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Vishwakarma C, Ansari A, Pratap JV. Distinct oligomerization and NADPH binding modes observed between L. donovani and human quinone oxidoreductases. Biochem Biophys Res Commun 2024; 690:149096. [PMID: 37988924 DOI: 10.1016/j.bbrc.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 11/23/2023]
Abstract
Electron-driven process helps the living organism in the generations of energy, biomass production and detoxification of synthetic compounds. Soluble quinone oxidoreductases (QORs) mediate the transfer of an electron from NADPH to various quinone and other compounds, helping in the detoxification of quinones. QORs play a crucial role in cellular metabolism and are thus potential targets for drug development. Here we report the crystal structure of the NADPH-dependent QOR from Leishmania donovani (LdQOR) at 2.05 Å. The enzyme exists as a homo-dimer, with each protomer consisting of two domains, responsible for binding NADPH cofactor and the substrate. Interestingly, the human QOR exists as a tetramer. Comparative analysis of the oligomeric interfaces of LdQOR with HsQOR shows no significant differences in the protomer/dimer assembly. The tetrameric interface of HsQOR is stabilized by salt bridges formed between Arg 169 and Glu 271 which is non-existent in LdQOR, with an Alanine replacing the glutamate. This distinct feature is conserved across other dimeric QORs, indicating the importance of this interaction for tetramer association. Among the homologs, the sequences of the loop region involved in the stabilization and binding of the adenine ring of the NADPH shows significant differences except for an Arginine & glycine residues. In dimer QORs, this Arginine acts as a gate to the co-factor, while the NADPH binding mode in the human homolog is distinct, stabilized by His 200 and Asn 229, which are not conserved in LdQOR. These distinct features have the potential to be utilized for therapeutic interventions.
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Affiliation(s)
- Chandan Vishwakarma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ahmadullah Ansari
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - J Venkatesh Pratap
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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Styczynski M, Rogowska A, Nyabayo C, Decewicz P, Romaniuk F, Pączkowski C, Szakiel A, Suessmuth R, Dziewit L. Heterologous production and characterization of a pyomelanin of Antarctic Pseudomonas sp. ANT_H4: a metabolite protecting against UV and free radicals, interacting with iron from minerals and exhibiting priming properties toward plant hairy roots. Microb Cell Fact 2022; 21:261. [PMID: 36527127 PMCID: PMC9756463 DOI: 10.1186/s12934-022-01990-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Antarctica has one of the most extreme environments in the world. This region is inhabited by specifically adapted microorganisms that produce various unique secondary metabolites (e.g. pigments) enabling their survival under the harsh environmental conditions. It was already shown that these natural, biologically active molecules may find application in various fields of biotechnology. RESULTS In this study, a cold-active brown-pigment-producing Pseudomonas sp. ANT_H4 strain was characterized. In-depth genomic analysis combined with the application of a fosmid expression system revealed two different pathways of melanin-like compounds biosynthesis by the ANT_H4 strain. The chromatographic behavior and Fourier-transform infrared spectroscopic analyses allowed for the identification of the extracted melanin-like compound as a pyomelanin. Furthermore, optimization of the production and thorough functional analyses of the pyomelanin were performed to test its usability in biotechnology. It was confirmed that ANT_H4-derived pyomelanin increases the sun protection factor, enables scavenging of free radicals, and interacts with the iron from minerals. Moreover, it was shown for the first time that pyomelanin exhibits priming properties toward Calendula officinalis hairy roots in in vitro cultures. CONCLUSIONS Results of the study indicate the significant biotechnological potential of ANT_H4-derived pyomelanin and open opportunities for future applications. Taking into account protective features of analyzed pyomelanin it may be potentially used in medical biotechnology and cosmetology. Especially interesting was showing that pyomelanin exhibits priming properties toward hairy roots, which creates a perspective for its usage for the development of novel and sustainable agrotechnical solutions.
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Affiliation(s)
- Michal Styczynski
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agata Rogowska
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Christine Nyabayo
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Przemyslaw Decewicz
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Filip Romaniuk
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Cezary Pączkowski
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Szakiel
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Roderich Suessmuth
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Lukasz Dziewit
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Yang C, Huang Z, Zhang X, Zhu C. Structural Insights into the NAD(P)H:Quinone Oxidoreductase from Phytophthora capsici. ACS OMEGA 2022; 7:25705-25714. [PMID: 35910145 PMCID: PMC9330140 DOI: 10.1021/acsomega.2c02954] [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: 05/12/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Soluble quinone oxidoreductases catalyze transfer of electrons from NADPH to quinones. Transfer of electrons is essential for detoxification of synthetic compounds. Here, we present the crystal structure of a NADPH-dependent QOR from Phytophthora capsici (Pc) complexed with NADPH at 2.4 Å resolution. The enzyme exhibits a bi-modular architecture, containing a NADPH-binding groove and a substrate-binding pocket in each subunit. In the crystal, each asymmetric unit of PcQOR contains two molecules stabilized by intermolecular interactions. Gel filtration and ultracentrifugation analyses reveal that it functions as a tetramer in solution. Alignment of homologous structures exhibits a conserved topology. However, the active sites vary among the homologues, indicating differences in substrate specificities. Enzymatic assays indicate that PcQOR tends to catalyze the large substrates, like 9,10-phenanthrenequinone. Computational simulation associated with site-directed mutagenesis and enzymatic activity analysis declares a potential quinone-binding channel. The ability to reduce quinones probably helps P. capsici to detoxify some harmful chemicals encountered during invasion.
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Affiliation(s)
- Cancan Yang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Zhenling Huang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Xiuguo Zhang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Chunyuan Zhu
- College
of Life Sciences, Shandong Agricultural
University, Taian 271018, China
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Ishikawa K, Hashimoto M, Komatsu K, Taguchi T, Okamoto S, Ichinose K. Characterization of stereospecific enoyl reductase ActVI-ORF2 for pyran ring formation in the actinorhodin biosynthesis of Streptomyces coelicolor A3(2). Bioorg Med Chem Lett 2022; 66:128727. [PMID: 35413414 DOI: 10.1016/j.bmcl.2022.128727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/02/2022]
Abstract
Actinorhodin (ACT) is a benzoisochromanequinone antibiotic produced by Streptomyces coelicolor A3(2), which has served as a favored model organism for comprehensive studies of antibiotic biosynthesis and its regulation. (S)-DNPA undergoes various modifications as an intermediate in the ACT biosynthetic pathway, including enoyl reduction to DDHK. It has been suggested that actVI-ORF2 encodes an enoyl reductase (ER). However, its function has not been characterized in vitro. In this study, biochemical analysis of recombinant ActVI-ORF2 revealed that (S)-DNPA is converted to DDHK in a stereospecific manner with NADPH acting as a cofactor. (R)-DNPA was also reduced to 3-epi-DDHK with the comparable efficacy as (S)-DNPA, suggesting that the stereospecificity of ActVI-ORF2 was not affected by the stereochemistry at the C-3 of DNPA. ActVI-ORF2 is a new example of a discrete ER, which is distantly related to known ERs according to phylogenetic analysis.
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Affiliation(s)
- Kazuki Ishikawa
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Makoto Hashimoto
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Kunpei Komatsu
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan; National Institute of Health Sciences 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Susumu Okamoto
- National Agriculture and Food Research Organization 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan.
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Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. mSystems 2021; 6:e0119421. [PMID: 34665012 PMCID: PMC8525567 DOI: 10.1128/msystems.01194-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.
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Hassan S, Sudhakar V, Nancy Mary MB, Babu R, Doble M, Dadar M, Hanna LE. Computational approach identifies protein off-targets for Isoniazid-NAD adduct: hypothesizing a possible drug resistance mechanism in Mycobacterium tuberculosis. J Biomol Struct Dyn 2019; 38:1697-1710. [PMID: 31094664 DOI: 10.1080/07391102.2019.1615987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Isoniazid is an important antitubercular molecule identified as a drug of choice in tuberculosis treatment. As such, INH is an inactive prodrug; it acquires an active conformation by forming an adduct with NAD. The adduct targets inhA protein, a reductase responsible for fatty acid chain elongation in the cell wall of Mycobacterium tuberculosis. Resistance to INH is majorly contributed by mutations in inhA, katG and geneic and non-geneic regions associated with efflux genes. Despite being widespread, the mechanism of resistance remains unknown in ∼15% of INH-resistant strains. Studies report that an intracellular increase in NADH concentration prevents inhA inhibition, leading to INH resistance. In the pursuit of finding possible resistance mechanisms, we set out to find NAD binding proteins to explore similarities in structure and NAD binding property of these proteins with that of inhA. We identified 172 NAD binding proteins, of which 53 were identified to have sequence or structural similarity to inhA. By performing docking analysis on selected proteins, we identified INH-adduct to have good binding affinity despite very minimal structural similarity to inhA. This analysis was further supported by principal component analysis, which identified 65 proteins with NAD binding conformation similar to that of inhA. These findings prompt us to hypothesize that upon exposure to INH, bacteria tries to reduce inhA susceptibility by inducing expression of these NAD binding proteins through increase in NADH concentration. This in turn favours off-target binding and leads to decreased binding and potency of INH, thus contributing indirectly to INH resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sameer Hassan
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of HIV, National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Vaishnavi Sudhakar
- Department of HIV, National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - M Benita Nancy Mary
- Department of HIV, National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Rajeshwari Babu
- Department of HIV, National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Mukesh Doble
- Department of Biotechnology, Indian Institute of Technology, Chennai, Tamil Nadu, India
| | - Maryam Dadar
- Education and Extension Organization, Razi Vaccine and Serum Research Institute, Agricultural Research, Karaj, Iran
| | - Luke Elizabeth Hanna
- Department of HIV, National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
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Bock T, Müller R, Blankenfeldt W. Crystal structure of AibC, a reductase involved in alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus. Acta Crystallogr F Struct Biol Commun 2016; 72:652-8. [PMID: 27487931 PMCID: PMC4973308 DOI: 10.1107/s2053230x16011146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
Isovaleryl coenzyme A (IV-CoA) performs a crucial role during development and fruiting-body formation in myxobacteria, which is reflected in the existence of a de novo biosynthetic pathway that is highly upregulated when leucine, the common precursor of IV-CoA, is limited. The final step in de novo IV-CoA biosynthesis is catalyzed by AibC, a medium-chain dehydrogenase/reductase. Here, the crystal structure of AibC from Myxococcus xanthus refined to 2.55 Å resolution is presented. The protein adopts two different conformations in the crystal lattice, which is a consequence of partial interaction with the purification tag. Based on this structure, it is suggested that AibC most probably uses a Zn(2+)-supported catalytic mechanism in which NADPH is preferred over NADH. Taken together, this study reveals structural details of the alternative IV-CoA-producing pathway in myxobacteria, which may serve as a base for further biotechnological research and biofuel production.
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Affiliation(s)
- Tobias Bock
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University, Universitätscampus E8 1, 66123 Saarbrücken, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institut für Biochemie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
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