Oxidizing enzymes as biocatalysts

This article describes oxidising enzymes used for biocatalytic applications. Redox biocatalysts are highly sought after because of the selectivity, controllability and economy of their reactions, in comparison with conventional chemical reactions. Increasing numbers of oxidative biotransformations are being reported, indicating wide variability in the biocatalyst characteristics and a range of potential and established applications. Several limitations apply to oxidative biotransformations, including the requirement for cofactor regeneration, and low stability and activities. Recent advances in addressing these problems include molecular and reaction engineering approaches.     

Review: Biocatalytic transformations of ferulic acid: An abundant aromatic natural product

In this review we examine the fascinating array of microbial and enzymatic transformations of ferulic acid. Ferulic acid is an extremely abundant, preformed phenolic aromatic chemical found widely in nature. Ferulic acid is viewed as a commodity scale, renewable chemical feedstock for biocatalytic conversion to other useful aromatic chemicals. Most attention is focused on bioconversions of ferulic acid itself. Topics covered include cinnamoyl side-chain cleavage; nonoxidative decarboxylation; mechanistic details of styrene formation; purification and characterization of ferulic acid decarboxylase; conversion of ferulic acid to vanillin;O-demethylation; and reduction reactions. Biotransformations of vinylgualacol are discussed, and selected biotransformations of vanillic acid including oxidative and nonoxidative decarboxylation are surveyed. Finally, enzymatic oxidative dimerization and polymerization reactions are reviewed.     

Contemporary proteomic strategies for cysteine redoxome profiling

Protein cysteine residues are susceptible to oxidative modifications that can affect protein functions. Proteomic techniques that comprehensively profile the cysteine redoxome, the repertoire of oxidized cysteine residues, are pivotal towards a better understanding of the protein redox signaling. Recent technical advances in chemical tools and redox proteomic strategies have greatly improved selectivity, in vivo applicability, and quantification of the cysteine redoxome. Despite this substantial progress, still many challenges remain. Here, we provide an update on the recent advances in proteomic strategies for cysteine redoxome profiling, compare the advantages and disadvantages of current methods and discuss the outstanding challenges and future perspectives for plant redoxome research.

Current cysteine redoxome profiling can characterize systematically diverse oxidative posttranslational modifications

Advances

• The chemical toolbox for Cys redoxome profiling has extensively expanded.
• Advanced chemoproteomic platforms have been applied to target specific Cys oxidative posttranslational modifications (OxiPTMs).
• Various reductomic workflows have been widely implemented for reversible Cys OxiPTMs quantification.
• Workflows have been integrated to measure the occupancy of multiple OxiPTMs simultaneously.
• Disulfide-based traps enable the in situ profiling for –SOH sites.

     

Aspects for the future of biotransformations

Biotransformations have gained extensive importance in practical use as a support for chemical synthesis or in the conversion of natural products. Biotransformations may present an enlargement, a sequential degradation or a specific modification of synthetic or natural compounds. The tools for biotransformations are principally mammalian, plant or microbial cells and their cell-free enzymes. In technical practice the biocatalysts are so far limited to the use of microorganisms and some cell-free enzymes of low cost. Although numerous microbial or enzymatical reactions were already developed for industrial processes, the capacities of biotransformations offer a broad field of inexhaustible possibilities for the future.

     

Chemical intermediates in α-methylnoradrenaline oxidation by tyrosinase—II. Kinetic study of process

• 1.1. The pathway for α-methylnoradrenaline oxidation to α-methylnoradrenochrome by tyrosinase. has been studied as a system of various chemical reactions coupled to an enzymatic reaction.
• 2.2. A theoretical and experimental kinetic approach was proposed for such a system, we named this type of mechanism as a mechanism enzymatic-chemical-chemical (E₂CC).
• 3.3. Rate constants for the implied chemical steps at different temperature and pH values, were evaluated from measurement of the lag period, arising from the accumulation of aminochroine, that took place when α-methylnoradrenaline was oxidized at acid pH.
• 4.4. The thermodynamic activation parameters of the chemical steps, the deprotonation and the internal cyclization of o-quinone into leukoaminochrome, were also calculated.

     

Advances in techniques for phosphorus analysis in biological sources

. Suites of analytical methods for detection and characterization of various forms of phosphorus present in biological sources.

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Highlights? We review the available methods for analyzing various forms of phosphorus. ? Biological, chemical, molecular and microscopic phosphorus analysis methods are summarized. ? Principles, advantages and limitations of each technique are discussed. ? Examples of applications for each technique are provided.     

White biotechnology for green chemistry: fermentative 2-oxocarboxylic acids as novel building blocks for subsequent chemical syntheses

Functionalized compounds, which are difficult to produce by classical chemical synthesis, are of special interest as biotechnologically available targets. They represent useful building blocks for subsequent organic syntheses, wherein they can undergo stereoselective or regioselective reactions. “White Biotechnology” (as defined by the European Chemical Industry [http://www.europabio.org/white_biotech.htm], as part of a sustainable “Green Chemistry,”) supports new applications of chemicals produced via biotechnology. Environmental aspects of this interdisciplinary combination include:

• Use of renewable feedstock

• Optimization of biotechnological processes by means of:

  • New “high performance” microorganisms

  • On-line measurement of substrates and products in bioreactors

  • Alternative product isolation, resulting in higher yields, and lower energy demand

In this overview we describe biotechnologically produced pyruvic, 2-oxopentaric and 2-oxohexaric acids as promising new building blocks for synthetic chemistry. In the first part, the microbial formation of 2-oxocarboxylic acids (2-OCAs) in general, and optimization of the fermentation steps required to form pyruvic acid, 2-oxoglutaric acid, and 2-oxo-d-gluconic acid are described, highlighting the fundamental advantages in comparison to chemical syntheses. In the second part, a set of chemical formula schemes demonstrate that 2-OCAs are applicable as building blocks in the chemical synthesis of, e.g., hydrophilic triazines, spiro-connected heterocycles, benzotriazines, and pyranoic amino acids. Finally, some perspectives are discussed.

     

Some Reactions of 4′-Thionucleosides and Their Sulfones

Abstract

We report interesting and novel reactions of 4′-thionucleosides and their sulfone derivatives when a good leaving group is present in the 5′-position. The results have important implications for the phosphorylation of these nucleoside analogues by standard chemical procedures. Possible mechanisms for these reactions are discussed.

     

Biotransformations by fungi

Summary The regio-and stereoselective characteristics of biotransformations involving oxidative ring expansion of bicyclo[3.2.0]hept-2-en-6-one have been characterised in various dematiaceous fungi of the generaCurvularia andDrechslera.     

Biotransformation of cycloalkanones: Controlled oxidative and reductive bioconversions by anAcinetobacter species

Summary Culture conditions have been optimised to enable resting cell cultures ofAcinetobacter calcoaceticus NCIMB 9871 to selectively undertake either oxidative or reductive biotransformations of various bicyclic ketones.     

Metabolic and contractile differentiation of rabbit muscles during growth

• 1.1. A study was carried out of post-natal evolution of the oxidative, glycolytic and contractile capacities in various types of rabbit muscle.
• 2.2. At birth, muscles are non-differentiated and present very limited metabolic and contractile activity, metabolism is mainly oxidative in all muscles.
• 3.3. Although muscular discrimination is manifest from the sixth week after birth, the glycolytic metabolism reaches its maximum capacity only after six to eight weeks.
• 4.4. Subsequently, oxidative metabolic capacity steadily decreases until adulthood.

     

Effect of Ageing on the Oxidative Browning of Sugar-Amino Acid Model Systems

Sugar-amino acid model systems were aged for 3 months under anaerobic or aerobic conditions. Subsequently, these aged model systems were stored for 2 weeks at 37°C under aerobic conditions to examine “oxidative browning.” The results obtained were as follows:

1. The oxidative browning of the model systems increased with increase of the ageing period. Fe²⁺ increased the effects of the ageing.

2. The model systems aged under anaerobic conditions darkened more than those aged under aerobic conditions during storage for 2 weeks.

3. An Amadori rearrangement product, 1-deoxy-1-glycino-d-fructcse was isolated from the aged glucose-glycine model system and it caused a marked increase in the rate of the oxidative browning. Therefore, Amadori rearrangement products are considered to be important precursors in the oxidative browning reaction.

     

Mining novel biosynthetic machineries of secondary metabolites from actinobacteria

ABSTRACT

Secondary metabolites produced by actinobacteria have diverse structures and important biological activities, making them a useful source of drug development. Diversity of the secondary metabolites indicates that the actinobacteria exploit various chemical reactions to construct a structural diversity. Thus, studying the biosynthetic machinery of these metabolites should result in discovery of various enzymes catalyzing interesting and useful reactions. This review summarizes our recent studies on the biosynthesis of secondary metabolites from actinobacteria, including the biosynthesis of nonproteinogenic amino acids used as building blocks of nonribosomal peptides, the type II polyketide synthase catalyzing polyene scaffold, the nitrous acid biosynthetic pathway involved in secondary metabolite biosynthesis and unique cytochrome P450 catalyzing nitrene transfer. These findings expand the knowledge of secondary metabolite biosynthesis machinery and provide useful tools for future bioengineering.     

Exploiting cell‐free systems: Implementation and debugging of a system of biotransformations

The orchestration of a multitude of enzyme catalysts allows cells to carry out complex and thermodynamically unfavorable chemical conversions. In an effort to recruit these advantages for in vitro biotransformations, we have assembled a 10‐step catalytic system—a system of biotransformations (SBT)—for the synthesis of unnatural monosaccharides based on the versatile building block dihydroxyacetone phosphate (DHAP). To facilitate the assembly of such a network, we have insulated a production pathway from Escherichia coli's central carbon metabolism. This pathway consists of the endogenous glycolysis without triose‐phosphate isomerase to enable accumulation of DHAP and was completed with lactate dehydrogenase to regenerate NAD⁺. It could be readily extended for the synthesis of unnatural sugar molecules, such as the unnatural monosaccharide phosphate 5,6,7‐trideoxy‐D ‐threo‐heptulose‐1‐phosphate from DHAP and butanal. Insulation required in particular inactivation of the amn gene encoding the AMP nucleosidase, which otherwise led to glucose‐independent DHAP production from adenosine phosphates. The work demonstrates that a sufficiently insulated in vitro multi‐step enzymatic system can be readily assembled from central carbon metabolism pathways. Biotechnol. Bioeng. 2010; 106: 376–389. © 2010 Wiley Periodicals, Inc.     

Ozone-induced damage of fibrinogen molecules: identification of oxidation sites by high-resolution mass spectrometry

Fibrinogen is highly susceptible to oxidation compared to other plasma proteins. Fibrinogen oxidation damages its structure and affects the protein function. Ozone-induced oxidative modifications of the fibrinogen Aα, Bβ, and γ polypeptide chains upon addition of various amounts of the oxidiser were studied by mass spectrometry. Amino acid residues located on all three chains and main structural parts of the protein were revealed to be involved in oxidation. The αC-connector was shown to be most vulnerable to oxidation as compared to other structural parts while the E region turned out to be the most protected area of the protein. For the first time, it was established that numerous amino acid residues responsible for the conversion of fibrinogen to fibrin remain unaffected upon fibrinogen oxidation. The data obtained in this study indicate that none of the identified residues, which are considered crucial for the binding of both hole “a” and hole “b” to knob “A” and knob “B”, respectively, as well as those responsible for the thrombin binding to fibrinogen E region, have been subjected to chemical alterations under moderate oxidation. The data on fibrinogen oxidation acquired in the current study enable one to assume that some of the structural fibrinogen parts and easily oxidisable residues could be endowed with antioxidant properties. New findings presented here could be essential for the detection of adaptive molecular mechanisms capable of mitigating the detrimental action of reactive oxygen species (ROS) on the functioning of oxidatively damaged fibrinogen. Data are available via ProteomeXchange with identifier PXD012046.

• Highlights

• Various oxidative modifications were detected in fibrinogen by mass spectrometry

• αC-connector has been shown to be most susceptible to oxidation

• E region proved to be least vulnerable to the action of the oxidising agent

• Some of the Met residues in the fibrinogen structure could operate as ROS scavengers

     

LCA in decision-making processes

Synthetic sulfuric acid is used in a wide range of applications in fine chemical industry. Despite an already performed optimization of input amounts, used sulfuric acid is still a quantitatively important waste by-product. As a result, different utilization technologies for used sulfuric acid exist:

1. production of gypsum
2. thermal reductive cracking
3. thermal cracking and oxidation

This makes an LCA study of this waste by-product quite interesting. In this paper:

? the starting point for a comparative LCA of the above mentioned utilization technologies at a concrete situation is explained, in a work of Ciba-Geigy Corp.

? a short summary of the comparative LCA is presented

? lessons learned from performing the LCA and using it in a decision process are described.

     

Development of strategies for the incorporation of biological pesticides into the integrated management of locusts and grasshoppers

• 1 Effective biological pesticides based on oil formulation of deuteromycete fungal spores have been developed for use against locusts and grasshoppers. The isolate IMI 330189 of Metarhizium anisopliae (flavoviride) var. acridum has been registered, extensively field tested and its operating characteristics explored. It should form an powerful component technology in the integrated management of locust and grasshopper pests.
• 2 The particular advantages of Metarhizium anisopliae were found to be efficacy and persistence, low vertebrate toxicity, little environmental impact, conservation of natural enemies and potential for recycling. Additional socio-economic advantages include the possibility of local production, ease of disposal and versatility in use. The principal disadvantages relate to operating characteristics such as slower speed of kill and slightly greater lability in storage than chemical pesticides.
• 3 Strategies are being developed to integrate biological control agents into locust and grasshopper management schemes; for Metarhizium the accent is placed on: (i) treating the pest before it invades crops and (ii) situations with a high premium on environmental issues.
• 4 For some pest situations, fast-acting chemical pesticides will still be necessary for crop protection.
• 5 A cheaper biological agent, such as Nosema locustae, with the capacity to persist in the pest insect population would be useful. Research is recommended on the long-term impact of Nosema in Africa.
• 6 An evaluation of the utility of the manual destruction of egg pods leads to the conclusion that we should consider the possibility of importing egg parasitoids, such as Scelio parvicornis from Australia, into Africa.
• 7 Further development work is needed to clarify the economics and politics of locust and grasshopper control; to improve the regulatory framework for biopesticides; to inform key decision makers of the availability and potential of Metarhizium; and to implement the bio-intensive IPM strategies described.

     

Candida parapsilosis: A versatile biocatalyst for organic oxidation-reduction reactions

This review highlights the importance of the biocatalyst, Candida parapsilosis for oxidation and reduction reactions of organic compounds and establishes its versatility to generate a variety of chiral synthons. Appropriately designed reactions using C. parapsilosis effect efficient catalysis of organic transformations such as deracemization, enantioselective reduction of prochiral ketones, imines, and kinetic resolution of racemic alcohols via selective oxidation. This review includes the details of these biotransformations, catalyzed by whole cells (wild type and recombinant strains), purified enzymes (oxidoreductases) and immobilized whole cells of C. parapsilosis. The review presents a bioorganic perspective as it discusses the chemo, regio and stereoselectivity of the biocatalyst along with the structure of the substrates and optical purity of the products. Fermentation scale biocatalysis using whole cells of C. parapsilosis for several biotransformations to synthesize important chiral synthons/industrial chemicals is included. A comparison of C. parapsilosis with other whole cell biocatalysts for biocatalytic deracemization and asymmetric reduction of carbonyl and imine groups in the synthesis of a variety of enantiopure products is presented which will provide a basis for the choice of a biocatalyst for a desired organic transformation. Thus, a wholesome perspective on the present status of C. parapsilosis mediated organic transformations and design of new reactions which can be considered for large scale operations is provided. Taken together, C. parapsilosis can now be considered a ‘reagent’ for the organic transformations discussed here.     

Interaction between macrophages and ferroptosis

AbstractFerroptosis, a newly discovered iron-dependent cell death pathway, is characterized by lipid peroxidation and GSH depletion mediated by iron metabolism and is morphologically, biologically and genetically different from other programmed cell deaths. Besides, ferroptosis is usually found accompanied by inflammatory reactions. So far, it has been found participating in the development of many kinds of diseases. Macrophages are a group of immune cells that widely exist in our body for host defense and play an important role in tissue homeostasis by mediating inflammation and regulating iron, lipid and amino acid metabolisms through their unique functions like phagocytosis and efferocytosis, cytokines secretion and ROS production under different polarization. According to these common points in ferroptosis characteristics and macrophages functions, it’s obvious that there must be relationship between macrophages and ferroptosis. Therefore, our review aims at revealing the interaction between macrophages and ferroptosis concerning three metabolisms and integrating the application of certain relationship in curing diseases, mostly cancer. Finally, we also provide inspirations for further studies in therapy for some diseases by targeting certain resident macrophages in distinct tissues to regulate ferroptosis.Facts

• Ferroptosis is considered as a newly discovered form characterized by its nonapoptotic and iron-dependent lipid hydroperoxide, concerning iron, lipid and amino acid metabolisms.
• Ferroptosis has been widely found playing a crucial part in various diseases, including hepatic diseases, neurological diseases, cancer, etc.
• Macrophages are phagocytic immune cells, widely existing and owning various functions such as phagocytosis and efferocytosis, cytokines secretion and ROS production.
• Macrophages are proved to participate in mediating metabolisms and initiating immune reactions to maintain balance in our body.
• Recent studies try to treat cancer by altering macrophages’ polarization which damages tumor microenvironment and induces ferroptosis of cancer cells.

Open questions

• How do macrophages regulate ferroptosis of other tissue cells specifically?
• Can we use the interaction between macrophages and ferroptosis in treating diseases other than cancer?
• What can we do to treat diseases related to ferroptosis by targeting macrophages?
• Is the use of the relationship between macrophages and ferroptosis more effective than other therapies when treating diseases?

Subject terms: Cell death and immune response, Cytokines, Cancer immunotherapy