The Copper Chaperone NosL Forms a Heterometal Site for Cu Delivery to Nitrous Oxide Reductase

Copper resistance in the cold: Genome analysis and characterisation of a PIB-1 ATPase in Bizionia argentinensis

Copper homeostasis is a fundamental process in organisms, characterised by unique pathways that have evolved to meet specific needs while preserving core resistance mechanisms. While these systems are well-documented in model bacteria, information on copper resistance in species adapted to cold environments is scarce. This study investigates the potential genes related to copper homeostasis in the genome of Bizionia argentinensis (JUB59-T), a psychrotolerant bacterium isolated from Antarctic seawater. We identified several genes encoding proteins analogous to those crucial for copper homeostasis, including three sequences of copper-transport P1B-type ATPases. One of these, referred to as BaCopA1, was chosen for cloning and expression in Saccharomyces cerevisiae. BaCopA1 was successfully integrated into yeast membranes and subsequently extracted with detergent. The purified BaCopA1 demonstrated the ability to catalyse ATP hydrolysis at low temperatures. Structural models of various BaCopA1 conformations were generated and compared with mesophilic and thermophilic homologous structures. The significant conservation of critical residues and structural similarity among these proteins suggest a shared reaction mechanism for copper transport. This study is the first to report a psychrotolerant P1B-ATPase that has been expressed and purified in a functional form.

Ascription of nosZ gene, pH and copper for mitigating N2O emissions in acidic soils

Soil nitrous oxide (N2O) emissions are alarming for global warming and climate change. N2O reduction is carried out only by nosZ gene encoded N2O-reductase, which is highly sensitive to acidic pH and copper (Cu) contents. Therefore, a microcosm study was conducted to examine the attribution of soil pH management, Cu supply and nosZ gene abundance for N2O emission mitigation. Cu was applied at the dose of 0, 10, 25 and 50 mg kg-1 to three acidic soils (Soil 1, 2 and 3) without and with dolomite (0 and 5 g kg-1). Cu application and soil pH increment substantially enlarged the abundance of nosZ gene, and consequently mitigated soil N2O emissions; highest reduction with 25 Cu mg kg-1. Decline in NH4+ and subsequently accumulation of NO3-, and large contents of MBC and DOC in dolomite treated soils led to a substantial N2O reduction. The cumulative N2O emissions were lowest in the treatment of 25 Cu mg kg-1 with dolomite application for each soil. Results suggest that soil pH increment, an adequate Cu supply, and nosZ gene abundance can potentially lower soil N2O emissions in acidic soils.

Cu4S Cluster in "0-Hole" and "1-Hole" States: Geometric and Electronic Structure Variations for the Active CuZ* Site of N2O Reductase

The active site of nitrous oxide reductase (N2OR), a key enzyme in denitrification, features a unique μ4-sulfido-bridged tetranuclear Cu cluster (the so-called CuZ or CuZ* site). Details of the catalytic mechanism have remained under debate and, to date, synthetic model complexes of the CuZ*/CuZ sites are extremely rare due to the difficulty in building the unique {Cu4(μ4-S)} core structure. Herein, we report the synthesis and characterization of [Cu4(μ4-S)]n+ (n = 2, 2; n = 3, 3) clusters, supported by a macrocyclic {py2NHC4} ligand (py = pyridine, NHC = N-heterocyclic carbene), in both their 0-hole (2) and 1-hole (3) states, thus mimicking the two active states of the CuZ* site during enzymatic N2O reduction. Structural and electronic properties of these {Cu4(μ4-S)} clusters are elucidated by employing multiple methods, including X-ray diffraction (XRD), nuclear magnetic resonance (NMR), UV/vis, electron paramagnetic resonance (EPR), Cu/S K-edge X-ray emission spectroscopy (XES), and Cu K-edge X-ray absorption spectroscopy (XAS) in combination with time-dependent density functional theory (TD-DFT) calculations. A significant geometry change of the {Cu4(μ4-S)} core occurs upon oxidation from 2 (τ4(S) = 0.46, seesaw) to 3 (τ4(S) = 0.03, square planar), which has not been observed so far for the biological CuZ(*) site and is unprecedented for known model complexes. The single electron of the 1-hole species 3 is predominantly delocalized over two opposite Cu ions via the central S atom, mediated by a π/π superexchange pathway. Cu K-edge XAS and Cu/S K-edge XES corroborate a mixed Cu/S-based oxidation event in which the lowest unoccupied molecular orbital (LUMO) has a significant S-character. Furthermore, preliminary reactivity studies evidence a nucleophilic character of the central μ4-S in the fully reduced 0-hole state.

Potential roles of the rhizospheric bacterial community in assisting Miscanthus floridulus in remediating multi-metal(loid)s contaminated soils

Phytoremediation technology is an important approach applied to heavy metal remediation, and how to improve its remediation efficiency is the key. In this study, we compared the rhizospheric bacterial communities and metals contents in Miscanthus floridulus (M. floridulus) of four towns, including Huayuan Town (HY), Longtan Town (LT), Maoer Village (ME), and Minle Town (ML) around the lead-zinc mining area in Huayuan County, China. The roles of rhizospheric bacterial communities in assisting the phytoremediation of M. floridulus were explored. It was found that the compositions of the rhizospheric bacterial community of M. floridulus differed in four regions, but majority of them were heavy metal-resistant bacteria that could promote plant growth. Results of bioconcentration factors showed the enrichment of Cu, Zn, and Pb by M. floridulus in these four regions were significantly different. The Zn enrichment capacity of ML was the strongest for Cu and stronger than LT and ME for Pb. The enrichment capacity of LT and ML was stronger than HY and ME. These bacteria may influence the different heavy metals uptake of M. floridulus by altering the soil physiochemical properties (e.g., soil peroxidase, pH and moisture content). In addition, co-occurrence network analysis also showed that LT and ML had higher network stability and complexity than HY and ME. Functional prediction analysis of the rhizospheric bacterial community showed that genes related to protein synthesis (e.g., zinc-binding alcohol dehydrogenase/oxidoreductase, Dtx R family transcriptional regulators and ACC deaminase) also contributed to phytoremediation in various ways. This study provides theoretical guidance for selecting suitable microorganisms to assist in the phytoremediation of heavy metals.

Structural biology of proteins involved in nitrogen cycling

Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.

Molecular interplay of an assembly machinery for nitrous oxide reductase

Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N₂O) from soils and industrial processes have increased considerably over the last decades^1-3. As the final step of bacterial denitrification, N₂O is reduced to chemically inert N₂ (refs. ^1,4) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N₂OR) (ref. ⁵). The assembly of its unique [4Cu:2S] active site cluster Cu_Z requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. ^4,6). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N₂OR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu⁺ ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to N₂OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N₂OR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme N₂OR.

Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil

Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated the highest methanol removal (73.28%) in terms of soluble chemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.

APEX2-based Proximity Labeling of Atox1 Identifies CRIP2 as a Nuclear Copper-binding Protein that Regulates Autophagy Activation

Mammalian cell nuclei contain copper, and cancer cells are known to accumulate aberrantly high copper levels, yet the mechanisms underlying nuclear accumulation and copper's broader functional significance remain poorly understood. Here, by combining APEX2-based proximity labeling focused on the copper chaperone Atox1 with mass spectrometry we identified a previously unrecognized nuclear copper binding protein, Cysteine-rich protein 2 (CRIP2), that interacts with Atox1 in the nucleus. We show that Atox1 transfers copper to CRIP2, which induces a change in CRIP2's secondary structure that ultimately promotes its ubiquitin-mediated proteasomal degradation. Finally, we demonstrate that depletion of CRIP2-as well as copper-induced CRIP2 degradation-elevates ROS levels and activates autophagy in H1299 cells. Thus, our study establishes that CRIP2 as an autophagic suppressor protein and implicates CRIP2-mediated copper metabolism in the activation of autophagy in cancer cells.