ENDOR and ESEEM investigation of the Ni-containing superoxide dismutase

Design of a minimal di-nickel hydrogenase peptide

Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.

Mutation of Leaf Senescence 1 Encoding a C2H2 Zinc Finger Protein Induces ROS Accumulation and Accelerates Leaf Senescence in Rice

Premature senescence of leaves causes a reduced yield and quality of rice by affecting plant growth and development. The regulatory mechanisms underlying early leaf senescence are still unclear. The Leaf senescence 1 (LS1) gene encodes a C2H2-type zinc finger protein that is localized to both the nucleus and cytoplasm. In this study, we constructed a rice mutant named leaf senescence 1 (ls1) with a premature leaf senescence phenotype using CRISPR/Cas9-mediated editing of the LS1 gene. The ls1 mutants exhibited premature leaf senescence and reduced chlorophyll content. The expression levels of LS1 were higher in mature or senescent leaves than that in young leaves. The contents of reactive oxygen species (ROS), malondialdehyde (MDA), and superoxide dismutase (SOD) were significantly increased and catalase (CAT) activity was remarkably reduced in the ls1 plants. Furthermore, a faster decrease in pigment content was detected in mutants than that in WT upon induction of complete darkness. TUNEL and staining experiments indicated severe DNA degradation and programmed cell death in the ls1 mutants, which suggested that excessive ROS may lead to leaf senescence and cell death in ls1 plants. Additionally, an RT-qPCR analysis revealed that most senescence-associated and ROS-scavenging genes were upregulated in the ls1 mutants compared with the WT. Collectively, our findings revealed that LS1 might regulate leaf development and function, and that disruption of LS1 function promotes ROS accumulation and accelerates leaf senescence and cell death in rice.

New insights into the mechanism of nickel superoxide degradation from studies of model peptides

A series of small, catalytically active metallopeptides, which were derived from the nickel superoxide dismutase (NiSOD) active site were employed to study the mechanism of superoxide degradation especially focusing on the role of the axial imidazole ligand. In the literature, there are contradicting propositions about the catalytic importance of the N-terminal histidine. Therefore, we studied the stability and activity of a set of eight NiSOD model peptides, which represent the major model systems discussed in the literature to date, yet differing in their length and their Ni-coordination. UV-Vis-coupled stopped-flow kinetic measurements and mass spectrometry analysis unveiled their high oxidation sensitivity in the presence of oxygen and superoxide resulting into a much faster Ni(II)-peptide degradation for the amine/amide Ni(II) coordination than for the catalytically inactive bis-amidate Ni(II) coordination. With respect to these results we determined the catalytic activities for all NiSOD mimics studied herein, which turned out to be in almost the same range of about 2 × 10⁶ M^-1 s^-1. From these experiments, we concluded that the amine/amide Ni(II) coordination is clearly the key factor for catalytic activity. Finally, we were able to clarify the role of the N-terminal histidine and to resolve the contradictory literature propositions, reported in previous studies.

Steric Enforcement about One Thiolate Donor Leads to New Oxidation Chemistry in a NiSOD Model Complex

Ni-containing superoxide dismutase (NiSOD) represents an unusual member of the SOD family due to the presence of oxygen-sensitive Ni-SCys bonds at its active site. Reported in this account is the synthesis and properties of the Ni^II complex of the N₃S₂ ligand [N₃S₂^Me2]^3- ([N₃S₂^Me2]^3- = deprotonated form of 2-((2-mercapto-2-methylpropyl)(pyridin-2-ylmethyl)amino)-N-(2-mercaptoethyl)acetamide), namely Na[Ni(N₃S₂^Me2)] (2), as a NiSOD model that features sterically robust gem-(CH₃)₂ groups on the thiolate α-C positioned trans to the carboxamide. The crystal structure of 2, coupled with spectroscopic measurements from ¹H NMR, X-ray absorption, IR, UV-vis, and mass spectrometry (MS), reveal a planar Ni^II (S = 0) ion coordinated by only the N₂S₂ basal donors of the N₃S₂ ligand. While the structure and spectroscopic properties of 2 resemble those of NiSOD_red and other models, the asymmetric S ligands open up new reaction paths upon chemical oxidation. One unusual oxidation product is the planar Ni^II-N₃S complex [Ni(L^ox)] (5; L^ox = 2-(5,5-dimethyl-2-(pyridin-2-yl)thiazolidin-3-yl)-N-(2-mercaptoethyl)acetamide), where two-electron oxidation takes place at the substituted thiolate and py-CH₂ carbon to generate a thiazolidine heterocycle. Electrochemical measurements of 2 reveal irreversible events wholly consistent with thiolate redox, which were identified by comparison to the Zn^II complex Na[Zn(N₃S₂^Me2)] (3). Although no reaction is observed between 2 and azide, reaction of 2 with superoxide produces multiple products on the basis of UV-vis and MS data, one of which is 5. Density functional theory (DFT) computations suggest that the HOMO in 2 is π* with primary contributions from Ni-dπ/S-pπ orbitals. These contributions can be modulated and biased toward Ni when electron-withdrawing groups are placed on the thiolate α-C. Analysis of the oxidized five-coordinate species 2^ox* by DFT reveal a singly occupied spin-up (α) MO that is largely thiolate based, which supports the proposed Ni^III-thiolate/Ni^II-thiyl radical intermediates that ultimately yield 5 and other products.

Reinventing the Wheel: The NiSOD Story

The most recently discovered SOD requires nickel in its active site – NiSOD. Among the available metals, nickel seems an unlikely redox center. This chapter discusses the protein adaptations required in order to use nickel for SOD catalysis. Cysteine ligands are employed for the first time in an SOD, to suppress the potential of the Ni(ii/iii) couple. However, this adaptation alone is not sufficient to produce an SOD, since thiolate ligands are sensitive to oxidation by H2O2 and O2. Additional adaptations include the use of two unusual backbone N-donor ligands, an amidate and the N-terminal amine. Yet merely producing a stable Ni redox center is not sufficient for SOD catalysis. A source of protons is needed to produce H2O2 and the pH-independent catalysis that is characteristic of SODs. Thus, the cysteine thiolates were also employed to provide a site for protonation. In restricting active site access, NiSOD appears to have utilized the same strategy employed by MnSOD and FeSOD – a “gateway” formed by Tyr residues. Thus, NiSOD represents evolution that converged on the same criteria for catalysis as other SODs, where the adaptations to the metal site are uniquely suited to using nickel as a redox center.