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How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes.
Martins, MC, Romão, CV, Folgosa, F, Borges, PT, Frazão, C, Teixeira, M
Free radical biology & medicine. 2019;:36-60
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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2.
Comparative review of the recent enzymatic methods used for selective assay of l-lysine.
Isobe, K, Matsui, D, Asano, Y
Analytical biochemistry. 2019;:113335
Abstract
l-Lysine is an essential amino acid important for maintaining human health. To date, many enzymatic methods for assay of l-lysine have been developed. The first method has been developed using l-lysine α-oxidase (l-LysOα). However, low specificity towards l-lysine of l-LysOα is a disadvantage inherent in this method. Recently, methods more specific to l-lysine were developed using newly discovered enzymes such as l-lysine ε-oxidase (l-LysOε), l-amino acid oxidase/monooxygenase (l-AAO/MOG) and l-lysine decarboxylase/oxidase (l-Lys-DC/OD). The present paper reviews recent enzymatic methods used for assay of l-lysine. These l-lysine selective assays rely on detecting and quantifying hydrogen peroxide, a product generated by the oxidase reaction of these enzymes. l-LysOε catalyzes the oxidative deamination of the ε-amino group of l-lysine, thus assays using this enzyme are more specific towards l-lysine than the ones using l-LysOα. The l-AAO/MOG has high substrate specificity towards l-lysine; however it exhibits l-lysine oxidase and monooxygenase activities. The sensitivity of l-AAO/MOG method was improved either by using its mutant, which has reduced monooxygenase activity, or by coupling with an aminoamide-oxidizing enzyme. The l-Lys-DC/OD exhibits both l-lysine decarboxylase and oxidase activities. The sensitivity of the l-Lys-DC/OD method was improved by using putrescine oxidase to oxidize the decarboxylation product of l-lysine.
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3.
Fungal PQQ-dependent dehydrogenases and their potential in biocatalysis.
Takeda, K, Umezawa, K, Várnai, A, Eijsink, VG, Igarashi, K, Yoshida, M, Nakamura, N
Current opinion in chemical biology. 2019;:113-121
Abstract
In 2014, the first fungal pyrroloquinoline-quinone (PQQ)-dependent enzyme was discovered as a pyranose dehydrogenase from the basidiomycete Coprinopsis cinerea (CcPDH). This discovery laid the foundation for a new Auxiliary Activities (AA) family, AA12, in the Carbohydrate-Active enZymes (CAZy) database and revealed a novel enzymatic activity potentially involved in biomass conversion. This review summarizes recent progress made in research on this fungal oxidoreductase and related enzymes. CcPDH consists of the catalytic PQQ-binding AA12 domain, an N-terminal cytochrome b AA8 domain, and a C-terminal family 1 carbohydrate-binding module (CBM1). CcPDH oxidizes 2-keto-d-glucose (d-glucosone), l-fucose, and rare sugars such as d-arabinose and l-galactose, and can activate lytic polysaccharide monooxygenases (LPMOs). Bioinformatic studies suggest a widespread occurrence of quinoproteins in eukaryotes as well as prokaryotes.
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4.
Multicopper oxidases: Biocatalysts in microbial pathogenesis and stress management.
Kaur, K, Sharma, A, Capalash, N, Sharma, P
Microbiological research. 2019;:1-13
Abstract
The acquisition of metal ions such as iron, copper and manganese is essential for the survival of microorganisms as these are constituents of metalloproteins including enzymes, storage proteins, structural elements, transcription factors and antimicrobial factors in various biological processes. However, excess of these metal ions is associated with significant toxicity due to spontaneous redox cycling of ions and obstruction of normal metabolic pathways. To overcome this, microbes have developed a variety of metal regulatory systems allowing them to adapt to the changing biotic and abiotic environments. Multi-copper oxidases (MCOs) such as ceruloplasmins, ferroxidases, laccases and nitrite reductases are such regulatory systems employed by microbes to resist the toxicity of metal ions by controlling their oxidation states under aerobic conditions. MCOs help pathogens survive during an infection by evasion of the toxic environment generated by the host immune system and thus are considered necessary determinants of virulence. This review summarizes the role of MCOs in metal homeostasis under stressful conditions and the extent to which these MCOs contribute to microbial virulence within the host that might prove as an esteemed avenue for the development of novel antimicrobial therapies.
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Alternative oxidase is an important player in the regulation of nitric oxide levels under normoxic and hypoxic conditions in plants.
Kumari, A, Pathak, PK, Bulle, M, Igamberdiev, AU, Gupta, KJ
Journal of experimental botany. 2019;(17):4345-4354
Abstract
Plant mitochondria possess two different pathways for electron transport from ubiquinol: the cytochrome pathway and the alternative oxidase (AOX) pathway. The AOX pathway plays an important role in stress tolerance and is induced by various metabolites and signals. Previously, several lines of evidence indicated that the AOX pathway prevents overproduction of superoxide and other reactive oxygen species. More recent evidence suggests that AOX also plays a role in regulation of nitric oxide (NO) production and signalling. The AOX pathway is induced under low phosphate, hypoxia, pathogen infections, and elicitor treatments. The induction of AOX under aerobic conditions in response to various stresses can reduce electron transfer through complexes III and IV and thus prevents the leakage of electrons to nitrite and the subsequent accumulation of NO. Excess NO under various stresses can inhibit complex IV; thus, the AOX pathway minimizes nitrite-dependent NO synthesis that would arise from enhanced electron leakage in the cytochrome pathway. By preventing NO generation, AOX can reduce peroxynitrite formation and tyrosine nitration. In contrast to its function under normoxia, AOX has a specific role under hypoxia, where AOX can facilitate nitrite-dependent NO production. This reaction drives the phytoglobin-NO cycle to increase energy efficiency under hypoxia.
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6.
An evolving view of methane metabolism in the Archaea.
Evans, PN, Boyd, JA, Leu, AO, Woodcroft, BJ, Parks, DH, Hugenholtz, P, Tyson, GW
Nature reviews. Microbiology. 2019;(4):219-232
Abstract
Methane is a key compound in the global carbon cycle that influences both nutrient cycling and the Earth's climate. A limited number of microorganisms control the flux of biologically generated methane, including methane-metabolizing archaea that either produce or consume methane. Methanogenic and methanotrophic archaea belonging to the phylum Euryarchaeota share a genetically similar, interrelated pathway for methane metabolism. The key enzyme in this pathway, the methyl-coenzyme M reductase (Mcr) complex, catalyses the last step in methanogenesis and the first step in methanotrophy. The discovery of mcr and divergent mcr-like genes in new euryarchaeotal lineages and novel archaeal phyla challenges long-held views of the evolutionary origin of this metabolism within the Euryarchaeota. Divergent mcr-like genes have recently been shown to oxidize short-chain alkanes, indicating that these complexes have evolved to metabolize substrates other than methane. In this Review, we examine the diversity, metabolism and evolutionary history of mcr-containing archaea in light of these recent discoveries.
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7.
Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles.
Ferlez, B, Sutter, M, Kerfeld, CA
mBio. 2019;(1)
Abstract
An increasing number of microbes are being identified that organize catabolic pathways within self-assembling proteinaceous structures known as bacterial microcompartments (BMCs). Most BMCs are characterized by their singular substrate specificity and commonly employ B12-dependent radical mechanisms. In contrast, a less-well-known BMC type utilizes the B12-independent radical chemistry of glycyl radical enzymes (GREs). Unlike B12-dependent enzymes, GREs require an activating enzyme (AE) as well as an external source of electrons to generate an adenosyl radical and form their catalytic glycyl radical. Organisms encoding these glycyl radical enzyme-associated microcompartments (GRMs) confront the challenge of coordinating the activation and maintenance of their GREs with the assembly of a multienzyme core that is encapsulated in a protein shell. The GRMs appear to enlist redox proteins to either generate reductants internally or facilitate the transfer of electrons from the cytosol across the shell. Despite this relative complexity, GRMs are one of the most widespread types of BMC, with distinct subtypes to catabolize different substrates. Moreover, they are encoded by many prominent gut-associated and pathogenic bacteria. In this review, we will focus on the diversity, function, and physiological importance of GRMs, with particular attention given to their associated and enigmatic redox proteins.
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8.
Flavin transferase: the maturation factor of flavin-containing oxidoreductases.
Bogachev, AV, Baykov, AA, Bertsova, YV
Biochemical Society transactions. 2018;(5):1161-1169
Abstract
Flavins, cofactors of many enzymes, are often covalently linked to these enzymes; for instance, flavin adenine mononucleotide (FMN) can form a covalent bond through either its phosphate or isoalloxazine group. The prevailing view had long been that all types of covalent attachment of flavins occur as autocatalytic reactions; however, in 2013, the first flavin transferase was identified, which catalyzes phosphoester bond formation between FMN and Na+-translocating NADHquinone oxidoreductase in certain bacteria. Later studies have indicated that this post-translational modification is widespread in prokaryotes and is even found in some eukaryotes. Flavin transferase can occur as a separate ∼40 kDa protein or as a domain within the target protein and recognizes a degenerate DgxtsAT/S motif in various target proteins. The purpose of this review was to summarize the progress already achieved by studies of the structure, mechanism, and specificity of flavin transferase and to encourage future research on this topic. Interestingly, the flavin transferase gene (apbE) is found in many bacteria that have no known target protein, suggesting the presence of yet unknown flavinylation targets.
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9.
Halogenase engineering and its utility in medicinal chemistry.
Fraley, AE, Sherman, DH
Bioorganic & medicinal chemistry letters. 2018;(11):1992-1999
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Abstract
Halogenation is commonly used in medicinal chemistry to improve the potency of pharmaceutical leads. While synthetic methods for halogenation present selectivity and reactivity challenges, halogenases have evolved over time to perform selective reactions under benign conditions. The optimization of halogenation biocatalysts has utilized enzyme evolution and structure-based engineering alongside biotransformation in a variety of systems to generate stable site-selective variants. The recent improvements in halogenase-catalyzed reactions has demonstrated the utility of these biocatalysts for industrial purposes, and their ability to achieve a broad substrate scope implies a synthetic tractability with increasing relevance in medicinal chemistry.
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10.
Pyrroloquinoline quinone-dependent dehydrogenases of acetic acid bacteria.
Matsutani, M, Yakushi, T
Applied microbiology and biotechnology. 2018;(22):9531-9540
Abstract
Pyrroloquinoline quinone (PQQ)-dependent dehydrogenases (quinoproteins) of acetic acid bacteria (AAB), such as the membrane-bound alcohol dehydrogenase (ADH) and the membrane-bound glucose dehydrogenase, contain PQQ as the prosthetic group. Most of them are located on the periplasmic surface of the cytoplasmic membrane, and function as primary dehydrogenases in cognate substance-oxidizing respiratory chains. Here, we have provided an overview on the function and molecular architecture of AAB quinoproteins, which can be categorized into six groups according to the primary amino acid sequences. Based on the genomic data, we discuss the types of quinoproteins found in AAB genome and how they are distributed. Our analyses indicate that a significant number of uncharacterized orphan quinoproteins are present in AAB. By reviewing recent experimental developments, we discuss how to characterize the as-yet-unknown enzymes. Moreover, our bioinformatics studies also provide insights on how quinoproteins have developed into intricate enzymes. ADH comprises at least two subunits: the quinoprotein dehydrogenase subunit encoded by adhA and the cytochrome subunit encoded by adhB, and the genes are located in a polycistronic transcriptional unit. Findings on stand-alone derivatives of adhA encourage us to speculate on a possible route for ADH development in the evolutional history of AAB. A combination of bioinformatics studies on big genome sequencing data and wet studies assisted with genetic engineering would unravel biochemical functions and physiological role of uncharacterized quinoproteins in AAB, or even in unculturable metagenome.