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Baumgartner JT, McCaughey CS, Fleming HS, Lentz AR, Sanchez LM, McKinnie SMK. Vanadium-dependent haloperoxidases from diverse microbes halogenate exogenous alkyl quinolone quorum sensing signals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606109. [PMID: 39131370 PMCID: PMC11312541 DOI: 10.1101/2024.07.31.606109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Site-selective vanadium-dependent haloperoxidases (VHPOs) are a unique enzyme family that catalyze selective halogenation reactions previously characterized within bacterial natural product biosynthetic pathways. However, the broader chemical roles and biological distribution of these halogenases remains to be explored. Using bioinformatic methods, we have defined a VHPO subfamily that regioselectively brominates alkyl quinolone (AQ) quorum sensing molecules. In vitro AQ halogenation activity was demonstrated from phylogenetically distinct bacteria lacking established AQ biosynthetic pathways and sourced from diverse environments. AQ-VHPOs show high sequence and biochemical similarities with negligible genomic synteny or biosynthetic gene cluster co-localization. Exposure of VHPO-containing microbes to synthetic AQs or established bacterial producers identifies the chemical and spatial response to subvert their bacteriostatic effects. The characterization of novel homologs from bacterial taxa without previously demonstrated vanadium enzymology suggests VHPO-mediated AQ bromination is a niche to manipulate the chemical ecology of microbial communities.
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Loan T, Vickers CE, Ayliffe M, Luo M. β-Dicarbonyls Facilitate Engineered Microbial Bromoform Biosynthesis. ACS Synth Biol 2024; 13:1492-1497. [PMID: 38525720 PMCID: PMC11106770 DOI: 10.1021/acssynbio.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
Ruminant livestock produce around 24% of global anthropogenic methane emissions. Methanogenesis in the animal rumen is significantly inhibited by bromoform, which is abundant in seaweeds of the genus Asparagopsis. This has prompted the development of livestock feed additives based on Asparagopsis to mitigate methane emissions, although this approach alone is unlikely to satisfy global demand. Here we engineer a non-native biosynthesis pathway to produce bromoform in vivo with yeast as an alternative biological source that may enable sustainable, scalable production of bromoform by fermentation. β-dicarbonyl compounds with low pKa values were identified as essential substrates for bromoform production and enabled bromoform synthesis in engineered Saccharomyces cerevisiae expressing a vanadate-dependent haloperoxidase gene. In addition to providing a potential route to the sustainable biological production of bromoform at scale, this work advances the development of novel microbial biosynthetic pathways for halogenation.
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Affiliation(s)
- Thomas
D. Loan
- CSIRO
Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
| | - Claudia E. Vickers
- ARC
Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre
of Agriculture and the Bioeconomy, School of Biology and Environmental
Science, Faculty of Science, Queensland
University of Technology, Brisbane, QLD 4000, Australia
| | - Michael Ayliffe
- CSIRO
Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
| | - Ming Luo
- CSIRO
Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
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Baumgartner JT, Lozano Salazar LI, Varga LA, Lefebre GH, McKinnie SMK. Vanadium haloperoxidases as noncanonical terpene synthases. Methods Enzymol 2024; 699:447-475. [PMID: 38942514 DOI: 10.1016/bs.mie.2024.03.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
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.
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Affiliation(s)
- Jackson T Baumgartner
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Lia I Lozano Salazar
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Lukas A Varga
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Gabriel H Lefebre
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Shaun M K McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, United States.
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Maldonado-Ruiz K, Pedroza-Islas R, Pedraza-Segura L. Blue Biotechnology: Marine Bacteria Bioproducts. Microorganisms 2024; 12:697. [PMID: 38674641 PMCID: PMC11051736 DOI: 10.3390/microorganisms12040697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The ocean is the habitat of a great number of organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent a vast and largely unexplored reservoir of bioactive compounds with diverse industrial applications like terrestrial microorganisms. This review examines the properties and potential applications of products derived from marine microorganisms, including bacteriocins, enzymes, exopolysaccharides, and pigments, juxtaposing them in some cases against their terrestrial counterparts. We discuss the distinct characteristics that set marine-derived products apart, including enhanced stability and unique structural features such as the amount of uronic acid and sulfate groups in exopolysaccharides. Further, we explore the uses of these marine-derived compounds across various industries, ranging from food and pharmaceuticals to cosmetics and biotechnology. This review also presents a broad description of biotechnologically important compounds produced by bacteria isolated from marine environments, some of them with different qualities compared to their terrestrial counterparts.
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Affiliation(s)
| | - Ruth Pedroza-Islas
- Department of Chemical, Industrial and Food Engineering, Universidad Iberoamericana, Prol. Paseo de la Reforma 880, Lomas de Santa Fe, Mexico City 01210, Mexico; (K.M.-R.); (L.P.-S.)
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McKinnie LJ, Cummins SF, Zhao M. Identification of Incomplete Annotations of Biosynthesis Pathways in Rhodophytes Using a Multi-Omics Approach. Mar Drugs 2023; 22:3. [PMID: 38276641 PMCID: PMC10817344 DOI: 10.3390/md22010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Rhodophytes (red algae) are an important source of natural products and are, therefore, a current research focus in terms of metabolite production. The recent increase in publicly available Rhodophyte whole genome and transcriptome assemblies provides the resources needed for in silico metabolic pathway analysis. Thus, this study aimed to create a Rhodophyte multi-omics resource, utilising both genomes and transcriptome assemblies with functional annotations to explore Rhodophyte metabolism. The genomes and transcriptomes of 72 Rhodophytes were functionally annotated and integrated with metabolic reconstruction and phylogenetic inference, orthology prediction, and gene duplication analysis to analyse their metabolic pathways. This resource was utilised via two main investigations: the identification of bioactive sterol biosynthesis pathways and the evolutionary analysis of gene duplications for known enzymes. We report that sterol pathways, including campesterol, β-sitosterol, ergocalciferol and cholesterol biosynthesis pathways, all showed incomplete annotated pathways across all Rhodophytes despite prior in vivo studies showing otherwise. Gene duplication analysis revealed high rates of duplication of halide-associated haem peroxidases in Florideophyte algae, which are involved in the biosynthesis of drug-related halogenated secondary metabolites. In summary, this research revealed trends in Rhodophyte metabolic pathways that have been under-researched and require further functional analysis. Furthermore, the high duplication of haem peroxidases and other peroxidase enzymes offers insight into the potential drug development of Rhodophyte halogenated secondary metabolites.
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Affiliation(s)
- Lachlan J. McKinnie
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
| | - Scott F. Cummins
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
| | - Min Zhao
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
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Recent development of biomimetic halogenation inspired by vanadium dependent haloperoxidase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Zheng J, Antrobus S, Feng W, Purdy TN, Moore BS, Pessah IN. Marine and Anthropogenic Bromopyrroles Alter Cellular Ca 2+ Dynamics of Murine Cortical Neuronal Networks by Targeting the Ryanodine Receptor and Sarco/Endoplasmic Reticulum Ca 2+-ATPase. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16023-16033. [PMID: 34788016 PMCID: PMC8813095 DOI: 10.1021/acs.est.1c05214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bromopyrroles (BrPyr) are synthesized naturally by marine sponge symbionts and produced anthropogenically as byproducts of wastewater treatment. BrPyr interact with ryanodine receptors (RYRs) and sarco/endoplasmic reticulum (SR/ER) Ca2+-ATPase (SERCA). Influences of BrPyr on the neuronal network activity remain uncharted. BrPyr analogues with differing spectra of RYR/SERCA activities were tested using RYR-null or RYR1-expressing HEK293 and murine cortical neuronal/glial cocultures (NGCs) loaded with Fluo-4 to elucidate their mechanisms altering Ca2+ dynamics. The NGC electrical spike activity (ESA) was measured from NGCs plated on multielectrode arrays. Nanomolar tetrabromopyrrole (TBP, 1) potentiated caffeine-triggered Ca2+ release independent of extracellular [Ca2+] in RYR1-HEK293, whereas higher concentrations produce slow and sustained rise in cytoplasmic [Ca2+] independent of RYR1 expression. TBP, 2,3,5-tribromopyrrole (2), pyrrole (3), 2,3,4-tribromopyrrole (4), and ethyl 4-bromopyrrole-2-carboxylate (5) added acutely to NGC showed differential potency; rank order TBP (IC50 ≈ 220 nM) > 2 ≫ 5, whereas 3 and 4 were inactive at 10 μM. TBP >2 μM elicited sustained elevation of cytoplasmic [Ca2+] and loss of neuronal viability. TBP did not alter network ESA. BrPyr from marine and anthropogenic sources are ecological signaling molecules and emerging anthropogenic pollutants of concern to environmental and human health that potently alter ER Ca2+ dynamics and warrant further investigation in vivo.
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Affiliation(s)
- Jing Zheng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | - Shane Antrobus
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | - Wei Feng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | - Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, California 92037, United States
- Scripps Institution of Oceanography, University of California, San Diego, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92037, United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, California 92037, United States
- Scripps Institution of Oceanography, University of California, San Diego, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92037, United States
| | - Isaac N Pessah
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
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Cyanobacteria and Cyanotoxins in a Changing Environment: Concepts, Controversies, Challenges. WATER 2021. [DOI: 10.3390/w13182463] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Concern is widely being published that the occurrence of toxic cyanobacteria is increasing in consequence of climate change and eutrophication, substantially threatening human health. Here, we review evidence and pertinent publications to explore in which types of waterbodies climate change is likely to exacerbate cyanobacterial blooms; whether controlling blooms and toxin concentrations requires a balanced approach of reducing not only the concentrations of phosphorus (P) but also those of nitrogen (N); how trophic and climatic changes affect health risks caused by toxic cyanobacteria. We propose the following for further discussion: (i) Climate change is likely to promote blooms in some waterbodies—not in those with low concentrations of P or N stringently limiting biomass, and more so in shallow than in stratified waterbodies. Particularly in the latter, it can work both ways—rendering conditions for cyanobacterial proliferation more favourable or less favourable. (ii) While N emissions to the environment need to be reduced for a number of reasons, controlling blooms can definitely be successful by reducing only P, provided concentrations of P can be brought down to levels sufficiently low to stringently limit biomass. Not the N:P ratio, but the absolute concentration of the limiting nutrient determines the maximum possible biomass of phytoplankton and thus of cyanobacteria. The absolute concentrations of N or P show which of the two nutrients is currently limiting biomass. N can be the nutrient of choice to reduce if achieving sufficiently low concentrations has chances of success. (iii) Where trophic and climate change cause longer, stronger and more frequent blooms, they increase risks of exposure, and health risks depend on the amount by which concentrations exceed those of current WHO cyanotoxin guideline values for the respective exposure situation. Where trophic change reduces phytoplankton biomass in the epilimnion, thus increasing transparency, cyanobacterial species composition may shift to those that reside on benthic surfaces or in the metalimnion, changing risks of exposure. We conclude that studying how environmental changes affect the genotype composition of cyanobacterial populations is a relatively new and exciting research field, holding promises for understanding the biological function of the wide range of metabolites found in cyanobacteria, of which only a small fraction is toxic to humans. Overall, management needs case-by-case assessments focusing on the impacts of environmental change on the respective waterbody, rather than generalisations.
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Investigating the Role of Vanadium-Dependent Haloperoxidase Enzymology in Microbial Secondary Metabolism and Chemical Ecology. mSystems 2021; 6:e0078021. [PMID: 34427499 PMCID: PMC8407465 DOI: 10.1128/msystems.00780-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
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.
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