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Sahu PN, Sen A. Preventing Cancer by Inhibiting Ornithine Decarboxylase: A Comparative Perspective on Synthetic vs. Natural Drugs. Chem Biodivers 2024; 21:e202302067. [PMID: 38404009 DOI: 10.1002/cbdv.202302067] [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: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/24/2024] [Indexed: 02/27/2024]
Abstract
This perspective delves into the investigation of synthetic and naturally occurring inhibitors, their patterns of inhibition, and the effectiveness of newly utilized natural compounds as inhibitors targeting the Ornithine decarboxylase enzyme. This enzyme is known to target the MYC oncogene, thereby establishing a connection between polyamine metabolism and oncogenesis in both normal and cancerous cells. ODC activation and heightened polyamine activity are associated with tumor development in numerous cancers and fluctuations in ODC protein levels exert a profound influence on cellular activity for inhibition or suppressing tumor cells. This perspective outlines efforts to develop novel drugs, evaluate natural compounds, and identify promising inhibitors to address gaps in cancer prevention, highlighting the potential of newly designed synthetic moieties and natural flavonoids as alternatives. It also discusses natural compounds with potential as enhanced inhibitors.
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Affiliation(s)
- Preeti Nanda Sahu
- Department of Chemistry, (CMDD Lab) GITAM (Deemed to be), University, Rushikonda, Visakhapatnam, 530045, India
| | - Anik Sen
- Department of Chemistry, (CMDD Lab) GITAM (Deemed to be), University, Rushikonda, Visakhapatnam, 530045, India
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Rastogi S, Chandra A. Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media. J Phys Chem B 2023; 127:8139-8149. [PMID: 37721415 DOI: 10.1021/acs.jpcb.3c04142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.
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Affiliation(s)
- Shreya Rastogi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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3
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Halwas K, Döring LM, Oehlert FV, Dohmen RJ. Hypusinated eIF5A Promotes Ribosomal Frameshifting during Decoding of ODC Antizyme mRNA in Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:ijms232112972. [PMID: 36361762 PMCID: PMC9656687 DOI: 10.3390/ijms232112972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022] Open
Abstract
Polyamines are essential biogenic poly-cations with important roles in many cellular processes and diseases such as cancer. A rate-limiting step early in the biosynthesis of polyamines is the conversion of ornithine to putrescine by the homodimeric enzyme ornithine decarboxylase (ODC). In a conserved mechanism of posttranslational regulation, ODC antizyme (OAZ) binds to ODC monomers promoting their ubiquitin-independent degradation by the proteasome. Decoding of OAZ mRNA is unusual in that it involves polyamine-regulated bypassing of an internal translation termination (STOP) codon by a ribosomal frameshift (RFS) event. Using Saccharomyces cerevisiae, we earlier showed that high polyamine concentrations lead to increased efficiency of OAZ1 mRNA translation by binding to nascent Oaz1 polypeptide. The binding of polyamines prevents stalling of the ribosomes on OAZ1 mRNA caused by nascent Oaz1 polypeptide thereby promoting synthesis of full-length Oaz1. Polyamine depletion, however, also inhibits RFS during the decoding of constructs bearing the OAZ1 shift site lacking sequences encoding the Oaz1 parts implicated in polyamine binding. Polyamine depletion is known to impair hypusine modification of translation factor eIF5A. Using a novel set of conditional mutants impaired in the function of eIF5A/Hyp2 or its hypusination, we show here that hypusinated eIF5A is required for efficient translation across the OAZ1 RFS site. These findings identify eIF5A as a part of Oaz1 regulation, and thereby of polyamine synthesis. Additional experiments with DFMO, however, show that depletion of polyamines inhibits translation across the OAZ1 RFS site not only by reducing Hyp2 hypusination, but in addition, and even earlier, by affecting RFS more directly.
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Tran JU, Brown BL. Structural Basis for Allostery in PLP-dependent Enzymes. Front Mol Biosci 2022; 9:884281. [PMID: 35547395 PMCID: PMC9081730 DOI: 10.3389/fmolb.2022.884281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are found ubiquitously in nature and are involved in a variety of biological pathways, from natural product synthesis to amino acid and glucose metabolism. The first structure of a PLP-dependent enzyme was reported over 40 years ago, and since that time, there is a steady wealth of structural and functional information revealed for a wide array of these enzymes. A functional mechanism that is gaining more appreciation due to its relevance in drug design is that of protein allostery, where binding of a protein or ligand at a distal site influences the structure, organization, and function at the active site. Here, we present a review of current structure-based mechanisms of allostery for select members of each PLP-dependent enzyme family. Knowledge of these mechanisms may have a larger potential for identifying key similarities and differences among enzyme families that can eventually be exploited for therapeutic development.
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Affiliation(s)
- Jenny U. Tran
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Breann L. Brown
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
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Carter NS, Kawasaki Y, Nahata SS, Elikaee S, Rajab S, Salam L, Alabdulal MY, Broessel KK, Foroghi F, Abbas A, Poormohamadian R, Roberts SC. Polyamine Metabolism in Leishmania Parasites: A Promising Therapeutic Target. Med Sci (Basel) 2022; 10:24. [PMID: 35645240 PMCID: PMC9149861 DOI: 10.3390/medsci10020024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 12/30/2022] Open
Abstract
Parasites of the genus Leishmania cause a variety of devastating and often fatal diseases in humans and domestic animals worldwide. The need for new therapeutic strategies is urgent because no vaccine is available, and treatment options are limited due to a lack of specificity and the emergence of drug resistance. Polyamines are metabolites that play a central role in rapidly proliferating cells, and recent studies have highlighted their critical nature in Leishmania. Numerous studies using a variety of inhibitors as well as gene deletion mutants have elucidated the pathway and routes of transport, revealing unique aspects of polyamine metabolism in Leishmania parasites. These studies have also shed light on the significance of polyamines for parasite proliferation, infectivity, and host-parasite interactions. This comprehensive review article focuses on the main polyamine biosynthetic enzymes: ornithine decarboxylase, S-adenosylmethionine decarboxylase, and spermidine synthase, and it emphasizes recent discoveries that advance these enzymes as potential therapeutic targets against Leishmania parasites.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sigrid C. Roberts
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR 97123, USA; (N.S.C.); (Y.K.); (S.S.N.); (S.E.); (S.R.); (L.S.); (M.Y.A.); (K.K.B.); (F.F.); (A.A.); (R.P.)
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Vicente-Barrueco A, Román ÁC, Ruiz-Téllez T, Centeno F. In Silico Research of New Therapeutics Rotenoids Derivatives against Leishmania amazonensis Infection. BIOLOGY 2022; 11:biology11010133. [PMID: 35053132 PMCID: PMC8772715 DOI: 10.3390/biology11010133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022]
Abstract
Yearly, 1,500,000 cases of leishmaniasis are diagnosed, causing thousands of deaths. To advance in its therapy, we present an interdisciplinary protocol that unifies ethnobotanical knowledge of natural compounds and the latest bioinformatics advances to respond to an orphan disease such as leishmaniasis and specifically the one caused by Leishmania amazonensis. The use of ethnobotanical information serves as a basis for the development of new drugs, a field in which computer-aided drug design (CADD) has been a revolution. Taking this information from Amazonian communities, located in the area with a high prevalence of this disease, a protocol has been designed to verify new leads. Moreover, a method has been developed that allows the evaluation of lead molecules, and the improvement of their affinity and specificity against therapeutic targets. Through this approach, deguelin has been identified as a good lead to treat the infection due to its potential as an ornithine decarboxylase (ODC) inhibitor, a key enzyme in Leishmania development. Using an in silico-generated combinatorial library followed by docking approaches, we have found deguelin derivatives with better affinity and specificity against ODC than the original compound, suggesting that this approach could be adapted for developing new drugs against leishmaniasis.
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Affiliation(s)
- Adrián Vicente-Barrueco
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Ángel Carlos Román
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
- Correspondence: (Á.C.R.); (F.C.)
| | - Trinidad Ruiz-Téllez
- Departamento de Biología Vegetal, Ecología y Ciencias de la Tierra, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Francisco Centeno
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain;
- Correspondence: (Á.C.R.); (F.C.)
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Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane. Biochem J 2021; 478:4137-4149. [PMID: 34796899 DOI: 10.1042/bcj20210647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022]
Abstract
Ornithine decarboxylase (ODC) is the rate-limiting enzyme for the synthesis of polyamines (PAs). PAs are oncometabolites that are required for proliferation, and pharmaceutical ODC inhibition is pursued for the treatment of hyperproliferative diseases, including cancer and infectious diseases. The most potent ODC inhibitor is 1-amino-oxy-3-aminopropane (APA). A previous crystal structure of an ODC-APA complex indicated that APA non-covalently binds ODC and its cofactor pyridoxal 5-phosphate (PLP) and functions by competing with the ODC substrate ornithine for binding to the catalytic site. We have revisited the mechanism of APA binding and ODC inhibition through a new crystal structure of APA-bound ODC, which we solved at 2.49 Å resolution. The structure unambiguously shows the presence of a covalent oxime between APA and PLP in the catalytic site, which we confirmed in solution by mass spectrometry. The stable oxime makes extensive interactions with ODC but cannot be catabolized, explaining APA's high potency in ODC inhibition. In addition, we solved an ODC/PLP complex structure with citrate bound at the substrate-binding pocket. These two structures provide new structural scaffolds for developing more efficient pharmaceutical ODC inhibitors.
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Barbareschi M, Benetti F, Gaio E, Angileri L, Veraldi S. Capryloyl glycine and soy isoflavonoids in hypertrichosis: An experimental and placebo-controlled clinical study. J Cosmet Dermatol 2021; 20 Suppl 1:18-22. [PMID: 33934471 PMCID: PMC8252421 DOI: 10.1111/jocd.14096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 11/29/2022]
Abstract
Background The management of acquired hypertrichosis (HT) is based on the search of the causes and subsequent specific treatment. However, simultaneous hair removal is important. No single method for hair removal is appropriate for all patients and skin areas. Treatment options are actually limited and clinical results are often unsatisfactory. Ornithine decarboxylase 1 (ODC1), an enzyme present in hair follicles, is considered as a potential target to inhibit hair growth. Only eflornithine hydrochloride, an inhibitor of ODC1, showed to be partially effective in the management of acquired HT. Aims The aim of our study was to evaluate the potential inhibition of ODC1 activity by a cream containing 4% capryloyl glycine, an ODC1 inhibitor, and 1% glycine soy‐fermented extract (soy isoflavonoids). Furthermore, we present the results of a placebo‐controlled clinical study that evaluated the efficacy and tolerability of this cream. Methods The ODC1 activity was detected by measuring absorbance at 340 nm. In the presence of ODC1 inhibitors, absorbance decreases as a function of inhibition. Difluoromethylornithine (DFMO) was provided as an inhibitor control. ODC1 activity inhibition was expressed as percentage of control (untreated sample). All data were presented as mean ± standard deviation of three independent experiments. To determine if statistically significant differences between treatments were present, a t test analysis was performed. The differences between groups were considered significant at p < 0.05. Twelve Caucasian female adult patients, with HT located on the forearms, were enrolled. The study cream (product A) was applied twice/day for four months on the right forearm. A placebo cream (product B) was applied twice/day for four months on the left forearm. Clinical efficacy was evaluated by means of macrophotography. Results The cream significantly inhibited ODC1 activity (35.1 ± 0.5% inhibition, equivalent to a 64.9 ± 0.5% ODC1 activity). DFMO completely abolished the enzymatic activity (100 ± 5% inhibition, equivalent to 0 ± 5% ODC1 activity). All patients were considered evaluable. In 11 out of 12 patients (91.7%), who were treated with product A, an improvement was observed. No improvement was observed in patients treated with product B. The global assessment showed good efficacy in 7 patients (58.3%) and moderate efficacy in 5 patients (41.7%) treated with the product A. No efficacy was detected in patients treated with product B. Conclusions The study cream showed to be effective in Caucasian, adult, female patients with hypertrichosis located on the forearms.
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Affiliation(s)
- Mauro Barbareschi
- Department of Pathophysiology and Transplantation, Università degli Studi, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Federico Benetti
- European Center for the Sustainable Impact of Nanotechnology (ECSIN), ECAMRICERT SRL, Padova, Italy
| | - Elisa Gaio
- European Center for the Sustainable Impact of Nanotechnology (ECSIN), ECAMRICERT SRL, Padova, Italy
| | - Luisa Angileri
- Department of Pathophysiology and Transplantation, Università degli Studi, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Veraldi
- Department of Pathophysiology and Transplantation, Università degli Studi, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Dual Role for Astroglial Copper-Assisted Polyamine Metabolism during Intense Network Activity. Biomolecules 2021; 11:biom11040604. [PMID: 33921742 PMCID: PMC8073386 DOI: 10.3390/biom11040604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
Astrocytes serve essential roles in human brain function and diseases. Growing evidence indicates that astrocytes are central players of the feedback modulation of excitatory Glu signalling during epileptiform activity via Glu-GABA exchange. The underlying mechanism results in the increase of tonic inhibition by reverse operation of the astroglial GABA transporter, induced by Glu-Na+ symport. GABA, released from astrocytes, is synthesized from the polyamine (PA) putrescine and this process involves copper amino oxidase. Through this pathway, putrescine can be considered as an important source of inhibitory signaling that counterbalances epileptic discharges. Putrescine, however, is also a precursor for spermine that is known to enhance gap junction channel communication and, consequently, supports long-range Ca2+ signaling and contributes to spreading of excitatory activity through the astrocytic syncytium. Recently, we presented the possibility of neuron-glia redox coupling through copper (Cu+/Cu2+) signaling and oxidative putrescine catabolism. In the current work, we explore whether the Cu+/Cu2+ homeostasis is involved in astrocytic control on neuronal excitability by regulating PA catabolism. We provide supporting experimental data underlying this hypothesis. We show that the blockade of copper transporter (CTR1) by AgNO3 (3.6 µM) prevents GABA transporter-mediated tonic inhibitory currents, indicating causal relationship between copper (Cu+/Cu2+) uptake and the catabolism of putrescine to GABA in astrocytes. In addition, we show that MnCl2 (20 μM), an inhibitor of the divalent metal transporter DMT1, also prevents the astrocytic Glu-GABA exchange. Furthermore, we observed that facilitation of copper uptake by added CuCl2 (2 µM) boosts tonic inhibitory currents. These findings corroborate the hypothesis that modulation of neuron-glia coupling by copper uptake drives putrescine → GABA transformation, which leads to subsequent Glu-GABA exchange and tonic inhibition. Findings may in turn highlight the potential role of copper signaling in fine-tuning the activity of the tripartite synapse.
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Marjanovic A, Ramírez-Palacios CJ, Masman MF, Drenth J, Otzen M, Marrink SJ, Janssen DB. Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase. Protein Eng Des Sel 2021; 34:gzab016. [PMID: 34258615 PMCID: PMC8277567 DOI: 10.1093/protein/gzab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/03/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Diaminopimelate decarboxylases (DAPDCs) are highly selective enzymes that catalyze the common final step in different lysine biosynthetic pathways, i.e. the conversion of meso-diaminopimelate (DAP) to L-lysine. We examined the modification of the substrate specificity of the thermostable decarboxylase from Thermotoga maritima with the aim to introduce activity with 2-aminopimelic acid (2-APA) since its decarboxylation leads to 6-aminocaproic acid (6-ACA), a building block for the synthesis of nylon-6. Structure-based mutagenesis of the distal carboxylate binding site resulted in a set of enzyme variants with new activities toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily acted as a 2-APA decarboxylase. We next used computational modeling to explain the observed shift in catalytic activities of the mutants. The results suggest that predictive computational protocols can support the redesign of the catalytic properties of this class of decarboxylating PLP-dependent enzymes.
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Affiliation(s)
- Antonija Marjanovic
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Carlos J Ramírez-Palacios
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Marcelo F Masman
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Van’t Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jeroen Drenth
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marleen Otzen
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert-Jan Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Zarei I, Baxter BA, Oppel RC, Borresen EC, Brown RJ, Ryan EP. Plasma and Urine Metabolite Profiles Impacted by Increased Dietary Navy Bean Intake in Colorectal Cancer Survivors: A Randomized-Controlled Trial. Cancer Prev Res (Phila) 2020; 14:497-508. [PMID: 33361317 DOI: 10.1158/1940-6207.capr-20-0270] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/28/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022]
Abstract
Navy beans contain bioactive phytochemicals with colon cancer prevention properties as demonstrated in carcinogen-induced animal models. Human studies support that dietary navy bean intake modulates metabolism by the gut microbiome. This study investigated the effect of navy bean ingestion on plasma and urine metabolite profiles of overweight and obese colorectal cancer survivors. Twenty participants completed a single-blinded, randomized-controlled dietary intervention with precooked navy beans (35 g bean powder/day) or control (0 g/day) for 4 weeks. Plasma and urine were collected at baseline, 2 weeks, and 4 weeks following consumption. Nontargeted metabolomics was applied to study meals and snacks, navy beans, plasma, and urine. Increased navy bean consumption was hypothesized to (i) delineate dietary biomarkers and (ii) promote metabolic shifts relevant for cancer protection in the plasma and urine metabolome. At 4 weeks, 16 plasma and 16 urine metabolites were significantly different in the navy bean intervention group compared with placebo control (P < 0.05). Increased plasma 2,3-dihydroxy-2-methylbutyrate (1.34-fold), S-methylcysteine (1.92-fold), and pipecolate (3.89-fold), and urine S-adenosylhomocysteine (2.09-fold) and cysteine (1.60-fold) represent metabolites with cancer-protective actions following navy bean consumption. Diet-derived metabolites were detected in plasma or urine and confirmed for presence in the navy bean intervention meals and snacks. These included 3-(4-hydroxyphenyl)propionate, betaine, pipecolate, S-methylcysteine, choline, eicosapentaenoate (20:5n3), benzoate, S-adenosylhomocysteine, N-delta-acetylornithine, cysteine, 3-(4-hydroxyphenyl)lactate, gentisate, hippurate, 4-hydroxyhippurate, and salicylate. The navy bean dietary intervention for 4 weeks showed changes to pathways of metabolic importance to colorectal cancer prevention and merit continued attention for dietary modulation in future high-risk cohort investigations. PREVENTION RELEVANCE: This clinical study suggests that increased consumption of navy beans would deliver bioactive metabolites to individuals at high risk for colorectal cancer recurrence and produce metabolic shifts in plasma and urine profiles.
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Affiliation(s)
- Iman Zarei
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - Bridget A Baxter
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - Renee C Oppel
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - Erica C Borresen
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - Regina J Brown
- University of Colorado School of Medicine, Aurora, Colorado
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado.
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Berardesca E, Cameli N, Piacentini M, Veraldi S, Celleno L. Assessment of the skin efficacy and acceptability of a cosmetic product in the treatment of the forearm hypertrichosis in female patients. J Cosmet Dermatol 2020; 20:2527-2530. [PMID: 33347705 DOI: 10.1111/jocd.13893] [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: 08/03/2020] [Revised: 11/20/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Treatment of unwanted body hair is a challenging area in cosmetic dermatology. Topical soy isoflavones and derivatives or eflornithine have been utilized in dermatocosmetology for their estrogenic and antiandrogenic activity. AIMS To evaluate the efficacy of a formulation containing capryloyl glycine 4% in decreasing hair growth on the forearms after topical application for 120 days vs placebo. METHODS A total of 69 female patients entered the study (age 37 ± 6). Hair growth was quantified using TrichoScan software on both forearms at 20-fold magnification (analyzed area 0.651 cm2). Hair density (number of hairs/cm2 ), density vellus hair, density terminal hair, and median length of hairs were evaluated. The data were analyzed using ANOVA for repeated measures to evaluate changes during the treatment (T0, T60, and T120) and Student's t test (placebo vs active). RESULTS There was a significant decrease on hair density, median, and terminal hair at the end of the treatment in the active-treated site (P < .001) as measured by TrichoScan software. Direct comparison between active and placebo-treated sites showed no significant differences at T0, but highly significant differences at T120 (P < .001). CONCLUSIONS The study shows that a cosmetic formulation based on capryloyl glycine 4% is highly effective in reducing several parameters related to hair growth and hair thickness vs placebo, thus showing efficacy in the treatment of hypertrichosis.
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Affiliation(s)
- Enzo Berardesca
- Phillip Frost Department of Dermatology, University of Miami, Miami, FL, USA
| | - Norma Cameli
- San Gallicano Dermatological Institute, Rome, Italy
| | | | - Stefano Veraldi
- Department of Pathophysiology and Transplantation, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Leonardo Celleno
- Department of Dermatology, Catholic University of Rome, Rome, Italy
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Oxygen reactivity with pyridoxal 5'-phosphate enzymes: biochemical implications and functional relevance. Amino Acids 2020; 52:1089-1105. [PMID: 32844248 PMCID: PMC7497351 DOI: 10.1007/s00726-020-02885-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 12/29/2022]
Abstract
The versatility of reactions catalyzed by pyridoxal 5'-phosphate (PLP) enzymes is largely due to the chemistry of their extraordinary catalyst. PLP is necessary for many reactions involving amino acids. Reaction specificity is controlled by the orientation of the external aldimine intermediate that is formed upon addition of the amino acidic substrate to the coenzyme. The breakage of a specific bond of the external aldimine gives rise to a carbanionic intermediate. From this point, the different reaction pathways diverge leading to multiple activities: transamination, decarboxylation, racemization, elimination, and synthesis. A significant novelty appeared approximately 30 years ago when it was reported that some PLP-dependent decarboxylases are able to consume molecular oxygen transforming an amino acid into a carbonyl compound. These side paracatalytic reactions could be particularly relevant for human health, also considering that some of these enzymes are responsible for the synthesis of important neurotransmitters such as γ-aminobutyric acid, dopamine, and serotonin, whose dysregulation under oxidative conditions could have important implications in neurodegenerative states. However, the reactivity of PLP enzymes with dioxygen is not confined to mammals/animals. In fact, some plant PLP decarboxylases have been reported to catalyze oxidative reactions producing carbonyl compounds. Moreover, other recent reports revealed the existence of new oxidase activities catalyzed by new PLP enzymes, MppP, RohP, Ind4, CcbF, PvdN, Cap15, and CuaB. These PLP enzymes belong to the bacterial and fungal kingdoms and are present in organisms synthesizing bioactive compounds. These new PLP activities are not paracatalytic and could only scratch the surface on a wider and unexpected catalytic capability of PLP enzymes.
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14
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Liang W, Yamahara K, Hernando-Erhard C, Lagies S, Wanner N, Liang H, Schell C, Kammerer B, Huber TB, Bork T. A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier. Kidney Int 2020; 98:1434-1448. [PMID: 32603735 DOI: 10.1016/j.kint.2020.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/07/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
Abstract
Podocyte maintenance and stress resistance are exquisitely based on high basal rates of autophagy making these cells a unique model to unravel mechanisms of autophagy regulation. Polyamines have key cellular functions such as proliferation, nucleic acid biosynthesis and autophagy. Here we test whether endogenous spermidine signaling is a driver of basal and dynamic autophagy in podocytes by using genetic and pharmacologic approaches to interfere with different steps of polyamine metabolism. Translational studies revealed altered spermidine signaling in focal segmental glomerulosclerosis in vivo and in vitro. Exogenous spermidine supplementation emerged as new treatment strategy by successfully activating autophagy in vivo via inhibition of EP300, a protein with an essential role in controlling cell growth, cell division and prompting cells to differentiate to take on specialized functions. Surprisingly, gas chromatography-mass spectroscopy based untargeted metabolomics of wild type and autophagy deficient primary podocytes revealed a positive feedback mechanism whereby autophagy itself maintains polyamine metabolism and spermidine synthesis. The transcription factor MAFB acted as an upstream regulator of polyamine metabolism. Thus, our data highlight a novel positive feedback loop of autophagy and spermidine signaling allowing maintenance of high basal levels of autophagy as a key mechanism to sustain the filtration barrier. Hence, spermidine supplementation may emerge as a new therapeutic to restore autophagy in glomerular disease.
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Affiliation(s)
- Wei Liang
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Kosuke Yamahara
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Medicine, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Camila Hernando-Erhard
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Simon Lagies
- Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Nicola Wanner
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Huan Liang
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Schell
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernd Kammerer
- Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany; BIOSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Tobias B Huber
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Tillmann Bork
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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15
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Semwal R, Aier I, Tyagi P, Varadwaj PK. DeEPn: a deep neural network based tool for enzyme functional annotation. J Biomol Struct Dyn 2020; 39:2733-2743. [PMID: 32274968 DOI: 10.1080/07391102.2020.1754292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
With the advancement of high throughput techniques, the discovery rate of enzyme sequences has increased significantly in the recent past. All of these raw sequences are required to be precisely mapped to their respective functional attributes, which helps in deciphering their biological role. In the recent past, various prediction models have been proposed to predict the enzyme functional class; however, all of these models were able to quantify at most six functional enzyme classes (EC1 to EC6) out of existing seven functional classes, making these approaches inappropriate for handling enzymes corresponding to the seventh functional class (EC7). In this study, a Deep Neural Network-based approach, DeEPn, has been proposed, which can quantify enzymes corresponding to all seven functional classes with high precision and accuracy. The proposed model was compared with two recently developed tools, ECPred and SVM-Prot. The result demonstrated that DeEPn outperformed ECPred and SVM-Prot in terms of predictive quality. The DeEPn tool has been hosted as a web-based tool at https://bioserver.iiita.ac.in/DeEPn/.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahul Semwal
- Department of Information Technology (Bioinformatics), Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Imlimaong Aier
- Department of Bioinformatics and Applied Science, Indian Institute of Information Technology, Allahabad, Allahabad, Uttar Pradesh, India
| | - Pankaj Tyagi
- Department of Information Technology (Bioinformatics), Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Pritish Kumar Varadwaj
- Department of Bioinformatics and Applied Science, Indian Institute of Information Technology, Allahabad, Allahabad, Uttar Pradesh, India
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16
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Tang J, Ju Y, Gu Q, Xu J, Zhou H. Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis. J Mol Biol 2019; 431:4868-4881. [PMID: 31634470 DOI: 10.1016/j.jmb.2019.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022]
Abstract
Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyzes the second step. Here, we report the X-ray crystal structures of S. aureus SbnH (SaSbnH) in complex with PLP, citrate, and the decarboxylation product citryl-diaminoethane (citryl-Dae). The overall structure of SaSbnH resembles those of the previously reported PLP-dependent amino acid decarboxylases, but the active site of SaSbnH showed unique structural features. Structural and mutagenesis analysis revealed that the citryl moiety of the substrate citryl-l-2,3-diaminopropionic acid (citryl-l-Dap) inserts into a narrow groove at the dimer interface of SaSbnH and forms hydrogen bonding interactions with both subunits. In the active site, a conserved lysine residue forms an aldimine linkage with the cofactor PLP, and a phenylalanine residue is essential for accommodating the l-configuration Dap of the substrate. Interestingly, the freestanding citrate molecule was found to bind to SaSbnH in a conformation inverse to that of the citryl group of citryl-Dae and efficiently inhibit SaSbnH. As an intermediate in the tricarboxylic acid (TCA) cycle, citrate is highly abundant in bacterial cells until iron depletion; thus, its inhibition of SaSbnH may serve as an iron-dependent regulatory mechanism in staphyloferrin B biosynthesis.
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Affiliation(s)
- Jieyu Tang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingchen Ju
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huihao Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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17
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Quantitative trait loci and candidate genes for the economic traits in meat-type chicken. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933914000348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Nogueira TCM, dos Santos Cruz L, Lourenço MC, de Souza MVN. Design, Synthesis and Anti-tuberculosis Activity of Hydrazones and N-acylhydrazones Containing Vitamin B6 and Different Heteroaromatic Nucleus. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180627122055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The term vitamin B6 refers to a set of six compounds, pyridoxine,pyridoxal
,and pyridoxamine and their phosphorylated forms, among which pyridoxal 5´-phosphate (PLP) is
the most important and active form acting as a critical cofactor. These compounds are very useful
in medicinal chemistry because of their structure and functionalities and are also used in bioinorganic
chemistry as ligands for complexation with metals.
Methods:
In this study, a series of hydrazones 1a-g and N-acylhydrazones 2a-f containing vitamin
B6 have been synthesized from commercial pyridoxal hydrochloride and the appropriate aromatic or
heteroaromatic hydrazine or N-acylhydrazine. All synthesized compounds have been fully characterized
and tested against Mycobacterium tuberculosis.
Results:
Among the N-acylhydrazones derivatives 2a-f, 2d (para- pyridine substituted Nacylhydrazone;
MIC = 10.90 µM) exhibited the best activity. The ortho-pyridine derivative 2b exhibited
intermediate activity (MIC = 87.32 µM), and the meta-pyridine derivative 2c was inactive.
In case of the hydrazone series 1a-g, 7-chloroquinoxaline derivative 1f (MIC = 72.72 µM) showed
the best result, indicating that the number of nitrogen and chlorine atoms in the radical moiety play an
important role in the anti-tuberculosis activity of the quinoxaline derivatives (1f and 1g).
Conclusion:
The data reported herein indicates that the isoniazid derivative 2d (MIC = 10.90 µM)
exhibited the best activity in the N-acylhydrazone series and; the quinoxaline nucleus derivative 1f
(MIC = 72.72 µM) was the most active compound in the hydrazone series.
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Affiliation(s)
- Thais Cristina Mendonça Nogueira
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos-Far-Manguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, Brazil
| | - Lucas dos Santos Cruz
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos-Far-Manguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, Brazil
| | - Maria Cristina Lourenço
- Fundacao Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Departamento de Bacteriologia, 21045-900, Manguinhos, Rio de Janeiro, Brazil
| | - Marcus Vinicius Nora de Souza
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos-Far-Manguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, Brazil
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19
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Liang J, Han Q, Tan Y, Ding H, Li J. Current Advances on Structure-Function Relationships of Pyridoxal 5'-Phosphate-Dependent Enzymes. Front Mol Biosci 2019; 6:4. [PMID: 30891451 PMCID: PMC6411801 DOI: 10.3389/fmolb.2019.00004] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 01/25/2019] [Indexed: 12/23/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP) functions as a coenzyme in many enzymatic processes, including decarboxylation, deamination, transamination, racemization, and others. Enzymes, requiring PLP, are commonly termed PLP-dependent enzymes, and they are widely involved in crucial cellular metabolic pathways in most of (if not all) living organisms. The chemical mechanisms for PLP-mediated reactions have been well elaborated and accepted with an emphasis on the pure chemical steps, but how the chemical steps are processed by enzymes, especially by functions of active site residues, are not fully elucidated. Furthermore, the specific mechanism of an enzyme in relation to the one for a similar class of enzymes seems scarcely described or discussed. This discussion aims to link the specific mechanism described for the individual enzyme to the same types of enzymes from different species with aminotransferases, decarboxylases, racemase, aldolase, cystathionine β-synthase, aromatic phenylacetaldehyde synthase, et al. as models. The structural factors that contribute to the reaction mechanisms, particularly active site residues critical for dictating the reaction specificity, are summarized in this review.
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Affiliation(s)
- Jing Liang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Institute of Agriculture and Forestry, Hainan University, Haikou, China
| | - Yang Tan
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haizhen Ding
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jianyong Li
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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20
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Du YL, Ryan KS. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat Prod Rep 2019; 36:430-457. [DOI: 10.1039/c8np00049b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review reactions catalyzed by pyridoxal phosphate-dependent enzymes, highlighting enzymes reported in the recent natural product biosynthetic literature.
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Affiliation(s)
- Yi-Ling Du
- Institute of Pharmaceutical Biotechnology
- Zhejiang University School of Medicine
- Hangzhou
- China
| | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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21
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Polyamines in Microalgae: Something Borrowed, Something New. Mar Drugs 2018; 17:md17010001. [PMID: 30577419 PMCID: PMC6356823 DOI: 10.3390/md17010001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/13/2023] Open
Abstract
Microalgae of different evolutionary origins are typically found in rivers, lakes, and oceans, providing more than 45% of global primary production. They provide not only a food source for animals, but also affect microbial ecosystems through symbioses with microorganisms or secretion of some metabolites. Derived from amino acids, polyamines are present in almost all types of organisms, where they play important roles in maintaining physiological functions or against stress. Microalgae can produce a variety of distinct polyamines, and the polyamine content is important to meet the physiological needs of microalgae and may also affect other species in the environment. In addition, some polyamines produced by microalgae have medical or nanotechnological applications. Previous studies on several types of microalgae have indicated that the putative polyamine metabolic pathways may be as complicated as the genomes of these organisms, which contain genes originating from plants, animals, and even bacteria. There are also several novel polyamine synthetic routes in microalgae. Understanding the nature of polyamines in microalgae will not only improve our knowledge of microalgal physiology and ecological function, but also provide valuable information for biotechnological applications.
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22
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A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora. J Struct Biol 2018; 202:236-249. [DOI: 10.1016/j.jsb.2018.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/30/2018] [Accepted: 02/07/2018] [Indexed: 01/01/2023]
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23
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Alam M, Srivastava A, Dutta A, Sau AK. Biochemical and biophysical studies ofHelicobacter pyloriarginine decarboxylase, an enzyme important for acid adaptation in host. IUBMB Life 2018; 70:658-669. [DOI: 10.1002/iub.1754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Mashkoor Alam
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Abhishek Srivastava
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Ankita Dutta
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Apurba Kumar Sau
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
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24
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Shinsky SA, Christianson DW. Polyamine Deacetylase Structure and Catalysis: Prokaryotic Acetylpolyamine Amidohydrolase and Eukaryotic HDAC10. Biochemistry 2018. [PMID: 29533602 DOI: 10.1021/acs.biochem.8b00079] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polyamines such as putrescine, spermidine, and spermine are small aliphatic cations that serve myriad biological functions in all forms of life. While polyamine biosynthesis and cellular trafficking pathways are generally well-defined, only recently has the molecular basis of reversible polyamine acetylation been established. In particular, enzymes that catalyze polyamine deacetylation reactions have been identified and structurally characterized: histone deacetylase 10 (HDAC10) from Homo sapiens and Danio rerio (zebrafish) is a highly specific N8-acetylspermidine deacetylase, and its prokaryotic counterpart, acetylpolyamine amidohydrolase (APAH) from Mycoplana ramosa, is a broad-specificity polyamine deacetylase. Similar to the greater family of HDACs, which mainly serve as lysine deacetylases, both enzymes adopt the characteristic arginase-deacetylase fold and employ a Zn2+-activated water molecule for catalysis. In contrast with HDACs, however, the active sites of HDAC10 and APAH are sterically constricted to enforce specificity for long, slender polyamine substrates and exclude bulky peptides and proteins containing acetyl-l-lysine. Crystal structures of APAH and D. rerio HDAC10 reveal that quaternary structure, i.e., dimer assembly, provides the steric constriction that directs the polyamine substrate specificity of APAH, whereas tertiary structure, a unique 310 helix defined by the P(E,A)CE motif, provides the steric constriction that directs the polyamine substrate specificity of HDAC10. Given the recent identification of HDAC10 and spermidine as mediators of autophagy, HDAC10 is rapidly emerging as a biomarker and target for the design of isozyme-selective inhibitors that will suppress autophagic responses to cancer chemotherapy, thereby rendering cancer cells more susceptible to cytotoxic drugs.
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Affiliation(s)
- Stephen A Shinsky
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
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Tremiño L, Forcada-Nadal A, Contreras A, Rubio V. Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B 6 -dependent epilepsy. FEBS Lett 2017; 591:3431-3442. [PMID: 28914444 DOI: 10.1002/1873-3468.12841] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/21/2017] [Accepted: 09/01/2017] [Indexed: 11/11/2022]
Abstract
The Synechococcus elongatus COG0325 gene pipY functionally interacts with the nitrogen regulatory gene pipX. As a first step toward a molecular understanding of such interactions, we characterized PipY. This 221-residue protein is monomeric and hosts pyridoxal phosphate (PLP), binding it with limited affinity and losing it upon incubation with D-cycloserine. PipY crystal structures with and without PLP reveal a single-domain monomer folded as the TIM barrel of type-III fold PLP enzymes, with PLP highly exposed, fitting a role for PipY in PLP homeostasis. The mobile PLP phosphate-anchoring C-terminal helix might act as a trigger for PLP exchange. Exploiting the universality of COG0325 functions, we used PipY in site-directed mutagenesis studies to shed light on disease causation by epilepsy-associated mutations in the human COG0325 gene PROSC.
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Affiliation(s)
- Lorena Tremiño
- Instituto de Biomedicina de Valencia (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain
| | - Alicia Forcada-Nadal
- Instituto de Biomedicina de Valencia (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain.,Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain
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26
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Agmatine: multifunctional arginine metabolite and magic bullet in clinical neuroscience? Biochem J 2017; 474:2619-2640. [DOI: 10.1042/bcj20170007] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022]
Abstract
Agmatine, the decarboxylation product of arginine, was largely neglected as an important player in mammalian metabolism until the mid-1990s, when it was re-discovered as an endogenous ligand of imidazoline and α2-adrenergic receptors. Since then, a wide variety of agmatine-mediated effects have been observed, and consequently agmatine has moved from a wallflower existence into the limelight of clinical neuroscience research. Despite this quantum jump in scientific interest, the understanding of the anabolism and catabolism of this amine is still vague. The purification and biochemical characterization of natural mammalian arginine decarboxylase and agmatinase still are open issues. Nevertheless, the agmatinergic system is currently one of the most promising candidates in order to pharmacologically interfere with some major diseases of the central nervous system, which are summarized in the present review. Particularly with respect to major depression, agmatine, its derivatives, and metabolizing enzymes show great promise for the development of an improved treatment of this common disease.
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27
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Characterization of an androgen-responsive, ornithine decarboxylase-related protein in mouse kidney. Biosci Rep 2017; 37:BSR20170163. [PMID: 28607032 PMCID: PMC5518511 DOI: 10.1042/bsr20170163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 01/26/2023] Open
Abstract
We have investigated and characterized a novel ornithine decarboxylase (ODC) related protein (ODCrp) also annotated as gm853. ODCrp shows 41% amino acid sequence identity with ODC and 38% with ODC antizyme inhibitor 1 (AZIN1). The Odcrp gene is selectively expressed in the epithelium of proximal tubuli of mouse kidney with higher expression in males than in females. Like Odc in mouse kidney, Odcrp is also androgen responsive with androgen receptor (AR)-binding loci within its regulatory region. ODCrp forms homodimers but does not heterodimerize with ODC. Although ODCrp contains 20 amino acid residues known to be necessary for the catalytic activity of ODC, no decarboxylase activity could be found with ornithine, lysine or arginine as substrates. ODCrp does not function as an AZIN, as it neither binds ODC antizyme 1 (OAZ1) nor prevents OAZ-mediated inactivation and degradation of ODC. ODCrp itself is degraded via ubiquination and mutation of Cys363 (corresponding to Cys360 of ODC) appears to destabilize the protein. Evidence for a function of ODCrp was found in ODC assays on lysates from transfected Cos-7 cells where ODCrp repressed the activity of endogenous ODC while Cys363Ala mutated ODCrp increased the enzymatic activity of endogenous ODC.
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Abstract
In trypanosomatids, polyamine and trypanothione pathways can be considered as a whole unique metabolism, where most enzymes are essential for parasitic survival and infectivity. Leishmania parasites and all the other members of the Trypanosomatids family depend on polyamines for growth and survival: the enzymes involved in the synthesis and utilization of spermidine and trypanothione, i.e., arginase, ornithine decarboxylase, S-adenosylmethionine decarboxylase, spermidine synthase and in particular trypanothione synthetase-amidase, trypanothione reductase and tryparedoxin-dependent peroxidase are promising targets for drug development. This review deals with recent structure-based studies on these enzymes, aimed at the discovery of inhibitors of this pathway.
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29
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Joshi RG, Ratna Prabha C. Degrons of yeast and mammalian ornithine decarboxylase enzymes make potent combination for regulated targeted protein degradation. Appl Microbiol Biotechnol 2016; 101:2905-2917. [DOI: 10.1007/s00253-016-8023-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/16/2016] [Indexed: 10/20/2022]
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Lima WR, Tessarin-Almeida G, Rozanski A, Parreira KS, Moraes MS, Martins DC, Hashimoto RF, Galante PAF, Garcia CRS. Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP. Genes Cancer 2016; 7:323-339. [PMID: 28050233 PMCID: PMC5115173 DOI: 10.18632/genesandcancer.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
According to the World Health Organization (WHO), Plasmodium falciparum is the deadliest parasite among all species. This parasite possesses the ability to sense molecules, including melatonin (MEL) and cAMP, and modulate its cell cycle accordingly. MEL synchronizes the development of this malaria parasite by activating several cascades, including the generation of the second messenger cAMP. Therefore, we performed RNA sequencing (RNA-Seq) analysis in P. falciparum erythrocytic stages (ring, trophozoite and schizont) treated with MEL and cAMP. To investigate the expression profile of P. falciparum genes regulated by MEL and cAMP, we performed RNA-Seq analysis in three P. falciparum strains (control, 3D7; protein kinase 7 knockout, PfPK7-; and PfPK7 complement, PfPK7C). In the 3D7 strain, 38 genes were differentially expressed upon MEL treatment; however, none of the genes in the trophozoite (T) stage PfPK7- knockout parasites were differentially expressed upon MEL treatment for 5 hours compared to untreated controls, suggesting that PfPK7 may be involved in the signaling leading to differential gene expression. Moreover, we found that MEL modified the mRNA expression of genes encoding membrane proteins, zinc ion-binding proteins and nucleic acid-binding proteins, which might influence numerous functions in the parasite. The RNA-Seq data following treatment with cAMP show that this molecule modulates different genes throughout the intraerythrocytic cycle, namely, 75, 101 and 141 genes, respectively, in the ring (R), T and schizont (S) stages. Our results highlight P. falciparum's perception of the external milieu through the signaling molecules MEL and cAMP, which are able to drive to changes in gene expression in the parasite.
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Affiliation(s)
- Wânia Rezende Lima
- Departamento de Fisiologia, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, Brazil.,Instituto de Ciências Exatas e Naturais (ICEN)- Medicina, Universidade Federal do Mato Grosso - Campus Rondonópolis, Brazil
| | | | - Andrei Rozanski
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Kleber S Parreira
- Departamento de Imunologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Brazil
| | - Miriam S Moraes
- Departamento de Fisiologia, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - David C Martins
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Paulo, Brazil
| | - Ronaldo F Hashimoto
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Célia R S Garcia
- Departamento de Fisiologia, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, Brazil
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31
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Jaenisch S, Squire M, Butler R, Yazbeck R. In vitro development and validation of a non-invasive (13)C-stable isotope assay for ornithine decarboxylase. J Breath Res 2016; 10:026009. [PMID: 27137347 DOI: 10.1088/1752-7155/10/2/026009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Oesophageal cancer is a significant cause of cancer related mortality, with increasing incidence worldwide. Ornithine decarboxylase (ODC) is an enzyme involved in polyamine synthesis and cellular proliferation, and ODC expression and activity has been implicated as a prognostic marker of oesophageal cancer. This study aimed to develop and optimise an in vitro (13)C-stable isotope assay for ODC activity as a non-invasive marker of oesophageal cancer. Experiments were performed in triplicate (n = 3/group/cell line) using Caco2, HeLa, Flo-1, OE33, TE7 and OE21 cell lines (colorectal, cervical, oesophageal adenocarcinoma and oesophageal squamous carcinoma respectively). Following addition of 2mM (13)C-ornithine to cells, 10 ml gas samples were collected from the headspace every 20 min for a total of five hours. Gas samples were analysed using isotope ratio mass spectrometry to quantify (13)CO2. Assay specificity was determined using the selective ODC inhibitor, N-(4'-Pyridoxil)-Ornithine(BOC)-OMe (POB). All data is expressed as δ (13)CO2 from baseline. High ODC activity was detected by (13)C-ornithine assay in Caco2 (32.00 ± 1.12 δ (13)CO2) in contrast to HeLa cells (5.44 ± 0.14 δ (13)CO2) cells. POB inhibited activity in Caco2 cells to 12.87 ± 1.10 δ (13)CO2. Differential ODC activity was detected in all oesophageal cancer cells, and 53 h incubation of cell lines with POB reduced activity by 72%, 56%, 64% and 69% in the Flo-1, OE33, OE21 and TE7 cell lines respectively. We have shown that ODC activity can be selectively detected by a non-invasive, stable-isotope (13)C-ornithine assay. ODC activity was detected in all oesophageal cancer cell lines in vitro. Further studies are indicated to quantify ODC activity in oesophageal cancer patients.
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Affiliation(s)
- Simone Jaenisch
- School of Medicine, Department of Surgery, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia. Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia, Australia
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Engineering degrons of yeast ornithine decarboxylase as vehicles for efficient targeted protein degradation. Biochim Biophys Acta Gen Subj 2015; 1850:2452-63. [DOI: 10.1016/j.bbagen.2015.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 09/03/2015] [Accepted: 09/08/2015] [Indexed: 11/18/2022]
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Hoefig CS, Wuensch T, Rijntjes E, Lehmphul I, Daniel H, Schweizer U, Mittag J, Köhrle J. Biosynthesis of 3-Iodothyronamine From T4 in Murine Intestinal Tissue. Endocrinology 2015; 156:4356-64. [PMID: 26348473 DOI: 10.1210/en.2014-1499] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The endogenous metabolite 3-iodothyronamine (3-T1AM) induces strong hypothermia and bradycardia at pharmacological doses. Although its biosynthesis from thyroid hormone precursors appears likely, the sequence and sites of reactions are still controversial: studies in T4-substituted thyroid cancer patients lacking functional thyroid tissue suggested extrathyroidal 3-T1AM production, whereas studies using labeled T4 in mice indicated intrathyroidal formation. However, because the patients received T4 orally, whereas the mice were injected ip, we hypothesized that 3-T1AM synthesis requires the intestinal passage of T4. Using the everted gut sac model in combination with mass spectrometry, we demonstrate 3-T1AM production from T4 in mouse intestine via several deiodination and decarboxylation steps. Gene expression analysis confirmed the expression of all 3 deiodinases as well as ornithine decarboxylase (ODC) in intestine. Subsequent experiments employing purified human ODC revealed that this enzyme can in fact mediate decarboxylation of 3,5-T2 and T4 to the respective thyronamines (TAMs), demonstrating that the intestine expresses the entire molecular machinery required for 3-T1AM biosynthesis. Interestingly, TAM production was strongly affected by the antithyroid treatment methimazole and perchlorate independently of thyroid status, limiting the validity of the respective mouse models in this context. Taken together, our data demonstrate intestinal 3-T1AM biosynthesis from T4 involving decarboxylation through ODC with subsequent deiodination, and explain the apparent discrepancy between 3-T1AM serum levels in patients substituted orally and mice injected ip with T4. Identifying ODC as the first enzyme capable of decarboxylating thyroid hormone, our findings open the path to further investigations of TAM metabolism on molecular and cellular levels.
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Affiliation(s)
- Carolin S Hoefig
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Tilo Wuensch
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Eddy Rijntjes
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Ina Lehmphul
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Hannelore Daniel
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Ulrich Schweizer
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Jens Mittag
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Josef Köhrle
- Institut für Experimentelle Endokrinologie (C.S.H., E.R., I.L., U.S., J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Karolinska Institutet (C.S.H., T.W., J.M.), Department of Cell and Molecular Biology, 17177 Stockholm, Sweden; Ziel Research Center of Nutrition and Food Science (T.W., H.D.), Abteilung Biochemie, Technische Universität München, 85354 Freising, Germany; Institut für Biochemie und Molekularbiologie (U.S.), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany; and Center of Brain, Behavior and Metabolism (J.M.), Medizinische Klinik 1, Universität zu Lübeck, 23562 Lübeck, Germany
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Structural basis of Ornithine Decarboxylase inactivation and accelerated degradation by polyamine sensor Antizyme1. Sci Rep 2015; 5:14738. [PMID: 26443277 PMCID: PMC4595762 DOI: 10.1038/srep14738] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/07/2015] [Indexed: 11/18/2022] Open
Abstract
Ornithine decarboxylase (ODC) catalyzes the first and rate-limiting step of polyamine biosynthesis in humans. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis. Excessive accumulation of polyamines has a cytotoxic effect on cells and elevated level of ODC activity is associated with cancer development. To maintain normal cellular proliferation, regulation of polyamine synthesis is imposed by Antizyme1 (AZ1). The expression of AZ1 is induced by a ribosomal frameshifting mechanism in response to increased intracellular polyamines. AZ1 regulates polyamine homeostasis by inactivating ODC activity and enhancing its degradation. Here, we report the structure of human ODC in complex with N-terminally truncated AZ1 (cAZ1). The structure shows cAZ1 binding to ODC, which occludes the binding of a second molecule of ODC to form the active homodimer. Consequently, the substrate binding site is disrupted and ODC is inactivated. Structural comparison shows that the binding of cAZ1 to ODC causes a global conformational change of ODC and renders its C-terminal region flexible, therefore exposing this region for degradation by the 26S proteasome. Our structure provides the molecular basis for the inactivation of ODC by AZ1 and sheds light on how AZ1 promotes its degradation.
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35
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Balaji S. Internal symmetry in protein structures: prevalence, functional relevance and evolution. Curr Opin Struct Biol 2015; 32:156-66. [PMID: 26093245 DOI: 10.1016/j.sbi.2015.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
Abstract
Symmetry has been found at various levels of biological organization in the protein structural universe. Numerous evolutionary studies have proposed connections between internal symmetry within protein tertiary structures, quaternary associations and protein functions. Recent computational methods, such as SymD and CE-Symm, facilitate a large-scale detection of internal symmetry in protein structures. Based on the results from these methods, about 20% of SCOP folds, superfamilies and families are estimated to have structures with internal symmetry (Figure 1d). All-β and membrane proteins fold classes contain a relatively high number of unique instances of internal symmetry. In addition to the axis of symmetry, anecdotal evidence suggests that, the region of connection or contact between symmetric units could coincide with functionally relevant sites within a fold. General principles that underlie protein internal symmetry and their connections to protein structural integrity and functions remain to be elucidated.
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Affiliation(s)
- Santhanam Balaji
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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36
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Lee CY, Liu YL, Lin CL, Liu GY, Hung HC. Functional roles of the dimer-interface residues in human ornithine decarboxylase. PLoS One 2014; 9:e104865. [PMID: 25140796 PMCID: PMC4139326 DOI: 10.1371/journal.pone.0104865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 07/13/2014] [Indexed: 01/06/2023] Open
Abstract
Ornithine decarboxylase (ODC) catalyzes the decarboxylation of ornithine to putrescine and is the rate-limiting enzyme in the polyamine biosynthesis pathway. ODC is a dimeric enzyme, and the active sites of this enzyme reside at the dimer interface. Once the enzyme dissociates, the enzyme activity is lost. In this paper, we investigated the roles of amino acid residues at the dimer interface regarding the dimerization, protein stability and/or enzyme activity of ODC. A multiple sequence alignment of ODC and its homologous protein antizyme inhibitor revealed that 5 of 9 residues (residues 165, 277, 331, 332 and 389) are divergent, whereas 4 (134, 169, 294 and 322) are conserved. Analytical ultracentrifugation analysis suggested that some dimer-interface amino acid residues contribute to formation of the dimer of ODC and that this dimerization results from the cooperativity of these interface residues. The quaternary structure of the sextuple mutant Y331S/Y389D/R277S/D332E/V322D/D134A was changed to a monomer rather than a dimer, and the Kd value of the mutant was 52.8 µM, which is over 500-fold greater than that of the wild-type ODC (ODC_WT). In addition, most interface mutants showed low but detectable or negligible enzyme activity. Therefore, the protein stability of these interface mutants was measured by differential scanning calorimetry. These results indicate that these dimer-interface residues are important for dimer formation and, as a consequence, are critical for enzyme catalysis.
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Affiliation(s)
- Chien-Yun Lee
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yi-Liang Liu
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
- Institute of Microbiology and Immunology and Division of Allergy, Immunology and Rheumatology, Chung Shan Medical University and Hospital, Taichung, Taiwan
| | - Chih-Li Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Guang-Yaw Liu
- Institute of Microbiology and Immunology and Division of Allergy, Immunology and Rheumatology, Chung Shan Medical University and Hospital, Taichung, Taiwan
- * E-mail: (HCH); (GYL)
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center (ABC), National Chung-Hsing University (NCHU), Taichung, Taiwan
- * E-mail: (HCH); (GYL)
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Ramos-Molina B, Lambertos A, Lopez-Contreras AJ, Kasprzak JM, Czerwoniec A, Bujnicki JM, Cremades A, Peñafiel R. Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2. FEBS Open Bio 2014; 4:510-21. [PMID: 24967154 PMCID: PMC4066113 DOI: 10.1016/j.fob.2014.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 01/11/2023] Open
Abstract
Ornithine decarboxylase (ODC) is the key enzyme in the polyamine biosynthetic pathway. ODC levels are controlled by polyamines through the induction of antizymes (AZs), small proteins that inhibit ODC and target it to proteasomal degradation without ubiquitination. Antizyme inhibitors (AZIN1 and AZIN2) are proteins homologous to ODC that bind to AZs and counteract their negative effect on ODC. Whereas ODC and AZIN1 are well-characterized proteins, little is known on the structure and stability of AZIN2, the lastly discovered member of this regulatory circuit. In this work we first analyzed structural aspects of AZIN2 by combining biochemical and computational approaches. We demonstrated that AZIN2, in contrast to ODC, does not form homodimers, although the predicted tertiary structure of the AZIN2 monomer was similar to that of ODC. Furthermore, we identified conserved residues in the antizyme-binding element, whose substitution drastically affected the capacity of AZIN2 to bind AZ1. On the other hand, we also found that AZIN2 is much more labile than ODC, but it is highly stabilized by its binding to AZs. Interestingly, the administration of the proteasome inhibitor MG132 caused differential effects on the three AZ-binding proteins, having no effect on ODC, preventing the degradation of AZIN1, but unexpectedly increasing the degradation of AZIN2. Inhibitors of the lysosomal function partially prevented the effect of MG132 on AZIN2. These results suggest that the degradation of AZIN2 could be also mediated by an alternative route to that of proteasome. These findings provide new relevant information on this unique regulatory mechanism of polyamine metabolism.
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Key Words
- AZ, antizyme
- AZBE, antizyme-binding element
- AZIN, antizyme inhibitor
- Antizyme
- Antizyme-binding element
- ERGIC, endoplasmic reticulum-Golgi intermediate compartment
- GDT_TS, global distance test total score
- HA, hemagglutinin
- HEK, human embryonic kidney
- Homology modeling
- ODC, ornithine decarboxylase
- PAGE, polyacrylamide gel electrophoresis
- Polyamines
- Proteasome inhibitors
- Protein degradation
- RMSD, root-mean-square deviation
- TGN, trans-Golgi network
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Affiliation(s)
- Bruno Ramos-Molina
- Department of Biochemistry and Molecular Biology B and Immunology, University of Murcia, Spain ; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Ana Lambertos
- Department of Biochemistry and Molecular Biology B and Immunology, University of Murcia, Spain ; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | | | - Joanna M Kasprzak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Anna Czerwoniec
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Asunción Cremades
- Department of Biochemistry and Molecular Biology B and Immunology, University of Murcia, Spain ; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Rafael Peñafiel
- Department of Biochemistry and Molecular Biology B and Immunology, University of Murcia, Spain ; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
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Lange I, Geerts D, Feith DJ, Mocz G, Koster J, Bachmann AS. Novel interaction of ornithine decarboxylase with sepiapterin reductase regulates neuroblastoma cell proliferation. J Mol Biol 2013; 426:332-46. [PMID: 24096079 DOI: 10.1016/j.jmb.2013.09.037] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 09/21/2013] [Accepted: 09/25/2013] [Indexed: 01/24/2023]
Abstract
Ornithine decarboxylase (ODC) is the sentinel enzyme in polyamine biosynthesis. Both ODC and polyamines regulate cell division, proliferation, and apoptosis. Sepiapterin reductase (SPR) catalyzes the last step in the biosynthesis of tetrahydrobiopterin (BH4), an essential cofactor of nitric oxide synthase, and has been implicated in neurological diseases but not yet in cancer. In this study, we present compelling evidence that native ODC and SPR physically interact, and we defined the individual amino acid residues involved in both enzymes using in silico protein-protein docking simulations. The resulting heterocomplex is a surprisingly compact structure, featuring two energetically and structurally equivalent binding modes both in monomer and in dimer conformations. The novel interaction between ODC and SPR proteins was confirmed under physiological conditions by co-immunoprecipitation and co-localization in neuroblastoma (NB) cells. Importantly, we showed that siRNA (small interfering RNA)-mediated knockdown of SPR expression significantly reduced endogenous ODC enzyme activity in NB cells, thus demonstrating the biological relevance of the ODC-SPR interaction. Finally, in a cohort of 88 human NB tumors, we found that high SPR mRNA expression correlated significantly with poor survival prognosis using a Kaplan-Meier analysis (log-rank test, P=5 × 10(-4)), suggesting an oncogenic role for SPR in NB tumorigenesis. In conclusion, we showed that ODC binds SPR and thus propose a new concept in which two well-characterized biochemical pathways converge via the interaction of two enzymes. We identified SPR as a novel regulator of ODC enzyme activity and, based on clinical evidence, present a model in which SPR drives ODC-mediated malignant progression in NB.
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Affiliation(s)
- Ingo Lange
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, USA
| | - Dirk Geerts
- Department of Pediatric Oncology/Hematology, Sophia Children's Hospital, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - David J Feith
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Gabor Mocz
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - André S Bachmann
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, USA; Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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39
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Kurosinski MA, Lüersen K, Ndjonka D, Younis AE, Brattig NW, Liebau E. Filarial parasites possess an antizyme but lack a functional ornithine decarboxylase. Acta Trop 2013; 126:167-76. [PMID: 23474393 DOI: 10.1016/j.actatropica.2013.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/08/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
In eukaryotes, the key player in polyamine metabolism is the ornithine decarboxylase (ODC) that catalyses the first and rate limiting step in cellular polyamine synthesis. The half life of ODC is strictly regulated by the antizyme (AZ), which promotes its degradation. Older reports on the polyamine situation in filarial parasites indicate a lack of ornithine decarboxylation activity and an increased uptake of polyamines. Our in silico analysis of the Brugia malayi genome revealed only an ODC-like protein that lacks essential residues. Consequently, the recombinant protein had no enzymatic ODC activity. Furthermore, only ODC-like genes were found in the available draft genomes of other filarial parasites. In this ODC-free scenario, we set out to investigate the AZ of O. volvulus (OvAZ). The expression of the recombinant protein allowed us to analyse the localization of OvAZ in different O. volvulus stages as well as to identify it as target for the human humoral immune response. Strong immunostaining was observed in the outer zone of the uterine epithelium as well as in the uterus lumen around the periphery of the developing parasite, indicating a potential role of the OvAZ in the control of polyamine levels during embryonic development. By employing a novel in vivo method using Caenorhabditis elegans, we postulate that the OvAZ enters the secretory pathway. Even though the ODCs are absent in filarial parasites, OvAZ has the ability to bind to various ODCs, thereby demonstrating the functionality of the conserved AZ-binding domains. Finally, pull-down assays show an interaction between B. malayi AZ and the B. malayi ODC-like protein, indicating that the B. malayi ODC-like protein might function as an AZI. Taken together, our results suggest that filarial species do not possess the ODC while retaining the ODC-regulatory proteins AZ and AZI. It is tempting to speculate that both proteins are retained for the regulation of polyamine transport systems.
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Structural insight into DFMO resistant ornithine decarboxylase from Entamoeba histolytica: an inkling to adaptive evolution. PLoS One 2013; 8:e53397. [PMID: 23326423 PMCID: PMC3543441 DOI: 10.1371/journal.pone.0053397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/28/2012] [Indexed: 11/19/2022] Open
Abstract
Background Polyamine biosynthetic pathway is a validated therapeutic target for large number of infectious diseases including cancer, giardiasis and African sleeping sickness, etc. α-Difluoromethylornithine (DFMO), a potent drug used for the treatment of African sleeping sickness is an irreversible inhibitor of ornithine decarboxylase (ODC), the first rate limiting enzyme of polyamine biosynthesis. The enzyme ODC of E. histolytica (EhODC) has been reported to exhibit resistance towards DFMO. Methodology/Principal Finding The basis for insensitivity towards DFMO was investigated by structural analysis of EhODC and conformational modifications at the active site. Here, we report cloning, purification and crystal structure determination of C-terminal truncated Entamoeba histolytica ornithine decarboxylase (EhODCΔ15). Structure was determined by molecular replacement method and refined to 2.8 Å resolution. The orthorhombic crystal exhibits P212121 symmetry with unit cell parameters a = 76.66, b = 119.28, c = 179.28 Å. Functional as well as evolutionary relations of EhODC with other ODC homologs were predicted on the basis of sequence analysis, phylogeny and structure. Conclusions/Significance We determined the tetrameric crystal structure of EhODCΔ15, which exists as a dimer in solution. Insensitivity towards DFMO is due to substitution of key substrate binding residues in active site pocket. Additionally, a few more substitutions similar to antizyme inhibitor (AZI), a non-functional homologue of ODCs, were identified in the active site. Here, we establish the fact that EhODC sequence has conserved PLP binding residues; in contrast few substrate binding residues are mutated similar to AZI. Further sequence analysis and structural studies revealed that EhODC may represent as an evolutionary bridge between active decarboxylase and inactive AZI.
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Kojima S, Kamio Y. Molecular basis for the maintenance of envelope integrity in Selenomonas ruminantium: cadaverine biosynthesis and covalent modification into the peptidoglycan play a major role. J Nutr Sci Vitaminol (Tokyo) 2012; 58:153-60. [PMID: 22878384 DOI: 10.3177/jnsv.58.153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Polyamine is a small organic polycation composed of a hydrocarbon backbone with multiple amino groups which ubiquitously exists in all living organisms from bacteria to higher animals. The critical step of polyamine biosynthesis generally includes the amino acid-decarboxylating reaction to produce the primary diamines, such as a synthesis of putrescine (NH(3)(+)·(CH(2))(4)·NH(3)(+)) from ornithine, and cadaverine (NH(3)(+)·(CH(2))(5)·NH(3)(+)) from lysine, which are catalyzed by pyridoxal-5'-phosphate (PLP; vitamin B(6))-dependent decarboxylases. Synthesized polyamines are implicated in a wide variety of cytoplasmic reactions such as DNA replication and protein synthesis, and are essential for proper growth of the organisms. However, in Selenomonas ruminantium, a strictly anaerobic Gram-negative bacterium dominant in sheep rumen, cadaverine displays its function in a quite distinctive scheme compared to the general bacteria reported. It serves as an essential constituent of the peptidoglycan for the maintenance of envelope integrity through an interaction with the periplasm-exposed SLH domain of Mep45, the outer membrane protein of this bacterium. Furthermore, cytoplasmic biosynthesis of cadaverine occurs totally in a eukaryotic-like manner rather than in a conventional way of bacteria. Lysine/ornithine decarboxylase (LDC/ODC), a PLP-dependent enzyme responsible for cadaverine synthesis in this bacterium, displays significant homology to the eukaryotic ODC but not to the general bacterial LDC nor ODC, and its activity is tightly regulated by antizyme-mediated proteolysis, a regulatory process generally found in eukaryotes. These findings represent the biological diversity of this bacterium beyond the preexisting knowledge related to the polyamine-physiology, cell envelope-architecture, and the regulatory system for the enzyme. In this review we will describe (i) the cadaverine-containing peptidoglycan of S. ruminantium: its chemical structure, biosynthesis, and biological function, and (ii) cellular biosynthesis of cadaverine by LDC/ODC and its antizyme-mediated regulation. In addition, we will briefly refer to (iii) the phylogenetic position and characteristics of S. ruminantium and its unique cadaverine-physiology.
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Affiliation(s)
- Seiji Kojima
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
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Chakraborty D, Saravanan P, Patra S, Dubey VK. Studies on ornithine decarboxylase of Leishmania donovani: structure modeling and inhibitor docking. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0035-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Erales J, Hoyt MA, Troll F, Coffino P. Functional asymmetries of proteasome translocase pore. J Biol Chem 2012; 287:18535-43. [PMID: 22493437 DOI: 10.1074/jbc.m112.357327] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Degradation by proteasomes involves coupled translocation and unfolding of its protein substrates. Six distinct but paralogous proteasome ATPase proteins, Rpt1 to -6, form a heterohexameric ring that acts on substrates. An axially positioned loop (Ar-Φ loop) moves in concert with ATP hydrolysis, engages substrate, and propels it into a proteolytic chamber. The aromatic (Ar) residue of the Ar-Φ loop in all six Rpts of S. cerevisiae is tyrosine; this amino acid is thought to have important functional contacts with substrate. Six yeast strains were constructed and characterized in which Tyr was individually mutated to Ala. The mutant cells were viable and had distinct phenotypes. rpt3, rpt4, and rpt5 Tyr/Ala mutants, which cluster on one side of the ATPase hexamer, were substantially impaired in their capacity to degrade substrates. In contrast, rpt1, rpt2, and rpt6 mutants equaled or exceeded wild type in degradation activity. However, rpt1 and rpt6 mutants had defects that limited cell growth or viability under conditions that stressed the ubiquitin proteasome system. In contrast, the rpt3 mutant grew faster than wild type and to a smaller size, a defect that has previously been associated with misregulation of G1 cyclins. This rpt3 phenotype probably results from altered degradation of cell cycle regulatory proteins. Finally, mutation of five of the Rpt subunits increased proteasome ATPase activity, implying bidirectional coupling between the Ar-Φ loop and the ATP hydrolysis site. The present observations assign specific functions to individual Rpt proteins and provide insights into the diverse roles of the axial loops of individual proteasome ATPases.
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Affiliation(s)
- Jenny Erales
- Department of Microbiology and Immunology, University of California, San Francisco, California 94127, USA
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Biochemical, mutational and in silico structural evidence for a functional dimeric form of the ornithine decarboxylase from Entamoeba histolytica. PLoS Negl Trop Dis 2012; 6:e1559. [PMID: 22389745 PMCID: PMC3289617 DOI: 10.1371/journal.pntd.0001559] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 01/21/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Entamoeba histolytica is responsible for causing amoebiasis. Polyamine biosynthesis pathway enzymes are potential drug targets in parasitic protozoan diseases. The first and rate-limiting step of this pathway is catalyzed by ornithine decarboxylase (ODC). ODC enzyme functions as an obligate dimer. However, partially purified ODC from E. histolytica (EhODC) is reported to exist in a pentameric state. METHODOLOGY AND RESULTS In present study, the oligomeric state of EhODC was re-investigated. The enzyme was over-expressed in Escherichia coli and purified. Pure protein was used for determination of secondary structure content using circular dichroism spectroscopy. The percentages of α-helix, β-sheets and random coils in EhODC were estimated to be 39%, 25% and 36% respectively. Size-exclusion chromatography and mass spectrophotometry analysis revealed that EhODC enzyme exists in dimeric form. Further, computational model of EhODC dimer was generated. The homodimer contains two separate active sites at the dimer interface with Lys57 and Cys334 residues of opposite monomers contributing to each active site. Molecular dynamic simulations were performed and the dimeric structure was found to be very stable with RMSD value ∼0.327 nm. To gain insight into the functional role, the interface residues critical for dimerization and active site formation were identified and mutated. Mutation of Lys57Ala or Cys334Ala completely abolished enzyme activity. Interestingly, partial restoration of the enzyme activity was observed when inactive Lys57Ala and Cys334Ala mutants were mixed confirming that the dimer is the active form. Furthermore, Gly361Tyr and Lys157Ala mutations at the dimer interface were found to abolish the enzyme activity and destabilize the dimer. CONCLUSION To our knowledge, this is the first report which demonstrates that EhODC is functional in the dimeric form. These findings and availability of 3D structure model of EhODC dimer opens up possibilities for alternate enzyme inhibition strategies by targeting the dimer disruption.
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Abstract
New drugs are urgently needed for the treatment of tropical and subtropical parasitic diseases, such as African sleeping sickness, Chagas' disease, leishmaniasis and malaria. Enzymes in polyamine biosynthesis and thiol metabolism, as well as polyamine transporters, are potential drug targets within these organisms. In the present review, the current knowledge of unique properties of polyamine metabolism in these parasites is outlined. These properties include prozyme regulation of AdoMetDC (S-adenosylmethionine decarboxylase) activity in trypanosomatids, co-expression of ODC (ornithine decarboxylase) and AdoMetDC activities in a single protein in plasmodia, and formation of trypanothione, a unique compound linking polyamine and thiol metabolism in trypanosomatids. Particularly interesting features within polyamine metabolism in these parasites are highlighted for their potential in selective therapeutic strategies.
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Morozov AV, Timofeev AV, Morozov VA, Karpov VL. Availability and canonical positioning of key amino acids of ornithine-decarboxylase degron is insufficient for alpha-fetoprotein degradation. Mol Biol 2011. [DOI: 10.1134/s0026893311030101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Liu YC, Liu YL, Su JY, Liu GY, Hung HC. Critical factors governing the difference in antizyme-binding affinities between human ornithine decarboxylase and antizyme inhibitor. PLoS One 2011; 6:e19253. [PMID: 21552531 PMCID: PMC3084279 DOI: 10.1371/journal.pone.0019253] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/24/2011] [Indexed: 12/18/2022] Open
Abstract
Both ornithine decarboxylase (ODC) and its regulatory protein, antizyme inhibitor (AZI), can bind with antizyme (AZ), but the latter has a higher AZ-binding affinity. The results of this study clearly identify the critical amino acid residues governing the difference in AZ-binding affinities between human ODC and AZI. Inhibition experiments using a series of ODC mutants suggested that residues 125 and 140 may be the key residues responsible for the differential AZ-binding affinities. The ODC_N125K/M140K double mutant demonstrated a significant inhibition by AZ, and the IC50 value of this mutant was 0.08 µM, three-fold smaller than that of ODC_WT. Furthermore, the activity of the AZ-inhibited ODC_N125K/M140K enzyme was hardly rescued by AZI. The dissociation constant (Kd) of the [ODC_N125K/M140K]-AZ heterodimer was approximately 0.02 µM, which is smaller than that of WT_ODC by approximately 10-fold and is very close to the Kd value of AZI_WT, suggesting that ODC_N125K/M140K has an AZ-binding affinity higher than that of ODC_WT and similar to that of AZI. The efficiency of the AZI_K125N/K140M double mutant in the rescue of AZ-inhibited ODC enzyme activity was less than that of AZI_WT. The Kd value of [AZI_K125N/K140M]-AZ was 0.18 µM, nine-fold larger than that of AZI_WT and close to the Kd value of ODC_WT, suggesting that AZI_K125N/K140M has an AZ-binding affinity lower than that of AZI_WT and similar to that of ODC. These data support the hypothesis that the differences in residues 125 and 140 in ODC and AZI are responsible for the differential AZ-binding affinities.
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Affiliation(s)
- Yen-Chin Liu
- Department of Life Sciences and Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan
| | - Yi-Liang Liu
- Department of Life Sciences and Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan
- Division of Allergy, Immunology and Rheumatology and Institute of Immunology, Chung-Shan Medical University and Hospital, Taichung, Taiwan
| | - Jia-Yang Su
- Department of Life Sciences and Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan
| | - Guang-Yaw Liu
- Division of Allergy, Immunology and Rheumatology and Institute of Immunology, Chung-Shan Medical University and Hospital, Taichung, Taiwan
- * E-mail: (HCH); (GYL)
| | - Hui-Chih Hung
- Department of Life Sciences and Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan
- * E-mail: (HCH); (GYL)
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Fuell C, Elliott KA, Hanfrey CC, Franceschetti M, Michael AJ. Polyamine biosynthetic diversity in plants and algae. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2010; 48:513-20. [PMID: 20227886 DOI: 10.1016/j.plaphy.2010.02.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Revised: 02/09/2010] [Accepted: 02/11/2010] [Indexed: 05/04/2023]
Abstract
Polyamine biosynthesis in plants differs from other eukaryotes because of the contribution of genes from the cyanobacterial ancestor of the chloroplast. Plants possess an additional biosynthetic route for putrescine formation from arginine, consisting of the enzymes arginine decarboxylase, agmatine iminohydrolase and N-carbamoylputrescine amidohydrolase, derived from the cyanobacterial ancestor. They also synthesize an unusual tetraamine, thermospermine, that has important developmental roles and which is evolutionarily more ancient than spermine in plants and algae. Single-celled green algae have lost the arginine route and are dependent, like other eukaryotes, on putrescine biosynthesis from the ornithine. Some plants like Arabidopsis thaliana and the moss Physcomitrella patens have lost ornithine decarboxylase and are thus dependent on the arginine route. With its dependence on the arginine route, and the pivotal role of thermospermine in growth and development, Arabidopsis represents the most specifically plant mode of polyamine biosynthesis amongst eukaryotes. A number of plants and algae are also able to synthesize unusual polyamines such as norspermidine, norspermine and longer polyamines, and biosynthesis of these amines likely depends on novel aminopropyltransferases similar to thermospermine synthase, with relaxed substrate specificity. Plants have a rich repertoire of polyamine-based secondary metabolites, including alkaloids and hydroxycinnamic amides, and a number of polyamine-acylating enzymes have been recently characterised. With the genetic tools available for Arabidopsis and other model plants and algae, and the increasing capabilities of comparative genomics, the biological roles of polyamines can now be addressed across the plant evolutionary lineage.
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Affiliation(s)
- Christine Fuell
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR47UA, UK
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Colotti G, Ilari A. Polyamine metabolism in Leishmania: from arginine to trypanothione. Amino Acids 2010; 40:269-85. [PMID: 20512387 DOI: 10.1007/s00726-010-0630-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 05/13/2010] [Indexed: 12/20/2022]
Abstract
Polyamines (PAs) are essential metabolites in eukaryotes, participating in a variety of proliferative processes, and in trypanosomatid protozoa play an additional role in the synthesis of the critical thiol trypanothione. The PAs are synthesized by a metabolic process which involves arginase (ARG), which catalyzes the enzymatic hydrolysis of L-arginine (L-Arg) to L-ornithine and urea, and ornithine decarboxylase (ODC), which catalyzes the enzymatic decarboxylation of L-ornithine in putrescine. The S-adenosylmethionine decarboxylase (AdoMetDC) catalyzes the irreversible decarboxylation of S-adenosylmethionine (AdoMet), generating the decarboxylated S-adenosylmethionine (dAdoMet), which is a substrate, together with putrescine, for spermidine synthase (SpdS). Leishmania parasites and all the other members of the trypanosomatid family depend on spermidine for growth and survival. They can synthesize PAs and polyamine precursors, and also scavenge them from the microenvironment, using specific transporters. In addition, Trypanosomatids have a unique thiol-based metabolism, in which trypanothione (N1-N8-bis(glutathionyl)spermidine, T(SH)(2)) and trypanothione reductase (TR) replace many of the antioxidant and metabolic functions of the glutathione/glutathione reductase (GR) and thioredoxin/thioredoxin reductase (TrxR) systems present in the host. Trypanothione synthetase (TryS) and TR are necessary for the protozoa survival. Consequently, enzymes involved in spermidine synthesis and its utilization, i.e. ARG, ODC, AdoMetDC, SpdS and, in particular, TryS and TR, are promising targets for drug development.
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Affiliation(s)
- Gianni Colotti
- Institute of Biology and Molecular Pathology, CNR, c/o Department of Biochemical Sciences, University Sapienza, P.le A. Moro 5, 00185, Rome, Italy.
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Ivanov IP, Firth AE, Atkins JF. Recurrent Emergence of Catalytically Inactive Ornithine Decarboxylase Homologous Forms That Likely Have Regulatory Function. J Mol Evol 2010; 70:289-302. [DOI: 10.1007/s00239-010-9331-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 02/17/2010] [Indexed: 10/19/2022]
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