Methylation potential associated with diet,genotype, protein,and metabolite levels in the Delta Obesity Vitamin Study

Micronutrient research typically focuses on analyzing the effects of single or a few nutrients on health by analyzing a limited number of biomarkers. The observational study described here analyzed micronutrients, plasma proteins, dietary intakes, and genotype using a systems approach. Participants attended a community-based summer day program for 6–14 year old in 2 years. Genetic makeup, blood metabolite and protein levels, and dietary differences were measured in each individual. Twenty-four-hour dietary intakes, eight micronutrients (vitamins A, D, E, thiamin, folic acid, riboflavin, pyridoxal, and pyridoxine) and 3 one-carbon metabolites [homocysteine (Hcy), S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH)], and 1,129 plasma proteins were analyzed as a function of diet at metabolite level, plasma protein level, age, and sex. Cluster analysis identified two groups differing in SAM/SAH and differing in dietary intake patterns indicating that SAM/SAH was a potential marker of nutritional status. The approach used to analyze genetic association with the SAM/SAH metabolites is called middle-out: SNPs in 275 genes involved in the one-carbon pathway (folate, pyridoxal/pyridoxine, thiamin) or were correlated with SAM/SAH (vitamin A, E, Hcy) were analyzed instead of the entire 1M SNP data set. This procedure identified 46 SNPs in 25 genes associated with SAM/SAH demonstrating a genetic contribution to the methylation potential. Individual plasma metabolites correlated with 99 plasma proteins. Fourteen proteins correlated with body mass index, 49 with group age, and 30 with sex. The analytical strategy described here identified subgroups for targeted nutritional interventions.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-014-0403-9) contains supplementary material, which is available to authorized users.     

Adenosine analogue inhibitors of S-adenosylhomocysteine hydrolase

Elevated plasma homocysteine (Hcy) levels are an independent risk factor for the onset and progression of Alzheimer’s disease. Reduction of Hcy to normal levels therefore presents a new approach for disease modification. Hcy is produced by the cytosolic enzyme S-adenosylhomocysteine hydrolase (AHCY), which converts S-adenosylhomocysteine (SAH) to Hcy and adenosine. Herein we describe the design and characterization of novel, substrate-based S-adenosylhomocysteine hydrolase inhibitors with low nanomolar potency in vitro and robust activity in vivo.     

Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response

The bacterial stringent response involves wide-ranging metabolic reprogramming aimed at increasing long-term survivability during stress conditions. One of the hallmarks of the stringent response is the production of a set of modified nucleotides, known as alarmones, which affect a multitude of cellular pathways in diverse ways. Production and degradation of these molecules depend on the activity of enzymes from the RelA/SpoT homologous family, which come in both bifunctional (containing domains to both synthesize and hydrolyze alarmones) and monofunctional (consisting of only synthetase or hydrolase domain) variants, of which the structure, activity, and regulation of the bifunctional RelA/SpoT homologs have been studied most intensely. Despite playing an important role in guanosine nucleotide homeostasis in particular, mechanisms of regulation of the small alarmone hydrolases (SAHs) are still rather unclear. Here, we present crystal structures of SAH enzymes from Corynebacterium glutamicum (RelH_Cg) and Leptospira levettii (RelH_Ll) and show that while being highly similar, structural differences in substrate access and dimer conformations might be important for regulating their activity. We propose that a varied dimer form is a general property of the SAH family, based on current structural information as well as prediction models for this class of enzymes. Finally, subtle structural variations between monofunctional and bifunctional enzymes point to how these different classes of enzymes are regulated.     

How Different Dietary Methionine Sources Could Modulate the Hepatic Metabolism in Rainbow Trout?

In aquafeeds in which plant proteins are used to replace fishmeal, exogenous methionine (Met) sources are demanded to balance the amino acid composition of diets and meet the metabolic fish requirements. Nonetheless, since different synthetic Met sources are commercially available, it is important to determine their bioavailability and efficacy. To address this issue, we conducted a two-month feeding trial with rainbow trout (Oncorhynchus mykiss), which were fed diets supplemented with five different forms of Met: Met-Met, L-Met, HMTBa, DL-Met, and Co DL-Met. No differences in growth performance were found in trout fed with different Met forms, but changes in the whole-body composition were found. In particular, Met-Met and L-Met promoted a significant body lipid reduction, whereas the protein retention was significantly increased in fish fed with HMTBa and Co DL-Met. The latter affected the hepatic Met metabolism promoting the trans-sulfuration pathway through the upregulation of CBS gene expression. Similarly, the L-Met enhanced the remethylation pathway through an increase in BHMT gene expression to maintain the cellular demand for Met. Altogether, our findings suggest an optimal dietary intake of all tested Met sources with similar promoting effects on fish growth and hepatic Met metabolism. Nevertheless, the mechanisms underlying these effects warrant further investigation.     

Evidence that a cAMP binding protein from Dictyostelium discoideum carries S-adenosyl-L-homocysteine hydrolase activity

A cAMP-adenosine binding protein partially purified from exponentially growing Dictyostelium discoideum cells carries S-adenosyl-L-homocysteine (SAH) hydrolase activity. This protein is present throughout the developmental cycle and has many properties in common with a cAMP binding activity previously reported from this laboratory (Gunzburg and Véron, 1981). Direct binding measurements with radioactive ligands indicate a dissociation constant of 0.2 microM for adenosine and 9 nM for cAMP, a value in good agreement with measurements of the rate constants for cAMP binding (k+1 = 2.4 X 10(4) M-1 sec-1) and dissociation (k-1 = 1.1 X 10(-4) sec-1). The binding of cAMP is completely abolished in the presence of 1 microM adenosine; a maximum 60 per cent inhibition of adenosine binding can be achieved with cAMP concentrations as high as 0.1 microM, suggesting that at least some of the cAMP and adenosine binding sites are not identical. The protein has a sedimentation coefficient of 9.2S and a native molecular weight of 190,000, as judged by gel filtration. Labeling with the photoaffinity ligand 8-azido-[3H]-cAMP followed by SDS polyacrylamide gel electrophoresis results in a single band of 47,000 MW, suggesting that the protein may be a tetramer. The physiological importance of the protein and its association with SAH hydrolase activity is discussed in relation to a possible role in the regulation of protein and phospholipid methylation that occurs during chemotaxis.     

Homocysteine and lipids: S-Adenosyl methionine as a key intermediate

An association between hyperlipidemia and hyperhomocysteinemia (HHCY) has been suggested. This link is clinically important in management of vascular risk factors especially in elderly people and patients with metabolic syndrome. Higher plasma homocysteine (Hcy) was associated with lower high-density lipoprotein (HDL)-cholesterol level. Moreover, HHCY was associated with disturbed plasma lipids or fatty liver. It seems that hypomethylation associated with HHCY is responsible for lipid accumulation in tissues. Decreased methyl group will decrease the synthesis of phosphatidylcholine, a major phospholipid required for very low-density lipoprotein (VLDL) assembly and homeostasis. The effect of Hcy on HDL-cholesterol is probably related to inhibiting enzymes or molecules participating in HDL-particle assembly.     

Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-Å X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-Å improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.     

Antifungal antibiotics and Siba inhibit 1-aminocyclopropane-1-carboxylic acid synthase activity

The antifungal antibiotics Sinefungin and A9145C isolated from Streptomyces griseolus and the synthetic nucleoside Siba, which are analogs of S-adenosylmethionine, inhibit the activity of 1-aminocyclopropane 1-carboxylic acid synthase from tomato fruits. Sinefungin and Siba were shown to be more potent inhibitors than A9145C. In extracts of green fruits, the enzyme activity was inhibited by Sinefungin with an I50 of 1 microM, which was similar to that caused by aminoethoxyvinylglycine, and by Siba with an I50 of 100 microM; in extracts from red tomatoes, the I50's were 25 microM and 100 microM, respectively. The inhibition of ACC synthase by these analogs could be reversed by gel filtration chromatography.