Abstract:Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. W… Show more
“…Recently, a new NrfA subclass was identified in G. lovleyi . Structural characterization indicates that unlike the previously characterized NrfA homologs, G. lovleyi NrfA has a critical arginine residue in the region otherwise occupied by Ca 2+ . Phylogenetic analysis helped confirm that this enzyme represents a new subclass of NrfA .…”
Section: The Nitrogen Cyclementioning
confidence: 99%
“…Phylogenetic analysis helped confirm that this enzyme represents a new subclass of NrfA . Like all available NrfA crystal structures, ,− G. lovleyi NrfA crystallizes as a homodimer (Figure ), but dynamic light scattering characterization suggests that the enzyme actually remains a monomer in solution, even up to a concentration of ∼300 μM, challenging the long held notion that NrfA is a functional dimer. , However, it should be noted that NrfA proteins form a complex with their physiological electron donors, NrfH or NrfBCD, and the exact composition of the resulting complex under physiological conditions is currently unknown. ,,− …”
Nitric oxide (NO)
is an important signaling molecule that is involved
in a wide range of physiological and pathological events in biology.
Metal coordination chemistry, especially with iron, is at the heart
of many biological transformations involving NO. A series of heme
proteins, nitric oxide synthases (NOS), soluble guanylate cyclase
(sGC), and nitrophorins, are responsible for the biosynthesis, sensing,
and transport of NO. Alternatively, NO can be generated from nitrite
by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing
small molecules such as nitrosothiols and dinitrosyl iron complexes
(DNICs) can serve as an alternative vehicle for NO storage and transport.
Once NO is formed, the rich reaction chemistry of NO leads to a wide
variety of biological activities including reduction of NO by heme
or non-heme iron-containing NO reductases and protein post-translational
modifications by DNICs. Much of our understanding of the reactivity
of metal sites in biology with NO and the mechanisms of these transformations
has come from the elucidation of the geometric and electronic structures
and chemical reactivity of synthetic model systems, in synergy with
biochemical and biophysical studies on the relevant proteins themselves.
This review focuses on recent advancements from studies on proteins
and model complexes that not only have improved our understanding
of the biological roles of NO but also have provided foundations for
biomedical research and for bio-inspired catalyst design in energy
science.
“…Recently, a new NrfA subclass was identified in G. lovleyi . Structural characterization indicates that unlike the previously characterized NrfA homologs, G. lovleyi NrfA has a critical arginine residue in the region otherwise occupied by Ca 2+ . Phylogenetic analysis helped confirm that this enzyme represents a new subclass of NrfA .…”
Section: The Nitrogen Cyclementioning
confidence: 99%
“…Phylogenetic analysis helped confirm that this enzyme represents a new subclass of NrfA . Like all available NrfA crystal structures, ,− G. lovleyi NrfA crystallizes as a homodimer (Figure ), but dynamic light scattering characterization suggests that the enzyme actually remains a monomer in solution, even up to a concentration of ∼300 μM, challenging the long held notion that NrfA is a functional dimer. , However, it should be noted that NrfA proteins form a complex with their physiological electron donors, NrfH or NrfBCD, and the exact composition of the resulting complex under physiological conditions is currently unknown. ,,− …”
Nitric oxide (NO)
is an important signaling molecule that is involved
in a wide range of physiological and pathological events in biology.
Metal coordination chemistry, especially with iron, is at the heart
of many biological transformations involving NO. A series of heme
proteins, nitric oxide synthases (NOS), soluble guanylate cyclase
(sGC), and nitrophorins, are responsible for the biosynthesis, sensing,
and transport of NO. Alternatively, NO can be generated from nitrite
by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing
small molecules such as nitrosothiols and dinitrosyl iron complexes
(DNICs) can serve as an alternative vehicle for NO storage and transport.
Once NO is formed, the rich reaction chemistry of NO leads to a wide
variety of biological activities including reduction of NO by heme
or non-heme iron-containing NO reductases and protein post-translational
modifications by DNICs. Much of our understanding of the reactivity
of metal sites in biology with NO and the mechanisms of these transformations
has come from the elucidation of the geometric and electronic structures
and chemical reactivity of synthetic model systems, in synergy with
biochemical and biophysical studies on the relevant proteins themselves.
This review focuses on recent advancements from studies on proteins
and model complexes that not only have improved our understanding
of the biological roles of NO but also have provided foundations for
biomedical research and for bio-inspired catalyst design in energy
science.
“…5 ) [ 164 ]. These characteristic basic features of NrfA, detected in nitrite reductase of S. deleyianum and W. succinogenes , have been also found in the NrfA structures of E. coli [ 165 , 166 ], D. desulfuricans ATCC27774 [ 167 , 168 ], S. oneidensis [ 169 ], the NrfA 4 H 2 complex of D. vulgaris [ 170 , 171 ], and most recently in NrfA of the bacterium Geobacter lovleyi [ 172 , 173 ]. Fig.…”
Section: Sulfur Respiration and Reduction Of Nitrite To Ammonia In
...mentioning
confidence: 89%
“…Furthermore, phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca 2+ -independent, Arg-containing NrfAgl represents a new subclass of pentaheme cytochrome c nitrite reductase [ 172 , 173 ].…”
Section: Structure Of Pentaheme Cytochrome
C
Nitri...mentioning
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2− is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2− to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
Graphical abstract
“…For example, out of all CHO molecular formulas within dry assemblages, we see that they contribute to convergence more frequently than CHONSP molecular formulas. Wang et al, 2018;Samaddar et al, 2019;Campeciño et al, 2020). Taken together, this potentially points to a combinatorial effect, whereby the functional development driven by N/P-containing formulas is tied to organismal selectivity (i.e., roles of Geobacteraceae in the N/P cycles).…”
Section: Homologous Series Disproportionately Contribute To Convergen...mentioning
Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTIfeat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTIfeat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTIfeat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTIfeat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTIfeat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.
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