-56, D. limi strain DSM17137, and D. soli strain GH2-10.
Lactobacillus paracasei subsp. tolerans, isolated from a traditional sourdough bread culture and previously shown to have antifungal activity against Fusarium species, was tested for inhibition of ...growth of Fusarium proliferatum M 5991 and M 5689 and F. graminearum R 4053 in a liquid medium setting. This isolate completely inhibited the growth of F. proliferatum M 5689 and M 5991 and F. graminearum R 4053, whereas such growth was not inhibited in the control in a supernatant agar plate assay. When this isolate was tested using 2M medium (MRS-modified Myro media) known for supporting Fusarium growth and trichothecene production, it was found to inhibit fungal growth but promote mycotoxin production at the same time. The antifungal activity was determined to be the result of organic acids and low pH. The mechanism of the mycotoxin production promotion requires further investigation.
Here we report the draft genome of Devosia sp. strain 17-2-E-8, isolated from Ontario agricultural soil (Canada) with promising deoxynivalenol biotransformation capabilities. In addition, we report ...the draft genome of Devosia riboflavina strain IFO13584, used as a control strain in our studies aimed at highlighting unique gene clusters involved in deoxynivalenol epimerization.
Holocarboxylase synthetase (HCS) catalyzes the binding of biotin to lysines in carboxylases and histones in two steps. First, HCS catalyzes the synthesis of biotinyl-5′-AMP; second, the biotinyl ...moiety is ligated to lysine residues. It has been proposed that step two is fairly promiscuous, and that protein biotinylation may occur in the absence of HCS as long as sufficient exogenous biotinyl-5′-AMP is provided. Here, we identified a novel polypeptide (Syn67) with a basic patch of lysines and arginines. Yeast-two-hybrid assays and limited proteolysis assays revealed that both N- and C-termini of HCS interact with Syn67. A potential target lysine in Syn67 was biotinylated by HCS only after arginine-to-glycine substitutions in Syn67 produced a histone-like peptide. We identified a Syn67 docking site near the active pocket of HCS by
in silico modeling and site-directed mutagenesis. Biotinylation of proteins by HCS is more specific than previously assumed.
Online Tools for Bioinformatics Analyses in Nutrition Sciences Malkaram, Sridhar A.; Hassan, Yousef I.; Zempleni, Janos
Advances in nutrition (Bethesda, Md.),
September 2012, 2012-Sep-01, 2012-09-00, 20120901, Letnik:
3, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Recent advances in “omics” research have resulted in the creation of large datasets that were generated by consortiums and centers, small datasets that were generated by individual investigators, and ...bioinformatics tools for mining these datasets. It is important for nutrition laboratories to take full advantage of the analysis tools to interrogate datasets for information relevant to genomics, epigenomics, transcriptomics, proteomics, and metabolomics. This review provides guidance regarding bioinformatics resources that are currently available in the public domain, with the intent to provide a starting point for investigators who want to take advantage of the opportunities provided by the bioinformatics field.
Holocarboxylase synthetase (HCS) mediates the binding of biotin to lysine (K) residues in histones H2A, H3 and H4; HCS knockdown disturbs gene regulation and decreases stress resistance and lifespan ...in eukaryotes. We tested the hypothesis that HCS interacts physically with histone H3 for subsequent biotinylation. Co-immunoprecipitation experiments were conducted and provided evidence that HCS co-localizes with histone H3 in human cells; physical interactions between HCS and H3 were confirmed using limited proteolysis assays. Yeast two-hybrid (Y2H) studies revealed that the N-terminal and C-terminal domains in HCS participate in H3 binding. Recombinant human HCS was produced and exhibited biological activity, as evidenced by biotinylation of its known substrate, recombinant p67. Recombinant histone H3.2 and synthetic H3-based peptides were also good targets for biotinylation by recombinant HCS (rHCS) in vitro, based on tracing histone-bound biotin with ³Hbiotin, streptavidin and anti-biotin antibody. Biotinylation site-specific antibodies were generated and revealed that both K9 and K18 in H3 were biotinylated by HCS. Collectively, these studies provide conclusive evidence that HCS interacts directly with histone H3, causing biotinylation of K9 and K18. We speculate that the targeting of HCS to distinct regions in human chromatin is mediated by DNA sequence, biotin, RNA, epigenetic marks or chromatin proteins.
Next-generation sequencing (NGS) technologies are increasingly being used by microbiologists for characterizing bacterial isolates. A draft genome can now be obtained within a few days. With the ...recent technological advancements in NGS, the affordability and feasibility of this technique promises to redirect such tasks from research laboratories to the daily practices of clinical and environmental microbiology laboratories in the near future. This short technical note will introduce the average microbiologist, who may have only limited knowledge of NGS technologies, to the most commonly used platforms currently on the market. The advantages and disadvantages of each platform and the technical-terminology essential to navigate the planning phase of any bacterial genome assembly are also highlighted.
Aluminium (Al) has been proposed as an environmental factor that may contribute to some diseases, affect several enzymes and other biomolecules and induced free radical-mediated cytotoxicity. Also, ...Al induced reproductive toxicity and exerted a significant adverse effect on the steroidogenesis. The antioxidant ascorbic acid (AA) plays an important role in various physiological processes in the body including detoxification of different toxic materials. Therefore, the present investigation aimed to elucidate possible protective effects of AA in alleviating the toxicity of aluminium chloride (AlCl
3) on reproductive performance, lipid peroxidation and enzyme activities in seminal plasma of male New Zealand white rabbits. Six rabbits per group were assigned to one of four treatment groups: 0
mg AA and 0
mg AlCl
3/kg body weight (BW) (control); 40
mg AA/kg BW; 34
mg AlCl
3/kg BW; 34
mg AlCl
3 plus 40
mg AA/kg BW. Rabbits were orally administered their respective doses every other day for 16 weeks. Results obtained showed that AlCl
3 significantly (
P
<
0.05) decreased libido (by increasing the reaction time), ejaculate volume, sperm concentration, total sperm output, sperm motility (%), total motile sperm per ejaculate (TMS), packed sperm volume (PSV), total functional sperm fraction (TFSF), normal and live sperm and semen initial fructose. While initial hydrogen ion concentration (pH) and dead and abnormal sperm were increased (
P
<
0.05). Live body weight (LBW), feed intake (FI) and relative weights of testes (RTW) and epididymis (REW) were significantly (
P
<
0.05) decreased. Concentrations of thiobarbituric acid-reactive substances (TBARS) were significantly (
P
<
0.05) increased in seminal plasma of rabbits treated with AlCl
3 compared with control. While, activities of glutathione
S-transferase (GST), aspartate aminotransferase (AST), alanine aminotransferase (ALT) and acid phosphatase (AcP) were significantly (
P
<
0.05) decreased. Ascorbic acid alone significantly increased LBW, FI, RTW, REW, semen characteristics and seminal plasma enzymes, and decreased the levels of free radicals. Also, the present study showed that ascorbic acid might be effective in the protection of aluminium-induced reproductive toxicity. It was suggested that AlCl
3 exerted a significant adverse effect on reproductive performance of male rabbits. Furthermore, AA could be able to antagonize the toxic effects of AlCl
3 and improved semen quality of male rabbit.
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