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Naletova I, Satriano C, Curci A, Margiotta N, Natile G, Arena G, La Mendola D, Nicoletti VG, Rizzarelli E. Cytotoxic phenanthroline derivatives alter metallostasis and redox homeostasis in neuroblastoma cells. Oncotarget 2018; 9:36289-36316. [PMID: 30555630 PMCID: PMC6284747 DOI: 10.18632/oncotarget.26346] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
Copper homeostasis is generally investigated focusing on a single component of the metallostasis network. Here we address several of the factors controlling the metallostasis for neuroblastoma cells (SH-SY5Y) upon treatment with 2,9-dimethyl-1,10-phenanthroline-5,6-dione (phendione) and 2,9-dimethyl-1,10-phenanthroline (cuproindione). These compounds bind and transport copper inside cells, exert their cytotoxic activity through the induction of oxidative stress, causing apoptosis and alteration of the cellular redox and copper homeostasis network. The intracellular pathway ensured by copper transporters (Ctr1, ATP7A), chaperones (CCS, ATOX, COX 17, Sco1, Sco2), small molecules (GSH) and transcription factors (p53) is scrutinised.
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Affiliation(s)
- Irina Naletova
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
| | - Cristina Satriano
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
| | - Alessandra Curci
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Chemistry, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Nicola Margiotta
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Chemistry, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Giovanni Natile
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Chemistry, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Giuseppe Arena
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
| | - Diego La Mendola
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Vincenzo Giuseppe Nicoletti
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Section of Medical Biochemistry, Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Enrico Rizzarelli
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
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Niranjanakumari S, Day-Storms JJ, Ahmed M, Hsieh J, Zahler NH, Venters RA, Fierke CA. Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage. RNA (NEW YORK, N.Y.) 2007; 13:521-35. [PMID: 17299131 PMCID: PMC1831860 DOI: 10.1261/rna.308707] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 12/21/2006] [Indexed: 05/03/2023]
Abstract
Bacterial ribonuclease P (RNase P) is a ribonucleoprotein complex composed of one catalytic RNA (PRNA) and one protein subunit (P protein) that together catalyze the 5' maturation of precursor tRNA. High-resolution X-ray crystal structures of the individual P protein and PRNA components from several species have been determined, and structural models of the RNase P holoenzyme have been proposed. However, holoenzyme models have been limited by a lack of distance constraints between P protein and PRNA in the holoenzyme-substrate complex. Here, we report the results of extensive cross-linking and affinity cleavage experiments using single-cysteine P protein variants derivatized with either azidophenacyl bromide or 5-iodoacetamido-1,10-o-phenanthroline to determine distance constraints and to model the Bacillus subtilis holoenzyme-substrate complex. These data indicate that the evolutionarily conserved RNR motif of P protein is located near (<15 Angstroms) the pre-tRNA cleavage site, the base of the pre-tRNA acceptor stem and helix P4 of PRNA, the putative active site of the enzyme. In addition, the metal binding loop and N-terminal region of the P protein are proximal to the P3 stem-loop of PRNA. Studies using heterologous holoenzymes composed of covalently modified B. subtilis P protein and Escherichia coli M1 RNA indicate that P protein binds similarly to both RNAs. Together, these data indicate that P protein is positioned close to the RNase P active site and may play a role in organizing the RNase P active site.
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Bales BC, Kodama T, Weledji YN, Pitié M, Meunier B, Greenberg MM. Mechanistic studies on DNA damage by minor groove binding copper-phenanthroline conjugates. Nucleic Acids Res 2005; 33:5371-9. [PMID: 16186134 PMCID: PMC1235636 DOI: 10.1093/nar/gki856] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Copper-phenanthroline complexes oxidatively damage and cleave nucleic acids. Copper bis-phenanthroline and copper complexes of mono- and bis-phenanthroline conjugates are used as research tools for studying nucleic acid structure and binding interactions. The mechanism of DNA oxidation and cleavage by these complexes was examined using two copper-phenanthroline conjugates of the sequence-specific binding molecule, distamycin. The complexes contained either one or two phenanthroline units that were bonded to the DNA-binding domain through a linker via the 3-position of the copper ligand. A duplex containing independently generated 2-deoxyribonolactone facilitated kinetic analysis of DNA cleavage. Oxidation rate constants were highly dependent upon the ligand environment but rate constants describing elimination of the alkali-labile 2-deoxyribonolactone intermediate were not. Rate constants describing DNA cleavage induced by each molecule were 11-54 times larger than the respective oxidation rate constants. The experiments indicate that DNA cleavage resulting from beta-elimination of 2-deoxyribonolactone by copper-phenanthroline complexes is a general mechanism utilized by this family of molecules. In addition, the experiments confirm that DNA damage mediated by mono- and bis-phenanthroline copper complexes proceeds through distinct species, albeit with similar outcomes.
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Affiliation(s)
| | - Tetsuya Kodama
- Department of Chemistry, Johns Hopkins University3400 North Charles Street, Baltimore, MD 21218, USA
| | - Yvonne N. Weledji
- Department of Chemistry, Johns Hopkins University3400 North Charles Street, Baltimore, MD 21218, USA
| | - Marguerite Pitié
- Laboratoire de Chimie de Coordination du CNRS205 route de Narbonne, 31 077 Toulouse Cedex 4, France
| | - Bernard Meunier
- Laboratoire de Chimie de Coordination du CNRS205 route de Narbonne, 31 077 Toulouse Cedex 4, France
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University3400 North Charles Street, Baltimore, MD 21218, USA
- To whom correspondence should be addressed. Tel: +33 410 516 8095; Fax: +33 410 616 7044;
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Qi D, Tann CM, Haring D, Distefano MD. Generation of new enzymes via covalent modification of existing proteins. Chem Rev 2001; 101:3081-111. [PMID: 11710063 DOI: 10.1021/cr000059o] [Citation(s) in RCA: 232] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D Qi
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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5
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Abstract
The oxidation of DNA and RNA provides a facile approach for investigating the interaction of nucleic acids with proteins and oligonucleotides. In this article, we have outlined our understanding of the mechanism of DNA scission by 1,10-phenanthroline-copper(I) in the presence of hydrogen peroxide. We also discuss results obtained by using 1,10-phenanthroline-oligonucleotide conjugates in probing the size of the transcriptionally active open complex. Finally, we outline an effective method for converting DNA-binding proteins into site-specific modification agents by using 1,10-phenanthroline-copper(I).
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Affiliation(s)
- C B Chen
- Molecular Biology Institute, University of California, Los Angeles Los Angeles, CA 90095-1570, USA
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Tzou WS, Hwang MJ. Modeling helix-turn-helix protein-induced DNA bending with knowledge-based distance restraints. Biophys J 1999; 77:1191-205. [PMID: 10465734 PMCID: PMC1300411 DOI: 10.1016/s0006-3495(99)76971-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A crucial element of many gene functions is protein-induced DNA bending. Computer-generated models of such bending have generally been derived by using a presumed bending angle for DNA. Here we describe a knowledge-based docking strategy for modeling the structure of bent DNA recognized by a major groove-inserting alpha-helix of proteins with a helix-turn-helix (HTH) motif. The method encompasses a series of molecular mechanics and dynamics simulations and incorporates two experimentally derived distance restraints: one between the recognition helix and DNA, the other between respective sites of protein and DNA involved in chemical modification-enabled nuclease scissions. During simulation, a DNA initially placed at a distance was "steered" by these restraints to dock with the binding protein and bends. Three prototype systems of dimerized HTH DNA binding were examined: the catabolite gene activator protein (CAP), the phage 434 repressor (Rep), and the factor for inversion stimulation (Fis). For CAP-DNA and Rep-DNA, the root mean square differences between model and x-ray structures in nonhydrogen atoms of the DNA core domain were 2.5 A and 1.6 A, respectively. An experimental structure of Fis-DNA is not yet available, but the predicted asymmetrical bending and the bending angle agree with results from a recent biochemical analysis.
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Affiliation(s)
- W S Tzou
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC
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7
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Toward the development of metal-based synthetic nucleases and peptidases: a rationale and progress report in applying the principles of coordination chemistry. Coord Chem Rev 1998. [DOI: 10.1016/s0010-8545(98)00157-x] [Citation(s) in RCA: 487] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chen CH, Landgraf R, Walts AD, Chan L, Schlonk PM, Terwilliger TC, Sigman DS. Scission of DNA at a preselected sequence using a single-strand-specific chemical nuclease. CHEMISTRY & BIOLOGY 1998; 5:283-92. [PMID: 9578634 DOI: 10.1016/s1074-5521(98)90621-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND We were interested in developing a protocol for cleaving large DNAs specifically. Previous attempts to develop such methods have failed to work because of high levels of nonspecific background scission. RESULTS R-loop formation was chosen for sequence-specific targeting, a method of hybridization whereby an RNA displaces a DNA strand of identical sequence in 70% formamide using Watson-Crick base-pairing, leading to a three-stranded structure. R-loops are stabilized in aqueous solution by modifying the bases with chemical reagents. The R-loop was cleaved using a novel nuclease prepared from the Thr48-->Cys mutant of the single-strand-specific M-13 gene V protein (GVP), which was alkylated with 5-(iodoacetamido-beta-alanyl)1,10-phenanthroline. The cleavage products of the pGEM plasmid were cloned in to the pCR 2.1-TOPO vector. Adenovirus 2 DNA (35.8 kb; tenfold larger than the pGEM plasmid) was also cleaved quantitatively at a preselected sequence. CONCLUSIONS A new method for cleaving duplex DNA at any preselected sequence was developed. The cleavage method relies on the chemical conversion of M-13 GVP into a nuclease, reflecting GVP's specificity for single-stranded DNA. The GVP chimera is the first example of a semisynthetic secondary structure specific nuclease. The chemical nuclease activity of 1,10-phenanthroline-copper is uniquely suited to this technique because it oxidizes the deoxyribose moiety without generating diffusible intermediates, providing clonable DNA fragments. The protocol could be useful in generating large DNA fragments for mapping the contiguity of probes or defining the exon-intron structure of transcription units.
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Affiliation(s)
- C H Chen
- Molecular Biology Institute, University of California, Los Angeles 90095-1570, USA
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Cox JM, Hayward MM, Sanchez JF, Gegnas LD, van der Zee S, Dennis JH, Sigler PB, Schepartz A. Bidirectional binding of the TATA box binding protein to the TATA box. Proc Natl Acad Sci U S A 1997; 94:13475-80. [PMID: 9391050 PMCID: PMC28330 DOI: 10.1073/pnas.94.25.13475] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
By selective attachment of a DNA cleavage agent to specific residues in the yeast TATA box binding protein (yTBP), we demonstrate that, in solution, yTBP binds to the TATA boxes of both the adenovirus major late promoter and the yeast CYC1 promoter with only a modest preference in orientation and binds well to several overlapping binding sites. The general factors TFIIA and TFIIB each increase the rotational and translational selectivity of yTBP but are not sufficient, at least individually, to confer a unique polarity to the preinitiation complex. We conclude that TBP alone cannot define the productive orientation of general factor assembly on a promoter.
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Affiliation(s)
- J M Cox
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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Muskhelishvili G, Travers A. Stabilization of DNA Microloops by FIS — A Mechanism for Torsional Transmission in Transcription Activation and DNA Inversion. MECHANISMS OF TRANSCRIPTION 1997. [DOI: 10.1007/978-3-642-60691-5_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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12
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Pai KS, Bussiere DE, Wang F, White SW, Bastia D. Structure of the replication terminus-terminator protein complex as probed by affinity cleavage. Proc Natl Acad Sci U S A 1996; 93:10647-52. [PMID: 8855233 PMCID: PMC38208 DOI: 10.1073/pnas.93.20.10647] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The replication terminator protein (RTP) of Bacillus subtilis is a homodimer that binds to each replication terminus and impedes replication fork movement in only one orientation with respect to the replication origin. The three-dimensional structure of the RTP-DNA complex needs to be determined to understand how structurally symmetrical dimers of RTP generate functional asymmetry. The functional unit of each replication terminus of Bacillus subtilis consists of four turns of DNA complexed with two interacting dimers of RTP. Although the crystal structure of the RTP apoprotein dimer has been determined at 2.6-A resolution, the functional unit of the terminus is probably too large and too flexible to lend itself to cocrystallization. We have therefore used an alternative strategy to delineate the three dimensional structure of the RTP-DNA complex by converting the protein into a site-directed chemical nuclease. From the pattern of base-specific cleavage of the terminus DNA by the chemical nuclease, we have mapped the amino acid to base contacts. Using these contacts as distance constraints, with the crystal structure of RTP, we have constructed a model of the DNA-protein complex. The biological implications of the model have been discussed.
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Affiliation(s)
- K S Pai
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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13
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Huang B, Schaeffer CJ, Li Q, Tsai MD. Splase: a new class IIS zinc-finger restriction endonuclease with specificity for Sp1 binding sites. JOURNAL OF PROTEIN CHEMISTRY 1996; 15:481-9. [PMID: 8895094 DOI: 10.1007/bf01886856] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new restriction endonuclease, named Splase, was constructed by genetically fusing the DNA-cleavage domain of the restriction endonuclease Fok1 with the zinc-finger DNA-binding domain of the transcription factor Sp1. The resulting protein was expressed in Escherichia coli., partially purified, and shown to selectively digest plasmid DNA harboring consensus Sp1 sites. Splase was also shown to selectively digest the long terminal repeat of the HIV-1 DNA at Sp1 sites. Splase recognizes a 10-bp DNA sequence and hydrolyzes phosphodiester bonds upstream of the binding sequence. The binding specificity of Splase makes this a "rare cutter" restriction enzyme which could be valuable in creating large DNA fragments for genome sequencing projects. The result also presents the opportunity to create other restriction enzymes by altering the binding specificity of the zinc-finger recognition helix.
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Affiliation(s)
- B Huang
- Ohio State Biochemistry Program, Ohio State University, Columbus 43210, USA
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14
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Bastia D. Structural aspects of protein-DNA interactions as revealed by conversion of the interacting protein into a sequence-specific cross-linking agent or a chemical nuclease. Structure 1996; 4:661-4. [PMID: 8805548 DOI: 10.1016/s0969-2126(96)00072-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- D Bastia
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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15
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Perrin DM, Mazumder A, Sigman DS. Oxidative chemical nucleases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 52:123-51. [PMID: 8821260 DOI: 10.1016/s0079-6603(08)60966-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- D M Perrin
- Department of Biological Chemistry, University of California, Los Angeles 90024, USA
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16
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Pan CQ, Landgraf R, Sigman DS. Drosophila engrailed-1,10-phenanthroline chimeras as probes of homeodomain-DNA complexes. Protein Sci 1995; 4:2279-88. [PMID: 8563624 PMCID: PMC2143021 DOI: 10.1002/pro.5560041105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have converted the Drosophila engrailed homeodomain into a sequence-specific nuclease by linking the protein to the chemical nuclease 1,10-phenanthroline-copper (OP-Cu). Unique cysteines were introduced at six positions into the homeodomain by site-directed mutagenesis for the covalent attachment of OP-Cu. The varied DNA-binding affinity and specificity of these mutants and the DNA cleavage pattern of their OP-Cu derivatives allowed us to assess the crystal structure of the engrailed homeodomain-DNA complex. We have also achieved site-specific double-stranded DNA scission with one of the homeodomain mutants, E28C, which has the potential of being used to identify engrailed binding sites in the genome. Because the homeodomain is so well conserved among members of the homeodomain-containing protein family, other homeodomain proteins can be converted into nucleases by attaching OP-Cu at position 28 of their homeodomains.
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Affiliation(s)
- C Q Pan
- Molecular Biology Institute, University of California at Los Angeles 90095-1570, USA
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Wu J, Perrin DM, Sigman DS, Kaback HR. Helix packing of lactose permease in Escherichia coli studied by site-directed chemical cleavage. Proc Natl Acad Sci U S A 1995; 92:9186-90. [PMID: 7568098 PMCID: PMC40949 DOI: 10.1073/pnas.92.20.9186] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Biotinylated lactose permease from Escherichia coli containing a single-cysteine residue at position 330 (helix X) or at position 147, 148, or 149 (helix V) was purified by avidin-affinity chromatography and derivatized with 5-(alpha-bromoacetamido)-1,10-phenanthroline-copper [OP(Cu)]. Studies with purified, OP(Cu)-labeled Leu-330 --> Cys permease in dodecyl-beta-D-maltopyranoside demonstrate that after incubation in the presence of ascorbate, cleavage products of approximately 19 and 6-8 kDa are observed on immunoblots with anti-C-terminal antibody. Remarkably, the same cleavage products are observed with permease embedded in the native membrane. Comparison with the C-terminal half of the permease expressed independently as a standard indicates that the 19-kDa product results from cleavage near the cytoplasmic end of helix VII, whereas the 6- to 8-kDa fragment probably results from fragmentation near the cytoplasmic end of helix XI. Results are entirely consistent with a tertiary-structure model of the C-terminal half of the permease derived from earlier site-directed fluorescence and site-directed mutagenesis studies. Similar studies with OP(Cu)-labeled Cys-148 permease exhibit cleavage products at approximately 19 kDa and at 15-16 kDa. The larger fragment probably reflects cleavage at a site near the cytoplasmic end of helix VII, whereas the 15- to 16-kDa fragment is consistent with cleavage near the cytoplasmic end of helix VIII. When OP(Cu) is moved 100 degrees to position 149 (Val-149 --> Cys permease), a single product is observed at 19 kDa, suggesting fragmentation at the cytoplasmic end of helix VII. However, when the reagent is moved 100 degrees in the other direction to position 147 (Gly-147 --> Cys permease), cleavage is not observed. The results suggest that helix V is in close proximity to helices VII and VIII with position 148 in the interface between the helices, position 149 facing helix VII, and position 147 facing the lipid bilayer.
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Affiliation(s)
- J Wu
- Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles 90095-1662, USA
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