1
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Shestakova A, Fatkulin A, Surkova D, Osmolovskiy A, Popova E. First Insight into the Degradome of Aspergillus ochraceus: Novel Secreted Peptidases and Their Inhibitors. Int J Mol Sci 2024; 25:7121. [PMID: 39000228 PMCID: PMC11241649 DOI: 10.3390/ijms25137121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024] Open
Abstract
Aspergillus fungi constitute a pivotal element within ecosystems, serving as both contributors of biologically active compounds and harboring the potential to cause various diseases across living organisms. The organism's proteolytic enzyme complex, termed the degradome, acts as an intermediary in its dynamic interaction with the surrounding environment. Using techniques such as genome and transcriptome sequencing, alongside protein prediction methodologies, we identified putative extracellular peptidases within Aspergillus ochraceus VKM-F4104D. Following manual annotation procedures, a total of 11 aspartic, 2 cysteine, 2 glutamic, 21 serine, 1 threonine, and 21 metallopeptidases were attributed to the extracellular degradome of A. ochraceus VKM-F4104D. Among them are enzymes with promising applications in biotechnology, potential targets and agents for antifungal therapy, and microbial antagonism factors. Thus, additional functionalities of the extracellular degradome, extending beyond mere protein substrate digestion for nutritional purposes, were demonstrated.
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Affiliation(s)
- Anna Shestakova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | - Artem Fatkulin
- Laboratory of Molecular Physiology, HSE University, Moscow 101000, Russia
| | - Daria Surkova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | | | - Elizaveta Popova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
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2
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Potok P, Zawada M, Potocki S. Determination of the role of specific amino acids in the binding of Zn(II), Ni(II), and Cu(II) to the active site of the M10 family metallopeptidase. J Inorg Biochem 2024; 253:112500. [PMID: 38301386 DOI: 10.1016/j.jinorgbio.2024.112500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Metallopeptidases are a group of metal-dependent enzymes that hydrolyze peptide bonds. These enzymes found in Streptococcus pneumoniae assist the pathogen in infecting the host by breaking down host tissues and extracellular matrix proteins. Considering metallopeptidases' significant role in bacterial virulence, inhibiting this enzyme represents a promising avenue for research. These enzymes are characterized by the presence of Zn(II) in the active site, proper coordination of which is essential for their catalytic function. This work aims to determine the significance of the specific amino acids in the metal binding domain of metallopeptidase from S. pneumoniae. For this purpose, we investigated the coordination chemistry of Zn(II), Ni(II), and Cu(II) ions with point-mutated peptide models of the metal-binding domain. Mutations were introduced at His-2 (L1) and Glu-1. Studies have shown that at pH 7.14 (pH of infected lungs by S. pneumoniae), point mutation on glutamic acid caused only minor effects on the binding of Zn(II) and Ni(II), while significantly improving Cu(II) binding. The stability of copper complexes is greater with the mutant Glu-1 → Gln-1 than with the original domain due to a hydrogen bonding network created by the Gln backbone with its side chain. Substituting histidine resulted in a significant reduction in metal binding for all metal ions, highlighting the crucial role of His-2 in metal coordination. Introduced mutations at neutral pH did not significantly affect the secondary structure of metal complexes. However, at alkaline pH, the peptides showed a higher percentage of antiparallel β-sheet structures upon the addition of Cu(II), Ni(II) and Zn(II).
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Affiliation(s)
- Paulina Potok
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Martyna Zawada
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland.
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3
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Wang Y. Erdr1 Drives Macrophage Programming via Dynamic Interplay with YAP1 and Mid1. Immunohorizons 2024; 8:198-213. [PMID: 38392560 PMCID: PMC10916360 DOI: 10.4049/immunohorizons.2400004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Erythroid differentiation regulator 1 (Erdr1) is a stress-induced, widely expressed, highly conserved secreted factor found in both humans and mice. Erdr1 is linked with the Hippo-YAP1 signaling. Initially identified as an inducer of hemoglobin synthesis, Erdr1 emerged as a multifunctional protein, especially in immune cells. Although Erdr1 has been implicated in regulating T cells and NK cell function, its role in macrophage remains unclear. This study explored the function and mechanism of Erdr1 in macrophage inflammatory response. The data demonstrated that Erdr1 could promote anti-inflammatory cytokine production, a function that also has been reported by previous research. However, I found Erdr1 also could play a proinflammatory role. The function of Erdr1 in macrophages depends on its dose and cell density. I observed that Erdr1 expression was inhibited in M1 macrophages but was upregulated in M2 macrophages compared with unpolarized macrophages. I hypothesized that Erdr1 balances the inflammatory response by binding with distinct adaptors dependent on varying concentrations. Mechanistically, I demonstrated YAP1 and Mid1 as the two adaptor proteins of Erdr1. The Erdr1-YAP1 interaction promotes anti-inflammatory cytokine production when Erdr1 levels are elevated, whereas the Erdr1-Mid1 interaction induces proinflammatory cytokine production when Erdr1 levels are decreased. This study highlights the effects of Erdr1 on regulating cytokine production from polarized macrophages potentially by regulating YAP1 in the nonclassical Hippo pathway.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology and Immunology, University of Iowa, IA City, IA
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4
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Feng S, Pan L, Li Q, Zhang Y, Mou F, Liu Z, Zhang Y, Duan L, Qin B, Hu Z. The Isolation, Identification and Immobilization Method of Three Novel Enzymes with Diosgenin-Producing Activity Derived from an Aspergillus flavus. Int J Mol Sci 2023; 24:17611. [PMID: 38139441 PMCID: PMC10743735 DOI: 10.3390/ijms242417611] [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: 10/28/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
Diosgenin is an important raw material used in the synthesis of steroid drugs, and it is widely used in the pharmaceutical industry. The traditional method of producing diosgenin is through using raw materials provided via the plant Dioscorea zingiberensis C. H. Wright (DZW), which is subsequently industrially hydrolyzed using a high quantity of hydrochloric and sulfuric acids at temperatures ranging from 70 °C to 175 °C. This process results in a significant amount of unmanageable wastewater, creates issues of severe environmental pollution and consumes high quantities of energy. As an alternative, the enzymolysis of DZW to produce diosgenin is an environmentally and friendly method with wide-ranging prospects for its application. However, there are still only a few enzymes that are suitable for production on an industrial scale. In this study, three new key enzymes, E1, E2, and E3, with a high conversion stability of diosgenin, were isolated and identified using an enzyme-linked-substrate autography strategy. HPLC-MS/MS identification showed that E1, a 134.45 kDa protein with 1019 amino acids (AAs), is a zinc-dependent protein similar to the M16 family. E2, a 97.89 kDa protein with 910 AAs, is a type of endo-β-1,3-glucanase. E3, a 51.6 kDa protein with 476 AAs, is a type of Xaa-Pro aminopeptidase. In addition, the method to immobilize these proteins was optimized, and stability was achieved. The results show that the optimal immobilization parameters are 3.5% sodium alginate, 3.45% calcium chloride concentration, 1.4 h fixed time, and pH 8.8; and the recovery rate of enzyme activity can reach 43.98%. A level of 70.3% relative enzyme activity can be obtained after employing six cycles of the optimized technology. Compared with free enzymes, immobilized enzymes have improved stability, acid and alkaline resistance and reusability, which are conducive to large-scale industrial production.
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Affiliation(s)
- Shirong Feng
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Lintao Pan
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Quanshun Li
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Yi Zhang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Fangyuan Mou
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Zhao Liu
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Yuanyuan Zhang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Longfei Duan
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Baofu Qin
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (S.F.); (L.P.); (Q.L.); (Y.Z.); (F.M.); (Z.L.); (Y.Z.); (L.D.)
| | - Zhongqiu Hu
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China
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5
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Potok P, Kola A, Valensin D, Capdevila M, Potocki S. Copper Forms a PPII Helix-Like Structure with the Catalytic Domains of Bacterial Zinc Metalloproteases. Inorg Chem 2023; 62:18425-18439. [PMID: 37909295 PMCID: PMC10647932 DOI: 10.1021/acs.inorgchem.3c02391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023]
Abstract
The rapid spread of antibiotic-resistant bacteria continuously raises concerns about the future ineffectiveness of current antimicrobial treatments against infectious diseases. To address this problem, new therapeutic strategies and antimicrobial drugs with unique modes of action are urgently needed. Inhibition of metalloproteases, bacterial virulence factors, is a promising target for the development of antibacterial treatments. In this study, the interaction among Zn(II), Cu(II), and the metal-binding domains of two metalloproteases, AprA (Pseudomonas aureginosa) and CpaA (Acinetobacter baumanii), was investigated. The objective was to determine the coordination sphere of Zn(II) with a peptide model of two zinc-dependent metalloproteases. Additionally, the study explored the formation of Cu(II) complexes with the domains, as Cu(II) has been shown to inhibit metalloproteases. The third aim was to understand the role of nonbinding amino acids in stabilizing the metal complexes formed by these proteases. This work identified specific coordination patterns (HExxHxxxxxH) for both Zn(II) and Cu(II) complexes, with AprA and CpaA exhibiting a higher affinity for Cu(II) compared to Zn(II). The study also found that the CpaA domain has greater stability for both Zn(II) and Cu(II) complexes compared to AprA. The nonbinding amino acids of CpaA surrounding the metal ion contribute to the increased thermodynamic stability of the metal-peptide complex through various intramolecular interactions. These interactions can also influence the secondary structures of the peptides. The presence of certain amino acids, such as tyrosine, arginine, and glutamic acid, and their interactions contribute to the stability and, only in the case of Cu(II) complexes, the formation of a rare protein structure called a left-handed polyproline II helix (PPII), which is known to play a role in the stability and function of various proteins. These findings provide valuable insights into the coordination chemistry of bacterial metalloproteases and expand our understanding of potential mechanisms for inhibiting these enzymes.
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Affiliation(s)
- Paulina Potok
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Arian Kola
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Daniela Valensin
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Merce Capdevila
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Sławomir Potocki
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
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6
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Singh R, Gautam P, Sharma C, Osmolovskiy A. Fibrin and Fibrinolytic Enzyme Cascade in Thrombosis: Unravelling the Role. Life (Basel) 2023; 13:2196. [PMID: 38004336 PMCID: PMC10672518 DOI: 10.3390/life13112196] [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: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Blood clot formation in blood vessels (thrombosis) is a major cause of life-threatening cardiovascular diseases. These clots are formed by αA-, βB-, and ϒ-peptide chains of fibrinogen joined together by isopeptide bonds with the help of blood coagulation factor XIIIa. These clot structures are altered by various factors such as thrombin, platelets, transglutaminase, DNA, histones, and red blood cells. Various factors are used to dissolve the blood clot, such as anticoagulant agents, antiplatelets drugs, fibrinolytic enzymes, and surgical operations. Fibrinolytic enzymes are produced by microorganisms (bacteria, fungi, etc.): streptokinase of Streptococcus hemolyticus, nattokinase of Bacillus subtilis YF 38, bafibrinase of Bacillus sp. AS-S20-I, longolytin of Arthrobotrys longa, versiase of Aspergillus versicolor ZLH-1, etc. They act as a thrombolytic agent by either enhancing the production of plasminogen activators (tissue or urokinase types), which convert inactive plasminogen to active plasmin, or acting as plasmin-like proteins themselves, forming fibrin degradation products which cause normal blood flow again in blood vessels. Fibrinolytic enzymes may be classified in two groups, as serine proteases and metalloproteases, based on their catalytic properties, consisting of a catalytic triad responsible for their fibrinolytic activity having different physiochemical properties (such as molecular weight, pH, and temperature). The analysis of fibrinolysis helps to detect hyperfibrinolysis (menorrhagia, renal failure, etc.) and hypofibrinolysis (diabetes, obesity, etc.) with the help of various fibrinolytic assays such as a fibrin plate assay, fibrin microplate assay, the viscoelastic method, etc. These fibrinolytic activities serve as a key aspect in the recognition of numerous cardiovascular diseases and can be easily produced on a large scale with a short generation time by microbes and are less expensive.
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Affiliation(s)
- Rajni Singh
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India; (P.G.); (C.S.)
| | - Prerna Gautam
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India; (P.G.); (C.S.)
| | - Chhavi Sharma
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India; (P.G.); (C.S.)
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7
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Matić A, Šupljika F, Brkić H, Jurasović J, Karačić Z, Tomić S. Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III. Int J Mol Sci 2023; 24:12747. [PMID: 37628928 PMCID: PMC10454320 DOI: 10.3390/ijms241612747] [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: 07/12/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the Kd values for the binding of Zn2+, Cu2+, and Co2+ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the Kd values for the binding of these metals to an additional binding site. The structure of the catalytic metal's binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn2+, Cu2+, Co2+, and Mn2+ using the QM approach. The structures of the additional binding sites for the Zn2+ and Cu2+ were also identified, and MD simulations showed that two Cu2+ ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn2+ ions bound to these sites.
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Affiliation(s)
- Antonia Matić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Filip Šupljika
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia;
| | - Hrvoje Brkić
- Faculty of Medicine, J. J. Strossmayer University of Osijek, 31000 Osijek, Croatia;
- Faculty of Dental Medicine and Health, J. J. Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Jasna Jurasović
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia;
| | - Zrinka Karačić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
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8
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Lloyd AC, Gregory KS, Isaac RE, Acharya KR. A Molecular Analysis of the Aminopeptidase P-Related Domain of PID-5 from Caenorhabditis elegans. Biomolecules 2023; 13:1132. [PMID: 37509168 PMCID: PMC10377022 DOI: 10.3390/biom13071132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical 'pita-bread fold'. However, the absence of conserved metal-coordinating residues indicates that only a single Zn2+ may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with C. elegans aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research.
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Affiliation(s)
- Anna C. Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
| | - Kyle S. Gregory
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
| | - R. Elwyn Isaac
- School of Biology, University of Leeds, Leeds LS2 9JT, UK;
| | - K. Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
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9
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Suri K, Rajput N, Sharma P, Omble AD, Kulkarni K, Gahlay GK. In silico identification and characterization of the SNPs in the human ASTL gene and their probable role in female infertility. Front Cell Dev Biol 2023; 11:1151672. [PMID: 37363721 PMCID: PMC10285486 DOI: 10.3389/fcell.2023.1151672] [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: 01/26/2023] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Ovastacin (ASTL), a zinc metalloprotease, is released from a fertilized egg during exocytosis of cortical granules which occurs minutes after the sperm and egg fuse. ASTL cleaves ZP2, one of the four primary glycoproteins of human zona pellucida, and this cleavage prevents polyspermy, causes zona pellucida hardening, and also protects the pre-implantation embryo. Any perturbation in the activity of ASTL can thus disturb this process and may lead to infertility without changing the gross morphology of the oocyte. A small amount of ASTL is also released by unfertilized oocytes but its catalytic activity is absent as it is bound by its inhibitor, Fetuin-B (FETUB). Pre-mature release of ASTL when FETUB is absent also causes infertility. To identify and understand the structural and functional effects of deleterious SNPs of ASTL on its interaction with ZP2 and FETUB and hence on fertility, a total of 4,748 SNPs from the dbSNP database were evaluated using a variety of in silico tools. All of the 40 shortlisted nsSNPs were present in the catalytic domain of the protein. Comparison of the wild type with mutants using MutPred2 suggests an alteration in the catalytic activity/zinc binding site in many SNPs. Docking studies show the involvement of hydrophobic interactions and H bonding between ASTL and ZP2 and also between ASTL and FETUB. Four positions in ASTL involved in the hydrophobic interactions (P105 and D200 between ASTL and ZP2; D198 and L278 between ASTL and FETUB) and 5 in H bonding (E75 and R159 between ASTL and ZP2; and K93, R159, and C281 between ASTL and FETUB) have SNP's associated with them validating their importance. Interestingly, a cluster of multiple SNPs was found in the motif 198DRD200, which is also a well-conserved region among several species. Statistical Coupling Analysis (SCA) suggested that the deleterious SNPs were present in the functionally important amino acid positions of ASTL and are evolutionarily coupled. Thus, these results attempt to identify the regions in ASTL, mutations in which can affect its binding with ZP2 or FETUB and cause female infertility.
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Affiliation(s)
- Kapali Suri
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Neha Rajput
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Priya Sharma
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Aishwarya D. Omble
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Gagandeep K. Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
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10
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Gao S, Campbell JX, Oas TG, Franz KJ. Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics. Inorg Chem 2023; 62:7087-7096. [PMID: 37083393 DOI: 10.1021/acs.inorgchem.3c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Histatin 5 (Hist5) is an antimicrobial peptide found in human saliva as part of the innate immune system. Hist5 can bind several metal ions in vitro, and Zn2+ has been shown to function as an inhibitory switch to regulate the peptide's biological activity against the opportunistic fungal pathogen Candida albicans in cell culture. Here, we studied Zn2+ binding to Hist5 at four temperatures from 15 to 37 °C using isothermal titration calorimetry to obtain thermodynamic parameters that were corrected for competing buffer effects. Hist5 bound Zn2+ with a buffer-dependent association constant of ∼105 M-1 and a buffer-independent association constant of ∼6 × 106 M-1 at pH 7.4 and at all temperatures tested. Zn2+ binding was both enthalpically and entropically favorable, with larger entropic contributions at 15 °C and larger enthalpic contributions at 37 °C. Additionally, the Zn:Hist5 binding stoichiometry increased from 1:1 to 2:1 as temperature increased. The enthalpy-entropy compensation and the variable stoichiometry lead us to propose a model in which the Zn-Hist5 complex exists in an equilibrium between two distinct binding modes with different Zn:Hist5 stoichiometries. The in-depth thermodynamic analysis presented herein may help illuminate the biophysical basis for Zn-dependent changes in the antifungal activity of Hist5.
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Affiliation(s)
- Sean Gao
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Joanna X Campbell
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G Oas
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Katherine J Franz
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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11
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Hugele A, Löffler S, Molina BH, Guillon M, Montaser AB, Auriola S, Huttunen KM. Aminopeptidase B can bioconvert L-type amino acid transporter 1 (LAT1)-utilizing amide prodrugs in the brain. Front Pharmacol 2022; 13:1034964. [PMID: 36339537 PMCID: PMC9631218 DOI: 10.3389/fphar.2022.1034964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
A prodrug approach is a powerful method to temporarily change the physicochemical and thus, pharmacokinetic properties of drugs. However, in site-selective targeted prodrug delivery, tissue or cell-specific bioconverting enzyme is needed to be utilized to release the active parent drug at a particular location. Unfortunately, ubiquitously expressed enzymes, such as phosphatases and carboxylesterases are well used in phosphate and ester prodrug applications, but less is known about enzymes selectively expressed, e.g., in the brain and enzymes that can hydrolyze more stable prodrug bonds, such as amides and carbamates. In the present study, L-type amino acid transporter 1 (LAT1)-utilizing amide prodrugs bioconverting enzyme was identified by gradually exploring the environment and possible determinants, such as pH and metal ions, that affect amide prodrug hydrolysis. Based on inducement by cobalt ions and slightly elevated pH (8.5) as well as localization in plasma, liver, and particularly in the brain, aminopeptidase B was proposed to be responsible for the bioconversion of the majority of the studied amino acid amide prodrugs. However, this enzyme hydrolyzed only those prodrugs that contained an aromatic promoiety (L-Phe), while leaving the aliphatic promoeities (L-Lys) and the smallest prodrug (with L-Phe promoiety) intact. Moreover, the parent drugs’ structure (flexibility and the number of aromatic rings) largely affected the bioconversion rate. It was also noticed in this study, that there were species differences in the bioconversion rate by aminopeptidase B (rodents > human), although the in vitro–in vivo correlation of the studied prodrugs was relatively accurate.
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12
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Campbell JX, Gao S, Anand KS, Franz KJ. Zinc Binding Inhibits Cellular Uptake and Antifungal Activity of Histatin-5 in Candida albicans. ACS Infect Dis 2022; 8:1920-1934. [PMID: 35997625 PMCID: PMC9671271 DOI: 10.1021/acsinfecdis.2c00289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Histatin-5 (Hist-5) is a polycationic, histidine-rich antimicrobial peptide with potent antifungal activity against the opportunistic fungal pathogen Candida albicans. Hist-5 can bind metals in vitro, and metals have been shown to alter the fungicidal activity of the peptide. Previous reports on the effect of Zn2+ on Hist-5 activity have been varied and seemingly contradictory. Here, we present data elucidating the dynamic role Zn2+ plays as an inhibitory switch to regulate Hist-5 fungicidal activity. A novel fluorescently labeled Hist-5 peptide (Hist-5*) was developed to visualize changes in internalization and localization of the peptide as a function of metal availability in the growth medium. Hist-5* was verified for use as a model peptide and retained antifungal activity and mode of action similar to native Hist-5. Cellular growth assays showed that Zn2+ had a concentration-dependent inhibitory effect on Hist-5 antifungal activity. Imaging by confocal microscopy revealed that equimolar concentrations of Zn2+ kept the peptide localized along the cell periphery rather than internalizing, thus preventing cytotoxicity and membrane disruption. However, the Zn-induced decrease in Hist-5 activity and uptake was rescued by decreasing the Zn2+ availability upon addition of a metal chelator EDTA or S100A12, a Zn-binding protein involved in the innate immune response. These results lead us to suggest a model wherein commensal C. albicans may exist in harmony with Hist-5 at concentrations of Zn2+ that inhibit peptide internalization and antifungal activity. Activation of host immune processes that initiate Zn-sequestering mechanisms of nutritional immunity could trigger Hist-5 internalization and cell killing.
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13
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Potok P, Potocki S. Bacterial M10 metallopeptidase as a medicinal target - coordination chemistry of possible metal-based inhibition. Dalton Trans 2022; 51:14882-14893. [PMID: 36056680 DOI: 10.1039/d2dt02265f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Streptococcus pneumoniae is the most frequent cause of fatal bacterial pneumonia infection worldwide. Due to the spreading of antibiotic-resistant pathogens, it is important to search for new therapeutic and prevention strategies against bacterial infections. It is believed that the search for effective inhibitors of bacterial and pathogenic metallopeptidases could be one of the innovative strategies for the design of new antibiotics. Most of them contain zinc in the metal-binding site of the protein, which is a critical component for the biological activity of the enzyme. The main goal of this work is to determine the specificity of the interactions between the binding domain of the metallopeptidase from S. pneumoniae, and Zn(II). Considering the observed inhibitory role of copper towards the metallopeptidases, the next step is to analyze the formation of complexes with Cu(II) and Ni(II). The thermodynamic properties of Zn(II), Cu(II), and Ni(II) complexes were examined by potentiometry, NMR, MS, UV-Vis, CD, and EPR. The results show a similar coordination pattern, HExxHxxxxxH, for all three studied metals below pH 7. Moreover, the primary binding sites were established as the N-terminus in all cases. However, at a pH value of 7.4, the coordination and geometry of the formed complexes differ. The comparison of the stability of the formed complexes reveals that both Cu(II) and Ni(II) are able to displace Zn(II) from its binding site in the whole studied pH range. It opens a discussion on the catalytic zinc ion displacement possibilities by other divalent metal ions and the importance of this process in enzymatic inhibition.
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Affiliation(s)
- Paulina Potok
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie St., 50-383 Wroclaw, Poland.
| | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie St., 50-383 Wroclaw, Poland.
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14
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A cryptic third active site in cyanophycin synthetase creates primers for polymerization. Nat Commun 2022; 13:3923. [PMID: 35798723 PMCID: PMC9262961 DOI: 10.1038/s41467-022-31542-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/14/2022] [Indexed: 12/25/2022] Open
Abstract
Cyanophycin is a nitrogen reserve biopolymer in many bacteria that has promising industrial applications. Made by cyanophycin synthetase 1 (CphA1), it has a poly-L-Asp backbone with L-Arg residues attached to each aspartate sidechain. CphA1s are thought to typically require existing segments of cyanophycin to act as primers for cyanophycin polymerization. In this study, we show that most CphA1s will not require exogenous primers and discover the surprising cause of primer independence: CphA1 can make minute quantities of cyanophycin without primer, and an unexpected, cryptic metallopeptidase-like active site in the N-terminal domain of many CphA1s digests these into primers, solving the problem of primer availability. We present co-complex cryo-EM structures, make mutations that transition CphA1s between primer dependence and independence, and demonstrate that primer dependence can be a limiting factor for cyanophycin production in heterologous hosts. In CphA1, domains with opposite catalytic activities combine into a remarkable, self-sufficient, biosynthetic nanomachine.
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15
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Abstract
Zn2+ ions are essential in many physiological processes, including enzyme catalysis, protein structural stabilization, and the regulation of many proteins. The affinities of proteins for Zn2+ ions span several orders of magnitude, with catalytic Zn2+ ions generally held more tightly than structural or regulatory ones. Metal carrier proteins, most of which are not specific for Zn2+, bind these ions with a broad range of affinities that overlap those of catalytic, structural, and regulatory Zn2+ ions and are thought to be responsible for distributing the metal through most cells, tissues, and fluid compartments. While little is known about how many proteins obtain or release these ions, there is now considerable experimental evidence suggesting that metal carrier proteins may be responsible for transferring metals to and from some Zn2+-dependent proteins, thus serving as a major regulatory factor for them. In this review, the biological roles of Zn2+ and structures of Zn2+ binding sites are examined, and experimental evidence demonstrating the direct participation of metal carrier proteins in enzyme regulation is discussed. Mechanisms of metal ion transfer are also offered, and the potential physiological significance of this phenomenon is explored.
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16
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Qiu J, Barrett K, Wilkens C, Meyer AS. Bioinformatics based discovery of new keratinases in protease family M36. N Biotechnol 2022; 68:19-27. [PMID: 35032710 DOI: 10.1016/j.nbt.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 10/19/2022]
Abstract
Keratinases are proteases that can catalyze the degradation of insoluble keratinous biomass. Keratinases in protease family M36 (MEROPS database) are endo-acting proteases. In total, 687 proteases are classified in family M36. In the present study, new keratinolytic enzymes were identified in protease family M36 using the bioinformatics tool Conserved Unique Peptide Patterns (CUPP). Via CUPP, M36 family members were classified into 11 groups, with CUPP group 1 containing the three currently known and sequenced family M36 keratinases (derived from the fungi Fusarium oxysporum, Microsporum canis and Onygena corvina) as well as an additional 71 uncharacterized M36 proteases. In order to assess the relevance of CUPP group 1 categorization to keratinolytic function, four uncharacterized M36 proteases and the known keratinase from F. oxysporum (in CUPP group 1) were selected for recombinant expression and keratinolytic activity assessment. The four hitherto unknown M36 proteases were from Phaeosphaeria nodorum, Aspergillus clavatus, Pseudogymnoascus pannorum and Nectria haematococca, and represent four different fungal taxonomical classes. The genes encoding the selected M36 proteases were individually expressed in Pichia pastoris and all proteases displayed keratinase activity on keratin azure. Additionally, the activity on different keratinase substrates, optimal reaction conditions and thermal stability were determined for the two most active new keratinases. The results validate the applicability of CUPP for function-based discovery of non-characterized keratinases and present new robust keratinases for potential use in keratin upgrading.
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Affiliation(s)
- Jingwen Qiu
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kristian Barrett
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Casper Wilkens
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Anne S Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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17
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Ren HN, Bai SJ, Wang Z, Han LL, Yan SW, Jiang P, Zhang X, Wang ZQ, Cui J. A metalloproteinase Tsdpy31 from Trichinella spiralis participates in larval molting and development. Int J Biol Macromol 2021; 192:883-894. [PMID: 34656542 DOI: 10.1016/j.ijbiomac.2021.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/20/2021] [Accepted: 10/04/2021] [Indexed: 01/07/2023]
Abstract
Trichinellosis is a serious food-borne zoonotic parasitic disease with global distribution, causing serious harm to public health and food safety. Molting is prerequisite for intestinal larval development in the life cycle of T. spiralis. Metalloproteinases play an important role in the molting process of T. spiralis intestinal infective larvae (IIL). In this study, the metalloproteinase Tsdpy31 was cloned, expressed and characterized. The results revealed that the Tsdpy31 was expressed at various T. spiralis stages and it was principally located in cuticle, hypodermis and embryos of the nematode. Recombinant Tsdpy31 (rTsdpy31) had the catalytic activity of natural metalloproteinase. Silencing of Tsdpy31 increased the permeability of larval new cuticle. When the mice were orally challenged with dsRNA treated- muscle larvae, the burden of intestinal adult and muscle larvae in Tsdpy31 dsRNA treatment group was significantly reduced, compared with the control green fluorescent protein (GFP) dsRNA and PBS groups (P < 0.05). Tsdpy31 may play a major role in the new cuticle synthesis and old cuticle shedding. Tsdpy31 also participates in T. spiralis embryonic development. We conclude that Tsdpy31 could be a candidate vaccine target molecule against intestinal T. spiralis ecdysis and development.
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Affiliation(s)
- Hua Nan Ren
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China
| | - Sheng Jie Bai
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China
| | - Zhen Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China
| | - Lu Lu Han
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China
| | - Shu Wei Yan
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China
| | - Peng Jiang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China
| | - Xi Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China
| | - Zhong Quan Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China.
| | - Jing Cui
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou 450052, PR China.
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18
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Redox signaling through zinc activates the radiation response in Deinococcus bacteria. Sci Rep 2021; 11:4528. [PMID: 33633226 PMCID: PMC7907104 DOI: 10.1038/s41598-021-84026-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and other DNA damage- and oxidative stress-generating conditions. An efficient SOS-independent response mechanism inducing expression of several DNA repair genes is essential for this resistance, and is controlled by metalloprotease IrrE that cleaves and inactivates transcriptional repressor DdrO. Here, we identify the molecular signaling mechanism that triggers DdrO cleavage. We show that reactive oxygen species (ROS) stimulate the zinc-dependent metalloprotease activity of IrrE in Deinococcus. Sudden exposure of Deinococcus to zinc excess also rapidly induces DdrO cleavage, but is not accompanied by ROS production and DNA damage. Further, oxidative treatment leads to an increase of intracellular free zinc, indicating that IrrE activity is very likely stimulated directly by elevated levels of available zinc ions. We conclude that radiation and oxidative stress induce changes in redox homeostasis that result in IrrE activation by zinc in Deinococcus. We propose that a part of the zinc pool coordinated with cysteine thiolates is released due to their oxidation. Predicted regulation systems involving IrrE- and DdrO-like proteins are present in many bacteria, including pathogens, suggesting that such a redox signaling pathway including zinc as a second messenger is widespread and participates in various stress responses.
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19
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Al-Mohanna T, Nejat N, Iannetta AA, Hicks LM, Popescu GV, Popescu SC. Arabidopsis thimet oligopeptidases are redox-sensitive enzymes active in the local and systemic plant immune response. J Biol Chem 2021; 296:100695. [PMID: 33894200 PMCID: PMC8215294 DOI: 10.1016/j.jbc.2021.100695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 01/22/2023] Open
Abstract
Upon pathogen infection, receptors in plants will activate a localized immune response, the effector-triggered immunity (ETI), and a systemic immune response, the systemic acquired response (SAR). Infection also induces oscillations in the redox environment of plant cells, triggering response mechanisms involving sensitive cysteine residues that subsequently alter protein function. Arabidopsis thaliana thimet oligopeptidases TOP1 and TOP2 are required for plant defense against pathogens and the oxidative stress response. Herein, we evaluated the biochemical attributes of TOP isoforms to determine their redox sensitivity using ex vivo Escherichia coli cultures and recombinant proteins. Moreover, we explored the link between their redox regulation and plant immunity in wild-type and mutant Arabidopsis lines. These analyses revealed that redox regulation of TOPs occurs through two mechanisms: (1) oxidative dimerization of full-length TOP1 via intermolecular disulfides engaging cysteines in the N-terminal signal peptide, and (2) oxidative activation of all TOPs via cysteines that are unique and conserved. Further, we detected increased TOP activity in wild-type plants undergoing ETI or SAR following inoculation with Pseudomonas syringae strains. Mutants unable to express the chloroplast NADPH-dependent thioredoxin reductase C (NTRC) showed elevated TOP activity under unstressed conditions and were SAR-incompetent. A top1top2 knockout mutant challenged with P. syringae exhibited misregulation of ROS-induced gene expression in pathogen-inoculated and distal tissues. Furthermore, TOP1 and TOP2 could cleave a peptide derived from the immune component ROC1 with distinct efficiencies at common and specific sites. We propose that Arabidopsis TOPs are thiol-regulated peptidases active in redox-mediated signaling of local and systemic immunity.
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Affiliation(s)
- Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Najmeh Nejat
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Anthony A Iannetta
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA.
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20
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ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range. PLoS Genet 2020; 16:e1008750. [PMID: 32348296 PMCID: PMC7213743 DOI: 10.1371/journal.pgen.1008750] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/11/2020] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Plasmids, when transferred by conjugation in natural environments, must overpass restriction-modification systems of the recipient cell. We demonstrate that protein ArdC, encoded by broad host range plasmid R388, was required for conjugation from Escherichia coli to Pseudomonas putida. Expression of ardC was required in the recipient cells, but not in the donor cells. Besides, ardC was not required for conjugation if the hsdRMS system was deleted in P. putida recipient cells. ardC was also required if the hsdRMS system was present in E. coli recipient cells. Thus, ArdC has antirestriction activity against the HsdRMS system and consequently broadens R388 plasmid host range. The crystal structure of ArdC was solved both in the absence and presence of Mn2+. ArdC is composed of a non-specific ssDNA binding N-terminal domain and a C-terminal metalloprotease domain, although the metalloprotease activity was not needed for the antirestriction function. We also observed by RNA-seq that ArdC-dependent conjugation triggered an SOS response in the P. putida recipient cells. Our findings give new insights, and open new questions, into the antirestriction strategies developed by plasmids to counteract bacterial restriction strategies and settle into new hosts. Horizontal gene transfer is the main mechanism by which bacteria acquire and disseminate new traits, such as antibiotic resistance genes, that allow adaptation and evolution. Here we identified a gene, ardC, that enables a plasmid to increase its conjugative host range, and thus positively contributes to plasmid fitness. The crystal structure of the antirestriction protein ArdC revealed a fold different from other antirestriction proteins. Our results have wide implications for understanding how a gene enlarges the environments a plasmid can colonize and point to new targets to harness the bacterial DNA uptake control.
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21
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Köhnlein K, Urban N, Guerrero-Gómez D, Steinbrenner H, Urbánek P, Priebs J, Koch P, Kaether C, Miranda-Vizuete A, Klotz LO. A Caenorhabditis elegans ortholog of human selenium-binding protein 1 is a pro-aging factor protecting against selenite toxicity. Redox Biol 2019; 28:101323. [PMID: 31557719 PMCID: PMC6812014 DOI: 10.1016/j.redox.2019.101323] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/30/2019] [Accepted: 09/07/2019] [Indexed: 12/21/2022] Open
Abstract
Human selenium-binding protein 1 (SELENBP1) was originally identified as a protein binding selenium, most likely as selenite. SELENBP1 is associated with cellular redox and thiol homeostasis in several respects, including its established role as a methanethiol oxidase that is involved in degradation of methanethiol, a methionine catabolite, generating hydrogen sulfide (H2S) and hydrogen peroxide (H2O2). As both H2S and reactive oxygen species (such as H2O2) are major regulators of Caenorhabditis elegans lifespan and stress resistance, we hypothesized that a SELENBP1 ortholog in C. elegans would likely be involved in regulating these aspects. Here we characterize Y37A1B.5, a putative selenium-binding protein 1 ortholog in C. elegans with 52% primary structure identity to human SELENBP1. While conferring resistance to toxic concentrations of selenite, Y37A1B.5 also attenuates resistance to oxidative stress and lowers C. elegans lifespan: knockdown of Y37A1B.5 using RNA interference resulted in an approx. 10% increase of C. elegans lifespan and an enhanced resistance against the redox cycler paraquat, as well as enhanced motility. Analyses of transgenic reporter strains suggest hypodermal expression and cytoplasmic localization of Y37A1B.5, whose expression decreases with worm age. We identify the transcriptional coregulator MDT-15 and transcription factor EGL-27 as regulators of Y37A1B.5 levels and show that the lifespan extending effect elicited by downregulation of Y37A1B.5 is independent of known MDT-15 interacting factors, such as DAF-16 and NHR-49. In summary, Y37A1B.5 is an ortholog of SELENBP1 that shortens C. elegans lifespan and lowers resistance against oxidative stress, while allowing for a better survival under toxic selenite concentrations.
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Affiliation(s)
- Karl Köhnlein
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich-Schiller-Universität Jena, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Nadine Urban
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - David Guerrero-Gómez
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Holger Steinbrenner
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Pavel Urbánek
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Josephine Priebs
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Philipp Koch
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | | | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Lars-Oliver Klotz
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich-Schiller-Universität Jena, Jena, Germany.
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22
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Fusco A, Savio V, De Filippis A, Tufano A, Donnarumma G. Induction of Different Apoptosis Pathways by Two Proteus mirabilis Clinical Isolates Strains in Prostatic Epithelial Cells. Front Physiol 2018; 9:1855. [PMID: 30618851 PMCID: PMC6306403 DOI: 10.3389/fphys.2018.01855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022] Open
Abstract
Bacterial prostatitis is believed to be the leading cause of recurrent urinary tract infections (UTIs) in men under 50 years of age and occurs both as an acute febrile disease responsive to antibiotics and as a chronic infection that is often unresponsive to antibiotic treatment. Proteusmirabilis is more commonly associated with UTIs in these abnormalities, especially in patients undergoing catheterisation. This pathogen is able to colonise the host’s tissues and to cause disease thanks to the production of many virulence factors such as fimbriae, flagella, immune avoidance, host-damaging factors, and the ability to form crystalline biofilms. In addition, Proteus lipid A may exhibit apoptotic activity and induce desquamation of epithelial cells. The aim of this work was to evaluate the ability of two clinically isolated strains of P. mirabilis that are phenotypically different, named PM1 of PM2, respectively, to induce apoptosis in human prostatic adenocarcinoma PC-3. Our results demonstrate that PM1 and PM2 are able to activate two different apoptotic pathways, and this different behaviour is confirmed by the expression level of the ZapA gene, molecular fingerprinting and different spectrum of antibiotic resistance. The identification and knowledge of relations between the microorganism and host may provide the basis for new solutions to clinical problems with regard to diagnosis and therapy.
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Affiliation(s)
- Alessandra Fusco
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Vittoria Savio
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Anna De Filippis
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Antonio Tufano
- Urology School, Sapienza University of Rome, Rome, Italy
| | - Giovanna Donnarumma
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania Luigi Vanvitelli, Naples, Italy
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23
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Fuchs ACD, Maldoner L, Wojtynek M, Hartmann MD, Martin J. Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system. Nat Commun 2018; 9:2696. [PMID: 30002364 PMCID: PMC6043591 DOI: 10.1038/s41467-018-05198-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/22/2018] [Indexed: 12/05/2022] Open
Abstract
While protein ubiquitination was long believed to be a truly eukaryotic feature, recently sequenced genomes revealed complete ubiquitin (Ub) modification operons in archaea. Here, we present the structural and mechanistic characterization of an archaeal Rpn11 deubiquitinase from Caldiarchaeum subterraneum, CsRpn11, and its role in the processing of CsUb precursor and ubiquitinated proteins. CsRpn11 activity is affected by the catalytic metal ion type, small molecule inhibitors, sequence characteristics at the cleavage site, and the folding state of CsUb-conjugated proteins. Comparison of CsRpn11 and CsRpn11-CsUb crystal structures reveals a crucial conformational switch in the CsRpn11 Ins-1 site, which positions CsUb for catalysis. The presence of this transition in a primordial soluble Rpn11 thus predates the evolution of eukaryotic Rpn11 immobilized in the proteasomal lid. Complementing phylogenetic studies, which designate CsRpn11 and CsUb as close homologs of the respective eukaryotic proteins, our results provide experimental support for an archaeal origin of protein ubiquitination.
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Affiliation(s)
- Adrian C D Fuchs
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Lorena Maldoner
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Matthias Wojtynek
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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24
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A novel fibrinolytic serine metalloprotease from the marine Serratia marcescens subsp. sakuensis: Purification and characterization. Int J Biol Macromol 2018; 112:110-118. [DOI: 10.1016/j.ijbiomac.2018.01.129] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/09/2018] [Accepted: 01/18/2018] [Indexed: 11/21/2022]
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25
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Young CJ, Richard K, Beruar A, Lo SY, Siemann S. An investigation of the pH dependence of copper-substituted anthrax lethal factor and its mechanistic implications. J Inorg Biochem 2018; 182:1-8. [PMID: 29407865 DOI: 10.1016/j.jinorgbio.2018.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/18/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
Abstract
Anthrax lethal factor (LF) is a zinc-dependent endopeptidase involved in the cleavage of proteins critical to the maintenance of host signaling pathways during anthrax infections. Although zinc is typically regarded as the native metal ion in vivo, LF is highly tolerant to metal substitution, with its replacement by copper yielding an enzyme (CuLF) 4.5-fold more active than the native zinc protein (at pH 7). The current study demonstrates that by careful choice of the buffer, ionic strength, pH and substrate, the activity ratio of CuLF and native LF can be increased to >40-fold. Using a fluorogenic LF substrate, such optimized assay conditions can be exploited to detect LF concentrations as low as 2 pM. In contrast to the zinc form, CuLF was found to be inhibited by bromide and iodide ions, to be resistant to metal loss under acidic conditions, and to display a sharp pH dependence with significantly shifted alkaline limb towards more acidic conditions. The alkaline limb in the enzyme's pH profile is suggested to originate from changes in the protonation state of the metal-bound water molecule which serves as the nucleophile in the catalytic mechanism. Based on these observations and studies on other zinc proteases, a minimal mechanism for LF is proposed.
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Affiliation(s)
- Calvin J Young
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Kaitlin Richard
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Ananya Beruar
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Suet Y Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada.
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26
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Sizochenko N, Leszczynska D, Leszczynski J. Modeling of Interactions between the Zebrafish Hatching Enzyme ZHE1 and A Series of Metal Oxide Nanoparticles: Nano-QSAR and Causal Analysis of Inactivation Mechanisms. NANOMATERIALS 2017; 7:nano7100330. [PMID: 29035311 PMCID: PMC5666495 DOI: 10.3390/nano7100330] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 12/14/2022]
Abstract
The quantitative relationships between the activity of zebrafish ZHE1 enzyme and a series of experimental and physicochemical features of 24 metal oxide nanoparticles were revealed. Vital characteristics of the nanoparticles’ structure were reflected using both experimental and theoretical descriptors. The developed quantitative structure–activity relationship model for nanoparticles (nano-QSAR) was capable of predicting the enzyme inactivation based on four descriptors: the hydrodynamic radius, mass density, the Wigner–Seitz radius, and the covalent index. The nano-QSAR model was calculated using the non-linear regression tree M5P algorithm. The developed model is characterized by high robustness R2bagging = 0.90 and external predictivity Q2EXT = 0.93. This model is in agreement with modern theories of aquatic toxicity. Dissolution and size-dependent characteristics are among the key driving forces for enzyme inactivation. It was proven that ZnO, CuO, Cr2O3, and NiO nanoparticles demonstrated strong inhibitory effects because of their solubility. The proposed approach could be used as a non-experimental alternative to animal testing. Additionally, methods of causal discovery were applied to shed light on the mechanisms and modes of action.
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Affiliation(s)
- Natalia Sizochenko
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA.
| | - Danuta Leszczynska
- Department of Civil and Environmental Engineering, Jackson State University, Jackson, MS 39217, USA.
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA.
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27
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Marion A, Groll M, Scharf DH, Scherlach K, Glaser M, Sievers H, Schuster M, Hertweck C, Brakhage AA, Antes I, Huber EM. Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase GliJ. ACS Chem Biol 2017; 12:1874-1882. [PMID: 28525266 DOI: 10.1021/acschembio.6b00847] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The formation of glutathione (GSH) conjugates, best known from the detoxification of xenobiotics, is a widespread strategy to incorporate sulfur into biomolecules. The biosynthesis of gliotoxin, a virulence factor of the human pathogenic fungus Aspergillus fumigatus, involves attachment of two GSH molecules and their sequential decomposition to yield two reactive thiol groups. The degradation of the GSH moieties requires the activity of the Cys-Gly carboxypeptidase GliJ, for which we describe the X-ray structure here. The enzyme forms a homodimer with each monomer comprising one active site. Two metal ions are present per proteolytic center, thus assigning GliJ to the diverse family of dinuclear metallohydrolases. Depending on availability, Zn2+, Fe2+, Fe3+, Mn2+, Cu2+, Co2+, or Ni2+ ions are accepted as cofactors. Despite this high metal promiscuity, a preference for zinc versus iron and manganese was noted. Mutagenesis experiments revealed details of metal coordination, and molecular modeling delivered insights into substrate recognition and processing by GliJ. The latter results suggest a reaction mechanism in which the two scissile peptide bonds of one gliotoxin precursor molecule are hydrolyzed sequentially and in a given order.
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Affiliation(s)
- Antoine Marion
- Center
for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Michael Groll
- Center
for Integrated Protein Science Munich at the Department Chemistry, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Daniel H. Scharf
- Department
of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
| | - Kirstin Scherlach
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
| | - Manuel Glaser
- Center
for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Holger Sievers
- Fachgruppe
Analytische Chemie, Technische Universität München, D-85748 Garching, Germany
| | - Michael Schuster
- Fachgruppe
Analytische Chemie, Technische Universität München, D-85748 Garching, Germany
| | - Christian Hertweck
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
- Chair of
Natural Product Chemistry, Friedrich Schiller University (FSU), D-07743 Jena, Germany
| | - Axel A. Brakhage
- Department
of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
- Department
of Microbiology and Molecular Biology, Friedrich Schiller University (FSU), D-07743 Jena, Germany
| | - Iris Antes
- Center
for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Eva M. Huber
- Center
for Integrated Protein Science Munich at the Department Chemistry, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
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28
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Blanchard L, Guérin P, Roche D, Cruveiller S, Pignol D, Vallenet D, Armengaud J, de Groot A. Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria. Microbiologyopen 2017; 6. [PMID: 28397370 PMCID: PMC5552922 DOI: 10.1002/mbo3.477] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/22/2017] [Accepted: 02/28/2017] [Indexed: 12/26/2022] Open
Abstract
The extreme radiation resistance of Deinococcus bacteria requires the radiation‐stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation‐induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo‐IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively. Binding of IrrE to RDRM‐containing DNA or interaction of IrrE with DNA‐bound DdrO was not observed. The data are in line with IrrE being a zinc peptidase, and indicate that increased zinc availability, caused by oxidative stress, triggers the in vivo cleavage of DdrO unbound to DNA. Transcriptomics and proteomics of Deinococcus deserti confirmed the IrrE‐dependent regulation of predicted RDR regulon genes and also revealed additional members of this regulon. Comparative analysis showed that the RDR regulon is largely well conserved in Deinococcus species, but also showed diversity in the regulon composition. Notably, several RDR genes with an important role in radiation resistance in Deinococcus radiodurans, for example pprA, are not conserved in some other radiation‐resistant Deinococcus species.
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Affiliation(s)
- Laurence Blanchard
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Philippe Guérin
- Laboratory "Innovative technologies for Detection and Diagnostic", CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Bagnols-sur-Cèze, France
| | - David Roche
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - Stéphane Cruveiller
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - David Pignol
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - David Vallenet
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - Jean Armengaud
- Laboratory "Innovative technologies for Detection and Diagnostic", CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Bagnols-sur-Cèze, France
| | - Arjan de Groot
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
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29
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Atas A, Seddon AM, Ford DC, Cooper IA, Wren BW, Oyston PCF, Karlyshev AV. YPTB3816 of Yersinia pseudotuberculosis strain IP32953 is a virulence-related metallo-oligopeptidase. BMC Microbiol 2016; 16:282. [PMID: 27887582 PMCID: PMC5124237 DOI: 10.1186/s12866-016-0900-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/17/2016] [Indexed: 12/03/2022] Open
Abstract
Background Although bacterial peptidases are known to be produced by various microorganisms, including pathogenic bacteria, their role in bacterial physiology is not fully understood. In particular, oligopeptidases are thought to be mainly involved in degradation of short peptides e.g. leader peptides released during classical protein secretion pathways. The aim of this study was to investigate effects of inactivation of an oligopeptidase encoding gene opdA gene of Yersinia pseudotuberculosis on bacterial properties in vivo and in vitro, and to test dependence of the enzymatic activity of the respective purified enzyme on the presence of different divalent cations. Results In this study we found that oligopeptidase OpdA of Yersinia pseudotuberculosis is required for bacterial virulence, whilst knocking out the respective gene did not have any effect on bacterial viability or growth rate in vitro. In addition, we studied enzymatic properties of this enzyme after expression and purification from E. coli. Using an enzyme depleted of contaminant divalent cations and different types of fluorescently labelled substrates, we found strong dependence of its activity on the presence of particular cations. Unexpectedly, Zn2+ showed stimulatory activity only at low concentrations, but inhibited the enzyme at higher concentrations. In contrast, Co2+, Ca2+ and Mn2+ stimulated activity at all concentrations tested, whilst Mg2+ revealed no effect on the enzyme activity at all concentrations used. Conclusions The results of this study provide valuable contribution to the investigation of bacterial peptidases in general, and that of metallo-oligopeptidases in particular. This is the first study demonstrating that opdA in Yersinia pseudotuberculsosis is required for pathogenicity. The data reported are important for better understanding of the role of OpdA-like enzymes in pathogenesis in bacterial infections. Characterisation of this protein may serve as a basis for the development of novel antibacterials based on specific inhibition of this peptidase activity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0900-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Atas
- School of Life Sciences, Pharmacy and Chemistry; Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Alan M Seddon
- School of Life Sciences, Pharmacy and Chemistry; Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Donna C Ford
- Biomedical Sciences, DSTL Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | - Ian A Cooper
- Biomedical Sciences, DSTL Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Petra C F Oyston
- Biomedical Sciences, DSTL Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | - Andrey V Karlyshev
- School of Life Sciences, Pharmacy and Chemistry; Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.
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30
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Identification and functional characterization of a putative IDE, C28F5.4 (ceIDE-1), in Caenorhabditis elegans: Implications for Alzheimer's disease. Biochim Biophys Acta Gen Subj 2016; 1860:2454-2462. [DOI: 10.1016/j.bbagen.2016.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/30/2016] [Accepted: 07/16/2016] [Indexed: 12/17/2022]
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31
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Lee RM, Jeong SM. Identification of a novel calcium (Ca2+)-activated chloride channel accessory gene in Xenopus laevis. Mol Biol 2016. [DOI: 10.1134/s0026893316010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Young CJ, Siemann S. Highly dynamic metal exchange in anthrax lethal factor involves the occupation of an inhibitory metal binding site. Chem Commun (Camb) 2016; 52:11748-51. [DOI: 10.1039/c6cc05460a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rapid metal exchange in anthrax lethal factor and potentially other zinc enzymes proceeds via the formation of transient bimetallic species.
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Affiliation(s)
- Calvin J. Young
- Department of Chemistry and Biochemistry
- Laurentian University
- Sudbury
- Canada
| | - Stefan Siemann
- Department of Chemistry and Biochemistry
- Laurentian University
- Sudbury
- Canada
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33
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Lee RM, Han KH, Han JS. rbCLCA1 is a putative metalloprotease family member: localization and catalytic domain identification. Amino Acids 2015; 48:707-720. [PMID: 26510883 DOI: 10.1007/s00726-015-2119-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 10/12/2015] [Indexed: 11/29/2022]
Abstract
Here, we identify the rat brain (rb) CLCA1 metalloprotease motif and its role in rbCLCA1 processing. GFP tagging or c-myc tagging adjacent to the rbCLCA1 signal sequence was used to detect rbCLCA1 expression and localization patterns if they matched those of other CLCA family members. Immunoblot analysis revealed that massive deletion of the metalloprotease motif affects the protein cleavage process by restricting two cleavage products to only one product. rbCLCA1 as well as the mutant proteins H155A, E156Q, H159A, D166A, E167A, E170A, and D171A overexpressed in HEK293T cells showed plasma membrane localization; and intracellular localizations of H159A and E167A were observed in permeabilized and non-permeabilized conditions. C-terminally GFP-tagged rbCLCA1 showed either ER localization or overall signal within the cells rather than on the cell surface. Cell surface biotinylation analysis was used to show that rbCLCA1, H155A, E156Q, D166A, E170A, and D171A reach the cell surface while little H159A and E167A reach the cell surface. Taken together, our findings indicate that the amino acids H159 and E167 in the rbCLCA1 metalloprotease motif are important in rbCLCA1 processing for localization to the cell surface. Our data demonstrate that rbCLCA1 localization is dependent on the H159 and E167, suggesting either the metalloprotease motif including H159 and E167 may be the key site for rbCLCA1 cellular processing or that a novel rbCLCA1 regulation mechanism exists with a metalloprotease activity.
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Affiliation(s)
- Ra Mi Lee
- Department of Biochemistry and Molecular Cell Biology, College of Veterinary Medicine, Konkuk University, 120 Neungdongro, Gwangjingu, Seoul, 05029, Republic of Korea.,The Institute for the 3Rs and Veterinary Science Research Institute, College of Veterinary Medicine, Konkuk University, 120 Neungdongro, Gwangjingu, Seoul, 05029, Republic of Korea
| | - Kyu Ho Han
- Department of Food Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Jin Soo Han
- The Institute for the 3Rs and Veterinary Science Research Institute, College of Veterinary Medicine, Konkuk University, 120 Neungdongro, Gwangjingu, Seoul, 05029, Republic of Korea.
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34
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Saxena R, Singh R. MALDI-TOF MS and CD spectral analysis for identification and structure prediction of a purified, novel, organic solvent stable, fibrinolytic metalloprotease from Bacillus cereus B80. BIOMED RESEARCH INTERNATIONAL 2015; 2015:527015. [PMID: 25802851 PMCID: PMC4352737 DOI: 10.1155/2015/527015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/25/2014] [Accepted: 09/30/2014] [Indexed: 12/01/2022]
Abstract
The ability to predict protein function from structure is becoming increasingly important; hence, elucidation and determination of protein structure become the major steps in proteomics. The present study was undertaken for identification of metalloprotease produced by Bacillus cereus B80 and recognition of characteristics that can be industrially exploited. The enzyme was purified in three steps combining precipitation and chromatographic methods resulting in 33.5% recovery with 13.1-fold purification of enzyme which was detected as a single band with a molecular mass of 26 kDa approximately in SDS-PAGE and zymogram. The MALDI-TOF MS showed that the enzyme exhibited 70-93% similarity with zinc metalloproteases from various strains Bacillus sp. specifically from Bacillus cereus group. The sequence alignment revealed the presence of zinc-binding region VVVHEMCHMV in the most conserved C terminus region. Secondary structure of the enzyme was obtained by CD spectra and I-TASSER. The enzyme kinetics revealed a Michaelis constant (Km) of 0.140 μmol/ml and Vmax of 2.11 μmol/min. The application studies showed that the enzyme was able to hydrolyze various proteins with highest affinity towards casein followed by BSA and gelatin. The enzyme exhibited strong fibrinolytic, collagenolytic, and gelatinolytic properties and stability in various organic solvents.
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Affiliation(s)
- Rajshree Saxena
- Amity Institute of Microbial Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh 201303, India
| | - Rajni Singh
- Amity Institute of Microbial Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh 201303, India
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35
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Na YR, Woo DJ, Choo H, Chung HS, Yang EG. Selective inhibition of the hypoxia-inducible factor prolyl hydroxylase PHD3 by Zn(ii). Chem Commun (Camb) 2015; 51:10730-3. [DOI: 10.1039/c5cc02143j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zn(ii) selectively inhibits PHD3 over PHD2 by interacting with Cys42 and Cys52 residues located distantly from the active site.
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Affiliation(s)
- Yu-Ran Na
- Center for Theragnosis
- Biomedical Research Institute
- Korea Institute of Science and Technology
- Seoul 136-791
- Republic of Korea
| | - Dustin J. Woo
- Center for Theragnosis
- Biomedical Research Institute
- Korea Institute of Science and Technology
- Seoul 136-791
- Republic of Korea
| | - Hyunah Choo
- Department of Biological Chemistry
- KIST Campus
- Korea University of Science and Technology (UST)
- Seoul 136-791
- Republic of Korea
| | - Hak Suk Chung
- Center for Theragnosis
- Biomedical Research Institute
- Korea Institute of Science and Technology
- Seoul 136-791
- Republic of Korea
| | - Eun Gyeong Yang
- Center for Theragnosis
- Biomedical Research Institute
- Korea Institute of Science and Technology
- Seoul 136-791
- Republic of Korea
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36
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Abstract
The metal dissociation constants of bovine carbonic anhydrase II, bovine carboxypeptidase A, rat aminopeptidase B, and rat dipeptidyl peptidase III were measured using metal buffer solutions. The zinc dissociation constants of bovine carbonic anhydrase II, bovine carboxypeptidase A, rat aminopeptidase B, and rat dipeptidyl peptidase III were 5.8×10(-14), 3.5×10(-12), 3.7×10(-13), and 1.9×10(-13) M, respectively. The ternary complex between metal derivatives of bovine carbonic anhydrase and various chelating agents were characterized using the kinetic method and visible and magnetic circular dichroism spectra. The coordination geometry of the ternary complex was in the equilibrium state between the five and the tetrahedral coordination geometry. The equilibrium state depends on the character of ligands. Dipeptidyl peptidase III which has an abnormal zinc binding motif (HEXXXH) was characterized using the point mutation and computer simulation methods. The abnormal zinc binding motif (HEXXXH) of rat dipeptidyl peptidase III has a large helix part. It is generally known that the cupric derivatives of the zinc peptidase loses enzyme activity, but the cupric derivative of dipeptidyl peptidase III surprisingly has enzyme activity. The measurement of the electron paramagnetic resonance spectra of the cupric rat dipeptidyl peptidase III in the presence of the substrate showed that the coordination geometry is very flexible. The flexibility of the coordination geometry in the cupric rat dipeptidyl peptidase III is important for the expression of enzyme activity. Docking simulation was used to identify the substrate binding site of aminopeptidase B, which is a powerful tool to estimate substrate binding residues in enzymes.
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Affiliation(s)
- Junzo Hirose
- Faculty of Pharmaceutical Sciences, Fukuyama University
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37
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Lo SY, Säbel CE, Webb MI, Walsby CJ, Siemann S. High metal substitution tolerance of anthrax lethal factor and characterization of its active copper-substituted analogue. J Inorg Biochem 2014; 140:12-22. [DOI: 10.1016/j.jinorgbio.2014.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/27/2014] [Accepted: 06/16/2014] [Indexed: 01/19/2023]
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38
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Raycroft MAR, Cimpean L, Neverov AA, Brown RS. Rapid Ni, Zn, and Cu Ion-Promoted Alcoholysis of N,N-Bis(2-picolyl)- and N,N-Bis((1H-benzimidazol-2-yl)methyl)-p-nitrobenzamides in Methanol and Ethanol. Inorg Chem 2014; 53:2211-21. [DOI: 10.1021/ic4028755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mark A. R. Raycroft
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
| | - Luana Cimpean
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
| | - Alexei A. Neverov
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
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39
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Lakshmi Bhargavi P, Prakasham R. A fibrinolytic, alkaline and thermostable metalloprotease from the newly isolated Serratia sp RSPB11. Int J Biol Macromol 2013; 61:479-86. [DOI: 10.1016/j.ijbiomac.2013.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 07/10/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
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40
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Lin S, Zhao Y, Ji Z, Ear J, Chang CH, Zhang H, Low-Kam C, Yamada K, Meng H, Wang X, Liu R, Pokhrel S, Mädler L, Damoiseaux R, Xia T, Godwin HA, Lin S, Nel AE. Zebrafish high-throughput screening to study the impact of dissolvable metal oxide nanoparticles on the hatching enzyme, ZHE1. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:1776-1785. [PMID: 23180726 PMCID: PMC4034474 DOI: 10.1002/smll.201202128] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Indexed: 05/19/2023]
Abstract
The zebrafish is emerging as a model organism for the safety assessment and hazard ranking of engineered nanomaterials. In this Communication, the implementation of a roboticized high-throughput screening (HTS) platform with automated image analysis is demonstrated to assess the impact of dissolvable oxide nanoparticles on embryo hatching. It is further demonstrated that this hatching interference is mechanistically linked to an effect on the metalloprotease, ZHE 1, which is responsible for degradation of the chorionic membrane. The data indicate that 4 of 24 metal oxide nanoparticles (CuO, ZnO, Cr2 O3 , and NiO) could interfere with embryo hatching by a chelator-sensitive mechanism that involves ligation of critical histidines in the ZHE1 center by the shed metal ions. A recombinant ZHE1 enzymatic assay is established to demonstrate that the dialysates from the same materials responsible for hatching interference also inhibit ZHE1 activity in a dose-dependent fashion. A peptide-based BLAST search identifies several additional aquatic species that express enzymes with homologous histidine-based catalytic centers, suggesting that the ZHE1 mechanistic paradigm could be used to predict the toxicity of a large number of oxide nanoparticles that pose a hazard to aquatic species.
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Affiliation(s)
- Sijie Lin
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
| | - Yan Zhao
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles
| | - Zhaoxia Ji
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
| | - Jason Ear
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles
| | - Chong Hyun Chang
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
| | - Haiyuan Zhang
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
| | - Cecile Low-Kam
- Department of Biostatistics, University of California, Los Angeles
| | - Kristin Yamada
- Department of Environmental Health Sciences, University of California, Los Angeles
| | - Huan Meng
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
- Division of NanoMedicine, Department of Medicine, University of California, Los Angeles
| | - Xiang Wang
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
| | - Rong Liu
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
| | - Suman Pokhrel
- IWT Foundation Institute of Materials Science, Department of Production Engineering, University of Bremen, Germany
| | - Lutz Mädler
- IWT Foundation Institute of Materials Science, Department of Production Engineering, University of Bremen, Germany
| | - Robert Damoiseaux
- Molecular Shared Screening Resources, California NanoSystem Institute, University of California, Los Angeles
| | - Tian Xia
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
- Division of NanoMedicine, Department of Medicine, University of California, Los Angeles
| | - Hilary A. Godwin
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
- Department of Environmental Health Sciences, University of California, Los Angeles
| | - Shuo Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles
| | - André E. Nel
- Center for Environmental Implications of Nanotechnology, University of California, Los Angeles
- Division of NanoMedicine, Department of Medicine, University of California, Los Angeles
- Prof. A. E. Nel, Department of Medicine, Division of NanoMedicine, UCLA School of Medicine, 52-175, CHS, 10833 Le Conte Ave, Los Angeles, CA 90095-1680. Tel: (310) 825-6620, Fax: (310) 206-8107,
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Berzigotti S, Benlafya K, Sépulchre J, Amoroso A, Joris B. Bacillus licheniformis BlaR1 L3 loop is a zinc metalloprotease activated by self-proteolysis. PLoS One 2012; 7:e36400. [PMID: 22623956 PMCID: PMC3356374 DOI: 10.1371/journal.pone.0036400] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 04/04/2012] [Indexed: 11/26/2022] Open
Abstract
In Bacillus licheniformis 749/I, BlaP β-lactamase is induced by the presence of a β-lactam antibiotic outside the cell. The first step in the induction mechanism is the detection of the antibiotic by the membrane-bound penicillin receptor BlaR1 that is composed of two functional domains: a carboxy-terminal domain exposed outside the cell, which acts as a penicillin sensor, and an amino-terminal domain anchored to the cytoplasmic membrane, which works as a transducer-transmitter. The acylation of BlaR1 sensor domain by the antibiotic generates an intramolecular signal that leads to the activation of the L3 cytoplasmic loop of the transmitter by a single-point cleavage. The exact mechanism of L3 activation and the nature of the secondary cytoplasmic signal launched by the activated transmitter remain unknown. However, these two events seem to be linked to the presence of a HEXXH zinc binding motif of neutral zinc metallopeptidases. By different experimental approaches, we demonstrated that the L3 loop binds zinc ion, belongs to Gluzincin metallopeptidase superfamily and is activated by self-proteolysis.
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Affiliation(s)
- Stéphanie Berzigotti
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Kamal Benlafya
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Jérémy Sépulchre
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Ana Amoroso
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Bernard Joris
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
- * E-mail:
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