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Zhong W, Agarwal V. Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty. Beilstein J Org Chem 2024; 20:1635-1651. [PMID: 39076296 PMCID: PMC11285056 DOI: 10.3762/bjoc.20.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Microbulbifer is a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation of Microbulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes.
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Affiliation(s)
- Weimao Zhong
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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2
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Hooe S, Thakur M, Lasarte-Aragonés G, Breger JC, Walper SA, Medintz IL, Ellis GA. Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues. ACS OMEGA 2024; 9:3894-3904. [PMID: 38284012 PMCID: PMC10809250 DOI: 10.1021/acsomega.3c08233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Evolution has gifted enzymes with the ability to synthesize an abundance of small molecules with incredible control over efficiency and selectivity. Central to an enzyme's role is the ability to selectively catalyze reactions in the milieu of chemicals within a cell. However, for chemists it is often desirable to extend the substrate scope of reactions to produce analogue(s) of a desired product and therefore some degree of enzyme promiscuity is often desired. Herein, we examine this dichotomy in the context of the violacein biosynthetic pathway. Importantly, we chose to interrogate this pathway with tryptophan analogues in vitro, to mitigate possible interference from cellular components and endogenous tryptophan. A total of nine tryptophan analogues were screened for by analyzing the substrate promiscuity of the initial enzyme, VioA, and compared to the substrate tryptophan. These results suggested that for VioA, substitutions at either the 2- or 4-position of tryptophan were not viable. The seven analogues that showed successful substrate conversion by VioA were then applied to the five enzyme cascade (VioABEDC) for the production of violacein, where l-tryptophan and 6-fluoro-l-tryptophan were the only substrates which were successfully converted to the corresponding violacein derivative(s). However, many of the other tryptophan analogues did convert to various substituted intermediaries. Overall, our results show substrate promiscuity with the initial enzyme, VioA, but much less for the full pathway. This work demonstrates the complexity involved when attempting to analyze substrate analogues within multienzymatic cascades, where each enzyme involved within the cascade possesses its own inherent promiscuity, which must be compatible with the remaining enzymes in the cascade for successful formation of a desired product.
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Affiliation(s)
- Shelby
L. Hooe
- National
Research Council, Washington, D.C. 20001, United States
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Meghna Thakur
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Guillermo Lasarte-Aragonés
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joyce C. Breger
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory A. Ellis
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Gardner ED, Johnson BP, Dimas DA, McClurg HE, Severance ZC, Burgett AW, Singh S. Unlocking New Prenylation Modes: Azaindoles as a New Substrate Class for Indole Prenyltransferases. ChemCatChem 2023; 15:e202300650. [PMID: 37954549 PMCID: PMC10634513 DOI: 10.1002/cctc.202300650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 11/14/2023]
Abstract
Aza-substitution, the replacement of aromatic CH groups with nitrogen atoms, is an established medicinal chemistry strategy for increasing solubility, but current methods of accessing functionalized azaindoles are limited. In this work, indole-alkylating aromatic prenyltransferases (PTs) were explored as a strategy to directly functionalize azaindole-substituted analogs of natural products. For this, a series of aza-l-tryptophans (Aza-Trp) featuring N-substitution of every aromatic CH position of the indole ring and their corresponding cyclic Aza-l-Trp-l-proline dipeptides (Aza-CyWP), were synthesized as substrate mimetics for the indole-alkylating PTs FgaPT2, CdpNPT, and FtmPT1. We then demonstrated most of these substrate analogs were accepted by a PT, and the regioselectivity of each prenylation was heavily influenced by the position of the N-substitution. Remarkably, FgaPT2 was found to produce cationic N-prenylpyridinium products, representing not only a new substrate class for indole PTs but also a previously unobserved prenylation mode. The discovery that nitrogenous indole bioisosteres can be accepted by PTs thus provides access to previously unavailable chemical space in the search for bioactive indolediketopiperazine analogs.
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Affiliation(s)
- Eric D. Gardner
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Bryce P. Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Dustin A. Dimas
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Heather E. McClurg
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Zachary C. Severance
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Anthony W. Burgett
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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4
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Wax N, Walke JB, Haak DC, Belden LK. Comparative genomics of bacteria from amphibian skin associated with inhibition of an amphibian fungal pathogen, Batrachochytrium dendrobatidis. PeerJ 2023; 11:e15714. [PMID: 37637170 PMCID: PMC10452622 DOI: 10.7717/peerj.15714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/16/2023] [Indexed: 08/29/2023] Open
Abstract
Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may alter infection outcomes. We completed whole genome sequencing of 40 bacterial isolates cultured from the skin of four amphibian species in the Eastern US. Each isolate was tested in vitro for the ability to inhibit Bd growth. The aim of this study was to identify genomic differences among the isolates and generate hypotheses about the genomic underpinnings of Bd growth inhibition. We identified sixty-five gene families that were present in all 40 isolates. Screening for common biosynthetic gene clusters revealed that this set of isolates contained a wide variety of clusters; the two most abundant clusters with potential antifungal activity were siderophores (N=17 isolates) and Type III polyketide synthases (N=22 isolates). We then examined various subsets of the 22 isolates in the phylum Proteobacteria for genes encoding specific compounds that may inhibit fungal growth, including chitinase and violacein. We identified differences in Agrobacterium and Sphingomonas isolates in the chitinase genes that showed some association with anti-Bd activity, as well as variation in the violacein genes in the Janthinobacterium isolates. Using a comparative genomics approach, we generated several testable hypotheses about differences among bacterial isolates from amphibian skin communities that could contribute to variation in the ability to inhibit Bd growth. Further work is necessary to explore and uncover the various mechanisms utilized by amphibian skin bacterial isolates to inhibit Bd.
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Affiliation(s)
- Noah Wax
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
- Department of Biology, Eastern Washington University, Cheney, WA, United States of America
| | - David C. Haak
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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Nemer G, Louka N, Rabiller Blandin P, Maroun RG, Vorobiev E, Rossignol T, Nicaud JM, Guénin E, Koubaa M. Purification of Natural Pigments Violacein and Deoxyviolacein Produced by Fermentation Using Yarrowia lipolytica. Molecules 2023; 28:4292. [PMID: 37298767 PMCID: PMC10254742 DOI: 10.3390/molecules28114292] [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: 03/30/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Violacein and deoxyviolacein are bis-indole pigments synthesized by a number of microorganisms. The present study describes the biosynthesis of a mixture of violacein and deoxyviolacein using a genetically modified Y. lipolytica strain as a production chassis, the subsequent extraction of the intracellular pigments, and ultimately their purification using column chromatography. The results show that the optimal separation between the pigments occurs using an ethyl acetate/cyclohexane mixture with different ratios, first 65:35 until both pigments were clearly visible and distinguishable, then 40:60 to create a noticeable separation between them and recover the deoxyviolacein, and finally 80:20, which allows the recovery of the violacein. The purified pigments were then analyzed by thin-layer chromatography and nuclear magnetic resonance.
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Affiliation(s)
- Georgio Nemer
- Université de Technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Centre de Recherche Royallieu—CS 60319, 60203 Compiègne CEDEX, France; (G.N.); (P.R.B.); (E.V.); (E.G.)
- Laboratoire CTA, UR TVA, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph, Beyrouth 1104 2020, Lebanon; (N.L.); (R.G.M.)
| | - Nicolas Louka
- Laboratoire CTA, UR TVA, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph, Beyrouth 1104 2020, Lebanon; (N.L.); (R.G.M.)
| | - Paul Rabiller Blandin
- Université de Technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Centre de Recherche Royallieu—CS 60319, 60203 Compiègne CEDEX, France; (G.N.); (P.R.B.); (E.V.); (E.G.)
| | - Richard G. Maroun
- Laboratoire CTA, UR TVA, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph, Beyrouth 1104 2020, Lebanon; (N.L.); (R.G.M.)
| | - Eugène Vorobiev
- Université de Technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Centre de Recherche Royallieu—CS 60319, 60203 Compiègne CEDEX, France; (G.N.); (P.R.B.); (E.V.); (E.G.)
| | - Tristan Rossignol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (T.R.); (J.-M.N.)
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (T.R.); (J.-M.N.)
| | - Erwann Guénin
- Université de Technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Centre de Recherche Royallieu—CS 60319, 60203 Compiègne CEDEX, France; (G.N.); (P.R.B.); (E.V.); (E.G.)
| | - Mohamed Koubaa
- Université de Technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Centre de Recherche Royallieu—CS 60319, 60203 Compiègne CEDEX, France; (G.N.); (P.R.B.); (E.V.); (E.G.)
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Combination of 2- tert-Butyl-1,4-Benzoquinone (TBQ) and ZnO Nanoparticles, a New Strategy To Inhibit Biofilm Formation and Virulence Factors of Chromobacterium violaceum. mSphere 2023; 8:e0059722. [PMID: 36645278 PMCID: PMC9942565 DOI: 10.1128/msphere.00597-22] [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] [Indexed: 01/17/2023] Open
Abstract
Drug-resistant bacteria have been raising serious social problems. Bacterial biofilms and different virulence factors are the main reasons for persistent infections. As a conditioned pathogen, Chromobacterium violaceum has evolved a vast network of regulatory mechanisms to modify and fine-tune biofilm development, contributing to multidrug resistance. However, there are few therapies to combat drug-resistant bacteria. Quorum sensing (QS) inhibitors (QSIs) are a promising strategy to solve antibiotic resistance. Our previous work suggested that 2-tert-butyl-1,4-benzoquinone (TBQ) is a potent QSI. In this study, the combination of zinc oxide nanoparticles (ZnO-NPs) and TBQ (ZnO-TBQ) was investigated for the treatment of Chromobacterium violaceum ATCC 12472 infection. ZnO-NPs attach to cell walls or biofilms, and the local dissolution of ZnO-NPs can lead to increased Zn2+ concentrations, which could destroy metal homeostasis, corresponding to disturbances in amino acid metabolism and nucleic acid metabolism. ZnO-NPs significantly improved the efficiency of TBQ in inhibiting the QS-related virulence factors and biofilm formation of C. violaceum ATCC 12472. ZnO-TBQ effectively reduces the expression of genes related to QS, which is conducive to limiting the infectivity of C. violaceum ATCC 12472. Caenorhabditis elegans nematodes treated with ZnO-TBQ presented a significant improvement in the survival rate by 46.7%. Overall, the combination of ZnO-NPs and TBQ offers a new strategy to attenuate virulence factors and biofilm formation synergistically in some drug-resistant bacteria. IMPORTANCE The combination of ZnO-NPs and TBQ (ZnO-TBQ) can compete with the inducer N-decanoyl-homoserine lactone (C10-HSL) by binding to CviR and downregulate genes related to the CviI/CviR system to interrupt the QS system of C. violaceum ATCC 12472. The downstream genes responding to cviR were also downregulated so that virulence factors and biofilm formation were inhibited. Furthermore, ZnO-TBQ presents multiple metabolic disturbances in C. violaceum ATCC 12472, which results in the reduced multidrug resistance and pathogenicity of C. violaceum ATCC 12472. In an in vivo assay, C. elegans nematodes treated with ZnO-TBQ presented a significant improvement in the survival rate by 46.7% by limiting the infectivity of C. violaceum ATCC 12472. In addition, ZnO-TBQ inhibited the generation of virulence factors and biofilm formation 2-fold compared to either ZnO-NPs or TBQ alone. The combination of ZnO-NPs with TBQ offers a potent synergistic strategy to reduce multidrug resistance and pathogenicity.
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Howan DHO, Jenei S, Szolomajer J, Endre G, Kondorosi É, Tóth GK. Enhanced Antibacterial Activity of Substituted Derivatives of NCR169C Peptide. Int J Mol Sci 2023; 24:ijms24032694. [PMID: 36769017 PMCID: PMC9917201 DOI: 10.3390/ijms24032694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Medicago truncatula in symbiosis with its rhizobial bacterium partner produces more than 700 nodule-specific cysteine-rich (NCR) peptides with diverse physicochemical properties. Most of the cationic NCR peptides have antimicrobial activity and the potential to tackle antimicrobial resistance with their novel modes of action. This work focuses on the antibacterial activity of the NCR169 peptide derivatives as we previously demonstrated that the C-terminal sequence of NCR169 (NCR169C17-38) has antifungal activity, affecting the viability, morphology, and biofilm formation of various Candida species. Here, we show that NCR169C17-38 and its various substituted derivatives are also able to kill ESKAPE pathogens such as Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. The replacement of the two cysteines with serines enhanced the antimicrobial activity against most of the tested bacteria, indicating that the formation of a disulfide bridge is not required. As tryptophan can play role in the interaction with bacterial membranes and thus in antibacterial activity, we replaced the tryptophans in the NCR169C17-38C12,17/S sequence with various modified tryptophans, namely 5-methyl tryptophan, 5-fluoro tryptophan, 6-fluoro tryptophan, 7-aza tryptophan, and 5-methoxy tryptophan, in the synthesis of NCR169C17-38C12,17/S analogs. The results demonstrate that the presence of modified fluorotryptophans can significantly enhance the antimicrobial activity without notable hemolytic effect, and this finding could be beneficial for the further development of new AMPs from the members of the NCR peptide family.
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Affiliation(s)
- Dian H. O. Howan
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
| | - Sándor Jenei
- Biological Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - János Szolomajer
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
| | - Gabriella Endre
- Biological Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - Éva Kondorosi
- Biological Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - Gábor K. Tóth
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- MTA-SZTE Biomimetic Systems Research Group, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Correspondence:
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Food-Grade Bacteria Combat Pathogens by Blocking AHL-Mediated Quorum Sensing and Biofilm Formation. Foods 2022; 12:foods12010090. [PMID: 36613306 PMCID: PMC9818890 DOI: 10.3390/foods12010090] [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: 11/20/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Disrupting bacterial quorum sensing (QS) signaling is a promising strategy to combat pathogenic biofilms without the development of antibiotic resistance. Here, we report that food-associated bacteria can interfere with the biofilm formation of a Gram-negative pathogenic bacterium by targeting its AHL (acyl-homoserine lactone) QS system. This was demonstrated by screening metabolic end-products of different lactobacilli and propionibacteria using Gram-negative and biofilm-forming Chromobacterium violaceum as the QS reporter and our anti-QS microscale screening platform with necessary modifications. The method was optimized in terms of the inoculation technique and the concentrations of D-glucose and L-tryptophan, two key factors controlling the synthesis of violacein, a purple pigment indicating the activation of the QS system in C. violaceum. These improvements resulted in ca. 16-times higher violacein yields and enabled revealing anti-QS effects of Lactobacillus acidophilus, Lentilactobacillus kefiri, Lacticaseibacillus rhamnosus and Propionibacterium freudenreichii, including new cheese-associated strains. Our findings also suggest that acetate and propionate excreted by these species are the main factors that interrupt the QS-mediated signaling and subsequent biofilm growth without affecting the cell viability of the C. violaceum reporter. Thus, the present study reports a revised anti-QS screening method to accurately define new bacteria with an ability to combat pathogens in a safe and sustainable way.
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Fermentation in Minimal Media and Fungal Elicitation Enhance Violacein and Deoxyviolacein Production in Two Janthinobacterium Strains. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Violacein and its biosynthesis by-product deoxyviolacein are valuable natural pigments with different biological activities. Various efforts have been made to enhance violacein and deoxyviolacein production in microbes. However, the effect of different culture media, agitation, and fungal elicitation on biosynthesis in Janthinobacterium has not been evaluated. In this study, the effect of eight different culture media, agitation, and fungal elicitation by Agaricus bisporus on violacein and deoxviolacein production in Janthinobacterium agaricidamnosum DSM 9628 and Janthinobacterium lividum DSM 1552 were examined. The results showed that violacein and deoxviolacein are produced at high-levels when Janthinobacterium is cultivated in minimal media such as Davis minimal broth with glycerol (DMBgly), shipworm basal medium (SBM), and MM9 media. A 50-fold increase was observed in violacein production when Janthinobacterium was cultivated in these media compared to cultivation in Luria–Bertani (LB), nutrient broth (NB), and King’s B (KB). Agitation reduces violacein and deoxyviolacein production, while fungal elicitation decreases violacein but increases deoxyviolacein when Janthinobacterium is cultured in KB media, SBM, and modified SBM (MSBM). An antibacterial assay using various pathogenic bacteria showed that violacein and deoxyviolacein extracted from Janthinobacterium are effective against both Gram-positive and Gram-negative pathogens, confirming their functionality as antibacterial agents. The findings suggest that cultivation in minimal media and fungal elicitation might invoke a stress response, enhancing the production of violacein and deoxviolacein in Janthinobacterium.
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Lyakhovchenko NS, Travkin VM, Senchenkov VY, Solyanikova IP. Bacterial Violacein: Properties, Biosynthesis and Application Prospects. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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11
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Xu KZ, Tan XJ, Chang ZY, Li JJ, Jia AQ. 2-tert-Butyl-1,4-benzoquinone, a food additive oxidant, reduces virulence factors of Chromobacterium violaceum. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113569] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Functional characterization of a novel violacein biosynthesis operon from Janthinobacterium sp. B9-8. Appl Microbiol Biotechnol 2022; 106:2903-2916. [PMID: 35445857 DOI: 10.1007/s00253-022-11929-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 11/02/2022]
Abstract
Violacein is a secondary metabolite mainly produced by Gram-negative bacteria that is formed from tryptophan by five enzymes encoded by a single operon. It is a broad-spectrum antibacterial pigment with various important biological activities such as anti-tumor, antiviral, and antioxidative effects. The newly discovered violacein operon vioABCDE was identified in the genome of the extremophile Janthinobacterium sp. B9-8. The key enzyme-encoding genes were cloned to construct the multigene coexpression plasmids pET-vioAB and pRSF-vioCDE. The violacein biosynthesis pathway was heterologously introduced into engineered Escherichia coli VioABCDE and VioABCDE-SD. The factors affecting violacein production, including temperature, pH, inoculum size, carbon and nitrogen source, precursor, and inducers were investigated. The violacein titer of VioABCDE-SD reached 107 mg/L in a two-stage fermentation process, representing a 454.4% increase over the original strain. The violacein operon from B9-8 provides a new microbial gene source for the analysis of the violacein synthesis mechanism, and the constructed engineering E. coli strains lay a foundation for the efficient and rapid synthesis of other natural products.Key points• The newly discovered violacein operon vioABCDE was identified in the genome of the extremophile Janthinobacterium sp. B9-8.• The violacein synthesis pathway was reconstructed in E. coli using two compatible plasmids.• A two-stage fermentation process was optimized for improved violacein accumulation.
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Gohil N, Bhattacharjee G, Gayke M, Narode H, Alzahrani KJ, Singh V. Enhanced production of violacein by Chromobacterium violaceum using agro-industrial waste soybean meal. J Appl Microbiol 2022; 132:1121-1133. [PMID: 34469627 DOI: 10.1111/jam.15277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/19/2021] [Accepted: 08/26/2021] [Indexed: 12/01/2022]
Abstract
AIMS The research is aimed at developing an economic and sustainable growth medium using abundantly available and highly nutritive agro-industrial waste soybean meal as the substrate for the production of violacein by Chromobacterium violaceum. METHODS AND RESULTS Violacein produced using soybean meal medium was compared with the commercial complex growth media. Upon utilization of 2% w/v soybean meal (SM2 ) medium, 496 mg/L crude violacein was achieved after 48-hr incubation time, which was 1.62-fold higher than the crude violacein produced in Luria-Bertani (LB) broth. Additionally, supplementation of 100 mg/L L-tryptophan to 1% and 2% w/v soybean meal (SMT1 and SMT2 ) medium yielded 1217 mg/L (3.96-fold higher as compared to LB) and 1198 mg/L (3.90-fold higher as compared to LB) crude violacein respectively. Optimization of culture conditions and concentration of L-tryptophan using Box-Behnken design (BBD) model produced as high as 1504.5 mg/L crude violacein. To the best of our knowledge, this is the highest crude violacein produced to date using agro-industrial-based waste as a substrate with minimal supplementation in a shake flask. CONCLUSIONS The study signifies the potentiality of soybean meal as a cost-effective growth medium for the production of violacein. Optimization of the fermentation parameters clearly demonstrated a surge in violacein production. SIGNIFICANCE AND IMPACT OF THE STUDY Utilization of soybean meal as an alternative to the expensive commercial media would surely promote the large-scale synthesis of this multifaceted compound.
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Affiliation(s)
- Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Manoj Gayke
- Department of Chemistry, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Hanuman Narode
- Department of Chemistry, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
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14
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Trisrivirat D, Sutthaphirom C, Pimviriyakul P, Chaiyen P. Dual activities of oxidation and oxidative decarboxylation by flavoenzymes. Chembiochem 2022; 23:e202100666. [PMID: 35040514 DOI: 10.1002/cbic.202100666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/17/2022] [Indexed: 11/07/2022]
Abstract
Specific flavoenzyme oxidases catalyze oxidative decarboxylation in addition to their classical oxidation reactions in the same active sites. The mechanisms underlying oxidative decarboxylation by these enzymes and how they control their two activities are not clearly known. This article reviews the current state of knowledge of four enzymes from the l-amino acid oxidase and l-hydroxy acid oxidase families, including l-tryptophan 2-monooxygenase, l-phenylalanine 2-oxidase and l-lysine oxidase/monooxygenase and lactate monooxygenase which catalyze substrate oxidation and oxidative decarboxylation. Apart from specific interactions to allow substrate oxidation by the flavin cofactor, specific binding of oxidized product in the active sites appears to be important for enabling subsequent decarboxylation by these enzymes. Based on recent findings of l-lysine oxidase/monooxygenase, we propose that nucleophilic attack of H2O2 on the imino acid product is the mechanism enabling oxidative decarboxylation.
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Affiliation(s)
- Duangthip Trisrivirat
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | - Chalermroj Sutthaphirom
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | | | - Pimchai Chaiyen
- Vidyasirimedhi Institute of Science and Technology (VISTEC), School of Biomolecular Science and Engineering, 555 Moo 1 Payupnai, 21210, Wangchan District, THAILAND
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15
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Ishida C, Miyata R, Hasebe F, Miyata A, Kumazawa S, Ito S, Nakano S. Reconstruction of Hyper‐Thermostable Ancestral L‐Amino Acid Oxidase to Perform Deracemization to D‐Amino Acids. ChemCatChem 2021. [DOI: 10.1002/cctc.202101296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chiharu Ishida
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Ryo Miyata
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Fumihito Hasebe
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Azusa Miyata
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Shigenori Kumazawa
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences University of Shizuoka Shizuoka 422-8526 Japan
- PREST, Japan Science and Technology Agency Saitama 332-0012 Japan
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16
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Han J, Lyutenko NV, Sorochinsky AE, Okawara A, Konno H, White S, Soloshonok VA. Tailor-Made Amino Acids in Pharmaceutical Industry: Synthetic Approaches to Aza-Tryptophan Derivatives. Chemistry 2021; 27:17510-17528. [PMID: 34913215 DOI: 10.1002/chem.202102485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/24/2021] [Indexed: 12/22/2022]
Abstract
Over the recent years there has been a noticeable upsurge of interest in aza-analogs of tryptophan which are isosteric to the latter and found numerous applications in medicinal, bioorganic chemistry, and peptide research. In the present review article, five aza-tryptophan derivatives are profiled, including aza-substitution in the positions 2, on the five-membered ring, as well as in positions 4, 5, 6, and 7 on the six-membered ring. A detailed and comprehensive literature overview of the synthetic methods for the preparation of these aza-tryptophans is presented and general facets of the biological properties and most promising applications are discussed.
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Affiliation(s)
- Jianlin Han
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and Materials College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P. R. China
| | - Nataliya V Lyutenko
- Department of Fine Organic Synthesis V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, The National Academy of Sciences of Ukraine, 1 Murmanska str., Kyiv, 02094, Ukraine
| | - Alexander E Sorochinsky
- Department of Fine Organic Synthesis V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, The National Academy of Sciences of Ukraine, 1 Murmanska str., Kyiv, 02094, Ukraine
| | - Ayaka Okawara
- Graduate School of Science and Engineering, Yamagata University, 4-3-16, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Hiroyuki Konno
- Graduate School of Science and Engineering, Yamagata University, 4-3-16, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Sarah White
- Oakwood Chemical, Inc., 730 Columbia Hwy. N, Estill, SC, 29918, USA
| | - Vadim A Soloshonok
- Department of Organic Chemistry I Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizábal 3, 20018, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, Plaza Bizkaia, 48013, Bilbao, Spain
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17
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Ahmed A, Ahmad A, Li R, AL-Ansi W, Fatima M, Mushtaq BS, Basharat S, Li Y, Bai Z. Recent Advances in Synthetic, Industrial and Biological Applications of Violacein and Its Heterologous Production. J Microbiol Biotechnol 2021; 31:1465-1480. [PMID: 34584039 PMCID: PMC9705886 DOI: 10.4014/jmb.2107.07045] [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: 07/27/2021] [Revised: 09/15/2021] [Accepted: 09/26/2021] [Indexed: 12/15/2022]
Abstract
Violacein, a purple pigment first isolated from a gram-negative coccobacillus Chromobacterium violaceum, has gained extensive research interest in recent years due to its huge potential in the pharmaceutic area and industry. In this review, we summarize the latest research advances concerning this pigment, which include (1) fundamental studies of its biosynthetic pathway, (2) production of violacein by native producers, apart from C. violaceum, (3) metabolic engineering for improved production in heterologous hosts such as Escherichia coli, Citrobacter freundii, Corynebacterium glutamicum, and Yarrowia lipolytica, (4) biological/pharmaceutical and industrial properties, (5) and applications in synthetic biology. Due to the intrinsic properties of violacein and the intermediates during its biosynthesis, the prospective research has huge potential to move this pigment into real clinical and industrial applications.
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Affiliation(s)
- Aqsa Ahmed
- School of Biotechnology, Jiangnan University, Wuxi 214122, P.R. China,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Abdullah Ahmad
- Department of Industrial Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad 44000, Pakistan
| | - Renhan Li
- School of Biotechnology, Jiangnan University, Wuxi 214122, P.R. China,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Waleed AL-Ansi
- School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.R. China,Department of Food Science and Technology, Faculty of Agriculture, Sana’a University, Sana’a, 725, Yemen
| | - Momal Fatima
- Department of Industrial Biotechnology, National Institute of Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
| | - Bilal Sajid Mushtaq
- School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.R. China
| | - Samra Basharat
- School of Biotechnology, Jiangnan University, Wuxi 214122, P.R. China
| | - Ye Li
- School of Biotechnology, Jiangnan University, Wuxi 214122, P.R. China,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, P.R. China,Corresponding authors Y. Li E-mail:
| | - Zhonghu Bai
- School of Biotechnology, Jiangnan University, Wuxi 214122, P.R. China,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, P.R. China,
Z. Bai Phone: +86510-85197983 Fax: +86510-85197983 E-mail:
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18
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Lai HE, Obled AMC, Chee SM, Morgan RM, Lynch R, Sharma SV, Moore SJ, Polizzi KM, Goss RJM, Freemont PS. GenoChemetic Strategy for Derivatization of the Violacein Natural Product Scaffold. ACS Chem Biol 2021; 16:2116-2123. [PMID: 34648268 PMCID: PMC8609527 DOI: 10.1021/acschembio.1c00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Natural products and their analogues are often challenging to synthesize due to their complex scaffolds and embedded functional groups. Solely relying on engineering the biosynthesis of natural products may lead to limited compound diversity. Integrating synthetic biology with synthetic chemistry allows rapid access to much more diverse portfolios of xenobiotic compounds, which may accelerate the discovery of new therapeutics. As a proof-of-concept, by supplementing an Escherichia coli strain expressing the violacein biosynthesis pathway with 5-bromo-tryptophan in vitro or tryptophan 7-halogenase RebH in vivo, six halogenated analogues of violacein or deoxyviolacein were generated, demonstrating the promiscuity of the violacein biosynthesis pathway. Furthermore, 20 new derivatives were generated from 5-brominated violacein analogues via the Suzuki-Miyaura cross-coupling reaction directly using the crude extract without prior purification. Herein we demonstrate a flexible and rapid approach to access a diverse chemical space that can be applied to a wide range of natural product scaffolds.
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Affiliation(s)
- Hung-En Lai
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Alan M. C. Obled
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Soo Mei Chee
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, London W12 0BZ, U.K
| | - Rhodri M. Morgan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Rosemary Lynch
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Sunil V. Sharma
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Simon J. Moore
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Karen M. Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Rebecca J. M. Goss
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, London W12 0BZ, U.K
- UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, U.K
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19
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Ramdass AC, Rampersad SN. Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism. BMC Microbiol 2021; 21:287. [PMID: 34670489 PMCID: PMC8527658 DOI: 10.1186/s12866-021-02346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Background Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment. Methods Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria. Results 16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch. Conclusions The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02346-4.
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Affiliation(s)
- Amanda C Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sephra N Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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20
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Sugiura S, Nakano S, Niwa M, Hasebe F, Matsui D, Ito S. Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining. J Biol Chem 2021; 297:101043. [PMID: 34358565 PMCID: PMC8405998 DOI: 10.1016/j.jbc.2021.101043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 11/23/2022] Open
Abstract
A large number of protein sequences are registered in public databases such as PubMed. Functionally uncharacterized enzymes are included in these databases, some of which likely have potential for industrial applications. However, assignment of the enzymes remained difficult tasks for now. In this study, we assigned a total of 28 original sequences to uncharacterized enzymes in the FAD-dependent oxidase family expressed in some species of bacteria including Chryseobacterium, Flavobacterium, and Pedobactor. Progenitor sequence of the assigned 28 sequences was generated by ancestral sequence reconstruction, and the generated sequence exhibited L-lysine oxidase activity; thus, we named the enzyme AncLLysO. Crystal structures of ligand-free and ligand-bound forms of AncLLysO were determined, indicating that the enzyme recognizes L-Lys by hydrogen bond formation with R76 and E383. The binding of L-Lys to AncLLysO induced dynamic structural change at a plug loop formed by residues 251 to 254. Biochemical assays of AncLLysO variants revealed the functional importance of these substrate recognition residues and the plug loop. R76A and E383D variants were also observed to lose their activity, and the kcat/Km value of G251P and Y253A mutations were approximately 800- to 1800-fold lower than that of AncLLysO, despite the indirect interaction of the substrates with the mutated residues. Taken together, our data demonstrate that combinational approaches to sequence classification from database and ancestral sequence reconstruction may be effective not only to find new enzymes using databases of unknown sequences but also to elucidate their functions.
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Affiliation(s)
- Sayaka Sugiura
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan; PREST, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Masazumi Niwa
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Fumihito Hasebe
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Daisuke Matsui
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
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21
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Durán N, Nakazato G, Durán M, Berti IR, Castro GR, Stanisic D, Brocchi M, Fávaro WJ, Ferreira-Halder CV, Justo GZ, Tasic L. Multi-target drug with potential applications: violacein in the spotlight. World J Microbiol Biotechnol 2021; 37:151. [PMID: 34398340 DOI: 10.1007/s11274-021-03120-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/02/2021] [Indexed: 11/28/2022]
Abstract
The aim of the current review is to address updated research on a natural pigment called violacein, with emphasis on its production, biological activity and applications. New information about violacein's action mechanisms as antitumor agent and about its synergistic action in drug delivery systems has brought new alternatives for anticancer therapy. Thus, violacein is introduced as reliable drug capable of overcoming at least three cancer hallmarks, namely: proliferative signaling, cell death resistance and metastasis. In addition, antimicrobial effects on several microorganisms affecting humans and other animals turn violacein into an attractive drug to combat resistant pathogens. Emphasis is given to effects of violacein combined with different agents, such as antibiotics, anticancer agents and nanoparticles. Although violacein is well-known for many decades, it remains an attractive compound. Thus, research groups have been making continuous effort to help improving its production in recent years, which can surely enable its pharmaceutical and chemical application as multi-task compound, even in the cosmetics and food industries.
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Affiliation(s)
- Nelson Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil. .,Nanomedicine Research Unit (Nanomed), Center for Natural and Human Sciences (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil.
| | - Gerson Nakazato
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Biology Sciences Center, Universidade Estadual de Londrina (UEL), Londrina, PR, Brazil
| | - Marcela Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil.,Nanomedicine Research Unit (Nanomed), Center for Natural and Human Sciences (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Ignasio R Berti
- Nanobiomaterials Laboratory, Department of Chemistry, School of Sciences, Institute of Applied Biotechnology CINDEFI (UNLPCONICET, CCT La Plata),, Universidad Nacional de La Plata, La Plata, Argentina
| | - Guillermo R Castro
- Nanobiomaterials Laboratory, Department of Chemistry, School of Sciences, Institute of Applied Biotechnology CINDEFI (UNLPCONICET, CCT La Plata),, Universidad Nacional de La Plata, La Plata, Argentina
| | - Danijela Stanisic
- Biological Chemistry Laboratory, Institute of Chemistry, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Brocchi
- Laboratory of Tropical Diseases, Department of Genetic, Evolution and Bioagents , Biology Institute, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Wagner J Fávaro
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Carmen V Ferreira-Halder
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Giselle Z Justo
- Departamento de Ciências Farmacêuticas (Campus Diadema) e Departamento de Bioquímica (Campus São Paulo), Universidade Federal de São Paulo (UNIFESP), 3 de Maio, 100, São Paulo, SP, 04044-020, Brazil.
| | - Ljubica Tasic
- Biological Chemistry Laboratory, Institute of Chemistry, Universidade Estadual de Campinas, Campinas, SP, Brazil
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22
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Park H, Park S, Yang YH, Choi KY. Microbial synthesis of violacein pigment and its potential applications. Crit Rev Biotechnol 2021; 41:879-901. [PMID: 33730942 DOI: 10.1080/07388551.2021.1892579] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Violacein is a pigment synthesized by Gram-negative bacteria such as Chromobacterium violaceum. It has garnered significant interest owing to its unique physiological and biological activities along with its synergistic effects with various antibiotics. In addition to C. violaceum, several microorganisms, including: Duganella sp., Pseudoalteromonas sp., Iodobacter sp., and Massilia sp., are known to produce violacein. Along with the identification of violacein-producing strains, the genetic regulation, quorum sensing mechanism, and sequence of the vio-operon involved in the biosynthesis of violacein have been elucidated. From an engineering perspective, the heterologous production of violacein using the genetically engineered Escherichia coli or Citrobacter freundii host has also been attempted. Genetic engineering of host cells involves the heterologous expression of genes involved in the vio operon and the optimization of metabolic pathways and gene regulation. Further, the crystallography of VioD and VioE was revealed, and mass production by enzyme engineering has been accelerated. In this review, we highlight the biologically assisted end-use applications of violacein (such as functional fabric development, nanoparticles, functional polymer composites, and sunscreen ingredients) and violacein activation mechanisms, production strains, and the results of mass production with engineered methods. The prospects for violacein research and engineering applications have also been discussed.
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Affiliation(s)
- HyunA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - SeoA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea.,Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Suwon, South Korea
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23
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Tran T, Dawrs SN, Norton GJ, Virdi R, Honda JR. Brought to you courtesy of the red, white, and blue-pigments of nontuberculous mycobacteria. AIMS Microbiol 2020; 6:434-450. [PMID: 33364537 PMCID: PMC7755587 DOI: 10.3934/microbiol.2020026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
Pigments are chromophores naturally synthesized by animals, plants, and microorganisms, as well as produced synthetically for a wide variety of industries such as food, pharmaceuticals, and textiles. Bacteria produce various pigments including melanin, pyocyanin, bacteriochlorophyll, violacein, prodigiosin, and carotenoids that exert diverse biological activities as antioxidants and demonstrate anti-inflammatory, anti-cancer, and antimicrobial properties. Nontuberculous mycobacteria (NTM) include over 200 environmental and acid-fast species; some of which can cause opportunistic disease in humans. Early in the study of mycobacteriology, the vast majority of mycobacteria were not known to synthesize pigments, particularly NTM isolates of clinical significance such as the Mycobacterium avium complex (MAC) species. This paper reviews the overall understanding of microbial pigments, their applications, as well as highlights what is currently known about pigments produced by NTM, the circumstances that trigger their production, and their potential roles in NTM survival and virulence.
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Affiliation(s)
- Tru Tran
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, Florida, USA
| | - Stephanie N Dawrs
- Center for Genes, Environment, and Health; Department of Immunology and Genomic Research, National Jewish Health, Denver, Colorado, USA
| | - Grant J Norton
- Center for Genes, Environment, and Health; Department of Immunology and Genomic Research, National Jewish Health, Denver, Colorado, USA
| | - Ravleen Virdi
- Center for Genes, Environment, and Health; Department of Immunology and Genomic Research, National Jewish Health, Denver, Colorado, USA
| | - Jennifer R Honda
- Center for Genes, Environment, and Health; Department of Immunology and Genomic Research, National Jewish Health, Denver, Colorado, USA
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24
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Durán N, Fávaro WJ, Brocchi M, Justo GZ, Castro GR, Durán M, Nakazato G. Patents on Violacein: A Compound with Great Diversity of Biological Activities and Industrial Potential. Recent Pat Biotechnol 2020; 15:102-111. [PMID: 33349223 DOI: 10.2174/2213476x07666201221111655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/15/2020] [Accepted: 11/16/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND This review outlines to envisage the current impact of violacein-derivative materials in several technological areas through patents. METHODS A comprehensive examination up to day patent databases on violacein demonstrated the relevance of this pigment, as well as the pertinent topics related to its technological development in order to obtain adaptable new pharmaceuticals, cosmetics and new quality fiber materials, together with others applications of violacein in different areas. RESULTS At present time, there is no efficient and economical feasible technique for violacein preparation at industrial scale. Many attempts have been developed but none have achieved the big challenge of being effective and inexpensive process. However, some potential applications of violacein in fields like biomedicine make the pigment worth to continuous the investigations. Particularly, violacein patents covering from biosynthesis to different applications were reported recently. CONCLUSION As unique pigment, violacein has been used in distinct areas of specialties, such as in medical and industrial fields. Then, this review through patents provides an update on violacein innovations useful for researchers working in an expandable and interesting field of biotechnology with natural pigments.
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Affiliation(s)
- Nelson Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Biology Institute, Department of Structural and Functional Biology, University of Campinas,Campinas, SP. Brazil
| | - Wagner J Fávaro
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Biology Institute, Department of Structural and Functional Biology, University of Campinas,Campinas, SP. Brazil
| | - Marcelo Brocchi
- Laboratory of Tropical Diseases, Institute of Biology, Department of Genetic, Evolution, Microbiology and Immunology. University of Campinas, Campinas, SP. Brazil
| | - Giselle Z Justo
- Department of Pharmaceutical Sciences and Department of Biochemistry, Federal University of São Paulo (UNIFESP). Brazil
| | - Guillermo R Castro
- Nanobiomaterials Laboratory, Institute of Applied Biotechnology CINDEFI (UNLP-CONICET, CCT La Plata), Department of Chemistry, School of Sciences, Universidad Nacional de La Plata, La Plata. Argentina
| | - Marcela Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Biology Institute, Department of Structural and Functional Biology, University of Campinas,Campinas, SP. Brazil
| | - Gerson Nakazato
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Biology Sciences Center, Londrina State University (UEL), Londrina. Brazil
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Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids. Commun Chem 2020; 3:181. [PMID: 36703379 PMCID: PMC9814856 DOI: 10.1038/s42004-020-00432-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
L-amino acid oxidases (LAAOs) can be applied to convert racemic amino acids to D-isomers, which are potential precursors of pharmaceuticals. However, this application is hampered by the lack of available stable and structure-determined LAAOs. In this study, we attempt to address this limitation by utilizing two ancestral LAAOs: AncLAAO-N4 and AncLAAO-N5. AncLAAO-N4 has the highest thermal and temporal stabilities among the designed LAAOs that can be used for deracemization and stereoinversion. AncLAAO-N5 can provide X-ray crystal structures, which are helpful to reveal substrate recognition and reaction mechanisms of LAAOs at the molecular level. Next, we attempted to improve activity of AncLAAO-N4 toward L-Val through a semi-rational protein engineering method. Three variants with enhanced activity toward L-Val were obtained. Taken together, we believe that the activity and substrate selectivity of AncLAAOs give them the potential to be key enzymes in various chemoenzymatic reactions.
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Velmurugan P, Venil CK, Veera Ravi A, Dufossé L. Marine Bacteria Is the Cell Factory to Produce Bioactive Pigments: A Prospective Pigment Source in the Ocean. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.589655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The course of investigations of bioactive compounds like bacterial pigments from the marine environment has greatly expanded in the recent decades. Despite the huge concern in secluding and collecting marine bacteria, microbial metabolites are progressively alluring to science due to their wide ranging applications in various fields, particularly those with distinctive color pigments. This review is a short appraisal of the studies undertaken over the past 5 years on the bacterial pigments sourced from the marine environment. Herein, we have reviewed the potential of different bacterial species isolated from marine environment in diverse studies that are producing bioactive pigments that have potential commercial applications.
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Sajjad W, Din G, Rafiq M, Iqbal A, Khan S, Zada S, Ali B, Kang S. Pigment production by cold-adapted bacteria and fungi: colorful tale of cryosphere with wide range applications. Extremophiles 2020; 24:447-473. [PMID: 32488508 PMCID: PMC7266124 DOI: 10.1007/s00792-020-01180-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022]
Abstract
Pigments are an essential part of everyday life on Earth with rapidly growing industrial and biomedical applications. Synthetic pigments account for a major portion of these pigments that in turn have deleterious effects on public health and environment. Such drawbacks of synthetic pigments have shifted the trend to use natural pigments that are considered as the best alternative to synthetic pigments due to their significant properties. Natural pigments from microorganisms are of great interest due to their broader applications in the pharmaceutical, food, and textile industry with increasing demand among the consumers opting for natural pigments. To fulfill the market demand of natural pigments new sources should be explored. Cold-adapted bacteria and fungi in the cryosphere produce a variety of pigments as a protective strategy against ecological stresses such as low temperature, oxidative stresses, and ultraviolet radiation making them a potential source for natural pigment production. This review highlights the protective strategies and pigment production by cold-adapted bacteria and fungi, their industrial and biomedical applications, condition optimization for maximum pigment extraction as well as the challenges facing in the exploitation of cryospheric microorganisms for pigment extraction that hopefully will provide valuable information, direction, and progress in forthcoming studies.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Ghufranud Din
- Department of Microbiology, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Awais Iqbal
- School of Life Sciences, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, People's Republic of China
| | - Suliman Khan
- The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sahib Zada
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
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28
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Trisrivirat D, Lawan N, Chenprakhon P, Matsui D, Asano Y, Chaiyen P. Mechanistic insights into the dual activities of the single active site of l-lysine oxidase/monooxygenase from Pseudomonas sp. AIU 813. J Biol Chem 2020; 295:11246-11261. [PMID: 32527725 DOI: 10.1074/jbc.ra120.014055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
l-Lysine oxidase/monooxygenase (l-LOX/MOG) from Pseudomonas sp. AIU 813 catalyzes the mixed bioconversion of l-amino acids, particularly l-lysine, yielding an amide and carbon dioxide by an oxidative decarboxylation (i.e. apparent monooxygenation), as well as oxidative deamination (hydrolysis of oxidized product), resulting in α-keto acid, hydrogen peroxide (H2O2), and ammonia. Here, using high-resolution MS and monitoring transient reaction kinetics with stopped-flow spectrophotometry, we identified the products from the reactions of l-lysine and l-ornithine, indicating that besides decarboxylating imino acids (i.e. 5-aminopentanamide from l-lysine), l-LOX/MOG also decarboxylates keto acids (5-aminopentanoic acid from l-lysine and 4-aminobutanoic acid from l-ornithine). The reaction of reduced enzyme and oxygen generated an imino acid and H2O2, with no detectable C4a-hydroperoxyflavin. Single-turnover reactions in which l-LOX/MOG was first reduced by l-lysine to form imino acid before mixing with various compounds revealed that under anaerobic conditions, only hydrolysis products are present. Similar results were obtained upon H2O2 addition after enzyme denaturation. H2O2 addition to active l-LOX/MOG resulted in formation of more 5-aminopentanoic acid, but not 5-aminopentamide, suggesting that H2O2 generated from l-LOX/MOG in situ can result in decarboxylation of the imino acid, yielding an amide product, and extra H2O2 resulted in decarboxylation only of keto acids. Molecular dynamics simulations and detection of charge transfer species suggested that interactions between the substrate and its binding site on l-LOX/MOG are important for imino acid decarboxylation. Structural analysis indicated that the flavoenzyme oxidases catalyzing decarboxylation of an imino acid all share a common plug loop configuration that may facilitate this decarboxylation.
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Affiliation(s)
- Duangthip Trisrivirat
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, Thailand
| | - Daisuke Matsui
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan.,Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand .,School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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Tararina MA, Allen KN. Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. J Mol Biol 2020; 432:3269-3288. [PMID: 32198115 DOI: 10.1016/j.jmb.2020.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/24/2020] [Accepted: 03/06/2020] [Indexed: 12/29/2022]
Abstract
The flavin-dependent amine oxidase (FAO) superfamily consists of over 9000 nonredundant sequences represented in all domains of life. Of the thousands of members identified, only 214 have been functionally annotated to date, and 40 unique structures are represented in the Protein Data Bank. The few functionally characterized members share a catalytic mechanism involving the oxidation of an amine substrate through transfer of a hydride to the FAD cofactor, with differences observed in substrate specificities. Previous studies have focused on comparing a subset of superfamily members. Here, we present a comprehensive analysis of the FAO superfamily based on reaction mechanism and substrate recognition. Using a dataset of 9192 sequences, a sequence similarity network, and subsequently, a genome neighborhood network were constructed, organizing the superfamily into eight subgroups that accord with substrate type. Likewise, through phylogenetic analysis, the evolutionary relationship of subgroups was determined, delineating the divergence between enzymes based on organism, substrate, and mechanism. In addition, using sequences and atomic coordinates of 22 structures from the Protein Data Bank to perform sequence and structural alignments, active-site elements were identified, showing divergence from the canonical aromatic-cage residues to accommodate large substrates. These specificity determinants are held in a structural framework comprising a core domain catalyzing the oxidation of amines with an auxiliary domain for substrate recognition. Overall, analysis of the FAO superfamily reveals a modular fold with cofactor and substrate-binding domains allowing for diversity of recognition via insertion/deletions. This flexibility allows facile evolution of new activities, as shown by reinvention of function between subfamilies.
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Affiliation(s)
- Margarita A Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Karen N Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA; Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA.
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30
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Asano Y, Yasukawa K. Identification and development of amino acid oxidases. Curr Opin Chem Biol 2019; 49:76-83. [DOI: 10.1016/j.cbpa.2018.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 12/23/2022]
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31
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Asano Y. Screening and development of enzymes for determination and transformation of amino acids. Biosci Biotechnol Biochem 2019; 83:1402-1416. [PMID: 30621552 DOI: 10.1080/09168451.2018.1559027] [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] [Indexed: 12/16/2022]
Abstract
The high stereo- and substrate specificities of enzymes have been utilized for micro-determination of amino acids. Here, I review the discovery of l-Phe dehydrogenase and its practical use in the diagnosis of phenylketonuria in more than 5,400,000 neonates over two decades in Japan. Screening and uses of other selective enzymes for micro-determination of amino acids have also been discussed. In addition, novel enzymatic assays with the systematic use of known enzymes, including assays based on a pyrophosphate detection system using pyrophosphate dikinase for a variety of l-amino acids with amino-acyl-tRNA synthetase have been reviewed. Finally, I review the substrate specificities of a few amino acid-metabolizing enzymes that have been altered, using protein engineering techniques, mainly for production of useful chemicals, thus enabling the wider use of natural enzymes.
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Affiliation(s)
- Yasuhisa Asano
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Toyama , Japan
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32
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Azman AS, Mawang CI, Abubakar S. Bacterial Pigments: The Bioactivities and as an Alternative for Therapeutic Applications. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801301240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Synthetic pigments have been widely used in various applications since the 1980s. However, the hyperallergenicity or carcinogenicity effects of synthetic dyes have led to the increased research on natural pigments. Among the natural resources, bacterial pigments are a good alternative to synthetic pigments because of their significant properties. Bacterial pigments are also one of the emerging fields of research since it offers promising opportunities for different applications. Besides its use as safe coloring agents in the cosmetic and food industry, bacterial pigments also possess biological properties such as antimicrobial, antiviral, antioxidant and anticancer activities. This review article highlights the various types of bacterial pigments, the latest studies on the discovery of bacterial pigments and the therapeutic insights of these bacterial pigments which hopefully provides useful information, guidance and improvement in future study.
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Affiliation(s)
- Adzzie-Shazleen Azman
- Tropical Infectious Diseases Research and Education Centre, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Christina-Injan Mawang
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Sazaly Abubakar
- Tropical Infectious Diseases Research and Education Centre, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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33
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Pillaiyar T, Gorska E, Schnakenburg G, Müller CE. General Synthesis of Unsymmetrical 3,3'-(Aza)diindolylmethane Derivatives. J Org Chem 2018; 83:9902-9913. [PMID: 30025207 DOI: 10.1021/acs.joc.8b01349] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diindolylmethane (DIM) and its derivatives have recently been in the focus of interest due to their significant biological activities, specifically in cancer prevention and therapy. Molecular targets of DIM have been identified, e.g., the immunostimulatory G protein-coupled receptor GPR84. However, most of the reported and investigated DIM derivatives are symmetrical because general methods for obtaining unsymmetrical DIMs have been lacking. To optimize the interaction of DIM derivatives with their protein targets, unsymmetrical substitution is required. In the present study we developed a new, mild and efficient access to unsymmetrically substituted 3,3'-DIMs by reaction of (3-indolylmethyl)trimethylammonium iodides with a wide range of substituted indole derivatives. 7-Azaindole also led to the 3,3'-connected DIM analogue, while 4- and 5-azaindoles reacted at the N1-nitrogen atom as confirmed by X-ray crystallography. The reactions were performed in water without the requirement of a catalyst or other additives. Wide substrate scope, operational simplicity, environmentally benign workup, and high yields are further advantages of the new method. The synthetic protocol proved to be suitable for upscaling to yield gram amounts for pharmacological studies. This procedure will allow the preparation of a broad range of novel, unsymmetrical DIM derivatives to exploit their potential as novel drugs.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , D-53121 Bonn , Germany
| | - Ewelina Gorska
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , D-53121 Bonn , Germany
| | - Gregor Schnakenburg
- Institute of Inorganic Chemistry , University of Bonn , Gerhard-Domagk-Str. 1 , D-53121 Bonn , Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , D-53121 Bonn , Germany
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Yamaguchi H, Tatsumi M, Takahashi K, Tagami U, Sugiki M, Kashiwagi T, Kameya M, Okazaki S, Mizukoshi T, Asano Y. Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis. J Biochem 2018; 164:359-367. [DOI: 10.1093/jb/mvy065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/23/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hiroki Yamaguchi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Moemi Tatsumi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Kazutoshi Takahashi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Uno Tagami
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Masayuki Sugiki
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Tatsuki Kashiwagi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Masafumi Kameya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, Japan
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| | - Seiji Okazaki
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Toshimi Mizukoshi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, Japan
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Bilsland E, Tavella TA, Krogh R, Stokes JE, Roberts A, Ajioka J, Spring DR, Andricopulo AD, Costa FTM, Oliver SG. Antiplasmodial and trypanocidal activity of violacein and deoxyviolacein produced from synthetic operons. BMC Biotechnol 2018; 18:22. [PMID: 29642881 PMCID: PMC5896143 DOI: 10.1186/s12896-018-0428-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/15/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Violacein is a deep violet compound that is produced by a number of bacterial species. It is synthesized from tryptophan by a pathway that involves the sequential action of 5 different enzymes (encoded by genes vioA to vioE). Violacein has antibacterial, antiparasitic, and antiviral activities, and also has the potential of inducing apoptosis in certain cancer cells. RESULTS Here, we describe the construction of a series of plasmids harboring the complete or partial violacein biosynthesis operon and their use to enable production of violacein and deoxyviolacein in E.coli. We performed in vitro assays to determine the biological activity of these compounds against Plasmodium, Trypanosoma, and mammalian cells. We found that, while deoxyviolacein has a lower activity against parasites than violacein, its toxicity to mammalian cells is insignificant compared to that of violacein. CONCLUSIONS We constructed E. coli strains capable of producing biologically active violacein and related compounds, and propose that deoxyviolacein might be a useful starting compound for the development of antiparasite drugs.
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Affiliation(s)
- Elizabeth Bilsland
- 0000000121885934grid.5335.0Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK ,0000 0001 0723 2494grid.411087.bDepartment of Structural and Functional Biology, Institute of Biology, UNICAMP, Campinas, SP Brazil ,0000 0001 0723 2494grid.411087.bLaboratory of Tropical Diseases – Prof. Dr. Luiz Jacintho da Silva - Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, SP Brazil
| | - Tatyana A. Tavella
- 0000 0001 0723 2494grid.411087.bLaboratory of Tropical Diseases – Prof. Dr. Luiz Jacintho da Silva - Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, SP Brazil
| | - Renata Krogh
- 0000 0004 1937 0722grid.11899.38Laboratory of Medicinal and Computational Chemistry, University of São Paulo, São Carlos, SP Brazil
| | - Jamie E. Stokes
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Annabelle Roberts
- 0000000121885934grid.5335.0Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - James Ajioka
- 0000000121885934grid.5335.0Department of Pathology, University of Cambridge, Cambridge, UK
| | - David R. Spring
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Adriano D. Andricopulo
- 0000 0004 1937 0722grid.11899.38Laboratory of Medicinal and Computational Chemistry, University of São Paulo, São Carlos, SP Brazil
| | - Fabio T. M. Costa
- 0000 0001 0723 2494grid.411087.bLaboratory of Tropical Diseases – Prof. Dr. Luiz Jacintho da Silva - Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, SP Brazil
| | - Stephen G. Oliver
- 0000000121885934grid.5335.0Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK
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36
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Banerjee D, Parmar D, Bhattacharya N, Ghanate AD, Panchagnula V, Raghunathan A. A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD +/NADH + imbalance. BMC SYSTEMS BIOLOGY 2017; 11:51. [PMID: 28446174 PMCID: PMC5405553 DOI: 10.1186/s12918-017-0427-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/21/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens using benign metabolites. RESULTS Controlled laboratory evolutions established chloramphenicol and streptomycin resistant pathogens of Chromobacterium. These resistant pathogens showed higher growth rates and required higher lethal doses of antibiotic. Growth and viability testing identified malate, maleate, succinate, pyruvate and oxoadipate as resensitising agents for antibiotic therapy. Resistant genes were catalogued through whole genome sequencing. Intracellular metabolomic profiling identified violacein as a potential biomarker for resistance. The temporal variance of metabolites captured the linearized dynamics around the steady state and correlated to growth rate. A constraints-based flux balance model of the core metabolism was used to predict the metabolic basis of antibiotic susceptibility and resistance. CONCLUSIONS The model predicts electron imbalance and skewed NAD/NADH ratios as a result of antibiotics - chloramphenicol and streptomycin. The resistant pathogen rewired its metabolic networks to compensate for disruption of redox homeostasis. We foresee the utility of such scalable workflows in identifying metabolites for clinical isolates as inevitable solutions to mitigate antibiotic resistance.
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Affiliation(s)
- Deepanwita Banerjee
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
| | | | | | - Avinash D. Ghanate
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
| | | | - Anu Raghunathan
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
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37
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Yi W, Yang K, Ye J, Long Y, Ke J, Ou H. Triphenyltin degradation and proteomic response by an engineered Escherichia coli expressing cytochrome P450 enzyme. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 137:29-34. [PMID: 27907843 DOI: 10.1016/j.ecoenv.2016.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Although triphenyltin (TPT) degradation pathway has been determined, information about the enzyme and protein networks involved was severely limited. To this end, a cytochrome P450 hydroxylase (CYP450) gene from Bacillus thuringiensis was cloned and expressed in Escherichia coli BL21 (DE3), namely E. coli pET32a-CYP450, whose dosage at 1gL-1 could degrade 54.6% TPT at 1mgL-1 within 6 d through attacking the carbon-tin bonds of TPT by CYP450. Sequence analysis verified that the CYP450 gene had a 1214bp open reading frame, encoding a protein with 404 amino acids. Proteomic analysis determined that 60 proteins were significantly differentially regulated expression in E. coli pET32a-CYP450 after TPT degradation. The up-regulated proteins enriched in a network related to transport, cell division, biosynthesis of amino acids and secondary metabolites, and microbial metabolism in diverse environments. The current findings demonstrated for the first time that P450 received electrons transferring from NADH could effectively cleave carbon-metal bonds.
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Affiliation(s)
- Wenying Yi
- Key Laboratory of Environmental Exposure and Health of Guangzhou City, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Kunliang Yang
- Key Laboratory of Environmental Exposure and Health of Guangzhou City, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangzhou City, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China; Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek 94598, CA, USA.
| | - Yan Long
- Key Laboratory of Environmental Exposure and Health of Guangzhou City, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jing Ke
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek 94598, CA, USA
| | - Huase Ou
- Key Laboratory of Environmental Exposure and Health of Guangzhou City, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
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