Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family

Background

It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5''-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.

Results

Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5''-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.

Conclusions

Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5''-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1584-3) contains supplementary material, which is available to authorized users.     

Social influences are associated with BMI and weight loss intentions in young adults

Christakis and colleagues have shown that health behaviors cluster in social networks and suggest social norms may account for the clustering. This study examined: (i) whether obesity clusters among young adults and whether social norms do in fact account for the clustering, and (ii) among overweight/obese (OW/OB) young adults, whether number of social contacts trying to lose weight is associated with weight loss intentions and whether social norms for weight loss account for this effect. Normal weight (NW) and OW/OB young adults (N = 288; 66% female; 75% white) completed measures assessing number of OW social contacts and social norms for obesity. OW/OB young adults also indicated number of OW social contacts currently trying to lose weight, social norms for weight loss, and weight loss intentions. Compared to NW, OW/OB young adults were more likely to have OW romantic partners and best friends and had more OW casual friends and family members (Ps < 0.05), but social norms for obesity did not differ between groups, and social norms did not mediate the relationship between OW social contacts and participants' weight status. However, among OW/OB young adults, having more social contacts trying to lose weight was associated with greater intention to lose weight (r = 0.20, P = 0.02) and social norms for weight loss fully mediated this effect (P < 0.01). This study is the first to show that social contacts and normative beliefs influence weight status and intentions for weight control in young adults. Findings underscore the importance of targeting social influence in the treatment and prevention of obesity in this high-risk age group.     

Effects of low-chloride solutions on action potentials of sheep cadiac purkinje fibers

The rapid repolarization during phase 1 of the action potential of sheep cardiac purkinje fibers has been attributed to a time- and voltage-dependent chloride current. In part, this conclusion was based on experiments that showed a substantial slowing of phase 1 when larger, presumably impermeant, anions were substituted for chloride in tyrode’s solution. We have re- examined the electrical effects of low-chloride solutions. We recorded action potentials of sheep cardiac purkinje fibers in normal tyrode’s solution and in low-chloride solutions made by substituting sodium propionate, acetylglycinate, methylsulfate, or methanesulfonate for the NaCl of Tyrode’s solution. Total calcium was adjusted to keep calcium ion activity of test solutions equal to that of control solutions. Propionate gave qualitatively variable results in preliminary experiments; it was not tested further. Low-chloride solutions made with the other anions gave much more consistent results: phase 1 and the notch that often occurs between phases 1 and 2 were usually unaffected, and the action potential duration usually increased. The only apparent change in the resting potential was a transient 3-6 mV depolarization when low-chloride solution was first admitted to the chamber, and a symmetrical transient hyperpolarization when chloride was returned to normal. If a time- and voltage-dependent chloride current exists in sheep cardiac purkinje fibers, our results suggest that it plays little role in generating phase 1 of the action potential.     

Degradation of Low-Ethoxylated Nonylphenols by a Stenotrophomonas Strain and Development of New Phylogenetic Probes for Stenotrophomonas spp. Detection

An aerobic bacterium (BCc6), isolated from nonylphenol polyethoxylates (NPEOs)-contaminated sludge, was shown to be capable of degrading low-ethoxylated NPEO mixtures. Sequencing of 16S rRNA gene (rDNA) showed that it clustered with Stenotrophomonas nitritireducens. Fluorescent in situ hybridization (FISH), performed on BCc6 strain and on the previously isolated Stenotrophomonas BCaL2, also involved in NPEO degradation but clustering with S. maltophilia, showed that strain BCc6 did not hybridize with the S. maltophilia-specific probe, and neither of the two strains hybridized with probes targeted to the Gammaproteobacteria site, rDNA analyses performed on the two strains evidenced two new polymorphisms, the first one at the 23S rRNA Gammaproteobacteria site, characterizing the known members of the Stenotrophomonas genus, and the other one at the 16S rRNA level, characteristic of S. nitritireducens. Two new FISH probes were designed accordingly, tested on control bacterial cultures, and employed for in situ monitoring of Stenotrophomonas representatives.     

Hypertension, cardiovascular risk and polymorphisms in genes controlling the cytochrome P450 pathway of arachidonic acid: A sex-specific relation?

Hypertension is a multifactorial disease in which the interplay of genetic and environmental factors that maintain blood pressure stable throughout life is altered. Cytochrome P450 (CYP)-derived metabolites of arachidonic acid such as epoxyeicosatrienoic acids (EETs) and 20-hydroxyeicosatetraenoic acid (20-HETE), active on vascular tone, endothelial function and renal sodium reapportion, have been identified as candidate mediators in the development of hypertension in several animal models, with remarkable sex-specific effect. Several SNPs, some recognized as functional, in human genes implicated in EETs/20-HETE biosynthesis and metabolism, such as CYP2J2 and CYP4A11, have been tested for association with blood pressure, hypertension and its long-term cardiovascular consequences in different populations, with conflicting results. A sex-specific effect, related to CYP4F2 polymorphisms and expression, has been observed in association studies. This finding indicates that altered 20-HETE bioactivity underlay the excess of hypertension and associated vascular events observed in men with respect to women and is consistent with the results from experimental models. Further epidemiological and mechanistic studies are required to confirm the effect of lipid mediators on blood pressure in humans and define the mechanisms of a putative sex-specific effect.