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Liu W, Hu X, Yan Y, Cai Y. Rational engineering of homospermidine synthase for enhanced catalytic efficiency toward spermidine synthesis. Synth Syst Biotechnol 2024; 9:549-557. [PMID: 38699566 PMCID: PMC11063116 DOI: 10.1016/j.synbio.2024.04.012] [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: 12/13/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Spermidine is a naturally occurring polyamine widely utilized in the prevention and treatment of various diseases. Current spermidine biosynthetic methods have problems such as low efficiency and complex multi-enzyme catalysis. Based on sequence-structure-function relationships, we engineered the widely studied homospermidine synthase from Blastochloris viridis (BvHSS) and obtained mutants that could catalyze the production of spermidine from 1,3-diaminopropane and putrescine. The specific activities of BvHSS and the mutants D361E and E232D + D361E (E232D-D) were 8.72, 46.04 and 48.30 U/mg, respectively. The optimal pH for both mutants was 9.0, and the optimal temperature was 50 °C. Molecular docking and dynamics simulations revealed that mutating aspartic acid at position 361 to glutamic acid narrowed the substrate binding pocket, promoting stable spermidine production. Conversely, mutating glutamic acid at position 232 to aspartic acid enlarged the substrate channel entrance, facilitating substrate entry into the active pocket and enhancing spermidine generation. In whole-cell catalysis lasting 6 h, D361E and E232D-D synthesized 725.3 and 933.5 mg/L of spermidine, respectively. This study offers a practical approach for single-enzyme catalyzed spermidine synthesis and sheds light on the crucial residues influencing homospermidine synthase catalytic activity in spermidine production.
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Affiliation(s)
- Wenjing Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xiaoxiang Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yi Yan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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2
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Rafi H, Rafiq H, Farhan M. Pharmacological profile of agmatine: An in-depth overview. Neuropeptides 2024; 105:102429. [PMID: 38608401 DOI: 10.1016/j.npep.2024.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Agmatine, a naturally occurring polyamine derived from arginine via arginine decarboxylase, has been shown to play multifaceted roles in the mammalian body, impacting a wide range of physiological and pathological processes. This comprehensive review delineates the significant insights into agmatine's pharmacological profile, emphasizing its structure and metabolism, neurotransmission and regulation, and pharmacokinetics and function. Agmatine's biosynthesis is highly conserved across species, highlighting its fundamental role in cellular functions. In the brain, comparable to established neurotransmitters, agmatine acts as a neuromodulator, influencing the regulation, metabolism, and reabsorption of neurotransmitters that are key to mood disorders, learning, cognition, and the management of anxiety and depression. Beyond its neuromodulatory functions, agmatine exhibits protective effects across various cellular and systemic contexts, including neuroprotection, nephroprotection, cardioprotection, and cytoprotection, suggesting a broad therapeutic potential. The review explores agmatine's interaction with multiple receptor systems, including NMDA, α2-adrenoceptors, and imidazoline receptors, elucidating its role in enhancing cell viability, neuronal protection, and synaptic plasticity. Such interactions underpin agmatine's potential in treating neurological diseases and mood disorders, among other conditions. Furthermore, agmatine's pharmacokinetics, including its absorption, distribution, metabolism, and excretion, are discussed, underlining the complexity of its action and the potential for therapeutic application. The safety and efficacy of agmatine supplementation, demonstrated through various animal and human studies, affirm its potential as a beneficial therapeutic agent. Conclusively, the diverse physiological and therapeutic effects of agmatine, spanning neurotransmission, protection against cellular damage, and modulation of various receptor pathways, position it as a promising candidate for further research and clinical application. This review underscores the imperative for continued exploration into agmatine's mechanisms of action and its potential in pharmacology and medicine, promising advances in the treatment of numerous conditions.
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Affiliation(s)
- Hira Rafi
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Biochemistry, University of Karachi, Pakistan.
| | - Hamna Rafiq
- Department of Biochemistry, University of Karachi, Pakistan
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3
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Kobayashi T, Sakamoto A, Hisano T, Kashiwagi K, Igarashi K, Takao K, Uemura T, Furuchi T, Sugita Y, Moriya T, Oshima T, Terui Y. Caldomycin, a new guanidopolyamine produced by a novel agmatine homocoupling enzyme involved in homospermidine biosynthesis. Sci Rep 2024; 14:7566. [PMID: 38555406 PMCID: PMC10981699 DOI: 10.1038/s41598-024-58296-0] [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: 12/06/2023] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
An extreme thermophilic bacterium, Thermus thermophilus produces more than 20 unusual polyamines, but their biosynthetic pathways, including homospermidine, are not yet fully understood. Two types of homospermidine synthases have been identified in plants and bacteria, which use spermidine and putrescine or two molecules of putrescine as substrates. However, homospermidine synthases with such substrate specificity have not been identified in T. thermophilus. Here we identified a novel agmatine homocoupling enzyme that is involved in homospermidine biosynthesis in T. thermophilus. The reaction mechanism is different from that of a previously described homospermidine synthase, and involves conjugation of two molecules of agmatine, which produces a diamidino derivative of homospermidine (caldomycin) as an immediate precursor of homospermidine. We conclude that there is a homospermidine biosynthetic pathway from agmatine via caldomycin synthase followed by ureohydrolase in T. thermophilus. Furthermore, it is shown that caldomycin is a novel compound existing in nature.
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Affiliation(s)
- Teruyuki Kobayashi
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Akihiko Sakamoto
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
- Department of Pathophysiology and Therapeutics, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa, Tokyo, Japan
| | - Tamao Hisano
- RIKEN Center for Biosystems Dynamics Research (BDR), Tsurumi, Kanagawa, Japan
| | - Keiko Kashiwagi
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Kazuei Igarashi
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba, Japan
| | - Koichi Takao
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Takeshi Uemura
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Takemitsu Furuchi
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Yoshiaki Sugita
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Toshiyuki Moriya
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | - Tairo Oshima
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan.
- School of Pharmacy, International University of Health and Welfare, Otawara, Tochigi, Japan.
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4
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Liu W, Hu X, Fang L, Cai Y. Insights into the Unusual Activity of a Novel Homospermidine Synthase with a Promising Application to Produce Spermidine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13024-13034. [PMID: 37622688 DOI: 10.1021/acs.jafc.3c03037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Spermidine is a naturally occurring polyamine with multiple biological activities and potential food and agricultural applications. However, sustainable and scalable spermidine production has not yet been attained. In this study, a homospermidine synthase (HSS) from Pseudomonas frederiksbergensis (PfHSS) capable of catalyzing the synthesis of spermidine from 1,3-diaminopropane and putrescine was identified based on multiple sequence alignment using Blastochloris viridis HSS (BvHSS) as a template. The optimal reaction pH and temperature for purified PfHSS were determined to be 8.5 and 45 °C, respectively, and K+ was able to promote the enzyme activity. Further analysis of the structural and functional relationships through molecular docking and molecular dynamics simulation indicates that glutamic acid at position 359 is the essential residue for the enzyme-catalyzed synthesis of spermidine. The whole-cell catalytic reaction yielded 1321.4 mg/L spermidine and 678.2 mg/L of homospermidine. This study presents a novel, promising, and sustainable biological method for producing spermidine.
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Affiliation(s)
- Wenjing Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiaoxiang Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Linghao Fang
- Zhongke Hengji (Hangzhou) Biotechnology Co., 501 Minhe Road, Hangzhou ,Zhejiang 311200, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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5
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Lee DF, Atencio N, Bouchey S, Shoemaker MR, Dodd JS, Satre M, Miller KA, McFarlane JS. Kinetic and structural characterization of carboxyspermidine dehydrogenase of polyamine biosynthesis. J Biol Chem 2023; 299:105033. [PMID: 37437886 PMCID: PMC10413350 DOI: 10.1016/j.jbc.2023.105033] [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: 03/11/2023] [Revised: 06/21/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
Polyamines are positively charged alkylamines ubiquitous among eukaryotes, prokaryotes, and archaea. Humans obtain polyamines through dietary intake, metabolic production, or uptake of polyamines made by gut microbes. The polyamine biosynthetic pathway used by most gut microbes differs from that used by human cells. This alternative pathway employs carboxyspermidine dehydrogenase (CASDH), an enzyme with limited characterization. Here, we solved a 1.94 Å X-ray crystal structure of Bacteroides fragilis CASDH by molecular replacement. BfCASDH is composed of three domains with a fold similar to saccharopine dehydrogenase but with a distinct active site arrangement. Using steady-state methods, we determined kcat and kcat/Km for BfCASDH and Clostridium leptum CASDH using putrescine, diaminopropane, aspartate semi-aldehyde, NADH, and NADPH as substrates. These data revealed evidence of cooperativity in BfCASDH. Putrescine is the likely polyamine substrate and NADPH is the coenzyme used to complete the reaction, forming carboxyspermidine as a product. These data provide the first kinetic characterization of CASDH-a key enzyme in the production of microbial polyamines.
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Affiliation(s)
- Danielle F Lee
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA
| | - Niko Atencio
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA
| | - Shade Bouchey
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA
| | - Madeline R Shoemaker
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA
| | - Joshua S Dodd
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA
| | - Meredith Satre
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA
| | - Kenneth A Miller
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA
| | - Jeffrey S McFarlane
- Department of Chemistry and Biochemistry, Fort Lewis College, Durango, Colorado, USA.
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6
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Functional polyamine metabolic enzymes and pathways encoded by the virosphere. Proc Natl Acad Sci U S A 2023; 120:e2214165120. [PMID: 36802435 PMCID: PMC9992855 DOI: 10.1073/pnas.2214165120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Viruses produce more viruses by manipulating the metabolic and replication systems of their host cells. Many have acquired metabolic genes from ancestral hosts and use the encoded enzymes to subvert host metabolism. The polyamine spermidine is required for bacteriophage and eukaryotic virus replication, and herein, we have identified and functionally characterized diverse phage- and virus-encoded polyamine metabolic enzymes and pathways. These include pyridoxal 5'-phosphate (PLP)-dependent ornithine decarboxylase (ODC), pyruvoyl-dependent ODC and arginine decarboxylase (ADC), arginase, S-adenosylmethionine decarboxylase (AdoMetDC/speD), spermidine synthase, homospermidine synthase, spermidine N-acetyltransferase, and N-acetylspermidine amidohydrolase. We identified homologs of the spermidine-modified translation factor eIF5a encoded by giant viruses of the Imitervirales. Although AdoMetDC/speD is prevalent among marine phages, some homologs have lost AdoMetDC activity and have evolved into pyruvoyl-dependent ADC or ODC. The pelagiphages that encode the pyruvoyl-dependent ADCs infect the abundant ocean bacterium Candidatus Pelagibacter ubique, which we have found encodes a PLP-dependent ODC homolog that has evolved into an ADC, indicating that infected cells would contain both PLP- and pyruvoyl-dependent ADCs. Complete or partial spermidine or homospermidine biosynthetic pathways are found encoded in the giant viruses of the Algavirales and Imitervirales, and in addition, some viruses of the Imitervirales can release spermidine from the inactive N-acetylspermidine. In contrast, diverse phages encode spermidine N-acetyltransferase that can sequester spermidine into its inactive N-acetyl form. Together, the virome-encoded enzymes and pathways for biosynthesis and release or biochemical sequestration of spermidine or its structural analog homospermidine consolidate and expand evidence supporting an important and global role of spermidine in virus biology.
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7
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Helfrich F, Scheidig AJ. Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-π interaction. Acta Crystallogr D Struct Biol 2021; 77:1317-1335. [PMID: 34605434 PMCID: PMC8489232 DOI: 10.1107/s2059798321008937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines influence medically relevant processes in the opportunistic pathogen Pseudomonas aeruginosa, including virulence, biofilm formation and susceptibility to antibiotics. Although homospermidine synthase (HSS) is part of the polyamine metabolism in various strains of P. aeruginosa, neither its role nor its structure has been examined so far. The reaction mechanism of the nicotinamide adenine dinucleotide (NAD+)-dependent bacterial HSS has previously been characterized based on crystal structures of Blastochloris viridis HSS (BvHSS). This study presents the crystal structure of P. aeruginosa HSS (PaHSS) in complex with its substrate putrescine. A high structural similarity between PaHSS and BvHSS with conservation of the catalytically relevant residues is demonstrated, qualifying BvHSS as a model for mechanistic studies of PaHSS. Following this strategy, crystal structures of single-residue variants of BvHSS are presented together with activity assays of PaHSS, BvHSS and BvHSS variants. For efficient homospermidine production, acidic residues are required at the entrance to the binding pocket (`ionic slide') and near the active site (`inner amino site') to attract and bind the substrate putrescine via salt bridges. The tryptophan residue at the active site stabilizes cationic reaction components by cation-π interaction, as inferred from the interaction geometry between putrescine and the indole ring plane. Exchange of this tryptophan for other amino acids suggests a distinct catalytic requirement for an aromatic interaction partner with a highly negative electrostatic potential. These findings substantiate the structural and mechanistic knowledge on bacterial HSS, a potential target for antibiotic design.
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Affiliation(s)
- F. Helfrich
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
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8
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Saccà ML, Manici LM. Honey bee-associated bacteria as producers of bioactive compounds for protecting hives. A biosynthetic gene-based approach. Microbiol Res 2021; 252:126860. [PMID: 34521052 DOI: 10.1016/j.micres.2021.126860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 12/25/2022]
Abstract
Honey bee-associated bacteria are a source of natural compounds of interest for controlling hive decline which is threatening bee health globally. Genes involved in the biosynthesis of a series of extracellular compounds released by bacteria living on the external surface of honey bees were investigated. A biosynthetic gene-based approach was adopted by developing a battery of primers to target the genes involved in the biosynthesis of four groups of bioactive compounds (pyrrolizidine alkaloids, surfactin, 2-heptanone and helveticin J). The primers were tested on 51 bacterial isolates belonging to Bacillus thuringiensis, Acetobacteraceae bacterium, Bifidobacterium asteroides and Apilactobacillus kunkeei. The developed primers led to species-specific detection and characterization of the functional genes involved in the production of three out of four groups of compounds selected for this study. The findings suggest that microbial populations inhabiting apiaries harbor genes involved in the biosynthesis of metabolites linked to the reduction of important honey bee pathogens such as Varroa destructor, Paenibacillus larvae and Nosema ceranae. The gene-based approach adopted for evaluating the biosynthetic potential of bioactive compounds in hives is promising for investigating further compounds for low input control strategies of bee enemies.
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Affiliation(s)
- Maria Ludovica Saccà
- Council for Agricultural Research and Economics (CREA), Research Center for Agriculture and Environment, Via di Corticella 133, 40128, Bologna, Italy.
| | - Luisa Maria Manici
- Council for Agricultural Research and Economics (CREA), Research Center for Agriculture and Environment, Via di Corticella 133, 40128, Bologna, Italy
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9
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Abstract
In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations at seawater pH produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells uptake and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, “Candidatus Pelagibacter” strain HTCC7211 and “Candidatus Pelagibacter ubique” strain HTCC1062. Both strains took up all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but polyamines did not fully substitute for their requirements of glycine (or related compounds) or pyruvate (or related compounds). Our data suggest that potABCD transports all five polyamines and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they metabolize.
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10
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Sousa FM, Lima LMP, Arnarez C, Pereira MM, Melo MN. Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies. J Chem Inf Model 2021; 61:335-346. [PMID: 33400529 DOI: 10.1021/acs.jcim.0c01077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleotides are structural units relevant not only in nucleic acids but also as substrates or cofactors in key biochemical reactions. The size- and timescales of such nucleotide-protein interactions fall well within the scope of coarse-grained molecular dynamics, which holds promise of important mechanistic insight. However, the lack of specific parameters has prevented accurate coarse-grained simulations of protein interactions with most nucleotide compounds. In this work, we comprehensively develop coarse-grained parameters for key metabolites/cofactors (FAD, FMN, riboflavin, NAD, NADP, ATP, ADP, AMP, and thiamine pyrophosphate) in different oxidation and protonation states as well as for smaller molecules derived from them (among others, nicotinamide, adenosine, adenine, ribose, thiamine, and lumiflavin), summing up a total of 79 different molecules. In line with the Martini parameterization methodology, parameters were tuned to reproduce octanol-water partition coefficients. Given the lack of existing data, we set out to experimentally determine these partition coefficients, developing two methodological approaches, based on 31P-NMR and fluorescence spectroscopy, specifically tailored to the strong hydrophilicity of most of the parameterized compounds. To distinguish the partition of each relevant protonation species, we further potentiometrically characterized the protonation constants of key molecules. This work successfully builds a comprehensive and relevant set of computational models that will boost the biochemical application of coarse-grained simulations. It does so based on the measurement of partition and acid-base physicochemical data that, in turn, covers important gaps in nucleotide characterization.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Luís M P Lima
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Clément Arnarez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal.,BIOISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
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11
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Roszczenko-Jasińska P, Vu HN, Subuyuj GA, Crisostomo RV, Cai J, Lien NF, Clippard EJ, Ayala EM, Ngo RT, Yarza F, Wingett JP, Raghuraman C, Hoeber CA, Martinez-Gomez NC, Skovran E. Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1. Sci Rep 2020; 10:12663. [PMID: 32728125 PMCID: PMC7391723 DOI: 10.1038/s41598-020-69401-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/09/2020] [Indexed: 11/08/2022] Open
Abstract
Lanthanide elements have been recently recognized as "new life metals" yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate. This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog, an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7. Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA
- Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Huong N Vu
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Gabriel A Subuyuj
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology and Molecular Genetics, University of California At Davis, Davis, CA, USA
| | - Ralph Valentine Crisostomo
- Department of Biological Sciences, San José State University, San José, CA, USA
- Molecular Biology Institute, University of California At Los Angeles, Los Angeles, CA, USA
| | - James Cai
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Nicholas F Lien
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Erik J Clippard
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Elena M Ayala
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Richard T Ngo
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Fauna Yarza
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Biochemistry and Biophysics, University of California At San Francisco, San Francisco, CA, USA
| | - Justin P Wingett
- Department of Biological Sciences, San José State University, San José, CA, USA
| | | | - Caitlin A Hoeber
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Norma C Martinez-Gomez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA.
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, USA.
| | - Elizabeth Skovran
- Department of Biological Sciences, San José State University, San José, CA, USA.
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12
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Mindt M, Walter T, Kugler P, Wendisch VF. Microbial Engineering for Production of N-Functionalized Amino Acids and Amines. Biotechnol J 2020; 15:e1900451. [PMID: 32170807 DOI: 10.1002/biot.201900451] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/04/2020] [Indexed: 01/04/2023]
Abstract
N-functionalized amines play important roles in nature and occur, for example, in the antibiotic vancomycin, the immunosuppressant cyclosporine, the cytostatic actinomycin, the siderophore aerobactin, the cyanogenic glucoside linamarin, and the polyamine spermidine. In the pharmaceutical and fine-chemical industries N-functionalized amines are used as building blocks for the preparation of bioactive molecules. Processes based on fermentation and on enzyme catalysis have been developed to provide sustainable manufacturing routes to N-alkylated, N-hydroxylated, N-acylated, or other N-functionalized amines including polyamines. Metabolic engineering for provision of precursor metabolites is combined with heterologous N-functionalizing enzymes such as imine or ketimine reductases, opine or amino acid dehydrogenases, N-hydroxylases, N-acyltransferase, or polyamine synthetases. Recent progress and applications of fermentative processes using metabolically engineered bacteria and yeasts along with the employed enzymes are reviewed and the perspectives on developing new fermentative processes based on insight from enzyme catalysis are discussed.
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Affiliation(s)
- Melanie Mindt
- Genetics of Prokaryotes, Biology and CeBiTec, Bielefeld University, Bielefeld, 33615, Germany.,BU Bioscience, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands
| | - Tatjana Walter
- Genetics of Prokaryotes, Biology and CeBiTec, Bielefeld University, Bielefeld, 33615, Germany
| | - Pierre Kugler
- Genetics of Prokaryotes, Biology and CeBiTec, Bielefeld University, Bielefeld, 33615, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Biology and CeBiTec, Bielefeld University, Bielefeld, 33615, Germany
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Suplatov D, Kopylov K, Sharapova Y, Švedas V. Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod. J Biomol Struct Dyn 2018; 37:2049-2060. [PMID: 29749295 DOI: 10.1080/07391102.2018.1475260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the 'out' state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod's binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry Suplatov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Kirill Kopylov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Yana Sharapova
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Vytas Švedas
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
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Annenkov VV, Verkhozina ON, Zelinskiy SN, Shishlyannikova TA, Bridoux MC, Danilovtseva EN. Unusual Polyamines from Baikalian Diatoms. ChemistrySelect 2018. [DOI: 10.1002/slct.201802032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vadim V. Annenkov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3; Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033 Russia
| | - Ol'ga N. Verkhozina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3; Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033 Russia
| | - Stanislav N. Zelinskiy
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3; Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033 Russia
| | - Tatyana A. Shishlyannikova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3; Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033 Russia
| | | | - Elena N. Danilovtseva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3; Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033 Russia
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Sharapova Y, Suplatov D, Švedas V. Neuraminidase A from Streptococcus pneumoniae has a modular organization of catalytic and lectin domains separated by a flexible linker. FEBS J 2018; 285:2428-2445. [PMID: 29704878 DOI: 10.1111/febs.14486] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 04/01/2018] [Accepted: 04/23/2018] [Indexed: 12/17/2022]
Abstract
Neuraminidase A (NanA) of the pathogen Streptococcus pneumoniae cleaves receptors of the human respiratory epithelial surface during bacterial colonization. The full-size structure of NanA that contains one lectin and one catalytic domain within a single polypeptide chain remains unresolved. Both domains are crucial for the microorganism's virulence and considered as promising antimicrobial targets. Methods of bioinformatics and molecular dynamics have been implemented to model NanA's structure and study interaction between the lectin and catalytic domains in three neuraminidases NanA, NanB, and NanC from Streptococcus pneumoniae. A significant difference in spatial organization of these homologous enzymes has been revealed. The lectin and catalytic domains of NanB and NanC form rigid globules stabilized by multiple interdomain interactions, whereas in NanA, the two domains are separated by a 16 amino acids long flexible linker - a characteristic of proteins that require conformational flexibility for their functioning. The biological role of this structural adaptation of NanA as a key virulence enzyme is discussed.
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Affiliation(s)
- Yana Sharapova
- Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Russia
| | - Dmitry Suplatov
- Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Russia
| | - Vytas Švedas
- Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Russia
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Evolution of biosynthetic diversity. Biochem J 2017; 474:2277-2299. [DOI: 10.1042/bcj20160823] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 12/16/2022]
Abstract
Since the emergence of the last common ancestor from which all extant life evolved, the metabolite repertoire of cells has increased and diversified. Not only has the metabolite cosmos expanded, but the ways in which the same metabolites are made have diversified. Enzymes catalyzing the same reaction have evolved independently from different protein folds; the same protein fold can produce enzymes recognizing different substrates, and enzymes performing different chemistries. Genes encoding useful enzymes can be transferred between organisms and even between the major domains of life. Organisms that live in metabolite-rich environments sometimes lose the pathways that produce those same metabolites. Fusion of different protein domains results in enzymes with novel properties. This review will consider the major evolutionary mechanisms that generate biosynthetic diversity: gene duplication (and gene loss), horizontal and endosymbiotic gene transfer, and gene fusion. It will also discuss mechanisms that lead to convergence as well as divergence. To illustrate these mechanisms, one of the original metabolisms present in the last universal common ancestor will be employed: polyamine metabolism, which is essential for the growth and cell proliferation of archaea and eukaryotes, and many bacteria.
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Structure and stability of complexes of agmatine with some functional receptor residues of proteins. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Biosynthesis of polyamines and polyamine-containing molecules. Biochem J 2016; 473:2315-29. [DOI: 10.1042/bcj20160185] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/22/2016] [Indexed: 12/16/2022]
Abstract
Polyamines are evolutionarily ancient polycations derived from amino acids and are pervasive in all domains of life. They are essential for cell growth and proliferation in eukaryotes and are essential, important or dispensable for growth in bacteria. Polyamines present a useful scaffold to attach other moieties to, and are often incorporated into specialized metabolism. Life has evolved multiple pathways to synthesize polyamines, and structural variants of polyamines have evolved in bacteria, archaea and eukaryotes. Among the complex biosynthetic diversity, patterns of evolutionary reiteration can be distinguished, revealing evolutionary recycling of particular protein folds and enzyme chassis. The same enzyme activities have evolved from multiple protein folds, suggesting an inevitability of evolution of polyamine biosynthesis. This review discusses the different biosynthetic strategies used in life to produce diamines, triamines, tetra-amines and branched and long-chain polyamines. It also discusses the enzymes that incorporate polyamines into specialized metabolites and attempts to place polyamine biosynthesis in an evolutionary context.
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Wang B, Pachaiyappan B, Gruber JD, Schmidt MG, Zhang YM, Woster PM. Antibacterial Diamines Targeting Bacterial Membranes. J Med Chem 2016; 59:3140-51. [PMID: 26964758 PMCID: PMC5927580 DOI: 10.1021/acs.jmedchem.5b01912] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Antibiotic resistance is a growing threat to human health exacerbated by a lack of new antibiotics. We now describe a series of substituted diamines that produce rapid bactericidal activity against both Gram-positive and Gram-negative bacteria, including methicillin-resistant Staphylococcus aureus and stationary-phase bacteria. These compounds reduce biofilm formation and promote biofilm dispersal in Pseudomonas aeruginosa. The most potent analogue, 3 (1,13-bis{[(2,2-diphenyl)-1-ethyl]thioureido}-4,10-diazatridecane), primarily acts by depolarization of the cytoplasmic membrane and permeabilization of the bacterial outer membrane. Transmission electron microscopy confirmed that 3 disrupts membrane integrity rapidly. Compound 3 is also synergistic with kanamycin, demonstrated by the checkerboard method and by time-kill kinetic experiments. In human cell toxicity assays, 3 showed limited adverse effects against the HEK293T human kidney embryonic cells and A549 human adenocarcinoma cells. In addition, 3 produced no adverse effects on Caenorhabditis elegans development, survival, and reproduction. Collectively, diamines related to 3 represent a new class of broad-spectrum antibacterials against drug-resistant pathogens.
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Affiliation(s)
- Bo Wang
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Boobalan Pachaiyappan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Jordon D. Gruber
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Michael G. Schmidt
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Yong-Mei Zhang
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Patrick M. Woster
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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