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1. QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase

   https://doi.org/10.1039/D0CP03053H  

   Cheng, Ronny; Wu, Chun; Cao, Zexing; Wang, Binju (September 2020, Physical Chemistry Chemical Physics)

   null (Ed.)

   Nitrite reductases are enzymes that aid in the denitrification process by catalyzing the reduction of nitrite to nitric oxide gas. Since this reaction is the first committed step that involves gas formation, it is regarded to be a vital step for denitrification. However, the mechanism of copper-containing nitrite reductase is still under debate due to the discrepancy between the theoretical and experimental data, especially in terms of the roles of secondary shell residues Asp98 and His255 and the electron transfer mechanism between the two copper sites. Herein, we revisited the nitrite reduction mechanism of A. faecalis copper nitrite reductase using QM(B3LYP)/MM-based metadynamics. It is found that the intramolecular electron transfer from T1-Cu to T2-Cu occurs via an asynchronous proton-coupled electron transfer (PCET) mechanism, with electron transfer (ET) preceding proton transfer (PT). In particular, we found that the ET process is driven by the conformation conversion of Asp98 from the gatekeeper to the proximal one, which is much more energy-demanding than the PCET itself. These results highlight that the inclusion of an electron donor is vital to investigate electron-transfer related processes such as PCET. 

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2. Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones

   https://doi.org/10.1093/ismejo/wrae160  

   Fortin, Samantha_G; Sun, Xin; Jayakumar, Amal; Ward, Bess_B (August 2024, The ISME Journal)

   Abstract Nitrite is a central molecule in the nitrogen cycle because nitrite oxidation to nitrate (an aerobic process) retains fixed nitrogen in a system and its reduction to dinitrogen gas (anaerobic) reduces the fixed nitrogen inventory. Despite its acknowledged requirement for oxygen, nitrite oxidation is observed in oxygen-depleted layers of the ocean’s oxygen minimum zones (OMZs), challenging the current understanding of OMZ nitrogen cycling. Previous attempts to determine whether nitrite-oxidizing bacteria in the anoxic layer differ from known nitrite oxidizers in the open ocean were limited by cultivation difficulties and sequencing depth. Here, we construct 31 draft genomes of nitrite-oxidizing bacteria from global OMZs. The distribution of nitrite oxidation rates, abundance and expression of nitrite oxidoreductase genes, and relative abundance of nitrite-oxidizing bacterial draft genomes from the same samples all show peaks in the core of the oxygen-depleted zone (ODZ) and are all highly correlated in depth profiles within the major ocean oxygen minimum zones. The ODZ nitrite oxidizers are not found in the Tara Oceans global dataset (the most complete oxic ocean dataset), and the major nitrite oxidizers found in the oxygenated ocean do not occur in ODZ waters. A pangenomic analysis shows the ODZ nitrite oxidizers have distinct gene clusters compared to oxic nitrite oxidizers and are microaerophilic. These findings all indicate the existence of nitrite oxidizers whose niche is oxygen-deficient seawater. Thus, specialist nitrite-oxidizing bacteria are responsible for fixed nitrogen retention in marine oxygen minimum zones, with implications for control of the ocean’s fixed nitrogen inventory. 

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3. All about nitrite: exploring nitrite sources and sinks in the eastern tropical North Pacific oxygen minimum zone

   https://doi.org/10.5194/bg-20-2499-2023  

   Tracey, John C.; Babbin, Andrew R.; Wallace, Elizabeth; Sun, Xin; DuRussel, Katherine L.; Frey, Claudia; Martocello III, Donald E.; Tamasi, Tyler; Oleynik, Sergey; Ward, Bess B. (January 2023, Biogeosciences)

   Abstract. Oxygen minimum zones (OMZs), due to their large volumes of perennially deoxygenated waters, are critical regions for understanding how the interplay between anaerobic and aerobic nitrogen (N) cycling microbial pathways affects the marine N budget. Here, we present a suite of measurements of the most significant OMZ N cycling rates, which all involve nitrite (NO2-) as a product, reactant, or intermediate, in the eastern tropical North Pacific (ETNP) OMZ. These measurements and comparisons to data from previously published OMZ cruisespresent additional evidence that NO3- reduction is the predominant OMZ N flux, followed by NO2- oxidation back to NO3-. The combined rates of both of these N recycling processes were observed to be much greater (up to nearly 200 times) thanthe combined rates of the N loss processes of anammox and denitrification, especially in waters near the anoxic–oxic interface. We also showthat NO2- oxidation can occur when O2 is maintained near 1 nM by a continuous-purge system, NO2-oxidation and O2 measurements that further strengthen the case for truly anaerobic NO2- oxidation. We also evaluate thepossibility that NO2- dismutation provides the oxidative power for anaerobic NO2- oxidation. The partitioning ofN loss between anammox and denitrification differed widely from stoichiometric predictions of at most 29 % anammox; in fact,N loss rates at many depths were entirely due to anammox. Our new NO3- reduction, NO2- oxidation, dismutation, andN loss data shed light on many open questions in OMZ N cycling research, especially the possibility of truly anaerobicNO2- oxidation. 

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4. Nitrite Formation at a Diiron Dinitrosyl Complex

   https://doi.org/10.1021/jacs.3c05155  

   Poptic, Anna L.; Klinger, Jeffrey K.; Carter, Samantha L.; Moore, Curtis E.; Zhang, Shiyu (October 2023, Journal of the American Chemical Society)
5. A Dinuclear Nickel Complex for Electrocatalytic Nitrite Reduction

   https://doi.org/10.1021/acs.inorgchem.5c00156  

   Partovi, Sheyda; Losovyj, Yaroslav; Yamamoto, Nobuyuki; Smith, Jeremy M (March 2025, Inorganic Chemistry)