Unspecific peroxygenase enabled formation of azoxy compounds.

Enzymes are making a significant impact on chemical synthesis. However, the range of chemical products achievable through biocatalysis is still limited compared to the vast array of products possible with organic synthesis. For instance, azoxy products have rarely been synthesized using enzyme catalysts. In this study, we discovered that fungal unspecific peroxygenases are promising catalysts for synthesizing azoxy products from simple aniline starting materials. The catalytic features (up to 48,450 turnovers and a turnover frequency of 6.7 s-1) and substrate transformations (up to 99% conversion with 98% chemoselectivity) highlight the synthetic potential. We propose a mechanism where peroxygenase-derived hydroxylamine and nitroso compounds spontaneously (non-enzymatically) form the desired azoxy products. This work expands the reactivity repertoire of biocatalytic transformations in the underexplored field of azoxy compound formation reactions.

Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap).

Proteins undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates critical protein-membrane and protein-protein interactions. The most widely used S-acylation assays, including acyl-biotin exchange and acyl resin-assisted capture, utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. These assays generally require >500 µg of protein input material per sample and numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome these limitations, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment. We show that the method is compatible with protein-level detection of S-acylated proteins (e.g., H-Ras) as well as S-acyl site identification and quantification using "on trap" isobaric labeling and LC-MS/MS from as little as 20 µg of protein input. In mouse brain, Acyl-Trap identified 279 reported sites of S-acylation and 1298 previously unreported putative sites. Also described are conditions for long-term hydroxylamine storage, which streamline the assay. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional protein detection and chemoproteomic workflows.

A highly sensitive and colorimetric fluorescent probe for visualizing hydroxylamine in immune cells.

BACKGROUND: Hydroxylamine (HA) is vital industrial raw material and pharmaceutical intermediate. In addition, HA is an important cellular metabolite, which is intermediate in the formation of nitric oxide and nitroxide. However, excessive amounts of HA are toxic to both animals and plants. Conventional methods for the detection of HA are cumbersome and complicated. The detection of HA with fluorescent probes is convenient and sensitive. There are few probes available for the detection of hydroxylamine. Therefore, a fluorescent probe for the sensitive and selective detection of HA was developed in this work. RESULTS: A coumarin derivative SWJT-22 was synthesized as a colorimetric fluorescent probe to detect hydroxylamine (HA), with high sensitivity and selectivity. The detection limit of the probe to HA was 0.15 µM, which was lower than most probes of HA. Upon the addition of HA to aqueous solution containing SWJT-22, the color of the solution changed from orange to yellow, and the fluorescence color also changed from orange to green. The reaction mechanism of SWJT-22 to HA was confirmed by 1H NMR titrations, mass spectrometry and round bottom flask experiments. Moreover, SWJT-22 had been fabricated into portable test strips for the detection of HA. SWJT-22 had been successfully used in cellular imaging and could detect both endogenous and exogenous HA in HeLa cells and RAW 264.7 cells. SIGNIFICANCE: Due to the physiological role of hydroxylamine in organisms, it is crucial to detect hydroxylamine selectively and sensitively. This work provided a convenient tool for the detection of hydroxylamine, not only to detect endogenous and exogenous HA in cells, but also made into portable test strips. The HA fluorescent probe SWJT-22 is expected to promote the study of HA in physiological processes.

A phenothiazine-based ratiometric fluorescence probe for the detection of hydroxylamine in real water and living cells.

In this study, a phenothiazine-based ratiometric fluorescent probe PCHO was developed for highly sensitive and specific detection of hydroxylamine (HA). In the presence of HA, the aldehyde group on the PCHO molecule underwent a specific nucleophilic addition with HA to form an oxime group, accompanied by significant changes in fluorescence from green to blue. This detection mechanism was well supported by 1H NMR titration, HRMS and DFT calculations. The probe PCHO exhibited high sensitivity for HA detection (LOD was 0.19 µM) with a rapid response time (1 min), high selectivity and strong anti-interference performance. Surprisingly, the probe PCHO could selectively distinguish HA from its similar competing agents such as hydrazine and amines. Moreover, paper strips loaded with PCHO were prepared and combined with a smartphone to achieve point-of-care and visual detection of HA. The probe PCHO was further applied for the detection of HA in real water samples, achieving a recovery rate of 98.90% to 104.86% and an RSD of 0.86% to 2.44%, confirming the accuracy and reliability of the method. Additionally, the probe PCHO was used for imaging analysis of HA in living cells, providing a powerful visualization tool for exploring the physiological functions of HA in vivo.

Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification.

Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, 15N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in Alcaligenes faecalis. We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that A. faecalis is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.

Dirammox-dominated microbial community for biological nitrogen removal from wastewater.

Direct ammonia oxidation (Dirammox) might be of great significance to advance the innovation of biological nitrogen removal process in wastewater treatment systems. However, it remains unknown whether Dirammox bacteria can be selectively enriched in activated sludge. In this study, a lab-scale bioreactor was established and operated for 2 months to treat synthetic wastewater with hydroxylamine as a selection pressure. Three Dirammox strains (Alcaligenes aquatilis SDU_AA1, Alcaligenes aquatilis SDU_AA2, and Alcaligenes sp. SDU_A2) were isolated from the activated sludge, and their capability to perform Dirammox process was confirmed. Although these three Dirammox bacteria were undetectable in the seed sludge (0%), their relative abundances rapidly increased after a month of operation, reaching 12.65%, 0.69%, and 0.69% for SDU_A2, SDU_AA1, and SDU_AA2, respectively. Among them, the most dominant Dirammox (SDU_A2) exhibited higher nitrogen removal rate (32.35%) than the other two strains (13.57% of SDU_AA1 and 14.52% of SDU_AA2). Comparative genomic analysis demonstrated that the most dominant Dirammox bacterium (SDU_A2) possesses fewer complete metabolic modules compared to the other two less abundant Alcaligenes strains. Our findings expanded the understanding of the application of Dirammox bacteria as key functional microorganisms in a novel biological nitrogen and carbon removal process if they could be well stabilized. KEY POINTS: • Dirammox-dominated microbial community was enriched in activated sludge bioreactor. • The addition of hydroxylamine played a role in Dirammox enrichment. • Three Dirammox bacterial strains, including one novel species, were isolated.

Intermittent hydroxylamine dosing to strengthen stability of partial nitrification and nitrogen removal efficiency through continuous-flow anaerobic-aerobic-anoxic reactor treating municipal wastewater.

Intermittent hydroxylamine (NH2OH) dosing strategy was applied to enhance the stability of partial nitrification and total nitrogen (N) removal efficiency (TNRE) in a continuous-flow process. The results showed 2 mg/L of NH2OH dosing (once every 6 h) could maintain stably partial nitrification with nitrite accumulation rate (NAR) of 91.6 % and TNRE of 92.6 %. The typical cycle suggested NH2OH dosing could promote simultaneous nitrification-denitrification (SND) and endogenous denitrification (END) while inhibit exogenous denitrification (EXD). Nitrification characteristics indicated the NH2OH dosing enhanced stability of partial nitrification by suppressing specific nitrite oxidation rate (SNOR), Nitrospira and nitrite oxidoreductase enzyme (Nxr). The microbial community suggested the aerobic denitrfiers, denitrifying glycogen accumulating organisms (DGAOs) and traditional denitrfiers were the potential contributor for advanced N removal. Moreover, NH2OH dosage was positively associated with NAR, SND and END. Overall, this study offers a feasible strategy to maintain sustainably partial nitrification that has great application potential.

A Hydroxylamine-Mediated Amidination of Lysine Residues That Retains the Protein's Positive Charge.

Lysine-specific peptide and protein modification strategies are widely used to study charge-related functions and applications. However, these strategies often result in the loss of the positive charge on lysine, significantly impacting the charge-related properties of proteins. Herein, we report a strategy to preserve the positive charge and selectively convert amines in lysine side chains to amidines using nitriles and hydroxylamine under aqueous conditions. Various unprotected peptides and proteins were successfully modified with a high conversion rate. Moreover, the reactive amidine moiety and derived modification site enable subsequent secondary modifications. Notably, positive charges were retained during the modification. Therefore, positive charge-related protein properties, such as liquid-liquid phase separation behaviour of α-synuclein, were not affected. This strategy was subsequently applied to a lysine rich protein to develop an amidine-containing coacervate DNA complex with outstanding mechanical properties. Overall, our innovative strategy provides a new avenue to explore the characteristics of positively charged proteins.

Digital colloid-enhanced Raman spectroscopy by single-molecule counting.

Quantitative detection of various molecules at very low concentrations in complex mixtures has been the main objective in many fields of science and engineering, from the detection of cancer-causing mutagens and early disease markers to environmental pollutants and bioterror agents1-5. Moreover, technologies that can detect these analytes without external labels or modifications are extremely valuable and often preferred6. In this regard, surface-enhanced Raman spectroscopy can detect molecular species in complex mixtures on the basis only of their intrinsic and unique vibrational signatures7. However, the development of surface-enhanced Raman spectroscopy for this purpose has been challenging so far because of uncontrollable signal heterogeneity and poor reproducibility at low analyte concentrations8. Here, as a proof of concept, we show that, using digital (nano)colloid-enhanced Raman spectroscopy, reproducible quantification of a broad range of target molecules at very low concentrations can be routinely achieved with single-molecule counting, limited only by the Poisson noise of the measurement process. As metallic colloidal nanoparticles that enhance these vibrational signatures, including hydroxylamine-reduced-silver colloids, can be fabricated at large scale under routine conditions, we anticipate that digital (nano)colloid-enhanced Raman spectroscopy will become the technology of choice for the reliable and ultrasensitive detection of various analytes, including those of great importance for human health.

Inhibition of kynurenine production by N,O-substituted hydroxylamine derivatives.

The inhibition of kynurenine production is considered a promising target for cancer immunotherapy. In this study, an amino acid derivative, compound 1 was discovered using a cell-based assay with our screening library. Compound 1 suppressed kynurenine production without inhibiting indoleamine 2,3-dioxygenase 1 (IDO1) activity. The activity of 1 was derived from the inhibition of IDO1 by a metabolite of 1, O-benzylhydroxylamine (OBHA, 2a). A series of N-substituted 2a derivatives that exhibit potent activity in cell-based assays may represent effective prodrugs. Therefore, we synthesized and evaluated novel N,O-substituted hydroxylamine derivatives. The structure-activity relationships revealed that N,O-substituted hydroxylamine 2c inhibits kynurenine production in a cell-based assay. We conducted an in vivo experiment with 2c, although the effectiveness of O-substituted hydroxylamine derivatives in vivo has not been previously reported. The results indicate that N,O-substituted hydroxylamine derivatives are promising IDO1 inhibitors.

Hydroxylamine supplementation accelerated the rates of cell growth, aerobic denitrification and nitrous oxide emission of Pseudomonas taiwanensis EN-F2.

Hydroxylamine can disrupt the protein translation process of most reported nitrogen-converting bacteria, and thus hinder the reproduction of bacteria and nitrogen conversion capacity. However, the effect of hydroxylamine on the denitrification ability of strain EN-F2 is unclear. In this study, the cell growth, aerobic denitrification ability, and nitrous oxide (N2O) emission by Pseudomonas taiwanensis were carefully investigated by addition of hydroxylamine at different concentrations. The results demonstrated that the rates of nitrate and nitrite reduction were enhanced by 2.51 and 2.78 mg/L/h after the addition of 8.0 and 12.0 mg/L hydroxylamine, respectively. The N2O production from nitrate and nitrite reaction systems were strongly promoted by 4.39 and 8.62 mg/L, respectively, through the simultaneous acceleration of cell growth and both of nitrite and nitrate reduction. Additionally, the enzymatic activities of nitrate reductase and nitrite reductase climbed from 0.13 and 0.01 to 0.22 and 0.04 U/mg protein when hydroxylamine concentration increased from 0 to 6.0 and 12.0 mg/L. This may be the main mechanism for controlling the observed higher denitrification rate and N2O release. Overall, hydroxylamine supplementation supported the EN-F2 strain cell growth, denitrification and N2O emission rates.

Nanopore Identification of N-Acetylation by Hydroxylamine Deacetylation (NINAHD).

N-Acetyl modification, a chemical modification commonly found on biomacromolecules, plays a crucial role in the regulation of cell activities and is related to a variety of diseases. However, due to the instability of N-acetyl modification, accurate and rapid identification of N-acetyl modification with a low measurement cost is still technically challenging. Here, based on hydroxylamine deacetylation and nanopore single molecule chemistry, a universal sensing strategy for N-acetyl modification has been developed. Acetohydroxamic acid (AHA), which is produced by the hydroxylamine deacetylation reaction and serves as a reporter for N-acetylation identification, is specifically sensed by a phenylboronic acid (PBA)-modified Mycobacterium smegmatis porin A (MspA). With this strategy, N-acetyl modifications on RNA, DNA, proteins, and glycans were identified, demonstrating its generality. Specifically, histones can be treated with hydroxylamine deacetylation, from which the generated AHA can represent the amount of N-acetyl modification detected by a nanopore sensor. The unique event features of AHA also demonstrate the robustness of sensing against other interfering analytes in the environment.

Electrochemical production of hydroxylamine from nitrate on metal electrodes: A comparative study of selectivity and efficiency.

Despite the great potential of electrochemical nitrate reduction as a hydroxylamine production method, this strategy has not been sufficiently examined, and the effects of electrode material type on the selectivity and efficiency of this reduction remain underexplored. To bridge this gap, the present study evaluated six metals (Ag, Cu, Ni, Sn, Ti, and Zn) as cathode materials for the electrochemical reduction of nitrate to hydroxylamine, showing that the selectivity of hydroxylamine production was maximal for Sn, while the corresponding faradaic and energy utilization efficiencies were maximal for Ti. Although all tested materials favored nitrate reduction over hydrogen evolution, the disparity in the onset potentials of these reactions did not adequately explain the variations in nitrate removal efficiency, which was found to be influenced by material resistance and charge-transfer properties. The rate constants of elementary nitrate reduction steps determined from the time-dependent concentrations of nitrate and its reduction products (nitrous acid, hydroxylamine, and ammonium) were used to calculate the selectivity and efficiency of hydroxylamine production for each electrode. In turn, these selectivities and efficiencies were correlated with the density functional theory-computed adsorption energies of a key hydroxylamine precursor on different electrodes to afford a volcano-type plot with Ti and Sn at its pinnacle. Thus, this study introduces valuable descriptors and methods for the further screening of electrocatalysts for hydroxylamine generation and the establishment of more environmentally friendly hydroxylamine production techniques utilizing sustainable electricity.

Successive Protein Extraction Using Hydroxylamine to Increase the Depth of Proteome Coverage in Fresh, Forensic, and Archaeological Bones.

Proteomics is continually being applied to a wider range of applications, now including the analysis of archaeological samples and anatomical specimens, particularly collagen-containing tissues such as bones and teeth. Here, we present the application of a chemical digestion-based proteomics sample preparation protocol to the analysis of fresh, anatomical, and archaeological samples. We describe and discuss two protocols: one that uses hydroxylamine as an additional step of the proteomic workflow, applied to the insoluble fraction, and another that applies hydroxylamine directly on demineralized bones and teeth. We demonstrate the additional information that can be extracted using both protocols, including an increase in the sequence coverage and number of peptides detected in modern and archaeological samples and an increase in the number of proteins identified in archaeological samples. By targeting research related to collagens or extracellular matrix proteins, the use of this protocol will open new insights, considering both fresh and ancient mineralized samples.

An overlooked effect of hydroxylamine on anammox granular sludge: Promoting granulation and boosting activity.

The exogenous hydroxylamine dosing has been proven to enhance nitrite supply for anammox bacteria. In this study, exogenous hydroxylamine was fed into a sequencing batch reactor to investigate its long-term effect on anammox granular sludge. The results showed that hydroxylamine enhanced the reactor's performance with an increase in total nitrogen removal rate from 0.23 to 0.52 kg N/m3/d and an increase in bacterial activity from 11.65 to 78.24 mg N/g VSS/h. Meanwhile, hydroxylamine promoted granulation by eluting flocs. And higher anammox activity and granulation were supported by extracellular polymeric substances (EPS) characteristics. Moreover, Candidatus Brocadia's abundance increased from 1.10 % to 3.03 %, and its symbiosis with heterotrophic bacteria was intensified. Additionally, molecular docking detailed the mechanism of the hydroxylamine effect. Overall, this study would provide new insights into the hydroxylamine dosing strategy application.

Eliminative Oximation of O-Glycans from Mucins.

The large variety and high concentration of O-glycans are characteristic properties of mucins and play a crucial role in their unique functions. Analyzing the O-glycans of mucins is essential for investigating the functions of mucins. Eliminative oximation is an aqueous reaction that can be used to obtain O-glycan oximes from mucins. Using diazabicyclo undec-7ene (DBU) as a base, an organic superbase that can be removed with an organic solvent during solid-phase extraction, and adding hydroxylamine to the reaction mixture in advance, the O-glycans released from the mucin are immediately converted to the corresponding glycan oximes. The glycan oxime can then be fluorescently labeled with a fluorescent labeling reagent and 2-picoline borane via reductive amination. O-glycans that have been fluorescently labeled can be analyzed using conventional HPLC techniques.

A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans.

The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.

Amino acid and protein specificity of protein fatty acylation in C. elegans.

Protein lipidation plays critical roles in regulating protein function and localization. However, the chemical diversity and specificity of fatty acyl group utilization have not been investigated using untargeted approaches, and it is unclear to what extent structures and biosynthetic origins of S-acyl moieties differ from N- and O-fatty acylation. Here, we show that fatty acylation patterns in Caenorhabditis elegans differ markedly between different amino acid residues. Hydroxylamine capture revealed predominant cysteine S-acylation with 15-methylhexadecanoic acid (isoC17:0), a monomethyl branched-chain fatty acid (mmBCFA) derived from endogenous leucine catabolism. In contrast, enzymatic protein hydrolysis showed that N-terminal glycine was acylated almost exclusively with straight-chain myristic acid, whereas lysine was acylated preferentially with two different mmBCFAs and serine was acylated promiscuously with a broad range of fatty acids, including eicosapentaenoic acid. Global profiling of fatty acylated proteins using a set of click chemistry-capable alkyne probes for branched- and straight-chain fatty acids uncovered 1,013 S-acylated proteins and 510 hydroxylamine-resistant N- or O-acylated proteins. Subsets of S-acylated proteins were labeled almost exclusively by either a branched-chain or a straight-chain probe, demonstrating acylation specificity at the protein level. Acylation specificity was confirmed for selected examples, including the S-acyltransferase DHHC-10. Last, homology searches for the identified acylated proteins revealed a high degree of conservation of acylation site patterns across metazoa. Our results show that protein fatty acylation patterns integrate distinct branches of lipid metabolism in a residue- and protein-specific manner, providing a basis for mechanistic studies at both the amino acid and protein levels.

Response of marine anammox bacteria to long-term hydroxylamine stress: Nitrogen removal performance and microbial community dynamics.

The response of anammox bacteria to hydroxylamine has not been well explained. Herein, hydroxylamine was long-term added as the sole substrate to marine anammox bacteria (MAB) in saline wastewater treatment for the first time. MAB could tolerate 5 mg/L hydroxylamine. However, MAB activity was inhibited by the high dose of hydroxylamine (40 mg/L), and hydroxylamine removal efficiency was only 3 %. Remarkably, when hydroxylamine reached 20 mg/L, ammonium was produced the most at 2.88 mg/L, mainly by the hydroxylamine and hydrazine disproportionations. Besides, the relative abundance of Candidatus Scalindua decreased from 4.6 % to 0.6 % as the hydroxylamine increased from 0 to 40 mg/L. MAB secreted more extracellular polymeric substances to resist hydroxylamine stress. However, long-term hydroxylamine loading led to the disintegration of MAB granules. This work shed light on the response of MAB to hydroxylamine in saline wastewater treatment.