Marine Vanadium-Dependent Haloperoxidases, Their Isolation, Characterization, and Application

Regioselective Halogenation of Lavanducyanin by a Site-Selective Vanadium-Dependent Chloroperoxidase

Halogenated phenazine meroterpenoids are a structurally unusual family of marine actinobacterial natural products that exhibit antibiotic, antibiofilm, and cytotoxic bioactivities. Despite a lack of established phenazine halogenation biochemistry, genomic analysis of Streptomyces sp. CNZ-289, a prolific lavanducyanin and C2-halogenated derivative producer, suggested the involvement of vanadium-dependent haloperoxidases. We subsequently discovered lavanducyanin halogenase (LvcH), characterized it in vitro as a regioselective vanadium-dependent chloroperoxidase, and applied it in late-stage chemoenzymatic synthesis.

Synthesis of Vanadyl Complexes of N-Confused Porphyrins and Their Bromoperoxidase-like Catalytic Activity

Two new vanadyl complexes of N-confused porphyrins (NCPs), [VONCTPP] (V-1) and [VONCP(OMe)8] (V-2), have been synthesized for the first time and investigated as a catalyst for the oxidative bromination reaction of phenol and its derivatives. This article further delineates crystal structures, photophysical, and redox properties of both the vanadyl complexes. Complexes V-1 and V-2 exhibited a significant red shift in their absorption spectra compared with their respective free bases. The single-crystal structure of V-1 revealed that the complex is in the 2H tautomeric form, while EPR studies revealed the +4 oxidation state of vanadium metal having an axial compression with dxy1 configuration. Catalytic potential for bromoperoxidases-like activity has been explored for both complexes V-1 and V-2 for the first time in NCP chemistry with excellent TOF values (4.7-6.3 s-1 for V-1 and 7.3-8.7 s-1 for V-2) using KBr as a source of bromine and H2O2 as a green oxidant in aqueous acidic medium at 298 K. Notably, both catalysts show excellent recyclability over five cycles. The vanadyl-metalated NCPs exhibit excellent stability in the air.

Photothermal conditions and upwelling enhance very short-lived brominated halocarbons emissions in the western tropical Pacific Ocean

Sea-to-air emissions of very short-lived brominated halocarbons (VSLBrHs) are known to contribute to 30 % of stratospheric and tropospheric ozone depletion. However, empirical data on their occurrence in open ocean are scarce, which makes it difficult to estimate the significant contribution of open ocean releases to the global budget of halocarbons. This study was conducted in 2022 to explore the spatial variations of VSLBrHs and their controlling factors in the western tropical Pacific Ocean (WTPO). The findings highlighted that high biological productivity and the resulting dissolved organic matter (DOM) as well as upwelling dynamics significantly influenced the distribution and production of VSLBrHs in seawater, with atmospheric levels primarily governed by oceanic emissions. Based on the simultaneous observation of seawater and atmospheric concentrations, the mean sea-to-air fluxes of CH2Br2, CHBr3, CHBrCl2, and CHBr2Cl were estimated to be 1.01, 6.65, 9.31, and 7.25 nmol m-2 d-1, respectively. Sea-to-air fluxes of these gases in the upwelling regions were 9.0, 4.6, 2.9, and 6.8 times those in the non-upwelling regions, respectively. Additionally, in-situ incubation experiments revealed that the enzymatic mediated biosynthesis pathways of VSLBrHs were enhanced under temperature and light-induced stress and in waters rich in humus-like substances. Therefore, we tentatively concluded that abundant photothermal conditions and the existence of upwelling in the WTPO made it a potential hotspot for the emission of VSLBrHs. This study offers critical insights into the environmental dynamics of VSLBrHs emissions and underscores the importance of regional oceanic conditions in influencing atmospheric greenhouse gas compositions.

Vanadium haloperoxidases as noncanonical terpene synthases

Vanadium-dependent haloperoxidases (VHPOs) are a unique family of enzymes that utilize vanadate, an aqueous halide ion, and hydrogen peroxide to produce an electrophilic halogen species that can be incorporated into electron rich organic substrates. This halogen species can react with terpene substrates and trigger halonium-induced cyclization in a manner reminiscent of class II terpene synthases. While not all VHPOs act in this capacity, several notable examples from algal and actinobacterial species have been characterized to catalyze regio- and enantioselective reactions on terpene and meroterpenoid substrates, resulting in complex halogenated cyclic terpenes through the action of single enzyme. In this article, we describe the expression, purification, and chemical assays of NapH4, a difficult to express characterized VHPO that catalyzes the chloronium-induced cyclization of its meroterpenoid substrate.

Heterologous Expression and Biochemical Characterization of a New Chloroperoxidase Isolated from the Deep-Sea Hydrothermal Vent Black Yeast Hortaea werneckii UBOCC-A-208029

The initiation of this study relies on a targeted genome-mining approach to highlight the presence of a putative vanadium-dependent haloperoxidase-encoding gene in the deep-sea hydrothermal vent fungus Hortaea werneckii UBOCC-A-208029. To date, only three fungal vanadium-dependent haloperoxidases have been described, one from the terrestrial species Curvularia inaequalis, one from the fungal plant pathogen Botrytis cinerea, and one from a marine derived isolate identified as Alternaria didymospora. In this study, we describe a new vanadium chloroperoxidase from the black yeast H. werneckii, successfully cloned and overexpressed in a bacterial host, which possesses higher affinity for bromide (Km = 26 µM) than chloride (Km = 237 mM). The enzyme was biochemically characterized, and we have evaluated its potential for biocatalysis by determining its stability and tolerance in organic solvents. We also describe its potential three-dimensional structure by building a model using the AlphaFold 2 artificial intelligence tool. This model shows some conservation of the 3D structure of the active site compared to the vanadium chloroperoxidase from C. inaequalis but it also highlights some differences in the active site entrance and the volume of the active site pocket, underlining its originality.

Marine enzymes: Classification and application in various industries

Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Nanozyme-based pollutant sensing and environmental treatment: Trends, challenges, and perspectives

Nanozymes are defined as nanomaterials exhibiting enzyme-like properties, and they possess both catalytic functions and nanomaterial's unique physicochemical characteristics. Due to the excellent stability and improved catalytic activity in comparison to natural enzymes, nanozymes have established a wide base for applications in environmental pollutants monitoring and remediation. Nanozymes have been applied in the detection of heavy metal ions, molecules, and organic compounds, both quantitatively and qualitatively. Additionally, within the natural environment, nanozymes can be employed for the degradation of organic and persistent pollutants such as antibiotics, phenols, and textile dyes. Further, the potential sphere of applications for nanozymes traverses from indoor air purification to anti-biofouling agents, and even they show promise in combatting pathogenic bacteria. However, nanozymes may have inherent toxicity, which can restrict their widespread utility. Thus, it is important to evaluate and monitor the interaction and transformation of nanozymes towards biosphere damage when employed within the natural environment in a cradle-to-grave manner, to assure their utmost safety. In this context, various studies have concluded that the green synthesis of nanozymes can efficiently overcome the toxicity limitations in real life applications, and nanozymes can be well utilized in the sensing and degradation of several toxic pollutants including metal ions, pesticides, and chemical warfare agents. In this seminal review, we have explored the great potential of nanozymes, whilst addressing a range of concerns, which have often been overlooked and currently restrict widespread applications and commercialization of nanozymes.

Climate change influence on the levels and trends of persistent organic pollutants (POPs) and chemicals of emerging Arctic concern (CEACs) in the Arctic physical environment - a review

Climate change brings about significant changes in the physical environment in the Arctic. Increasing temperatures, sea ice retreat, slumping permafrost, changing sea ice regimes, glacial loss and changes in precipitation patterns can all affect how contaminants distribute within the Arctic environment and subsequently impact the Arctic ecosystems. In this review, we summarized observed evidence of the influence of climate change on contaminant circulation and transport among various Arctic environment media, including air, ice, snow, permafrost, fresh water and the marine environment. We have also drawn on parallel examples observed in Antarctica and the Tibetan Plateau, to broaden the discussion on how climate change may influence contaminant fate in similar cold-climate ecosystems. Significant knowledge gaps on indirect effects of climate change on contaminants in the Arctic environment, including those of extreme weather events, increase in forests fires, and enhanced human activities leading to new local contaminant emissions, have been identified. Enhanced mobilization of contaminants to marine and freshwater ecosystems has been observed as a result of climate change, but better linkages need to be made between these observed effects with subsequent exposure and accumulation of contaminants in biota. Emerging issues include those of Arctic contamination by microplastics and higher molecular weight halogenated natural products (hHNPs) and the implications of such contamination in a changing Arctic environment is explored.

Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis

Vanadium-dependent haloperoxidases (VHPOs) from Streptomyces bacteria differ from their counterparts in fungi, macroalgae, and other bacteria by catalyzing organohalogenating reactions with strict regiochemical and stereochemical control. While this group of enzymes collectively uses hydrogen peroxide to oxidize halides for incorporation into electron-rich organic molecules, the mechanism for the controlled transfer of highly reactive chloronium ions in the biosynthesis of napyradiomycin and merochlorin antibiotics sets the Streptomyces vanadium-dependent chloroperoxidases apart. Here we report high-resolution crystal structures of two homologous VHPO family members associated with napyradiomycin biosynthesis, NapH1 and NapH3, that catalyze distinctive chemical reactions in the construction of meroterpenoid natural products. The structures, combined with site-directed mutagenesis and intact protein mass spectrometry studies, afforded a mechanistic model for the asymmetric alkene and arene chlorination reactions catalyzed by NapH1 and the isomerase activity catalyzed by NapH3. A key lysine residue in NapH1 situated between the coordinated vanadate and the putative substrate binding pocket was shown to be essential for catalysis. This observation suggested the involvement of the ε-NH2, possibly through formation of a transient chloramine, as the chlorinating species much as proposed in structurally distinct flavin-dependent halogenases. Unexpectedly, NapH3 is modified post-translationally by phosphorylation of an active site His (τ-pHis) consistent with its repurposed halogenation-independent, α-hydroxyketone isomerase activity. These structural studies deepen our understanding of the mechanistic underpinnings of VHPO enzymes and their evolution as enantioselective biocatalysts.

Coastal observation of halocarbons in the Yellow Sea and East China Sea during winter: Spatial distribution and influence of different factors on the enzyme-mediated reactions

Volatile brominated compounds are important trace gases for stratospheric ozone chemistry. In this study, the spatial variations of dibromomethane (CH₂Br₂), bromodichloromethane (CHBrCl₂), dibromochloromethane (CHBr₂Cl) and bromoform (CHBr₃) in the seawater and overlying atmosphere were measured in the Yellow Sea (YS) and the East China Sea (ECS) in winter. The air-sea fluxes of CH₂Br₂, CHBrCl₂, CHBr₂Cl and CHBr₃ ranged from -11.46 to 25.33, -4.68 to 7.91, -8.60 to 4.08 and -88.57 to 8.84 nmol m^-2·d^-1, respectively. In order to understand the mechanism of halocarbons production, we measured bromoperoxidase (BrPO) activity (39.18-186.74 μU·L^-1) in the YS and ECS for the first time using an aminophenyl fluorescein (APF) method and performed in-situ incubation experiments in BrPO-treated seawater. The production rates of CH₂Br₂, CHBrCl₂, CHBr₂Cl and CHBr₃ ranged from 14.21 to 94.74, 0.00 to 19.74, 0.00 to 30.62 and 6.18-72.75 pmol L^-1·h^-1, respectively, in BrPO-treated seawater. There were significantly higher production rates in coastal waters compared with the open sea (P = 0.016) because of higher DOC levels near the coast. Moreover, the production rates of halocarbons increased with BrPO activity and H₂O₂ concentration. The results showed that enzyme-mediated reaction was an important source for the production of halocarbons in seawater. The present research is of great significance for understanding the production mechanisms of halocarbons in seawater and global oceanic halocarbons emissions.

Investigating the Role of Vanadium-Dependent Haloperoxidase Enzymology in Microbial Secondary Metabolism and Chemical Ecology

The chemical diversity of natural products is established by an elegant network of biosynthetic machinery and controlled by a suite of intracellular and environmental cues. Advances in genomics, transcriptomics, and metabolomics have provided useful insight to understand how organisms respond to abiotic and biotic factors to adjust their chemical output; this has permitted researchers to begin asking bigger-picture questions regarding the ecological significance of these molecules to the producing organism and its community. Our lab is motivated by understanding how select microbes construct and manipulate bioactive molecules by utilizing vanadium-dependent haloperoxidase (VHPO) enzymology. This commentary will give perspective into our efforts to understand the unique VHPO-catalyzed conversions which modulate the activities within two ecologically relevant natural product families. Through enhancing our knowledge of microbial natural product biosynthesis, we can understand how and why these bioactive molecules are created.

Diterpene Biosynthesis in Catenulispora acidiphila: On the Mechanism of Catenul-14-en-6-ol Synthase

A new diterpene synthase from the actinomycete Catenulispora acidiphila was identified and the structures of its products were elucidated, including the absolute configurations by an enantioselective deuteration approach. The mechanism of the cationic terpene cyclisation cascade was deeply studied through the use of isotopically labelled substrates and of substrate analogues with partially blocked reactivity, resulting in derailment products that gave further insights into the intermediates along the cascade. Their chemistry was studied, leading to the biomimetic synthesis of a diterpenoid analogue of a brominated sesquiterpene known from the red seaweed Laurencia microcladia.

A Fluorescence-Based Assay System for the Determination of Haloperoxidase-Activity Using a Two-Dimensional Calibration Ap-proach

Screening for an interesting biocatalyst and its subsequent kinetic characterization depends on a reliable activity assay. In this work, a fluorometric assay based on the halogenation of 4-methyl-7-diethylamino-coumarin was established to monitor haloperoxidase-activity. Since haloperoxidases utilize hydrogen peroxide and halide ions to halogenate a broad range of substrates by releasing hypohalous acids, a direct quantification of haloperoxidase-activity remains difficult. With the system presented here, 3-bromo-4-methyl-7-diethylaminocoumarin is preferentially formed and monitored by fluorescence measurements. As starting material and product share similar spectroscopical properties, a two-dimensional calibration ap-proach was utilized to allow for quantification of each compound within a single measurement. To validate the system, the two-dimensional Michaelis-Menten kinetics of a vanadium-dependent chloroperoxidase from Curvularia inaequalis were recorded, yielding the first overall kinetic parameters for this enzyme. With limits of detection and quantification in the low μm range, this assay may provide a reliable alternative system for the quantification of haloperoxidase-activity.

Genetic and Biochemical Reconstitution of Bromoform Biosynthesis in Asparagopsis Lends Insights into Seaweed Reactive Oxygen Species Enzymology

Marine macroalgae, seaweeds, are exceptionally prolific producers of halogenated natural products. Biosynthesis of halogenated molecules in seaweeds is inextricably linked to reactive oxygen species (ROS) signaling as hydrogen peroxide serves as a substrate for haloperoxidase enzymes that participate in the construction these halogenated molecules. Here, using red macroalga Asparagopsis taxiformis, a prolific producer of the ozone depleting molecule bromoform, we provide the discovery and biochemical characterization of a ROS-producing NAD(P)H oxidase from seaweeds. This discovery was enabled by our sequencing of Asparagopsis genomes, in which we find the gene encoding the ROS-producing enzyme to be clustered with genes encoding bromoform-producing haloperoxidases. Biochemical reconstitution of haloperoxidase activities establishes that fatty acid biosynthesis can provide viable hydrocarbon substrates for bromoform production. The ROS production haloperoxidase enzymology that we describe here advances seaweed biology and biochemistry by providing the molecular basis for decades worth of physiological observations in ROS and halogenated natural product biosyntheses.

Will Climate Change Influence Production and Environmental Pathways of Halogenated Natural Products?

Thousands of halogenated natural products (HNPs) pervade the terrestrial and marine environment. HNPs are generated by biotic and abiotic processes and range in complexity from low molecular mass natural halocarbons (nHCs, mostly halomethanes and haloethanes) to compounds of higher molecular mass which often contain oxygen and/or nitrogen atoms in addition to halogens (hHNPs). nHCs have a key role in regulating tropospheric and stratospheric ozone, while some hHNPs bioaccumulate and have toxic properties similar those of anthropogenic-persistent organic pollutants (POPs). Both chemical classes have common sources: biosynthesis by marine bacteria, phytoplankton, macroalgae, and some invertebrate animals, and both may be similarly impacted by alteration of production and transport pathways in a changing climate. The nHCs scientific community is advanced in investigating sources, atmospheric and oceanic transport, and forecasting climate change impacts through modeling. By contrast, these activities are nascent or nonexistent for hHNPs. The goals of this paper are to (1) review production, sources, distribution, and transport pathways of nHCs and hHNPs through water and air, pointing out areas of commonality, (2) by analogy to nHCs, argue that climate change may alter these factors for hHNPs, and (3) suggest steps to improve linkage between nHCs and hHNPs science to better understand and predict climate change impacts.

Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases

Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.

New Napyradiomycin Analogues from Streptomyces sp. Strain CA-271078

As part of our continuing efforts to discover new bioactive compounds from microbial sources, a reinvestigation of extracts of scaled-up cultures of the marine-derived Streptomyces sp. strain CA-271078 resulted in the isolation and structural elucidation of four new napyradiomycins (1-3, 5). The known napyradiomycin SC (4), whose structural details had not been previously described in detail, and another ten related known compounds (6-15). The structures of the new napyradiomycins were characterized by HRMS and 1D- and 2D-NMR spectroscopies and their relative configurations were established through a combination of molecular modelling with nOe and coupling constants NMR analysis. The absolute configuration of each compound is also proposed based on biosynthetic arguments and the comparison of specific rotation data with those of related compounds. Among the new compounds, 1 was determined to be the first non-halogenated member of napyradiomycin A series containing a functionalized prenyl side chain, while 2-4 harbor in their structures the characteristic chloro-cyclohexane ring of the napyradiomycin B series. Remarkably, compound 5 displays an unprecedented 14-membered cyclic ether ring between the prenyl side chain and the chromophore, thus representing the first member of a new class of napyradiomycins that we have designated as napyradiomycin D1. Anti-infective and cytotoxic properties for all isolated compounds were evaluated against a set of pathogenic microorganisms and the HepG2 cell line, respectively. Among the new compounds, napyradiomycin D1 exhibited significant growth-inhibitory activity against methicillin-resistant Staphylococcus aureus, Mycobacterium tuberculosis, and HepG2.

Bromotryptophan and its Analogs in Peptides from Marine Animals

Bromotryptophan is a nonstandard amino acid that is rarely incorporated in ribosomally synthesized and post-translationally modified peptides (ribosomal peptides). Bromotryptophan and its analogs sometimes occur in non-ribosomal peptides. This paper presents an overview of ribosomal and non-ribosomal peptides that are known to contain bromotryptophan and its analogs. This work further covers the biological activities and therapeutic potential of some of these peptides.

Total Enzyme Syntheses of Napyradiomycins A1 and B1

The biosynthetic route to the napyradiomycin family of bacterial meroterpenoids has been fully described 32 years following their original isolation and 11 years after their gene cluster discovery. The antimicrobial and cytotoxic natural products napyradiomycins A1 and B1 are produced using three organic substrates (1,3,6,8-tetrahydroxynaphthalene, dimethylallyl pyrophosphate, and geranyl pyrophosphate), and catalysis via five enzymes: two aromatic prenyltransferases (NapT8 and T9); and three vanadium dependent haloperoxidase (VHPO) homologues (NapH1, H3, and H4). Building upon the previous characterization of NapH1, H3, and T8, we herein describe the initial (NapT9, H1) and final (NapH4) steps required for napyradiomycin construction. This remarkably streamlined biosynthesis highlights the utility of VHPO enzymology in complex natural product generation, as NapH4 efficiently performs a unique chloronium-induced terpenoid cyclization to establish two stereocenters and a new carbon-carbon bond, and dual-acting NapH1 catalyzes chlorination and etherification reactions at two distinct stages of the pathway. Moreover, we employed recombinant napyradiomycin biosynthetic enzymes to chemoenzymatically synthesize milligram quantities in one pot in 1 day. This method represents a viable enantioselective approach to produce complex halogenated metabolites, like napyradiomycin B1, that have yet to be chemically synthesized.

Characterization and Biochemical Assays of Streptomyces Vanadium-Dependent Chloroperoxidases

Vanadium-dependent haloperoxidases (VHPOs) are fascinating enzymes that facilitate electrophilic halogen incorporation into electron-rich substrates, simply requiring vanadate, a halide source, and cosubstrate hydrogen peroxide for activity. Initially characterized in fungi and red algae, VHPOs were long believed to have limited regio-, chemo-, and enantioselectivity in the production of halogenated metabolites. However, the recent discovery of homologues in the biosynthetic gene clusters of the stereoselectively halogenated meroterpenoids from marine-derived Streptomyces bacteria has revised this paradigm. Their intriguing transformations have both enhanced and contributed to the fields of synthetic organic and natural product chemistry. We, herein, describe the expression, purification, and chemical assays of two characterized vanadium-dependent chloroperoxidase enzymes (NapH1 and Mcl24), and one homologue devoid of chlorination activity (NapH3), involved in the biosyntheses of halogenated meroterpenoid products.