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De Angelis M, Schobesberger S, Selinger F, Sedlmayr VL, Frauenlob M, Corcione O, Dong S, Gilardi G, Ertl P, Sadeghi SJ. A multi-channel microfluidic platform based on human flavin-containing monooxygenase 3 for personalised medicine. RSC Adv 2024; 14:13209-13217. [PMID: 38655484 PMCID: PMC11037025 DOI: 10.1039/d4ra01516a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024] Open
Abstract
Human flavin-containing monooxygenase 3 (FMO3) is a drug-metabolizing enzyme (DME) which is known to be highly polymorphic. Some of its polymorphic variants are associated with inter-individual differences that contribute to drug response. In order to measure these differences, the implementation of a quick and efficient in vitro assay is highly desirable. To this end, in this work a microfluidic immobilized enzyme reactor (μ-IMER) was developed with four separate serpentines where FMO3 and its two common polymorphic variants (V257M and E158K) were covalently immobilized via glutaraldehyde cross-linking in the presence of a polylysine coating. Computational fluid dynamics simulations were performed to calculate the selected substrate retention time in serpentines with different surface areas at various flow rates. The oxidation of tamoxifen, an anti-breast cancer drug, was used as a model reaction to characterize the new device in terms of available surface area for immobilization, channel coating, and applied flow rate. The highest amount of product was obtained when applying a 10 μL min-1 flow rate on polylysine-coated serpentines with a surface area of 90 mm2 each. Moreover, these conditions were used to test the device as a multi-enzymatic platform by simultaneously assessing the conversion of tamoxifen by FMO3 and its two polymorphic variants immobilized on different serpentines of the same chip. The results obtained demonstrate that the differences observed in the conversion of tamoxifen within the chip are similar to those already published (E158K > WT > V257M). Therefore, this microfluidic platform provides a feasible option for fabricating devices for personalised medicine.
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Affiliation(s)
- Melissa De Angelis
- Department of Life Sciences and Systems Biology, University of Torino via Accademia Albertina 13 10123 Torino Italy
| | | | - Florian Selinger
- TU Wien, Faculty of Technical Chemistry Getreidemarkt 9 1060 Vienna Austria
| | | | - Martin Frauenlob
- TU Wien, Faculty of Technical Chemistry Getreidemarkt 9 1060 Vienna Austria
| | - Orsola Corcione
- Department of Life Sciences and Systems Biology, University of Torino via Accademia Albertina 13 10123 Torino Italy
| | - Shiman Dong
- Department of Life Sciences and Systems Biology, University of Torino via Accademia Albertina 13 10123 Torino Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino via Accademia Albertina 13 10123 Torino Italy
| | - Peter Ertl
- TU Wien, Faculty of Technical Chemistry Getreidemarkt 9 1060 Vienna Austria
| | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino via Accademia Albertina 13 10123 Torino Italy
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2
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Yin CF, Nie Y, Li T, Zhou NY. AlmA involved in the long-chain n-alkane degradation pathway in Acinetobacter baylyi ADP1 is a Baeyer-Villiger monooxygenase. Appl Environ Microbiol 2024; 90:e0162523. [PMID: 38168668 PMCID: PMC10807437 DOI: 10.1128/aem.01625-23] [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: 09/14/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Many Acinetobacter species can grow on n-alkanes of varying lengths (≤C40). AlmA, a unique flavoprotein in these Acinetobacter strains, is the only enzyme proven to be required for the degradation of long-chain (LC) n-alkanes, including C32 and C36 alkanes. Although it is commonly presumed to be a terminal hydroxylase, its role in n-alkane degradation remains elusive. In this study, we conducted physiological, biochemical, and bioinformatics analyses of AlmA to determine its role in n-alkane degradation by Acinetobacter baylyi ADP1. Consistent with previous reports, gene deletion analysis showed that almA was vital for the degradation of LC n-alkanes (C26-C36). Additionally, enzymatic analysis revealed that AlmA catalyzed the conversion of aliphatic 2-ketones (C10-C16) to their corresponding esters, but it did not conduct n-alkane hydroxylation under the same conditions, thus suggesting that AlmA in strain ADP1 possesses Baeyer-Villiger monooxygenase (BVMO) activity. These results were further confirmed by bioinformatics analysis, which revealed that AlmA was closer to functionally identified BVMOs than to hydroxylases. Altogether, the results of our study suggest that LC n-alkane degradation by strain ADP1 possibly follows a novel subterminal oxidation pathway that is distinct from the terminal oxidation pathway followed for short-chain n-alkane degradation. Furthermore, our findings suggest that AlmA catalyzes the third reaction in the LC n-alkane degradation pathway.IMPORTANCEMany microbial studies on n-alkane degradation are focused on the genes involved in short-chain n-alkane (≤C16) degradation; however, reports on the genes involved in long-chain (LC) n-alkane (>C20) degradation are limited. Thus far, only AlmA has been reported to be involved in LC n-alkane degradation by Acinetobacter spp.; however, its role in the n-alkane degradation pathway remains elusive. In this study, we conducted a detailed characterization of AlmA in A. baylyi ADP1 and found that AlmA exhibits Baeyer-Villiger monooxygenase activity, thus indicating the presence of a novel LC n-alkane biodegradation mechanism in strain ADP1.
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Affiliation(s)
- Chao-Fan Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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3
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Bitzenhofer NL, Höfel C, Thies S, Weiler AJ, Eberlein C, Heipieper HJ, Batra‐Safferling R, Sundermeyer P, Heidler T, Sachse C, Busche T, Kalinowski J, Belthle T, Drepper T, Jaeger K, Loeschcke A. Exploring engineered vesiculation by Pseudomonas putida KT2440 for natural product biosynthesis. Microb Biotechnol 2024; 17:e14312. [PMID: 37435812 PMCID: PMC10832525 DOI: 10.1111/1751-7915.14312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/25/2023] [Indexed: 07/13/2023] Open
Abstract
Pseudomonas species have become promising cell factories for the production of natural products due to their inherent robustness. Although these bacteria have naturally evolved strategies to cope with different kinds of stress, many biotechnological applications benefit from engineering of optimised chassis strains with specially adapted tolerance traits. Here, we explored the formation of outer membrane vesicles (OMV) of Pseudomonas putida KT2440. We found OMV production to correlate with the recombinant production of a natural compound with versatile beneficial properties, the tripyrrole prodigiosin. Further, several P. putida genes were identified, whose up- or down-regulated expression allowed controlling OMV formation. Finally, genetically triggering vesiculation in production strains of the different alkaloids prodigiosin, violacein, and phenazine-1-carboxylic acid, as well as the carotenoid zeaxanthin, resulted in up to three-fold increased product yields. Consequently, our findings suggest that the construction of robust strains by genetic manipulation of OMV formation might be developed into a useful tool which may contribute to improving limited biotechnological applications.
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Affiliation(s)
- Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology (IMET)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Carolin Höfel
- Institute of Molecular Enzyme Technology (IMET)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology (IMET)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Andrea Jeanette Weiler
- Institute of Molecular Enzyme Technology (IMET)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Christian Eberlein
- Department of Environmental BiotechnologyHelmholtz Centre for Environmental Research (UFZ)LeipzigGermany
| | - Hermann J. Heipieper
- Department of Environmental BiotechnologyHelmholtz Centre for Environmental Research (UFZ)LeipzigGermany
| | - Renu Batra‐Safferling
- Institute of Biological Information Processing – Structural Biochemistry (IBI‐7: Structural Biochemistry)Forschungszentrum JülichJülichGermany
| | - Pia Sundermeyer
- Ernst‐Ruska Centre for Microscopy and Spectroscopy with Electrons (ER‐C‐3/Structural Biology)Forschungszentrum JülichJülichGermany
- Institute for Biological Information Processing 6 (IBI‐6/ Structural Cellular Biology)Forschungszentrum JülichJülichGermany
| | - Thomas Heidler
- Ernst‐Ruska Centre for Microscopy and Spectroscopy with Electrons (ER‐C‐3/Structural Biology)Forschungszentrum JülichJülichGermany
- Institute for Biological Information Processing 6 (IBI‐6/ Structural Cellular Biology)Forschungszentrum JülichJülichGermany
| | - Carsten Sachse
- Ernst‐Ruska Centre for Microscopy and Spectroscopy with Electrons (ER‐C‐3/Structural Biology)Forschungszentrum JülichJülichGermany
- Institute for Biological Information Processing 6 (IBI‐6/ Structural Cellular Biology)Forschungszentrum JülichJülichGermany
- Department of BiologyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
- Bielefeld University, Medical School East Westphalia‐LippeBielefeld UniversityBielefeldGermany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Thomke Belthle
- DWI─Leibniz‐Institute for Interactive MaterialsAachenGermany
- Functional and Interactive Polymers, Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityAachenGermany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology (IMET)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET)Heinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyForschungszentrum JülichJülichGermany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology (IMET)Heinrich Heine University DüsseldorfDüsseldorfGermany
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Saadon S, Ali MSM, Kamarudin NHA, Latip W, Ishak SNH, Basri RS, Johan UUM, Shukri NSA, Rosli NE, Rahman RNZRA. Benefitting multi-enzyme system for the purpose of improving the flow properties of waxy oil. GEOENERGY SCIENCE AND ENGINEERING 2023; 230:212221. [DOI: 10.1016/j.geoen.2023.212221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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5
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Dong C, Wei L, Wang J, Lai Q, Huang Z, Shao Z. Genome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus. Front Microbiol 2022; 13:1051202. [PMID: 36605514 PMCID: PMC9807766 DOI: 10.3389/fmicb.2022.1051202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus. Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1 T and 59MF3M-4 T , for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.
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Affiliation(s)
- Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Lin Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China,*Correspondence: Zongze Shao,
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6
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Catucci G, Turella S, Cheropkina H, De Angelis M, Gilardi G, Sadeghi SJ. Green production of indigo and indirubin by an engineered Baeyer–Villiger monooxygenase. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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7
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Perera M, Wijesundera S, Wijayarathna CD, Seneviratne G, Jayasena S. Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis. Front Microbiol 2022; 13:898456. [PMID: 36110294 PMCID: PMC9468676 DOI: 10.3389/fmicb.2022.898456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyzed using a computational approach. By analyzing publicly available protein databases, we identified six uncharacterized proteins in A. flavus NRRL 3357, of which five were identified as class LadAα and one as class LadAβ, which are eukaryotic homologs of bacterial long-chain alkane monooxygenase (LadA). Computational models of A. flavus LadAα homologs (Af1-Af5) showed overall structural similarity to the bacterial LadA and the unique sequence and structural elements that bind the cofactor Flavin mononucleotide (FMN). A receptor-cofactor-substrate docking protocol was established and validated to demonstrate the substrate binding in the A. flavus LadAα homologs. The modeled Af1, Af3, Af4, and Af5 captured long-chain n-alkanes inside the active pocket, above the bound FMN. Isoalloxazine ring of reduced FMN formed a π–alkyl interaction with the terminal carbon atom of captured alkanes, C16–C30, in Af3–Af5 and C16–C24 in Af1. Our results confirmed the ability of identified A. flavus LadAα monooxygenases to bind long-chain alkanes inside the active pocket. Hence A. flavus LadAα monooxygenases potentially initiate the degradation of long-chain alkanes by oxidizing bound long-chain alkanes into their corresponding alcohol.
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Affiliation(s)
- Madushika Perera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Sulochana Wijesundera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | | | | | - Sharmila Jayasena
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- *Correspondence: Sharmila Jayasena,
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8
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Zadjelovic V, Erni-Cassola G, Obrador-Viel T, Lester D, Eley Y, Gibson MI, Dorador C, Golyshin PN, Black S, Wellington EMH, Christie-Oleza JA. A mechanistic understanding of polyethylene biodegradation by the marine bacterium Alcanivorax. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129278. [PMID: 35739790 DOI: 10.1016/j.jhazmat.2022.129278] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Polyethylene (PE) is one of the most recalcitrant carbon-based synthetic materials produced and, currently, the most ubiquitous plastic pollutant found in nature. Over time, combined abiotic and biotic processes are thought to eventually breakdown PE. Despite limited evidence of biological PE degradation and speculation that hydrocarbon-degrading bacteria found within the plastisphere is an indication of biodegradation, there is no clear mechanistic understanding of the process. Here, using high-throughput proteomics, we investigated the molecular processes that take place in the hydrocarbon-degrading marine bacterium Alcanivorax sp. 24 when grown in the presence of low density PE (LDPE). As well as efficiently utilising and assimilating the leachate of weathered LDPE, the bacterium was able to reduce the molecular weight distribution (Mw from 122 to 83 kg/mol) and overall mass of pristine LDPE films (0.9 % after 34 days of incubation). Most interestingly, Alcanivorax acquired the isotopic signature of the pristine plastic and induced an extensive array of metabolic pathways for aliphatic compound degradation. Presumably, the primary biodegradation of LDPE by Alcanivorax sp. 24 is possible via the production of extracellular reactive oxygen species as observed both by the material's surface oxidation and the measurement of superoxide in the culture with LDPE. Our findings confirm that hydrocarbon-biodegrading bacteria within the plastisphere may in fact have a role in degrading PE.
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Affiliation(s)
- Vinko Zadjelovic
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Gabriel Erni-Cassola
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Program Man-Society-Environment (MGU), University of Basel, 4051 Basel, Switzerland
| | - Theo Obrador-Viel
- Department of Biology, University of the Balearic Islands, Palma 07122, Spain
| | - Daniel Lester
- Polymer Characterisation Research Technology Platform, University of Warwick, Coventry CV4 7AL, UK
| | - Yvette Eley
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Chile; Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta Angamos 601, Antofagasta, Chile; Centre for Biotechnology & Bioengineering (CeBiB) Santiago, Chile
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Stuart Black
- Department of Geography and Environmental Science, University of Reading, UK
| | | | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Department of Biology, University of the Balearic Islands, Palma 07122, Spain.
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Biodegradation of used motor oil by Streptomyces ginkgonis KM-1-2, isolated from soil polluted by waste oils in the region of Azzaba (Skikda-Algeria). J Biotechnol 2022; 349:1-11. [DOI: 10.1016/j.jbiotec.2022.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 03/05/2022] [Accepted: 03/15/2022] [Indexed: 12/28/2022]
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Rhizosphere Bacterium Rhodococcus sp. P1Y Metabolizes Abscisic Acid to Form Dehydrovomifoliol. Biomolecules 2021; 11:biom11030345. [PMID: 33668728 PMCID: PMC7996341 DOI: 10.3390/biom11030345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/22/2022] Open
Abstract
The phytohormone abscisic acid (ABA) plays an important role in plant growth and in response to abiotic stress factors. At the same time, its accumulation in soil can negatively affect seed germination, inhibit root growth and increase plant sensitivity to pathogens. ABA is an inert compound resistant to spontaneous hydrolysis and its biological transformation is scarcely understood. Recently, the strain Rhodococcus sp. P1Y was described as a rhizosphere bacterium assimilating ABA as a sole carbon source in batch culture and affecting ABA concentrations in plant roots. In this work, the intermediate product of ABA decomposition by this bacterium was isolated and purified by preparative HPLC techniques. Proof that this compound belongs to ABA derivatives was carried out by measuring the molar radioactivity of the conversion products of this phytohormone labeled with tritium. The chemical structure of this compound was determined by instrumental techniques including high-resolution mass spectrometry, NMR spectrometry, FTIR and UV spectroscopies. As a result, the metabolite was identified as (4RS)-4-hydroxy-3,5,5-trimethyl-4-[(E)-3-oxobut-1-enyl]cyclohex-2-en-1-one (dehydrovomifoliol). Based on the data obtained, it was concluded that the pathway of bacterial degradation and assimilation of ABA begins with a gradual shortening of the acyl part of the molecule.
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Rodrigues AM, Kubitschek-Barreira PH, Pinheiro BG, Teixeira-Ferreira A, Hahn RC, de Camargo ZP. Immunoproteomic Analysis Reveals Novel Candidate Antigens for the Diagnosis of Paracoccidioidomycosis Due to Paracoccidioides lutzii. J Fungi (Basel) 2020; 6:jof6040357. [PMID: 33322269 PMCID: PMC7770604 DOI: 10.3390/jof6040357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic infection caused by the fungal pathogen Paracoccidioides brasiliensis and related species. Whole-genome sequencing and stage-specific proteomic analysis of Paracoccidioides offer the opportunity to profile humoral immune responses against P. lutzii and P. brasiliensis s. str. infection using innovative screening approaches. Here, an immunoproteomic approach was used to identify PCM-associated antigens that elicit immune responses by combining 2-D electrophoresis of P. lutzii and P. brasiliensis proteomes, immunological detection using a gold-standard serum, and mass spectrometry analysis. A total of 16 and 25 highly immunoreactive proteins were identified in P. lutzii and P. brasiliensis, respectively, and 29 were shown to be the novel antigens for Paracoccidioides species, including seven uncharacterized proteins. Among the panel of proteins identified, most are involved in metabolic pathways, carbon metabolism, and biosynthesis of secondary metabolites in both immunoproteomes. Remarkably, six isoforms of the surface-associated enolase in the range of 54 kDa were identified as the major antigens in human PCM due to P. lutzii. These novel immunoproteomes of Paracoccidioides will be employed to develop a sensitive and affordable point-of-care diagnostic assay and an effective vaccine to identify infected hosts and prevent infection and development of human PCM. These findings provide a unique opportunity for the refinement of diagnostic tools of this important neglected systemic mycosis, which is usually associated with poverty.
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Affiliation(s)
- Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil;
- Correspondence: (A.M.R.); (Z.P.d.C.); Tel.: +55-1155764551 (ext. 1540) (A.M.R.); +55-1155764551 (ext. 1512) (Z.P.d.C.)
| | - Paula Helena Kubitschek-Barreira
- Department of Cellular Biology, Roberto Alcantara Gomes Institute of Biology, Rio de Janeiro State University (UERJ), Rio de Janeiro 20511010, Brazil;
| | - Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil;
| | - André Teixeira-Ferreira
- Toxinology Laboratory, Department of Physiology and Pharmacodynamics, Fiocruz, Rio de Janeiro 21040900, Brazil;
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá 78060900, Brazil;
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá 78048902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil;
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Correspondence: (A.M.R.); (Z.P.d.C.); Tel.: +55-1155764551 (ext. 1540) (A.M.R.); +55-1155764551 (ext. 1512) (Z.P.d.C.)
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12
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Insights into the Mechanism of Ethionamide Resistance in Mycobacterium tuberculosis through an in silico Structural Evaluation of EthA and Mutants Identified in Clinical Isolates. Catalysts 2020. [DOI: 10.3390/catal10050543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mutation in the ethionamide (ETH) activating enzyme, EthA, is the main factor determining resistance to this drug, used to treat TB patients infected with MDR and XDR Mycobacterium tuberculosis isolates. Many mutations in EthA of ETH resistant (ETH-R) isolates have been described but their roles in resistance remain uncharacterized, partly because structural studies on the enzyme are lacking. Thus, we took a two-tier approach to evaluate two mutations (Y50C and T453I) found in ETH-R clinical isolates. First, we used a combination of comparative modeling, molecular docking, and molecular dynamics to build an EthA model in complex with ETH that has hallmark features of structurally characterized homologs. Second, we used free energy computational calculations for the reliable prediction of relative free energies between the wild type and mutant enzymes. The ΔΔG values for Y50C and T453I mutant enzymes in complex with FADH2-NADP-ETH were 3.34 (+/−0.55) and 8.11 (+/−0.51) kcal/mol, respectively, compared to the wild type complex. The positive ΔΔG values indicate that the wild type complex is more stable than the mutants, with the T453I complex being the least stable. These are the first results shedding light on the molecular basis of ETH resistance, namely reduced complex stability of mutant EthA.
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Genome of Alcanivorax sp. 24: A hydrocarbon degrading bacterium isolated from marine plastic debris. Mar Genomics 2020. [DOI: 10.1016/j.margen.2019.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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SadrAzodi SM, Shavandi M, Amoozegar MA, Mehrnia MR. Biodegradation of long chain alkanes in halophilic conditions by Alcanivorax sp. strain Est-02 isolated from saline soil. 3 Biotech 2019; 9:141. [PMID: 30944788 DOI: 10.1007/s13205-019-1670-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 03/09/2019] [Indexed: 10/27/2022] Open
Abstract
In this study, through a multistep enrichment and isolation procedure, a halophilic bacterial strain was isolated from unpolluted saline soil, which was able to effectively and preferentially degrade long chain alkanes (especially tetracosane and octacosane). The strain was identified by 16S rRNA gene sequence as an Alcanivorax sp. The growth of strain Est-02 was optimized at the presence of tetracosane in different NaCl concentrations, temperatures, and pH. The consumption of different heavy alkanes was also investigated. Optimal culture conditions of the strain were determined to be as follows: 10% NaCl, temperature 25-35 °C and pH 7. Alcanivorax sp. strain Est-02 was able to use a wide range of aliphatic substrates ranging from C14 to C28 with clear tendency to utilize heavy chain hydrocarbons of C24 and C28. During growth on a mixture of alkanes (C14-C28), the strain consumed 60% and 65% of tetracosane and octacosane, respectively, while only about 40% of the lower chain alkanes were degraded. This unique ability of the strain Est-02 in efficient and selective biodegradation of long chain hydrocarbons could be further exploited for remediation of wax and heavy oil contaminated soils or upgrading of heavy crude oils. Comparison of the sequence of alkane hydroxylase gene (alkB) of strain Est-02 with previously reported sequences for Alcanivorax spp. and other hydrocarbon degraders, showed a remarkable phylogenetic distance between the sequence alkB of Est-02 and other alkane-degrading bacteria.
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Tolmie C, Smit MS, Opperman DJ. Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Nat Prod Rep 2019; 36:326-353. [DOI: 10.1039/c8np00054a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.
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Affiliation(s)
- Carmien Tolmie
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
| | - Martha S. Smit
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Front Microbiol 2018; 9:3130. [PMID: 30619200 PMCID: PMC6304351 DOI: 10.3389/fmicb.2018.03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 02/02/2023] Open
Abstract
The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom.,School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, United Kingdom
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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Integrated analysis of ethionamide resistance loci in Mycobacterium tuberculosis clinical isolates. Tuberculosis (Edinb) 2018; 113:163-174. [DOI: 10.1016/j.tube.2018.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/15/2018] [Accepted: 08/22/2018] [Indexed: 01/31/2023]
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18
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Kim HS, Dong K, Kim J, Lee SS. Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment. Microbiologyopen 2018; 8:e00754. [PMID: 30338941 PMCID: PMC6562140 DOI: 10.1002/mbo3.754] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 01/01/2023] Open
Abstract
Crude oil is a major pollutant of marine and coastal ecosystems, and it causes environmental problems more seriously. It is believed ultimate and complete degradation is accomplished mainly by microorganisms. In this study, we aim to search out for bacterial strains with high ability in degrading crude oil. From sediments contaminated by the petroleum spilled in 2007, an accident in Taean, South Korea, we isolated thirty‐one bacterial strains in total with potential application in crude oil contamination remediation. In terms of removal percentage after 7 days, one of the strains, Co17, showed the highest removal efficiency with 84.2% of crude oil in Bushnell‐Haas media. The Co17 strain even exhibited outstanding ability removing crude oil at a high salt concentration. Through the whole genome sequencing annotation results, many genes related with n‐alkane degradation in the genome of Gordonia sp. Co17, revealed alkane‐1‐monooxygenase, alcohol dehydrogenase, and Baeyer–Villiger monooxygenase. Specially, for confirmation of gene‐level, alkB gene encoding alkane hydroxylase (alkane‐1‐monooxygenase) was found in the strain Co17. The expression of alkB upregulated 125‐fold after 18 hr accompany with the removal of n‐alkanes of 48.9%. We therefore propose the strain Gordonia iterans Co17, isolated from crude oil‐contaminated marine sediment, could be used to offer a new strategy for bioremediation with high efficiency.
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Affiliation(s)
- Hyun-Sook Kim
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea
| | - Ke Dong
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Jinsoo Kim
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Sang-Seob Lee
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea.,Department of Life Science, Kyonggi University, Suwon-si, Korea
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Liu YF, Galzerani DD, Mbadinga SM, Zaramela LS, Gu JD, Mu BZ, Zengler K. Metabolic capability and in situ activity of microorganisms in an oil reservoir. MICROBIOME 2018; 6:5. [PMID: 29304850 PMCID: PMC5756336 DOI: 10.1186/s40168-017-0392-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/19/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. RESULTS Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery. CONCLUSION Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, 200237, People's Republic of China
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA
| | - Daniela Domingos Galzerani
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA
| | - Serge Maurice Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, 200237, People's Republic of China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, 200237, People's Republic of China
| | - Livia S Zaramela
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, 200237, People's Republic of China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, 200237, People's Republic of China.
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0436, USA.
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Chemical applications of Class B flavoprotein monooxygenases. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2016. [DOI: 10.1007/s12210-016-0583-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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21
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Catucci G, Zgrablic I, Lanciani F, Valetti F, Minerdi D, Ballou DP, Gilardi G, Sadeghi SJ. Characterization of a new Baeyer-Villiger monooxygenase and conversion to a solely N-or S-oxidizing enzyme by a single R292 mutation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1177-1187. [DOI: 10.1016/j.bbapap.2016.06.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/27/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
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Escherichia coli Overexpressing a Baeyer-Villiger Monooxygenase from Acinetobacter radioresistens Becomes Resistant to Imipenem. Antimicrob Agents Chemother 2015; 60:64-74. [PMID: 26459905 DOI: 10.1128/aac.01088-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance is a global issue currently resulting in the deaths of hundreds of thousands of people a year worldwide. Data present in the literature illustrate the emergence of many bacterial species that display resistance to known antibiotics; Acinetobacter spp. are a good example of this. We report here that Acinetobacter radioresistens has a Baeyer-Villiger monooxygenase (Ar-BVMO) with 100% amino acid sequence identity to the ethionamide monooxygenase of multidrug-resistant (MDR) Acinetobacter baumannii. Both enzymes are only distantly phylogenetically related to other canonical bacterial BVMO proteins. Ar-BVMO not only is capable of oxidizing two anticancer drugs metabolized by human FMO3, danusertib and tozasertib, but also can oxidize other synthetic drugs, such as imipenem. The latter is a member of the carbapenems, a clinically important antibiotic family used in the treatment of MDR bacterial infections. Susceptibility tests performed by the Kirby-Bauer disk diffusion method demonstrate that imipenem-sensitive Escherichia coli BL21 cells overexpressing Ar-BVMO become resistant to this antibiotic. An agar disk diffusion assay proved that when imipenem reacts with Ar-BVMO, it loses its antibiotic property. Moreover, an NADPH consumption assay with the purified Ar-BVMO demonstrates that this antibiotic is indeed a substrate, and its product is identified by liquid chromatography-mass spectrometry to be a Baeyer-Villiger (BV) oxidation product of the carbonyl moiety of the β-lactam ring. This is the first report of an antibiotic-inactivating BVMO enzyme that, while mediating its usual BV oxidation, also operates by an unprecedented mechanism of carbapenem resistance.
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The Origin and Evolution of Baeyer-Villiger Monooxygenases (BVMOs): An Ancestral Family of Flavin Monooxygenases. PLoS One 2015; 10:e0132689. [PMID: 26161776 PMCID: PMC4498894 DOI: 10.1371/journal.pone.0132689] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/18/2015] [Indexed: 12/13/2022] Open
Abstract
The Baeyer-Villiger Monooxygenases (BVMOs) are enzymes belonging to the "Class B" of flavin monooxygenases and are capable of performing exquisite selective oxidations. These enzymes have been studied from a biotechnological perspective, but their physiological substrates and functional roles are widely unknown. Here, we investigated the origin, taxonomic distribution and evolutionary history of the BVMO genes. By using in silico approaches, 98 BVMO encoding genes were detected in the three domains of life: Archaea, Bacteria and Eukarya. We found evidence for the presence of these genes in Metazoa (Hydra vulgaris, Oikopleura dioica and Adineta vaga) and Haptophyta (Emiliania huxleyi) for the first time. Furthermore, a search for other "Class B" monooxygenases (flavoprotein monooxygenases--FMOs--and N-hydroxylating monooxygenases--NMOs) was conducted. These sequences were also found in the three domains of life. Phylogenetic analyses of all "Class B" monooxygenases revealed that NMOs and BVMOs are monophyletic, whereas FMOs form a paraphyletic group. Based on these results, we propose that BVMO genes were already present in the last universal common ancestor (LUCA) and their current taxonomic distribution is the result of differential duplication and loss of paralogous genes.
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Sun LH, Zhang NY, Sun RR, Gao X, Gu C, Krumm CS, Qi DS. A novel strain of Cellulosimicrobium funkei can biologically detoxify aflatoxin B1 in ducklings. Microb Biotechnol 2015; 8:490-8. [PMID: 25616109 PMCID: PMC4408181 DOI: 10.1111/1751-7915.12244] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/13/2014] [Accepted: 10/22/2014] [Indexed: 12/11/2022] Open
Abstract
Two experiments were conducted to screen microorganisms with aflatoxin B1 (AFB1 ) removal potential from soils and to evaluate their ability in reducing the toxic effects of AFB1 in ducklings. In experiment 1, we screened 11 isolates that showed the AFB1 biodegradation ability, and the one exhibited the highest AFB1 removal ability (97%) was characterized and identified as Cellulosimicrobium funkei (C. funkei). In experiment 2, 80 day-old Cherry Valley ducklings were divided into four groups with four replicates of five birds each and were used in a 2 by 2 factorial trial design, in which the main factors included administration of AFB1 versus solvent and C. funkei versus solvent for 2 weeks. The AFB1 treatment significantly decreased the body weight gain, feed intake and impaired feed conversion ratio. AFB1 also decreased serum albumin and total protein concentration, while it increased activities of alanine aminotransferase and aspartate aminotransferase and liver damage in the ducklings. Supplementation of C. funkei alleviated the adverse effects of AFB1 on growth performance, and provided protective effects on the serum biochemical indicators, and decreased hepatic injury in the ducklings. Conclusively, our results suggest that the novel isolated C. funkei strain could be used to mitigate the negative effects of aflatoxicosis in ducklings.
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Affiliation(s)
- Lv-Hui Sun
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural UniversityWuhan, Hubei, 430070, China
| | - Ni-Ya Zhang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural UniversityWuhan, Hubei, 430070, China
| | - Ran-Ran Sun
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural UniversityWuhan, Hubei, 430070, China
| | - Xin Gao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural UniversityWuhan, Hubei, 430070, China
| | - Changqin Gu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural UniversityWuhan, Hubei, 430070, China
| | | | - De-Sheng Qi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural UniversityWuhan, Hubei, 430070, China
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Minerdi D, Sadeghi SJ, Di Nardo G, Rua F, Castrignanò S, Allegra P, Gilardi G. CYP116B5: a new class VII catalytically self-sufficient cytochrome P450 from Acinetobacter radioresistens that enables growth on alkanes. Mol Microbiol 2014; 95:539-54. [PMID: 25425282 DOI: 10.1111/mmi.12883] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2014] [Indexed: 11/27/2022]
Abstract
A gene coding for a class VII cytochrome P450 monooxygenase (CYP116B5) was identified from Acinetobacter radioresistens S13 growing on media with medium (C14, C16) and long (C24, C36) chain alkanes as the sole energy source. Phylogenetic analysis of its N- and C-terminal domains suggests an evolutionary model involving a plasmid-mediated horizontal gene transfer from the donor Rhodococcus jostii RHA1 to the receiving A. radioresistens S13. This event was followed by fusion and integration of the new gene in A. radioresistens chromosome. Heterologous expression of CYP116B5 in Escherichia coli BL21, together with the A. radioresistens Baeyer-Villiger monooxygenase, allowed the recombinant bacteria to grow on long- and medium-chain alkanes, showing that CYP116B5 is involved in the first step of terminal oxidation of medium-chain alkanes overlapping AlkB and in the first step of sub-terminal oxidation of long-chain alkanes. It was also demonstrated that CYP116B5 is a self-sufficient cytochrome P450 consisting of a heme domain (aa 1-392) involved in the oxidation step of n-alkanes degradation, and its reductase domain (aa 444-758) comprising the NADPH-, FMN- and [2Fe2S]-binding sites. To our knowledge, CYP116B5 is the first member of this class to have its natural substrate and function identified.
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Affiliation(s)
- Daniela Minerdi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
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26
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Bisagni S, Smuś J, Chávez G, Hatti-Kaul R, Mamo G. Cloning and expression of a Baeyer–Villiger monooxygenase oxidizing linear aliphatic ketones from Dietzia sp. D5. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Ceccoli RD, Bianchi DA, Rial DV. Flavoprotein monooxygenases for oxidative biocatalysis: recombinant expression in microbial hosts and applications. Front Microbiol 2014; 5:25. [PMID: 24567729 PMCID: PMC3915288 DOI: 10.3389/fmicb.2014.00025] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/14/2014] [Indexed: 11/21/2022] Open
Abstract
External flavoprotein monooxygenases comprise a group of flavin-dependent oxidoreductases that catalyze the insertion of one atom of molecular oxygen into an organic substrate and the second atom is reduced to water. These enzymes are involved in a great number of metabolic pathways both in prokaryotes and eukaryotes. Flavoprotein monooxygenases have attracted the attention of researchers for several decades and the advent of recombinant DNA technology caused a great progress in the field. These enzymes are subjected to detailed biochemical and structural characterization and some of them are also regarded as appealing oxidative biocatalysts for the production of fine chemicals and valuable intermediates toward active pharmaceutical ingredients due to their high chemo-, stereo-, and regioselectivity. Here, we review the most representative reactions catalyzed both in vivo and in vitro by prototype flavoprotein monooxygenases, highlighting the strategies employed to produce them recombinantly, to enhance the yield of soluble proteins, and to improve cofactor regeneration in order to obtain versatile biocatalysts. Although we describe the most outstanding features of flavoprotein monooxygenases, we mainly focus on enzymes that were cloned, expressed and used for biocatalysis during the last years.
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Affiliation(s)
- Romina D Ceccoli
- Área Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario CONICET, Rosario, Argentina
| | - Dario A Bianchi
- Instituto de Química Rosario (IQUIR, CONICET-UNR), Área Análisis de Medicamentos, Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
| | - Daniela V Rial
- Área Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario CONICET, Rosario, Argentina
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Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
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