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1.
Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide.
Chen, J, Xie, P, Huang, Y, Gao, H
International journal of molecular sciences. 2022;(2)
Abstract
Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.
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2.
4-Deoxy-l-erythro-5-hexoseulose Uronate (DEH) and DEH Reductase: Key Molecule and Enzyme for the Metabolism and Utilization of Alginate.
Kawai, S, Hashimoto, W
Molecules (Basel, Switzerland). 2022;(2)
Abstract
4-Deoxy-l-erythro-5-hexoseulose uronate (DEH), DEH reductase, and alginate lyase have key roles in the metabolism of alginate, a promising carbon source in brown macroalgae for biorefinery. In contrast to the widely reviewed alginate lyase, DEH and DEH reductase have not been previously reviewed. Here, we summarize the current understanding of DEH and DEH reductase, with emphasis on (i) the non-enzymatic and enzymatic formation and structure of DEH and its reactivity to specific amino groups, (ii) the molecular identification, classification, function, and structure, as well as the structural determinants for coenzyme specificity of DEH reductase, and (iii) the significance of DEH for biorefinery. Improved understanding of this and related fields should lead to the practical utilization of alginate for biorefinery.
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3.
Enzymatic modifications of gluten protein: Oxidative enzymes.
Pourmohammadi, K, Abedi, E
Food chemistry. 2021;:129679
Abstract
Oxidative enzymes treat weak flours in order to restore the gluten network of damaged wheat flour and reduce the economic and technological losses. The present review concentrates on oxidative exogenous enzymes (transglutaminase, laccase, glucose oxidase, hexose oxidase) and oxidative endogenous enzymes (tyrosinase, peroxidase, catalase, sulfhydryl oxidase, lipoxygenase, lipase, protein disulfide isomerase, NAD(P)H-dependent dehydrogenase, thioredoxin reductase and glutathione reductase) and their effects on the rheological, functional, and conformational features of gluten and its subunits. Overall, transglutaminase is used in wheat-based foods through introducing isopeptide bonds (ε-γ glutamyl-lysine). Glucose oxidase, hexose oxidase, peroxidase, sulfhydryl oxidase, lipase, and lipoxygenase form disulfide and nondisulfide bonds through producing hydrogen peroxide. Laccase, tyrosinase, and protein disulfide isomerase form cross-links between tyrosine and cysteine residues by generating radicals. Thioredoxin reductase and glutathione reductase create new inter disulfide bonds. The effect of oxidative enzymes on the formation of covalent cross-linkages were substantially more than non-covalent bonds in gluten structure.
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4.
Anaerobic bacterial response to nitric oxide stress: Widespread misconceptions and physiologically relevant responses.
Cole, JA
Molecular microbiology. 2021;(1):29-40
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Abstract
How anaerobic bacteria protect themselves against nitric oxide-induced stress is controversial, not least because far higher levels of stress were used in the experiments on which most of the literature is based than bacteria experience in their natural environments. This results in chemical damage to enzymes that inactivates their physiological function. This review illustrates how transcription control mechanisms reveal physiological roles of the encoded gene products. Evidence that the hybrid cluster protein, Hcp, is a major high affinity NO reductase in anaerobic bacteria is reviewed: if so, its trans-nitrosation activity is a nonspecific secondary consequence of chemical inactivation. Whether the flavorubredoxin, NorV, is equally effective at such low [NO] is unknown. YtfE is proposed to be an enzyme rather than a source of iron for the repair of iron-sulfur proteins damaged by nitrosative stress. Any reaction catalyzed by YtfE needs to be revealed. The concentration of NO that accumulates in the cytoplasm of anaerobic bacteria is unknown, but indirect evidence indicates that it is in the pM to low nM range. Also unknown are the functions of the NO-inducible cytoplasmic proteins YgbA, YeaR, or YoaG. Experiments to resolve some of these questions are proposed.
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5.
Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling.
Reed, CJ, Lam, QN, Mirts, EN, Lu, Y
Chemical Society reviews. 2021;(4):2486-2539
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Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
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6.
Reduction of NO by diiron complexes in relation to flavodiiron nitric oxide reductases.
Pal, N, Jana, M, Majumdar, A
Chemical communications (Cambridge, England). 2021;(70):8682-8698
Abstract
Reduction of nitric oxide (NO) to nitrous oxide (N2O) is associated with immense biological and health implications. Flavodiiron nitric oxide reductases (FNORs) are diiron containing enzymes that catalyze the two electron reduction of NO to N2O and help certain pathogenic bacteria to survive under "nitrosative stress" in anaerobic growth conditions. Consequently, invading bacteria can proliferate inside the body of mammals by bypassing the immune defense mechanism involving NO and may thus lead to harmful infections. Various mechanisms, namely the direct reduction, semireduction, superreduction and hyponitrite mechanisms, have been proposed over time for catalytic NO reduction by FNORs. Model studies in relation to the diiron active site of FNORs have immensely helped to replicate the minimal structure-reactivity relationship and to understand the mechanism of NO reduction. A brief overview of the FNOR activity and the proposed reaction mechanisms followed by a systematic description and detailed analysis of the model studies is presented, which describes the development in the area of NO reduction by diiron complexes and its implications. A great deal of successful modeling chemistry as well as the shortcomings related to the synthesis and reactivity studies is discussed in detail. Finally, future prospects in this particular area of research are proposed, which in due course may bring more clarity in the understanding of this important redox reaction.
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7.
Methionine dependence in tumor cells: The potential role of cobalamin and MMACHC.
Sorin, M, Watkins, D, Gilfix, BM, Rosenblatt, DS
Molecular genetics and metabolism. 2021;(3):155-161
Abstract
Methionine dependence of tumor cell lines, the inability to grow in tissue culture media lacking methionine but supplemented with homocysteine, has been known for decades, but an understanding of the mechanism underlying this phenomenon remains incomplete. Methionine dependence of certain glioma and melanoma cell lines has been linked to alterations in the metabolism of cobalamin (vitamin B12). In the MeWo LC1 melanoma line, complementation analysis demonstrated that the genetic defect affected the same locus mutated in the cblC inborn error of cobalamin metabolism; hypermethylation of the MMACHC promoter was subsequently demonstrated. Analysis of data in the Cancer Cell Line Encyclopedia showed increased MMACHC methylation levels in melanoma lines compared to other types of cancer. RNA sequencing data from isolated tumors, tabulated at the cBioPortal for Cancer Genomics website, showed decreased MMACHC expression compared to other tumors; and methylation data tabulated at the TGGA Wanderer website demonstrated increased MMACHC methylation. These data suggest that disruptions in cobalamin metabolism might play a more general role in methionine dependence, and potentially in the pathogenesis of melanoma cell lines and primary tumors.
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8.
Fluorine biocatalysis.
Wu, L, Maglangit, F, Deng, H
Current opinion in chemical biology. 2020;:119-126
Abstract
The introduction of fluorine atoms into organic molecules has received considerable attention as these organofluorines have often found widespread applications in bioorganic chemistry, medicinal chemistry and biomaterial science. Despite innovation of synthetic C-F forming methodologies, selective fluorination is still extremely challenging. Therefore, a biotransformation approach using fluorine biocatalysts is needed to selectively introduce fluorine into structurally diverse molecules. Yet, there are few ways that enable incorporation of fluorine into structurally complex bioactive molecules. One is to extend the substrate scope of the existing enzyme inventory. Another is to expand the biosynthetic pathways to accept fluorinated precursors for producing fluorinated bioactive molecules. Finally, an understanding of the physiological roles of fluorometabolites in the producing microorganisms will advance our ability to engineer a microorganism to produce novel fluorinated commodities. Here, we review the fluorinase biotechnology and fluorine biocatalysts that incorporate fluorine motifs to generate fluorinated molecules, and highlight areas for future developments.
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9.
Cytokinin dehydrogenase: a genetic target for yield improvement in wheat.
Chen, L, Zhao, J, Song, J, Jameson, PE
Plant biotechnology journal. 2020;(3):614-630
Abstract
The plant hormone group, the cytokinins, is implicated in both qualitative and quantitative components of yield. Cytokinins have opposing actions in shoot and root growth-actions shown to involve cytokinin dehydrogenase (CKX), the enzyme that inactivates cytokinin. We revise and provide unambiguous names for the CKX gene family members in wheat, based on the most recently released wheat genome database, IWGSC RefSeq v1.0 & v2.0. We review expression data of CKX gene family members in wheat, revealing tissue-specific gene family member expression as well as sub-genome-specific expression. Manipulation of CKX in cereals shows clear impacts on yield, root growth and orientation, and Zn nutrition, but this also emphasizes the necessity to unlink promotive effects on grain yield from negative effects of cytokinin on root growth and uptake of mineral nutrients, particularly Zn and Fe. Wheat is the most widely grown cereal crop globally, yet is under-research compared with rice and maize. We highlight gaps in our knowledge of the involvement of CKX for wheat. We also highlight the necessity for accurate analysis of endogenous cytokinins, acknowledging why this is challenging, and provide examples where inadequate analyses of endogenous cytokinins have led to unjustified conclusions. We acknowledge that the allohexaploid nature of bread wheat poses challenges in terms of uncovering useful mutations. However, we predict TILLING followed by whole-exome sequencing will uncover informative mutations and we indicate the potential for stacking mutations within the three genomes to modify yield components. We model a wheat ideotype based on CKX manipulation.
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10.
An enzymatic method for precise oxygen affinity measurements over nanomolar-to-millimolar concentration regime.
Sanyal, R, Bhagi-Damodaran, A
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry. 2020;(2):181-186
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Abstract
Oxygen affinity is an important property of metalloproteins that helps elucidate their reactivity profile and mechanism. Heretofore, oxygen affinity values were determined either using flash photolysis and polarography techniques that require expensive instrumentation, or using oxygen titration methods which are erroneous at low nanomolar and at high millimolar oxygen concentrations. Here, we describe an inexpensive, easy-to-setup, and a one-pot method for oxygen affinity measurements that uses the enzyme chlorite dismutase (Cld) as a precise in situ oxygen source. Using this method, we measure thermodynamic and kinetic oxygen affinities (Kd and KM) of different classes of heme and non-heme metalloproteins involved in oxygen transport, sensing, and catalysis. The method enables oxygen affinity measurements over a wide concentration range from 10 nM to 5 mM which is unattainable by simply diluting oxygen-saturated buffers. In turn, we were able to precisely measure oxygen affinities of a model set of eight different metalloproteins with affinities ranging from 48 ± 3 nM to 1.18 ± 0.03 mM. Overall, the Cld method is easy and inexpensive to set up, requires significantly lower quantities of protein, enables precise oxygen affinity measurements, and is applicable for proteins exhibiting nanomolar-to-millimolar affinity values.