1
|
Toft CJ, Sorenson AE, Schaeffer PM. A soft Tus-Ter interaction is hiding a fail-safe lock in the replication fork trap of Dickeya paradisiaca. Microbiol Res 2022; 263:127147. [PMID: 35914414 DOI: 10.1016/j.micres.2022.127147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022]
Abstract
A variety of replication fork traps have recently been characterised in Enterobacterales, unveiling two different types of architecture. Of these, the degenerate type II fork traps are commonly found in Enterobacteriaceae such as Escherichia coli. The newly characterised type I fork traps are found almost exclusively outside Enterobacteriaceae within Enterobacterales and include several archetypes of possible ancestral architectures. Dickeya paradisiaca harbours a somewhat degenerate type I fork trap with a unique Ter1 adjacent to tus gene on one side of the circular chromosome and three putative Ter2-4 sites on the other side of the fork trap. The two innermost Ter1 and Ter2 sites are only separated by 18 kb, which is the shortest distance between two innermost Ter sites of any chromosomal fork trap identified so far. Of note, the dif site is located between these two sites, coinciding with a sharp GC-skew flip. Here we examined and compared the binding modalities of E. coli and D. paradisiaca Tus proteins for these Ter sites. Surprisingly, while Ter1-3 were functional, no significant Tus binding was observed for Ter4 even in low salt conditions, which is in stark contrast with the significant non-specific protein-DNA interactions that occur with E. coli Tus. Even more surprising was the finding that D. paradisiaca Tus has a relatively moderate binding affinity to double-stranded Ter while retaining an extremely high affinity to Ter-lock sequences. Our data revealed major differences in the salt resistance and stability between the D. paradisiaca and E. coli Tus protein complexes, suggesting that while Tus protein evolution can be quite flexible regarding the initial Ter binding step, it requires a highly stringent purifying selection for its final locked complex formation.
Collapse
Affiliation(s)
- Casey J Toft
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Alanna E Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Patrick M Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia.
| |
Collapse
|
2
|
Berghuis BA, Raducanu VS, Elshenawy MM, Jergic S, Depken M, Dixon NE, Hamdan SM, Dekker NH. What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments. Crit Rev Biochem Mol Biol 2017; 53:49-63. [DOI: 10.1080/10409238.2017.1394264] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bojk A. Berghuis
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Vlad-Stefan Raducanu
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohamed M. Elshenawy
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Martin Depken
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nicholas E. Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Samir M. Hamdan
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nynke H. Dekker
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
3
|
Moolman MC, Tiruvadi Krishnan S, Kerssemakers JWJ, de Leeuw R, Lorent V, Sherratt DJ, Dekker NH. The progression of replication forks at natural replication barriers in live bacteria. Nucleic Acids Res 2016; 44:6262-73. [PMID: 27166373 PMCID: PMC5291258 DOI: 10.1093/nar/gkw397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 01/07/2023] Open
Abstract
Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus-ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus-ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus-ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression.
Collapse
Affiliation(s)
- M Charl Moolman
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Sriram Tiruvadi Krishnan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Roy de Leeuw
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Vincent Lorent
- Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, CNRS, (UMR 7538), F-93430 Villetaneuse, France
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| |
Collapse
|
4
|
Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM. Replisome speed determines the efficiency of the Tus−Ter replication termination barrier. Nature 2015; 525:394-8. [DOI: 10.1038/nature14866] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/26/2015] [Indexed: 11/09/2022]
|
5
|
Berghuis BA, Dulin D, Xu ZQ, van Laar T, Cross B, Janissen R, Jergic S, Dixon NE, Depken M, Dekker NH. Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier. Nat Chem Biol 2015; 11:579-85. [PMID: 26147356 DOI: 10.1038/nchembio.1857] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 05/20/2015] [Indexed: 01/30/2023]
Abstract
The bidirectional replication of a circular chromosome by many bacteria necessitates proper termination to avoid the head-on collision of the opposing replisomes. In Escherichia coli, replisome progression beyond the termination site is prevented by Tus proteins bound to asymmetric Ter sites. Structural evidence indicates that strand separation on the blocking (nonpermissive) side of Tus-Ter triggers roadblock formation, but biochemical evidence also suggests roles for protein-protein interactions. Here DNA unzipping experiments demonstrate that nonpermissively oriented Tus-Ter forms a tight lock in the absence of replicative proteins, whereas permissively oriented Tus-Ter allows nearly unhindered strand separation. Quantifying the lock strength reveals the existence of several intermediate lock states that are impacted by mutations in the lock domain but not by mutations in the DNA-binding domain. Lock formation is highly specific and exceeds reported in vivo efficiencies. We postulate that protein-protein interactions may actually hinder, rather than promote, proper lock formation.
Collapse
Affiliation(s)
- Bojk A Berghuis
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Zhi-Qiang Xu
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Bronwen Cross
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
6
|
Askin SP, Morin I, Schaeffer PM. Development of a protease activity assay using heat-sensitive Tus-GFP fusion protein substrates. Anal Biochem 2011; 415:126-33. [PMID: 21570945 DOI: 10.1016/j.ab.2011.04.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 04/19/2011] [Accepted: 04/19/2011] [Indexed: 11/28/2022]
Abstract
Proteases are implicated in various diseases and several have been identified as potential drug targets or biomarkers. As a result, protease activity assays that can be performed in high throughput are essential for the screening of inhibitors in drug discovery programs. Here we describe the development of a simple, general method for the characterization of protease activity and its use for inhibitor screening. GFP was genetically fused to a comparatively unstable Tus protein through an interdomain linker containing a specially designed protease site, which can be proteolyzed. When this Tus-GFP fusion protein substrate is proteolyzed it releases GFP, which remains in solution after a short heat denaturation and centrifugation step used to eliminate uncleaved Tus-GFP. Thus, the increase in GFP fluorescence is directly proportional to protease activity. We validated the protease activity assay with three different proteases, i.e., trypsin, caspase 3, and neutrophil elastase, and demonstrated that it can be used to determine protease activity and the effect of inhibitors with small sample volumes in just a few simple steps using a fluorescence plate reader.
Collapse
Affiliation(s)
- Samuel P Askin
- Comparative Genomics Centre, School of Pharmacy and Molecular Sciences, James Cook University, DB 21, James Cook Drive, Townsville, QLD 4811, Australia
| | | | | |
Collapse
|
7
|
Nitharwal RG, Verma V, Dasgupta S, Dhar SK. Helicobacter pylori chromosomal DNA replication: current status and future perspectives. FEBS Lett 2010; 585:7-17. [PMID: 21093441 DOI: 10.1016/j.febslet.2010.11.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/03/2010] [Accepted: 11/12/2010] [Indexed: 11/30/2022]
Abstract
Helicobacter pylori causes gastritis, gastric ulcer and gastric cancer. Though DNA replication and its control are central to bacterial proliferation, pathogenesis, virulence and/or dormancy, our knowledge of DNA synthesis in slow growing pathogenic bacteria like H. pylori is still preliminary. Here, we review the current understanding of DNA replication, replication restart and recombinational repair in H. pylori. Several differences have been identified between the H. pylori and Escherichia coli replication machineries including the absence of DnaC, the helicase loader usually conserved in gram-negative bacteria. These differences suggest different mechanisms of DNA replication at initiation and restart of stalled forks in H. pylori.
Collapse
Affiliation(s)
- Ram Gopal Nitharwal
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | | | | | | |
Collapse
|
8
|
Abstract
The Tus-Ter protein-DNA complex of Escherichia coli blocks progression of DNA replication from only one direction at the replication terminus. As the replication fork helicase unwinds one side of Ter, a conserved cytosine flips out of the duplex and binds to Tus, thereby creating a locked complex that blocks the advancing helicase.
Collapse
Affiliation(s)
- Daniel L Kaplan
- Vanderbilt University, Department of Biological Sciences, VU Station B, Box 35-1634, Nashville, Tennessee 37235, USA.
| |
Collapse
|
9
|
Mulcair MD, Schaeffer PM, Oakley AJ, Cross HF, Neylon C, Hill TM, Dixon NE. A molecular mousetrap determines polarity of termination of DNA replication in E. coli. Cell 2006; 125:1309-19. [PMID: 16814717 DOI: 10.1016/j.cell.2006.04.040] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 03/16/2006] [Accepted: 04/26/2006] [Indexed: 11/24/2022]
Abstract
During chromosome synthesis in Escherichia coli, replication forks are blocked by Tus bound Ter sites on approach from one direction but not the other. To study the basis of this polarity, we measured the rates of dissociation of Tus from forked TerB oligonucleotides, such as would be produced by the replicative DnaB helicase at both the fork-blocking (nonpermissive) and permissive ends of the Ter site. Strand separation of a few nucleotides at the permissive end was sufficient to force rapid dissociation of Tus to allow fork progression. In contrast, strand separation extending to and including the strictly conserved G-C(6) base pair at the nonpermissive end led to formation of a stable locked complex. Lock formation specifically requires the cytosine residue, C(6). The crystal structure of the locked complex showed that C(6) moves 14 A from its normal position to bind in a cytosine-specific pocket on the surface of Tus.
Collapse
Affiliation(s)
- Mark D Mulcair
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | | | | | | | | | | | | |
Collapse
|
10
|
Neylon C, Kralicek AV, Hill TM, Dixon NE. Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex. Microbiol Mol Biol Rev 2005; 69:501-26. [PMID: 16148308 PMCID: PMC1197808 DOI: 10.1128/mmbr.69.3.501-526.2005] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The arrest of DNA replication in Escherichia coli is triggered by the encounter of a replisome with a Tus protein-Ter DNA complex. A replication fork can pass through a Tus-Ter complex when traveling in one direction but not the other, and the chromosomal Ter sites are oriented so replication forks can enter, but not exit, the terminus region. The Tus-Ter complex acts by blocking the action of the replicative DnaB helicase, but details of the mechanism are uncertain. One proposed mechanism involves a specific interaction between Tus-Ter and the helicase that prevents further DNA unwinding, while another is that the Tus-Ter complex itself is sufficient to block the helicase in a polar manner, without the need for specific protein-protein interactions. This review integrates three decades of experimental information on the action of the Tus-Ter complex with information available from the Tus-TerA crystal structure. We conclude that while it is possible to explain polar fork arrest by a mechanism involving only the Tus-Ter interaction, there are also strong indications of a role for specific Tus-DnaB interactions. The evidence suggests, therefore, that the termination system is more subtle and complex than may have been assumed. We describe some further experiments and insights that may assist in unraveling the details of this fascinating process.
Collapse
Affiliation(s)
- Cameron Neylon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.
| | | | | | | |
Collapse
|
11
|
Kapur A, Beck JL, Brown SE, Dixon NE, Sheil MM. Use of electrospray ionization mass spectrometry to study binding interactions between a replication terminator protein and DNA. Protein Sci 2002; 11:147-57. [PMID: 11742131 PMCID: PMC2368767 DOI: 10.1110/ps.27702] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Tus protein binds tightly to specific DNA sequences (Ter) on the Escherichia coli chromosome halting replication. We report here conditions for detecting the 1 : 1 Tus-Ter complex by electrospray ionization mass spectrometry (ESI-MS). ESI mass spectra of a mixture of Tus and nonspecific DNA showed ions predominantly from uncomplexed Tus protein, indicating that the Tus-Ter complex observed in the gas phase was the result of a specific interaction rather than nonspecific associations in the ionization source. The Tus-Ter complex was very stable using a spray solvent of 10 mM ammonium acetate at pH 8.0, and initial attempts to distinguish binding affinities of Tus and mutant Tus proteins for Ter DNA were unsuccessful. Increasing the ammonium acetate concentration in the electrospray solvent (800 mM at pH 8.0) increased the dissociation constants sufficiently such that relative orders of binding affinity for Tus and various mutant Tus proteins for various DNA sequences could be determined. These were in agreement with the dissociation constants determined in solution studies. A dissociation constant of 700 x 10(-9) M for the binding of the mutant Tus protein A173T (where residue 173 is changed from alanine to threonine) to Ter DNA was estimated, compared with a value of <or=2 x 10(-9) M for Tus where A173 was unchanged. This is the first example in which ESI-MS has been used to compare binding affinities of a DNA-binding protein with mutant proteins for specific DNA recognition sequences. It was also possible to estimate the strength of the interaction between Tus and a DNA sequence (TerH) that had been identified by database searching.
Collapse
Affiliation(s)
- Amit Kapur
- Department of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | | | | | | | | |
Collapse
|
12
|
Coskun-Ari FF, Hill TM. Sequence-specific interactions in the Tus-Ter complex and the effect of base pair substitutions on arrest of DNA replication in Escherichia coli. J Biol Chem 1997; 272:26448-56. [PMID: 9334221 DOI: 10.1074/jbc.272.42.26448] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Arrest of DNA replication in Escherichia coli is mediated by specific interactions between the Tus protein and terminator (Ter) sequences. Binding of Tus to a Ter site forms a asymmetric protein-DNA complex that arrests DNA replication in an orientation-dependent fashion. In this study, mutant Ter sites carrying single base pair substitutions at 16 different positions were examined for their ability to bind purified Tus protein and arrest DNA replication. In vitro competition assays demonstrated that base pair substitutions at positions 8-19 had significant effects on the free energy of Tus binding (DeltaDeltaG0 of 1.5 to >4. 0 kcal/mol). Concomitant with loss of binding affinity, mutations at these positions also showed significantly lower or undetectable replication arrest activities in vivo. Substitutions at positions 6, 20, and 21 had moderate effects on Tus-Ter interactions, suggesting that these base pairs contribute to, but are not absolutely critical for, Tus binding. Even though the effects on binding were minimal, these Ter mutants were not as efficient as wild type Tus-TerB complexes at arresting replication forks. Three new potential Ter sites, referred to as TerH, TerI, and TerJ, were identified by searching the E. coli genome for sequence similarity to a consensus Ter site sequence.
Collapse
Affiliation(s)
- F F Coskun-Ari
- Department of Microbiology and Immunology, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9037, USA
| | | |
Collapse
|
13
|
|
14
|
Skokotas A, Hiasa H, Marians KJ, O'Donnell L, Hill TM. Mutations in the Escherichia coli Tus protein define a domain positioned close to the DNA in the Tus-Ter complex. J Biol Chem 1995; 270:30941-8. [PMID: 8537350 DOI: 10.1074/jbc.270.52.30941] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A new genetic screen for mutations in the tus gene of Escherichia coli has been devised that selects for Tus proteins with altered ability to arrest DNA replication. We report here the characterization of three such mutants: TusP42S, TusE49K, and TusH50Y. TusP42S and TusE49K arrest DNA replication in vivo at 36% of the efficiency of wild-type Tus, whereas TusH50Y functions at 78% efficiency. The loss of replication arrest activity did not correlate with changes in the stability of the Tus-TerB complexes formed by the mutant proteins. TusE49K formed a more stable protein-DNA complex than wild-type Tus (t1/2 of 178 versus 149 min, respectively) and TusP42 had a 9-min half-life, yet these two mutants showed identical efficiencies for replication arrest. When tested in vitro using a helicase assay or an oriC replication system, we observed a general, but imperfect, correlation between the in vivo and in vitro assays. Finally, the half-lives of the mutant protein-DNA complexes suggested that the domain of Tus where these mutations are located is positioned close to the DNA in the Tus-Ter complex.
Collapse
Affiliation(s)
- A Skokotas
- Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | |
Collapse
|
15
|
Duggan LJ, Hill TM, Wu S, Garrison K, Zhang X, Gottlieb PA. Using modified nucleotides to map the DNA determinants of the Tus-TerB complex, the protein-DNA interaction associated with termination of replication in Escherichia coli. J Biol Chem 1995; 270:28049-54. [PMID: 7499290 DOI: 10.1074/jbc.270.47.28049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A series of modified nucleotides was used to map the hydrogen-bonding and hydrophobic sites of the TerB DNA required for Tus interaction. Each of four consensus guanine residues in the TerB-binding site was replaced by 7-deazaguanine, 2-aminopurine, or inosine nucleobase analogues, and each thymine by a uracil analogue. The observable equilibrium dissociation constant for the Tus protein-TerB DNA complex was measured at pH 7.5, 25 degrees C, and 150 mM potassium glutamate using a competition binding method. Substitutions made at position 10 with a 7-deazaguanine, 2-aminopurine, or inosine analogue had a large effect on the stability of the complex, approximately +3 kcal/mol in each case. Substitutions made at positions 13 and 17 had a varied response. For uracil substitutions, potential hydrophobic sites were identified at six positions in the TerB DNA. The energetic penalty for the removal of a single methyl group ranged between +1 and +2 kcal/mol. Rate dissociation measurements agree with these results. Overall, major and minor groove determinants are required for binding. An unusual result was that the conserved nucleotide at position 6 did not significantly affect in vitro binding of the complex.
Collapse
Affiliation(s)
- L J Duggan
- Department of Chemistry and Biochemistry, University of Delaware, Newark 19716, USA
| | | | | | | | | | | |
Collapse
|
16
|
Skokotas A, Wrobleski M, Hill T. Isolation and characterization of mutants of Tus, the replication arrest protein of Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32013-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|