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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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Shi WT, Zhang B, Li ML, Liu KH, Jiao J, Tian CF. The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes. Nucleic Acids Res 2022; 50:8580-8598. [PMID: 36007892 PMCID: PMC9410896 DOI: 10.1093/nar/gkac664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial adaptation is largely shaped by horizontal gene transfer, xenogeneic silencing mediated by lineage-specific DNA bridgers (H-NS, Lsr2, MvaT and Rok), and various anti-silencing mechanisms. No xenogeneic silencing DNA bridger is known for α-proteobacteria, from which mitochondria evolved. By investigating α-proteobacterium Sinorhizobium fredii, a facultative legume microsymbiont, here we report the conserved zinc-finger bearing MucR as a novel xenogeneic silencing DNA bridger. Self-association mediated by its N-terminal domain (NTD) is required for DNA–MucR–DNA bridging complex formation, maximizing MucR stability, transcriptional silencing, and efficient symbiosis in legume nodules. Essential roles of NTD, CTD (C-terminal DNA-binding domain), or full-length MucR in symbiosis can be replaced by non-homologous NTD, CTD, or full-length protein of H-NS from γ-proteobacterium Escherichia coli, while NTD rather than CTD of Lsr2 from Gram-positive Mycobacterium tuberculosis can replace the corresponding domain of MucR in symbiosis. Chromatin immunoprecipitation sequencing reveals similar recruitment profiles of H-NS, MucR and various functional chimeric xenogeneic silencers across the multipartite genome of S. fredii, i.e. preferring AT-rich genomic islands and symbiosis plasmid with key symbiosis genes as shared targets. Collectively, the convergently evolved DNA bridger MucR predisposed α-proteobacteria to integrate AT-rich foreign DNA including symbiosis genes, horizontal transfer of which is strongly selected in nature.
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Affiliation(s)
- Wen-Tao Shi
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Biliang Zhang
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Meng-Lin Li
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Ke-Han Liu
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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Soares LW, Bailão AM, Soares CMDA, Bailão MGS. Zinc at the Host-Fungus Interface: How to Uptake the Metal? J Fungi (Basel) 2020; 6:jof6040305. [PMID: 33233335 PMCID: PMC7711662 DOI: 10.3390/jof6040305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/31/2022] Open
Abstract
Zinc is an essential nutrient for all living organisms. However, firm regulation must be maintained since micronutrients also can be toxic in high concentrations. This notion is reinforced when we look at mechanisms deployed by our immune system, such as the use of chelators or membrane transporters that capture zinc, when threatened with pathogens, like fungi. Pathogenic fungi, on the other hand, also make use of a variety of transporters and specialized zinc captors to survive these changes. In this review, we sought to explain the mechanisms, grounded in experimental analysis and described to date, utilized by pathogenic fungi to maintain optimal zinc levels.
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Rodriguez J, Mosquera J, Learte-Aymamı́ S, Vázquez ME, Mascareñas JL. Stimuli-Responsive DNA Binding by Synthetic Systems. Acc Chem Res 2020; 53:2286-2298. [PMID: 32997936 DOI: 10.1021/acs.accounts.0c00415] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA is the molecule responsible for the storage and transmission of the genetic information in living organisms. The expression of this information is highly regulated. In eukaryotes, it is achieved mainly at the transcription level thanks to specialized proteins called transcription factors (TFs) that recognize specific DNA sequences, thereby promoting or inhibiting the transcription of particular genes. In many cases, TFs are present in the cell in an inactive form but become active in response to an external signal, which might modify their localization and DNA binding properties or modulate their interactions with the rest of the transcriptional machinery. As a result of the crucial role of TFs, the design of synthetic peptides or miniproteins that can emulate their DNA binding properties and eventually respond to external stimuli is of obvious interest. On the other hand, although the B-form double helix is the most common DNA secondary structure, it is not the only one with an essential biological function. Guanine quadruplexes (GQs) have received considerable attention due to their critical role in the regulation of gene expression, which is usually associated with a change in the GQ conformation. Thus, the development of GQ probes whose properties can be controlled using external signals is also of significant relevance.In this Account, we present a summary of the recent efforts toward the development of stimuli-responsive synthetic DNA binders with a particular emphasis on our own contributions. We first introduce the structure of B and GQ DNAs, and some of the main factors underlying their selective recognition. We then discuss some of the different approaches used for the design of stimulus-mediated DNA binders. We have organized our discussion according to whether the interaction takes place with duplex or guanine quadruplex DNAs, and each section is divided according to the nature of the stimulus (i.e., physical or chemical). Regarding physical stimuli, light (through the incorporation of photolabile protecting groups or photoisomerizable agents) is the most common input for the activation/deactivation of DNA binding events. With respect to chemical signals, the use of metals (through the incorporation of metal-coordinating groups in the DNA binding agent) has allowed the development of a wide range of stimuli-responsive DNA binders. More recently, redox-based systems have also been used to control DNA interactions.This Account ends with a "Conclusions and Outlook" section highlighting some of the general lessons that have been learned and future directions toward further advancing the field.
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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, 15782 Santiago de Compostela, Spain
| | - Jesús Mosquera
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Soraya Learte-Aymamı́
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José Luis Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Learte‐Aymamí S, Rodríguez J, Vázquez ME, Mascareñas JL. Assembly of a Ternary Metallopeptide Complex at Specific DNA Sites Mediated by an AT‐Hook Adaptor. Chemistry 2020; 26:8875-8878. [DOI: 10.1002/chem.202001277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Soraya Learte‐Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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Zhou Y, Wu R, Wang D, Hu P, Jin Y. Single-Molecule Translocation Conformational Sensing of Multiarm DNA Concatemers Using Glass Capillary Nanopore. ACS Sens 2019; 4:3119-3123. [PMID: 31797666 DOI: 10.1021/acssensors.9b01880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glass capillary-based nanopore is exploited for single-molecule conformational sensing of multiarm DNA concatemers during translocation. Both translocation frequency and orientation preference were found related with the number of arms of the DNA concatemers.
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Affiliation(s)
- Ya Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Ruiping Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Dandan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Ping Hu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
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Bonome EL, Cecconi F, Chinappi M. Translocation intermediates of ubiquitin through an α-hemolysin nanopore: implications for detection of post-translational modifications. NANOSCALE 2019; 11:9920-9930. [PMID: 31069350 DOI: 10.1039/c8nr10492a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopore based sensors constitute a promising approach to single molecule protein characterization being able, in principle, to detect sequences, structural elements and folding states of proteins and polypeptide chains. In narrow nanopores, one of the open issues concerns the coupling between unfolding and translocation. Here, we studied the ubiquitin translocation in an α-hemolysin nanopore, the most widely used pore for nanopore sensing, via all-atom molecular dynamics simulations. We completely characterize the co-translocational unfolding pathway finding that robust translocation intermediates are associated with the rearrangement of secondary structural elements, as also confirmed by coarse grained simulations. An interesting recurrent pattern is the clogging of the α-hemolysin constriction by an N-terminal β-hairpin. This region of ubiquitin is the target of several post-translational modifications. We propose a strategy to detect post-translational modifications at the N-terminal using the α-hemolysin nanopore based on the comparison of the co-translocational unfolding signals associated with modified and unmodified proteins.
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Affiliation(s)
- Emma Letizia Bonome
- Dipartimento di Ingegneria Meccanica e Aerospaziale Sapienza Università di Roma, Roma, 00185, Italy
| | - Fabio Cecconi
- CNR-Istituto dei Sistemi Complessi UoS Sapienza, Via dei Taurini 19, Roma, 00185, Italy
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Roma, 00133, Italy.
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D’Souza A, Torres J, Bhattacharjya S. Expanding heme-protein folding space using designed multi-heme β-sheet mini-proteins. Commun Chem 2018. [DOI: 10.1038/s42004-018-0078-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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