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Xiong Z, Zhang N, Xu L, Deng Z, Limwachiranon J, Guo Y, Han Y, Yang W, Scharf DH. Urease of Aspergillus fumigatus Is Required for Survival in Macrophages and Virulence. Microbiol Spectr 2023; 11:e0350822. [PMID: 36916906 PMCID: PMC10100864 DOI: 10.1128/spectrum.03508-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/09/2023] [Indexed: 03/16/2023] Open
Abstract
The number of patients suffering from fungal diseases has constantly increased during the last decade. Among the fungal pathogens, the airborne filamentous fungus Aspergillus fumigatus can cause chronic and fatal invasive mold infections. So far, only three major classes of drugs (polyenes, azoles, and echinocandins) are available for the treatment of life-threatening fungal infections, and all present pharmacological drawbacks (e.g., low solubility or toxicity). Meanwhile, clinical antifungal-resistant isolates are continuously emerging. Therefore, there is a high demand for novel antifungal drugs, preferentially those that act on new targets. We studied urease and the accessory proteins in A. fumigatus to determine their biochemical roles and their influence on virulence. Urease is crucial for the growth on urea as the sole nitrogen source, and the transcript and protein levels are elevated on urea media. The urease deficient mutant displays attenuated virulence, and its spores are more susceptible to macrophage-mediated killing. We demonstrated that this observation is associated with an inability to prevent the acidification of the phagosome. Furthermore, we could show that a nickel-chelator inhibits growth on urea. The nickel chelator is also able to reverse the effects of urease on macrophage killing and phagosome acidification, thereby reducing virulence in systemic and trachea infection models. IMPORTANCE The development of antifungal drugs is an urgent task, but it has proven to be difficult due to many similarities between fungal and animal cells. Here, we characterized the urease system in A. fumigatus, which depends on nickel for activity. Notably, nickel is not a crucial element for humans. Therefore, we went further to explore the role of nickel-dependent urease in host-pathogen interactions. We were able to show that urease is important in preventing the acidification of the phagosome and therefore reduces the killing of conidia by macrophages. Furthermore, the deletion of urease shows reduced virulence in murine infection models. Taken together, we identified urease as an essential virulence factor of A. fumigatus. We were able to show that the application of the nickel-chelator dimethylglyoxime is effective in both in vitro and in vivo infection models. This suggests that nickel chelators or urease inhibitors are potential candidates for the development of novel antifungal drugs.
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Affiliation(s)
- Zhenzhen Xiong
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Nan Zhang
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Liru Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiduo Deng
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jarukitt Limwachiranon
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaojie Guo
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Han
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Yang
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Daniel H. Scharf
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- Key Laboratory of Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou, China
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2
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Wang K. GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability. Brief Bioinform 2023; 24:6987821. [PMID: 36642411 DOI: 10.1093/bib/bbac620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 01/17/2023] Open
Abstract
Accurately predicting the interaction modes for metalloproteins remains extremely challenging in structure-based drug design and mechanism analysis of enzymatic catalysis due to the complexity of metal coordination in metalloproteins. Here, we report a docking method for metalloproteins based on geometric probability (GPDOCK) with unprecedented accuracy. The docking tests of 10 common metal ions with 9360 metalloprotein-ligand complexes demonstrate that GPDOCK has an accuracy of 94.3% in predicting binding pose. What is more, it can accurately realize the docking of metalloproteins with ligand when one or two water molecules are engaged in the metal ion coordination. Since GPDOCK only depends on the three-dimensional structure of metalloprotein and ligand, structure-based machine learning model is employed for the scoring of binding poses, which significantly improves computational efficiency. The proposed docking strategy can be an effective and efficient tool for drug design and further study of binding mechanism of metalloproteins. The manual of GPDOCK and the code for the logistical regression model used to re-rank the docking results are available at https://github.com/wangkai-zhku/GPDOCK.git.
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Affiliation(s)
- Kai Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China.,Abinitio Technology Company, Ltd, Guangzhou 510640, P. R. China
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3
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Abstract
Hydrogenases and ureases play vital metabolic functions in all three domains of life. However, nickel ions are cytotoxic because they can inactivate enzymes that require less competitive ions (e.g. Mg2+) in the Irving-Williams series to function. Life has evolved elegant mechanisms to solve the problem of delivering the toxic metal to the active site of nickel-containing enzymes inside the cells. Here, we review our current understanding of nickel trafficking along the hydrogenase and urease maturation pathways. Metallochaperones and accessory proteins (SlyD, HypA, HypB, UreD, UreE, UreF, and UreG) form specific protein complexes to allow the transfer of nickel from one protein to another without releasing the toxic metal into the cytoplasm. The role of SlyD is not fully understood, but it can interact with and transfer its nickel to HypB. In the hydrogenase maturation pathway, nickel is transferred from HypB to HypA, which can then deliver its nickel to the hydrogenase large subunit precursor. In Helicobacter pylori, the urease maturation pathway receives its nickel from HypA of the hydrogenase maturation pathway via the formation of a HypA/UreE2 complex. Guanosine triphosphate (GTP) binding promotes the formation of a UreE2G2 complex, where UreG receives a nickel from UreE. In the final step of the urease maturation, nickel/GTP-bound UreG forms an activation complex with UreF, UreD, and apo-urease. Upon GTP hydrolysis, nickel is released from UreG to the urease. Finally, some common themes learned from the hydrogenase-urease maturation pathway are discussed.
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Affiliation(s)
- Ka Lung Tsang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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4
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Broll V, Perin APA, Lopes FC, Martinelli AHS, Moyetta NR, Fruttero LL, Grahl MV, Uberti AF, Demartini DR, Ligabue-Braun R, Carlini CR. Non-enzymatic properties of Proteus mirabilis urease subunits. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Nickel as a virulence factor in the Class I bacterial carcinogen, Helicobacter pylori. Semin Cancer Biol 2021; 76:143-155. [PMID: 33865991 DOI: 10.1016/j.semcancer.2021.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 01/16/2023]
Abstract
Helicobacter pylori is a human bacterial pathogen that causes peptic ulcers and has been designated a Class I carcinogen by the International Agency for Research on Cancer (IARC). Its ability to survive in the acid environment of the stomach, to colonize the stomach mucosa, and to cause cancer, are linked to two enzymes that require nickel-urease and hydrogenase. Thus, nickel is an important virulence factor and the proteins involved in nickel trafficking are potential antibiotic targets. This review summarizes the nickel biochemistry of H. pylori with a focus on the roles of nickel in virulence, nickel homeostasis, maturation of urease and hydrogenase, and the unique nickel trafficking that occurs between the hydrogenase maturation pathway and urease nickel incorporation that is mediated by the metallochaperone HypA and its partner, HypB.
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6
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Pierro A, Etienne E, Gerbaud G, Guigliarelli B, Ciurli S, Belle V, Zambelli B, Mileo E. Nickel and GTP Modulate Helicobacter pylori UreG Structural Flexibility. Biomolecules 2020; 10:E1062. [PMID: 32708696 PMCID: PMC7408563 DOI: 10.3390/biom10071062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
UreG is a P-loop GTP hydrolase involved in the maturation of nickel-containing urease, an essential enzyme found in plants, fungi, bacteria, and archaea. This protein couples the hydrolysis of GTP to the delivery of Ni(II) into the active site of apo-urease, interacting with other urease chaperones in a multi-protein complex necessary for enzyme activation. Whereas the conformation of Helicobacter pylori (Hp) UreG was solved by crystallography when it is in complex with two other chaperones, in solution the protein was found in a disordered and flexible form, defining it as an intrinsically disordered enzyme and indicating that the well-folded structure found in the crystal state does not fully reflect the behavior of the protein in solution. Here, isothermal titration calorimetry and site-directed spin labeling coupled to electron paramagnetic spectroscopy were successfully combined to investigate HpUreG structural dynamics in solution and the effect of Ni(II) and GTP on protein mobility. The results demonstrate that, although the protein maintains a flexible behavior in the metal and nucleotide bound forms, concomitant addition of Ni(II) and GTP exerts a structural change through the crosstalk of different protein regions.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy;
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy;
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
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7
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Targeting the Protein Tunnels of the Urease Accessory Complex: A Theoretical Investigation. Molecules 2020; 25:molecules25122911. [PMID: 32599898 PMCID: PMC7355429 DOI: 10.3390/molecules25122911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Urease is a nickel-containing enzyme that is essential for the survival of several and often deadly pathogenic bacterial strains, including Helicobacter pylori. Notwithstanding several attempts, the development of direct urease inhibitors without side effects for the human host remains, to date, elusive. The recently solved X-ray structure of the HpUreDFG accessory complex involved in the activation of urease opens new perspectives for structure-based drug discovery. In particular, the quaternary assembly and the presence of internal tunnels for nickel translocation offer an intriguing possibility to target the HpUreDFG complex in the search of indirect urease inhibitors. In this work, we adopted a theoretical framework to investigate such a hypothesis. Specifically, we searched for putative binding sites located at the protein–protein interfaces on the HpUreDFG complex, and we challenged their druggability through structure-based virtual screening. We show that, by virtue of the presence of tunnels, some protein–protein interfaces on the HpUreDFG complex are intrinsically well suited for hosting small molecules, and, as such, they possess good potential for future drug design endeavors.
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8
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Xu YY, Huang CJ, Xu L, Jiang XW, Xu XW, Xu XW. Complete Genome Sequences of Leclercia sp. W6 and W17 Isolated from a Gastric Cancer Patient. Curr Microbiol 2020; 77:2775-2782. [PMID: 32533320 DOI: 10.1007/s00284-020-02075-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 06/04/2020] [Indexed: 11/26/2022]
Abstract
Leclercia sp. W6 and W17, which belong to the Enterobacteriaceae, were isolated from a stomach sample from a 78-year-old female gastric cancer patient, and genomic sequencing and analysis were performed. The genome of Leclercia sp. W6 consists of one chromosome with a size of 4,945,486 bp, while that of Leclercia sp. W17 contains one chromosome and two plasmids with a total size of 5,125,645 bp. Average nucleotide identity (ANI) calculations indicated that strains W6 and W17 exhibited similarities < 91.0% to other strains within the Enterobacteriaceae, except for six Leclercia strains. Phylogenomic analysis based on core-genome showed that strains W6 and W17 belong to the genus Leclercia, and phylogenetic analysis based on ANI values revealed that strains W6 and W17 formed an independent clade from those six Leclercia strains. Furthermore, comparative genomic analysis revealed that strains W6 and W17 had 5086 orthologous clusters (OCs) in their pan-genomes, and 59 exclusive OCs which were absent in their closest relatives. Genomic annotations revealed that the genomes of strains W6 and W17 encoded genes related to multidrug resistance clusters, multiple antibiotic resistance loci, and multidrug efflux pumps and had an identical urease gene cluster and a dissimilatory nitrate reduction pathway. Bioinformatic analyses indicated that strains W6 and W17 represented a novel species within the genus Leclercia. Genomic annotations revealed that these strains encoded genes related to multidrug resistance, nitrate reduction, and urease activity, which contribute to gastric malignant transformation. This will broaden our knowledge of the genetic mechanisms of the Enterobacteriaceae and help improve the clinical conditions of gastric cancer patients.
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Affiliation(s)
- Yun-Yun Xu
- Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, People's Republic of China
| | - Chao-Jie Huang
- Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, People's Republic of China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xia-Wei Jiang
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310012, People's Republic of China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Xiao-Wu Xu
- Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, People's Republic of China.
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Xuhui District, 274th Dong'an Road, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
- Shanghai Pancreatic Cancer Institute, Shanghai, 200032, People's Republic of China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China.
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9
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Jamwal S, Ranote S, Dautoo U, Chauhan GS. Improving activity and stabilization of urease by crosslinking to nanoaggregate forms for herbicide degradation. Int J Biol Macromol 2020; 158:521-529. [PMID: 32360462 DOI: 10.1016/j.ijbiomac.2020.04.224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/13/2020] [Accepted: 04/25/2020] [Indexed: 01/14/2023]
Abstract
Bioremediation is the most effective green protocol for degradation of environmental contaminants. Present study involves carrier free urease immobilization with synthesis of its new crosslinked aggregates using two different crosslinkers, divinyl benzene (DVB) and tripropyleneglycol dimethacrylate (TPGDA) via free radical mechanism. Resulting crosslinked ureases were further converted to nanoform (CLUNAs) using solvent evaporation technique. The activity of free and the crosslinked ureases was studied as a function of operational parameters viz. temperature (20-80), pH (2-11) and substrate concentration (5-20 mM) using urea as substrate at contact time of 10 min. Storability study of the pristine urease and CLUNAs was carried out for 40 days, and the CLUNAs were reused in 10 repeat cycles to assess their reusability. Isoproturone degradation was studied under the above-cited range of pH and temperature and results were recorded after 24 h.
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Affiliation(s)
- Shivani Jamwal
- Himachal Pradesh University, Department of Chemistry, Summerhill, Shimla 171005, Himachal Pradesh, India
| | - Sunita Ranote
- Himachal Pradesh University, Department of Chemistry, Summerhill, Shimla 171005, Himachal Pradesh, India
| | - Umesh Dautoo
- Himachal Pradesh University, Department of Chemistry, Summerhill, Shimla 171005, Himachal Pradesh, India
| | - Ghanshyam S Chauhan
- Himachal Pradesh University, Department of Chemistry, Summerhill, Shimla 171005, Himachal Pradesh, India.
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10
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Zambelli B, Mazzei L, Ciurli S. Intrinsic disorder in the nickel-dependent urease network. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:307-330. [DOI: 10.1016/bs.pmbts.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Abstract
Maturation of urease involves post-translational insertion of nickel ions to form an active site with a carbamylated lysine ligand and is assisted by urease accessory proteins UreD, UreE, UreF and UreG. Here, we review our current understandings on how these urease accessory proteins facilitate the urease maturation. The urease maturation pathway involves the transfer of Ni2+ from UreE → UreG → UreF/UreD → urease. To avoid the release of the toxic metal to the cytoplasm, Ni2+ is transferred from one urease accessory protein to another through specific protein–protein interactions. One central theme depicts the role of guanosine triphosphate (GTP) binding/hydrolysis in regulating the binding/release of nickel ions and the formation of the protein complexes. The urease and [NiFe]-hydrogenase maturation pathways cross-talk with each other as UreE receives Ni2+ from hydrogenase maturation factor HypA. Finally, the druggability of the urease maturation pathway is reviewed.
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12
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Sgrignani J, Chen J, Alimonti A, Cavalli A. How phosphorylation influences E1 subunit pyruvate dehydrogenase: A computational study. Sci Rep 2018; 8:14683. [PMID: 30279533 PMCID: PMC6168537 DOI: 10.1038/s41598-018-33048-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022] Open
Abstract
Pyruvate (PYR) dehydrogenase complex (PDC) is an enzymatic system that plays a crucial role in cellular metabolism as it controls the entry of carbon into the Krebs cycle. From a structural point of view, PDC is formed by three different subunits (E1, E2 and E3) capable of catalyzing the three reaction steps necessary for the full conversion of pyruvate to acetyl-CoA. Recent investigations pointed out the crucial role of this enzyme in the replication and survival of specific cancer cell lines, renewing the interest of the scientific community. Here, we report the results of our molecular dynamics studies on the mechanism by which posttranslational modifications, in particular the phosphorylation of three serine residues (Ser-264-α, Ser-271-α, and Ser-203-α), influence the enzymatic function of the protein. Our results support the hypothesis that the phosphorylation of Ser-264-α and Ser-271-α leads to (1) a perturbation of the catalytic site structure and dynamics and, especially in the case of Ser-264-α, to (2) a reduction in the affinity of E1 for the substrate. Additionally, an analysis of the channels connecting the external environment with the catalytic site indicates that the inhibitory effect should not be due to the occlusion of the access/egress pathways to/from the active site.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - JingJing Chen
- Institute of Research in Oncology (IOR), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Andrea Alimonti
- Institute of Research in Oncology (IOR), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Kappaun K, Piovesan AR, Carlini CR, Ligabue-Braun R. Ureases: Historical aspects, catalytic, and non-catalytic properties - A review. J Adv Res 2018; 13:3-17. [PMID: 30094078 PMCID: PMC6077230 DOI: 10.1016/j.jare.2018.05.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 12/11/2022] Open
Abstract
Urease (urea amidohydrolase, EC 3.5.1.5) is a nickel-containing enzyme produced by plants, fungi, and bacteria that catalyzes the hydrolysis of urea into ammonia and carbamate. Urease is of historical importance in Biochemistry as it was the first enzyme ever to be crystallized (1926). Finding nickel in urease's active site (1975) was the first indication of a biological role for this metal. In this review, historical and structural features, kinetics aspects, activation of the metallocenter and inhibitors of the urea hydrolyzing activity of ureases are discussed. The review also deals with the non-enzymatic biological properties, whose discovery 40 years ago started a new chapter in the study of ureases. Well recognized as virulence factors due to the production of ammonia and alkalinization in diseases by urease-positive microorganisms, ureases have pro-inflammatory, endocytosis-inducing and neurotoxic activities that do not require ureolysis. Particularly relevant in plants, ureases exert insecticidal and fungitoxic effects. Data on the jack bean urease and on jaburetox, a recombinant urease-derived peptide, have indicated that interactions with cell membrane lipids may be the basis of the non-enzymatic biological properties of ureases. Altogether, with this review we wanted to invite the readers to take a second look at ureases, very versatile proteins that happen also to catalyze the breakdown of urea into ammonia and carbamate.
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Affiliation(s)
- Karine Kappaun
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Angela Regina Piovesan
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Celia Regina Carlini
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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14
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The synthesis and evaluation of phenoxyacylhydroxamic acids as potential agents for Helicobacter pylori infections. Bioorg Med Chem 2018; 26:4145-4152. [DOI: 10.1016/j.bmc.2018.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 12/11/2022]
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15
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Tarsia C, Danielli A, Florini F, Cinelli P, Ciurli S, Zambelli B. Targeting Helicobacter pylori urease activity and maturation: In-cell high-throughput approach for drug discovery. Biochim Biophys Acta Gen Subj 2018; 1862:2245-2253. [PMID: 30048738 DOI: 10.1016/j.bbagen.2018.07.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/12/2018] [Accepted: 07/18/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Helicobacter pylori is a bacterium strongly associated with gastric cancer. It thrives in the acidic environment of the gastric niche of large portions of the human population using a unique adaptive mechanism that involves the catalytic activity of the nickel-dependent enzyme urease. Targeting urease represents a key strategy for drug design and H. pylori eradication. METHOD Here, we describe a novel method to screen, directly in the cellular environment, urease inhibitors. A ureolytic Escherichia coli strain was engineered by cloning the entire urease operon in an expression plasmid and used to test in-cell urease inhibition with a high-throughput colorimetric assay. A two-plasmid system was further developed to evaluate the ability of small peptides to block the protein interactions that lead to urease maturation. RESULTS The developed assay is a robust cellular model to test, directly in the cell environment, urease inhibitors. The efficacy of a co-expressed peptide to affect the interaction between UreF and UreD, two accessory proteins necessary for urease activation, was observed. This event involves a process that occurs through folding upon binding, pointing to the importance of intrinsically disordered hot spots in protein interfaces. CONCLUSIONS The developed system allows the concomitant screening of a large number of drug candidates that interfere with the urease activity both at the level of the enzyme catalysis and maturation. GENERAL SIGNIFICANCE As inhibition of urease has the potential of being a global antibacterial strategy for a large number of infections, this work paves the way for the development of new candidates for antibacterial drugs.
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Affiliation(s)
- Cinzia Tarsia
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Alberto Danielli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Francesca Florini
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Paolo Cinelli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Stefano Ciurli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Barbara Zambelli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy.
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Hu HQ, Huang HT, Maroney MJ. The Helicobacter pylori HypA·UreE 2 Complex Contains a Novel High-Affinity Ni(II)-Binding Site. Biochemistry 2018; 57:2932-2942. [PMID: 29708738 DOI: 10.1021/acs.biochem.8b00127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Helicobacter pylori is a human pathogen that colonizes the stomach, is the major cause of ulcers, and has been associated with stomach cancers. To survive in the acidic environment of the stomach, H. pylori uses urease, a nickel-dependent enzyme, to produce ammonia for maintenance of cellular pH. The bacteria produce apo-urease in large quantities and activate it by incorporating nickel under acid shock conditions. Urease nickel incorporation requires the urease-specific metallochaperone UreE and the (UreFGH)2 maturation complex. In addition, the H. pylori nickel urease maturation pathway recruits accessory proteins from the [NiFe] hydrogenase maturation pathway, namely, HypA and HypB. HypA and UreE dimers (UreE2) are known to form a protein complex, the role of which in urease maturation is largely unknown. Herein, we examine the nickel-binding properties and protein-protein interactions of HypA and UreE2 using isothermal titration calorimetry and fluorometric methods under neutral and acidic pH conditions to gain insight into the roles played by HypA in urease maturation. The results reveal that HypA and UreE2 form a stable complex with micromolar affinity that protects UreE from hydrolytic degradation. The HypA·UreE2 complex contains a unique high-affinity (nanomolar) Ni2+-binding site that is maintained under conditions designed to mimic acid shock (pH 6.3). The data are interpreted in terms of a proposed mechanism wherein HypA and UreE2 act as co-metallochaperones that target the delivery of Ni2+ to apo-urease with high fidelity.
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17
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Mazzei L, Cianci M, Gonzalez Vara A, Ciurli S. The structure of urease inactivated by Ag(i): a new paradigm for enzyme inhibition by heavy metals. Dalton Trans 2018; 47:8240-8247. [DOI: 10.1039/c8dt01190g] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular details of the inactivation of urease, a nickel-dependent virulence factor for human pathogens and negatively affecting the efficiency of soil nitrogen fertilization, are elucidated through the crystal structure of the enzyme complex with Ag(i).
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- I-40127 Bologna
- Italy
| | - Michele Cianci
- Department of Agricultural
- Food and Environmental Sciences
- Marche Polytechnic University
- Ancona
- Italy
| | | | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- I-40127 Bologna
- Italy
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18
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Structural insights into how GTP-dependent conformational changes in a metallochaperone UreG facilitate urease maturation. Proc Natl Acad Sci U S A 2017; 114:E10890-E10898. [PMID: 29203664 DOI: 10.1073/pnas.1712658114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ability of metallochaperones to allosterically regulate the binding/release of metal ions and to switch protein-binding partners along the metal delivery pathway is essential to the metallation of the metalloenzymes. Urease, catalyzing the hydrolysis of urea into ammonia and carbon dioxide, contains two nickel ions bound by a carbamylated lysine in its active site. Delivery of nickel ions for urease maturation is dependent on GTP hydrolysis and is assisted by four urease accessory proteins UreE, UreF, UreG, and UreH(UreD). Here, we determined the crystal structure of the UreG dimer from Klebsiella pneumoniae in complex with nickel and GMPPNP, a nonhydrolyzable analog of GTP. Comparison with the structure of the GDP-bound Helicobacter pylori UreG (HpUreG) in the UreG2F2H2 complex reveals large conformational changes in the G2 region and residues near the 66CPH68 metal-binding motif. Upon GTP binding, the side chains of Cys66 and His68 from each of the UreG protomers rotate toward each other to coordinate a nickel ion in a square-planar geometry. Mutagenesis studies on HpUreG support the conformational changes induced by GTP binding as essential to dimerization of UreG, GTPase activity, in vitro urease activation, and the switching of UreG from the UreG2F2H2 complex to form the UreE2G2 complex with the UreE dimer. The nickel-charged UreE dimer, providing the sole source of nickel, and the UreG2F2H2 complex could activate urease in vitro in the presence of GTP. Based on our results, we propose a mechanism of how conformational changes of UreG during the GTP hydrolysis/binding cycle facilitate urease maturation.
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Masetti M, Musiani F, Bernetti M, Falchi F, Cavalli A, Ciurli S, Recanatini M. Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data. J Comput Chem 2017; 38:1834-1843. [PMID: 28558120 DOI: 10.1002/jcc.24827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 12/14/2022]
Abstract
Force-field parameters are developed for a multisite model of Ni(II) ions to be used in molecular dynamics simulations combined to enhanced sampling methods. The performances of two charge-partitioning schemes are validated by taking into account structural, thermodynamic, and kinetic observables. One of the two models, featuring partial charges on the dummy atoms only, matches both Ni(II) free energy of solvation and water exchange rates. Such model is particularly suited to study complexation events at a fully dynamic description. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Matteo Masetti
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 40, Bologna, I-40127, Italy
| | - Mattia Bernetti
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
- Compunet, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
| | - Federico Falchi
- Compunet, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
| | - Andrea Cavalli
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
- Compunet, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 40, Bologna, I-40127, Italy
| | - Maurizio Recanatini
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
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