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Michieletto D, Fosado YAG, Melas E, Baiesi M, Tubiana L, Orlandini E. Dynamic and facilitated binding of topoisomerase accelerates topological relaxation. Nucleic Acids Res 2022; 50:4659-4668. [PMID: 35474478 PMCID: PMC9071436 DOI: 10.1093/nar/gkac260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expected of proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc. Intriguingly, this in turn implies that the timescale of topological relaxation is virtually independent of the substrate length. We then discover that considering binding biases due to facilitated diffusion on looped substrates steers the sampling of the topological space closer to the boundaries between different topoisomers yielding an optimally fast topological relaxation. We discuss our findings in the context of topological simplification in vitro and in vivo.
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Affiliation(s)
| | | | - Elias Melas
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy,INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Luca Tubiana
- Physics Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy,Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy,INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
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2
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DNA-Topology Simplification by Topoisomerases. Molecules 2021; 26:molecules26113375. [PMID: 34204901 PMCID: PMC8199745 DOI: 10.3390/molecules26113375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022] Open
Abstract
The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems.
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3
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Seddek A, Annamalai T, Tse-Dinh YC. Type IA Topoisomerases as Targets for Infectious Disease Treatments. Microorganisms 2021; 9:E86. [PMID: 33401386 PMCID: PMC7823277 DOI: 10.3390/microorganisms9010086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
Infectious diseases are one of the main causes of death all over the world, with antimicrobial resistance presenting a great challenge. New antibiotics need to be developed to provide therapeutic treatment options, requiring novel drug targets to be identified and pursued. DNA topoisomerases control the topology of DNA via DNA cleavage-rejoining coupled to DNA strand passage. The change in DNA topological features must be controlled in vital processes including DNA replication, transcription, and DNA repair. Type IIA topoisomerases are well established targets for antibiotics. In this review, type IA topoisomerases in bacteria are discussed as potential targets for new antibiotics. In certain bacterial pathogens, topoisomerase I is the only type IA topoisomerase present, which makes it a valuable antibiotic target. This review will summarize recent attempts that have been made to identify inhibitors of bacterial topoisomerase I as potential leads for antibiotics and use of these inhibitors as molecular probes in cellular studies. Crystal structures of inhibitor-enzyme complexes and more in-depth knowledge of their mechanisms of actions will help to establish the structure-activity relationship of potential drug leads and develop potent and selective therapeutics that can aid in combating the drug resistant bacterial infections that threaten public health.
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Affiliation(s)
- Ahmed Seddek
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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4
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Shoura MJ, Giovan SM, Vetcher AA, Ziraldo R, Hanke A, Levene SD. Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination. Nucleic Acids Res 2020; 48:4371-4381. [PMID: 32182357 PMCID: PMC7192630 DOI: 10.1093/nar/gkaa153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/24/2020] [Accepted: 02/29/2020] [Indexed: 11/12/2022] Open
Abstract
In Cre site-specific recombination, the synaptic intermediate is a recombinase homotetramer containing a pair of loxP DNA target sites. The enzyme system's strand-exchange mechanism proceeds via a Holliday-junction (HJ) intermediate; however, the geometry of DNA segments in the synapse has remained highly controversial. In particular, all crystallographic structures are consistent with an achiral, planar Holliday-junction (HJ) structure, whereas topological assays based on Cre-mediated knotting of plasmid DNAs are consistent with a right-handed chiral junction. We use the kinetics of loop closure involving closely spaced (131-151 bp) loxP sites to investigate the in-aqueo ensemble of conformations for the longest-lived looped DNA intermediate. Fitting the experimental site-spacing dependence of the loop-closure probability, J, to a statistical-mechanical theory of DNA looping provides evidence for substantial out-of-plane HJ distortion, which unequivocally stands in contrast to the square-planar intermediate geometry from Cre-loxP crystal structures and those of other int-superfamily recombinases. J measurements for an HJ-isomerization-deficient Cre mutant suggest that the apparent geometry of the wild-type complex is consistent with temporal averaging of right-handed and achiral structures. Our approach connects the static pictures provided by crystal structures and the natural dynamics of macromolecules in solution, thus advancing a more comprehensive dynamic analysis of large nucleoprotein structures and their mechanisms.
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Affiliation(s)
- Massa J Shoura
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Stefan M Giovan
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Alexandre A Vetcher
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Riccardo Ziraldo
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Andreas Hanke
- Department of Physics, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Stephen D Levene
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
- Physics, University of Texas at Dallas, Richardson, TX 75080, USA
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Ziraldo R, Shoura MJ, Fire AZ, Levene SD. Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications. Nucleic Acids Res 2019; 47:e92. [PMID: 31226202 PMCID: PMC6895257 DOI: 10.1093/nar/gkz534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/10/2019] [Accepted: 06/06/2019] [Indexed: 11/12/2022] Open
Abstract
Next-generation DNA-sequencing (NGS) technologies, which are designed to streamline the acquisition of massive amounts of sequencing data, are nonetheless dependent on various preparative steps to generate DNA fragments of required concentration, purity and average size (molecular weight). Current automated electrophoresis systems for DNA- and RNA-sample quality control, such as Agilent's Bioanalyzer® and TapeStation® products, are costly to acquire and use; they also provide limited information for samples having broad size distributions. Here, we describe a software tool that helps determine the size distribution of DNA fragments in an NGS library, or other DNA sample, based on gel-electrophoretic line profiles. The software, developed as an ImageJ plug-in, allows for straightforward processing of gel images, including lane selection and fitting of univariate functions to intensity distributions. The user selects the option of fitting either discrete profiles in cases where discrete gel bands are visible or continuous profiles, having multiple bands buried under a single broad peak. The method requires only modest imaging capabilities and is a cost-effective, rigorous alternative characterization method to augment existing techniques for library quality control.
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Affiliation(s)
- Riccardo Ziraldo
- Department of Bioengineering, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Massa J Shoura
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.,Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.,Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Stephen D Levene
- Department of Bioengineering, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Physics, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
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6
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Aedo SJ, Orman MA, Brynildsen MP. Stationary phase persister formation in Escherichia coli can be suppressed by piperacillin and PBP3 inhibition. BMC Microbiol 2019; 19:140. [PMID: 31234796 PMCID: PMC6591824 DOI: 10.1186/s12866-019-1506-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 05/31/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Persisters are rare phenotypic variants within a bacterial population that are capable of tolerating lethal antibiotic concentrations. Passage through stationary phase is associated with the formation of persisters (type I), and a major physiological response of Escherichia coli during stationary phase is cell wall restructuring. Given the concurrence of these processes, we sought to assess whether perturbation to cell wall synthesis during stationary phase impacts type I persister formation. RESULTS We tested a panel of cell wall inhibitors and found that piperacillin, which primarily targets penicillin binding protein 3 (PBP3 encoded by ftsI), resulted in a significant reduction in both β-lactam (ampicillin, carbenicillin) and fluoroquinolone (ofloxacin, ciprofloxacin) persister levels. Further analyses showed that piperacillin exposure through stationary phase resulted in cells with more ATP, DNA, RNA, and protein (including PBPs) than untreated controls; and that their physiology led to more rapid resumption of DNA gyrase supercoiling activity, translation, and cell division upon introduction into fresh media. Previously, PBP3 inhibition had been linked to antibiotic efficacy through the DpiBA two component system; however, piperacillin suppressed persister formation in ΔdpiA to the same extent as it did in wild-type, suggesting that DpiBA is not required for the phenomenon reported here. To test the generality of PBP3 inhibition on persister formation, we expressed FtsI Ser307Ala to genetically inhibit PBP3, and suppression of persister formation was also observed, although not to the same magnitude as that seen for piperacillin treatment. CONCLUSIONS From these data we conclude that stationary phase PBP3 activity is important to type I persister formation in E. coli.
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Affiliation(s)
- Sandra J Aedo
- Department of Chemical and Biological Engineering, Princeton University, Hoyt Laboratory, 25 William Street, Princeton, NJ, 08544, USA
| | - Mehmet A Orman
- Department of Chemical and Biological Engineering, Princeton University, Hoyt Laboratory, 25 William Street, Princeton, NJ, 08544, USA.,Present Address: Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Hoyt Laboratory, 25 William Street, Princeton, NJ, 08544, USA.
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Piili J, Marenduzzo D, Kaski K, Linna RP. Sedimentation of knotted polymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:012728. [PMID: 23410380 DOI: 10.1103/physreve.87.012728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/20/2012] [Indexed: 06/01/2023]
Abstract
We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n(c) of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov et al. [J. Mol. Biol. 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration R(g)(-1), more specifically with the inverse of the R(g) component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, R(g)(-1) remains to a good precision linearly dependent on n(c). Therefore, R(g)(-1) is a good measure of a knot's complexity.
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Affiliation(s)
- J Piili
- Department of Biomedical Engineering and Computational Science, Aalto University, P.O. Box 12200, FI-00076 Aalto, Finland
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8
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Portillo J, Diao Y, Scharein R, Arsuaga J, Vazquez M. On the mean and variance of the writhe of random polygons. JOURNAL OF PHYSICS. A, MATHEMATICAL AND THEORETICAL 2011; 44:275004. [PMID: 25685182 PMCID: PMC4324762 DOI: 10.1088/1751-8113/44/27/275004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We here address two problems concerning the writhe of random polygons. First, we study the behavior of the mean writhe as a function length. Second, we study the variance of the writhe. Suppose that we are dealing with a set of random polygons with the same length and knot type, which could be the model of some circular DNA with the same topological property. In general, a simple way of detecting chirality of this knot type is to compute the mean writhe of the polygons; if the mean writhe is non-zero then the knot is chiral. How accurate is this method? For example, if for a specific knot type K the mean writhe decreased to zero as the length of the polygons increased, then this method would be limited in the case of long polygons. Furthermore, we conjecture that the sign of the mean writhe is a topological invariant of chiral knots. This sign appears to be the same as that of an "ideal" conformation of the knot. We provide numerical evidence to support these claims, and we propose a new nomenclature of knots based on the sign of their expected writhes. This nomenclature can be of particular interest to applied scientists. The second part of our study focuses on the variance of the writhe, a problem that has not received much attention in the past. In this case, we focused on the equilateral random polygons. We give numerical as well as analytical evidence to show that the variance of the writhe of equilateral random polygons (of length n) behaves as a linear function of the length of the equilateral random polygon.
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Affiliation(s)
- J Portillo
- Department of Mathematics, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132
| | - Y Diao
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - R Scharein
- Department of Mathematics, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132
| | - J Arsuaga
- Department of Mathematics, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132
| | - M Vazquez
- Department of Mathematics, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132
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9
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Vetcher AA, McEwen AE, Abujarour R, Hanke A, Levene SD. Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity. Biophys Chem 2010; 148:104-11. [PMID: 20346570 PMCID: PMC2867096 DOI: 10.1016/j.bpc.2010.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 02/25/2010] [Accepted: 02/26/2010] [Indexed: 11/15/2022]
Abstract
Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk (but different values of the excess linking number, DeltaLk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution.
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Affiliation(s)
- Alexandre A. Vetcher
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Abbye E. McEwen
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Ramzey Abujarour
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Andreas Hanke
- Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, TX 78520 USA
| | - Stephen D. Levene
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
- Department of Physics, University of Texas at Dallas, Richardson, TX 75083 USA
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