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.     

Randomized trial on 14 versus 7 days of esomeprazole, moxifloxacin, and amoxicillin for second-line or rescue treatment of Helicobacter pylori infection

Background: Triple therapy with a proton pump inhibitor, moxifloxacin, and amoxicillin has been proven effective in first‐line treatment of Helicobacter pylori infection. Aim: To explore 1, the value of triple therapy with esomeprazole, moxifloxacin, and amoxicillin in second‐line or rescue treatment of Caucasian patients and 2, the impact of treatment duration on eradication success. Methods: H. pylori‐infected patients with at least one previous treatment failure were randomized to oral esomeprazole 20 mg b.i.d., moxifloxacin 400 mg o.d., and amoxicillin 1000 mg b.i.d. for either 7 (EMA‐7) or 14 days (EMA‐14). Eradication was confirmed by 13C urea breath test. Antimicrobial susceptibility testing was performed in all patients at baseline and in patients who failed treatment. Results: Eighty patients were randomized, and 60% had ≥2 previous treatment failures. Pretreatment resistance against clarithromycin and metronidazole was found in 70.5 and 61.5% of cases, respectively. The intention‐to‐treat eradication rate was significantly higher after EMA‐14 compared with EMA‐7 (95.0 vs 78.9%, p = .036). No independent risk factor for treatment failure could be identified. There were no serious adverse events. Five of the EMA‐14 patients (12.5%) compared with none of the EMA‐7 patients discontinued prematurely because of adverse events (p = .031). Post‐treatment resistance against moxifloxacin was found in one of seven patients with isolated organisms (14.3%). Conclusion: Second‐line/rescue H. pylori eradication therapy with esomeprazole, moxifloxacin, and amoxicillin is very effective and well tolerated. Fourteen days of treatment significantly increase the eradication rate but also the rate of adverse events.     

Exertional rhabdomyolysis in an adolescent athlete during preseason conditioning: a perfect storm

Cleary, MA, Sadowski, KA, Lee, SY-C, Miller, GL, and Nichols, AW. Exertional rhabdomyolysis in an adolescent athlete during preseason conditioning: a perfect storm. J Strength Cond Res 25(12): 3506-3513, 2011-The purpose of this brief review is to present a case of a healthy, male adolescent athlete (age = 16 years, body mass = 67.9 kg, height = 165.5 cm) who participated in a 3-day preseason wrestling camp which resulted in hospitalization for exertional rhabdomyolysis. As part of the preseason conditioning program directed by the coaches, the athlete completed 60 minutes of short, intense intervals of wall-sits, squats, sit-ups, push-ups, lunges, and plyometric jumps. The following day, the athlete continued his vigorous training consisting of running drills. That night he noticed voiding dark brown urine the color of cola. The day after the camp ended, the athlete reported to his Athletic Trainers with the chief complaint of severe bilateral leg pain in his quadriceps. Two days after the initial assessment, he was admitted to the hospital where he was diagnosed with exertional rhabdomyolysis based on creatine kinase (CK) levels that peaked at 146,000 IU·L, elevated far beyond normal (normal range = 58-280 IU·L). The athlete was hospitalized for 6 days where he received intravenous normal saline for rehydration, and his CK levels were assessed daily. Athletic Trainers, personal trainers, physical education teachers, and coaches should be aware that exertional rhabdomyolysis is the most common form of rhabdomyolysis and affects individuals who participate in novel and intense exercise to which they are unaccustomed. Stressful ambient conditions may lead to dehydration and exacerbation of the condition, particularly when the individual is not accustomed to the exercise intensity.     

The seated medicine ball throw as a test of upper body power in older adults

Practitioners training the older adult may benefit from a low-cost, easy-to-administer field test of upper body power. This study evaluated validity and reliability of the seated medicine ball throw (SMBT) in older adults. Subjects (n = 33; age 72.4 ± 5.2 years) completed 6 trials of an SMBT in each of 2 testing days and 2 ball masses (1.5 and 3.0 kg). Subjects also completed 6 trials of an explosive push-up (EPU) on a force plate over 2 testing days. Validity was assessed via a Pearson Product-Moment correlation (PPM) between SMBT and EPU maximal vertical force. Reliability of the SMBT was determined using PPMs (r), Intraclass correlation (ICC, R) and Bland-Altman plots (BAPs). For validity, the association between the SMBT and the EPU revealed a PPM of r = 0.641 and r = 0.614 for the 1.5- and 3.0-kg medicine balls, respectively. Test-retest reliability of the 1.5- and 3.0-kg SMBT was r = 0.967 and r = 0.958, respectively. The ICC values of the 1.5- and 3.0-kg SMBT were R = 0.994 and 0.989, respectively. The BAPs revealed 94% of the differences between day 1 and 2 scores were within the 95% confidence interval of the mean difference. Test-retest reliability for the EPU was r = 0.944, R = 0.969. The BAPs showed 94% of the differences between day 1 and 2 scores were within the 95% confidence interval of the mean difference, for both medicine ball throws. In conclusion, for the older adult, the SMBT appears to be highly reliable test of upper body power. Its validity relative to the maximal force exerted during the EPU is modest. The SMBT is an inexpensive, safe, and repeatable measure of upper body power for the older adult.     

A web of imprinting in stem cells

Imprinted genes are the prototypical epigenetically regulated genes. On the basis of findings in adult lung stem cells, Zacharek et?al. (2011) suggest in this issue of Cell Stem Cell that epigenetic silencing of imprinted genes is a common requirement for maintaining self-renewal in adult stem cell populations.     

Examining the evidence for chytridiomycosis in threatened amphibian species

Extinction risks are increasing for amphibians due to rising threats and minimal conservation efforts. Nearly one quarter of all threatened/extinct amphibians in the IUCN Red List is purportedly at risk from the disease chytridiomycosis. However, a closer look at the data reveals that Batrachochytrium dendrobatidis (the causal agent) has been identified and confirmed to cause clinical disease in only 14% of these species. Primary literature surveys confirm these findings; ruling out major discrepancies between Red List assessments and real-time science. Despite widespread interest in chytridiomycosis, little progress has been made between assessment years to acquire evidence for the role of chytridiomycosis in species-specific amphibian declines. Instead, assessment teams invoke the precautionary principle when listing chytridiomycosis as a threat. Precaution is valuable when dealing with the world's most threatened taxa, however scientific research is needed to distinguish between real and predicted threats in order to better prioritize conservation efforts. Fast paced, cost effective, in situ research to confirm or rule out chytridiomycosis in species currently hypothesized to be threatened by the disease would be a step in the right direction. Ultimately, determining the manner in which amphibian conservation resources are utilized is a conversation for the greater conservation community that we hope to stimulate here.     

Water availability alters the tri-trophic consequences of a plant-fungal symbiosis

Plant–microbe protection symbioses occur when a symbiont defends its host against enemies (e.g., insect herbivores); these interactions can have important influences on arthropod abundance and composition. Understanding factors that generate context-dependency in protection symbioses will improve predictions on when and where symbionts are most likely to affect the ecology and evolution of host species and their associated communities. Of particular relevance are changes in abiotic contexts that are projected to accompany global warming. For example, increased drought stress can enhance the benefits of fungal symbiosis in plants, which may have multi-trophic consequences for plant-associated arthropods. Here, we tracked colonization of fungal endophyte-symbiotic and aposymbiotic Poa autumnalis (autumn bluegrass) by Rhopalosiphum padi (bird-cherry-oat aphids) and their parasitoids (Aphelinus sp.) following manipulations of soil water levels. Endophyte symbiosis significantly reduced plant colonization by aphids. Under low water, symbiotic plants also supported a significantly higher proportion of aphids that were parasitized by Aphelinus and had higher above-ground biomass than aposymbiotic plants, but these endophyte-mediated effects disappeared under high water. Thus, the multi-trophic consequences of plant-endophyte symbiosis were contingent on the abiotic context, suggesting the potential for complex responses in the arthropod community under future climate shifts.     

Serum uric acid and coronary heart disease in 9,458 incident cases and 155,084 controls: prospective study and meta-analysis

BackgroundIt has been suggested throughout the past fifty years that serum uric acid concentrations can help predict the future risk of coronary heart disease (CHD), but the epidemiological evidence is uncertain.ConclusionsMeasurement of serum uric acid levels is unlikely to enhance usefully the prediction of CHD, and this factor is unlikely to be a major determinant of the disease in general populations.     

Ethanol synthesis and aerobic respiration in the laboratory by leader segments of Douglas-fir seedlings from winter and spring

Stem segments from terminal leaders of Douglas-fir, Pseudotsuga menziesii (Mirb.) Franco, seedlings were sampled in mid-December when cambial cells were dormant. The residual, debudded leaders were resampled again in early May when the cambium was metabolically active. May stems had higher constitutive ethanol concentrations than December stems. This was not the result of cambial hypoxia generated by rapid spring respiration rates, because when aerobic respiration was stimulated by incubating the stems in air at 30 degrees C ethanol production was induced in December, but not in May. Rapid respiration rates at 30 degrees C may have depleted O(2) supplies and induced ethanol production in December stems because dormant, thick-walled cambial cells may be less permeable to CO(2) and O(2), compared with metabolically active, thin-walled cambial cells in May. December stem segments incubated in a N(2) atmosphere at 30 degrees C synthesized 1.8 times more ethanol than segments from May, most likely because spring growth had reduced the soluble sugars available for fermentation. CO(2) efflux from May stems (after 5.5 h of incubation at 30 degrees C) was equal to December stems per unit volume, but greater than December stems per unit surface area. N(2)-induced ethanol concentrations were positively related with CO(2) efflux per unit volume, indicating that rapidly respiring leaders can maintain rapid fermentation rates, provided soluble sugars are readily available. N(2)-induced ethanol and CO(2) efflux per unit volume declined with increasing leader diameter in both seasons, whereas there were no relationships between CO(2) efflux per unit surface area and diameter. Cambium physiology and phenology influence the induction of fermentation and concentrations of ethanol produced in terminal leaders of Douglas-fir, and probably other conifers as well. This needs to be considered when comparing fermentation among species, or comparing individuals from different seasons, or disparate ages within a species.