1
|
Lulli M, Trabocchi A, Roviello G, Catalano M, Papucci L, Parenti A, Molli A, Napoli C, Landini I, Schiavone N, Lapucci A. Targeting z-Crystallin by aspirin restores the sensitivity to cisplatin in resistant A2780 ovarian cancer cells. Front Pharmacol 2024; 15:1377028. [PMID: 39021835 PMCID: PMC11252033 DOI: 10.3389/fphar.2024.1377028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/16/2024] [Indexed: 07/20/2024] Open
Abstract
Ovarian cancer is the deadliest gynaecologic malignancies worldwide. Platinum based chemotherapy is the mainstay treatment for ovarian cancer; however, frequent recurrence and chemoresistance onset in patients with advanced diseases remain a therapeutic challenge. Although mechanisms underlying the development of chemoresistance are still ambiguous, the B-cell lymphoma-2 (Bcl-2) family is closely associated with chemoresistance in ovarian cancer. We previously disclosed that Zeta-Crystallin (CryZ) is a post-transcriptional regulator of Bcl-2 gene expression, by binding to Bcl-2 mRNA and increasing its half-life. Here, we investigated the role of CryZ as a novel therapeutic target in A2780 ovarian carcinoma cells by modulating the protein activity with acetylsalicylic acid (ASA) to restore chemosensitivity. Molecular docking and fragment-mapping based approach revealed potential interaction of ASA within CryZ protein. Inhibition of CryZ binding activity to Bcl-2 and Bcl-xl mRNA targets by ASA was demonstrated in A375 cells. Cytotoxicity assays were conducted in A2780S and A2780R ovarian cancer cells to evaluate if CryZ binding activity inhibition and CryZ silencing were able to reverse cisplatin resistance. ASA-treatment determined a downregulation of Bcl-2 and Bcl-xl mRNA levels in A2780S and A2780R cells. ASA-treatment or CryZ silencing were able to increase and restore the chemosensitivity in both sensitive and resistant A2780 ovarian cancer cells, respectively. In this research article we demonstrated that the pharmacological or genetic inhibition of CryZ restores the sensitivity to cisplatin in a model of sensitive or resistant ovarian cancer cells. These findings suggest a new gene-targeted chemotherapeutic approach to restore the cytotoxicity in drug-resistant ovarian cancers and increase the sensitivity in non-resistant cells.
Collapse
Affiliation(s)
- Matteo Lulli
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Section of Experimental Pathology and Oncology, University of Florence, Florence, Italy
| | - Andrea Trabocchi
- Department of Chemistry “Ugo Schiff”, University of Florence, Florence, Italy
| | - Giandomenico Roviello
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Florence, Italy
| | - Martina Catalano
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Florence, Italy
| | - Laura Papucci
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Section of Experimental Pathology and Oncology, University of Florence, Florence, Italy
| | - Astrid Parenti
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Florence, Italy
| | - Alice Molli
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Florence, Italy
| | - Cristina Napoli
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Florence, Italy
| | - Ida Landini
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Florence, Italy
| | - Nicola Schiavone
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Section of Experimental Pathology and Oncology, University of Florence, Florence, Italy
| | - Andrea Lapucci
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Florence, Italy
| |
Collapse
|
2
|
Gandra RM, Johnson CJ, Nett JE, Konopka JB. The Candida albicans ζ-crystallin homolog Zta1 promotes resistance to oxidative stress. mSphere 2023; 8:e0050723. [PMID: 38032185 PMCID: PMC10732081 DOI: 10.1128/msphere.00507-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Candida albicans is an important human pathogen that can cause lethal systemic infections. The ability of C. albicans to colonize and establish infections is closely tied to its highly adaptable nature and capacity to resist various types of stress, including oxidative stress. Previous studies showed that four C. albicans proteins belonging to the flavodoxin-like protein family of quinone reductases are needed for resistance to quinones and virulence. Therefore, in this study, we examined the role of a distinct type of quinone reductase, Zta1, and found that it acts in conjunction with the flavodoxin-like proteins to protect against oxidative stress.
Collapse
Affiliation(s)
- Rafael M. Gandra
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Chad J. Johnson
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeniel E. Nett
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James B. Konopka
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| |
Collapse
|
3
|
Gandra RM, Johnson CJ, Nett JE, Konopka JB. The Candida albicans ζ-crystallin homolog Zta1 promotes resistance to oxidative stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556406. [PMID: 37732195 PMCID: PMC10508745 DOI: 10.1101/2023.09.05.556406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The fungal pathogen Candida albicans is capable of causing lethal infections in humans. Its pathogenic potential is due in part to the ability to resist various stress conditions in the host, including oxidative stress. Recent studies showed that a family of four flavodoxin-like proteins (Pst1, Pst2, Pst3, Ycp4) that function as quinone reductases promotes resistance to oxidation and is needed for virulence. Therefore, in this study Zta1 was examined because it belongs to a structurally distinct family of quinone reductases that are highly conserved in eukaryotes and have been called the ζ-crystallins. The levels of Zta1 in C. albicans rapidly increased after exposure to oxidants, consistent with a role in resisting oxidative stress. Accumulation of reactive oxygen species was significantly higher in cells lacking ZTA1 upon exposure to quinones and other oxidants. Furthermore, deletion of ZTA1 in a mutant lacking the four flavodoxin-like proteins, resulted in further increased susceptibility to quinones, indicating that these distinct quinone reductases work in combination. These results demonstrate that Zta1 contributes to C. albicans survival after exposure to oxidative conditions, which increases the understanding of how C. albicans resists stressful conditions in the host.
Collapse
Affiliation(s)
- Rafael M. Gandra
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
| | | | - Jeniel E. Nett
- University of Wisconsin-Madison, Department of Medicine
- University of Wisconsin-Madison, Department of Medical Microbiology & Immunology
| | - James B. Konopka
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
| |
Collapse
|
4
|
Yang C, Huang Z, Zhang X, Zhu C. Structural Insights into the NAD(P)H:Quinone Oxidoreductase from Phytophthora capsici. ACS OMEGA 2022; 7:25705-25714. [PMID: 35910145 PMCID: PMC9330140 DOI: 10.1021/acsomega.2c02954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Soluble quinone oxidoreductases catalyze transfer of electrons from NADPH to quinones. Transfer of electrons is essential for detoxification of synthetic compounds. Here, we present the crystal structure of a NADPH-dependent QOR from Phytophthora capsici (Pc) complexed with NADPH at 2.4 Å resolution. The enzyme exhibits a bi-modular architecture, containing a NADPH-binding groove and a substrate-binding pocket in each subunit. In the crystal, each asymmetric unit of PcQOR contains two molecules stabilized by intermolecular interactions. Gel filtration and ultracentrifugation analyses reveal that it functions as a tetramer in solution. Alignment of homologous structures exhibits a conserved topology. However, the active sites vary among the homologues, indicating differences in substrate specificities. Enzymatic assays indicate that PcQOR tends to catalyze the large substrates, like 9,10-phenanthrenequinone. Computational simulation associated with site-directed mutagenesis and enzymatic activity analysis declares a potential quinone-binding channel. The ability to reduce quinones probably helps P. capsici to detoxify some harmful chemicals encountered during invasion.
Collapse
Affiliation(s)
- Cancan Yang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Zhenling Huang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Xiuguo Zhang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Chunyuan Zhu
- College
of Life Sciences, Shandong Agricultural
University, Taian 271018, China
| |
Collapse
|
5
|
Transcriptome Analysis Reveals Candidate Genes Involved in Light-Induced Primordium Differentiation in Pleurotus eryngii. Int J Mol Sci 2021; 23:ijms23010435. [PMID: 35008859 PMCID: PMC8745762 DOI: 10.3390/ijms23010435] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/29/2022] Open
Abstract
Pleurotus eryngii, a highly valued edible fungus, is one of the major commercially cultivated mushrooms in China. The development of P. eryngii, especially during the stage of primordium differentiation, is easily affected by light. However, the molecular mechanism underlying the response of primordium differentiation to light remains unknown. In the present study, primordium expression profiles under blue-light stimulation, red-light stimulation, and exposure to darkness were compared using high-throughput sequencing. A total of 16,321 differentially expressed genes (DEGs) were identified from three comparisons. GO enrichment analysis showed that a large number of DEGs were related to light stimulation and amino acid biosynthesis. KEGG analyses demonstrated that the MAPK signaling pathway, oxidative phosphorylation pathway, and RNA transport were most active during primordium differentiation. Furthermore, it was predicted that the blue-light photoreceptor WC-1 and Deoxyribodipyrimidine photolyase PHR play important roles in the primordium differentiation of P. eryngii. Taken together, the results of this study provide a speculative mechanism that light induces primordium differentiation and a foundation for further research on fruiting body development in P. eryngii.
Collapse
|
6
|
Abstract
Drug metabolizing enzymes catalyze the biotransformation of many of drugs and chemicals. The drug metabolizing enzymes are distributed among several evolutionary families and catalyze a range of detoxication reactions, including oxidation/reduction, conjugative, and hydrolytic reactions that serve to detoxify potentially toxic compounds. This detoxication function requires that drug metabolizing enzymes exhibit substrate promiscuity. In addition to their catalytic functions, many drug metabolizing enzymes possess functions unrelated to or in addition to catalysis. Such proteins are termed 'moonlighting proteins' and are defined as proteins with multiple biochemical or biophysical functions that reside in a single protein. This review discusses the diverse moonlighting functions of drug metabolizing enzymes and the roles they play in physiological functions relating to reproduction, vision, cell signaling, cancer, and transport. Further research will likely reveal new examples of moonlighting functions of drug metabolizing enzymes.
Collapse
Affiliation(s)
- Philip G Board
- John Curtin School of Medical Research, ANU College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, NY, USA
| |
Collapse
|
7
|
Lulli M, Nencioni D, Papucci L, Schiavone N. Zeta-crystallin: a moonlighting player in cancer. Cell Mol Life Sci 2020; 77:965-976. [PMID: 31563996 PMCID: PMC11104887 DOI: 10.1007/s00018-019-03301-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022]
Abstract
Crystallins were firstly found as structural proteins of the eye lens. To this family belong proteins, such as ζ-crystallin, expressed ubiquitously, and endowed with enzyme activity. ζ-crystallin is a moonlighting protein endowed with two main different functions: (1) mRNA binding with stabilizing activity; (2) NADPH:quinone oxidoreductase. ζ-crystallin has been clearly demonstrated to stabilize mRNAs encoding proteins involved in renal glutamine catabolism during metabolic acidosis resulting in ammoniagenesis and bicarbonate ion production that concur to compensate such condition. ζ-crystallin binds also mRNAs encoding for antiapoptotic proteins, such as Bcl-2 in leukemia cells. On the other hand, the physiological role of its enzymatic activity is still elusive. Gathering research evidences and data mined from public databases, we provide a framework where all the known ζ-crystallin properties are called into question, making it a hypothetical pivotal player in cancer, allowing cells to hijack or subjugate the acidity response mechanism to increase their ability to resist oxidative stress and apoptosis, while fueling their glutamine addicted metabolism.
Collapse
Affiliation(s)
- Matteo Lulli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy.
| | - Daniele Nencioni
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy
| | - Laura Papucci
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy
| | - Nicola Schiavone
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy.
| |
Collapse
|
8
|
Braesel J, Lee JH, Arnould B, Murphy BT, Eustáquio AS. Diazaquinomycin Biosynthetic Gene Clusters from Marine and Freshwater Actinomycetes. JOURNAL OF NATURAL PRODUCTS 2019; 82:937-946. [PMID: 30896942 PMCID: PMC6902439 DOI: 10.1021/acs.jnatprod.8b01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Tuberculosis is an infectious disease of global concern. Members of the diazaquinomycin (DAQ) class of natural products have shown potent and selective activity against drug-resistant Mycobacterium tuberculosis. However, poor solubility has prevented further development of this compound class. Understanding DAQ biosynthesis may provide a viable route for the generation of derivatives with improved properties. We have sequenced the genomes of two actinomycete bacteria that produce distinct DAQ derivatives. While software tools for automated biosynthetic gene cluster (BGC) prediction failed to detect DAQ BGCs, comparative genomics using MAUVE alignment led to the identification of putative BGCs in the marine Streptomyces sp. F001 and in the freshwater Micromonospora sp. B006. Deletion of the identified daq BGC in strain B006 using CRISPR-Cas9 genome editing abolished DAQ production, providing experimental evidence for BGC assignment. A complete model for DAQ biosynthesis is proposed based on the genes identified. Insufficient knowledge of natural product biosynthesis is one of the major challenges of productive genome mining approaches. The results reported here fill a gap in knowledge regarding the genetic basis for the biosynthesis of DAQ antibiotics. Moreover, identification of the daq BGC shall enable future generations of improved derivatives using biosynthetic methods.
Collapse
Affiliation(s)
- Jana Braesel
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jung-Ho Lee
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Benoit Arnould
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian T. Murphy
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| |
Collapse
|
9
|
Structure, biochemical and kinetic properties of recombinant Pst2p from Saccharomyces cerevisiae, a FMN-dependent NAD(P)H:quinone oxidoreductase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1046-1056. [PMID: 28499769 DOI: 10.1016/j.bbapap.2017.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/09/2023]
Abstract
The genome of the yeast Saccharomyces cerevisiae encodes four flavodoxin-like proteins, namely Lot6p, Pst2p, Rfs1p and Ycp4p. Thus far only Lot6p was characterized in detail demonstrating that the enzyme possesses NAD(P)H:quinone oxidoreductase activity. In the present study, we heterologously expressed PST2 in Escherichia coli and purified the produced protein to conduct a detailed biochemical and structural characterization. Determination of the three-dimensional structure by X-ray crystallography revealed that Pst2p adopts the flavodoxin-like fold and forms tetramers independent of cofactor binding. The lack of electron density for FMN indicated weak binding, which was confirmed by further biochemical analysis yielding a dissociation constant of 20±1μM. The redox potential of FMN bound to Pst2p was determined to -89±3mV and is thus 119mV more positive than that of free FMN indicating that reduced FMN binds ca. five orders of magnitude tighter to Pst2p than oxidized FMN. Due to this rather positive redox potential Pst2p is unable to reduce free FMN or azo dyes as reported for other members of the flavodoxin-like protein family. On the other hand, Pst2p efficiently catalyzes the NAD(P)H dependent two-electron reduction of natural and artificial quinones. The kinetic mechanism follows a ping-pong bi-bi reaction scheme. In vivo experiments with a PST2 knock out and overexpressing strain demonstrated that Pst2p enables yeast cells to cope with quinone-induced damage suggesting a role of the enzyme in managing oxidative stress.
Collapse
|
10
|
Mas y mas S, Curien G, Giustini C, Rolland N, Ferrer JL, Cobessi D. Crystal Structure of the Chloroplastic Oxoene Reductase ceQORH from Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:329. [PMID: 28337214 PMCID: PMC5343027 DOI: 10.3389/fpls.2017.00329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/24/2017] [Indexed: 05/17/2023]
Abstract
Enzymatic and non-enzymatic peroxidation of polyunsaturated fatty acids give rise to accumulation of aldehydes, ketones, and α,β-unsaturated carbonyls of various lengths, known as oxylipins. Oxylipins with α,β-unsaturated carbonyls are reactive electrophile species and are toxic. Cells have evolved several mechanisms to scavenge reactive electrophile oxylipins and decrease their reactivity such as by coupling with glutathione, or by reduction using NAD(P)H-dependent reductases and dehydrogenases of various substrate specificities. Plant cell chloroplasts produce reactive electrophile oxylipins named γ-ketols downstream of enzymatic lipid peroxidation. The chloroplast envelope quinone oxidoreductase homolog (ceQORH) from Arabidopsis thaliana was previously shown to reduce the reactive double bond of γ-ketols. In marked difference with its cytosolic homolog alkenal reductase (AtAER) that displays a high activity toward the ketodiene 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE) and the ketotriene 13-oxo-9(Z), 11(E), 15(Z)-octadecatrienoic acid (13-KOTE), ceQORH binds, but does not reduce, 13-KODE and 13-KOTE. Crystal structures of apo-ceQORH and ceQORH bound to 13-KOTE or to NADP+ and 13-KOTE have been solved showing a large ligand binding site, also observed in the structure of the cytosolic alkenal/one reductase. Positioning of the α,β-unsaturated carbonyl of 13-KOTE in ceQORH-NADP+-13-KOTE, far away from the NADP+ nicotinamide ring, provides a rational for the absence of activity with the ketodienes and ketotrienes. ceQORH is a monomeric enzyme in solution whereas other enzymes from the quinone oxidoreductase family are stable dimers and a structural explanation of this difference is proposed. A possible in vivo role of ketodienes and ketotrienes binding to ceQORH is also discussed.
Collapse
Affiliation(s)
- Sarah Mas y mas
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS)Grenoble, France
| | - Gilles Curien
- Laboratoire de Physiologie Cellulaire & Végétale, BIG, Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS), INRAGrenoble, France
| | - Cécile Giustini
- Laboratoire de Physiologie Cellulaire & Végétale, BIG, Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS), INRAGrenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire & Végétale, BIG, Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS), INRAGrenoble, France
| | - Jean-Luc Ferrer
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS)Grenoble, France
| | - David Cobessi
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS)Grenoble, France
- *Correspondence: David Cobessi
| |
Collapse
|
11
|
Franklin MC, Cheung J, Rudolph MJ, Burshteyn F, Cassidy M, Gary E, Hillerich B, Yao ZK, Carlier PR, Totrov M, Love JD. Structural genomics for drug design against the pathogen Coxiella burnetii. Proteins 2015; 83:2124-36. [PMID: 26033498 DOI: 10.1002/prot.24841] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 05/01/2015] [Accepted: 05/19/2015] [Indexed: 11/11/2022]
Abstract
Coxiella burnetii is a highly infectious bacterium and potential agent of bioterrorism. However, it has not been studied as extensively as other biological agents, and very few of its proteins have been structurally characterized. To address this situation, we undertook a study of critical metabolic enzymes in C. burnetii that have great potential as drug targets. We used high-throughput techniques to produce novel crystal structures of 48 of these proteins. We selected one protein, C. burnetii dihydrofolate reductase (CbDHFR), for additional work to demonstrate the value of these structures for structure-based drug design. This enzyme's structure reveals a feature in the substrate binding groove that is different between CbDHFR and human dihydrofolate reductase (hDHFR). We then identified a compound by in silico screening that exploits this binding groove difference, and demonstrated that this compound inhibits CbDHFR with at least 25-fold greater potency than hDHFR. Since this binding groove feature is shared by many other prokaryotes, the compound identified could form the basis of a novel antibacterial agent effective against a broad spectrum of pathogenic bacteria.
Collapse
Affiliation(s)
| | - Jonah Cheung
- Special Projects Division, New York Structural Biology Center, New York
| | - Michael J Rudolph
- Special Projects Division, New York Structural Biology Center, New York
| | - Fiana Burshteyn
- Special Projects Division, New York Structural Biology Center, New York
| | - Michael Cassidy
- Special Projects Division, New York Structural Biology Center, New York
| | - Ebony Gary
- Special Projects Division, New York Structural Biology Center, New York
| | - Brandan Hillerich
- Special Projects Division, New York Structural Biology Center, New York
| | - Zhong-Ke Yao
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | - Paul R Carlier
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | | | - James D Love
- Special Projects Division, New York Structural Biology Center, New York
| |
Collapse
|
12
|
Guo PC, Ma XX, Bao ZZ, Ma JD, Chen Y, Zhou CZ. Structural insights into the cofactor-assisted substrate recognition of yeast quinone oxidoreductase Zta1. J Struct Biol 2011; 176:112-8. [PMID: 21820057 DOI: 10.1016/j.jsb.2011.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/14/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
Abstract
Quinone oxidoreductase (QOR EC1.6.5.5) catalyzes the reduction of quinone to hydroxyquinone using NADPH as a cofactor. Here we present the crystal structure of the ζ-crystallin-like QOR Zta1 from Saccharomycescerevisiae in apo-form at 2.00 Å and complexed with NADPH at 1.59 Å resolution. Zta1 forms a homodimer, with each subunit containing a catalytic and a cofactor-binding domain. Upon NADPH binding to the interdomain cleft, the two domains shift towards each other, producing a better fit for NADPH, and tightening substrate binding. Computational simulation combined with site-directed mutagenesis and enzymatic activity analysis defined a potential quinone-binding site that determines the stringent substrate specificity. Moreover, multiple-sequence alignment and kinetics assays implied that a single-residue change from Arg in lower organisms to Gly in vertebrates possibly resulted in elevation of enzymatic activity of ζ-crystallin-like QORs throughout evolution.
Collapse
Affiliation(s)
- Peng-Chao Guo
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, People's Republic of China
| | | | | | | | | | | |
Collapse
|
13
|
Porté S, Moeini A, Reche I, Shafqat N, Oppermann U, Farrés J, Parés X. Kinetic and structural evidence of the alkenal/one reductase specificity of human ζ-crystallin. Cell Mol Life Sci 2011; 68:1065-77. [PMID: 20835842 PMCID: PMC11114546 DOI: 10.1007/s00018-010-0508-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/04/2010] [Accepted: 08/10/2010] [Indexed: 12/01/2022]
Abstract
Human ζ-crystallin is a Zn(2+)-lacking medium-chain dehydrogenase/reductase (MDR) included in the quinone oxidoreductase (QOR) family because of its activity with quinones. In the present work a novel enzymatic activity was characterized: the double bond α,β-hydrogenation of medium-chain 2-alkenals and 3-alkenones. The enzyme is especially active with lipid peroxidation products such as 4-hydroxyhexenal, and a role in their detoxification is discussed. This specificity is novel in the QOR family, and it is similar to that described in the distantly related alkenal/one reductase family. Moreover, we report the X-ray structure of ζ-crystallin, which represents the first structure solved for a tetrameric Zn(2+)-lacking MDR, and which allowed the identification of the active-site lining residues. Docking simulations suggest a role for Tyr53 and Tyr59 in catalysis. The kinetics of Tyr53Phe and Tyr59Phe mutants support the implication of Tyr53 in binding/catalysis of alkenal/one substrates, while Tyr59 is involved in the recognition of 4-OH-alkenals.
Collapse
Affiliation(s)
- Sergio Porté
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
| | - Agrin Moeini
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
| | - Irene Reche
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
| | - Naeem Shafqat
- Structural Genomics Consortium, University of Oxford, Old Road Research Campus, Oxford, OX3 7DQ UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Research Campus, Oxford, OX3 7DQ UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Oxford, OX3 7DQ UK
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
| |
Collapse
|
14
|
Bandaranayake PC, Filappova T, Tomilov A, Tomilova NB, Jamison-McClung D, Ngo Q, Inoue K, Yoder JI. A single-electron reducing quinone oxidoreductase is necessary to induce haustorium development in the root parasitic plant Triphysaria. THE PLANT CELL 2010; 22:1404-19. [PMID: 20424175 PMCID: PMC2879752 DOI: 10.1105/tpc.110.074831] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 03/19/2010] [Accepted: 04/07/2010] [Indexed: 05/18/2023]
Abstract
Parasitic plants in the Orobanchaceae develop haustoria in response to contact with host roots or chemical haustoria-inducing factors. Experiments in this manuscript test the hypothesis that quinolic-inducing factors activate haustorium development via a signal mechanism initiated by redox cycling between quinone and hydroquinone states. Two cDNAs were previously isolated from roots of the parasitic plant Triphysaria versicolor that encode distinct quinone oxidoreductases. QR1 encodes a single-electron reducing NADPH quinone oxidoreductase similar to zeta-crystallin. The QR2 enzyme catalyzes two electron reductions typical of xenobiotic detoxification. QR1 and QR2 transcripts are upregulated in a primary response to chemical-inducing factors, but only QR1 was upregulated in response to host roots. RNA interference technology was used to reduce QR1 and QR2 transcripts in Triphysaria roots that were evaluated for their ability to form haustoria. There was a significant decrease in haustorium development in roots silenced for QR1 but not in roots silenced for QR2. The infrequent QR1 transgenic roots that did develop haustoria had levels of QR1 similar to those of nontransgenic roots. These experiments implicate QR1 as one of the earliest genes on the haustorium signal transduction pathway, encoding a quinone oxidoreductase necessary for the redox bioactivation of haustorial inducing factors.
Collapse
Affiliation(s)
- Pradeepa C.G. Bandaranayake
- Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka 20400
- Department of Plant Sciences, University of California, Davis, California 96516
| | - Tatiana Filappova
- Department of Plant Sciences, University of California, Davis, California 96516
| | - Alexey Tomilov
- Department of Plant Sciences, University of California, Davis, California 96516
| | - Natalya B. Tomilova
- Department of Plant Sciences, University of California, Davis, California 96516
| | | | - Quy Ngo
- Department of Plant Sciences, University of California, Davis, California 96516
| | - Kentaro Inoue
- Department of Plant Sciences, University of California, Davis, California 96516
| | - John I. Yoder
- Department of Plant Sciences, University of California, Davis, California 96516
| |
Collapse
|
15
|
Lapucci A, Lulli M, Amedei A, Papucci L, Witort E, Di Gesualdo F, Bertolini F, Brewer G, Nicolin A, Bevilacqua A, Schiavone N, Morello D, Donnini M, Capaccioli S. zeta-Crystallin is a bcl-2 mRNA binding protein involved in bcl-2 overexpression in T-cell acute lymphocytic leukemia. FASEB J 2010; 24:1852-65. [PMID: 20103721 DOI: 10.1096/fj.09-140459] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The human antiapoptotic bcl-2 gene has been discovered in t(14;18) B-cell leukemias/lymphomas because of its overexpression caused at a transcriptional control level by the bcl-2/IgH fusion gene. We were the first to disclose the post-transcriptional control of bcl-2 expression mediated by interactions of an adenine + uracil (AU)-rich element (ARE) in the 3'-UTR of bcl-2 mRNA with AU-binding proteins (AUBPs). Here, we identify and characterize zeta-crystallin as a new bcl-2 AUBP, whose silencing or overexpression has impact on bcl-2 mRNA stability. An increased Bcl-2 level observed in normal phytohemagglutinin (PHA)-activated T lymphocytes, acute lymphatic leukemia (ALL) T-cell lines, and T cells of patients with leukemia in comparison with normal non-PHA-activated T lymphocytes was concomitant with an increase in zeta-crystallin level. The specific association of zeta-crystallin with the bcl-2 ARE was significantly enhanced in T cells of patients with ALL, which accounts for the higher stability of bcl-2 mRNA and suggests a possible contribution of zeta-crystallin to bcl-2 overexpression occurring in this leukemia.
Collapse
Affiliation(s)
- Andrea Lapucci
- Department of Experimental Pathology and Oncology, University of Florence, Florence, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Pilka ES, Niesen FH, Lee WH, El-Hawari Y, Dunford JE, Kochan G, Wsol V, Martin HJ, Maser E, Oppermann U. Structural basis for substrate specificity in human monomeric carbonyl reductases. PLoS One 2009; 4:e7113. [PMID: 19841672 PMCID: PMC2741203 DOI: 10.1371/journal.pone.0007113] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 08/24/2009] [Indexed: 11/18/2022] Open
Abstract
Carbonyl reduction constitutes a phase I reaction for many xenobiotics and is carried out in mammals mainly by members of two protein families, namely aldo-keto reductases and short-chain dehydrogenases/reductases. In addition to their capacity to reduce xenobiotics, several of the enzymes act on endogenous compounds such as steroids or eicosanoids. One of the major carbonyl reducing enzymes found in humans is carbonyl reductase 1 (CBR1) with a very broad substrate spectrum. A paralog, carbonyl reductase 3 (CBR3) has about 70% sequence identity and has not been sufficiently characterized to date. Screening of a focused xenobiotic compound library revealed that CBR3 has narrower substrate specificity and acts on several orthoquinones, as well as isatin or the anticancer drug oracin. To further investigate structure-activity relationships between these enzymes we crystallized CBR3, performed substrate docking, site-directed mutagenesis and compared its kinetic features to CBR1. Despite high sequence similarities, the active sites differ in shape and surface properties. The data reveal that the differences in substrate specificity are largely due to a short segment of a substrate binding loop comprising critical residues Trp229/Pro230, Ala235/Asp236 as well as part of the active site formed by Met141/Gln142 in CBR1 and CBR3, respectively. The data suggest a minor role in xenobiotic metabolism for CBR3. Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.
Collapse
Affiliation(s)
- Ewa S. Pilka
- Structural Genomics Consortium, University of Oxford, Headington, United Kingdom
| | - Frank H. Niesen
- Structural Genomics Consortium, University of Oxford, Headington, United Kingdom
| | - Wen Hwa Lee
- Structural Genomics Consortium, University of Oxford, Headington, United Kingdom
| | | | - James E. Dunford
- Nuffield Department of Orthopedic Surgery, Rheumatology and Musculoskeletal Sciences, Botnar Research Center, Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
| | - Grazyna Kochan
- Structural Genomics Consortium, University of Oxford, Headington, United Kingdom
| | - Vladimir Wsol
- Faculty of Pharmacy, Charles University, Hradec Kralove, Czech Republic
| | | | | | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Headington, United Kingdom
- Nuffield Department of Orthopedic Surgery, Rheumatology and Musculoskeletal Sciences, Botnar Research Center, Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|