1
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Tants JN, Oberstrass L, Weigand JE, Schlundt A. Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger. Nucleic Acids Res 2024:gkae555. [PMID: 38953172 DOI: 10.1093/nar/gkae555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024] Open
Abstract
Zinc finger (ZnF) domains appear in a pool of structural contexts and despite their small size achieve varying target specificities, covering single-stranded and double-stranded DNA and RNA as well as proteins. Combined with other RNA-binding domains, ZnFs enhance affinity and specificity of RNA-binding proteins (RBPs). The ZnF-containing immunoregulatory RBP Roquin initiates mRNA decay, thereby controlling the adaptive immune system. Its unique ROQ domain shape-specifically recognizes stem-looped cis-elements in mRNA 3'-untranslated regions (UTR). The N-terminus of Roquin contains a RING domain for protein-protein interactions and a ZnF, which was suggested to play an essential role in RNA decay by Roquin. The ZnF domain boundaries, its RNA motif preference and its interplay with the ROQ domain have remained elusive, also driven by the lack of high-resolution data of the challenging protein. We provide the solution structure of the Roquin-1 ZnF and use an RBNS-NMR pipeline to show that the ZnF recognizes AU-rich RNAs. We systematically refine the contributions of adenines in a poly(U)-background to specific complex formation. With the simultaneous binding of ROQ and ZnF to a natural target transcript of Roquin, our study for the first time suggests how Roquin integrates RNA shape and sequence features through the ROQ-ZnF tandem.
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Affiliation(s)
- Jan-Niklas Tants
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Lasse Oberstrass
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany
| | - Julia E Weigand
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- University of Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
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2
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He Z, Wang Z, Lu Z, Gao C, Wang Y. An electrophoretic mobility shift assay using the protein isolated from host plants. PLANT METHODS 2024; 20:68. [PMID: 38735938 PMCID: PMC11089672 DOI: 10.1186/s13007-024-01201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND The electrophoretic mobility shift assay (EMSA) is a common technology to detect DNA-protein interactions. However, in most cases, the protein used in EMSA is obtained via prokaryotic expression, and rarely from plants. At the same time, the proteins expressed from prokaryotic systems usually cannot fold naturally and have no post translationally modification, which may affect the binding of proteins to DNA. RESULTS Here, we develop a technique to quickly isolate proteins of interest from host plants and then analyze them using fluorescent EMSA. This technology system is called: protein from plants fluorescent EMSA method (PPF-EMSA). In PPF-EMSA, a special transient transformation method is employed to transiently deliver genes into the plant, enabling efficient synthesis the encoded proteins. Then, the target protein is isolated using immunoprecipitation, and the DNA probes were labeled with cyanine 3 (Cy3). Both fluorescent EMSA and super-shift fluorescent EMSA can be performed using the proteins from plants. Three kinds of plants, Betula platyphylla, Populus. davidiana×P. bolleana and Arabidopsis thaliana, are used in this study. The proteins isolated from plants are in a natural state, can fold naturally and are posttranslationally modified, enabling true binding to their cognate DNAs. CONCLUSION As transient transformation can be performed quickly and not depended on whether stable transformation is available or not, we believe this method will have a wide application, enabling isolation of proteins from host plant conveniently.
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Affiliation(s)
- Zihang He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhangguo Lu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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3
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Alcalde-Ordóñez A, Barreiro-Piñeiro N, McGorman B, Gómez-González J, Bouzada D, Rivadulla F, Vázquez ME, Kellett A, Martínez-Costas J, López MV. A copper(ii) peptide helicate selectively cleaves DNA replication foci in mammalian cells. Chem Sci 2023; 14:14082-14091. [PMID: 38098723 PMCID: PMC10718067 DOI: 10.1039/d3sc03303a] [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: 06/29/2023] [Accepted: 10/25/2023] [Indexed: 12/17/2023] Open
Abstract
The use of copper-based artificial nucleases as potential anticancer agents has been hampered by their poor selectivity in the oxidative DNA cleavage process. An alternative strategy to solve this problem is to design systems capable of selectively damaging noncanonical DNA structures that play crucial roles in the cell cycle. We designed an oligocationic CuII peptide helicate that selectively binds and cleaves DNA three-way junctions (3WJs) and induces oxidative DNA damage via a ROS-mediated pathway both in vitro and in cellulo, specifically at DNA replication foci of the cell nucleus, where this DNA structure is transiently generated. To our knowledge, this is the first example of a targeted chemical nuclease that can discriminate with high selectivity 3WJs from other forms of DNA both in vitro and in mammalian cells. Since the DNA replication process is deregulated in cancer cells, this approach may pave the way for the development of a new class of anticancer agents based on copper-based artificial nucleases.
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Affiliation(s)
- Ana Alcalde-Ordóñez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Natalia Barreiro-Piñeiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Bríonna McGorman
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Francisco Rivadulla
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Física, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Andrew Kellett
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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4
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Gunitseva N, Evteeva M, Korzhenkov A, Patrushev M. A New RNA-Dependent Cas12g Nuclease. Int J Mol Sci 2023; 24:17105. [PMID: 38069429 PMCID: PMC10707612 DOI: 10.3390/ijms242317105] [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: 09/25/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
The development of RNA-targeting CRISPR-Cas systems represents a major step forward in the field of gene editing and regulation. RNA editing presents a viable alternative to genome editing in certain scenarios as it offers a reversible and manageable approach, reducing the likelihood of runaway mutant variants. One of the most promising applications is in the treatment of genetic disorders caused by mutations in RNA molecules. In this study, we investigate a previously undescribed Cas12g nuclease which was found in metagenomes from promising thermophilic microbial communities during the expedition to the Republic of North Ossetia-Alania in 2020. The method outlined in this study can be applied to other Cas orthologs and variants, leading to a better understanding of the CRISPR-Cas system and its enzymatic activities. The cis-cleavage activity of the new type V-G Cas effector was indicated by in vitro RNA cleavage experiments. While CRISPR-Cas systems are known for their high specificity, there is still a risk of unintended cleavage of nontargeted RNA molecules. Ultimately, the search for new genome editing tools and the study of their properties will remove barriers to research in this area. With continued research and development, we may be able to unlock their full potential.
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Affiliation(s)
- Natalia Gunitseva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia (M.P.)
| | - Martha Evteeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia (M.P.)
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5
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Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL. Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA. RSC Chem Biol 2023; 4:486-493. [PMID: 37415868 PMCID: PMC10320839 DOI: 10.1039/d3cb00053b] [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: 04/12/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
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Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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6
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Malaga Gadea FC, Nikolova EN. Structural Plasticity of Pioneer Factor Sox2 and DNA Bendability Modulate Nucleosome Engagement and Sox2-Oct4 Synergism. J Mol Biol 2023; 435:167916. [PMID: 36495920 PMCID: PMC10184184 DOI: 10.1016/j.jmb.2022.167916] [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: 09/01/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Pioneer transcription factors (pTFs) can bind directly to silent chromatin and promote vital transcriptional programs. Here, by integrating high-resolution nuclear magnetic resonance (NMR) spectroscopy with biochemistry, we reveal new structural and mechanistic insights into the interaction of pluripotency pTFs and functional partners Sox2 and Oct4 with nucleosomes. We find that the affinity and conformation of Sox2 for solvent-exposed nucleosome sites depend strongly on their position and DNA sequence. Sox2, which is partially disordered but becomes structured upon DNA binding and bending, forms a super-stable nucleosome complex at superhelical location +5 (SHL+5) with similar affinity and conformation to that with naked DNA. However, at suboptimal internal and end-positioned sites where DNA may be harder to deform, Sox2 favors partially unfolded and more dynamic states that are encoded in its intrinsic flexibility. Importantly, Sox2 structure and DNA bending can be stabilized by synergistic Oct4 binding, but only on adjacent motifs near the nucleosome edge and with the full Oct4 DNA-binding domain. Further mutational studies reveal that strategically impaired Sox2 folding is coupled to reduced DNA bending and inhibits nucleosome binding and Sox2-Oct4 cooperation, while increased nucleosomal DNA flexibility enhances Sox2 association. Together, our findings fit a model where the site-specific DNA bending propensity and structural plasticity of Sox2 govern distinct modes of nucleosome engagement and modulate Sox2-Oct4 synergism. The principles outlined here can potentially guide pTF site selection in the genome and facilitate interaction with other chromatin factors or chromatin opening in vivo.
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Affiliation(s)
- Fabiana C Malaga Gadea
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Evgenia N Nikolova
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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7
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Thakur M, Parulekar RS, Barale SS, Sonawane KD, Muniyappa K. Interrogating the substrate specificity landscape of UvrC reveals novel insights into its non-canonical function. Biophys J 2022; 121:3103-3125. [PMID: 35810330 PMCID: PMC9463653 DOI: 10.1016/j.bpj.2022.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/23/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
Although it is relatively unexplored, accumulating data highlight the importance of tripartite crosstalk between nucleotide excision repair (NER), DNA replication, and recombination in the maintenance of genome stability; however, elucidating the underlying mechanisms remains challenging. While Escherichia coli uvrA and uvrB can fully complement polAΔ cells in DNA replication, uvrC attenuates this alternative DNA replication pathway, but the exact mechanism by which uvrC suppresses DNA replication is unknown. Furthermore, the identity of bona fide canonical and non-canonical substrates for UvrCs are undefined. Here, we reveal that Mycobacterium tuberculosis UvrC (MtUvrC) strongly binds to, and robustly cleaves, key intermediates of DNA replication/recombination as compared with the model NER substrates. Notably, inactivation of MtUvrC ATPase activity significantly attenuated its endonuclease activity, thus suggesting a causal link between these two functions. We built an in silico model of the interaction of MtUvrC with the Holliday junction (HJ), using a combination of homology modeling, molecular docking, and molecular dynamic simulations. The model predicted residues that were potentially involved in HJ binding. Six of these residues were mutated either singly or in pairs, and the resulting MtUvrC variants were purified and characterized. Among them, residues Glu595 and Arg597 in the helix-hairpin-helix motif were found to be crucial for the interaction between MtUvrC and HJ; consequently, mutations in these residues, or inhibition of ATP hydrolysis, strongly abrogated its DNA-binding and endonuclease activities. Viewed together, these findings expand the substrate specificity landscape of UvrCs and provide crucial mechanistic insights into the interplay between NER and DNA replication/recombination.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.
| | | | - Sagar S Barale
- Structural Bioinformatics Unit, Shivaji University, Kolhapur, India
| | - Kailas D Sonawane
- Department of Microbiology, Shivaji University, Kolhapur, India; Structural Bioinformatics Unit, Shivaji University, Kolhapur, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.
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8
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Charlier D, Bervoets I. Separation and Characterization of Protein-DNA Complexes by EMSA and In-Gel Footprinting. Methods Mol Biol 2022; 2516:169-199. [PMID: 35922628 DOI: 10.1007/978-1-0716-2413-5_11] [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] [Indexed: 06/15/2023]
Abstract
In-gel footprinting enables the precise identification of protein binding sites on the DNA after separation of free and protein-bound DNA molecules by gel electrophoresis in native conditions and subsequent digestion by the nuclease activity of the 1,10-phenanthroline-copper ion [(OP)2-Cu+] within the gel matrix. Hence, the technique combines the resolving power of protein-DNA complexes in the electrophoretic mobility shift assay (EMSA) with the precision of target site identification by chemical footprinting. This approach is particularly well suited to characterize distinct molecular assemblies in a mixture of protein-DNA complexes and to identify individual binding sites within composite operators, when the concentration-dependent occupation of binding sites, with a different affinity, results in the generation of complexes with a distinct stoichiometry and migration velocity in gel electrophoresis.
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Affiliation(s)
- Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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9
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Racca JD, Chatterjee D, Chen YS, Rai RK, Yang Y, Georgiadis MM, Haas E, Weiss MA. Tenuous transcriptional threshold of human sex determination. II. SRY exploits water-mediated clamp at the edge of ambiguity. Front Endocrinol (Lausanne) 2022; 13:1029177. [PMID: 36568077 PMCID: PMC9771472 DOI: 10.3389/fendo.2022.1029177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Y-encoded transcription factor SRY initiates male differentiation in therian mammals. This factor contains a high-mobility-group (HMG) box, which mediates sequence-specific DNA binding with sharp DNA bending. A companion article in this issue described sex-reversal mutations at box position 72 (residue 127 in human SRY), invariant as Tyr among mammalian orthologs. Although not contacting DNA, the aromatic ring seals the domain's minor wing at a solvent-exposed junction with a basic tail. A seeming paradox was posed by the native-like biochemical properties of inherited Swyer variant Y72F: its near-native gene-regulatory activity is consistent with the father's male development, but at odds with the daughter's XY female somatic phenotype. Surprisingly, aromatic rings (Y72, F72 or W72) confer higher transcriptional activity than do basic or polar side chains generally observed at solvated DNA interfaces (Arg, Lys, His or Gln). Whereas biophysical studies (time-resolved fluorescence resonance energy transfer and heteronuclear NMR spectroscopy) uncovered only subtle perturbations, dissociation of the Y72F complex was markedly accelerated relative to wild-type. Studies of protein-DNA solvation by molecular-dynamics (MD) simulations of an homologous high-resolution crystal structure (SOX18) suggest that Y72 para-OH anchors a network of water molecules at the tail-DNA interface, perturbed in the variant in association with nonlocal conformational fluctuations. Loss of the Y72 anchor among SRY variants presumably "unclamps" its basic tail, leading to (a) rapid DNA dissociation despite native affinity and (b) attenuated transcriptional activity at the edge of sexual ambiguity. Conservation of Y72 suggests that this water-mediated clamp operates generally among SRY and metazoan SOX domains.
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Affiliation(s)
- Joseph D. Racca
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Joseph D. Racca, ; Michael A. Weiss,
| | - Deepak Chatterjee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ratan K. Rai
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yanwu Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elisha Haas
- Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Joseph D. Racca, ; Michael A. Weiss,
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10
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Naumenko NV, Petruseva IO, Lomzov AA, Lavrik OI. Recognition and removal of clustered DNA lesions via nucleotide excision repair. DNA Repair (Amst) 2021; 108:103225. [PMID: 34562718 DOI: 10.1016/j.dnarep.2021.103225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/25/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
Clustered damage of DNA consists of two or more lesions located within one or two turns of the DNA helix. Clusters consisting of lesions of various structures can arise under the influence of strong damaging factors, especially if the cells have a compromised repair status. In this work, we analyzed how the presence of an analog of the apurinic/apyrimidinic site - a non-nucleoside residue consisting of diethylene glycol phosphodiester (DEG) - affects the recognition and removal of a bulky lesion (a non-nucleoside site of the modified DNA strand containing a fluorescein residue, nFlu) from DNA by a mammalian nucleotide excision repair system. Here we demonstrated that the efficiency of nFlu removal decreases in the presence of DEG in the complementary strand and is completely suppressed when the DEG is located opposite the nFlu. By contrast, protein factor XPC-RAD23B, which initiates global genomic nucleotide excision repair, has higher affinity for DNA containing clustered damage as compared to DNA containing a single bulky lesion; the affinity of XPC strengthens as the positions of DEG and nFlu become closer. The changes in the double-stranded DNA's geometry caused by the presence of clustered damage were also assessed. The obtained experimental data together with the results of molecular dynamics simulations make it possible to get insight into the structural features of DNA containing clustered lesions that determine the efficiency of repair. Speaking more broadly, this study should help to understand the probable fate of bulky adduct-containing clusters of various topologies in the mammalian cell.
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Affiliation(s)
- N V Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - I O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.
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11
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Vasantha Niranjan C, Retnaraj Samue SJ, Saravanakumar V, Jackson Durairaj S. Novel and Efficient Protocol for DNA Coating-Based Identification of DNA-Protein Interaction by Antibody-Mediated Immunodetection. Rep Biochem Mol Biol 2021; 9:264-269. [PMID: 33649719 DOI: 10.29252/rbmb.9.3.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Background Studying protein-protein and protein-DNA interactions are prerequisites for the identification of function and mechanistic role of various proteins in the cell. Protocols for analyzing DNA-based Protein-Protein and Protein-DNA interactions are complicated and need to be simplified for efficient tracking of binding capabilities of various proteins to specific DNA molecules. Here, we demonstrated a simple yet efficient protocol for the identification of DNA coating-based Protein-DNA interaction using antibodymediated immunodetection. Methods Briefly, we have coated specific DNA in the microtiter plate followed by incubating with protein lysate. Specific protein-DNA and/or protein-protein bind with DNA interactions are identified using specific fluorophore-conjugated antibodies. Antibodies are used to detect a protein that is bound to the DNA. Results Fluorescent-based detection identifies the specific interaction between Protein-DNA with respect to coated DNA fragments. The protocol uses indirect conjugated antibodies and hence the technique is sensitive for effective identification of Protein-DNA interactions. Conclusion Based on the results we conclude that the demonstrated protocol is simple, efficient and sensitive for identification of Protein-DNA interactions.
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Affiliation(s)
- Chellathurai Vasantha Niranjan
- This The two authors are considered as the first author.,Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre,Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Selvan Johnson Retnaraj Samue
- This The two authors are considered as the first author.,Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre,Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Venkatachalam Saravanakumar
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre,Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Selvan Jackson Durairaj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre,Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
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12
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Gómez-González J, Pérez Y, Sciortino G, Roldan-Martín L, Martínez-Costas J, Maréchal JD, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*. Angew Chem Int Ed Engl 2021; 60:8859-8866. [PMID: 33290612 DOI: 10.1002/anie.202013039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/12/2020] [Indexed: 01/03/2023]
Abstract
Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as FeII and CoII . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled FeII helicate was internalized and selectively stains DNA replication factories in functional cells.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Yolanda Pérez
- NMR Facility, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Lorena Roldan-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
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13
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Muniyandi P, Palaninathan V, Veeranarayanan S, Ukai T, Maekawa T, Hanajiri T, Mohamed MS. ECM Mimetic Electrospun Porous Poly (L-lactic acid) (PLLA) Scaffolds as Potential Substrates for Cardiac Tissue Engineering. Polymers (Basel) 2020; 12:E451. [PMID: 32075089 PMCID: PMC7077699 DOI: 10.3390/polym12020451] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 11/16/2022] Open
Abstract
Cardiac tissue engineering (CTE) aims to generate potential scaffolds to mimic extracellular matrix (ECM) for recreating the injured myocardium. Highly porous scaffolds with properties that aid cell adhesion, migration and proliferation are critical in CTE. In this study, electrospun porous poly (l-lactic acid) (PLLA) porous scaffolds were fabricated and modified with different ECM derived proteins such as collagen, gelatin, fibronectin and poly-L-lysine. Subsequently, adult human cardiac fibroblasts (AHCF) were cultured on the protein modified and unmodified fibers to study the cell behavior and guidance. Further, the cytotoxicity and reactive oxygen species (ROS) assessments of the respective fibers were performed to determine their biocompatibility. Excellent cell adhesion and proliferation of the cardiac fibroblasts was observed on the PLLA porous fibers regardless of the surface modifications. The metabolic rate of cells was on par with the conventional cell culture ware while the proliferation rate surpassed the latter by nearly two-folds. Proteome profiling revealed that apart from being an anchorage platform for cells, the surface topography has modulated significant expression of the cellular proteome with many crucial proteins responsible for cardiac fibroblast growth and proliferation.
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Affiliation(s)
- Priyadharshni Muniyandi
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama 350-8585, Japan; (P.M.); (T.U.); (T.M.); (T.H.)
| | - Vivekanandan Palaninathan
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama 350-8585, Japan; (V.P.); (S.V.)
| | - Srivani Veeranarayanan
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama 350-8585, Japan; (V.P.); (S.V.)
| | - Tomofumi Ukai
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama 350-8585, Japan; (P.M.); (T.U.); (T.M.); (T.H.)
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama 350-8585, Japan; (V.P.); (S.V.)
| | - Toru Maekawa
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama 350-8585, Japan; (P.M.); (T.U.); (T.M.); (T.H.)
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama 350-8585, Japan; (V.P.); (S.V.)
| | - Tatsuro Hanajiri
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama 350-8585, Japan; (P.M.); (T.U.); (T.M.); (T.H.)
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama 350-8585, Japan; (V.P.); (S.V.)
| | - Mohamed Sheikh Mohamed
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama 350-8585, Japan; (P.M.); (T.U.); (T.M.); (T.H.)
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama 350-8585, Japan; (V.P.); (S.V.)
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14
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Guynet C, Nicolas E, Ton-Hoang B, Bouet JY, Hallet B. First Biochemical Steps on Bacterial Transposition Pathways. Methods Mol Biol 2020; 2075:157-177. [PMID: 31584162 DOI: 10.1007/978-1-4939-9877-7_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Transposons are found in a wide variety of forms throughout the prokaryotic world where they actively contribute to the adaptive strategies of bacterial communities and hence, to the continuous emergence of new multiresistant pathogens. Contrasting with their biological and societal impact, only a few bacterial transposons have been the subject of detailed molecular studies. In this chapter, we propose a set of reliable biochemical methods as a primary route for studying new transposition mechanisms. These methods include (a) a straightforward approach termed "thermal shift induction" to produce the transposase in a soluble and properly folded configuration prior to its purification, (b) an adaptation of classical electrophoretic mobility shift assays (EMSA) combined to fluorescently labeled DNA substrates to determine the DNA content of different complexes assembled by the transposase, and (c) a highly sensitive "in-gel" DNA footprinting assay to further characterize these complexes at the base pair resolution level. A combination of these approaches was recently applied to decipher the molecular organization of key intermediates in the Tn3-family transposition pathway, a mechanism that has long been refractory to biochemical studies.
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Affiliation(s)
- Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France.
| | - Emilien Nicolas
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology-URBE, University of Namur (UNamur), Namur, Belgium
| | - Bao Ton-Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Bernard Hallet
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium.
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15
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Wang C, Du X, Xie T, Li H. Label- and modification-free-based in situ selection of bovine serum albumin specific aptamer. J Sep Sci 2019; 42:3571-3578. [PMID: 31550414 DOI: 10.1002/jssc.201900620] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
Abstract
Systematic evolution of ligands by exponential enrichment is a traditional approach to select aptamer, which has a great potential in biosensing field. However, chemical modifications of DNA library or targets before selection might block the real recognition and binding sites between aptamers and their targets. In this study, a label- and modification-free-based in situ selection strategy was developed to overcome this limitation. The strategy is an attempt to screen bovine serum albumin aptamers according to the principle of electrophoretic mobility shift assay, and allowed single-stranded DNA sequence to be fully exposed to interact with bovine serum albumin which was mixed with the agarose gel beforehand. After eight rounds of selection, specific aptamer with low dissociation constant (Kd ) value of 69.44 ± 7.60 nM was selected and used for subsequent establishment of fluorescence biosensor. After optimization, the optimal aptasensor exhibited a high sensitivity toward bovine serum albumin with a limit of detection of 0.24 ng/mL (linear range from 1 to 120 ng/mL). These results indicated that the label- and modification-free-based in situ selection strategy proposed in this work could effectively select specific aptamer to develop aptasensor for sensitive detection of bovine serum albumin or other targets in actual complicated samples.
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Affiliation(s)
- Chuchu Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Xiaoyan Du
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Tiantian Xie
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Hao Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
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16
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Paolini A, Leoni L, Giannicchi I, Abbaszadeh Z, D'Oria V, Mura F, Dalla Cort A, Masotti A. MicroRNAs delivery into human cells grown on 3D-printed PLA scaffolds coated with a novel fluorescent PAMAM dendrimer for biomedical applications. Sci Rep 2018; 8:13888. [PMID: 30224665 PMCID: PMC6141561 DOI: 10.1038/s41598-018-32258-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/03/2018] [Indexed: 11/25/2022] Open
Abstract
Many advanced synthetic, natural, degradable or non-degradable materials have been employed to create scaffolds for cell culture for biomedical or tissue engineering applications. One of the most versatile material is poly-lactide (PLA), commonly used as 3D printing filament. Manufacturing of multifunctional scaffolds with improved cell growth proliferation and able to deliver oligonucleotides represents an innovative strategy for controlled and localized gene modulation that hold great promise and could increase the number of applications in biomedicine. Here we report for the first time the synthesis of a novel Rhodamine derivative of a poly-amidoamine dendrimer (G = 5) able to transfect cells and to be monitored by confocal microscopy that we also employed to coat a 3D-printed PLA scaffold. The coating do not modify the oligonucleotide binding ability, toxicity or transfection properties of the scaffold that is able to increase cell proliferation and deliver miRNA mimics (i.e., pre-mir-503) into human cells. Although further experiments are required to optimize the dendrimer/miRNA ratio and improve transfection efficiency, we demonstrated the effectiveness of this promising and innovative 3D-printed transfection system to transfer miRNAs into human cells for future biomedical applications.
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Affiliation(s)
- Alessandro Paolini
- Bambino Gesù Children's Hospital-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy.
| | - Luca Leoni
- Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Ilaria Giannicchi
- Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Zeinab Abbaszadeh
- Bambino Gesù Children's Hospital-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy
| | - Valentina D'Oria
- Bambino Gesù Children's Hospital-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy
| | - Francesco Mura
- Center for the Nanotechnology applied to the Engineering of La Sapienza (CNIS), Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Antonella Dalla Cort
- Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Andrea Masotti
- Bambino Gesù Children's Hospital-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy.
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17
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Rodríguez J, Learte-Aymamí S, Mosquera J, Celaya G, Rodríguez-Larrea D, Vázquez ME, Mascareñas JL. DNA-binding miniproteins based on zinc fingers. Assessment of the interaction using nanopores. Chem Sci 2018; 9:4118-4123. [PMID: 29780541 PMCID: PMC5941273 DOI: 10.1039/c7sc05441f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/23/2018] [Indexed: 12/18/2022] Open
Abstract
We report a synthetic miniprotein that combines zinc finger modules of the transcription factor GAGA with the AT-hook peptide. This designed chimera binds to extended DNA sites with high affinity and selectivity, as shown by nanopore force spectroscopy.
Obtaining artificial proteins that mimic the DNA binding properties of natural transcription factors could open new ways of manipulating gene expression at will. In this context it is particularly interesting to develop simple synthetic systems. Inspired by the modularity of natural transcription factors, we have designed synthetic miniproteins that combine the zinc finger module of the transcription factor GAGA and AT-hook peptide domains. These constructs are capable of binding to composite DNA sequences of up to 14 base pairs with high affinity and good selectivity. In particular, we have synthesized three different chimeras and characterized their DNA binding properties by electrophoresis and fluorescence anisotropy. We have also used, for the first time in the study of peptide-based DNA binders, nanopore force spectroscopy to obtain further data on the DNA interaction.
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Garbiñe Celaya
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU) , Leioa 48940 , Spain
| | - David Rodríguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU) , Leioa 48940 , Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
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18
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Celluzzi A, Paolini A, D'Oria V, Risoluti R, Materazzi S, Pezzullo M, Casciardi S, Sennato S, Bordi F, Masotti A. Biophysical and biological contributions of polyamine-coated carbon nanotubes and bidimensional buckypapers in the delivery of miRNAs to human cells. Int J Nanomedicine 2018. [PMID: 29296082 DOI: 10.2147/ijn.s144155.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recent findings in nanomedicine have revealed that carbon nanotubes (CNTs) can be used as potential drug carriers, therapeutic agents and diagnostics tools. Moreover, due to their ability to cross cellular membranes, their nanosize dimension, high surface area and relatively good biocompatibility, CNTs have also been employed as a novel gene delivery vector system. In our previous work, we functionalized CNTs with two polyamine polymers, polyethyleneimine (PEI) and polyamidoamine dendrimer (PAMAM). These compounds have low cytotoxicity, ability to conjugate microRNAs (such as miR-503) and, at the same time, transfect efficiently endothelial cells. The parameters contributing to the good efficiency of transfection that we observed were not investigated in detail. In fact, the diameter and length of CNTs are important parameters to be taken into account when evaluating the effects on drug delivery efficiency. In order to investigate the biophysical and biological contributions of polymer-coated CNTs in delivery of miRNAs to human cells, we decided to investigate three different preparations, characterized by different dimensions and aspect ratios. In particular, we took into account very small CNTs, a suspension of CNTs starting from the commercial product and a 2D material based on CNTs (ie, buckypapers [BPs]) to examine the transfection efficiency of a rigid scaffold. In conclusion, we extensively investigated the biophysical and biological contributions of polyamine-coated CNTs and bidimensional BPs in the delivery of miRNAs to human cells, in order to optimize the transfection efficiency of these compounds to be employed as efficient drug delivery vectors in biomedical applications.
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Affiliation(s)
| | | | | | | | | | - Marco Pezzullo
- Bambino Gesù Children's Hospital, IRCCS, Research Laboratories
| | - Stefano Casciardi
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, National Institution for Insurance Against Accidents at Work (INAIL Research), Monte Porzio Catone
| | - Simona Sennato
- CNR-ISC UOS Roma, Department of Physics, Sapienza University of Rome, Roma, Italy
| | - Federico Bordi
- CNR-ISC UOS Roma, Department of Physics, Sapienza University of Rome, Roma, Italy
| | - Andrea Masotti
- Bambino Gesù Children's Hospital, IRCCS, Research Laboratories
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19
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Celluzzi A, Paolini A, D'Oria V, Risoluti R, Materazzi S, Pezzullo M, Casciardi S, Sennato S, Bordi F, Masotti A. Biophysical and biological contributions of polyamine-coated carbon nanotubes and bidimensional buckypapers in the delivery of miRNAs to human cells. Int J Nanomedicine 2017; 13:1-18. [PMID: 29296082 PMCID: PMC5739113 DOI: 10.2147/ijn.s144155] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recent findings in nanomedicine have revealed that carbon nanotubes (CNTs) can be used as potential drug carriers, therapeutic agents and diagnostics tools. Moreover, due to their ability to cross cellular membranes, their nanosize dimension, high surface area and relatively good biocompatibility, CNTs have also been employed as a novel gene delivery vector system. In our previous work, we functionalized CNTs with two polyamine polymers, polyethyleneimine (PEI) and polyamidoamine dendrimer (PAMAM). These compounds have low cytotoxicity, ability to conjugate microRNAs (such as miR-503) and, at the same time, transfect efficiently endothelial cells. The parameters contributing to the good efficiency of transfection that we observed were not investigated in detail. In fact, the diameter and length of CNTs are important parameters to be taken into account when evaluating the effects on drug delivery efficiency. In order to investigate the biophysical and biological contributions of polymer-coated CNTs in delivery of miRNAs to human cells, we decided to investigate three different preparations, characterized by different dimensions and aspect ratios. In particular, we took into account very small CNTs, a suspension of CNTs starting from the commercial product and a 2D material based on CNTs (ie, buckypapers [BPs]) to examine the transfection efficiency of a rigid scaffold. In conclusion, we extensively investigated the biophysical and biological contributions of polyamine-coated CNTs and bidimensional BPs in the delivery of miRNAs to human cells, in order to optimize the transfection efficiency of these compounds to be employed as efficient drug delivery vectors in biomedical applications.
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Affiliation(s)
| | | | | | | | | | - Marco Pezzullo
- Bambino Gesù Children's Hospital, IRCCS, Research Laboratories
| | - Stefano Casciardi
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, National Institution for Insurance Against Accidents at Work (INAIL Research), Monte Porzio Catone
| | - Simona Sennato
- CNR-ISC UOS Roma, Department of Physics, Sapienza University of Rome, Roma, Italy
| | - Federico Bordi
- CNR-ISC UOS Roma, Department of Physics, Sapienza University of Rome, Roma, Italy
| | - Andrea Masotti
- Bambino Gesù Children's Hospital, IRCCS, Research Laboratories
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20
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Hovland E, Beyene GT, Frye SA, Homberset H, Balasingham SV, Gómez-Muñoz M, Derrick JP, Tønjum T, Ambur OH. DprA from Neisseria meningitidis: properties and role in natural competence for transformation. MICROBIOLOGY-SGM 2017; 163:1016-1029. [PMID: 28696187 PMCID: PMC5817196 DOI: 10.1099/mic.0.000489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA processing chain A (DprA) is a DNA-binding protein that is ubiquitous in bacteria and expressed in some archaea. DprA is active in many bacterial species that are competent for transformation of DNA, but its role in Neisseriameningitidis (Nm) is not well characterized. An Nm mutant lacking DprA was constructed, and the phenotypes of the wild-type and ΔdprA mutant were compared. The salient feature of the phenotype of dprA null cells is the total lack of competence for genetic transformation shown by all of the donor DNA substrates tested in this study. Here, Nm wild-type and dprA null cells appeared to be equally resistant to genotoxic stress. The gene encoding DprANm was cloned and overexpressed, and the biological activities of DprANm were further investigated. DprANm binds ssDNA more strongly than dsDNA, but lacks DNA uptake sequence-specific DNA binding. DprANm dimerization and interaction with the C-terminal part of the single-stranded binding protein SSBNmwere demonstrated. dprA is co-expressed with smg, a downstream gene of unknown function, and the gene encoding topoisomerase 1, topA.
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Affiliation(s)
- Eirik Hovland
- Department of Microbiology, University of Oslo, Oslo, Norway.,Present address: Lovisenberg Diaconal Hospital, Oslo, Norway
| | | | - Stephan A Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Jeremy P Derrick
- Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ole H Ambur
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Present address: Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, Norway
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21
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Glick Y, Orenstein Y, Chen D, Avrahami D, Zor T, Shamir R, Gerber D. Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities. Nucleic Acids Res 2015; 44:e51. [PMID: 26635393 PMCID: PMC4824076 DOI: 10.1093/nar/gkv1327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 11/14/2015] [Indexed: 01/16/2023] Open
Abstract
Protein binding to DNA is a fundamental process in gene regulation. Methodologies such as ChIP-Seq and mapping of DNase I hypersensitive sites provide global information on this regulation in vivo In vitro methodologies provide valuable complementary information on protein-DNA specificities. However, current methods still do not measure absolute binding affinities. There is a real need for large-scale quantitative protein-DNA affinity measurements. We developed QPID, a microfluidic application for measuring protein-DNA affinities. A single run is equivalent to 4096 gel-shift experiments. Using QPID, we characterized the different affinities of ATF1, c-Jun, c-Fos and AP-1 to the CRE consensus motif and CRE half-site in two different genomic sequences on a single device. We discovered that binding of ATF1, but not of AP-1, to the CRE half-site is highly affected by its genomic context. This effect was highly correlated with ATF1 ChIP-seq and PBM experiments. Next, we characterized the affinities of ATF1 and ATF3 to 128 genomic CRE and CRE half-site sequences. Our affinity measurements explained that in vivo binding differences between ATF1 and ATF3 to CRE and CRE half-sites are partially mediated by differences in the minor groove width. We believe that QPID would become a central tool for quantitative characterization of biophysical aspects affecting protein-DNA binding.
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Affiliation(s)
- Yair Glick
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Yaron Orenstein
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Dana Chen
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Dorit Avrahami
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Tsaffrir Zor
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Doron Gerber
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
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22
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Song C, Zhang S, Huang H. Choosing a suitable method for the identification of replication origins in microbial genomes. Front Microbiol 2015; 6:1049. [PMID: 26483774 PMCID: PMC4588119 DOI: 10.3389/fmicb.2015.01049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. Using various in silico approaches such as Ori-Finder, and databases such as DoriC, researchers have predicted the locations of replication origins sites for thousands of bacterial chromosomes and archaeal genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.
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Affiliation(s)
- Chengcheng Song
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Shaocun Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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Functional manipulations of the tetramycin positive regulatory gene ttmRIV to enhance the production of tetramycin A and nystatin A1 in Streptomyces ahygroscopicus. J Ind Microbiol Biotechnol 2015; 42:1273-82. [PMID: 26233316 DOI: 10.1007/s10295-015-1660-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/23/2015] [Indexed: 01/05/2023]
Abstract
A putative regulatory gene ttmRIV located in the tetramycin biosynthetic gene cluster was found in Streptomyces ahygroscopicus. In-frame deletion of ttmRIV led to abolishment of tetramycin and significant enhancement of nystatin A1, whose production reached 2.1-fold of the H42 parental strain. Gene complementation by an integrative plasmid carrying ttmRIV restored tetramycin biosynthesis revealed that ttmRIV was indispensable to tetramycin biosynthesis. Gene expression analysis of the H42 strain and its mutant strain ΔttmRIV via reverse transcriptase-PCR of the tetramycin gene cluster demonstrated that the expression levels of most biosynthetic genes were reduced in ΔttmRIV. Results of electrophoretic mobility shift assays showed that TtmRIV bound the putative promoters of several genes in the tetramycin pathway. Thus, TtmRIV is a pathway-specific positive regulator activating the transcription of the tetramycin gene cluster in S. ahygroscopicus. Providing an additional copy of ttmRIV under the control of the ermEp* promoter in the H42 strain boosted tetramycin A production to 3.3-fold.
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24
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Rodríguez J, Mosquera J, Couceiro JR, Vázquez ME, Mascareñas JL. The AT-Hook motif as a versatile minor groove anchor for promoting DNA binding of transcription factor fragments. Chem Sci 2015; 6:4767-4771. [PMID: 26290687 PMCID: PMC4538796 DOI: 10.1039/c5sc01415h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022] Open
Abstract
We report the development of chimeric DNA binding peptides comprising a DNA binding fragment of natural transcription factors (the basic region of a bZIP protein or a monomeric zinc finger module) and an AT-Hook peptide motif. The resulting peptide conjugates display high DNA affinity and excellent sequence selectivity. Furthermore, the AT-Hook motif also favors the cell internalization of the conjugates.
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - Jose R. Couceiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Fax: +34 981 595 012 ; Tel: +34 981 576541 ext. 14405
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25
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Brunet A, Chevalier S, Destainville N, Manghi M, Rousseau P, Salhi M, Salomé L, Tardin C. Probing a label-free local bend in DNA by single molecule tethered particle motion. Nucleic Acids Res 2015; 43:e72. [PMID: 25765645 PMCID: PMC4477641 DOI: 10.1093/nar/gkv201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/01/2015] [Indexed: 02/07/2023] Open
Abstract
Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.
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Affiliation(s)
- Annaël Brunet
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Sébastien Chevalier
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Nicolas Destainville
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Manoel Manghi
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Philippe Rousseau
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Maya Salhi
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Laurence Salomé
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Catherine Tardin
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
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26
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Mostaghaci B, Susewind J, Kickelbick G, Lehr CM, Loretz B. Transfection system of amino-functionalized calcium phosphate nanoparticles: in vitro efficacy, biodegradability, and immunogenicity study. ACS APPLIED MATERIALS & INTERFACES 2015; 7:5124-5133. [PMID: 25692576 DOI: 10.1021/am507193a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many methods have been developed in order to use calcium phosphate (CaP) for delivering nucleotides into living cells. Surface functionalization of CaP nanoparticles (CaP NPs) with N-(2-aminoethyl)-3-aminopropyltrimethoxysilane was shown recently to achieve dispersed NPs with a positive surface charge, capable of transfection (Chem. Mater. 2013, 25 (18), 3667). In this study, different crystal structures of amino-modified CaP NPs (brushite and hydroxyapatite) were investigated for their interaction in cell culture systems in more detail. Qualitative (confocal laser scanning microscopy) and quantitative (flow cytometry) transfection experiments with two cell lines showed the higher transfection efficacy of brushite versus hydroxyapatite. The transfection also revealed a cell type dependency. HEK293 cells were easier to transfect compared to A549 cells. This result was supported by the cytotoxicity results. A549 cells showed a higher degree of tolerance toward the CaP NPs. Further, the impact of the surface modification on the interaction with macrophages and complement as two important components of the innate immune system were considered. The amine surface functionalization had an effect of decreasing the release of proinflammatory cytokines. The complement interaction investigated by a C3a complement activation assay did show no significant differences between CaP NPs without or with amine modification and overall weak interaction. Finally, the degradation of CaP NPs in biological media was studied with respect to the two crystal structures and at acidic and neutral pH. Both amino-modified CaP NPs disintegrate within days at neutral pH, with a notable faster disintegration of brushite NPs at acidic pH. In summary, the fair transfection capability of this amino functionalized CaP NPs together with the excellent biocompatibility, biodegradability, and low immunogenicity make them interesting candidates for further evaluation.
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Affiliation(s)
- Babak Mostaghaci
- Department of Drug Delivery (DDEL), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University , 66123 Saarbrücken, Germany
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27
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Guzman-Villanueva D, El-Sherbiny IM, Vlassov AV, Herrera-Ruiz D, Smyth HD. Enhanced cellular uptake and gene silencing activity of siRNA molecules mediated by chitosan-derivative nanocomplexes. Int J Pharm 2014; 473:579-90. [DOI: 10.1016/j.ijpharm.2014.07.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 07/14/2014] [Accepted: 07/20/2014] [Indexed: 01/01/2023]
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28
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An ArsR/SmtB family member is involved in the regulation by arsenic of the arsenite oxidase operon in Thiomonas arsenitoxydans. Appl Environ Microbiol 2014; 80:6413-26. [PMID: 25107975 DOI: 10.1128/aem.01771-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic organization of the aioBA operon, encoding the arsenite oxidase of the moderately acidophilic and facultative chemoautotrophic bacterium Thiomonas arsenitoxydans, is different from that of the aioBA operon in the other arsenite oxidizers, in that it encodes AioF, a metalloprotein belonging to the ArsR/SmtB family. AioF is stabilized by arsenite, arsenate, or antimonite but not molybdate. Arsenic is tightly attached to AioF, likely by cysteine residues. When loaded with arsenite or arsenate, AioF is able to bind specifically to the regulatory region of the aio operon at two distinct positions. In Thiomonas arsenitoxydans, the promoters of aioX and aioB are convergent, suggesting that transcriptional interference occurs. These results indicate that the regulation of the aioBA operon is more complex in Thiomonas arsenitoxydans than in the other aioBA containing arsenite oxidizers and that the arsenic binding protein AioF is involved in this regulation. On the basis of these data, a model to explain the tight control of aioBA expression by arsenic in Thiomonas arsenitoxydans is proposed.
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29
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The 'Densitometric Image Analysis Software' and its application to determine stepwise equilibrium constants from electrophoretic mobility shift assays. PLoS One 2014; 9:e85146. [PMID: 24465496 PMCID: PMC3897411 DOI: 10.1371/journal.pone.0085146] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/24/2013] [Indexed: 11/29/2022] Open
Abstract
Current software applications for densitometric analysis, such as ImageJ, QuantityOne (BioRad) and the Intelligent or Advanced Quantifier (Bio Image) do not allow to take the non-linearity of autoradiographic films into account during calibration. As a consequence, quantification of autoradiographs is often regarded as problematic, and phosphorimaging is the preferred alternative. However, the non-linear behaviour of autoradiographs can be described mathematically, so it can be accounted for. Therefore, the ‘Densitometric Image Analysis Software’ has been developed, which allows to quantify electrophoretic bands in autoradiographs, as well as in gels and phosphorimages, while providing optimized band selection support to the user. Moreover, the program can determine protein-DNA binding constants from Electrophoretic Mobility Shift Assays (EMSAs). For this purpose, the software calculates a chosen stepwise equilibrium constant for each migration lane within the EMSA, and estimates the errors due to non-uniformity of the background noise, smear caused by complex dissociation or denaturation of double-stranded DNA, and technical errors such as pipetting inaccuracies. Thereby, the program helps the user to optimize experimental parameters and to choose the best lanes for estimating an average equilibrium constant. This process can reduce the inaccuracy of equilibrium constants from the usual factor of 2 to about 20%, which is particularly useful when determining position weight matrices and cooperative binding constants to predict genomic binding sites. The MATLAB source code, platform-dependent software and installation instructions are available via the website http://micr.vub.ac.be.
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30
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Churion K, Liu Y, Hsiao HC, Matthews KS, Bondos SE. Measuring Hox-DNA binding by electrophoretic mobility shift analysis. Methods Mol Biol 2014; 1196:211-230. [PMID: 25151166 DOI: 10.1007/978-1-4939-1242-1_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding gene regulation by Hox transcription factors requires understanding the forces that underlie DNA binding by these proteins. Electrophoretic mobility shift analysis (EMSA) not only allows measurement of protein affinity and cooperativity but also permits visualization of differently migrating protein-DNA complexes, including complexes with different compositions or complexes with identical compositions yet assembled in different geometries. Furthermore, protein activity can be measured, allowing correction of binding constants for the percentage of protein that is properly folded and capable of binding DNA. Protocols for measuring protein activity and the equilibrium DNA-binding dissociation constant (K d) are provided. This versatile assay system can be adjusted based on specific needs to measure other parameters, including the kinetic association and dissociation constants (k a and k d) and the formation of heterologous protein-protein interactions.
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Affiliation(s)
- Kelly Churion
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843-1114, USA
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31
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Guo L, Ding J, Guo R, Hou Y, Wang DC, Huang L. Biochemical and structural insights into RNA binding by Ssh10b, a member of the highly conserved Sac10b protein family in Archaea. J Biol Chem 2013; 289:1478-90. [PMID: 24307170 DOI: 10.1074/jbc.m113.521351] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Proteins of the Sac10b family are highly conserved in Archaea. Ssh10b, a member of the Sac10b family from the hyperthermophilic crenarchaeon Sulfolobus shibatae, binds to RNA in vivo. Here we show that binding by Ssh10b destabilizes RNA secondary structure. Structural analysis of Ssh10b in complex with a 25-bp RNA duplex containing local distortions reveals that Ssh10b binds the two RNA strands symmetrically as a tetramer with each dimer bound asymmetrically to a single RNA strand. Amino acid residues involved in double-stranded RNA binding are similar, but non-identical, to those in dsDNA binding. The dimer-dimer interaction mediated by the intermolecular β-sheet appears to facilitate the destabilization of base pairing in the secondary structure of RNA. Our results suggest that proteins of the Sac10b family may play important roles in RNA transactions requiring destabilization of RNA secondary structure in Sulfolobus.
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Affiliation(s)
- Li Guo
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology and
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32
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Daddaoua A, Krell T, Ramos JL. Transcriptional control by two interacting regulatory proteins: identification of the PtxS binding site at PtxR. Nucleic Acids Res 2013; 41:10150-6. [PMID: 24019239 PMCID: PMC3905896 DOI: 10.1093/nar/gkt773] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The PtxS and PtxR regulators control the expression of the glucose dehydrogenase genes from the Pgad promoter in Pseudomonas aeruginosa. These regulators bind to their cognate operators, that are separated by ∼50 nt, within the promoter region and interact with each other creating a DNA-loop that prevents RNA polymerase promoter access. Binding of the 2-ketogluconate effector to PtxS caused PtxS/PtxR complex dissociation and led to the dissolution of the repression loop facilitating the entry of the RNA polymerase and enabling the transcription of the gad gene. We have identified a hydrophobic surface patch on the PtxR putative surface that was hypothesized to correspond to the binding site for PtxS. Two surface-exposed residues in this patch, V173 and W269, were replaced by alanine. Isothermal titration calorimetry assays showed that PtxS does not interact with the mutant variants of PtxR. Electrophoretic mobility shift assay and DNAase I footprinting assays proved that both regulators bind to their target operators and that failure to interact with each other prevented the formation of the DNA-loop. In vitro transcription showed that PtxS per se is sufficient to inhibit transcription from the Pgad promoter, but that affinity of PtxS for its effector is modulated by PtxR.
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Affiliation(s)
- Abdelali Daddaoua
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Calle Profesor Albareda 1, E-18008 Granada, Spain
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33
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Nagore LI, Nadeau RJ, Guo Q, Jadhav YLA, Jarrett HW, Haskins WE. Purification and characterization of transcription factors. MASS SPECTROMETRY REVIEWS 2013; 32:386-398. [PMID: 23832591 PMCID: PMC3758410 DOI: 10.1002/mas.21369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 11/19/2012] [Accepted: 11/19/2012] [Indexed: 06/02/2023]
Abstract
Transcription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography-tandem mass spectrometry and protein database searching. Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements (REs) on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and penetrance of the TF proteome. For example, trapping of TF complexes specific for particular REs has been achieved by recovering the element DNA-protein complex on solid supports. Additional methods for improving dynamic range include two- and three-dimensional gel electrophoresis incorporating electrophoretic mobility shift assays and Southwestern blotting for detection. Here we review methods for TF purification and characterization. We fully expect that future investigations will apply these and other methods to illuminate this important but challenging proteome.
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Affiliation(s)
- LI Nagore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
| | - RJ Nadeau
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Q Guo
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - YLA Jadhav
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - HW Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
| | - WE Haskins
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Biology, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Medicine, Division of Hematology & Medical Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
- Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
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Abstract
The band-shift assay using polyacrylamide gel electrophoresis is a powerful technique used to investigate DNA-protein interactions. The basis of the method is the separation of free DNA from DNA-protein complexes by virtue of differences in charge, size, and shape. The band-shift assay can be used to determine thermodynamic and kinetic binding constants and also to analyze the composition and stoichiometries of DNA-protein complexes.
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Affiliation(s)
- Lynn Powell
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
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35
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Arbab M, Mahony S, Cho H, Chick JM, Rolfe PA, van Hoff JP, Morris VW, Gygi SP, Maas RL, Gifford DK, Sherwood RI. A multi-parametric flow cytometric assay to analyze DNA-protein interactions. Nucleic Acids Res 2012; 41:e38. [PMID: 23143268 PMCID: PMC3554230 DOI: 10.1093/nar/gks1034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Interactions between DNA and transcription factors (TFs) guide cellular function and
development, yet the complexities of gene regulation are still far from being understood.
Such understanding is limited by a paucity of techniques with which to probe
DNA–protein interactions. We have devised magnetic protein immobilization on
enhancer DNA (MagPIE), a simple, rapid, multi-parametric assay using flow cytometric
immunofluorescence to reveal interactions among TFs, chromatin structure and DNA. In
MagPIE, synthesized DNA is bound to magnetic beads, which are then incubated with nuclear
lysate, permitting sequence-specific binding by TFs, histones and methylation by native
lysate factors that can be optionally inhibited with small molecules. Lysate
protein–DNA binding is monitored by flow cytometric immunofluorescence, which allows
for accurate comparative measurement of TF-DNA affinity. Combinatorial fluorescent
staining allows simultaneous analysis of sequence-specific TF-DNA interaction and
chromatin modification. MagPIE provides a simple and robust method to analyze complex
epigenetic interactions in vitro.
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Affiliation(s)
- Mandana Arbab
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Mahony
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - Hyunjii Cho
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - Joel M. Chick
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - P. Alexander Rolfe
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - John Peter van Hoff
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - Viveca W.S. Morris
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - Steven P. Gygi
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - Richard L. Maas
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - David K. Gifford
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and
Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA
02115, Computer Science and Artificial Intelligence Laboratory, Massachusetts
Institute of Technology, Cambridge, MA 02139 and Department of Cell Biology,
Harvard Medical School, Boston, MA 02115, USA
- *To whom correspondence should be addressed. Tel:
+1 617 525 4772; Fax: +1 617 525 4751;
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36
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LUEGO: a cost and time saving gel shift procedure. Biotechniques 2012; 51:267-9. [PMID: 21988693 DOI: 10.2144/000113751] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/08/2011] [Indexed: 11/23/2022] Open
Abstract
We developed a new approach to prepare DNA probes for electrophoretic mobility gel shift assays that presents a number of advantages compared with the classical approach. The method relies on two complementary oligonucleotides containing the desired transcription factor binding sequence, one of them being extended at its 3' end with a universal tail that complements a third, short oligonucleotide labeled with a fluorophore or any other label. The use of this third "universal" oligonucleotide allows labeling many different probes with minimal time, effort and cost. We show that probes prepared this way are as effective and reliable as probes prepared by conventional methods. We refer to this short oligonucleotide as LUEGO for labeled universal electrophoretic gel shift oligonucleotide.
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Wassarman KM. Native gel electrophoresis to study the binding and release of RNA polymerase by 6S RNA. Methods Mol Biol 2012; 905:259-271. [PMID: 22736010 DOI: 10.1007/978-1-61779-949-5_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RNA-protein interactions are critical in diverse aspects of gene expression and often serve to mediate regulatory events. Many procedures are available to gain information about RNA-protein interactions. They span from initial identification of an interaction, such as through co-immunoprecipitation studies, to highly detailed atomic resolution definition of the interaction gained from crystallographic and NMR studies. One of the most versatile techniques uses native gel electrophoresis to study RNA-protein complexes, which is often called band shift, gel retardation, or electrophoretic mobility shift assays. Gel shift assays have been used to study a plethora of RNA-protein interactions in all organisms, but here we will use the 6S RNA:RNA polymerase interaction from Escherichia coli as an example to direct discussion of questions that can be addressed, including the ability to follow the dynamics of complexes over time.
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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38
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Schallon A, Synatschke CV, Pergushov DV, Jérôme V, Müller AHE, Freitag R. DNA melting temperature assay for assessing the stability of DNA polyplexes intended for nonviral gene delivery. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12042-51. [PMID: 21770418 DOI: 10.1021/la201803c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Many synthetic polycations have the ability to form complexes with the polyanion DNA, yet only a few, most notably poly(ethylene imine) (PEI), are efficient gene-delivery vehicles. Although a common explanation of this observation relies on the buffering capacity of the polycation, the intracellular stability of the complex may also play a role and should not be neglected. Assays typically used to follow complex formation, however, often do not provide the required information on stability. In this article, we propose the change in the DNA melting temperature observable after complex formation to be a significant indicator of complex stability. For a given DNA/polycation ratio, changes in the melting temperature are shown to depend on the polycation chemistry but not on the DNA topology or the polycation architecture. Effects of changes in the DNA/polycation ratio as well as the effect of polycation quaternization can be interpreted using the melting temperature assay. Finally, the assay was used to follow the displacement of DNA from the complexes by poly(methacrylic acid) or short single-stranded DNA sequences as competing polyanions.
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Affiliation(s)
- Anja Schallon
- Chair for Process Biotechnology, University of Bayreuth, Germany
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39
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Mach-Aigner AR, Grosstessner-Hain K, Poças-Fonseca MJ, Mechtler K, Mach RL. From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach. BMC Genomics 2010; 11:644. [PMID: 21087492 PMCID: PMC3012607 DOI: 10.1186/1471-2164-11-644] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/18/2010] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Hypocrea jecorina (anamorph Trichoderma reesei) is a filamentous ascomycete of industrial importance due to its hydrolases (e.g., xylanases and cellulases). The regulation of gene expression can influence the composition of the hydrolase cocktail, and thus, transcription factors are a major target of current research. Here, we design an approach for identifying a repressor of a xylanase-encoding gene. RESULTS We used streptavidin affinity chromatography to isolate the Xylanase promoter-binding protein 1 (Xpp1). The optimal conditions and templates for the chromatography step were chosen according to the results of an electrophoretic mobility shift assay performed under repressing conditions, which yielded a DNA-protein complex specific to the AGAA-box (the previously identified, tetranucleotide cis-acting element). After isolating AGAA-box binding proteins, the eluted proteins were identified with Nano-HPLC/tandem MS-coupled detection. We compared the identified peptides to sequences in the H. jecorina genome and predicted in silico the function and DNA-binding ability of the identified proteins. With the results from these analyses, we eliminated all but three candidate proteins. We verified the transcription of these candidates and tested their ability to specifically bind the AGAA-box. In the end, only one candidate protein remained. We generated this protein with in vitro translation and used an EMSA to demonstrate the existence of an AGAA-box-specific protein-DNA complex. We found that the expression of this gene is elevated under repressing conditions relative to de-repressing or inducing conditions. CONCLUSIONS We identified a putative transcription factor that is potentially involved in repressing xylanase 2 expression. We also identified two additional potential regulatory proteins that bind to the xyn2 promoter. Thus, we succeeded in identifying novel, putative transcription factors for the regulation of xylanase expression in H. jecorina.
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Affiliation(s)
- Astrid R Mach-Aigner
- Department of Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Wien, Austria.
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40
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Rousseau P, Tardin C, Tolou N, Salomé L, Chandler M. A model for the molecular organisation of the IS911 transpososome. Mob DNA 2010; 1:16. [PMID: 20553579 PMCID: PMC2909936 DOI: 10.1186/1759-8753-1-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 06/16/2010] [Indexed: 11/10/2022] Open
Abstract
Tight regulation of transposition activity is essential to limit damage transposons may cause by generating potentially lethal DNA rearrangements. Assembly of a bona fide protein-DNA complex, the transpososome, within which transposition is catalysed, is a crucial checkpoint in this regulation. In the case of IS911, a member of the large IS3 bacterial insertion sequence family, the transpososome (synaptic complex A; SCA) is composed of the right and left inverted repeated DNA sequences (IRR and IRL) bridged by the transposase, OrfAB (the IS911-encoded enzyme that catalyses transposition). To characterise further this important protein-DNA complex in vitro, we used different tagged and/or truncated transposase forms and analysed their interaction with IS911 ends using gel electrophoresis. Our results allow us to propose a model in which SCA is assembled with a dimeric form of the transposase. Furthermore, we present atomic force microscopy results showing that the terminal inverted repeat sequences are probably assembled in a parallel configuration within the SCA. These results represent the first step in the structural description of the IS911 transpososome, and are discussed in comparison with the very few other transpososome examples described in the literature.
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Affiliation(s)
- Philippe Rousseau
- Centre National de la Recherche Scientifique, LMGM, F-31000 Toulouse, France.
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41
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Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 2010; 20:861-73. [PMID: 20378718 PMCID: PMC2877582 DOI: 10.1101/gr.100552.109] [Citation(s) in RCA: 312] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 03/22/2010] [Indexed: 01/15/2023]
Abstract
The genetic code-the binding specificity of all transfer-RNAs--defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the approximately 1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers.
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Affiliation(s)
- Arttu Jolma
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Teemu Kivioja
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Jarkko Toivonen
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Lu Cheng
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Gonghong Wei
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Martin Enge
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Mikko Taipale
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Juan M. Vaquerizas
- EMBL–European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Jian Yan
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Mikko J. Sillanpää
- Department of Mathematics and Statistics, FI-00014 University of Helsinki, Helsinki, Finland
| | - Martin Bonke
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Kimmo Palin
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Shaheynoor Talukder
- Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M4T 2J4, Canada
| | - Timothy R. Hughes
- Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M4T 2J4, Canada
| | | | - Esko Ukkonen
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
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Philonenko ES, Klochkov DB, Borunova VV, Gavrilov AA, Razin SV, Iarovaia OV. TMEM8 - a non-globin gene entrapped in the globin web. Nucleic Acids Res 2010; 37:7394-406. [PMID: 19820109 PMCID: PMC2794187 DOI: 10.1093/nar/gkp838] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
For more than 30 years it was believed that globin gene domains included only genes encoding globin chains. Here we show that in chickens, the domain of α-globin genes also harbor the non-globin gene TMEM8. It was relocated to the vicinity of the α-globin cluster due to inversion of an ∼170-kb genomic fragment. Although in humans TMEM8 is preferentially expressed in resting T-lymphocytes, in chickens it acquired an erythroid-specific expression profile and is upregulated upon terminal differentiation of erythroblasts. This correlates with the presence of erythroid-specific regulatory elements in the body of chicken TMEM8, which interact with regulatory elements of the α-globin genes. Surprisingly, TMEM8 is not simply recruited to the α-globin gene domain active chromatin hub. An alternative chromatin hub is assembled, which includes some of the regulatory elements essential for the activation of globin gene expression. These regulatory elements should thus shuttle between two different chromatin hubs.
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Affiliation(s)
- Elena S Philonenko
- Institute of Gene Biology of the Russian Academy of Sciences, Vavilov street 34/5, 119334 Moscow, Russia
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43
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Recruitment of the ParG segregation protein to different affinity DNA sites. J Bacteriol 2009; 191:3832-41. [PMID: 19376860 DOI: 10.1128/jb.01630-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The segrosome is the nucleoprotein complex that mediates accurate plasmid segregation. In addition to its multifunctional role in segrosome assembly, the ParG protein of multiresistance plasmid TP228 is a transcriptional repressor of the parFG partition genes. ParG is a homodimeric DNA binding protein, with C-terminal regions that interlock into a ribbon-helix-helix fold. Antiparallel beta-strands in this fold are presumed to insert into the O(F) operator major groove to exert transcriptional control as established for other ribbon-helix-helix factors. The O(F) locus comprises eight degenerate tetramer boxes arranged in a combination of direct and inverted orientation. Each tetramer motif likely recruits one ParG dimer, implying that the fully bound operator is cooperatively coated by up to eight dimers. O(F) was subdivided experimentally into four overlapping 20-bp sites (A to D), each of which comprises two tetramer boxes separated by AT-rich spacers. Extensive interaction studies demonstrated that sites A to D individually are bound with different affinities by ParG (C > A approximately B >> D). Moreover, comprehensive scanning mutagenesis revealed the contribution of each position in the site core and flanking sequences to ParG binding. Natural variations in the tetramer box motifs and in the interbox spacers, as well as in flanking sequences, each influence ParG binding. The O(F) operator apparently has evolved with sites that bind ParG dissimilarly to produce a nucleoprotein complex fine-tuned for optimal interaction with the transcription machinery. The association of other ribbon-helix-helix proteins with complex recognition sites similarly may be modulated by natural sequence variations between subsites.
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Studies of the interaction of the viral suppressor of RNA silencing protein p19 with small RNAs using fluorescence polarization. Biochemistry 2008; 47:8130-8. [PMID: 18597480 DOI: 10.1021/bi800401y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tombusviruses use a 19 kDa protein (p19) as a suppressor of the RNA silencing pathway during infection. The p19 protein binds to short-interfering RNA (siRNA) as a dimer and shows a high selectivity for short duplex RNAs over other RNA species. Since p19 can bind to synthetic and RNA silencing generated small RNAs with little sequence dependence and with size selectivity, this protein has utility as a tool for studying RNA silencing pathways in eukaryotes. However, the ability of p19 to serve as a tool for studying RNA silencing pathways may be complicated by the presence of other endogenous small RNAs such as micro-RNAs (miRNAs). To understand the importance of endogenous small RNA components with respect to p19's ability to bind to siRNAs, we examined the interactions of p19 with human miR-122, a 23-nucleotide duplex miRNA containing several mismatched base pairs that is highly abundant in the liver. The binding characteristics were compared with those of an siRNA optimized against the human kinase CSK. The binding studies were performed using fluorescence polarization experiments on duplex oligonucleotides containing Cy3 dye labels at the 5'-end of one of the strands of RNA as well as electrophoretic gel mobility shift assays. Both methods indicate that the synthetic siRNA with no mismatches in base pairing bound with >3-fold selectivity over that of miR-122. Our results suggest that p19 can distinguish between siRNAs and miRNA species, although the difference in binding constants is not so large that interactions with endogenous miRNAs can be totally ignored.
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45
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Zhang B, Morace G, Gauss-Müller V, Kusov Y. Poly(A) binding protein, C-terminally truncated by the hepatitis A virus proteinase 3C, inhibits viral translation. Nucleic Acids Res 2007; 35:5975-84. [PMID: 17726047 PMCID: PMC2034478 DOI: 10.1093/nar/gkm645] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/02/2007] [Accepted: 08/03/2007] [Indexed: 12/30/2022] Open
Abstract
Proteolytic cleavage of translation initiation factors is a means to interfere with mRNA circularization and to induce translation arrest during picornaviral replication or apoptosis. It was shown that the regulated cleavages of eukaryotic initiation factor (eIF) 4G and poly(A)-binding protein (PABP) by viral proteinases correlated with early and late arrest of host cap-dependent and viral internal ribosome entry site (IRES)-dependent translation, respectively. Here we show that in contrast to coxsackievirus, eIF4G is not a substrate of proteinase 3C of hepatitis A virus (HAV 3C(pro)). However, PABP is cleaved by HAV 3C(pro) in vitro and in vivo, separating the N-terminal RNA-binding domain (NTD) of PABP from the C-terminal protein-interaction domain. In vitro, NTD has a dominant negative effect on HAV IRES-dependent translation and an enhanced binding affinity to the RNA structural element pY1 in the 5' nontranslated region of the HAV RNA that is essential for viral genome replication. The results point to a regulatory role of PABP cleavage in RNA template switching of viral translation to RNA synthesis.
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Affiliation(s)
- Bo Zhang
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
| | - Graziella Morace
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
| | - Verena Gauss-Müller
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
| | - Yuri Kusov
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
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46
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Hellman LM, Fried MG. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2007; 2:1849-61. [PMID: 17703195 PMCID: PMC2757439 DOI: 10.1038/nprot.2007.249] [Citation(s) in RCA: 741] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The gel electrophoresis mobility shift assay (EMSA) is used to detect protein complexes with nucleic acids. It is the core technology underlying a wide range of qualitative and quantitative analyses for the characterization of interacting systems. In the classical assay, solutions of protein and nucleic acid are combined and the resulting mixtures are subjected to electrophoresis under native conditions through polyacrylamide or agarose gel. After electrophoresis, the distribution of species containing nucleic acid is determined, usually by autoradiography of 32P-labeled nucleic acid. In general, protein-nucleic acid complexes migrate more slowly than the corresponding free nucleic acid. In this protocol, we identify the most important factors that determine the stabilities and electrophoretic mobilities of complexes under assay conditions. A representative protocol is provided and commonly used variants are discussed. Expected outcomes are briefly described. References to extensions of the method and a troubleshooting guide are provided.
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Affiliation(s)
- Lance M. Hellman
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 S. Limestone Street, Lexington, Kentucky, 40536-0509, USA
| | - Michael G. Fried
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 S. Limestone Street, Lexington, Kentucky, 40536-0509, USA
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47
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Pouget N, Turlan C, Destainville N, Salomé L, Chandler M. IS911 transpososome assembly as analysed by tethered particle motion. Nucleic Acids Res 2006; 34:4313-23. [PMID: 16923775 PMCID: PMC1636345 DOI: 10.1093/nar/gkl420] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Initiation of transposition requires formation of a synaptic complex between both transposon ends and the transposase (Tpase), the enzyme which catalyses DNA cleavage and strand transfer and which ensures transposon mobility. We have used a single-molecule approach, tethered particle motion (TPM), to observe binding of a Tpase derivative, OrfAB[149], amputated for its C-terminal catalytic domain, to DNA molecules carrying one or two IS911 ends. Binding of OrfAB[149] to a single IS911 end provoked a small shortening of the DNA. This is consistent with a DNA bend introduced by protein binding to a single end. This was confirmed using a classic gel retardation assay with circularly permuted DNA substrates. When two ends were present on the tethered DNA in their natural, inverted, configuration, Tpase not only provoked the short reduction in length but also generated species with greatly reduce effective length consistent with DNA looping between the ends. Once formed, this 'looped' species was very stable. Kinetic analysis in real-time suggested that passage from the bound unlooped to the looped state could involve another species of intermediate length in which both transposon ends are bound. DNA carrying directly repeated ends also gave rise to the looped species but the level of the intermediate species was significantly enhanced. Its accumulation could reflect a less favourable synapse formation from this configuration than for the inverted ends. This is compatible with a model in which Tpase binds separately to and bends each end (the intermediate species) and protein-protein interactions then lead to synapsis (the looped species).
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Affiliation(s)
- N. Pouget
- Laboratoire de Microbiologie et Génétique Moléculaire (UMR CNRS 5100)118 route de Narbonne, 31062 Toulouse cedex, France
- Institut de Pharmacologie et Biologie Structurale (UMR CNRS 5089)205 route de Narbonne 31077 Toulouse cedex, France
| | - C. Turlan
- Laboratoire de Microbiologie et Génétique Moléculaire (UMR CNRS 5100)118 route de Narbonne, 31062 Toulouse cedex, France
| | - N. Destainville
- Laboratoire de Physique Théorique (UMR CNRS 5152), IRSAMC, Université Paul Sabatier118 route de Narbonne, 31062 Toulouse cedex, France
| | - L. Salomé
- Institut de Pharmacologie et Biologie Structurale (UMR CNRS 5089)205 route de Narbonne 31077 Toulouse cedex, France
| | - M. Chandler
- Laboratoire de Microbiologie et Génétique Moléculaire (UMR CNRS 5100)118 route de Narbonne, 31062 Toulouse cedex, France
- To whom correspondence should be addressed. Tel: +33 5 61 33 58 61; Fax: +33 5 61 33 58 58.
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Dobryszycki P, Grad I, Krusiński T, Michaluk P, Sawicka D, Kowalska A, Orłowski M, Jakób M, Rymarczyk G, Kochman M, Ozyhar A. The DNA-binding domain of the ultraspiracle drives deformation of the response element whereas the DNA-binding domain of the ecdysone receptor is responsible for a slight additional change of the preformed structure. Biochemistry 2006; 45:668-75. [PMID: 16411742 DOI: 10.1021/bi051354b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ecdysteroids control molting and metamorphosis in insects via a heterodimeric complex of two nuclear receptors, the ecdysone receptor (EcR) and ultraspiracle protein (Usp). We used fluorescence resonance energy transfer (FRET) to study the topology of the natural pseudopalindromic element from the hsp27 gene (hsp27pal) in complex with the DNA-binding domains of Usp and EcR (UspDBD and EcRDBD, respectively). Steady-state data revealed shortening of the end-to-end distance of the hsp27pal-derived probe. For the 70.8 +/- 0.6 A distance obtained for the UspDBD-complexed DNA a bend of about 23.1 +/- 2.9 degrees was measured. Nearly the same value (23.0 +/- 3.4 degrees) was obtained for the DNA complexed with the UspDBD/EcRDBD heterodimer. The respective bend angles estimated using fluorescence decay measurements were 19.0 +/- 2.1 degrees and 20.9 +/- 3.6 degrees . Thus, the FRET data suggest for the first time that the UspDBD defines the architecture of the UspDBD/EcRDBD heterocomplex due to the significant deformation of the hsp27pal. This suggestion has been further reinforced using gel retardation experiments, which, in conjunction with high-resolution DNase I footprinting, indicate that the main contribution to the observed bend is given by the UspDBD itself, while binding of the EcRDBD molecule brings on a slight additional change of the preformed structure.
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Affiliation(s)
- Piotr Dobryszycki
- Division of Biochemistry, Institute of Organic Chemistry, Biochemistry and Biotechnology, Wrocław University of Technology, Wybrzeze Wyspiańskiego 27, 50-370 Wrocław, Poland
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Peeters E, Willaert R, Maes D, Charlier D. Ss-LrpB from Sulfolobus solfataricus condenses about 100 base pairs of its own operator DNA into globular nucleoprotein complexes. J Biol Chem 2006; 281:11721-8. [PMID: 16522627 DOI: 10.1074/jbc.m600383200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ss-LrpB from the hyperthermoacidophilic crenarchaeote Sulfolobus solfataricus P2 is a member of the Lrp-like family of Bacterial/Archaeal transcription regulators that binds its own control region at three regularly spaced and partially conserved 15-bp-long imperfect palindromes. We have used atomic force microscopy to analyze the architecture of Ss-LrpB.DNA complexes with a different stoichiometry formed with the wild type operator and with an operator mutant. Binding of dimeric Ss-LrpB to all three target sites is accompanied by the formation of globular complexes, in which the protein induces strong DNA deformations. Furthermore, DNA contour length foreshortening of these complexes indicates DNA wrapping, with about 100 bp being condensed. The average bending angle is 260 degrees . The establishment of protein-protein contacts between Ss-LrpB dimers in these globular complexes will contribute to the cooperativity of the binding. The profound remodeling of the control region is expected to have a strong impact on gene expression and might constitute the key element in the autoregulatory process.
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Affiliation(s)
- Eveline Peeters
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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Powell LM, Zur Lage PI, Prentice DRA, Senthinathan B, Jarman AP. The proneural proteins Atonal and Scute regulate neural target genes through different E-box binding sites. Mol Cell Biol 2004; 24:9517-26. [PMID: 15485919 PMCID: PMC522279 DOI: 10.1128/mcb.24.21.9517-9526.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For a particular functional family of basic helix-loop-helix (bHLH) transcription factors, there is ample evidence that different factors regulate different target genes but little idea of how these different target genes are distinguished. We investigated the contribution of DNA binding site differences to the specificities of two functionally related proneural bHLH transcription factors required for the genesis of Drosophila sense organ precursors (Atonal and Scute). We show that the proneural target gene, Bearded, is regulated by both Scute and Atonal via distinct E-box consensus binding sites. By comparing with other Ato-dependent enhancer sequences, we define an Ato-specific binding consensus that differs from the previously defined Scute-specific E-box consensus, thereby defining distinct E(Ato) and E(Sc) sites. These E-box variants are crucial for function. First, tandem repeats of 20-bp sequences containing E(Ato) and E(Sc) sites are sufficient to confer Atonal- and Scute-specific expression patterns, respectively, on a reporter gene in vivo. Second, interchanging E(Ato) and E(Sc) sites within enhancers almost abolishes enhancer activity. While the latter finding shows that enhancer context is also important in defining how proneural proteins interact with these sites, it is clear that differential utilization of DNA binding sites underlies proneural protein specificity.
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Affiliation(s)
- Lynn M Powell
- Division of Biomedical Sciences, University of Edinburgh, George Square, Edinburgh EH8 9XD, United Kingdom
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