Datamining approaches for examining the low prevalence of N-acetylglutamate synthase deficiency and understanding transcriptional regulation of urea cycle genes

Ammonia, which is toxic to the brain, is converted into non-toxic urea, through a pathway of six enzymatically catalyzed steps known as the urea cycle. In this pathway, N-acetylglutamate synthase (NAGS, EC 2.3.1.1) catalyzes the formation of N-acetylglutamate (NAG) from glutamate and acetyl coenzyme A. NAGS deficiency (NAGSD) is the rarest of the urea cycle disorders, yet is unique in that ureagenesis can be restored with the drug N-carbamylglutamate (NCG). We investigated whether the rarity of NAGSD could be due to low sequence variation in the NAGS genomic region, high NAGS tolerance for amino acid replacements, and alternative sources of NAG and NCG in the body. We also evaluated whether the small genomic footprint of the NAGS catalytic domain might play a role. The small number of patients diagnosed with NAGSD could result from the absence of specific disease biomarkers and/or short NAGS catalytic domain. We screened for sequence variants in NAGS regulatory regions in patients suspected of having NAGSD and found a novel NAGS regulatory element in the first intron of the NAGS gene. We applied the same datamining approach to identify regulatory elements in the remaining urea cycle genes. In addition to the known promoters and enhancers of each gene, we identified several novel regulatory elements in their upstream regions and first introns. The identification of cis-regulatory elements of urea cycle genes and their associated transcription factors holds promise for uncovering shared mechanisms governing urea cycle gene expression and potentially leading to new treatments for urea cycle disorders.

Denitrification and N2O Emission in Estuarine Sediments in Response to Ocean Acidification: From Process to Mechanism

Global estuarine ecosystems are experiencing severe nitrogen pollution and ocean acidification (OA) simultaneously. Sedimentary denitrification is an important way of reactive nitrogen removal but at the same time leads to the emission of large amounts of nitrous oxide (N₂O), a potent greenhouse gas. It is known that OA in estuarine regions could impact denitrification and N₂O production; however, the underlying mechanism is still underexplored. Here, sediment incubation and pure culture experiments were conducted to explore the OA impacts on microbial denitrification and the associated N₂O emissions in estuarine sediments. Under neutral (in situ) conditions, fungal N₂O emission dominated in the sediment, while the bacterial and fungal sources had a similar role under acidification. This indicated that acidification decreased the sedimentary fungal denitrification and likely inhibited the activity of fungal denitrifiers. To explore molecular mechanisms, a denitrifying fungal strain of Penicillium janthinellum was isolated from the sediments. By using deuterium-labeled single-cell Raman spectroscopy and isobaric tags for relative and absolute quantitation proteomics, we found that acidification inhibited electron transfers in P. janthinellum and downregulated expressions of the proteins related to energy production and conservation. Two collaborative pathways of energy generation in the P. janthinellum were further revealed, that is, aerobic oxidative phosphorylation and TCA cycle and anoxic pyruvate fermentation. This indicated a distinct energy supply strategy from bacterial denitrification. Our study provides insights into fungi-mediated nitrogen cycle in acidifying aquatic ecosystems.

Denitrification and Nitrogen Burial in Swiss Lakes

Earth's nitrogen (N) cycle is imbalanced because of excessive anthropogenic inputs. Freshwater lakes efficiently remove N from surface waters by transformation of NO₃^- to atmospheric N₂ and/or N₂O (denitrification; DN) and by burial of organic N in sediments (net sedimentation; NS). However, relatively little is known about the controlling environmental conditions, and few long-term measurements on individual lakes are available to quantify conversion rates. We report N-elimination rates in 21 Swiss lakes estimated from whole-lake N budgets covering up to ∼20 years of monitoring. The NO₃^- concentration in the bottom water was the main predictor of DN. Additionally, DN rates were positively correlated with external N load and the area-specific hydraulic loading rate (mean depth/water residence time; Q_s). NS of N was strongly related to total phosphorus (P) concentration. Nitrogen removal efficiency (NRE), the fraction of the load of dissolved N to a lake removed by DN and NS, was strongly negatively related to Q_s. This previously unconsidered variable improves the predictability of NRE and does not require knowledge of N and P loading rates or concentrations. We conclude that P management alone intended to oligotrophy lakes only slightly increases N export unless it is accompanied by N management.

[Screening and Nitrogen Removing Characteristics of Heterotrophic Nitrification-Aerobic Denitrification Bacteria SLWX2 from Sea Water]

In this study, an efficient heterotrophic nitrifying-aerobic denitrifying bacteria strain SLWX₂ was screened from 7 strains isolated from Stichopus japonicus culture ponds, with removal rates of NH₄⁺-N, NO₂^--N and NO₃^--N up to 100%, 99.5% and 85.6% within 24 h, respectively. Through morphologic observation, physiological characteristics and 16S rDNA sequence analysis, strain SLWX₂ was identified as Bacillus hwajinpoensis. The results of nitrogen removal characterization experiments indicated that, when NH₄⁺-N, NO₂^--N and NO₃^--N existed at the same time, SLWX₂ utilized NH₄⁺-N firstly, then utilized NO₂^--N and NO₃^--N, and removed almost all the inorganic nitrogen within 72 h, suggesting that it could achieve simultaneous nitrification and denitrification itself. The results of nitrogen tolerance examination indicated that strain SLWX₂ showed perfect nitrogen removal ability when the ammonia load was not above 500 mg·L^-1, nitrite load was not above 100 mg·L^-1 and nitrate load was not above 200 mg·L^-1, the maximal removal of ammonia nitrogen, nitrite nitrogen and nitrate nitrogen withinn 96 h reached 180 mg, 30 mg and 120 mg, respectively. Moreover, there was no NO₂^--N accumulation during nitrification. This strain showed great potential in biological nitrogen removal of wastewater with high salt and nitrogen from mariculture and industries.

Socioeconomic driving factors of nitrogen load from food consumption and preventive measures

To diagnose environmental nitrogen (N) load from food consumption and to suggest preventive measures, this study identified relationships between nitrogen load from food consumption and driving factors by examining six representative countries and regions for the period 1970-2009 as an example. The logarithmic mean Divisia index technique was used to disassemble nitrogen load growth into four driving factors: population, economic activity, food intensity of the economy, and nitrogen content of food. In all study areas, increased economic activity was the main factor driving nitrogen load increase. The positive effect of population growth was relatively small but not negligible and changes in food intensity had a decreasing effect on nitrogen load. Changes in nitrogen content of food varied between areas. Broad strategies to reduce and mitigate nitrogen loading and decouple nitrogen load from economic growth in both developed and developing countries are suggested.