1
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Jacobs RQ, Schneider DA. Transcription elongation mechanisms of RNA polymerases I, II, and III and their therapeutic implications. J Biol Chem 2024; 300:105737. [PMID: 38336292 PMCID: PMC10907179 DOI: 10.1016/j.jbc.2024.105737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Transcription is a tightly regulated, complex, and essential cellular process in all living organisms. Transcription is comprised of three steps, transcription initiation, elongation, and termination. The distinct transcription initiation and termination mechanisms of eukaryotic RNA polymerases I, II, and III (Pols I, II, and III) have long been appreciated. Recent methodological advances have empowered high-resolution investigations of the Pols' transcription elongation mechanisms. Here, we review the kinetic similarities and differences in the individual steps of Pol I-, II-, and III-catalyzed transcription elongation, including NTP binding, bond formation, pyrophosphate release, and translocation. This review serves as an important summation of Saccharomyces cerevisiae (yeast) Pol I, II, and III kinetic investigations which reveal that transcription elongation by the Pols is governed by distinct mechanisms. Further, these studies illustrate how basic, biochemical investigations of the Pols can empower the development of chemotherapeutic compounds.
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Affiliation(s)
- Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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2
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Recoulat Angelini AA, Incicco JJ, Melian NA, González-Flecha FL. Susceptibility of Cu(I) transport ATPases to sodium dodecyl sulfate. Relevance of the composition of the micellar phase. Arch Biochem Biophys 2023; 745:109704. [PMID: 37527700 DOI: 10.1016/j.abb.2023.109704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/11/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
Sodium dodecyl sulfate (SDS) is a well-known protein denaturing agent. A less known property of this detergent is that it can activate or inactivate some enzymes at sub-denaturing concentrations. In this work we explore the effect of SDS on the ATPase activity of a hyper-thermophilic and a mesophilic Cu(I) ATPases reconstituted in mixed micelles of phospholipids and a non-denaturing detergent. An iterative procedure was used to evaluate the partition of SDS between the aqueous and the micellar phases, allowing to determine the composition of micelles prepared from phospholipid/detergent mixtures. The incubation of enzymes with SDS in the presence of different amounts of phospholipids reveals that higher SDS concentrations are required to obtain the same degree of inactivation when the initial concentration of phospholipids is increased. Remarkably, we found that, if represented as a function of the mole fraction of SDS in the micelle, the degree of inactivation obtained at different amounts of amphiphiles converges to a single inactivation curve. To interpret this result, we propose a simple model involving active and inactive enzyme molecules in equilibrium. This model allowed us to estimate the Gibbs free energy change for the inactivation process and its derivative with respect to the mole fraction of SDS in the micellar phase, the latter being a measure of the susceptibility of the enzyme to SDS. Our results showed that the inactivation free energy changes are similar for both proteins. Conversely, susceptibility to SDS is significantly lower for the hyperthermophilic ATPase, suggesting an inverse relation between thermophilicity and susceptibility to SDS.
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Affiliation(s)
- Alvaro A Recoulat Angelini
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - J Jeremías Incicco
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - Noelia A Melian
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - F Luis González-Flecha
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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3
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Gong GQ, Bilanges B, Allsop B, Masson GR, Roberton V, Askwith T, Oxenford S, Madsen RR, Conduit SE, Bellini D, Fitzek M, Collier M, Najam O, He Z, Wahab B, McLaughlin SH, Chan AWE, Feierberg I, Madin A, Morelli D, Bhamra A, Vinciauskaite V, Anderson KE, Surinova S, Pinotsis N, Lopez-Guadamillas E, Wilcox M, Hooper A, Patel C, Whitehead MA, Bunney TD, Stephens LR, Hawkins PT, Katan M, Yellon DM, Davidson SM, Smith DM, Phillips JB, Angell R, Williams RL, Vanhaesebroeck B. A small-molecule PI3Kα activator for cardioprotection and neuroregeneration. Nature 2023; 618:159-168. [PMID: 37225977 PMCID: PMC7614683 DOI: 10.1038/s41586-023-05972-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/17/2023] [Indexed: 05/26/2023]
Abstract
Harnessing the potential beneficial effects of kinase signalling through the generation of direct kinase activators remains an underexplored area of drug development1-5. This also applies to the PI3K signalling pathway, which has been extensively targeted by inhibitors for conditions with PI3K overactivation, such as cancer and immune dysregulation. Here we report the discovery of UCL-TRO-1938 (referred to as 1938 hereon), a small-molecule activator of the PI3Kα isoform, a crucial effector of growth factor signalling. 1938 allosterically activates PI3Kα through a distinct mechanism by enhancing multiple steps of the PI3Kα catalytic cycle and causes both local and global conformational changes in the PI3Kα structure. This compound is selective for PI3Kα over other PI3K isoforms and multiple protein and lipid kinases. It transiently activates PI3K signalling in all rodent and human cells tested, resulting in cellular responses such as proliferation and neurite outgrowth. In rodent models, acute treatment with 1938 provides cardioprotection from ischaemia-reperfusion injury and, after local administration, enhances nerve regeneration following nerve crush. This study identifies a chemical tool to directly probe the PI3Kα signalling pathway and a new approach to modulate PI3K activity, widening the therapeutic potential of targeting these enzymes through short-term activation for tissue protection and regeneration. Our findings illustrate the potential of activating kinases for therapeutic benefit, a currently largely untapped area of drug development.
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Affiliation(s)
- Grace Q Gong
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Benoit Bilanges
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Ben Allsop
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Glenn R Masson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Victoria Roberton
- UCL Centre for Nerve Engineering, UCL School of Pharmacy, University College London, London, UK
| | - Trevor Askwith
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Sally Oxenford
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Ralitsa R Madsen
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Sarah E Conduit
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Dom Bellini
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martina Fitzek
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | - Matt Collier
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | - Osman Najam
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Zhenhe He
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Ben Wahab
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff, UK
| | | | - A W Edith Chan
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | | | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Daniele Morelli
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Amandeep Bhamra
- Proteomics Research Translational Technology Platform, Cancer Institute, University College London, London, UK
| | - Vanesa Vinciauskaite
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | | | - Silvia Surinova
- Proteomics Research Translational Technology Platform, Cancer Institute, University College London, London, UK
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | | | - Matthew Wilcox
- UCL Centre for Nerve Engineering, UCL School of Pharmacy, University College London, London, UK
| | - Alice Hooper
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Chandni Patel
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Maria A Whitehead
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | | | | | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Derek M Yellon
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Sean M Davidson
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - David M Smith
- Emerging Innovations, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - James B Phillips
- UCL Centre for Nerve Engineering, UCL School of Pharmacy, University College London, London, UK
| | - Richard Angell
- Drug Discovery Group, Translational Research Office, University College London, London, UK
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff, UK
| | - Roger L Williams
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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Henderson IM, Zeng F, Bhuiyan NH, Luo D, Martinez M, Smoake J, Bi F, Perera C, Johnson D, Prisinzano TE, Wang W, Uhl GR. Structure-activity studies of PTPRD phosphatase inhibitors identify a 7-cyclopentymethoxy illudalic acid analog candidate for development. Biochem Pharmacol 2022; 195:114868. [PMID: 34863978 PMCID: PMC9248268 DOI: 10.1016/j.bcp.2021.114868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 12/30/2022]
Abstract
Interest in development of potent, selective inhibitors of the phosphatase from the receptor type protein tyrosine phosphatase PTPRD as antiaddiction agents is supported by human genetics, mouse models and studies of our lead compound PTPRD phosphatase inhibitor, 7-butoxy illudalic acid analog 1 (7-BIA). We now report structure-activity relationships for almost 70 7-BIA-related compounds and results that nominate a 7- cyclopentyl methoxy analog as a candidate for further development. While efforts to design 7-BIA analogs with substitutions for other parts failed to yield potent inhibitors of PTPRD's phosphatase, ten 7-position substituted analogs displayed greater potency at PTPRD than 7-BIA. Several were more selective for PTPRD vs the receptor type protein tyrosine phosphatases S, F and J or the nonreceptor type protein tyrosine phosphatase N1 (PTPRS, PTPRF, PTPRJ or PTPN1/PTP1B), phosphatases at which 7-BIA displays activity. In silico studies aided design of novel analogs. A 7-position cyclopentyl methoxy substituted 7-BIA analog termed NHB1109 displayed 600-700 nM potencies in inhibiting PTPRD and PTPRS, improved selectivity vs PTPRS, PTPRF, PTPRJ or PTPN1/PTP1B phosphatases, no substantial potency at other protein tyrosine phosphatases screened, no significant potency at any of the targets of clinically-useful drugs identified in EUROFINS screens and significant oral bioavailability. Oral doses up to 200 mg/kg were well tolerated by mice, though higher doses resulted in reduced weight and apparent ileus without clear organ histopathology. NHB1109 provides a good candidate to advance to in vivo studies in addiction paradigms and toward human use to reduce reward from addictive substances.
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Affiliation(s)
- Ian M Henderson
- Biomedical Research Institute of New Mexico, Albuquerque, NM, United States; New Mexico VA Healthcare System, Albuquerque, NM, United States
| | - Fanxun Zeng
- College of Pharmacy, University of Arizona, Tucson, AZ, United States
| | - Nazmul H Bhuiyan
- College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Dan Luo
- College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Maria Martinez
- Biomedical Research Institute of New Mexico, Albuquerque, NM, United States; New Mexico VA Healthcare System, Albuquerque, NM, United States
| | - Jane Smoake
- Biomedical Research Institute of New Mexico, Albuquerque, NM, United States; New Mexico VA Healthcare System, Albuquerque, NM, United States
| | - Fangchao Bi
- College of Pharmacy, University of Arizona, Tucson, AZ, United States
| | | | | | | | - Wei Wang
- College of Pharmacy, University of Arizona, Tucson, AZ, United States.
| | - George R Uhl
- Biomedical Research Institute of New Mexico, Albuquerque, NM, United States; New Mexico VA Healthcare System, Albuquerque, NM, United States; Departments of Neurology, Neuroscience and Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, United States; Departments of Neurology and Pharmacology, University of Maryland School of Medicine, Baltimore, MD, United States; VA Maryland Healthcare System, Baltimore, MD, United States.
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5
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Maniak H, Talma M, Giurg M. Inhibitory Potential of New Phenolic Hydrazide-Hydrazones with a Decoy Substrate Fragment towards Laccase from a Phytopathogenic Fungus: SAR and Molecular Docking Studies. Int J Mol Sci 2021; 22:ijms222212307. [PMID: 34830189 PMCID: PMC8617976 DOI: 10.3390/ijms222212307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 01/22/2023] Open
Abstract
Laccase from pathogenic fungi participates in both the delignification and neutralization of phytoantibiotics. Furthermore, it interferes with the hormone signaling in plants and catalyzes melanization. Infections of these pathogens contribute to loss in forestry, agriculture, and horticulture. As there is still a need to expand knowledge on efficient defense strategies against phytopathogenic fungi, the present study aimed to reveal more information on the molecular mechanisms of laccase inhibition with natural and natural-like carboxylic acid semi-synthetic derivatives. A set of hydrazide-hydrazones derived from carboxylic acids, generally including electron-rich arene units that serve as a decoy substrate, was synthesized and tested with laccase from Trametes versicolor. The classic synthesis of the title inhibitors proceeded with good to almost quantitative yield. Ninety percent of the tested molecules were active in the range of KI = 8–233 µM and showed different types of action. Such magnitude of inhibition constants qualified the hydrazide-hydrazones as strong laccase inhibitors. Molecular docking studies supporting the experimental data explained the selected derivatives’ interactions with the enzyme. The results are promising in developing new potential antifungal agents mitigating the damage scale in the plant cultivation, gardening, and horticulture sectors.
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Affiliation(s)
- Halina Maniak
- Department of Micro, Nano and Bioprocess Engineering, Faculty of Chemistry, Wroclaw University of Science and Technology, Norwida 4/6, 50-373 Wrocław, Poland
- Correspondence: (H.M.); (M.G.); Tel.: +48-713203314 (H.M.); +48-713203616 (M.G.)
| | - Michał Talma
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (H.M.); (M.G.); Tel.: +48-713203314 (H.M.); +48-713203616 (M.G.)
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6
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de Rosa M, Nonnis S, Aliverti A. Covalent inhibition of P. falciparum ferredoxin-NADP + reductase: Exploring alternative strategies for the development of new antimalarial drugs. Biochem Biophys Res Commun 2021; 577:89-94. [PMID: 34509083 DOI: 10.1016/j.bbrc.2021.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022]
Abstract
The protozoan Plasmodium falciparum is the main aetiological agent of tropical malaria. Characteristic of the phylum is the presence of a plastid-like organelle which hosts several homologs of plant proteins, including a ferredoxin (PfFd) and its NADPH-dependent reductase (PfFNR). The PfFNR/PfFd redox system is essential for the parasite, while mammals share no homologous proteins, making the enzyme an attractive target for novel and much needed antimalarial drugs. Based on previous findings, three chemically reactive residues important for PfFNR activity were identified: namely, the active-site Cys99, responsible for hydride transfer; Cys284, whose oxidation leads to an inactive dimeric form of the protein; and His286, which is involved in NADPH binding. These amino acid residues were probed by several residue-specific reagents and the two cysteines were shown to be promising targets for covalent inhibition. The quantitative and qualitative description of the reactivity of few compounds, including a repurposed drug, set the bases for the development of more potent and specific antimalarial leads.
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Affiliation(s)
- Matteo de Rosa
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy.
| | - Simona Nonnis
- DIMEVET - Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy; CRC "Innovation for Well-Beeing and Environment" (I-WE), Università degli Studi di Milano, Milano, Italy
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7
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Mai Z, Wang L, Zeng Q. Characterization of a novel isoflavone glycoside-hydrolyzing β-glucosidase from mangrove soil metagenomic library. Biochem Biophys Res Commun 2021; 569:61-65. [PMID: 34229124 DOI: 10.1016/j.bbrc.2021.06.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 11/21/2022]
Abstract
For the beneficial pharmacological properties of isoflavonoids and their related glycoconjugates, there is increasingly interest in their enzymatic conversion. In this study, a novel β-glucosidase gene isolated from metagenomic library of mangrove sediment was cloned and overexpressed in Escherichia coli BL21(DE3). The purified recombination β-glucosidase, designated as r-Bgl66, showed high catalytic activity for soy isoflavone glycosides. It converted soy isoflavone flour extract with the productivities of 0.87 mM/h for daidzein, 0.59 mM/h for genistein and 0.42 mM/h for glycitein. The kcat/Km values for daidzin, genistin and glycitin were 208.73, 222.37 and 288.07 mM-1 s-1, respectively. In addition, r-Bgl66 also exhibited the characteristic of glucose-tolerance, and the inhibition constant Ki was 471.4 mM. These properties make it a good candidate in the enzymatic hydrolysis of soy isoflavone glycosides. This study also highlights the utility of metagenomic approach in discovering novel β-glucosidase for soy isoflavone glycosides hydrolysis.
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Affiliation(s)
- Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qi Zeng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Giuliani V, Miller MA, Liu CY, Hartono SR, Class CA, Bristow CA, Suzuki E, Sanz LA, Gao G, Gay JP, Feng N, Rose JL, Tomihara H, Daniele JR, Peoples MD, Bardenhagen JP, Geck Do MK, Chang QE, Vangamudi B, Vellano C, Ying H, Deem AK, Do KA, Genovese G, Marszalek JR, Kovacs JJ, Kim M, Fleming JB, Guccione E, Viale A, Maitra A, Emilia Di Francesco M, Yap TA, Jones P, Draetta G, Carugo A, Chedin F, Heffernan TP. PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma. Nat Commun 2021; 12:4626. [PMID: 34330913 PMCID: PMC8324870 DOI: 10.1038/s41467-021-24798-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/05/2021] [Indexed: 12/11/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer that has remained clinically challenging to manage. Here we employ an RNAi-based in vivo functional genomics platform to determine epigenetic vulnerabilities across a panel of patient-derived PDAC models. Through this, we identify protein arginine methyltransferase 1 (PRMT1) as a critical dependency required for PDAC maintenance. Genetic and pharmacological studies validate the role of PRMT1 in maintaining PDAC growth. Mechanistically, using proteomic and transcriptomic analyses, we demonstrate that global inhibition of asymmetric arginine methylation impairs RNA metabolism, which includes RNA splicing, alternative polyadenylation, and transcription termination. This triggers a robust downregulation of multiple pathways involved in the DNA damage response, thereby promoting genomic instability and inhibiting tumor growth. Taken together, our data support PRMT1 as a compelling target in PDAC and informs a mechanism-based translational strategy for future therapeutic development.Statement of significancePDAC is a highly lethal cancer with limited therapeutic options. This study identified and characterized PRMT1-dependent regulation of RNA metabolism and coordination of key cellular processes required for PDAC tumor growth, defining a mechanism-based translational hypothesis for PRMT1 inhibitors.
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Affiliation(s)
- Virginia Giuliani
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Meredith A Miller
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chiu-Yi Liu
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Caleb A Class
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN, USA
| | | | - Erika Suzuki
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Guang Gao
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason P Gay
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ningping Feng
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Johnathon L Rose
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hideo Tomihara
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgery, Kindai University Nara Hospital, Nara, JP, USA
| | - Joseph R Daniele
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael D Peoples
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer P Bardenhagen
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mary K Geck Do
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qing E Chang
- ORBIT, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bhavatarini Vangamudi
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Exo Therapeutics, Cambridge, MA, USA
| | - Christopher Vellano
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haoqiang Ying
- Department of Cellular and Molecular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Angela K Deem
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph R Marszalek
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey J Kovacs
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason B Fleming
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Division of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Ernesto Guccione
- Department of Oncological Sciences and Pharmacological Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Emilia Di Francesco
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Philip Jones
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio Draetta
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessandro Carugo
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frederic Chedin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Timothy P Heffernan
- Traction, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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9
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Herbst S, Lewis PA. From structure to ætiology: a new window on the biology of leucine-rich repeat kinase 2 and Parkinson's disease. Biochem J 2021; 478:2945-2951. [PMID: 34328508 PMCID: PMC8331089 DOI: 10.1042/bcj20210383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 01/20/2023]
Abstract
Since the discovery of mutations in leucine-rich repeat kinase 2 (LRRK2) as an underlying genetic cause for the development of Parkinson's disease (PD) in 2004 (Neuron 44, 601-607; Neuron 44, 595-600), and subsequent efforts to develop LRRK2 kinase inhibitors as a therapy for Parkinson's (Expert Opin. Ther. Targets 21, 751-753), elucidating the atomic resolution structure of LRRK2 has been a major goal of research into this protein. At over 250 kDa, the large size and complicated domain organisation of LRRK2 has made this a highly challenging target for structural biologists, however, a number of recent studies using both in vitro and in situ approaches (Nature 588, 344-349; Cell 182, 1508-1518.e1516; Cell 184, 3519-3527.e3510) have provided important new insights into LRRK2 structure and the complexes formed by this protein.
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Affiliation(s)
- Susanne Herbst
- Department of Comparative Biomedical Science, Royal Veterinary College, Royal College Street, London, U.K
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, U.S.A
| | - Patrick A. Lewis
- Department of Comparative Biomedical Science, Royal Veterinary College, Royal College Street, London, U.K
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, U.S.A
- Correspondence: Patrick A. Lewis ()
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10
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Sousa AC, Martins LO, Robalo MP. Laccases: Versatile Biocatalysts for the Synthesis of Heterocyclic Cores. Molecules 2021; 26:3719. [PMID: 34207073 PMCID: PMC8234338 DOI: 10.3390/molecules26123719] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
Laccases are multicopper oxidases that have shown a great potential in various biotechnological and green chemistry processes mainly due to their high relative non-specific oxidation of phenols, arylamines and some inorganic metals, and their high redox potentials that can span from 500 to 800 mV vs. SHE. Other advantages of laccases include the use of readily available oxygen as a second substrate, the formation of water as a side-product and no requirement for cofactors. Importantly, addition of low-molecular-weight redox mediators that act as electron shuttles, promoting the oxidation of complex bulky substrates and/or of higher redox potential than the enzymes themselves, can further expand their substrate scope, in the so-called laccase-mediated systems (LMS). Laccase bioprocesses can be designed for efficiency at both acidic and basic conditions since it is known that fungal and bacterial laccases exhibit distinct optimal pH values for the similar phenolic and aromatic amines. This review covers studies on the synthesis of five- and six-membered ring heterocyclic cores, such as benzimidazoles, benzofurans, benzothiazoles, quinazoline and quinazolinone, phenazine, phenoxazine, phenoxazinone and phenothiazine derivatives. The enzymes used and the reaction protocols are briefly outlined, and the mechanistic pathways described.
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Affiliation(s)
- Ana Catarina Sousa
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal;
- Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - M. Paula Robalo
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal;
- Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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11
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Yin S, Liu L, Brobbey C, Palanisamy V, Ball LE, Olsen SK, Ostrowski MC, Gan W. PRMT5-mediated arginine methylation activates AKT kinase to govern tumorigenesis. Nat Commun 2021; 12:3444. [PMID: 34103528 PMCID: PMC8187744 DOI: 10.1038/s41467-021-23833-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 05/19/2021] [Indexed: 02/05/2023] Open
Abstract
AKT is involved in a number of key cellular processes including cell proliferation, apoptosis and metabolism. Hyperactivation of AKT is associated with many pathological conditions, particularly cancers. Emerging evidence indicates that arginine methylation is involved in modulating AKT signaling pathway. However, whether and how arginine methylation directly regulates AKT kinase activity remain unknown. Here we report that protein arginine methyltransferase 5 (PRMT5), but not other PRMTs, promotes AKT activation by catalyzing symmetric dimethylation of AKT1 at arginine 391 (R391). Mechanistically, AKT1-R391 methylation cooperates with phosphatidylinositol 3,4,5 trisphosphate (PIP3) to relieve the pleckstrin homology (PH)-in conformation, leading to AKT1 membrane translocation and subsequent activation by phosphoinositide-dependent kinase-1 (PDK1) and the mechanistic target of rapamycin complex 2 (mTORC2). As a result, deficiency in AKT1-R391 methylation significantly suppresses AKT1 kinase activity and tumorigenesis. Lastly, we show that PRMT5 inhibitor synergizes with AKT inhibitor or chemotherapeutic drugs to enhance cell death. Altogether, our study suggests that R391 methylation is an important step for AKT activation and its oncogenic function.
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Affiliation(s)
- Shasha Yin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Liu Liu
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Charles Brobbey
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Lauren E Ball
- Department of Cell and Molecular Pharmacology, and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Michael C Ostrowski
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
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12
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Janská P, Knejzlík Z, Perumal AS, Jurok R, Tokárová V, Nicolau DV, Štěpánek F, Kašpar O. Effect of physicochemical parameters on the stability and activity of garlic alliinase and its use for in-situ allicin synthesis. PLoS One 2021; 16:e0248878. [PMID: 33740023 PMCID: PMC7978267 DOI: 10.1371/journal.pone.0248878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/09/2021] [Indexed: 11/18/2022] Open
Abstract
Garlic is a well-known example of natural self-defence system consisting of an inactive substrate (alliin) and enzyme (alliinase) which, when combined, produce highly antimicrobial allicin. Increase of alliinase stability and its activity are of paramount importance in various applications relying on its use for in-situ synthesis of allicin or its analogues, e.g., pulmonary drug delivery, treatment of superficial injuries, or urease inhibitors in fertilizers. Here, we discuss the effect of temperature, pH, buffers, salts, and additives, i.e. antioxidants, chelating agents, reducing agents and cosolvents, on the stability and the activity of alliinase extracted from garlic. The effects of the storage temperature and relative humidity on the stability of lyophilized alliinase was demonstrated. A combination of the short half-life, high reactivity and non-specificity to particular proteins are reasons most bacteria cannot deal with allicin's mode of action and develop effective defence mechanism, which could be the key to sustainable drug design addressing serious problems with escalating emergence of multidrug-resistant (MDR) bacterial strains.
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Affiliation(s)
- Petra Janská
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Zdeněk Knejzlík
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Radek Jurok
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Viola Tokárová
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Dan V. Nicolau
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - František Štěpánek
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Ondřej Kašpar
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
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13
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Abstract
Pharmacological inhibition of vacuolar-type H+-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Although there are many V-ATPase structures reported, the molecular basis of specific inhibitors on V-ATPase remains unknown. Here, we report the cryo-EM structure of bafilomycin A1 bound intact bovine V-ATPase at an overall resolution of 3.6-Å. The structure reveals six bafilomycin A1 molecules bound to the c-ring. One bafilomycin A1 molecule engages with two c subunits and disrupts the interactions between the c-ring and subunit a, thereby preventing proton translocation. Structural and sequence analyses demonstrate that the bafilomycin A1-binding residues are conserved in yeast and mammalian species and the 7'-hydroxyl group of bafilomycin A1 acts as a unique feature recognized by subunit c.
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Affiliation(s)
- Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jin Wang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abdirahman Hassan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiao-Song Xie
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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14
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Langella E, Buonanno M, De Simone G, Monti SM. Intrinsically disordered features of carbonic anhydrase IX proteoglycan-like domain. Cell Mol Life Sci 2021; 78:2059-2067. [PMID: 33201250 PMCID: PMC11072538 DOI: 10.1007/s00018-020-03697-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/26/2020] [Accepted: 10/31/2020] [Indexed: 12/25/2022]
Abstract
hCA IX is a multi-domain protein belonging to the family of hCAs which are ubiquitous zinc enzymes that catalyze the reversible hydration of CO2 to HCO3- and H+. hCA IX is a tumor-associated enzyme with a limited distribution in normal tissues, but over-expressed in many tumors, and is a promising drug target. Although many studies concerning the CA IX catalytic domain were performed, little is known about the proteoglycan-like (PG-like) domain of hCA IX which has been poorly investigated so far. Here we attempt to fill this gap by providing an overview on the functional, structural and therapeutic studies of the PG-like domain of hCA IX which represents a unique feature within the CA family. The main studies and recent advances concerning PG role in modulating hCA IX catalytic activity as well as in tumor spreading and migration are here reported. Special attention has been paid to the newly discovered disordered features of the PG domain which open new perspectives about its molecular mechanisms of action under physiological and pathological conditions, since disorder is likely involved in mediating interactions with partner proteins. The emerged disordered features of PG domain will be explored for putative diagnostic and therapeutic applications involving CA IX targeting in tumors.
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Affiliation(s)
- Emma Langella
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy.
| | - Martina Buonanno
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Giuseppina De Simone
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Simona Maria Monti
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy.
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15
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Saikia K, Rathankumar AK, Vaithyanathan VK, Cabana H, Vaidyanathan VK. Preparation of highly diffusible porous cross-linked lipase B from Candida antarctica conjugates: Advances in mass transfer and application in transesterification of 5-Hydroxymethylfurfural. Int J Biol Macromol 2020; 170:583-592. [PMID: 33385453 DOI: 10.1016/j.ijbiomac.2020.12.178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022]
Abstract
The present work pronounces the three phase partitioning (TPP)-facilitated preparation of porous cross-linked Candida antarctica lipase B (CaLB) aggregates (pCLEAs) for 5-Hydroxymethylfurfural (HMF) esters synthesis. CLEAs and pCLEAs of CaLB were prepared with eupergit as the support under the optimized conditions of pH 8.0, eupergit/protein ratio of 3.0:1.0, 50 mM cross-linker concentration and 3.3 mg/mL BSA concentration in 4 h. The optimum starch concentration for pCLEAs was 0.20%, m/v. The maximum biocatalytic load was 650 U/g (CLEAs) and 721 U/g (pCLEAs), and the immobilized biocatalysts were stable over a pH range of 6.0-9.0 and temperature range of (40-60)°C. The BET surface area of CLEAs and pCLEAs were 21.3 and 29.1 m2/g, respectively, and the catalytic efficiency of pCLEAs was 2.2-fold higher than that of CLEAs. Subsequently, the pCLEAs of CaLB were utilized for the manufacturing of industrially significant HMF esters. Under the optimized transesterification conditions, HMF conversion with pCLEAs CaLB was 1.41- and 1.25-fold higher than with free and CLEAs CaLB, respectively. The pCLEAs were reused upto 8 consecutive transesterification cycles and the produced HMF esters reduced the surface tension of water from 72 mN/m to 32.6 mN/m, proving its potential application as surface-active compounds.
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Affiliation(s)
- Kongkona Saikia
- Integrated Bioprocessing Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Tamil Nadu 603 203, India; Laboratoire de génie de l'environnement, Faculté de génie, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Abiram Karanam Rathankumar
- Integrated Bioprocessing Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Tamil Nadu 603 203, India; Laboratoire de génie de l'environnement, Faculté de génie, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Vasanth Kumar Vaithyanathan
- Laboratoire de génie de l'environnement, Faculté de génie, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Hubert Cabana
- Laboratoire de génie de l'environnement, Faculté de génie, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Vinoth Kumar Vaidyanathan
- Integrated Bioprocessing Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Tamil Nadu 603 203, India; Laboratoire de génie de l'environnement, Faculté de génie, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada.
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16
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Deniston CK, Salogiannis J, Mathea S, Snead DM, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Böhning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL, Leschziner AE. Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. Nature 2020; 588:344-349. [PMID: 32814344 PMCID: PMC7726071 DOI: 10.1038/s41586-020-2673-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease1 and is also linked to its idiopathic form2. LRRK2 has been proposed to function in membrane trafficking3 and colocalizes with microtubules4. Despite the fundamental importance of LRRK2 for understanding and treating Parkinson's disease, structural information on the enzyme is limited. Here we report the structure of the catalytic half of LRRK2, and an atomic model of microtubule-associated LRRK2 built using a reported cryo-electron tomography in situ structure5. We propose that the conformation of the LRRK2 kinase domain regulates its interactions with microtubules, with a closed conformation favouring oligomerization on microtubules. We show that the catalytic half of LRRK2 is sufficient for filament formation and blocks the motility of the microtubule-based motors kinesin 1 and cytoplasmic dynein 1 in vitro. Kinase inhibitors that stabilize an open conformation relieve this interference and reduce the formation of LRRK2 filaments in cells, whereas inhibitors that stabilize a closed conformation do not. Our findings suggest that LRRK2 can act as a roadblock for microtubule-based motors and have implications for the design of therapeutic LRRK2 kinase inhibitors.
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Affiliation(s)
- C K Deniston
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - J Salogiannis
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - S Mathea
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - D M Snead
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - I Lahiri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, India
| | - M Matyszewski
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - O Donosa
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - R Watanabe
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - J Böhning
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- Sir William Dunn School of Pathology, Oxford University, Oxford, UK
| | - A K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S Knapp
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - E Villa
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA.
| | - A E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA.
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17
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Arroyo M, Cañuelo A, Calahorra J, Hastert F, Sánchez A, Clarke DJ, Marchal J. Mitotic entry upon Topo II catalytic inhibition is controlled by Chk1 and Plk1. FEBS J 2020; 287:4933-4951. [PMID: 32144855 PMCID: PMC7483426 DOI: 10.1111/febs.15280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/11/2022]
Abstract
Catalytic inhibition of topoisomerase II during G2 phase delays onset of mitosis due to the activation of the so-called decatenation checkpoint. This checkpoint is less known compared with the extensively studied G2 DNA damage checkpoint and is partially compromised in many tumor cells. We recently identified MCPH1 as a key regulator that confers cells with the capacity to adapt to the decatenation checkpoint. In the present work, we have explored the contributions of checkpoint kinase 1 (Chk1) and polo-like kinase 1 (Plk1), in order to better understand the molecular basis of decatenation checkpoint. Our results demonstrate that Chk1 function is required to sustain the G2 arrest induced by catalytic inhibition of Topo II. Interestingly, Chk1 loss of function restores adaptation in cells lacking MCPH1. Furthermore, we demonstrate that Plk1 function is required to bypass the decatenation checkpoint arrest in cells following Chk1 inhibition. Taken together, our data suggest that MCPH1 is critical to allow checkpoint adaptation by counteracting Chk1-mediated inactivation of Plk1. Importantly, we also provide evidence that MCPH1 function is not required to allow recovery from this checkpoint, which lends support to the notion that checkpoint adaptation and recovery are different mechanisms distinguished in part by specific effectors.
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Affiliation(s)
- M. Arroyo
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - A. Cañuelo
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - J. Calahorra
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - F.D. Hastert
- Department of Biology, Technische Universität Darmstadt, Germany
| | - A. Sánchez
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - D. J. Clarke
- Department of Genetics, Cell Biology and Development, University of Minnesota, US
| | - J.A. Marchal
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
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18
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Gavara L, Verdirosa F, Legru A, Mercuri PS, Nauton L, Sevaille L, Feller G, Berthomieu D, Sannio F, Marcoccia F, Tanfoni S, De Luca F, Gresh N, Galleni M, Docquier JD, Hernandez JF. 4-( N-Alkyl- and -Acyl-amino)-1,2,4-triazole-3-thione Analogs as Metallo-β-Lactamase Inhibitors: Impact of 4-Linker on Potency and Spectrum of Inhibition. Biomolecules 2020; 10:E1094. [PMID: 32717907 PMCID: PMC7465886 DOI: 10.3390/biom10081094] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 11/17/2022] Open
Abstract
To fight the increasingly worrying bacterial resistance to antibiotics, the discovery and development of new therapeutics is urgently needed. Here, we report on a new series of 1,2,4-triazole-3-thione compounds as inhibitors of metallo-β-lactamases (MBLs), which represent major resistance determinants to β-lactams, and especially carbapenems, in Gram-negative bacteria. These molecules are stable analogs of 4-amino-1,2,4-triazole-derived Schiff bases, where the hydrazone-like bond has been reduced (hydrazine series) or the 4-amino group has been acylated (hydrazide series); the synthesis and physicochemical properties thereof are described. The inhibitory potency was determined on the most clinically relevant acquired MBLs (IMP-, VIM-, and NDM-types subclass B1 MBLs). When compared with the previously reported hydrazone series, hydrazine but not hydrazide analogs showed similarly potent inhibitory activity on VIM-type enzymes, especially VIM-2 and VIM-4, with Ki values in the micromolar to submicromolar range. One of these showed broad-spectrum inhibition as it also significantly inhibited VIM-1 and NDM-1. Restoration of β-lactam activity in microbiological assays was observed for one selected compound. Finally, the binding to the VIM-2 active site was evaluated by isothermal titration calorimetry and a modeling study explored the effect of the linker structure on the mode of binding with this MBL.
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Affiliation(s)
- Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
| | - Federica Verdirosa
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Alice Legru
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
| | - Paola Sandra Mercuri
- Laboratoire des Macromolécules Biologiques, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, Institute of Chemistry B6 a, Sart-Tilman, 4000 Liège, Belgium; (P.S.M.); (M.G.)
| | - Lionel Nauton
- Institut de Chimie de Clermont-Ferrand, Université Clermont-Auvergne, CNRS, SIGMA Clermont, 63000 Clermont-Ferrand, France;
| | - Laurent Sevaille
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
| | - Georges Feller
- Laboratoire de Biochimie, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, B6, Sart-Tilman, 4000 Liège, Belgium;
| | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR5253, CNRS, Université de Montpellier, ENSCM, Cedex 5, 34296 Montpellier, France;
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Francesca Marcoccia
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Silvia Tanfoni
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Filomena De Luca
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616, Sorbonne Université, CNRS, 75252 Paris, France;
| | - Moreno Galleni
- Laboratoire des Macromolécules Biologiques, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, Institute of Chemistry B6 a, Sart-Tilman, 4000 Liège, Belgium; (P.S.M.); (M.G.)
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy; (F.V.); (F.S.); (F.M.); (S.T.); (F.D.L.)
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 34093 Montpellier, France; (A.L.); (L.S.)
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19
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Wang Y, Wang R, Tang DD. Ste20-like Kinase-mediated Control of Actin Polymerization Is a New Mechanism for Thin Filament-associated Regulation of Airway Smooth Muscle Contraction. Am J Respir Cell Mol Biol 2020; 62:645-656. [PMID: 31913659 PMCID: PMC7193783 DOI: 10.1165/rcmb.2019-0310oc] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/07/2020] [Indexed: 12/26/2022] Open
Abstract
It has been reported that actin polymerization is regulated by protein tyrosine phosphorylation in smooth muscle on contractile stimulation. The role of protein serine/threonine phosphorylation in modulating actin dynamics is underinvestigated. SLK (Ste20-like kinase) is a serine/threonine protein kinase that plays a role in apoptosis, cell cycle, proliferation, and migration. The function of SLK in smooth muscle is mostly unknown. Here, SLK knockdown (KD) inhibited acetylcholine (ACh)-induced actin polymerization and contraction without affecting myosin light chain phosphorylation at Ser-19 in human airway smooth muscle. Stimulation with ACh induced paxillin phosphorylation at Ser-272, which was reduced in SLK KD cells. However, SLK did not catalyze paxillin Ser-272 phosphorylation in vitro. But, SLK KD attenuated Plk1 (polo-like kinase 1) phosphorylation at Thr-210. Plk1 mediated paxillin phosphorylation at Ser-272 in vitro. Expression of the nonphosphorylatable paxillin mutant S272A (substitution of alanine at Ser-272) attenuated the agonist-enhanced F-actin/G-actin ratios without affecting myosin light chain phosphorylation. Because N-WASP (neuronal Wiskott-Aldrich Syndrome Protein) phosphorylation at Tyr-256 (an indication of its activation) promotes actin polymerization, we also assessed the role of paxillin phosphorylation in N-WASP activation. S272A paxillin inhibited the ACh-enhanced N-WASP phosphorylation at Tyr-256. Together, these results suggest that SLK regulates paxillin phosphorylation at Ser-272 via Plk1, which modulates N-WASP activation and actin polymerization in smooth muscle. SLK-mediated actin cytoskeletal reorganization may facilitate force transmission between the contractile units and the extracellular matrix.
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Affiliation(s)
- Yinna Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Ruping Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Dale D Tang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
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20
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Yang J, Bak G, Burgin T, Barnes WJ, Mayes HB, Peña MJ, Urbanowicz BR, Nielsen E. Biochemical and Genetic Analysis Identify CSLD3 as a beta-1,4-Glucan Synthase That Functions during Plant Cell Wall Synthesis. Plant Cell 2020; 32:1749-1767. [PMID: 32169960 PMCID: PMC7203914 DOI: 10.1105/tpc.19.00637] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/11/2020] [Accepted: 03/10/2020] [Indexed: 05/24/2023]
Abstract
In plants, changes in cell size and shape during development fundamentally depend on the ability to synthesize and modify cell wall polysaccharides. The main classes of cell wall polysaccharides produced by terrestrial plants are cellulose, hemicelluloses, and pectins. Members of the cellulose synthase (CESA) and cellulose synthase-like (CSL) families encode glycosyltransferases that synthesize the β-1,4-linked glycan backbones of cellulose and most hemicellulosic polysaccharides that comprise plant cell walls. Cellulose microfibrils are the major load-bearing component in plant cell walls and are assembled from individual β-1,4-glucan polymers synthesized by CESA proteins that are organized into multimeric complexes called CESA complexes, in the plant plasma membrane. During distinct modes of polarized cell wall deposition, such as in the tip growth that occurs during the formation of root hairs and pollen tubes or de novo formation of cell plates during plant cytokinesis, newly synthesized cell wall polysaccharides are deposited in a restricted region of the cell. These processes require the activity of members of the CESA-like D subfamily. However, while these CSLD polysaccharide synthases are essential, the nature of the polysaccharides they synthesize has remained elusive. Here, we use a combination of genetic rescue experiments with CSLD-CESA chimeric proteins, in vitro biochemical reconstitution, and supporting computational modeling and simulation, to demonstrate that Arabidopsis (Arabidopsis thaliana) CSLD3 is a UDP-glucose-dependent β-1,4-glucan synthase that forms protein complexes displaying similar ultrastructural features to those formed by CESA6.
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Affiliation(s)
- Jiyuan Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Gwangbae Bak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Tucker Burgin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109
| | - William J Barnes
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Heather B Mayes
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109
| | - Maria J Peña
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Erik Nielsen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
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21
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Sousa BC, Ahmed T, Dann WL, Ashman J, Guy A, Durand T, Pitt AR, Spickett CM. Short-chain lipid peroxidation products form covalent adducts with pyruvate kinase and inhibit its activity in vitro and in breast cancer cells. Free Radic Biol Med 2019; 144:223-233. [PMID: 31173844 DOI: 10.1016/j.freeradbiomed.2019.05.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/10/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
Pyruvate kinase catalyses the last step in glycolysis and has been suggested to contribute to the regulation of aerobic glycolysis in cancer cells. It can be inhibited by oxidation of cysteine residues in vitro and in vivo, which is relevant to the more pro-oxidant state in cancer and proliferating tissues. These conditions also favour lipid peroxidation and the formation of electrophilic fragmentation products, including short-chain aldehydes that can covalently modify proteins. However, as yet few studies have investigated their interactions with pyruvate kinase, so we investigated the effects of three different aldehydes, acrolein, malondialdehyde and 4-hydroxy-2(E)-hexenal (HHE), on the structure and activity of the enzyme. Analysis by LC-MS/MS showed unique modification profiles for each aldehyde, but Cys152, Cys423 and Cys474 were the residues most susceptible to electrophilic modification. Analysis of enzymatic activity under these conditions showed that acrolein was the strongest inhibitor, and at incubation times longer than 2 h, pathophysiological concentrations induced significant effects. Treatment of MCF-7 cells with the aldehydes caused similar losses of pyruvate kinase activity to those observed in vitro, and at lower concentrations than those required to cause cell death, with time and dose-dependent effects; acrolein adducts on Cys152 and Cys358 were detected. Cys358 and Cys474 are located at or near the allosteric or active sites, and formation of adducts on these residues probably contributes to loss of activity at low treatment concentrations. This study provides the first detailed analysis of the structure-activity relationship of C3 and C6 aldehydes with pyruvate kinase, and suggests that reactive short-chain aldehydes generated in diseases with an oxidative aetiology or from environmental exposure such as smoking could be involved in the metabolic alterations observed in cancer cells, through alteration of pyruvate kinase activity.
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Affiliation(s)
- Bebiana C Sousa
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Tanzim Ahmed
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - William L Dann
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Jed Ashman
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Alexandre Guy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK.
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22
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Shahid F, Javed U, Aman A, Ul Qader SA. REPORT- Role of metal ions on the catalytic efficiency of dextran hydrolyzing biocatalyst. Pak J Pharm Sci 2019; 32:2761-2764. [PMID: 31969313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hydrothermal spring isolate Bacillus megaterium KIBGE-IB31was utilized to produce dextranase. Enzyme was partially purified up to 11.8 fold after dialysis. Different metals ions were tested to explore their behavior with dextranase. It was noticed that cobalt (Co+2), copper (Cu+2), magnesium (Mg+2), manganese (Mn+2), nickle (Ni+2) and zinc (Zn+2) act as activator whilst potassium (K+), sodium (Na+), barium (Ba+), calcium (Ca+), mercury (Hg+), vanadium (V+2), aluminum (Al+3) and ferric (Fe+3) ions display inhibitory action.
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Affiliation(s)
- Faiza Shahid
- Department of Biochemistry, University of Karachi, Karachi, Pakistan
| | - Urooj Javed
- Department of Biochemistry, University of Karachi, Karachi, Pakistan
| | - Afsheen Aman
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan
| | - Shah Ali Ul Qader
- Department of Biochemistry, University of Karachi, Karachi, Pakistan
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23
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Mayer M, Fey K, Heinze E, Wick CR, Abboud MI, Yeh TL, Tumber A, Orth N, Schley G, Buchholz B, Clark T, Schofield CJ, Willam C, Burzlaff N. A Fluorescent Benzo[g]isoquinoline-Based HIF Prolyl Hydroxylase Inhibitor for Cellular Imaging. ChemMedChem 2019; 14:94-99. [PMID: 30380199 DOI: 10.1002/cmdc.201800483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/08/2018] [Indexed: 12/19/2022]
Abstract
Prolyl hydroxylation domain (PHD) enzymes catalyze the hydroxylation of the transcription factor hypoxia-inducible factor (HIF) and serve as cellular oxygen sensors. HIF and the PHD enzymes regulate numerous potentially tissue-protective target genes which can adapt cells to metabolic and ischemic stress. We describe a fluorescent PHD inhibitor (1-chloro-4-hydroxybenzo[g]isoquinoline-3-carbonyl)glycine which is suited to fluorescence-based detection assays and for monitoring PHD inhibitors in biological systems. In cell-based assays, application of the fluorescent PHD inhibitor allowed co-localization with a cellular PHD enzyme and led to live cell imaging of processes involved in cellular oxygen sensing.
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Affiliation(s)
- Marleen Mayer
- Department of Chemistry and Pharmacy, Inorganic and Organometallic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058, Erlangen, Germany
| | - Kerstin Fey
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054, Erlangen, Germany
| | - Eva Heinze
- Department of Chemistry and Pharmacy, Inorganic and Organometallic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058, Erlangen, Germany
| | - Christian R Wick
- Department of Chemistry and Pharmacy, Computer Chemistry Center (CCC), Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany
- Institute for Theoretical Physics I, PULS Group, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 49b, 91052, Erlangen, Germany
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tzu-Lan Yeh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Nicole Orth
- Department of Chemistry and Pharmacy, Inorganic and Organometallic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058, Erlangen, Germany
| | - Gunnar Schley
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054, Erlangen, Germany
| | - Björn Buchholz
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054, Erlangen, Germany
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer Chemistry Center (CCC), Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Carsten Willam
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054, Erlangen, Germany
| | - Nicolai Burzlaff
- Department of Chemistry and Pharmacy, Inorganic and Organometallic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058, Erlangen, Germany
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24
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Stefanucci A, Angeli A, Dimmito MP, Luisi G, Del Prete S, Capasso C, Donald WA, Mollica A, Supuran CT. Activation of β- and γ-carbonic anhydrases from pathogenic bacteria with tripeptides. J Enzyme Inhib Med Chem 2018; 33:945-950. [PMID: 29747543 PMCID: PMC6009936 DOI: 10.1080/14756366.2018.1468530] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Six tripeptides incorporating acidic amino acid residues were prepared for investigation as activators of β- and γ-carbonic anhydrases (CAs, EC 4.2.1.1) from the pathogenic bacteria Vibrio cholerae, Mycobacterium tuberculosis, and Burkholderia pseudomallei. The primary amino acid residues that are involved in the catalytic mechanisms of these CA classes are poorly understood, although glutamic acid residues near the active site appear to be involved. The tripeptides that contain Glu or Asp residues can effectively activate VchCAβ and VchCAγ (enzymes from V. cholerae), Rv3273 CA (mtCA3, a β-CA from M. tuberculosis) and BpsCAγ (γ-CA from B. pseudomallei) at 0.21-18.1 µM levels. The position of the acidic residues in the peptide sequences can significantly affect bioactivity. For three of the enzymes, tripeptides were identified that are more effective activators than both l-Glu and l-Asp. The tripeptides are also relatively selective because they do not activate prototypical α-CAs (human carbonic anhydrases I and II). Because the role of CA activators in the pathogenicity and life cycles of these infectious bacteria are poorly understood, this study provides new molecular probes to explore such processes.
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Affiliation(s)
- Azzurra Stefanucci
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Andrea Angeli
- Department of Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche, Sesto Fiorentino, Florence, Italy
| | - Marilisa Pia Dimmito
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Grazia Luisi
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Sonia Del Prete
- Department of Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche, Sesto Fiorentino, Florence, Italy
- Istituto di Bioscienze e Biorisorse, CNR, Napoli, Italy
| | | | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Adriano Mollica
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Claudiu T. Supuran
- Department of Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche, Sesto Fiorentino, Florence, Italy
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
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25
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Solé M, Rivera-Ingraham G, Freitas R. The use of carboxylesterases as biomarkers of pesticide exposure in bivalves: A methodological approach. Comp Biochem Physiol C Toxicol Pharmacol 2018; 212:18-24. [PMID: 29902568 DOI: 10.1016/j.cbpc.2018.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/18/2018] [Accepted: 06/03/2018] [Indexed: 12/13/2022]
Abstract
Bivalves are worldwide sentinels of anthropogenic pollution. The inclusion of biomarker responses in chemical monitoring is a recommended practise that has to overcome some difficulties. One of them is the time frame between sample collection and sample processing in order to ensure the preservation of enzymatic activities. In the present study, three bivalve species of commercial interest (mussel, Mytilus galloprovincialis, razor shell, Solen marginatus, and cockle, Cerastoderma edule) were processed within <2 h after being retrieved from their natural habitat, and 24 h after being transported in air under cold conditions (6-8 °C) to laboratory facilities. The enzymatic activities were compared in the three species submitted to both conditions revealing no differences in terms of carboxylesterase dependent activities (CEs) using different substrates: p-nitrophenyl acetate (pNPA), p-nitrophenyl butyrate (pNPB), 1-naphthyl acetate (1-NA), 1-naphthyl butyrate (1-NB) and 2-naphthyl acetate (2-NA). In mussels, three tissues were selected (haemolymph, gills and digestive gland). For comparative purposes, in razor shell and cockle only digestive gland was considered as it is the main metabolic organ. Baseline enzymatic activities for CEs were characterised in the digestive gland of the three bivalves using four out of the five selected CE substrates as well as the kinetic parameters (Vmax and Km) and catalytic efficiency. The in vitro sensitivity to the organophosphorus metabolite chlorpyrifos oxon was also calculated. IC50 values (pM-nM range) were lower than those obtained for vertebrate groups which suggest that bivalves have high protection efficiency against this pesticide as well as species dependent particularities.
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Affiliation(s)
- Montserrat Solé
- Institute of Marine Sciences (ICM-CSIC), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | | | - Rosa Freitas
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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26
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Alfieri C, Chang L, Barford D. Mechanism for remodelling of the cell cycle checkpoint protein MAD2 by the ATPase TRIP13. Nature 2018; 559:274-278. [PMID: 29973720 PMCID: PMC6057611 DOI: 10.1038/s41586-018-0281-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/16/2018] [Indexed: 11/09/2022]
Abstract
The maintenance of genome stability during mitosis is coordinated by the spindle assembly checkpoint (SAC) through its effector the mitotic checkpoint complex (MCC), an inhibitor of the anaphase-promoting complex (APC/C, also known as the cyclosome)1,2. Unattached kinetochores control MCC assembly by catalysing a change in the topology of the β-sheet of MAD2 (an MCC subunit), thereby generating the active closed MAD2 (C-MAD2) conformer3-5. Disassembly of free MCC, which is required for SAC inactivation and chromosome segregation, is an ATP-dependent process driven by the AAA+ ATPase TRIP13. In combination with p31comet, an SAC antagonist6, TRIP13 remodels C-MAD2 into inactive open MAD2 (O-MAD2)7-10. Here, we present a mechanism that explains how TRIP13-p31comet disassembles the MCC. Cryo-electron microscopy structures of the TRIP13-p31comet-C-MAD2-CDC20 complex reveal that p31comet recruits C-MAD2 to a defined site on the TRIP13 hexameric ring, positioning the N terminus of C-MAD2 (MAD2NT) to insert into the axial pore of TRIP13 and distorting the TRIP13 ring to initiate remodelling. Molecular modelling suggests that by gripping MAD2NT within its axial pore, TRIP13 couples sequential ATP-driven translocation of its hexameric ring along MAD2NT to push upwards on, and simultaneously rotate, the globular domains of the p31comet-C-MAD2 complex. This unwinds a region of the αA helix of C-MAD2 that is required to stabilize the C-MAD2 β-sheet, thus destabilizing C-MAD2 in favour of O-MAD2 and dissociating MAD2 from p31comet. Our study provides insights into how specific substrates are recruited to AAA+ ATPases through adaptor proteins and suggests a model of how translocation through the axial pore of AAA+ ATPases is coupled to protein remodelling.
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Affiliation(s)
| | - Leifu Chang
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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27
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Joanitti GA, Sawant RS, Torchilin VP, Freitas SMD, Azevedo RB. Optimizing liposomes for delivery of Bowman-Birk protease inhibitors - Platforms for multiple biomedical applications. Colloids Surf B Biointerfaces 2018; 167:474-482. [PMID: 29723819 DOI: 10.1016/j.colsurfb.2018.04.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 04/02/2018] [Accepted: 04/16/2018] [Indexed: 11/19/2022]
Abstract
One of the major challenges in the administration of therapeutic proteins involves delivery limitations. Liposomes are well-known drug delivery systems (DDS) that have been used to overcome this drawback; nevertheless, low protein entrapment efficiency (EE) still limits their wide biomedical application on a commercial scale. In the present work, different methods for protein entrapment into liposomes were tested in order to obtain tailored DDS platforms for multiple biomedical applications. The protein used as model was the Black-eyed pea Trypsin and Chymotrypsin Inhibitor (BTCI), a member of the Bowman-Birk protease inhibitor family (BBIs), which has been largely explored for its potential application in many biomedical therapies. We optimized reverse-phase evaporation (REV) and freeze/thaw (F/T) entrapment methods, using a cationic lipid matrix to entrap expressive amounts of BTCI (∼100 μM) in stable liposomes without affecting its protease inhibition activity. The influence of various parameters (e.g. entrapment method, liposome composition, buffer type) on particle size, charge, polydispersity, and EE of liposomes was investigated to provide an insight on how to control such parameters in view of obtaining a high entrapment yield. In addition, BTCI liposome platforms obtained herein showed to be versatile vesicles, allowing surface modification with moieties/polymers of interest (e.g. PEG, transferrin). The aforementioned results are relevant to focusing on the entrapment of other promising BBIs or protein agents sharing similar structural features. These findings encourage future studies to investigate the advantages of using the liposome platforms presented herein to broaden the use of this type of DDS for BBI biomedical applications.
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Affiliation(s)
- Graziella Anselmo Joanitti
- Laboratory of Nanobiotecnology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil; Universidade de Brasília (UnB), Campus Ceilândia (FCE) Centro Metropolitano, Conjunto A - Lote 01, Brasília, DF, 72220-900, Brazil.
| | - Rupa S Sawant
- Center for Pharmaceutical Biotechnology and Nanomedicine, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA; Vertex Pharmaceuticals, Boston, MA 02210, USA.
| | - Vladimir P Torchilin
- Center for Pharmaceutical Biotechnology and Nanomedicine, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.
| | - Sonia Maria de Freitas
- Laboratory of Biophysics, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil.
| | - Ricardo Bentes Azevedo
- Laboratory of Nanobiotecnology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil.
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Xiong W, Ye T, Yao X, Liu X, Ma S, Chen X, Chen ML, Feng YQ, Wu Y. The dioxygenase GIM2 functions in seed germination by altering gibberellin production in Arabidopsis. J Integr Plant Biol 2018; 60:276-291. [PMID: 29205921 DOI: 10.1111/jipb.12619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023]
Abstract
The phytohormones gibberellic acid (GA) and abscisic acid (ABA) antagonistically control seed germination. High levels of GA favor seed germination, whereas high levels of ABA hinder this process. The direct relationship between GA biosynthesis and seed germination ability need further investigation. Here, we identified the ABA-insensitive gain-of-function mutant germination insensitive to ABA mutant 2 (gim2) by screening a population of XVE T-DNA-tagged mutant lines. Based on two loss-of-function gim2-ko mutant lines, the disruption of GIM2 function caused a delay in seed germination. By contrast, upregulation of GIM2 accelerated seed germination, as observed in transgenic lines overexpressing GIM2 (OE). We detected a reduction in endogenous bioactive GA levels and an increase in endogenous ABA levels in the gim2-ko mutants compared to wild type. Conversely, the OE lines had increased endogenous bioactive GA levels and decreased endogenous ABA levels. The expression levels of a set of GA- and/or ABA-related genes were altered in both the gim2-ko mutants and the OE lines. We confirmed that GIM2 has dioxygenase activity using an in vitro enzyme assay, observing that GIM2 can oxidize GA12 . Hence, our characterization of GIM2 demonstrates that it plays a role in seed germination by affecting the GA metabolic pathway in Arabidopsis.
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Affiliation(s)
- Wei Xiong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tiantian Ye
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Xuan Yao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiong Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Sheng Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ming-Luan Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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de Souza PR, de Souza KS, de Assis CRD, de Araújo MC, Silva KCC, de Fátima Xavier da Silva J, Ferreira ACM, da Silva VL, Adam ML, de Carvalho LB, de Souza Bezerra R. Acetylcholinesterase of mangrove oyster Crassostrea rhizophorae: A highly thermostable enzyme with promising features for estuarine biomonitoring. Aquat Toxicol 2018; 197:109-121. [PMID: 29462762 DOI: 10.1016/j.aquatox.2018.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/09/2018] [Indexed: 06/08/2023]
Abstract
Enzyme biomarkers from several aquatic organisms have been used for assessing the exposure to contaminants at sublethal levels. Amongst them, the cholinesterases are commonly extracted from several organisms to evaluate/measure organophosphate and carbamate neurotoxic effects. Acetylcholinesterase (AChE; EC 3.1.1.7) is an enzyme of the group of serine esterases that acts on the hydrolysis of the neurotransmitter acetylcholine allowing the intermittence of the nerve impulses responsible for the neuronal communication. This enzyme is the main target for the action of some pesticides and the inhibition of its activity in bivalve mollusks may be used as biomarker due to their filter-feeding habit. In this context, the present study aimed to characterize physicochemical and kinetic parameters of the AChE extracted from gills and viscera of the oyster Crassostrea rhizophorae and investigate the in vitro effect of pesticides (dichlorvos, diazinon, chlorpyrifos, methyl-parathion, temephos, carbaryl, carbofuran, aldicarb, diflubenzuron and novaluron) in search for assessing its potential as biomarker. Specific substrates and inhibitors evidenced the predominance of AChE in both tissues. The optimum pH found for gills and viscera AChE were 8.0 and 8.5, respectively. The maximum peak of activity occurred at 70 °C for gill AChE and 75 °C for viscera AChE. The enzymes of both tissues presented remarkable thermostability. The Michaelis-Menten constant for both enzymes were 1.32 ± 0.20 mM for gills and 0.43 ± 0.12 mM for viscera. The Vmax values for gills and viscera were 53.57 ± 1.72 and 27.71 ± 1.15 mU/mg, respectively. The enzymes were able to reduce the activation energy to 9.75 kcal mol-1 (gills) and 11.87 kcal mol-1 (viscera) obtaining rate enhancements of 3.57 × 105 and 1.01 × 104, respectively, in relation to non-catalyzed reactions. Among the pesticides under study, the carbamates carbaryl and carbofuran exerted the strongest inhibitory effects on the enzyme activity achieving important degrees of inhibition at concentrations below national and international current regulations. The first observation of the effects of benzoylurea pesticides (diflubenzuron and novaluron) on AChE from mollusks is reported here. The gills AChE of C. rhizophorae showed potential to be specific biomarker for the carbamate carbaryl while the viscera AChE showed it for carbofuran. According to their features, these enzymes may be proposed as promising tools for estuarine monitoring as well as biocomponent of biosensor devices.
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Affiliation(s)
- Paula Rayane de Souza
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Kelma Sirleide de Souza
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Caio Rodrigo Dias de Assis
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil; Laboratório de Imunopatologia Keizo Asami - LIKA, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil.
| | - Marlyete Chagas de Araújo
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Kaline Catiely Campos Silva
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil; Departamento de Educação, Colegiado de Biologia, Universidade do Estado da Bahia - UNEB, Paulo Afonso, BA, Brazil
| | - Juliett de Fátima Xavier da Silva
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil; Laboratório de Tecnologia do Pescado - LATEPE, Departamento de Engenharia de Pesca, Universidade Federal de Alagoas - UFAL, Penedo, AL, Brazil
| | - Andreia Cybelle Marques Ferreira
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Valdir Luna da Silva
- Laboratório de Fisiologia Comparada e Comportamento Animal - LabFCCA, Departamento de Fisiologia e Farmacologia, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Mônica Lúcia Adam
- Centro Acadêmico de Vitória de Santo Antão - CAV, Universidade Federal de Pernambuco - UFPE, Vitória de Santo Antão, PE, Brazil
| | - Luiz Bezerra de Carvalho
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil; Laboratório de Imunopatologia Keizo Asami - LIKA, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Ranilson de Souza Bezerra
- Laboratório de Enzimologia - LABENZ, Departamento de Bioquímica e Biofísica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
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Ferrari S, Severi L, Pozzi C, Quotadamo A, Ponterini G, Losi L, Marverti G, Costi MP. Human Thymidylate Synthase Inhibitors Halting Ovarian Cancer Growth. Vitam Horm 2018; 107:473-513. [PMID: 29544641 DOI: 10.1016/bs.vh.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human thymidylate synthase (hTS) has an important role in DNA biosynthesis, thus it is essential for cell survival. TS is involved in the folate pathways, specifically in the de novo pyrimidine biosynthesis. Structure and functions are intimately correlated, account for cellular activity and, in a broader view, with in vivo mechanisms. hTS is a target for anticancer agents, some of which are clinical drugs. The understanding of the detailed mechanism of TS inhibition by currently used drugs and of the interaction with the mechanism of action of other anticancer agents can suggest new perspective of TS inhibition able to improve the anticancer effect and to overcome drug resistance. TS-targeting drugs in therapy today are inhibitors that bind at the active site and that mostly resemble the substrates. Nonsubstrate analogs offer an opportunity for allosteric binding and novel mode of inhibition in the cancer cells. This chapter illustrates the relationship among the large number of hTS actions at molecular and clinical levels, its role as a target for ovarian cancer therapy, in particular in cases of overexpression of hTS and other folate proteins such as those induced by platinum drug treatments, and address the potential combination of TS inhibitors with other suitable anticancer agents.
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Affiliation(s)
| | - Leda Severi
- University of Modena and Reggio Emilia, Modena, Italy
| | | | | | | | - Lorena Losi
- University of Modena and Reggio Emilia, Modena, Italy
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Koschmieder J, Fehling-Kaschek M, Schaub P, Ghisla S, Brausemann A, Timmer J, Beyer P. Plant-type phytoene desaturase: Functional evaluation of structural implications. PLoS One 2017; 12:e0187628. [PMID: 29176862 PMCID: PMC5703498 DOI: 10.1371/journal.pone.0187628] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/04/2017] [Indexed: 11/19/2022] Open
Abstract
Phytoene desaturase (PDS) is an essential plant carotenoid biosynthetic enzyme and a prominent target of certain inhibitors, such as norflurazon, acting as bleaching herbicides. PDS catalyzes the introduction of two double bonds into 15-cis-phytoene, yielding 9,15,9'-tri-cis-ζ-carotene via the intermediate 9,15-di-cis-phytofluene. We present the necessary data to scrutinize functional implications inferred from the recently resolved crystal structure of Oryza sativa PDS in a complex with norflurazon. Using dynamic mathematical modeling of reaction time courses, we support the relevance of homotetrameric assembly of the enzyme observed in crystallo by providing evidence for substrate channeling of the intermediate phytofluene between individual subunits at membrane surfaces. Kinetic investigations are compatible with an ordered ping-pong bi-bi kinetic mechanism in which the carotene and the quinone electron acceptor successively occupy the same catalytic site. The mutagenesis of a conserved arginine that forms a hydrogen bond with norflurazon, the latter competing with plastoquinone, corroborates the possibility of engineering herbicide resistance, however, at the expense of diminished catalytic activity. This mutagenesis also supports a "flavin only" mechanism of carotene desaturation not requiring charged residues in the active site. Evidence for the role of the central 15-cis double bond of phytoene in determining regio-specificity of carotene desaturation is presented.
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Affiliation(s)
| | | | - Patrick Schaub
- University of Freiburg, Faculty of Biology, Freiburg, Germany
| | - Sandro Ghisla
- University of Konstanz, Department of Biology, Konstanz, Germany
| | - Anton Brausemann
- University of Freiburg, Institute for Biochemistry, Freiburg, Germany
| | - Jens Timmer
- University of Freiburg, Department of Physics, Freiburg, Germany
- University of Freiburg, BIOSS Center for Biological Signaling Studies, Freiburg, Germany
- * E-mail: (PB); (JT)
| | - Peter Beyer
- University of Freiburg, Faculty of Biology, Freiburg, Germany
- University of Freiburg, BIOSS Center for Biological Signaling Studies, Freiburg, Germany
- * E-mail: (PB); (JT)
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32
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Barauskas O, Xing W, Aguayo E, Willkom M, Sapre A, Clarke M, Birkus G, Schultz BE, Sakowicz R, Kwon H, Feng JY. Biochemical characterization of recombinant influenza A polymerase heterotrimer complex: Polymerase activity and mechanisms of action of nucleotide analogs. PLoS One 2017; 12:e0185998. [PMID: 29020100 PMCID: PMC5636120 DOI: 10.1371/journal.pone.0185998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/22/2017] [Indexed: 12/02/2022] Open
Abstract
Influenza polymerase is a heterotrimer protein with both endonuclease and RNA-dependent RNA polymerase (RdRp) activity. It plays a critical role in viral RNA replication and transcription and has been targeted for antiviral drug development. In this study, we characterized the activity of recombinant RdRp purified at 1:1:1 ratio in both ApG-primed RNA replication and mRNA-initiated RNA transcription. The heterotrimer complex showed comparable activity profiles to that of viral particle derived crude replication complex, and in contrast to the crude replication complex, was suitable for detailed mechanistic studies of nucleotide incorporation. The recombinant RdRp was further used to examine distinct modes of inhibition observed with five different nucleotide analog inhibitors, and the apparent steady-state binding affinity Kapp was measured for selected analogs to correlate antiviral activity and enzymatic inhibition with substrate efficiency.
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Affiliation(s)
- Ona Barauskas
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Weimei Xing
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Esmeralda Aguayo
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Madeleine Willkom
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Annapurna Sapre
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Michael Clarke
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Gabriel Birkus
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Brian E. Schultz
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Roman Sakowicz
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - HyockJoo Kwon
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail: (HJK); (JYF)
| | - Joy Y. Feng
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail: (HJK); (JYF)
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Maseko SB, Padayachee E, Govender T, Sayed Y, Kruger G, Maguire GEM, Lin J. I36T↑T mutation in South African subtype C (C-SA) HIV-1 protease significantly alters protease-drug interactions. Biol Chem 2017; 398:1109-1117. [PMID: 28525359 DOI: 10.1515/hsz-2017-0107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022]
Abstract
The efficacy of HIV-1 protease (PR) inhibition therapies is often compromised by the emergence of mutations in the PR molecule that reduces the binding affinity of inhibitors while maintaining viable catalytic activity and affinity for natural substrates. In the present study, we used a recombinant HIV-1 C-SA PR and a recently reported variant for inhibition (Ki, IC50) and thermodynamic studies against nine clinically used inhibitors. This is the first time that binding free energies for C-SA PR and the mutant are reported. This variant PR harbours a mutation and insertion (I36T↑T) at position 36 of the C-SA HIV-1 PR, and did not show a significant difference in the catalytic effect of the HIV-1 PR. However, the nine clinically approved HIV PR drugs used in this study demonstrated weaker inhibition and lower binding affinities toward the variant when compared to the wild type HIV-1 PR. All the protease inhibitors (PIs), except Amprenavir and Ritonavir exhibited a significant decrease in binding affinity (p<0.0001). Darunavir and Nelfinavir exhibited the weakest binding affinity, 155- and 95-fold decreases respectively, toward the variant. Vitality values for the variant PR, against the seven selected PIs, confirm the impact of the mutation and insertion on the South African HIV-1 subtype C PR. This information has important clinical implications for thousands of patients in Sub-Saharan Africa.
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Rodionova MV, Zharmukhamedov SK, Karacan MS, Venedik KB, Shitov AV, Tunç T, Mamaş S, Kreslavski VD, Karacan N, Klimov VV, Allakhverdiev SI. Evaluation of new Cu(II) complexes as a novel class of inhibitors against plant carbonic anhydrase, glutathione reductase, and photosynthetic activity in photosystem II. Photosynth Res 2017; 133:139-153. [PMID: 28497193 DOI: 10.1007/s11120-017-0392-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Increasing inefficiency of production of important agricultural plants raises one of the biggest problems in the modern world. Herbicide application is still the best method of weed management. Traditional herbicides blocking only one of the plant metabolic pathways is ineffective due to the rapid growth of herbicide-resistant weeds. The synthesis of novel compounds effectively suppressing several metabolic processes, and therefore achieving the synergism effect would serve as the alternative approach to weed problem. For this reason, recently, we synthesized a series of nine novel Cu(II) complexes and four ligands, characterized them with different analyses techniques, and carried out their primary evaluation as inhibitors of photosynthetic electron transfer in spinach thylakoids (design, synthesis, and evaluation of a series of Cu(II) based metal-organic complexes as possible inhibitors of photosynthesis, J Photochem Photobiol B, submitted). Here, we evaluated in vitro inhibitory potency of these agents against: photochemistry and carbonic anhydrase activity of photosystem II (PSII); α-carbonic anhydrase from bovine erythrocytes; as well as glutathione reductase from chloroplast and baker's yeast. Our results show that all Cu(II) complexes excellently inhibit glutathione reductase and PSII carbonic anhydrase activity. Some of them also decently inhibit PSII photosynthetic activity.
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Affiliation(s)
- Margarita V Rodionova
- Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, Russia, 127276
| | - Sergei K Zharmukhamedov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, Pushchino, Moscow Region, Russia, 142290
| | - Mehmet Sayım Karacan
- Department of Chemistry, Science Faculty, Gazi University, Teknikokullar, Ankara, Turkey
| | - Kubra Begum Venedik
- Department of Chemistry, Science Faculty, Gazi University, Teknikokullar, Ankara, Turkey
| | - Alexandr V Shitov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, Pushchino, Moscow Region, Russia, 142290
| | - Turgay Tunç
- Department of Chemistry and Process Engineering, Faculty of Engineering-Architecture, Ahi Evran University, Kirsehir, Turkey
| | - Serhat Mamaş
- Department of Chemistry, Science Faculty, Gazi University, Teknikokullar, Ankara, Turkey
| | - Vladimir D Kreslavski
- Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, Russia, 127276
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, Pushchino, Moscow Region, Russia, 142290
| | - Nurcan Karacan
- Department of Chemistry, Science Faculty, Gazi University, Teknikokullar, Ankara, Turkey.
| | - Vyacheslav V Klimov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, Pushchino, Moscow Region, Russia, 142290
| | - Suleyman I Allakhverdiev
- Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, Russia, 127276.
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, Pushchino, Moscow Region, Russia, 142290.
- Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow, Russia, 119991.
- Bionanotechnology Laboratory, Institute of Molecular Biology and Biotechnology, Azerbaijan National Academy of Sciences, Baku, Azerbaijan.
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Eprintsev AT, Fedorin DN, Dobychina MA, Igamberdiev AU. Expression and promoter methylation of succinate dehydrogenase and fumarase genes in maize under anoxic conditions. J Plant Physiol 2017; 216:197-201. [PMID: 28710913 DOI: 10.1016/j.jplph.2017.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 06/07/2023]
Abstract
Succinate dehydrogenase (SDH) and fumarase enzyme activity and expression of genes encoding the SDH subunits A (Sdh1-2), B (Sdh2-3), C (Sdh3), D (Sdh4) and the mitochondrial (Fum1) and cytosolic (Fum2) isoforms of fumarase were quantified in maize (Zea mays L.) seedlings exposed to atmospheres of air (control), N2, and CO2. The catalytic activity of SDH gradually declined in plants exposed to N2 atmospheres, with ∼40% activity remaining after 24h. In seedlings incubated in CO2, the suppression was even more pronounced. Fumarase activity was more stable, decreasing by one third after 24h of anoxia. The level of Sdh1-2 transcripts in seedlings declined significantly under N2 and even more rapidly upon exposure to CO2, with a concomitant increase in methylation of the corresponding promoters. The level of Sdh2-3 and Sdh3 transcripts also decreased under N2 and CO2, but the changes in promoter methylation were less pronounced, whereas the changes in the level of Sdh4 expression and promoter methylation were minor. Expression of Fum1 and Fum2 was affected by N2 and CO2 atmospheres, however without changes in corresponding promoter methylation. It is concluded that, under conditions of oxygen deficiency, succinate accumulates mainly due to downregulation of SDH gene expression and reduction of enzyme activity, and to a lesser extent due to the decrease of fumarase gene expression.
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Affiliation(s)
- Alexander T Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394006 Voronezh, Russia
| | - Dmitry N Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394006 Voronezh, Russia
| | - Maria A Dobychina
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394006 Voronezh, Russia
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1 B 3X9, Canada.
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Rodríguez MM, Herman R, Ghiglione B, Kerff F, D’Amico González G, Bouillenne F, Galleni M, Handelsman J, Charlier P, Gutkind G, Sauvage E, Power P. Crystal structure and kinetic analysis of the class B3 di-zinc metallo-β-lactamase LRA-12 from an Alaskan soil metagenome. PLoS One 2017; 12:e0182043. [PMID: 28750094 PMCID: PMC5531557 DOI: 10.1371/journal.pone.0182043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 12/02/2022] Open
Abstract
We analyzed the kinetic properties of the metagenomic class B3 β-lactamase LRA-12, and determined its crystallographic structure in order to compare it with prevalent metallo-β-lactamases (MBLs) associated with clinical pathogens. We showed that LRA-12 confers extended-spectrum resistance on E. coli when expressed from recombinant clones, and the MIC values for carbapenems were similar to those observed in enterobacteria expressing plasmid-borne MBLs such as VIM, IMP or NDM. This was in agreement with the strong carbapenemase activity displayed by LRA-12, similar to GOB β-lactamases. Among the chelating agents evaluated, dipicolinic acid inhibited the enzyme more strongly than EDTA, which required pre-incubation with the enzyme to achieve measurable inhibition. Structurally, LRA-12 contains the conserved main structural features of di-zinc class B β-lactamases, and presents unique structural signatures that differentiate this enzyme from others within the family: (i) two loops (α3-β7 and β11-α5) that could influence antibiotic entrance and remodeling of the active site cavity; (ii) a voluminous catalytic cavity probably responsible for the high hydrolytic efficiency of the enzyme; (iii) the absence of disulfide bridges; (iv) a unique Gln116 at metal-binding site 1; (v) a methionine residue at position 221that replaces Cys/Ser found in other B3 β-lactamases in a predominantly hydrophobic environment, likely playing a role in protein stability. The structure of LRA-12 indicates that MBLs exist in wild microbial populations in extreme environments, or environments with low anthropic impact, and under the appropriate antibiotic selective pressure could be captured and disseminated to pathogens.
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Affiliation(s)
- María Margarita Rodríguez
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Raphaël Herman
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Barbara Ghiglione
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Frédéric Kerff
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Gabriela D’Amico González
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fabrice Bouillenne
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Moreno Galleni
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Jo Handelsman
- Department of Molecular, Cellular and Development Biology, Yale University, New Haven, CT, United States of America
| | - Paulette Charlier
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Gabriel Gutkind
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eric Sauvage
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Pablo Power
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
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Roy A, Lim L, Srivastava S, Lu Y, Song J. Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants. PLoS One 2017; 12:e0180632. [PMID: 28700665 PMCID: PMC5503262 DOI: 10.1371/journal.pone.0180632] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 12/20/2022] Open
Abstract
The recent Zika viral (ZIKV) epidemic has been associated with severe neurological pathologies such as neonatal microcephaly and Guillain-Barre syndrome but unfortunately no vaccine or medication is effectively available yet. Zika NS2B-NS3pro is essential for the proteolysis of the viral polyprotein and thereby viral replication. Thus NS2B-NS3pro represents an attractive target for anti-Zika drug discovery/design. Here, we have characterized the solution conformations and catalytic parameters of both linked and unlinked Zika NS2B-NS3pro complexes and found that the unlinked complex manifested well-dispersed NMR spectra. Subsequently with selective isotope-labeling using NMR spectroscopy, we demonstrated that C-terminal residues (R73-K100) of NS2B is highly disordered without any stable tertiary and secondary structures in the Zika NS2B-NS3pro complex in the free state. Upon binding to the well-characterized serine protease inhibitor, bovine pancreatic trypsin inhibitor (BPTI), only the extreme C-terminal residues (L86-K100) remain disordered. Additionally, we have identified five flavonoids and one natural phenol rich in edible plants including fruits and vegetables, which inhibit Zika NS2B-NS3pro in a non-competitive mode, with Ki ranging from 770 nM for Myricetin to 34.02 μM for Apigenin. Molecular docking showed that they all bind to a pocket on the back of the active site and their structure-activity relationship was elucidated. Our study provides valuable insights into the solution conformation of Zika NS2B-NS3pro and further deciphers its susceptibility towards allosteric inhibition by natural products. As these natural product inhibitors fundamentally differ from the currently-known active site inhibitors in terms of both inhibitory mode and chemical scaffold, our finding might open a new avenue for development of better allosteric inhibitors to fight ZIKV infection.
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Affiliation(s)
- Amrita Roy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Shagun Srivastava
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yimei Lu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- * E-mail:
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Jennings S, Chenevert M, Liu L, Mottamal M, Wojcik EJ, Huckaba TM. Characterization of kinesin switch I mutations that cause hereditary spastic paraplegia. PLoS One 2017; 12:e0180353. [PMID: 28678816 PMCID: PMC5498027 DOI: 10.1371/journal.pone.0180353] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/14/2017] [Indexed: 11/18/2022] Open
Abstract
Kif5A is a neuronally-enriched isoform of the Kinesin-1 family of cellular transport motors. 23 separate mutations in the motor domain of Kif5A have been identified in patients with the complicated form of hereditary spastic paraplegia (HSP). We performed in vitro assays on dimeric recombinant Kif5A with HSP-causing mutations in the Switch I domain, which participates in the coordination and hydrolysis of ATP by kinesin. We observed a variety of significantly reduced catalytic and mechanical activities as a result of each mutation, with the shared phenotype from each that motility was significantly reduced. Substitution of Mn2+ for Mg2+ in our reaction buffers provides a dose-dependent rescue in both the catalytic and ensemble mechanical properties of the S203C mutant. This work provides mechanistic insight into the cause of HSP in patients with these mutations and points to future experiments to further dissect the root cause of this disease.
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Affiliation(s)
- Scott Jennings
- Department of Biology, Xavier University of Louisiana, New Orleans, Louisiana, United States of America
| | - Madeline Chenevert
- Department of Biology, Xavier University of Louisiana, New Orleans, Louisiana, United States of America
| | - Liqiong Liu
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Madhusoodanan Mottamal
- RCMI Molecular Modeling Core, Xavier University of Louisiana, New Orleans, Louisiana, United States of America
| | - Edward J. Wojcik
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Thomas M. Huckaba
- Department of Biology, Xavier University of Louisiana, New Orleans, Louisiana, United States of America
- * E-mail:
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Aljameeli A, Thakkar A, Shah G. Calcitonin receptor increases invasion of prostate cancer cells by recruiting zonula occludens-1 and promoting PKA-mediated TJ disassembly. Cell Signal 2017; 36:1-13. [PMID: 28428082 DOI: 10.1016/j.cellsig.2017.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 12/16/2022]
Abstract
Almost all primary prostate cancers (PCs) and PC cell lines express calcitonin (CT) and/or its receptor (CTR), and their co-expression positively correlates with their invasiveness. Activation of the CT-CTR axis in non-invasive LNCaP cells induces an invasive phenotype. In contrast, silencing of CT/CTR expression in highly metastatic PC-3M cells markedly reduces their tumorigenicity and abolishes their ability to form distant metastases in nude mice. Our recent studies suggest that CTR interacts with zonula occludens 1 (ZO-1) through PDZ interaction to destabilize tight junctions and increase invasion of PC cells. Our results show that CTR activates AKAP2-anchored cAMP-dependent protein kinase A, which then phosphorylates tight junction proteins ZO-1 and claudin 3. Moreover, PKA-mediated phosphorylation of tight unction proteins required CTR-ZO-1 interaction, suggesting that the interaction may bring CTR-activated PKA in close proximity of tight junction proteins. Furthermore, inhibition of PKA activity attenuated CT-induced loss of TJ functionality and invasion, suggesting that the phosphorylation of TJ proteins is responsible for TJ disassembly. Finally, we show that the prevention of CTR-ZO-1 interaction abolishes CT-induced invasion, and can serve as a novel therapeutic tool to treat aggressive prostate cancers. In brief, the present study identifies the significance of CTR-ZO-1 interaction in progression of prostate cancer to its metastatic form.
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Affiliation(s)
- Ahmed Aljameeli
- Pharmacology, University of Louisiana College of Pharmacy, Monroe, LA 71209, USA
| | - Arvind Thakkar
- Pharmacology, University of Louisiana College of Pharmacy, Monroe, LA 71209, USA
| | - Girish Shah
- Pharmacology, University of Louisiana College of Pharmacy, Monroe, LA 71209, USA.
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Verhoeven MD, Lee M, Kamoen L, van den Broek M, Janssen DB, Daran JMG, van Maris AJA, Pronk JT. Mutations in PMR1 stimulate xylose isomerase activity and anaerobic growth on xylose of engineered Saccharomyces cerevisiae by influencing manganese homeostasis. Sci Rep 2017; 7:46155. [PMID: 28401919 PMCID: PMC5388867 DOI: 10.1038/srep46155] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/09/2017] [Indexed: 01/04/2023] Open
Abstract
Combined overexpression of xylulokinase, pentose-phosphate-pathway enzymes and a heterologous xylose isomerase (XI) is required but insufficient for anaerobic growth of Saccharomyces cerevisiae on d-xylose. Single-step Cas9-assisted implementation of these modifications yielded a yeast strain expressing Piromyces XI that showed fast aerobic growth on d-xylose. However, anaerobic growth required a 12-day adaptation period. Xylose-adapted cultures carried mutations in PMR1, encoding a Golgi Ca2+/Mn2+ ATPase. Deleting PMR1 in the parental XI-expressing strain enabled instantaneous anaerobic growth on d-xylose. In pmr1 strains, intracellular Mn2+ concentrations were much higher than in the parental strain. XI activity assays in cell extracts and reconstitution experiments with purified XI apoenzyme showed superior enzyme kinetics with Mn2+ relative to other divalent metal ions. This study indicates engineering of metal homeostasis as a relevant approach for optimization of metabolic pathways involving metal-dependent enzymes. Specifically, it identifies metal interactions of heterologous XIs as an underexplored aspect of engineering xylose metabolism in yeast.
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Affiliation(s)
- Maarten D Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Misun Lee
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Lycka Kamoen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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41
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Yu H, Dranchak P, Li Z, MacArthur R, Munson MS, Mehzabeen N, Baird NJ, Battalie KP, Ross D, Lovell S, Carlow CKS, Suga H, Inglese J. Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases. Nat Commun 2017; 8:14932. [PMID: 28368002 PMCID: PMC5382265 DOI: 10.1038/ncomms14932] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/13/2017] [Indexed: 11/22/2022] Open
Abstract
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.
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Affiliation(s)
- Hao Yu
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Zhiru Li
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts 01938, USA
| | - Ryan MacArthur
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Matthew S. Munson
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Nurjahan Mehzabeen
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | - Nathan J. Baird
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin P. Battalie
- IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Scott Lovell
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
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Jadaun JS, Sangwan NS, Narnoliya LK, Singh N, Bansal S, Mishra B, Sangwan RS. Over-expression of DXS gene enhances terpenoidal secondary metabolite accumulation in rose-scented geranium and Withania somnifera: active involvement of plastid isoprenogenic pathway in their biosynthesis. Physiol Plant 2017; 159:381-400. [PMID: 27580641 DOI: 10.1111/ppl.12507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 05/08/2023]
Abstract
Rose-scented geranium (Pelargonium spp.) is one of the most important aromatic plants and is well known for its diverse perfumery uses. Its economic importance is due to presence of fragrance rich essential oil in its foliage. The essential oil is a mixture of various volatile phytochemicals which are mainly terpenes (isoprenoids) in nature. In this study, on the geranium foliage genes related to isoprenoid biosynthesis (DXS, DXR and HMGR) were isolated, cloned and confirmed by sequencing. Further, the first gene of 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway, 1-deoxy-d-xylulose-5-phosphate synthase (GrDXS), was made full length by using rapid amplification of cDNA ends strategy. GrDXS contained a 2157 bp open reading frame that encoded a polypeptide of 792 amino acids having calculated molecular weight 77.5 kDa. This study is first report on heterologous expression and kinetic characterization of any gene from this economically important plant. Expression analysis of these genes was performed in different tissues as well as at different developmental stages of leaves. In response to external elicitors, such as methyl jasmonate, salicylic acid, light and wounding, all the three genes showed differential expression profiles. Further GrDXS was over expressed in the homologous (rose-scented geranium) as well as in heterologous (Withania somnifera) plant systems through genetic transformation approach. The over-expression of GrDXS led to enhanced secondary metabolites production (i.e. essential oil in rose-scented geranium and withanolides in W. somnifera). To the best of our knowledge, this is the first report showing the expression profile of the three genes related to isoprenoid biosynthesis pathways operated in rose-scented geranium as well as functional characterization study of any gene from rose-scented geranium through a genetic transformation system.
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Affiliation(s)
- Jyoti Singh Jadaun
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Neelam S Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Lokesh K Narnoliya
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Neha Singh
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Shilpi Bansal
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Bhawana Mishra
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Rajender Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
- Center of Innovative and Applied Bioprocessing (A National Institute under Department of Biotechnology, Govt. of India), C-127, Phase-8, Industrial Area, S.A.S. Nagar, Mohali - 160071, Punjab, India
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Liu ZQ, Dong SC, Yin HH, Xue YP, Tang XL, Zhang XJ, He JY, Zheng YG. Enzymatic synthesis of an ezetimibe intermediate using carbonyl reductase coupled with glucose dehydrogenase in an aqueous-organic solvent system. Bioresour Technol 2017; 229:26-32. [PMID: 28092733 DOI: 10.1016/j.biortech.2016.12.098] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/23/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
(4S)-3-[(5S)-5-(4-Fluorophenyl)-5-hydroxypentanoyl]-4-phenyl-1,3-oxazolidin-2-one ((S)-ET-5) is an important chiral intermediate in the synthesis of chiral side chain of ezetimibe. Recombinant Escherichia coli expressing carbonyl reductase (CBR) was successfully constructed in this study. The total E. coli biomass and the specific activity of recombinant CBR in 5L fermenter culture were 10.9gDCWL-1 and 14900.3Ug-1DCW, respectively. The dual-enzyme coupled biocatalytic process in an aqueous-organic biphasic solvent system was first constructed using p-xylene as the optimal organic phase under optimized reaction conditions, and 150gL-1 (4S)-3-[5-(4-fluorophenyl)-1,5-dioxophentyl]-4-phenyl-1,3-oxazolidin-2-one (ET-4) was successfully converted to (S)-ET-5 with a conversion of 99.1% and diastereomeric excess of 99% after 24-h, which are the highest values reported to date for the production of (S)-ET-5.
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Affiliation(s)
- Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Si-Chuan Dong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Huan-Huan Yin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiao-Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiao-Jian Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jun-Yao He
- School of Pharmaceutical Engineering, Zhejiang Pharmaceutical College, Ningbo 315100, PR China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
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Guerrero C, Vera C, Illanes A. Synthesis of lactulose in batch and repeated-batch operation with immobilized β-galactosidase in different agarose functionalized supports. Bioresour Technol 2017; 230:56-66. [PMID: 28160659 DOI: 10.1016/j.biortech.2017.01.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Lactulose synthesis was done in repeated-batch mode with Aspergillus oryzae β-galactosidase immobilized in glyoxyl-agarose (GA-βG), amino-glyoxyl-agarose (Am-GA-βG) and chelate-glyoxyl-agarose (Che-GA-βG), at fructose/lactose molar ratios of 4, 12 and 20. Highest yields of lactulose in batch were obtained with Che-GA-βG (0.21, 0.29 and 0.32g·g-1) for 4, 12 and 20 fructose/lactose molar ratios respectively; when operating in 10 repeated batches highest product to biocatalyst mass ratios were obtained with Am-GA-βG (1.82, 2.52 and 2.7g·mg-1), while the lowest were obtained with Che-GA-βG (0.25, 0.33 and 0.39g·mg-1). Operational stability of Am-GA-βG was higher than GA-βG and Che-GA-βG and much higher than that of the free enzyme, at all fructose/lactose molar ratios evaluated. Efficiency of biocatalyst use for GA-βG were 64.4, 35.5 and 18.4kglactulose/gprotein, for fructose/lactose molar ratios of 4, 12 and 20 respectively, while for Che-GA-βG were 1.46, 1.05 and 0.96kglactulose/gprotein.
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Affiliation(s)
- Cecilia Guerrero
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso (PUCV), Valparaíso, Chile.
| | - Carlos Vera
- Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Andrés Illanes
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso (PUCV), Valparaíso, Chile
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Jadaun JS, Sangwan NS, Narnoliya LK, Tripathi S, Sangwan RS. Withania coagulans tryptophan decarboxylase gene cloning, heterologous expression, and catalytic characteristics of the recombinant enzyme. Protoplasma 2017; 254:181-192. [PMID: 26795344 DOI: 10.1007/s00709-015-0929-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/10/2015] [Indexed: 05/14/2023]
Abstract
Tryptophan decarboxylase (EC 4.1.1.28) catalyzes pyridoxal 5'-phosphate (PLP)-dependent decarboxylation of tryptophan to produce tryptamine for recruitment in a myriad of biosynthetic pathways of metabolites possessing indolyl moiety. A recent report of certain indolyl metabolites in Withania species calls for a possible predominant functional role of tryptophan decarboxylase (TDC) in the genome of Withania species to facilitate production of the indolyl progenitor molecule, tryptamine. Therefore, with this metabolic prospection, we have identified and cloned a full-length cDNA sequence of TDC from aerial tissues of Withania coagulans. The functional WcTDC gene comprises of 1506 bp open reading frame (ORF) encoding a 502 amino acid protein with calculated molecular mass and pI value of 56.38 kDa and 8.35, respectively. The gene was expressed in Escherichia coli, and the recombinant enzyme was affinity-purified to homogeneity to discern its kinetics of catalysis. The enzyme (WcTDC) exhibited much higher Km value for tryptophan than for pyridoxal 5'-phosphate and was dedicated to catalyze decarboxylation of only tryptophan or, to a limited extent, of its analogue (like 5-hydroxy tryptophan). The observed optimal catalytic functionality of the enzyme on the slightly basic side of the pH scale and at slightly higher temperatures reflected adaptability of the plant to hot and arid regions, the predominant natural habitat of the herb. This pertains to be the first report on cloning and characterization of heterologously expressed recombinant enzyme from W. coagulans and forms a starting point to further understanding of withanamide biosynthesis.
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Affiliation(s)
- Jyoti Singh Jadaun
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Neelam Singh Sangwan
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Lokesh Kumar Narnoliya
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Sandhya Tripathi
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Rajender Singh Sangwan
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India.
- Center of Innovative and Applied Bioprocessing (CIAB), C-127, Phase-8, Industrial Area, S.A.S. Nagar, Mohali, 160071, Punjab, India.
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Wang X, Huang H, Xie X, Ma R, Bai Y, Zheng F, You S, Zhang B, Xie H, Yao B, Luo H. Improvement of the catalytic performance of a hyperthermostable GH10 xylanase from Talaromyces leycettanus JCM12802. Bioresour Technol 2016; 222:277-284. [PMID: 27723474 DOI: 10.1016/j.biortech.2016.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/30/2016] [Accepted: 10/01/2016] [Indexed: 05/07/2023]
Abstract
A xylanase gene of GH 10, Tlxyn10A, was cloned from Talaromyces leycettanus JCM12802 and expressed in Pichia pastoris. Purified recombinant TlXyn10A was acidic and hyperthermophilic, and retained stable over the pH range of 2.0-6.0 and at 90°C. Sequence analysis of TlXyn10A identified seven residues probably involved in substrate contacting. Three mutants (TlXyn10A_P, _N and _C) were then constructed by substituting some or all of the residues with corresponding ones of hyperthermal Xyl10C from Bispora sp. MEY-1. TlXyn10A_P with mutations at subsites +2 to +4 exhibited improved specific activity (by 0.44-fold) and pH stability (2.0-10.0). Molecular dynamics simulation analysis indicated that mutations E229I and F232E probably weaken the substrate affinity at subsites +3 to +4, and G149D may introduce a new hydrogen bond. These modifications altogether account for the improved performance of TlXyn10A_P. Moreover, TlXyn10A_P was able to hydrolyze wheat straw persistently, and has the application potentials in various industries.
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Affiliation(s)
- Xiaoyu Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Xiangming Xie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Fei Zheng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China
| | - Shuai You
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Bingyu Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Huifang Xie
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China.
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47
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Yin S, Kong JQ. Transcriptome-guided gene isolation and functional characterization of UDP-xylose synthase and UDP-D-apiose/UDP-D-xylose synthase families from Ornithogalum caudatum Ait. Plant Cell Rep 2016; 35:2403-2421. [PMID: 27591771 DOI: 10.1007/s00299-016-2044-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The present study first identified the involvement of OcUAXS2 and OcUXS1-3 in anticancer polysaccharides biosynthesis in O. caudatum. UDP-xylose synthase (UXS) and UDP-D-apiose/UDP-D-xylose synthase (UAXS), both capable of converting UDP-D-glucuronic acid to UDP-D-xylose, are believed to transfer xylosyl residue to anticancer polysaccharides biosynthesis in Ornithogalum caudatum Ait. However, the cDNA isolation and functional characterization of genes encoding the two enzymes from O. caudatum has never been documented. Previously, the transcriptome sequencing of O. caudatum was performed in our laboratory. In this study, a total of six and two unigenes encoding UXS and UAXS were first retrieved based on RNA-Seq data. The eight putative genes were then successfully isolated from transcriptome of O. caudatum by reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis revealed the six putative UXS isoforms can be classified into three types, one soluble and two distinct putative membrane-bound. Moreover, the two UAXS isoenzymes were predicted to be soluble forms. Subsequently, these candidate cDNAs were characterized to be bona fide genes by functional expression in Escherichia coli individually. Although UXS and UAXS catalyzed the same reaction, their biochemical properties varied significantly. It is worth noting that a ratio switch of UDP-D-xylose/UDP-D-apiose for UAXS was established, which is assumed to be helpful for its biotechnological application. Furthermore, a series of mutants were generated to test the function of NAD+ binding motif GxxGxxG. Most importantly, the present study determined the involvement of OcUAXS2 and OcUXS1-3 in xylose-containing polysaccharides biosynthesis in O. caudatum. These data provide a comprehensive knowledge for UXS and UAXS families in plants.
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Affiliation(s)
- Sen Yin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian-Qiang Kong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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48
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Yu C, Kim BS, Kim E. FAF1 mediates regulated necrosis through PARP1 activation upon oxidative stress leading to dopaminergic neurodegeneration. Cell Death Differ 2016; 23:1873-1885. [PMID: 27662363 PMCID: PMC5071579 DOI: 10.1038/cdd.2016.99] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 07/29/2016] [Accepted: 08/17/2016] [Indexed: 02/02/2023] Open
Abstract
Cumulative damage caused by oxidative stress results in diverse pathological conditions. Therefore, elucidating the molecular mechanisms underlying cell death following oxidative stress is important. Here, we describe a novel role for Fas-associated factor 1 (FAF1) as a crucial regulator of necrotic cell death elicited by hydrogen peroxide. Upon oxidative insult, FAF1 translocated from the cytoplasm to the nucleus and promoted the catalytic activation of poly(ADP-ribose) polymerase 1 (PARP1) through physical interaction. Moreover, FAF1 depletion prevented PARP1-linked downstream events involved in the triggering of cell death, including energetic collapse, mitochondrial depolarization and nuclear translocation of apoptosis-inducing factor (AIF), implying that FAF1 has a key role in PARP1-dependent necrosis in response to oxidative stress. We further investigated whether FAF1 might contribute to the pathogenesis of Parkinson's disease through excessive PARP1 activation. Indeed, the overexpression of FAF1 using a recombinant adeno-associated virus system in the mouse ventral midbrain promoted PARP1 activation and dopaminergic neurodegeneration in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of Parkinson's disease. Collectively, our data demonstrate the presence of an FAF1-PARP1 axis that is involved in oxidative stress-induced necrosis and in the pathology of Parkinson's disease.
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Affiliation(s)
- Changsun Yu
- Department of Biological Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Bok-seok Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Eunhee Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 305-764, Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 305-764, Korea
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49
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Karthikeyan R, Krishnaraj N, Selvam A, Wong JWC, Lee PKH, Leung MKH, Berchmans S. Effect of composites based nickel foam anode in microbial fuel cell using Acetobacter aceti and Gluconobacter roseus as a biocatalysts. Bioresour Technol 2016; 217:113-120. [PMID: 26970695 DOI: 10.1016/j.biortech.2016.02.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 06/05/2023]
Abstract
This study explores the use of materials such as chitosan (chit), polyaniline (PANI) and titanium carbide (TC) as anode materials for microbial fuel cells. Nickel foam (NF) was used as the base anode substrate. Four different types of anodes (NF, NF/PANI, NF/PANI/TC, NF/PANI/TC/Chit) are thus prepared and used in batch type microbial fuel cells operated with a mixed consortium of Acetobacter aceti and Gluconobacter roseus as the biocatalysts and bad wine as a feedstock. A maximum power density of 18.8Wm(-3) (≈2.3 times higher than NF) was obtained in the case of the anode modified with a composite of PANI/TC/Chit. The MFCs running under a constant external resistance of (50Ω) yielded 14.7% coulombic efficiency with a maximum chemical oxygen demand (COD) removal of 87-93%. The overall results suggest that the catalytic materials embedded in the chitosan matrix show the best performance and have potentials for further development.
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Affiliation(s)
- Rengasamy Karthikeyan
- Electrodics and Electrocatalysis (EEC) Division, Central Electrochemical Research Institute (CSIR-CECRI), Karaikudi 630 006, Tamil Nadu, India; Ability R&D Energy Research Center, School of Energy and Environment, City University of Hong Kong, Hong Kong, China; Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong, China.
| | - Navanietha Krishnaraj
- Electrodics and Electrocatalysis (EEC) Division, Central Electrochemical Research Institute (CSIR-CECRI), Karaikudi 630 006, Tamil Nadu, India
| | - Ammaiyappan Selvam
- Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong, China
| | - Jonathan Woon-Chung Wong
- Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong, China
| | - Patrick K H Lee
- Ability R&D Energy Research Center, School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Michael K H Leung
- Ability R&D Energy Research Center, School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Sheela Berchmans
- Electrodics and Electrocatalysis (EEC) Division, Central Electrochemical Research Institute (CSIR-CECRI), Karaikudi 630 006, Tamil Nadu, India
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50
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Zhang H, Du C, Wang Y, Wang J, Zheng L, Wang Y. The Reaumuria trigyna leucoanthocyanidin dioxygenase (RtLDOX) gene complements anthocyanidin synthesis and increases the salt tolerance potential of a transgenic Arabidopsis LDOX mutant. Plant Physiol Biochem 2016; 106:278-87. [PMID: 27219053 DOI: 10.1016/j.plaphy.2016.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 05/27/2023]
Abstract
Reaumuria trigyna is a typical, native desert halophyte that grows under extreme conditions in Inner Mongolia. In a previous transcriptomic profiling analysis, flavonoid pathway-related genes in R. trigyna showed significant differences in transcript abundance under salt stress. Leucoanthocyanidin dioxygenase (LDOX, EC 1.14.11.19) is one of three dioxygenases in the flavonoid pathway that catalyzes the formation of anthocyanidins from leucoanthocyanidins. In this study, we cloned the full-length cDNA of R. trigyna LDOX (RtLDOX), and found RtLDOX recombinant protein was able to replace flavanone-3-hydroxylase (F3H, EC 1.14.11.9), another dioxygenase in the flavonoid pathway, to convert naringenin to dihydrokaempferol in vitro. R. trigyna LDOX can complement the Arabidopsis LDOX mutant transparent testa11 (tt11-11), which has reduced proanthocyanin (PA) and anthocyanin levels in seeds, to accumulate these two compounds. Thus, RtLDOX acts as a multifunctional dioxygenase to effect the synthesis of PA and anthocyanins and can perform F3H dioxygenase activities in the flavonoid biosynthesis pathway. The RtLDOX promoter harbored many cis-acting elements that might be recognized and bound by transcription factors related to stress response. RtLDOX expression was strongly increased under salt stress, and RtLDOX transgenic Arabidopsis mutant under NaCl stress accumulated the content of flavonoids leading to an increased antioxidant activities and plant biomass. These results suggest that RtLDOX as a multifunctional dioxygenase in flavonoid biosynthesis involves in enhancing plant response to NaCl stress.
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MESH Headings
- Amino Acid Sequence
- Anthocyanins/biosynthesis
- Arabidopsis/genetics
- Arabidopsis/physiology
- Biocatalysis/drug effects
- Electrophoresis, Polyacrylamide Gel
- Flavanones/metabolism
- Flavonoids/metabolism
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant
- Genetic Complementation Test
- Mutation/genetics
- Oxygenases/chemistry
- Oxygenases/genetics
- Oxygenases/metabolism
- Phylogeny
- Plants, Genetically Modified
- Proanthocyanidins/metabolism
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Salt Tolerance/drug effects
- Salt Tolerance/genetics
- Seeds/drug effects
- Seeds/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sodium Chloride/pharmacology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Tamaricaceae/drug effects
- Tamaricaceae/enzymology
- Tamaricaceae/genetics
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Affiliation(s)
- Huirong Zhang
- Key Laboratory of Herbage & Endemic Crop Biotechnology, College of Life Sciences, Inner Mongolia University, Hohhot 010020, People's Republic of China.
| | - Chao Du
- Key Laboratory of Herbage & Endemic Crop Biotechnology, College of Life Sciences, Inner Mongolia University, Hohhot 010020, People's Republic of China.
| | - Yan Wang
- Key Laboratory of Herbage & Endemic Crop Biotechnology, College of Life Sciences, Inner Mongolia University, Hohhot 010020, People's Republic of China.
| | - Jia Wang
- Key Laboratory of Herbage & Endemic Crop Biotechnology, College of Life Sciences, Inner Mongolia University, Hohhot 010020, People's Republic of China.
| | - Linlin Zheng
- Key Laboratory of Herbage & Endemic Crop Biotechnology, College of Life Sciences, Inner Mongolia University, Hohhot 010020, People's Republic of China.
| | - Yingchun Wang
- Key Laboratory of Herbage & Endemic Crop Biotechnology, College of Life Sciences, Inner Mongolia University, Hohhot 010020, People's Republic of China.
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