51
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Jin L, Nawab S, Xia M, Ma X, Huo Y. Context-dependency of synthetic minimal promoters in driving gene expression: a case study. Microb Biotechnol 2019; 12:1476-1486. [PMID: 31578818 PMCID: PMC6801132 DOI: 10.1111/1751-7915.13489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022] Open
Abstract
Synthetic promoters are considered ideal candidates in driving robust gene expression. Most of the available synthetic promoters are minimal promoters, for which the upstream sequence of the 5' end of the core region is usually excluded. Although the upstream sequence has been shown to mediate transcription of natural promoters, its impact on synthetic promoters has not been widely studied. Here, a library of chromosomal DNA fragments is randomly fused with the 5' end of the J23119 synthetic promoter, and the transcriptional performance of the promoter is evaluated through β-galactosidase assay, fluorescence intensity and chemical biosynthesis. Results show that changes in the upstream sequence can induce significant variation in the promoter strength of up to 5.8-fold. The effect is independent of the length of the insertions and the number of potential transcription factor binding sites. Several DNA fragments that are able to enhance the transcription of both the natural and the synthetic promoters are identified. This study indicates that the synthetic minimal promoters are susceptible to the surrounding sequence context. Therefore, the upstream sequence should be treated as an indispensable component in the design and application of synthetic promoters, or as an independent genetic part for the fine-tuning of gene expression.
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Affiliation(s)
- Liyuan Jin
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Said Nawab
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Mengli Xia
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Yi‐Xin Huo
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
- UCLA Institute for Technology Advancement (Suzhou)10 Yueliangwan Road, Suzhou Industrial ParkSuzhou215123China
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52
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Schärfen L, Schlierf M. Real-time monitoring of protein-induced DNA conformational changes using single-molecule FRET. Methods 2019; 169:11-20. [DOI: 10.1016/j.ymeth.2019.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/21/2018] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
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53
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Mukhortava A, Pöge M, Grieb MS, Nivina A, Loot C, Mazel D, Schlierf M. Structural heterogeneity of attC integron recombination sites revealed by optical tweezers. Nucleic Acids Res 2019; 47:1861-1870. [PMID: 30566629 PMCID: PMC6393395 DOI: 10.1093/nar/gky1258] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/02/2018] [Accepted: 12/04/2018] [Indexed: 11/12/2022] Open
Abstract
A predominant tool for adaptation in Gram-negative bacteria is the functional genetic platform called integron. Integrons capture and rearrange promoterless gene cassettes in a unique recombination process involving the recognition of folded single-stranded DNA hairpins—so-called attC sites—with a strong preference for the attC bottom strand. While structural elements have been identified to promote this preference, their mechanistic action remains incomplete. Here, we used high-resolution single-molecule optical tweezers (OT) to characterize secondary structures formed by the attC bottom (\documentclass[12pt]{minimal}
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}{}${{att}}{{{C}}_{{\rm{bs}}}}$\end{document}) and top (\documentclass[12pt]{minimal}
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}{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document}) strands of the paradigmatic attCaadA7 site. We found for both sequences two structures—a straight, canonical hairpin and a kinked hairpin. Remarkably, the recombination-preferred \documentclass[12pt]{minimal}
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}{}${{att}}{{{C}}_{{\rm{bs}}}}$\end{document} predominantly formed the straight hairpin, while the \documentclass[12pt]{minimal}
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}{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document} preferentially adopted the kinked structure, which exposes only one complete recombinase binding box. By a mutational analysis, we identified three bases in the unpaired central spacer, which could invert the preferred conformations and increase the recombination frequency of the \documentclass[12pt]{minimal}
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}{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document}in vivo. A bioinformatics screen revealed structural bias toward a straight, canonical hairpin conformation in the bottom strand of many antibiotic resistance cassettes attC sites. Thus, we anticipate that structural fine tuning could be a mechanism in many biologically active DNA hairpins.
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Affiliation(s)
- Ann Mukhortava
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Matthias Pöge
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Maj Svea Grieb
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Aleksandra Nivina
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr Roux, 75015 Paris, France.,CNRS, UMR3525, 28 Rue du Dr Roux, 75015 Paris, France.,Paris Descartes University, 75006 Paris, France
| | - Celine Loot
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr Roux, 75015 Paris, France.,CNRS, UMR3525, 28 Rue du Dr Roux, 75015 Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr Roux, 75015 Paris, France.,CNRS, UMR3525, 28 Rue du Dr Roux, 75015 Paris, France
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307 Dresden, Germany
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54
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Patra S, Schuabb V, Kiesel I, Knop JM, Oliva R, Winter R. Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study. Nucleic Acids Res 2019; 47:981-996. [PMID: 30418613 PMCID: PMC6344865 DOI: 10.1093/nar/gky1122] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/23/2018] [Indexed: 12/19/2022] Open
Abstract
We investigated the volumetric and kinetic profile of the conformational landscape of a poly dA loop DNA hairpin (Hp) in the presence of salts, osmolytes and crowding media, mimicking the intracellular milieu, using single-molecule FRET methodology. Pressure modulation was applied to explore the volumetric and hydrational characteristics of the free-energy landscape of the DNA Hp, but also because pressure is a stress factor many organisms have to cope with, e.g. in the deep sea where pressures even up to the kbar level are encountered. Urea and pressure synergistically destabilize the closed conformation of the DNA Hp due to a lower molar partial volume in the unfolded state. Conversely, multivalent salts, trimethylamine-N-oxide and Ficoll strongly populate the closed state and counteract deteriorating effects of pressure. Complementary smFRET measurements under immobilized conditions at ambient pressure allowed us to dissect the equilibrium data in terms of folding and unfolding rate constants of the conformational transitions, leading to a deeper understanding of the stabilization mechanisms of the cosolutes. Our results show that the free-energy landscape of the DNA Hp is a rugged one, which is markedly affected by the ionic strength of the solution, by preferential interaction and exclusion of cosolvents as well as by pressure.
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Affiliation(s)
- Satyajit Patra
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Vitor Schuabb
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Irena Kiesel
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Jim-Marcel Knop
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cinita, 80126 Naples, Italy
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
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55
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Satange R, Chang CK, Hou MH. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res 2019; 46:6416-6434. [PMID: 29945186 PMCID: PMC6061790 DOI: 10.1093/nar/gky561] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
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56
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Miele SAB, Cerrudo CS, Parsza CN, Nugnes MV, Mengual Gómez DL, Belaich MN, Ghiringhelli PD. Identification of Multiple Replication Stages and Origins in the Nucleopolyhedrovirus of Anticarsia gemmatalis. Viruses 2019; 11:E648. [PMID: 31311127 PMCID: PMC6669502 DOI: 10.3390/v11070648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
To understand the mechanism of replication used by baculoviruses, it is essential to describe all the factors involved, including virus and host proteins and the sequences where DNA synthesis starts. A lot of work on this topic has been done, but there is still confusion in defining what sequence/s act in such functions, and the mechanism of replication is not very well understood. In this work, we performed an AgMNPV replication kinetics into the susceptible UFL-Ag-286 cells to estimate viral genome synthesis rates. We found that the viral DNA exponentially increases in two different phases that are temporally separated by an interval of 5 h, probably suggesting the occurrence of two different mechanisms of replication. Then, we prepared a plasmid library containing virus fragments (0.5-2 kbp), which were transfected and infected with AgMNPV in UFL-Ag-286 cells. We identified 12 virus fragments which acted as origins of replication (ORI). Those fragments are in close proximity to core genes. This association to the core genome would ensure vertical transmission of ORIs. We also predict the presence of common structures on those fragments that probably recruit the replication machinery, a structure also present in previously reported ORIs in baculoviruses.
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Affiliation(s)
- Solange A B Miele
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
- Institute for Integrative Biology of the Cell (I2BC), Evolution and Maintenance of Circular Chromosomes, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, 91190 Saint-Aubin, France
| | - Carolina S Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - Cintia N Parsza
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - María Victoria Nugnes
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - Diego L Mengual Gómez
- Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - Mariano N Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina.
| | - P Daniel Ghiringhelli
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
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57
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Wumaier M, Shi JJ, Yao TM, Hu XC, Gao RR, Shi S. G-quadruplex and duplex DNA binding studies of novel Ruthenium(II) complexes containing ascididemin ligands. J Inorg Biochem 2019; 196:110681. [DOI: 10.1016/j.jinorgbio.2019.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 11/29/2022]
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58
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A Novel G-Quadruplex Binding Protein in Yeast-Slx9. Molecules 2019; 24:molecules24091774. [PMID: 31067825 PMCID: PMC6539110 DOI: 10.3390/molecules24091774] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 01/01/2023] Open
Abstract
G-quadruplex (G4) structures are highly stable four-stranded DNA and RNA secondary structures held together by non-canonical guanine base pairs. G4 sequence motifs are enriched at specific sites in eukaryotic genomes, suggesting regulatory functions of G4 structures during different biological processes. Considering the high thermodynamic stability of G4 structures, various proteins are necessary for G4 structure formation and unwinding. In a yeast one-hybrid screen, we identified Slx9 as a novel G4-binding protein. We confirmed that Slx9 binds to G4 DNA structures in vitro. Despite these findings, Slx9 binds only insignificantly to G-rich/G4 regions in Saccharomyces cerevisiae as demonstrated by genome-wide ChIP-seq analysis. However, Slx9 binding to G4s is significantly increased in the absence of Sgs1, a RecQ helicase that regulates G4 structures. Different genetic and molecular analyses allowed us to propose a model in which Slx9 recognizes and protects stabilized G4 structures in vivo.
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59
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Detection of nucleotide sequences capable of forming non-canonical DNA structures: Application of automata theory. Comput Biol Chem 2019; 80:278-283. [PMID: 31054540 DOI: 10.1016/j.compbiolchem.2019.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 11/24/2022]
Abstract
In this study, we develop a program that allows us to reveal DNA receptors, i.e. nucleotide sequences that may form more than one non-canonical structure. The data obtained may be analysed either experimentally or using DNA banks, and refers to the coding, non-coding or promotor region of the gene. These results provide a better understanding of the role that non-canonical structures play in pathological modifications of the genetic apparatus, resulting in tumour formation or inherited disease. They also reveal the effect of single nucleotide polymorphisms on gene expression, indicate so-called "risk regions" in which the substitution of a single nucleotide may lead to increased formation of non-canonical structures, and elucidate the epigenetic mechanisms of microorganism adaptation.
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60
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Bukovska G, Ugorcakova J, Halgasova N, Bocanova L, Tkacova A. The BFK20 phage replication origin confers a phage-encoded resistance phenotype to the industrial strain Brevibacterium flavum. FEMS Microbiol Lett 2019; 366:5480461. [DOI: 10.1093/femsle/fnz090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/25/2019] [Indexed: 01/21/2023] Open
Affiliation(s)
- Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Jana Ugorcakova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Nora Halgasova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Adela Tkacova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia
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61
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Abdollah-Nia F, Gelfand MP, Van Orden A. Three-State DNA Hairpin Conformational Dynamics Revealed by Higher-Order Fluorescence Correlation Spectroscopy. J Phys Chem B 2019; 123:1491-1504. [DOI: 10.1021/acs.jpcb.8b10703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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62
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Cechová J, Lýsek J, Bartas M, Brázda V. Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability. Bioinformatics 2019; 34:1081-1085. [PMID: 29126205 PMCID: PMC6030915 DOI: 10.1093/bioinformatics/btx729] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/07/2017] [Indexed: 01/08/2023] Open
Abstract
Motivation The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. Results IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. Availability and implementation Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jana Cechová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Jirí Lýsek
- Department of Informatics, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Martin Bartas
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic.,Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 701 03 Ostrava, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
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63
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Roth E, Glick Azaria A, Girshevitz O, Bitler A, Garini Y. Measuring the Conformation and Persistence Length of Single-Stranded DNA Using a DNA Origami Structure. NANO LETTERS 2018; 18:6703-6709. [PMID: 30352164 DOI: 10.1021/acs.nanolett.8b02093] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Measuring the mechanical properties of single-stranded DNA (ssDNA) is a challenge that has been addressed by different methods lately. The short persistence length, fragile structure, and the appearance of stem loops complicate the measurement, and this leads to a large variability in the measured values. Here we describe an innovative method based on DNA origami for studying the biophysical properties of ssDNA. By synthesizing a DNA origami structure that consists of two rigid rods with an ssDNA segment between them, we developed a method to characterize the effective persistence length of a random-sequence ssDNA while allowing the formation of stem loops. We imaged the structure with an atomic force microscope (AFM); the rigid rods provide a means for the exact identification of the ssDNA ends. This leads to an accurate determination of the end-to-end distance of each ssDNA segment, and by fitting the measured distribution to the ideal chain polymer model we measured an effective persistence length of 1.98 ± 0.72 nm. This method enables one to measure short or long strands of ssDNA, and it can cope with the formation of stem loops that are often formed along ssDNA. We envision that this method can be used for measuring stem loops for determining the effect of repetitive nucleotide sequences and environmental conditions on the mechanical properties of ssDNA and the effect of interacting proteins with ssDNA. We further noted that the method can be extended to nanoprobes for measuring the interactions of specific DNA sequences, because the DNA origami rods (or similar structures) can hold multiple fluorescent probes that can be easily detected.
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Affiliation(s)
- Efrat Roth
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Alex Glick Azaria
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Olga Girshevitz
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Arkady Bitler
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Yuval Garini
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
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64
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Akhlaq S, Panicker NG, Philip PS, Ali LM, Dudley JP, Rizvi TA, Mustafa F. A cis-Acting Element Downstream of the Mouse Mammary Tumor Virus Major Splice Donor Critical for RNA Elongation and Stability. J Mol Biol 2018; 430:4307-4324. [PMID: 30179605 DOI: 10.1016/j.jmb.2018.08.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND The mouse mammary tumor virus (MMTV) encodes a functional signal peptide, a cleavage product of envelope and Rem proteins. Signal peptide interacts with a 3' cis-acting RNA element, the Rem-responsive element (RmRE), to facilitate expression of both unspliced genomic (gRNA) and spliced mRNAs. An additional RmRE has been proposed at the 5' end of the genome, facilitating nuclear export of the unspliced gRNA, whereas the 3' RmRE could facilitate translation of all other mRNAs, including gRNA. RESULTS To address this hypothesis, a series of mutations were introduced into a 24-nt region found exclusively in the unspliced gRNA. Mutant clones using MMTV or human cytomegalovirus promoters were tested in both transient and stable transfections to determine their effect on gRNA nuclear export, stability, and translation. Nuclear export of the gRNA was affected only in a small mutant subset in stably transfected Jurkat T cells. Quantitative real-time RT-PCR of actinomycin D-treated cells expressing MMTV revealed that multiple mutants were severely compromised for RNA expression and stability. Both genomic and spliced nuclear RNAs were reduced, leading to abrogation of Gag and Env protein expressed from unspliced and spliced mRNAs, respectively. RT-PCRs with multiple primer pairs indicated failure to elongate genomic MMTV transcripts beyond ~500 nt compared to the wild type in a cell line-dependent manner. CONCLUSIONS MMTV contains a novel cis-acting element downstream of the major splice donor critical for facilitating MMTV gRNA elongation and stability. Presence of a mirror repeat within the element may represent important viral/host factor binding site(s) within MMTV gRNA.
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Affiliation(s)
- Shaima Akhlaq
- Department of Biochemistry, College of Medicine and Health Sciences, UAE University, Tawam Hospital Complex, P.O. Box 17666, Al Ain, United Arab Emirates.
| | - Neena G Panicker
- Department of Biochemistry, College of Medicine and Health Sciences, UAE University, Tawam Hospital Complex, P.O. Box 17666, Al Ain, United Arab Emirates.
| | - Pretty S Philip
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, UAE University, Tawam Hospital Complex, P.O. Box 17666, Al Ain, United Arab Emirates.
| | - Lizna M Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, UAE University, Tawam Hospital Complex, P.O. Box 17666, Al Ain, United Arab Emirates.
| | - Jaquelin P Dudley
- LaMontagne Center for Infectious Diseases, The University of Texas at Austin, 100 East 24th Street, NHB 2.616, Austin, TX 78712, USA.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, UAE University, Tawam Hospital Complex, P.O. Box 17666, Al Ain, United Arab Emirates.
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences, UAE University, Tawam Hospital Complex, P.O. Box 17666, Al Ain, United Arab Emirates.
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65
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Carr CE, Marky LA. Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges. Biophys J 2018; 114:2764-2774. [PMID: 29925014 PMCID: PMC6026347 DOI: 10.1016/j.bpj.2018.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/25/2018] [Accepted: 05/01/2018] [Indexed: 12/20/2022] Open
Abstract
Intramolecular junctions are a ubiquitous structure within DNA and RNA; three-way junctions in particular have high strain around the junction because of the lack of flexibility, preventing the junctions from adopting conformations that would allow for optimal folding. In this work, we used a combination of calorimetric and spectroscopic techniques to study the unfolding of four intramolecular three-way junctions. The control three-way junction, 3H, has the sequence d(GAAATTGCGCT5GCGCGTGCT5GCACAATTTC), which has three arms of different sequences. We studied three other three-way junctions in which one (2HS1H), two (HS12HS1), and three (HS1HS1HS1) cytosine bulges were placed at the junction to allow the arms to adopt a wider range of conformations that may potentially relieve strain. Through calorimetric studies, it was concluded that bulges produce only minor effects on the enthalpic and thermal stability at physiological salt concentrations for 2HS1H and HS1HS1HS1. HS12HS1 displays the strongest effect, with the GTGC stem lacking a defined transition. In addition to unfolding thermodynamics, the differential binding of counterions, water, and protons was determined. It was found that with each bulge, there was a large increase in the binding of counterions; this correlated with a decrease in the immobilization of structural water molecules. The increase in counterion uptake upon folding likely displaces binding of structural water, which is measured by the osmotic stress method, in favor of electrostricted waters. The cytosine bulges do not affect the binding of protons; this finding indicates that the bulges are not forming base-triplet stacks. These results indicate that bulges in junctions do not affect the unfolding profile or the enthalpy of oligonucleotides but do affect the number and amount of molecules immobilized by the junction.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska.
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66
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Integrase-Mediated Recombination of the bel-1 Gene Cassette Encoding the Extended-Spectrum β-Lactamase BEL-1. Antimicrob Agents Chemother 2018; 62:AAC.00030-18. [PMID: 29483118 DOI: 10.1128/aac.00030-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/08/2018] [Indexed: 11/20/2022] Open
Abstract
Integrons are genetic elements that can acquire and rearrange gene cassettes. The blaBEL-1 gene encodes an extended-spectrum β-lactamase, BEL-1, that is present at the second position of the variable region of class 1 integrons identified in Pseudomonas aeruginosa The mobility of the bel-1 gene cassette was analyzed under physiological conditions and with the integrase gene being overexpressed. Cassette mobility in Escherichia coli was detected by excision/integration into the recipient integron In3 on the conjugative plasmid R388 with the overproduced integrase. Despite several antibiotic pressures, the bel-1 cassette remained at the second position in the integron, highlighting its stability in P. aeruginosa Overexpression of the integrase gene in E. coli induced bel-1 cassette recombination. However, cassettes containing two genes (blaBEL-1 and smr2 or blaBEL-1 and aacA4) were excised, suggesting that the bel-1 cassette attC site was defective. We show that bel-1 is a stable gene cassette under physiological growth conditions, irrespective of the selective antibiotic pressure, that may be mobilized upon overexpression of the integrase gene.
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67
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Non-canonical DNA structures: Comparative quantum mechanical study. Biophys Chem 2018; 235:19-28. [DOI: 10.1016/j.bpc.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 11/21/2022]
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68
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Lorenzo-Díaz F, Fernández-López C, Guillén-Guío B, Bravo A, Espinosa M. Relaxase MobM Induces a Molecular Switch at Its Cognate Origin of Transfer. Front Mol Biosci 2018; 5:17. [PMID: 29600250 PMCID: PMC5863519 DOI: 10.3389/fmolb.2018.00017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/09/2018] [Indexed: 11/13/2022] Open
Abstract
The MOBV1 family of relaxases is broadly distributed in plasmids and other mobile genetic elements isolated from staphylococci, enterococci, and streptococci. The prototype of this family is protein MobM encoded by the streptococcal promiscuous plasmid pMV158. MobM cleaves the phosphodiester bond of a specific dinucleotide within the origin of transfer (oriT) to initiate conjugative transfer. Differently from other relaxases, MobM and probably other members of the family, cleaves its target single-stranded DNA through a histidine residue rather than the commonly used tyrosine. The oriT of the MOBV1 family differs from other well-known conjugative systems since it has sequences with three inverted repeats, which were predicted to generate three mutually-exclusive hairpins on supercoiled DNA. In this work, such hypothesis was evaluated through footprinting experiments on supercoiled plasmid DNA. We have found a change in hairpin extrusion mediated by protein MobM. This conformational change involves a shift from the main hairpin generated on “naked” DNA to a different hairpin in which the nick site is positioned in a single-stranded configuration. Our results indicate that the oriTpMV158 acts as a molecular switch in which, depending on the inverted repeat recognized by MobM, pMV158 mobilization could be turned “on” or “off.”
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Affiliation(s)
- Fabián Lorenzo-Díaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Beatriz Guillén-Guío
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Alicia Bravo
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
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69
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Carr CE, Marky LA. Effect of GCAA stabilizing loops on three- and four-way intramolecular junctions. Phys Chem Chem Phys 2018; 20:5046-5056. [PMID: 29388988 DOI: 10.1039/c7cp08329g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tetraloops are a common way of changing the melting behavior of a DNA or RNA structure without changing the sequence of the stem. Because of the ubiquitous nature of tetraloops, our goal is to understand the effect a GCAA tetraloop, which belongs to the GNRA family of tetraloops, has on the unfolding thermodynamics of intramolecular junctions. Specifically, we have described the melting behavior of intramolecular three-way and four-way junctions where a T5 loop has been replaced with a GCAA tetraloops in different positions. Their thermodynamic profiles, including ΔnNa+ and ΔnW, were analyzed based on the position of the tetraloop. We obtained between -16.7 and -27.5 kcal mol-1 for all junctions studied. The experimental data indicates the influence of the GCAA tetraloop is primarily dictated by the native unfolding of the junction; if the tetraloop is placed on a stem that unfolds as a single domain when the tetraloop is not present, it will unfold as a single domain when the tetraloop is present but with a higher thermal stability. Conversely, if the tetraloop is placed on a stem which unfolds cooperatively with other stems when the tetraloop is not present, the tetraloop will increase the thermal stability of all the stems in the melting domain. The oligonucleotide structure and not the tetraloop itself affects ion uptake; three-way junctions do not gain an increase in ion uptake, but four-way junctions do. This is not the case for water immobilization, where the position of the tetraloop dictates the amount of water immobilized.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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70
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McDonald MC, Ahren D, Simpfendorfer S, Milgate A, Solomon PS. The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana. MOLECULAR PLANT PATHOLOGY 2018; 19:432-439. [PMID: 28093843 PMCID: PMC6638140 DOI: 10.1111/mpp.12535] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 05/18/2023]
Abstract
Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene, which has been associated previously with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis. Analysis of the regions flanking ToxA within B. sorokiniana revealed that it was embedded within a 12-kb genomic element nearly identical to the corresponding regions in P. nodorum and P. tritici-repentis. A screen of 35 Australian B. sorokiniana isolates confirmed that ToxA was present in 12 isolates. Sequencing of the ToxA genes within these isolates revealed two haplotypes, which differed by a single non-synonymous nucleotide substitution. Pathogenicity assays showed that a B. sorokiniana isolate harbouring ToxA was more virulent on wheat lines that contained the sensitivity gene when compared with a non-ToxA isolate. This work demonstrates that proteins that confer host-specific virulence can be horizontally acquired across multiple species. This acquisition can dramatically increase the virulence of pathogenic strains on susceptible cultivars, which, in an agricultural setting, can have devastating economic and social impacts.
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Affiliation(s)
- Megan C. McDonald
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityCanberra2601Australia
| | - Dag Ahren
- Department of BiologyLund UniversityLund22101Sweden
| | - Steven Simpfendorfer
- SW Department of Primary IndustriesTamworth Agricultural InstituteTamworthNSW2340Australia
| | - Andrew Milgate
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNSW2650Australia
| | - Peter S. Solomon
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityCanberra2601Australia
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71
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Xu Y, Xu C, Li X, Sun B, Eldin AA, Jia Y. A combinational optimization method for efficient synthesis of tetramethylpyrazine by the recombinant Escherichia coli. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2017.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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72
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Appukutti N, Serpell CJ. High definition polyphosphoesters: between nucleic acids and plastics. Polym Chem 2018. [DOI: 10.1039/c8py00251g] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nucleic acids and synthetic polyphosphoester materials have been distinct fields – this review shows how these areas now comprise a continuum.
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73
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Cui Y, Han X, An R, Zhou G, Komiyama M, Liang X. Cyclization of secondarily structured oligonucleotides to single-stranded rings by using Taq DNA ligase at high temperatures. RSC Adv 2018; 8:18972-18979. [PMID: 35539641 PMCID: PMC9080623 DOI: 10.1039/c8ra02804d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 05/10/2018] [Indexed: 11/21/2022] Open
Abstract
Single-stranded DNA rings play important roles in nanoarchitectures, molecular machines, DNA detection, etc. Although T4 DNA ligase has been widely employed to cyclize single-stranded oligonucleotides into rings, the cyclization efficiency is very low when the oligonucleotides (l-DNAs) take complicated secondary structures at ambient temperatures. In the present study, this problem has been solved by using Thermus aquaticus DNA ligase (Taq DNA ligase) at higher temperatures (65 and 70 °C) where the secondary structures are less stable or completely destroyed. This method is based on our new finding that this ligase successfully functions even when the splint strand is short and forms no stable duplex with l-DNA (at least in the absence of the enzyme). In order to increase the efficiency of cyclization, various operation factors (lengths and sequences of splint, as well as the size of the DNA ring) have been investigated. Based on these results, DNA rings have been successfully synthesized from secondarily structured oligonucleotides in high yields and high selectivity. The present methodology is applicable to the preparation of versatile DNA rings involving complicated secondary structures, which should show novel properties and greatly widen the scope of DNA-based nanotechnology. We have achieved the efficient preparation of single-stranded DNA rings from secondarily structured oligonucleotides.![]()
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Affiliation(s)
- Yixiao Cui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Xutiange Han
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Ran An
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
| | - Guangqing Zhou
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Makoto Komiyama
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- National Institute for Materials Science (NIMS)
| | - Xingguo Liang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
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74
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Escudero JA, Nivina A, Cambray G, López-Igual R, Loot C, Mazel D. Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation. Biotechnol Bioeng 2018; 115:184-191. [DOI: 10.1002/bit.26450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/23/2017] [Accepted: 09/08/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Jose A. Escudero
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
- Departamento de Sanidad Animal; Facultad de Veterinaria; Universidad Complutense de Madrid; Madrid Spain
- VISAVET Health Surveillance Centre; Universidad Complutense Madrid; Madrid Spain
| | - Aleksandra Nivina
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
- Université Paris Descartes; Sorbonne Paris Cité; Paris France
| | | | - Rocío López-Igual
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
| | - Celine Loot
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
| | - Didier Mazel
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
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75
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Swadling JB, Ishii K, Tahara T, Kitao A. Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation. Phys Chem Chem Phys 2018; 20:2990-3001. [DOI: 10.1039/c7cp06355e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Temperature REMD reveals how local chemical changes can result in markedly differing conformational landscapes for DNA and RNA hairpin loops.
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Affiliation(s)
- Jacob B. Swadling
- School of Life Science and Technology
- Tokyo Institute of Technology
- Tokyo 152-8550
- Japan
| | | | | | - Akio Kitao
- School of Life Science and Technology
- Tokyo Institute of Technology
- Tokyo 152-8550
- Japan
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76
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Patra S, Anders C, Schummel PH, Winter R. Antagonistic effects of natural osmolyte mixtures and hydrostatic pressure on the conformational dynamics of a DNA hairpin probed at the single-molecule level. Phys Chem Chem Phys 2018; 20:13159-13170. [DOI: 10.1039/c8cp00907d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Osmolyte mixtures from deep sea organisms are able to rescue nucleic acids from pressure-induced unfolding.
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Affiliation(s)
- Satyajit Patra
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Christian Anders
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Paul Hendrik Schummel
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
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77
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Yang KA, Chun H, Zhang Y, Pecic S, Nakatsuka N, Andrews AM, Worgall TS, Stojanovic MN. High-Affinity Nucleic-Acid-Based Receptors for Steroids. ACS Chem Biol 2017; 12:3103-3112. [PMID: 29083858 DOI: 10.1021/acschembio.7b00634] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Artificial receptors for hydrophobic molecules usually have moderate affinities and limited selectivities. We describe three new classes of high affinity hydrophobic receptors for nonaromatic steroids based on deoxyribonucleotides, obtained through five high stringency selections coupled with tailored counter-selections. The isolation of multiple classes of high affinity steroid receptors demonstrates the surprising breadth of moderately sized hydrophobic binding motifs (<40 nucleotides) available to natural nucleic acids. Studies of interactions with analogs indicate that two classes, four-way junctions and 4XGN motifs, comprise receptors with shapes that prevent binding of specific steroid conjugates used in counter-selections. Furthermore, they strongly prefer nonhydroxylated steroid cores, which is typical for hydrophobic receptors. The third new class accommodates hydroxyl groups in high-affinity, high-selectivity binding pockets, thus reversing the preferences of the first two classes. The high-affinity binding of aptamers to targets efficiently inhibits double-helix formation in the presence of the complementary oligonucleotides. The high affinity of some of these receptors and tailored elimination of binding through counter-selections ensures that these new aptamers will enable clinical chemistry applications.
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Affiliation(s)
| | - Hyosun Chun
- School
of Computer Science and Engineering, Seoul National University, Seoul 08826, Korea
| | | | | | - Nako Nakatsuka
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Anne M. Andrews
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience
and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, California 90095, United States
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78
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Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes. Curr Biol 2017; 27:3771-3782.e6. [PMID: 29199074 DOI: 10.1016/j.cub.2017.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/28/2022]
Abstract
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Kenny A Bogaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine, Québec City, QC G1V 0A6, Canada
| | - Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, New Kirk Building, Kelburn Parade, P.O. Box 600, Wellington 6012, New Zealand
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Juan M Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35484-0345, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Professors Walk, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium.
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79
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Abstract
The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C-G loop-closing base pairs are more stabilizing than T-A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.
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Affiliation(s)
- Yuan Liu
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories Hong Kong
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80
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Grieb MS, Nivina A, Cheeseman BL, Hartmann A, Mazel D, Schlierf M. Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality. Nucleic Acids Res 2017; 45:10555-10563. [PMID: 28985409 PMCID: PMC5737091 DOI: 10.1093/nar/gkx670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/22/2017] [Indexed: 11/22/2022] Open
Abstract
Biologically functional DNA hairpins are found in archaea, prokaryotes and eukaryotes, playing essential roles in various DNA transactions. However, during DNA replication, hairpin formation can stall the polymerase and is therefore prevented by the single-stranded DNA binding protein (SSB). Here, we address the question how hairpins maintain their functional secondary structure despite SSB’s presence. As a model hairpin, we used the recombinogenic form of the attC site, essential for capturing antibiotic-resistance genes in the integrons of bacteria. We found that attC hairpins have a conserved high GC-content near their apical loop that creates a dynamic equilibrium between attC fully opened by SSB and a partially structured attC-6–SSB complex. This complex is recognized by the recombinase IntI, which extrudes the hairpin upon binding while displacing SSB. We anticipate that this intriguing regulation mechanism using a base pair distribution to balance hairpin structure formation and genetic stability is key to the dissemination of antibiotic resistance genes among bacteria and might be conserved among other functional hairpins.
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Affiliation(s)
- Maj Svea Grieb
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Aleksandra Nivina
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 rue du Dr. Roux, 75724 Paris, France.,CNRS UMR3525, 75724 Paris, France.,Paris Descartes University, 75006 Paris, France
| | - Bevan L Cheeseman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 rue du Dr. Roux, 75724 Paris, France.,CNRS UMR3525, 75724 Paris, France
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
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81
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Zou X, Morganella S, Glodzik D, Davies H, Li Y, Stratton MR, Nik-Zainal S. Short inverted repeats contribute to localized mutability in human somatic cells. Nucleic Acids Res 2017; 45:11213-11221. [PMID: 28977645 PMCID: PMC5737083 DOI: 10.1093/nar/gkx731] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/14/2017] [Accepted: 08/10/2017] [Indexed: 01/09/2023] Open
Abstract
Selected repetitive sequences termed short inverted repeats (SIRs) have the propensity to form secondary DNA structures called hairpins. SIRs comprise palindromic arm sequences separated by short spacer sequences that form the hairpin stem and loop respectively. Here, we show that SIRs confer an increase in localized mutability in breast cancer, which is domain-dependent with the greatest mutability observed within spacer sequences (∼1.35-fold above background). Mutability is influenced by factors that increase the likelihood of formation of hairpins such as loop lengths (of 4-5 bp) and stem lengths (of 7-15 bp). Increased mutability is an intrinsic property of SIRs as evidenced by how almost all mutational processes demonstrate a higher rate of mutagenesis of spacer sequences. We further identified 88 spacer sequences showing enrichment from 1.8- to 90-fold of local mutability distributed across 283 sites in the genome that intriguingly, can be used to inform the biological status of a tumor.
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Affiliation(s)
- Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Yilin Li
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
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82
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Carr CE, Marky LA. Melting Behavior of a DNA Four-Way Junction Using Spectroscopic and Calorimetric Techniques. J Am Chem Soc 2017; 139:14443-14455. [DOI: 10.1021/jacs.7b06429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carolyn E. Carr
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Luis A. Marky
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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83
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Mukherjee D, Bhattacharyya D. Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation. J Mol Model 2017; 23:300. [DOI: 10.1007/s00894-017-3470-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
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84
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Carr CE, Marky LA. Investigation of the Melting Behavior of DNA Three-Way Junctions in the Closed and Open States. Biophys J 2017; 113:529-539. [PMID: 28793208 DOI: 10.1016/j.bpj.2017.06.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/09/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022] Open
Abstract
Intramolecular three-way junctions are commonly found in both DNA and RNA. These structures are functionally relevant in ribozymes, riboswitches, rRNA, and during replication. In this work, we present a thermodynamic description of the unfolding of DNA intramolecular three-way junctions. We used a combination of spectroscopic and calorimetric techniques to investigate the folding/unfolding thermodynamics of two three-way junctions with a closed (Closed-J) or open (Open-J) junction and their appropriate control stem-loop motifs (GAAATT-Hp, CTATC-Hp, and Dumbbell). The overall results show that both junctions are stable over a wide range of salt concentrations. However, Open-J is more stable due to a higher enthalpy contribution from the formation of a higher number of basepair stacks whereas Closed-J has a defined structure and retains the basepair stacking of all three stems. The comparison of the experimental results of Closed-J and Open-J with those of their component stem-loop motifs allowed us to be more specific about their cooperative unfolding. For instance, Closed-J sacrifices thermal stability of the Dumbbell structure to maintain an overall folded state. At higher salt concentration, the simultaneous unfolding of the above domains is lost, resulting in the unfolding of the three separate stems. In contrast, the junction of Open-J in low salt retains the thermal and enthalpic stability of the Dumbbell structure although sacrificing stability of the CTATC stem. The relative stability of Dumbbell is the primary reason for the higher ΔG°(5), or free energy, value seen for Open-J at low salt. Higher salt not only maintains thermal stability of the Dumbbell structure in Open-J but causes the CTATC stem to fully fold.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, Nebraska.
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85
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Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion. Proc Natl Acad Sci U S A 2017; 114:9535-9540. [PMID: 28827328 DOI: 10.1073/pnas.1708691114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.
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86
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DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein of Bacillus thuringiensis. BMC BIOPHYSICS 2017; 10:4. [PMID: 28540040 PMCID: PMC5441083 DOI: 10.1186/s13628-017-0036-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 05/11/2017] [Indexed: 12/26/2022]
Abstract
Background The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy \documentclass[12pt]{minimal}
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\begin{document}$$ \left(\overline{\varDelta G}\right) $$\end{document}ΔG¯ were determined by an in silico analysis using different experimental DNA shuffling scenarios. In terms of spontaneity, shuffling efficiency was directly proportional to the formation of secondary structures but inversely proportional to ∆G. Results The results showed a shared thermodynamic pattern for each cluster and relationships among sequences that are phylogenetically close at the protein level. The regions of the cry11Aa, Ba and Bb genes that encode domain I showed more spontaneity and thus a greater tendency to form secondary structures (<∆G). In the region of domain III; this tendency was lower (>∆G) in the cry11Ba and Bb genes. Proteins that are phylogenetically closer to Cry11Ba and Cry11Bb, such as Cry2Aa and Cry18Aa, maintained the same thermodynamic pattern. More distant proteins, such as Cry1Aa, Cry1Ab, Cry30Aa and Cry30Ca, featured different thermodynamic patterns in their DNA. Conclusion These results suggest the presence of thermodynamic variations associated to the formation of secondary structures and an evolutionary relationship with regions that encode highly conserved domains in Cry proteins. The findings of this study may have a role in the in silico design of cry gene assembly by DNA shuffling techniques.
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87
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Núñez-Villanueva D, Iadevaia G, Stross AE, Jinks MA, Swain JA, Hunter CA. H-Bond Self-Assembly: Folding versus Duplex Formation. J Am Chem Soc 2017; 139:6654-6662. [PMID: 28470070 PMCID: PMC5469522 DOI: 10.1021/jacs.7b01357] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 01/05/2023]
Abstract
Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Alexander E. Stross
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Michael A. Jinks
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Jonathan A. Swain
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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88
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Oppold AM, Schmidt H, Rose M, Hellmann SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M. Chironomus riparius
(Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Mol Ecol 2017; 26:3256-3275. [DOI: 10.1111/mec.14111] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Ann-Marie Oppold
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Hanno Schmidt
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Marcel Rose
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
| | - Sören Lukas Hellmann
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Florian Dolze
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Fabian Ripp
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Bettina Weich
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy; University of Chicago; 920 E. 58th Street, 1061C Chicago IL 60637 USA
| | - Erwin Schmidt
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Robert Kofler
- Institut für Populationsgenetik; Vetmeduni Vienna 1210 Vienna Austria
| | - Thomas Hankeln
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Markus Pfenninger
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
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89
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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90
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017; 56:5045-5049. [DOI: 10.1002/anie.201701420] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/03/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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91
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Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance. mBio 2017; 8:mBio.02296-16. [PMID: 28351923 PMCID: PMC5371416 DOI: 10.1128/mbio.02296-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrons ensure a rapid and "on demand" response to environmental stresses driving bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes due to site-specific recombination catalyzed by their integrase. Integrons can be either sedentary and chromosomally located or mobile when they are associated with transposons and plasmids. They are respectively called sedentary chromosomal integrons (SCIs) and mobile integrons (MIs). MIs are key players in the dissemination of antibiotic resistance genes. Here, we used in silico and in vivo approaches to study cassette excision dynamics in MIs and SCIs. We show that the orientation of cassette arrays relative to replication influences attC site folding and cassette excision by placing the recombinogenic strands of attC sites on either the leading or lagging strand template. We also demonstrate that stability of attC sites and their propensity to form recombinogenic structures also regulate cassette excision. We observe that cassette excision dynamics driven by these factors differ between MIs and SCIs. Cassettes with high excision rates are more commonly found on MIs, which favors their dissemination relative to SCIs. This is especially true for SCIs carried in the Vibrio genus, where maintenance of large cassette arrays and vertical transmission are crucial to serve as a reservoir of adaptive functions. These results expand the repertoire of known processes regulating integron recombination that were previously established and demonstrate that, in terms of cassette dynamics, a subtle trade-off between evolvability and genetic capacitance has been established in bacteria.IMPORTANCE The integron system confers upon bacteria a rapid adaptation capability in changing environments. Specifically, integrons are involved in the continuous emergence of bacteria resistant to almost all antibiotic treatments. The international situation is critical, and in 2050, the annual number of deaths caused by multiresistant bacteria could reach 10 million, exceeding the incidence of deaths related to cancer. It is crucial to increase our understanding of antibiotic resistance dissemination and therefore integron recombination dynamics to find new approaches to cope with the worldwide problem of multiresistance. Here, we studied the dynamics of recombination and dissemination of gene encoding cassettes carried on integrons. By combining in silico and in vivo analyses, we show that cassette excision is highly regulated by replication and by the intrinsic properties of cassette recombination sites. We also demonstrated differences in the dynamics of cassette recombination between mobile and sedentary chromosomal integrons (MIs and SCIs). For MIs, a high cassette recombination rate is favored and timed to conditions when generating diversity (upon which selection can act) allows for a rapid response to environmental conditions and stresses. In contrast, for SCIs, cassette excisions are less frequent, limiting cassette loss and ensuring a large pool of cassettes. We therefore confirm a role of SCIs as reservoirs of adaptive functions and demonstrate that the remarkable adaptive success of integron recombination system is due to its intricate regulation.
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92
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Abstract
All plasmids that spread by conjugative transfer encode a relaxase. That includes plasmids that encode the type IV secretion machinery necessary to mediate cell to cell transfer, as well as mobilizable plasmids that exploit the existence of other plasmids' type IV secretion machinery to enable their own lateral spread. Relaxases perform key functions in plasmid transfer by first binding to their cognate plasmid as part of a multiprotein complex called the relaxosome, which is then specifically recognized by a receptor protein at the opening of the secretion channel. Relaxases catalyze a site- and DNA-strand-specific cleavage reaction on the plasmid then pilot the single strand of plasmid DNA through the membrane-spanning type IV secretion channel as a nucleoprotein complex. In the recipient cell, relaxases help terminate the transfer process efficiently and stabilize the incoming plasmid DNA. Here, we review the well-studied MOBF family of relaxases to describe the biochemistry of these versatile enzymes and integrate current knowledge into a mechanistic model of plasmid transfer in Gram-negative bacteria.
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93
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Wassenaar TM, Ussery DW, Ingmer H. The qacC Gene Has Recently Spread between Rolling Circle Plasmids of Staphylococcus, Indicative of a Novel Gene Transfer Mechanism. Front Microbiol 2016; 7:1528. [PMID: 27729906 PMCID: PMC5037232 DOI: 10.3389/fmicb.2016.01528] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/12/2016] [Indexed: 11/13/2022] Open
Abstract
Resistance of Staphylococcus species to quaternary ammonium compounds, frequently used as disinfectants and biocides, can be attributed to qac genes. Most qac gene products belong to the Small Multidrug Resistant (SMR) protein family, and are often encoded by rolling-circle (RC) replicating plasmids. Four classes of SMR-type qac gene families have been described in Staphylococcus species: qacC, qacG, qacJ, and qacH. Within their class, these genes are highly conserved, but qacC genes are extremely conserved, although they are found in variable plasmid backgrounds. The lower degree of sequence identity of these plasmids compared to the strict nucleotide conservation of their qacC means that this gene has recently spread. In the absence of insertion sequences or other genetic elements explaining the mobility, we sought for an explanation of mobilization by sequence comparison. Publically available sequences of qac genes, their flanking genes and the replication gene that is invariably present in RC-plasmids were compared to reconstruct the evolutionary history of these plasmids and to explain the recent spread of qacC. Here we propose a new model that explains how qacC is mobilized and transferred to acceptor RC-plasmids without assistance of other genes, by means of its location in between the Double Strand replication Origin (DSO) and the Single-Strand replication Origin (SSO). The proposed mobilization model of this DSO-qacC-SSO element represents a novel mechanism of gene mobilization in RC-plasmids, which has also been employed by other genes, such as lnuA (conferring lincomycin resistance). The proposed gene mobility has aided to the wide spread of clinically relevant resistance genes in Staphylococcus populations.
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Affiliation(s)
| | - David W Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
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94
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Nivina A, Escudero JA, Vit C, Mazel D, Loot C. Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features of attC recombination sites. Nucleic Acids Res 2016; 44:7792-803. [PMID: 27496283 PMCID: PMC5027507 DOI: 10.1093/nar/gkw646] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/05/2016] [Accepted: 07/10/2016] [Indexed: 01/29/2023] Open
Abstract
The integron is a bacterial recombination system that allows acquisition, stockpiling and expression of cassettes carrying protein-coding sequences, and is responsible for the emergence and rise of multiresistance in Gram-negative bacteria. The functionality of this system depends on the insertion of promoterless cassettes in correct orientation, allowing their expression from the promoter located upstream of the cassette array. Correct orientation is ensured by strand selectivity of integron integrases for the bottom strand of cassette recombination sites (attC), recombined in form of folded single-stranded hairpins. Here, we investigated the basis of such strand selectivity by comparing recombination of wild-type and mutated attC sites with different lengths, sequences and structures. We show that all three unpaired structural features that distinguish the bottom and top strands contribute to strand selectivity. The localization of Extra-Helical Bases (EHBs) directly favors integrase binding to the bottom strand. The Unpaired Central Spacer (UCS) and the Variable Terminal Structure (VTS) influence strand selectivity indirectly, probably through the stabilization of the bottom strand and the resulting synapse due to the nucleotide skew between the two strands. These results underscore the importance of the single-stranded nature of the attC site that allows such tight control over integron cassette orientation.
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Affiliation(s)
- Aleksandra Nivina
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - José Antonio Escudero
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Claire Vit
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Didier Mazel
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Céline Loot
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
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95
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Abstract
The non-B DNA structures formed by short tandem repeats on the nascent strand during DNA replication have been proposed to be the structural intermediates that lead to repeat expansion mutations. Tetranucleotide TTTA and CCTG repeat expansions have been known to cause reduction in biofilm formation in Staphylococcus aureus and myotonic dystrophy type 2 in human, respectively. In this study, we report the first three-dimensional minidumbbell (MDB) structure formed by natural DNA sequences containing two TTTA or CCTG repeats. The formation of MDB provides possible pathways for strand slippage to occur, which ultimately leads to repair escape and thus expansion mutations. Our result here shows that MDB is a highly compact structure composed of two type II loops. In addition to the typical stabilizing interactions in type II loops, MDB shows extensive stabilizing forces between the two loops, including two distinctive modes of interactions between the minor groove residues. The formation of MDB enriches the structural diversity of natural DNA sequences, reveals the importance of loop-loop interactions in unusual DNA structures, and provides insights into novel mechanistic pathways of DNA repeat expansion mutations.
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Affiliation(s)
- Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
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96
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Pastrana CL, Carrasco C, Akhtar P, Leuba SH, Khan SA, Moreno-Herrero F. Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules. Nucleic Acids Res 2016; 44:8885-8896. [PMID: 27488190 PMCID: PMC5062986 DOI: 10.1093/nar/gkw689] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/22/2016] [Indexed: 11/14/2022] Open
Abstract
Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep) that directly binds to the plasmid double-stranded origin and remains covalently bound to its substrate 5′-end via a phosphotyrosine linkage. It has been proposed that the inverted DNA sequences at the nick site form a cruciform structure that facilitates DNA cleavage. However, the role of Rep proteins in the formation of this cruciform and the implication for its nicking and religation functions is unclear. Here, we have used magnetic tweezers to directly measure the DNA nicking and religation activities of RepC, the replication initiator protein of plasmid pT181, in plasmid sized and torsionally-constrained linear DNA molecules. Nicking by RepC occurred only in negatively supercoiled DNA and was force- and twist-dependent. Comparison with a type IB topoisomerase in similar experiments highlighted a relatively inefficient religation activity of RepC. Based on the structural modeling of RepC and on our experimental evidence, we propose a model where RepC nicking activity is passive and dependent upon the supercoiling degree of the DNA substrate.
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Affiliation(s)
- Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Parvez Akhtar
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Sanford H Leuba
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Saleem A Khan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
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97
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Chakraborty K, Khatua P, Bandyopadhyay S. Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies. Phys Chem Chem Phys 2016; 18:15899-910. [PMID: 27241311 DOI: 10.1039/c6cp00663a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One crucial issue in DNA hydration is the effect of salts on its conformational features. This has relevance in biology as cations present in the cellular environment shield the negative charges on the DNA backbone, thereby reducing the repulsive force between them. By screening the negative charges along the backbone, cations stabilize the folded structure of DNA. To study the effect of the added salt on single-stranded DNA (ss-DNA) conformations, we have performed room temperature molecular dynamics simulations of an aqueous solution containing the ss-DNA dodecamer with the 5'-CGCGAATTCGCG-3' sequence in the presence of 0.2, 0.5, and 0.8 M NaCl. Our calculations reveal that in the presence of the salt, the DNA molecule forms more collapsed coil-like conformations due to the screening of negative charges along the backbone. Additionally, we demonstrated that the formation of an octahedral inner-sphere complex by the strongly bound ion plays an important role in the stabilization of such folded conformation of DNA. Importantly, it is found that ion-DNA interactions can also explain the formation of non-sequential base stackings with longer lifetimes. Such non-sequential base stackings further stabilize the collapsed coil-like folded form of the DNA oligomer.
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Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India.
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98
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Charnavets T, Nunvar J, Nečasová I, Völker J, Breslauer KJ, Schneider B. Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases. Biopolymers 2016; 103:585-96. [PMID: 25951997 PMCID: PMC4690160 DOI: 10.1002/bip.22666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/05/2015] [Indexed: 01/19/2023]
Abstract
Repetitive extragenic palindrome (REP)—associated tyrosine transposase enzymes (RAYTs) bind REP DNA domains and catalyze their cleavage. Genomic sequence analyses identify potential noncoding REP sequences associated with RAYT-encoding genes. To probe the conformational space of potential RAYT DNA binding domains, we report here spectroscopic and calorimetric measurements that detect and partially characterize the solution conformational heterogeneity of REP oligonucleotides from six bacterial species. Our data reveal most of these REP oligonucleotides adopt multiple conformations, suggesting that RAYTs confront a landscape of potential DNA substrates in dynamic equilibrium that could be selected, enriched, and/or induced via differential binding. Thus, the transposase-bound DNA motif may not be the predominant conformation of the isolated REP domain. Intriguingly, for several REPs, the circular dichroism spectra suggest guanine tetraplexes as potential alternative or additional RAYT recognition elements, an observation consistent with these REP domains being highly nonrandom, with tetraplex-favoring 5′-G and 3′-C-rich segments. In fact, the conformational heterogeneity of REP domains detected and reported here, including the formation of noncanonical DNA secondary structures, may reflect a general feature required for recognition by RAYT transposases. Based on our biophysical data, we propose guanine tetraplexes as an additional DNA recognition element for binding by RAYT transposase enzymes. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 585–596, 2015.
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Affiliation(s)
- Tatsiana Charnavets
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Jaroslav Nunvar
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Iva Nečasová
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
| | - Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ, 08854
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ, 08854.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08903
| | - Bohdan Schneider
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska, 1083, 142 20 Prague, Czech Republic
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99
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Bi H, Yin Y, Pan B, Li G, Zhao XS. Scanning Single-Molecule Fluorescence Correlation Spectroscopy Enables Kinetics Study of DNA Hairpin Folding with a Time Window from Microseconds to Seconds. J Phys Chem Lett 2016; 7:1865-1871. [PMID: 27140004 DOI: 10.1021/acs.jpclett.6b00720] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule fluorescence measurements have been widely used to explore kinetics and dynamics of biological systems. Among them, single-molecule imaging (SMI) is good at tracking processes slower than tens of milliseconds, whereas fluorescence correlation spectroscopy (FCS) is good at probing processes faster than submilliseconds. However, there is still shortage of simple yet effective single-molecule fluorescence method to cover the time-scale between submilliseconds and tens of milliseconds. To effectively bridge this millisecond gap, we developed a single-molecule fluorescence correlation spectroscopy (smFCS) method that works on surface-immobilized single molecules through surface scanning. We validated it by monitoring the classical DNA hairpin folding process. With a wide time window from microseconds to seconds, the experimental data are well fitted to the two-state folding model. All relevant molecular parameters, including the relative fluorescence brightness, equilibrium constant, and reaction rate constants, were uniquely determined.
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Affiliation(s)
- Huimin Bi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Yandong Yin
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Bailong Pan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Geng Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China
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100
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Flood BE, Fliss P, Jones DS, Dick GJ, Jain S, Kaster AK, Winkel M, Mußmann M, Bailey J. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity. Front Microbiol 2016; 7:603. [PMID: 27199933 PMCID: PMC4853749 DOI: 10.3389/fmicb.2016.00603] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/11/2016] [Indexed: 11/23/2022] Open
Abstract
The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group I intron also carried a MITE sequence that, like the hupL MITE family, occurs broadly across the genome. The presence of a high degree of mobile elements in genes central to Thiomargarita's core metabolism has not been previously reported in free-living bacteria and suggests a highly mutable genome.
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Affiliation(s)
- Beverly E Flood
- Department of Earth Sciences, University of Minnesota Minneapolis, MN, USA
| | - Palmer Fliss
- Department of Earth Sciences, University of Minnesota Minneapolis, MN, USA
| | - Daniel S Jones
- Department of Earth Sciences, University of MinnesotaMinneapolis, MN, USA; Biotechnology Institute, University of MinnesotaSt. Paul, MN, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Sunit Jain
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Anne-Kristin Kaster
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ Braunschweig, Germany
| | - Matthias Winkel
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Marc Mußmann
- Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Jake Bailey
- Department of Earth Sciences, University of Minnesota Minneapolis, MN, USA
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