Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome

New insights in uranium bioremediation by cytochromes of the bacterium G. uraniireducens

The bacterium Geotalea uraniireducens, commonly found in uranium-contaminated environments, plays a key role in bioremediation strategies by converting the soluble hexavalent form of uranium (UVI) into less soluble forms (e.g. UIV.). While most of the reduction and concomitant precipitation of uranium occur outside the cells, there have been reports of important reduction processes taking place in the periplasm. In any case, the triheme periplasmic cytochromes are crucial players, either by ensuring an effective interface between the cell´s interior and exterior or by directly participating in the reduction of the metal. Therefore, understanding the functional mechanism of the highly abundant G. uraniireducens' triheme cytochromes is crucial to assist the elucidation on the respiratory pathways in this bacterium. In this work, a detailed functional characterization of the triheme cytochromes PpcA and PpcB from G. uraniireducens was conducted using NMR and visible spectroscopy techniques. Despite sharing high amino acid sequence and structural homology with their counterparts from G. sulfurreducens, the results obtained showed that the heme reduction potential values are less negative, the order of oxidation of the hemes is distinct, and the redox and redox-Bohr network of interactions revealed unprecedented functional mechanisms of the G. uraniireducens cytochromes. In these cytochromes, the reduction potential values of the three heme groups are much more similar, hence covering a narrow range of values, features that facilitate the directional electron flow from the inner membrane, thereby favouring the optimal reduction of uranium.

Novel insights into self-defense function of anammox sludge under magnesium ions (Mg2+) stress based on Mg2+ transport system

Magnesium ion (Mg2+) plays an important role in the accumulation and stability of anaerobic ammonium-oxidizing bacteria (AnAOB). In this study, the response of anammox sludge to Mg2+ was comprehensively investigated by performance evaluation and metagenomics analysis. Appropriate Mg2+ (0.8 mmol/L) could improve the nitrogen removal performance, AnAOB activity, and the synthesis potential of some hydrophobic substances, while high Mg2+ (>1.6 mmol/L) has a negative effect. Meanwhile, Mg2+ transmembrane transport theory was introduced to reveal the response principle of AnAOB to Mg2+ from a novel insight. AnAOB may have a self-defense function based on the PhoQ/PhoP-MgtAB system. Low extracellular Mg2+ will activate this function to enhance Mg2+ influx, thereby improving the intracellular metabolism of AnAOB. Excessive Mg2+, however, dormant this function and induces Mg2+ efflux, which may decrease the intracellular Mg2+ and thus affect AnAOB metabolism. These findings provide valuable references for the Mg2+ regulation of anammox-based process.

Electron transfer in biological systems

Examples of how metalloproteins feature in electron transfer processes in biological systems are reviewed. Attention is focused on the electron transport chains of cellular respiration and photosynthesis, and on metalloproteins that directly couple electron transfer to a chemical reaction. Brief mention is also made of extracellular electron transport. While covering highlights of the recent and the current literature, this review is aimed primarily at introducing the senior undergraduate and the novice postgraduate student to this important aspect of bioinorganic chemistry.

A survey of the Desulfuromonadia "cytochromome" provides a glimpse of the unexplored diversity of multiheme cytochromes in nature

BACKGROUND

Multiheme cytochromes c (MHC) provide prokaryotes with a broad metabolic versatility that contributes to their role in the biogeochemical cycling of the elements and in energy production in bioelectrochemical systems. However, MHC have only been isolated and studied in detail from a limited number of species. Among these, Desulfuromonadia spp. are particularly MHC-rich. To obtain a broad view of the diversity of MHC, we employed bioinformatic tools to study the cytochromome encoded in the genomes of the Desulfuromonadia class.

RESULTS

We found that the distribution of the MHC families follows a different pattern between the two orders of the Desulfuromonadia class and that there is great diversity in the number of heme-binding motifs in MHC. However, the vast majority of MHC have up to 12 heme-binding motifs. MHC predicted to be extracellular are the least conserved and show high diversity, whereas inner membrane MHC are well conserved and show lower diversity. Although the most prevalent MHC have homologues already characterized, nearly half of the MHC families in the Desulforomonadia class have no known characterized homologues. AlphaFold2 was employed to predict their 3D structures. This provides an atlas of novel MHC, including examples with high beta-sheet content and nanowire MHC with unprecedented high numbers of putative heme cofactors per polypeptide.

CONCLUSIONS

This work illuminates for the first time the universe of experimentally uncharacterized cytochromes that are likely to contribute to the metabolic versatility and to the fitness of Desulfuromonadia in diverse environmental conditions and to drive biotechnological applications of these organisms.

The adaptive regulation mechanism of Anammox granule sludge under calcium ions stress: Defense modes transformation

Anammox granular sludge (AnGS) has received considerable attention due to its low carbon footprint (less aeration energy and carbon source consumption) and high biomass density, but growth rate and stability are still the bottlenecks of AnGS process. Calcium ion (Ca2+) is essential for the growth of anaerobic ammonium oxidation bacteria (AnAOB) and plays an important role in the formation and stability of AnGS. Response of AnGS to Ca2+ under different concentrations was comprehensively investigated by multi-spectral and metagenomics analysis in four aspects: nitrogen removal performance, surface morphology, extracellular polymeric substance (EPS) composition and characterization, and microbial community. The nitrogen removal efficiency was significantly enhanced at appropriate Ca2+ concentration (2 mmol/L), owning to the more favorable morphology and functional microbial composition of AnGS. However, the nitrogen removal performance of AnGS declined with the Ca2+concentration increased from 2 to 8 mmol/L, due to the negative effects of excess Ca2+on EPS, mass transfer efficiency, and functional microorganisms. Meanwhile, an unexpected slight "rebound" of nitrogen removal efficiency was observed at Ca2+ = 6 mmol/L and attributed to the defense mode transformation of AnGS (from "ion stabilization" to "precipitate shield" modes) against excess Ca2+ stress. Based on the findings, the response mechanism of AnGS to Ca2+ with different concentrations was established. Our results enhanced the understanding of the interaction between AnGS and Ca2+, which may be valuable for filling the theoretical gap in enhancing the granulation and stability of AnGS and providing a reference for the practical operation of the AnGS process.

Ferroheme/Ferriheme Directly Involved in the Synthesis and Decomposition of Hydrazine as an Electron Carrier during Anammox

Anammox bacteria performed the reaction of NH4+ and NO with hydrazine synthase to produce N2H4, followed by the decomposition of N2H4 with hydrazine dehydrogenase to generate N2. Ferroheme/ferriheme, which serves as the active center of both hydrazine synthase and hydrazine dehydrogenase, is thought to play a crucial role in the synthesis and decomposition of N2H4 during Anammox due to its high redox activity. However, this has yet to be proven and the exact mechanisms by which ferroheme/ferriheme is involved in the Anammox process remain unclear. In this study, abiotic and biological assays confirmed that ferroheme participated in NH4+ and NO reactions to generate N2H4 and ferriheme, and the produced N2H4 reacted with ferriheme to generate N2 and ferroheme. In other words, the ferroheme/ferriheme cycle drove the continuous reaction between NH4+ and NO. Raman, ultraviolet-visible spectroscopy, and X-ray absorption fine structure spectroscopy confirmed that ferroheme/ferriheme is involved in the synthesis and decomposition of N2H4 via the core FeII/FeIII cycle. The mechanism of ferroheme/ferriheme participation in the synthesis and decomposition of N2H4 was proposed by density functional theory calculations. These findings revealed for the first time the heme electron transfer mechanisms, which are of great significance for deepening the understanding of Anammox.

Environmental proteomics as a useful methodology for early-stage detection of stress in anammox engineered systems

Anammox bacteria are widely applied worldwide for denitrification of urban wastewater. Differently, their application in the case of industrial effluents has been more limited. Those frequently present high loads of contaminants, demanding an individual evaluation of their treatability by anammox technologies. Bioreactors setting up and recovery after contaminants-derived perturbations are slow. Also, toxicity is frequently not acute but cumulative, which causes negative macroscopic effects to appear only after medium or long-term operations. All these particularities lead to relevant economic and time losses. We hypothesized that contaminants cause changes at anammox proteome level before perturbations in the engineered systems are detectable by macroscopic analyses. In this study, we explored the usefulness of short-batch tests combined with environmental proteomics for the early detection of those changes. Copper was used as a model of stressor contaminant, and anammox granules were exposed to increasing copper concentrations including previously reported IC50 values. The proteomic results revealed that specific anammox proteins involved in stress response (bacterioferritin, universal stress protein, or superoxide dismutase) were overexpressed in as short a time as 28 h at the higher copper concentrations. Consequently, EPS production was also increased, as indicated by the alginate export family protein, polysaccharide biosynthesis protein, and sulfotransferase increased expression. The described workflow can be applied to detect early-stage stress biomarkers of the negative effect of other metals, organics, or even changes in physical-chemical parameters such as pH or temperature on anammox-engineered systems. On an industrial level, it can be of great value for decision-making, especially before dealing with new effluents on facilities, deriving important economic and time savings.

Unraveling potential mechanism of different metal ions effect on anammox through big data analysis, molecular docking and molecular dynamics simulation

Heavy metals (HMs) have been widely reported to pose an adverse effect on anaerobic ammonia oxidation (anammox) bacteria, yet the underlying mechanisms remain unclear. This study provides new insights into the potential mechanisms of interaction between HMs and functional enzymes through big date analysis, molecular docking and molecular dynamics simulation. The statistical analysis indicated that 10 mg/L Cu(II) and Cd(II) reduced nitrogen removal rate (NRR) by 85% and 43%, while 5 mg/L Fe(II) enhanced NRR by 29%. Additionally, the results of molecular simulations provided a microscopic interpretation for these macroscopic data. Molecular docking revealed that Hg(II) formed a distinctive binding site on ferritin, while other HMs resided at iron oxidation sites. Furthermore, HMs exhibited distinct binding sites on hydrazine dehydrogenase. Concurrently, the molecular dynamics simulation results further substantiated their capacity to form complexes. Cu(II) displayed the strongest binding affinity with ferritin for -1576 ± 79 kJ/mol in binding free energy calculation. Moreover, Cd(II) bound to ferritin and HDH for -1052.67 ± 58.49 kJ/mol, -290.02 ± 49.68 kJ/mol, respectively. This research addressed a crucial knowledge gap, shedding light on potential applications for remediating heavy metal-laden industrial wastewater.

Chameleon-like Anammox Bacteria for Surface Color Change after Suffering Starvation

Bacteria are often exposed to long-term starvation during transportation and storage, during which a series of enzymes and metabolic pathways are activated to ensure survival. However, why the surface color of the bacteria changes during starvation is still not well-known. In this study, we found black anammox consortia suffering from long-term starvation contained 0.86 mmol gVSS-1 cytochrome c, which had no significant discrepancy compared with the red anammox consortia (P > 0.05), indicating cytochrome c was not the key issue for chromaticity change. Conversely, we found that under starvation conditions cysteine degradation is an important metabolic pathway for the blackening of the anammox consortia for H2S production. In particular, anammox bacteria contain large amounts of iron-rich nanoparticles, cytochrome c, and other iron-sulfur clusters that are converted to produce free iron. H2S combines with free iron in bacteria to form Fe-S compounds, which eventually exist stably as FeS2, mainly in the extracellular space. Interestingly, FeS2 could be oxidized by air aeration, which makes the consortia turn red again. The unique self-protection mechanism makes the whole consortia appear black, avoiding inhibition by high concentrations of H2S and achieving Fe storage. This study expands the understanding of the metabolites of anammox bacteria as well as the bacterial survival mechanism during starvation.

Insights into heavy metals shock on anammox systems: Cell structure-based mechanisms and new challenges

Anaerobic ammonium oxidation (anammox) as a low-carbon and energy-saving technology, has shown unique advantages in the treatment of high ammonia wastewater. However, wastewater usually contains complex heavy metals (HMs), which pose a potential risk to the stable operation of the anammox system. This review systematically re-evaluates the HMs toxicity level from the inhibition effects and the inhibition recovery process, which can provide a new reference for engineering. From the perspective of anammox cell structure (extracellular, anammoxosome membrane, anammoxosome), the mechanism of HMs effects on cellular substances and metabolism is expounded. Furthermore, the challenges and research gaps for HMs inhibition in anammox research are also discussed. The clarification of material flow, energy flow and community succession under HMs shock will help further reveal the inhibition mechanism. The development of new recovery strategies such as bio-accelerators and bio-augmentation is conductive to breaking through the engineered limitations of HMs on anammox. This review provides a new perspective on the recognition of toxicity and mechanism of HMs in the anammox process, as well as the promotion of engineering applicability.

Use of iron-loaded biochar to alleviate anammox performance inhibition under PFOA stress conditions: Integrated analysis of sludge characteristics and metagenomics

The negative effects of perfluorooctanoic acid (PFOA) on biological nitrogen removal performance in wastewater treatment plants, are receiving increasing attention due to the widespread reporting of this issue. In this study, pomelo peel iron-loaded biochar (Fe-PBC) was added to an anammox bioreactor to alleviate the negative effects of PFOA. Results showed that the addition of Fe-PBC increased the ammonia and nitrite removal efficiencies from 77.7 ± 9.6 % and 79.5 ± 5.6 % to 94.45 ± 5.1 % and 95.9 ± 5.0 %, respectively. In addition, Fe-PBC promoted the removal of PFOA from wastewater, increasing the PFOA removal efficiency from 5.2 % to 29.2 ± 4.3 % from 100 to 200 days. The introduction of iron-loaded biochar into the anammox bioreactor increased the CO ratio by 13.64 % by 150 days. In addition, a CO fitting peak was detected in the Fe-PBC, indicating that the Fe-PBC was loaded with microorganisms. Microbial community analysis showed a decrease in the relative abundances of Proteobacteria and Nitrospirae from 31 % and 3.4 % to 16.8 % and 0.9 %, respectively, while the relative abundance of Planctomycetes increased from 26.8 % to 44.1 %. Metagenomic analysis found that the functional genes hzsB and hdh increased from 98,666 ± 11,400 and 3190 ± 460 to 119,333 ± 15,534 and 138,650 ± 11,233 copy numbers/MLSS. The increase in anammox biomass may be attributed to the presence of iron, an essential element for the synthesis of key anammox enzyme. Furthermore, iron was also associated with the enhanced extracellular electron transfer in the anammox system induced by Fe-PBC.

Metagenomic and extracellular polymeric substances analysis reveals the mechanism of exogenous N-hexanoyl-L-homoserine lactone in alleviating the inhibition of perfluorooctanoic acid on anammox process

To alleviate the negative effects of perfluorooctanoic acid (PFOA) on nitrogen removal via anaerobic ammonia oxidation (anammox), an exogenous signaling factor (N-hexanoyl-L-homoserine lactone, C₆-HSL) was introduced into an anammox reactor. Results showed that 2 μmol/L C₆-HSL promoted the nitrogen removal efficiency of the anammox reactor under PFOA stress, with the removal efficiencies of ammonia and nitrite increasing from 79.7 ± 4.8 % and 80.8 ± 3.8 %, to 94.4 ± 4.3 % and 97.1 ± 3.8 %. Exogenous C₆-HSL enhanced the compactness of the extracellular proteins, and improved the sludge hydrophobicity. Meanwhile, C₆-HSL resulted in a microbial shift, with the relative abundance of Planctomycetes increasing from 30.2 % to 49.5 %. Candidatus Kuenenia stuttgartiensis replaced Candidatus Brocadia sp. BL1 as the dominant species, while the available space for other nitrogen-removing bacteria was reduced. Exogenous C₆-HSL promoted the expression of anammox-related genes, such as hzsB and hdh, while denitrifying genes were down-regulated. In addition, the relative abundance of HdtS, which synthesizes AHLs, increased by 0.02446%.

Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance

In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems.

Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs

Uncovering conserved 3D protein-ligand binding patterns on the basis of functional groups (FGs) shared by a variety of small molecules can greatly expand our knowledge of protein-ligand interactions. Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature, large-scale identification and evaluation of FG-based 3D binding motifs are still lacking. Here, we propose a computational method, Automatic FG-based Three-dimensional Motif Extractor (AFTME), for automatic mapping of 3D motifs to different FGs of a specific ligand. Applying our method to 233 naturally-occurring ligands, we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets. Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities. Finally, we show that our FG-motif map can be used to nominate FGs that potentially bind to specific drug targets, thus providing useful insights and guidance for rational design of small-molecule drugs.

Promotion of anammox process by different graphene-based materials: Roles of particle size and oxidation degree

Graphene oxide (GO) and reduced graphene oxide (RGO) have been applied in the anaerobic ammonium oxidation (anammox) process for nitrogen removal as electron shuttles. However, there is still controversy about their efficacy. In this study, nine graphene-based materials with a gradient of three particle sizes (large (l), medium (m) and small (s) sizes) and oxidation degrees, were used to compare their effects on the anammox process efficiency. The graphene-based materials include GO and its reduced products (RGO250 and RGO800) obtained at temperatures of 250 °C and 800 °C respectively. It was observed that their enhancements on the anammox process were in the order of GO > RGO800 > RGO250. In detail, at the dose of 100 mg/L, specific anammox activities (SAA) were promoted by 6.7% (l-GO), 4.9% (l-RGO800), 11.5% (m-GO), 7.3% (m-RGO800), 13.2% (s-GO) and 8.3% (s-RGO800) compared to the control respectively; while RGO250 with the same dose inhibited the process. In addition, the enhancement of the anammox process was increasing with the decreasing size of GO and RGO800. The nitrite reductase (NIR) activity was greatly increased by up to 24.9% with the presence of GO, which might be attributed to organized and specific electron transport with oxygen functional groups. The finding of hydroxyl on RGO and increasing content of oxygen determined after reaction detected by Fourier transform infrared spectroscopy and energy dispersive spectrometer respectively, indicated the essential condition for RGO's function on transferring electrons for key enzymes in annamox bacteria. Most importantly, O/C (Oxygen/Carbon) ratios of graphene-based materials had greater effects on the promotion of the anammox process than the particle size and electrical conductivity.

Insight into the structure and metabolic function of iron-rich nanoparticles in anammox bacteria

Anaerobic ammonium-oxidizing (anammox) bacteria are iron abundant and depend heavily on iron-binding proteins. The iron demand of anammox bacteria is relatively large. However, it still remains some doubts where these large quantities of available iron come from and how they are regulated in anammox bacteria. Herein, iron-rich nanoparticles in anammoxosomes were detected by synchrotron soft X-ray tomography coupled with scanning transmission X-ray microscopy (STXM). The iron-rich nanoparticles were identified as ferric oxide (α-Fe₂O₃) mineral cores, and the local atomic structure of iron-rich nanoparticles was obtained by X-ray absorption fine-structure (XAFS) spectra. The bacterioferritin of Q1Q315 and Q1Q5F8 were detected by proteomics analysis. On this basis, the metabolic pathway centered on iron-rich nanoparticles was proposed.

Structural and functional insights of GSU0105, a unique multiheme cytochrome from G. sulfurreducens

Geobacter sulfurreducens possesses over 100 cytochromes that assure an effective electron transfer to the cell exterior. The most abundant group of cytochromes in this microorganism is the PpcA family, composed of five periplasmic triheme cytochromes with high structural homology and identical heme coordination (His-His). GSU0105 is a periplasmic triheme cytochrome synthetized by G. sulfurreducens in Fe(III)-reducing conditions but is not present in cultures grown on fumarate. This cytochrome has a low sequence identity with the PpcA family cytochromes and a different heme coordination, based on the analysis of its amino acid sequence. In this work, amino acid sequence analysis, site-directed mutagenesis, and complementary biophysical techniques, including ultraviolet-visible, circular dichroism, electron paramagnetic resonance, and nuclear magnetic resonance spectroscopies, were used to characterize GSU0105. The cytochrome has a low percentage of secondary structural elements, with features of α-helices and β-sheets. Nuclear magnetic resonance shows that the protein contains three low-spin hemes (Fe(II), S = 0) in the reduced state. Electron paramagnetic resonance shows that, in the oxidized state, one of the hemes becomes high-spin (Fe(III), S = 5/2), whereas the two others remain low-spin (Fe(III), S = 1/2). The data obtained also indicate that the heme groups have distinct axial coordination. The apparent midpoint reduction potential of GSU0105 (-154 mV) is pH independent in the physiological range. However, the pH modulates the reduction potential of the heme that undergoes the low- to high-spin interconversion. The reduction potential values of cytochrome GSU0105 are more distinct compared to those of the PpcA family members, providing the protein with a larger functional working redox potential range. Overall, the results obtained, together with an amino acid sequence analysis of different multiheme cytochrome families, indicate that GSU0105 is a member of a new group of triheme cytochromes.

Activities and metabolic versatility of distinct anammox bacteria in a full-scale wastewater treatment system

Anaerobic ammonium oxidation (anammox) is a key N₂-producing process in the global nitrogen cycle. Major progress in understanding the core mechanism of anammox bacteria has been made, but our knowledge of the survival strategies of anammox bacteria in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Here, by combining metagenomics with in situ metatranscriptomics, complex anammox-driven nitrogen cycles in an anoxic tank and a granular activated carbon (GAC) biofilm module of a full-scale WWTP treating landfill leachate were constructed. Four distinct anammox metagenome-assembled genomes (MAGs), representing a new genus named Ca. Loosdrechtii, a new species in Ca. Kuenenia, a new species in Ca. Brocadia, and a new strain in "Ca. Kuenenia stuttgartiensis", were simultaneously retrieved from the GAC biofilm. Metabolic reconstruction revealed that all anammox organisms highly expressed the core metabolic enzymes and showed a high metabolic versatility. Pathways for dissimilatory nitrate reduction to ammonium (DNRA) coupled to volatile fatty acids (VFAs) oxidation likely assist anammox bacteria to survive unfavorable conditions and facilitate switches between lifestyles in oxygen fluctuating environments. The new Ca. Kuenenia species dominated the anammox community of the GAC biofilm, specifically may be enhanced by the uniquely encoded flexible ammonium and iron acquisition strategies. The new Ca. Brocadia species likely has an extensive niche distribution that is simultaneously established in the anoxic tank and the GAC biofilm, the two distinct niches. The highly diverse and impressive metabolic versatility of anammox bacteria revealed in this study advance our understanding of the survival and application of anammox bacteria in the full-scale wastewater treatment system.

Specificity of Small c-Type Cytochromes in Anaerobic Ammonium Oxidation

Anaerobic ammonium oxidation (anammox) is a bacterial process in which ammonium and nitrite are combined into dinitrogen gas and water, yielding energy for the cell. This process relies on a series of redox reactions catalyzed by a set of enzymes, with electrons being shuttled to and from these enzymes, likely by small cytochrome c proteins. For this system to work productively, these electron carriers require a degree of specificity toward the various possible redox partners they encounter in the cell. Here, we compare two cytochrome c proteins from the anammox model organism Kuenenia stuttgartiensis. We show that they are highly homologous, are expressed at comparable levels, share the same fold, and display highly similar redox potentials, yet one of them accepts electrons from the metabolic enzyme hydroxylamine oxidase (HAO) efficiently, whereas the other does not. An analysis of the crystal structures supplemented by Monte Carlo simulations of the transient redox interactions suggests that this difference is at least partly due to the electrostatic field surrounding the proteins, illustrating one way in which the electron carriers in anammox could attain the required specificity. Moreover, the simulations suggest a different "outlet" for electrons on HAO than has traditionally been assumed.

Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link

The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.

Nitrogen management in landfill leachate using single-stage anammox process-illustrating key nitrogen pathways under an ecogenomics framework

Simultaneous functional gene expressions using mRNA, rate measurements, and biochemical analysis proved the consistent contribution of ammonia oxidizers, heterotrophic denitrifiers, and anammox bacteria in a single-stage attached growth partial nitritation/anammox system for nitrogen management in landfill leachate. Average removal efficiencies of ammonia-nitrogen, total inorganic nitrogen, and COD were 94%, 88%, and 26%, respectively, in the reactor. Off-gas N₂O fluxes increased at relatively higher dissolved oxygen. Batch activity tests revealed the occurrence of significant anammox activity even in the presence of high concentrations of organic carbon in the influent. mRNA based functional expressions of nitrite reductase (nirK and nirS) and hydrazine synthase (hzsA) suggested simultaneous active heterotrophic denitrification and anammox, respectively. 16S rRNA amplicon sequencing revealed Proteobacteria (36-56%), Planctomycetes (10-31%), and Bacteroidetes (6-39%) as dominant phyla in the reactor. Candidatus brocadia was observed as the most abundant genus representing anammox community.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

Role of multiheme cytochromes involved in extracellular anaerobic respiration in bacteria

Heme containing proteins are involved in a broad range of cellular functions, from oxygen sensing and transport to catalyzing oxidoreductive reactions. The two major types of cytochrome (b-type and c-type) only differ in their mechanism of heme attachment, but this has major implications for their cellular roles in both localization and mechanism. The b-type cytochromes are commonly cytoplasmic, or are within the cytoplasmic membrane, while c-type cytochromes are always found outside of the cytoplasm. The mechanism of heme attachment allows for complex c-type multiheme complexes, having the capacity to hold multiple electrons, to be assembled. These are increasingly being identified as secreted into the extracellular environment. For organisms that respire using extracellular substrates, these large multiheme cytochromes allow for electron transfer networks from the cytoplasmic membrane to the cell exterior for the reduction of extracellular electron acceptors. In this review the structures and functions of these networks and the mechanisms by which electrons are transferred to extracellular substrates is described.