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Kaguni JM. The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery. Antibiotics (Basel) 2018. [PMID: 29538288 PMCID: PMC5872134 DOI: 10.3390/antibiotics7010023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
DNA replication is an essential process. Although the fundamental strategies to duplicate chromosomes are similar in all free-living organisms, the enzymes of the three domains of life that perform similar functions in DNA replication differ in amino acid sequence and their three-dimensional structures. Moreover, the respective proteins generally utilize different enzymatic mechanisms. Hence, the replication proteins that are highly conserved among bacterial species are attractive targets to develop novel antibiotics as the compounds are unlikely to demonstrate off-target effects. For those proteins that differ among bacteria, compounds that are species-specific may be found. Escherichia coli has been developed as a model system to study DNA replication, serving as a benchmark for comparison. This review summarizes the functions of individual E. coli proteins, and the compounds that inhibit them.
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Affiliation(s)
- Jon M Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA.
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2
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Hood IV, Berger JM. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication. eLife 2016; 5. [PMID: 27244442 PMCID: PMC4887207 DOI: 10.7554/elife.14158] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/20/2016] [Indexed: 12/18/2022] Open
Abstract
Replisome assembly requires the loading of replicative hexameric helicases onto origins by AAA+ ATPases. How loader activity is appropriately controlled remains unclear. Here, we use structural and biochemical analyses to establish how an antimicrobial phage protein interferes with the function of the Staphylococcus aureus replicative helicase loader, DnaI. The viral protein binds to the loader’s AAA+ ATPase domain, allowing binding of the host replicative helicase but impeding loader self-assembly and ATPase activity. Close inspection of the complex highlights an unexpected locus for the binding of an interdomain linker element in DnaI/DnaC-family proteins. We find that the inhibitor protein is genetically coupled to a phage-encoded homolog of the bacterial helicase loader, which we show binds to the host helicase but not to the inhibitor itself. These findings establish a new approach by which viruses can hijack host replication processes and explain how loader activity is internally regulated to prevent aberrant auto-association. DOI:http://dx.doi.org/10.7554/eLife.14158.001 Cells must copy their DNA in order to grow and divide. DNA replication begins when a small region of the DNA double helix is unwound to expose single strands of DNA. A protein called a helicase is then shepherded onto the unwound DNA regions by other proteins known as loaders. Once loaded, the helicase can unwind long stretches of the chromosome in which the DNA is packaged, producing the template required by the replication machinery to duplicate the DNA. This process must be accurately executed to avoid generating errors that could damage the DNA and potentially cause cells to die. DnaI is a helicase loader protein that is found in some types of bacteria. In the disease-causing bacterial species Staphylococcus aureus (S. aureus), an inhibitor protein from a virus that infects the bacteria can interact with DnaI and halt S. aureus DNA replication, leading to cell death. However, it has not been understood how this viral protein controls the activity of the loader molecules. DnaI consists of three regions: one that binds to the helicase, a short 'linker' region, and a third element that harnesses chemical energy (in the form of a small high-energy molecule called ATP) to drive the loader’s activity. Using biochemical and structural techniques, Hood and Berger now show that the viral inhibitor protein interacts with the DnaI loader from S. aureus by binding to the loader's ATP-binding region. When the two proteins are bound together, the loader can still bind to its target helicase but it cannot interact with other loader molecules. This defect prevents the loaders from self-assembling into a structure that is required for them to load the replicative helicase. Hood and Berger also found that the region of DnaI targeted by the inhibitor is important for normally ensuring that the loader molecules self-assemble at the correct place and time. A second unexpected discovery was that the virus encodes its own helicase loader, which binds to the bacterial helicase but not to the viral inhibitor protein. The next stage of work will be to determine whether the regions on the helicase loader that are targeted by the inhibitor and that are important for regulating self-assembly can be selectively disrupted by small molecules to interfere with DNA replication in bacteria. DOI:http://dx.doi.org/10.7554/eLife.14158.002
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Affiliation(s)
- Iris V Hood
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
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3
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Abstract
The initiation of chromosomal DNA replication starts at a replication origin, which in bacteria is a discrete locus that contains DNA sequence motifs recognized by an initiator protein whose role is to assemble the replication fork machinery at this site. In bacteria with a single chromosome, DnaA is the initiator and is highly conserved in all bacteria. As an adenine nucleotide binding protein, DnaA bound to ATP is active in the assembly of a DnaA oligomer onto these sites. Other proteins modulate DnaA oligomerization via their interaction with the N-terminal region of DnaA. Following the DnaA-dependent unwinding of an AT-rich region within the replication origin, DnaA then mediates the binding of DnaB, the replicative DNA helicase, in a complex with DnaC to form an intermediate named the prepriming complex. In the formation of this intermediate, the helicase is loaded onto the unwound region within the replication origin. As DnaC bound to DnaB inhibits its activity as a DNA helicase, DnaC must dissociate to activate DnaB. Apparently, the interaction of DnaB with primase (DnaG) and primer formation leads to the release of DnaC from DnaB, which is coordinated with or followed by translocation of DnaB to the junction of the replication fork. There, DnaB is able to coordinate its activity as a DNA helicase with the cellular replicase, DNA polymerase III holoenzyme, which uses the primers made by primase for leading strand DNA synthesis.
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Affiliation(s)
- S Chodavarapu
- Michigan State University, East Lansing, MI, United States
| | - J M Kaguni
- Michigan State University, East Lansing, MI, United States.
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Felczak MM, Sage JM, Hupert-Kocurek K, Aykul S, Kaguni JM. Substitutions of Conserved Residues in the C-terminal Region of DnaC Cause Thermolability in Helicase Loading. J Biol Chem 2016; 291:4803-12. [PMID: 26728455 DOI: 10.1074/jbc.m115.708586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Indexed: 11/06/2022] Open
Abstract
The DnaB-DnaC complex binds to the unwound DNA within the Escherichia coli replication origin in the helicase loading process, but the biochemical events that lead to its stable binding are uncertain. This study characterizes the function of specific C-terminal residues of DnaC. Genetic and biochemical characterization of proteins bearing F231S and W233L substitutions of DnaC reveals that their activity is thermolabile. Because the mutants remain able to form a complex with DnaB at 30 and 37 °C, their thermolability is not explained by an impaired interaction with DnaB. Photo-cross-linking experiments and biosensor analysis show an altered affinity of these mutants compared with wild type DnaC for single-stranded DNA, suggesting that the substitutions affect DNA binding. Despite this difference, their activity in DNA binding is not thermolabile. The substitutions also drastically reduce the affinity of DnaC for ATP as measured by the binding of a fluorescent ATP analogue (MANT-ATP) and by UV cross-linking of radiolabeled ATP. Experiments show that an elevated temperature substantially inhibits both mutants in their ability to load the DnaB-DnaC complex at a DnaA box. Because a decreased ATP concentration exacerbates their thermolabile behavior, we suggest that the F231S and W233L substitutions are thermolabile in ATP binding, which correlates with defective helicase loading at an elevated temperature.
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Affiliation(s)
- Magdalena M Felczak
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Jay M Sage
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Katarzyna Hupert-Kocurek
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Senem Aykul
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Jon M Kaguni
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
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5
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Chodavarapu S, Jones AD, Feig M, Kaguni JM. DnaC traps DnaB as an open ring and remodels the domain that binds primase. Nucleic Acids Res 2015; 44:210-20. [PMID: 26420830 PMCID: PMC4705694 DOI: 10.1093/nar/gkv961] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/11/2015] [Indexed: 11/23/2022] Open
Abstract
Helicase loading at a DNA replication origin often requires the dynamic interactions between the DNA helicase and an accessory protein. In E. coli, the DNA helicase is DnaB and DnaC is its loading partner. We used the method of hydrogen/deuterium exchange mass spectrometry to address the importance of DnaB–DnaC complex formation as a prerequisite for helicase loading. Our results show that the DnaB ring opens and closes, and that specific amino acids near the N-terminus of DnaC interact with a site in DnaB's C-terminal domain to trap it as an open ring. This event correlates with conformational changes of the RecA fold of DnaB that is involved in nucleotide binding, and of the AAA+ domain of DnaC. DnaC also causes an alteration of the helical hairpins in the N-terminal domain of DnaB, presumably occluding this region from interacting with primase. Hence, DnaC controls the access of DnaB by primase.
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Affiliation(s)
- Sundari Chodavarapu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA Department of Chemistry, Michigan State University, East Lansing, MI 48824-1319, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA Department of Chemistry, Michigan State University, East Lansing, MI 48824-1319, USA
| | - Jon M Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
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6
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Bell SP, Kaguni JM. Helicase loading at chromosomal origins of replication. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a010124. [PMID: 23613349 DOI: 10.1101/cshperspect.a010124] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Loading of the replicative DNA helicase at origins of replication is of central importance in DNA replication. As the first of the replication fork proteins assemble at chromosomal origins of replication, the loaded helicase is required for the recruitment of the rest of the replication machinery. In this work, we review the current knowledge of helicase loading at Escherichia coli and eukaryotic origins of replication. In each case, this process requires both an origin recognition protein as well as one or more additional proteins. Comparison of these events shows intriguing similarities that suggest a similar underlying mechanism, as well as critical differences that likely reflect the distinct processes that regulate helicase loading in bacterial and eukaryotic cells.
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Affiliation(s)
- Stephen P Bell
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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7
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Arias-Palomo E, O'Shea VL, Hood IV, Berger JM. The bacterial DnaC helicase loader is a DnaB ring breaker. Cell 2013; 153:438-48. [PMID: 23562643 DOI: 10.1016/j.cell.2013.03.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/03/2012] [Accepted: 03/01/2013] [Indexed: 11/26/2022]
Abstract
Dedicated AAA+ ATPases deposit hexameric ring-shaped helicases onto DNA to promote replication in cellular organisms. To understand how loading occurs, we used electron microscopy and small angle X-ray scattering (SAXS) to determine the ATP-bound structure of the intact E. coli DnaB⋅DnaC helicase/loader complex. The 480 kDa dodecamer forms a three-tiered assembly, in which DnaC adopts a spiral configuration that remodels N-terminal scaffolding and C-terminal motor regions of DnaB to produce a clear break in the helicase ring. Surprisingly, DnaC's AAA+ fold is dispensable for ring remodeling because the DnaC isolated helicase-binding domain can both load DnaB onto DNA and increase the efficiency by which the helicase acts on substrates in vitro. Our data demonstrate that DnaC opens DnaB by a mechanism akin to that of polymerase clamp loaders and indicate that bacterial replicative helicases, like their eukaryotic counterparts, possess autoregulatory elements that influence how hexameric motor domains are loaded onto and unwind DNA.
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Affiliation(s)
- Ernesto Arias-Palomo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
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8
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Abstract
The initiation of DNA replication represents a committing step to cell proliferation. Appropriate replication onset depends on multiprotein complexes that help properly distinguish origin regions, generate nascent replication bubbles, and promote replisome formation. This review describes initiation systems employed by bacteria, archaea, and eukaryotes, with a focus on comparing and contrasting molecular mechanisms among organisms. Although commonalities can be found in the functional domains and strategies used to carry out and regulate initiation, many key participants have markedly different activities and appear to have evolved convergently. Despite significant advances in the field, major questions still persist in understanding how initiation programs are executed at the molecular level.
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Affiliation(s)
- Alessandro Costa
- Clare Hall Laboratories, London Research Institute, Cancer Research UK, Hertfordshire, EN6 3LD United Kingdom
| | - Iris V. Hood
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - James M. Berger
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
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9
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Replication initiation at the Escherichia coli chromosomal origin. Curr Opin Chem Biol 2011; 15:606-13. [PMID: 21856207 DOI: 10.1016/j.cbpa.2011.07.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/20/2011] [Accepted: 07/22/2011] [Indexed: 11/24/2022]
Abstract
To initiate DNA replication, DnaA recognizes and binds to specific sequences within the Escherichia coli chromosomal origin (oriC), and then unwinds a region within oriC. Next, DnaA interacts with DnaB helicase in loading the DnaB-DnaC complex on each separated strand. Primer formation by primase (DnaG) induces the dissociation of DnaC from DnaB, which involves the hydrolysis of ATP bound to DnaC. Recent evidence indicates that DnaC acts as a checkpoint in the transition from initiation to the elongation stage of DNA replication. Freed from DnaC, DnaB helicase unwinds the parental duplex DNA while interacting the cellular replicase, DNA polymerase III holoenzyme, and primase as it intermittently forms primers that are extended by the replicase in duplicating the chromosome.
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10
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Pérez Audero ME, Podoroska BM, Ibáñez MM, Cauerhff A, Checa SK, Soncini FC. Target transcription binding sites differentiate two groups of MerR-monovalent metal ion sensors. Mol Microbiol 2010; 78:853-65. [PMID: 20807206 DOI: 10.1111/j.1365-2958.2010.07370.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The evolution of bacterial regulatory circuits often involves duplication of genes encoding transcription factors that may suffer both modifications in their detected signals, as well as, rewiring of their target operators. This, and subsequent horizontal gene transfer events contribute to generate a diverse array of regulatory pathways. In Salmonella, two homologous transcription factors CueR and GolS are responsible for Cu and Au sensing and resistance respectively. They share similarities not only in their sequence but also in their target binding sites, although they cluster separately among MerR-monovalent metal sensors. Here, we demonstrate that CueR and GolS can selectively distinguish their target binding sites by recognizing bases at positions 3' and 3 of their cognate operators. Swap of these bases results in switching regulator dependency. The differences in promoter architecture plus the environmentally controlled regulator's cytoplasmic availability warrant intra-regulon regulator-operator selectivity, and the proper response to metal injury. Furthermore, the presence of the distinctive operators' bases is widely extended among the two groups of MerR-monovalent metal sensors, providing evidence of the co-evolution of these factors and their target operators. This approach allows the prediction of regulator's dependency and the identification of transcription modules among groups of homologous transcription factors.
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Affiliation(s)
- María E Pérez Audero
- Instituto de Biología Molecular, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Suipacha 531, S2002LRK-Rosario, Argentina
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11
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Makowska-Grzyska M, Kaguni JM. Primase directs the release of DnaC from DnaB. Mol Cell 2010; 37:90-101. [PMID: 20129058 DOI: 10.1016/j.molcel.2009.12.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 09/03/2009] [Accepted: 12/18/2009] [Indexed: 10/20/2022]
Abstract
An AAA+ ATPase, DnaC, delivers DnaB helicase at the E. coli chromosomal origin by a poorly understood process. This report shows that mutant proteins bearing alanine substitutions for two conserved arginines in a motif named box VII are defective in DNA replication, but this deficiency does not arise from impaired interactions with ATP, DnaB, or single-stranded DNA. Despite their ability to deliver DnaB to the chromosomal origin to form the prepriming complex, this intermediate is inactive. Quantitative analysis of the prepriming complex suggests that the DnaB-DnaC complex contains three DnaC monomers per DnaB hexamer and that the interaction of primase with DnaB and primer formation triggers the release of DnaC, but not the mutants, from DnaB. The interaction of primase with DnaB and the release of DnaC mark discrete events in the transition from initiation to the elongation stage of DNA replication.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
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12
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Gupta MK, Atkinson J, McGlynn P. DNA structure specificity conferred on a replicative helicase by its loader. J Biol Chem 2009; 285:979-87. [PMID: 19880515 DOI: 10.1074/jbc.m109.072520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prokaryotic and eukaryotic replicative helicases can translocate along single-stranded and double-stranded DNA, with the central cavity of these multimeric ring helicases being able to accommodate both forms of DNA. Translocation by such helicases along single-stranded DNA results in the unwinding of forked DNA by steric exclusion and appears critical in unwinding of parental strands at the replication fork, whereas translocation over double-stranded DNA has no well-defined role. We have found that the accessory factor, DnaC, that promotes loading of the Escherichia coli replicative helicase DnaB onto single-stranded DNA may also act to confer DNA structure specificity on DnaB helicase. When present in excess, DnaC inhibits DnaB translocation over double-stranded DNA but not over single-stranded DNA. Inhibition of DnaB translocation over double-stranded DNA requires the ATP-bound form of DnaC, and this inhibition is relieved during translocation over single-stranded DNA indicating that stimulation of DnaC ATPase is responsible for this DNA structure specificity. These findings demonstrate that DnaC may provide the DNA structure specificity lacking in DnaB, limiting DnaB translocation to bona fide replication forks. The ability of other replicative helicases to translocate along single-stranded and double-stranded DNA raises the possibility that analogous regulatory mechanisms exist in other organisms.
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Affiliation(s)
- Milind K Gupta
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
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13
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Tsai KL, Lo YH, Sun YJ, Hsiao CD. Molecular interplay between the replicative helicase DnaC and its loader protein DnaI from Geobacillus kaustophilus. J Mol Biol 2009; 393:1056-69. [PMID: 19744498 DOI: 10.1016/j.jmb.2009.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 09/02/2009] [Accepted: 09/03/2009] [Indexed: 10/20/2022]
Abstract
Helicase loading factors are thought to transfer the hexameric ring-shaped helicases onto the replication fork during DNA replication. However, the mechanism of helicase transfer onto DNA remains unclear. In Bacillus subtilis, the protein DnaI, which belongs to the AAA+ family of ATPases, is responsible for delivering the hexameric helicase DnaC onto DNA. Here we investigated the interaction between DnaC and DnaI from Geobacillus kaustophilus HTA426 (GkDnaC and GkDnaI, respectively) and determined that GkDnaI forms a stable complex with GkDnaC with an apparent stoichiometry of GkDnaC(6)-GkDnaI(6) in the absence of ATP. Surface plasmon resonance analysis indicated that GkDnaI facilitates loading of GkDnaC onto single-stranded DNA (ssDNA) and supports complex formation with ssDNA in the presence of ATP. Additionally, the GkDnaI C-terminal AAA+ domain alone could bind ssDNA, and binding was modulated by nucleotides. We also determined the crystal structure of the C-terminal AAA+ domain of GkDnaI in complex with ADP at 2.5 A resolution. The structure not only delineates the binding of ADP in the expected Walker A and B motifs but also reveals a positively charged region that may be involved in ssDNA binding. These findings provide insight into the mechanism of replicative helicase loading onto ssDNA.
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Affiliation(s)
- Kuang-Lei Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, ROC
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14
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Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell 2008; 135:623-34. [PMID: 19013274 DOI: 10.1016/j.cell.2008.09.058] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/18/2008] [Accepted: 09/26/2008] [Indexed: 11/23/2022]
Abstract
The loading of oligomeric helicases onto replication origins marks an essential step in replisome assembly. In cells, dedicated AAA+ ATPases regulate loading, however, the mechanism by which these factors recruit and deposit helicases has remained unclear. To better understand this process, we determined the structure of the ATPase region of the bacterial helicase loader DnaC from Aquifex aeolicus to 2.7 A resolution. The structure shows that DnaC is a close paralog of the bacterial replication initiator, DnaA, and unexpectedly shares an ability to form a helical assembly similar to that of ATP-bound DnaA. Complementation and ssDNA-binding assays validate the importance of homomeric DnaC interactions, while pull-down experiments show that the DnaC and DnaA AAA+ domains interact in a nucleotide-dependent manner. These findings implicate DnaC as a molecular adaptor that uses ATP-activated DnaA as a docking site for regulating the recruitment and correct spatial deposition of the DnaB helicase onto origins.
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15
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Hupert-Kocurek K, Sage JM, Makowska-Grzyska M, Kaguni JM. Genetic method to analyze essential genes of Escherichia coli. Appl Environ Microbiol 2007; 73:7075-82. [PMID: 17873068 PMCID: PMC2074942 DOI: 10.1128/aem.01756-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic analysis of essential genes has been generally restricted to the use of conditional mutations, or inactivating chromosomal mutations, which require a complementing plasmid that must either be counterselected or lost to measure a phenotype. These approaches are limited because they do not permit the analysis of mutations suspected to affect a specific function of a protein, nor do they take advantage of the increasing abundance of structural and bioinformatics data for proteins. Using the dnaC gene as an example, we developed a genetic method that should permit the mutational analysis of other essential genes of Escherichia coli and related enterobacteria. The method consists of using a strain carrying a large deletion of the dnaC gene, which is complemented by a wild-type copy expressed from a plasmid that requires isopropyl-beta-d-thiogalactopyranoside for maintenance. Under conditions in which this resident plasmid is lost, the method measures the function of a dnaC mutation encoded by a second plasmid. This methodology should be widely applicable to the genetic analysis of other essential genes.
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Affiliation(s)
- Katarzyna Hupert-Kocurek
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
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16
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Biswas SB, Biswas-Fiss EE. Quantitative analysis of binding of single-stranded DNA by Escherichia coli DnaB helicase and the DnaB x DnaC complex. Biochemistry 2006; 45:11505-13. [PMID: 16981710 DOI: 10.1021/bi060118d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DnaB helicase is responsible for unwinding duplex DNA during chromosomal DNA replication and is an essential component of the DNA replication apparatus in Escherichia coli. We have analyzed the mechanism of binding of single-stranded DNA (ssDNA) by the DnaB x DnaC complex and DnaB helicase. Binding of ssDNA to DnaB helicase was significantly modulated by nucleotide cofactors, and the modulation was distinctly different for its complex with DnaC. DnaB helicase bound ssDNA with a high affinity [Kd = (5.09 +/- 0.32) x 10(-8) M] only in the presence of ATPgammaS, a nonhydrolyzable analogue of ATP, but not other nucleotides. The binding was sensitive to ionic strength but not to changes in temperature in the range of 30-37 degrees C. On the other hand, ssDNA binding in the presence of ADP was weaker than that observed with ATPgammaS, and the binding was insensitive to ionic strength. DnaC protein hexamerizes to form a 1:1 complex with the DnaB hexamer and loads it onto the ssDNA by forming a DnaB6 x DnaC6 dodecameric complex. Our results demonstrate that the DnaB6 x DnaC6 complex bound ssDNA with a high affinity [Kd = (6.26 +/- 0.65) x 10(-8) M] in the presence of ATP, unlike the DnaB hexamer. In the presence of ATPgammaS or ADP, binding of ssDNA by the DnaB6 x DnaC6 complex was a lower-affinity process. In summary, our results suggest that in the presence of ATP in vivo, the DnaB6 x DnaC6 complex should be more efficient in binding DNA as well as in loading DnaB onto the ssDNA than DnaB helicase itself.
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Affiliation(s)
- Subhasis B Biswas
- Department of Molecular Biology, School of Medicine and Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Stratford, New Jersey 08084, USA.
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17
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Abstract
The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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