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The DnaE polymerase from Deinococcus radiodurans features RecA-dependent DNA polymerase activity. Biosci Rep 2016; 36:BSR20160364. [PMID: 27789781 PMCID: PMC5137535 DOI: 10.1042/bsr20160364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/25/2022] Open
Abstract
We report in the present study on the catalytic properties of Deinococcus radiodurans DnaE polymerase, whose DNA elongation efficiency was compared with the homologous Escherichia coli polymerase. Contrary to the latter, the deinococcal enzyme was found to be strictly dependent on RecA recombinase. We report in the present study on the catalytic properties of the Deinococcus radiodurans DNA polymerase III α subunit (αDr). The αDr enzyme was overexpressed in Escherichia coli, both in soluble form and as inclusion bodies. When purified from soluble protein extracts, αDr was found to be tightly associated with E. coli RNA polymerase, from which αDr could not be dissociated. On the contrary, when refolded from inclusion bodies, αDr was devoid of E. coli RNA polymerase and was purified to homogeneity. When assayed with different DNA substrates, αDr featured slower DNA extension rates when compared with the corresponding enzyme from E. coli (E. coli DNA Pol III, αEc), unless under high ionic strength conditions or in the presence of manganese. Further assays were performed using a ssDNA and a dsDNA, whose recombination yields a DNA substrate. Surprisingly, αDr was found to be incapable of recombination-dependent DNA polymerase activity, whereas αEc was competent in this action. However, in the presence of the RecA recombinase, αDr was able to efficiently extend the DNA substrate produced by recombination. Upon comparing the rates of RecA-dependent and RecA-independent DNA polymerase activities, we detected a significant activation of αDr by the recombinase. Conversely, the activity of αEc was found maximal under non-recombination conditions. Overall, our observations indicate a sharp contrast between the catalytic actions of αDr and αEc, with αDr more performing under recombination conditions, and αEc preferring DNA substrates whose extension does not require recombination events.
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Dohrmann PR, Correa R, Frisch RL, Rosenberg SM, McHenry CS. The DNA polymerase III holoenzyme contains γ and is not a trimeric polymerase. Nucleic Acids Res 2016; 44:1285-97. [PMID: 26786318 PMCID: PMC4756838 DOI: 10.1093/nar/gkv1510] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
There is widespread agreement that the clamp loader of the Escherichia coli replicase has the composition DnaX3δδ’χψ. Two DnaX proteins exist in E. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds DNA polymerase III tightly; γ does not. There is a controversy as to whether or not DNA polymerase III holoenzyme (Pol III HE) contains γ. A three-τ form of Pol III HE would contain three Pol IIIs. Proponents of the three-τ hypothesis have claimed that γ found in Pol III HE might be a proteolysis product of τ. To resolve this controversy, we constructed a strain that expressed only τ from a mutated chromosomal dnaX. γ containing a C-terminal biotinylation tag (γ-Ctag) was provided in trans at physiological levels from a plasmid. A 2000-fold purification of Pol III* (all Pol III HE subunits except β) from this strain contained one molecule of γ-Ctag per Pol III* assembly, indicating that the dominant form of Pol III* in cells is Pol III2τ2 γδδ’χψ. Revealing a role for γ in cells, mutants that express only τ display sensitivity to ultraviolet light and reduction in DNA Pol IV-dependent mutagenesis associated with double-strand-break repair, and impaired maintenance of an F’ episome.
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Affiliation(s)
- Paul R Dohrmann
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | - Raul Correa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan L Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
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Hochkoeppler A. Expanding the landscape of recombinant protein production in Escherichia coli. Biotechnol Lett 2013; 35:1971-81. [DOI: 10.1007/s10529-013-1396-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/26/2013] [Indexed: 12/11/2022]
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Karata K, Vaisman A, Goodman MF, Woodgate R. Simple and efficient purification of Escherichia coli DNA polymerase V: cofactor requirements for optimal activity and processivity in vitro. DNA Repair (Amst) 2012; 11:431-40. [PMID: 22341652 DOI: 10.1016/j.dnarep.2012.01.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 01/23/2012] [Indexed: 11/18/2022]
Abstract
Most damage induced mutagenesis in Escherichia coli is dependent upon the UmuD'(2)C protein complex, which comprises DNA polymerase V (pol V). Biochemical characterization of pol V has been hindered by the fact that the enzyme is notoriously difficult to purify, largely because overproduced UmuC is insoluble. Here, we report a simple and efficient protocol for the rapid purification of milligram quantities of pol V from just 4 L of bacterial culture. Rather than over producing the UmuC protein, it was expressed at low basal levels, while UmuD'(2)C was expressed in trans from a high copy-number plasmid with an inducible promoter. We have also developed strategies to purify the β-clamp and γ-clamp loader free from contaminating polymerases. Using these highly purified proteins, we determined the cofactor requirements for optimal activity of pol V in vitro and found that pol V shows robust activity on an SSB-coated circular DNA template in the presence of the β/γ-complex and a RecA nucleoprotein filament (RecA*) formed in trans. This strong activity was attributed to the unexpectedly high processivity of pol V Mut (UmuD'(2)C · RecA · ATP), which was efficiently recruited to a primer terminus by SSB.
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Affiliation(s)
- Kiyonobu Karata
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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Abstract
Bacterial replicases are complex, tripartite replicative machines. They contain a polymerase, polymerase III (Pol III), a β₂ processivity factor, and a DnaX complex ATPase that loads β₂ onto DNA and chaperones Pol III onto the newly loaded β₂. Bacterial replicases are highly processive, yet cycle rapidly during Okazaki fragment synthesis in a regulated way. Many bacteria encode both a full-length τ and a shorter γ form of DnaX by a variety of mechanisms. γ appears to be uniquely placed in a single position relative to two τ protomers in a pentameric ring. The polymerase catalytic subunit of Pol III, α, contains a PHP domain that not only binds to a prototypical ε Mg²⁺-dependent exonuclease, but also contains a second Zn²⁺-dependent proofreading exonuclease, at least in some bacteria. This review focuses on a critical evaluation of recent literature and concepts pertaining to the above issues and suggests specific areas that require further investigation.
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Affiliation(s)
- Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA.
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6
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Dohrmann PR, Manhart CM, Downey CD, McHenry CS. The rate of polymerase release upon filling the gap between Okazaki fragments is inadequate to support cycling during lagging strand synthesis. J Mol Biol 2011; 414:15-27. [PMID: 21986197 DOI: 10.1016/j.jmb.2011.09.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/16/2011] [Accepted: 09/24/2011] [Indexed: 10/17/2022]
Abstract
Upon completion of synthesis of an Okazaki fragment, the lagging strand replicase must recycle to the next primer at the replication fork in under 0.1 s to sustain the physiological rate of DNA synthesis. We tested the collision model that posits that cycling is triggered by the polymerase encountering the 5'-end of the preceding Okazaki fragment. Probing with surface plasmon resonance, DNA polymerase III holoenzyme initiation complexes were formed on an immobilized gapped template. Initiation complexes exhibit a half-life of dissociation of approximately 15 min. Reduction in gap size to 1 nt increased the rate of dissociation 2.5-fold, and complete filling of the gap increased the off-rate an additional 3-fold (t(1/2)~2 min). An exogenous primed template and ATP accelerated dissociation an additional 4-fold in a reaction that required complete filling of the gap. Neither a 5'-triphosphate nor a 5'-RNA terminated oligonucleotide downstream of the polymerase accelerated dissociation further. Thus, the rate of polymerase release upon gap completion and collision with a downstream Okazaki fragment is 1000-fold too slow to support an adequate rate of cycling and likely provides a backup mechanism to enable polymerase release when the other cycling signals are absent. Kinetic measurements indicate that addition of the last nucleotide to fill the gap is not the rate-limiting step for polymerase release and cycling. Modest (approximately 7 nt) strand displacement is observed after the gap between model Okazaki fragments is filled. To determine the identity of the protein that senses gap filling to modulate affinity of the replicase for the template, we performed photo-cross-linking experiments with highly reactive and non-chemoselective diazirines. Only the α subunit cross-linked, indicating that it serves as the sensor.
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Affiliation(s)
- Paul R Dohrmann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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Heli H, Mirtorabi S, Karimian K. Advances in iron chelation: an update. Expert Opin Ther Pat 2011; 21:819-56. [PMID: 21449664 DOI: 10.1517/13543776.2011.569493] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Oxidative stress (caused by excess iron) can result in tissue damage, organ failure and finally death, unless treated by iron chelators. The causative factor in the etiology of a variety of disease states is the presence of iron-generated reactive oxygen species (ROS), which can result in cell damage or which can affect the signaling pathways involved in cell necrosis-apoptosis or organ fibrosis, cancer, neurodegeneration and cardiovascular, hepatic or renal dysfunctions. Iron chelators can reduce oxidative stress by the removal of iron from target tissues. Equally as important, removal of iron from the active site of enzymes that play key roles in various diseases can be of considerable benefit to the patients. AREAS COVERED This review focuses on iron chelators used as therapeutic agents. The importance of iron in oxidative damage is discussed, along with the three clinically approved iron chelators. EXPERT OPINION A number of iron chelators are used as approved therapeutic agents in the treatment of thalassemia major, asthma, fungal infections and cancer. However, as our knowledge about the biochemistry of iron and its role in etiologies of seemingly unrelated diseases increases, new applications of the approved iron chelators, as well as the development of new iron chelators, present challenging opportunities in the areas of drug discovery and development.
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Affiliation(s)
- Hossein Heli
- Islamic Azad University, Science and Research Branch, Department of Chemistry, Fars, 7348113111, Iran
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8
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Downey CD, McHenry CS. Chaperoning of a replicative polymerase onto a newly assembled DNA-bound sliding clamp by the clamp loader. Mol Cell 2010; 37:481-91. [PMID: 20188667 DOI: 10.1016/j.molcel.2010.01.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/03/2009] [Accepted: 11/12/2009] [Indexed: 11/29/2022]
Abstract
Cellular replicases contain multiprotein ATPases that load sliding clamp processivity factors onto DNA. We reveal an additional role for the DnaX clamp loader: chaperoning of the replicative polymerase onto a clamp newly bound to DNA. We show that chaperoning confers distinct advantages, including marked acceleration of initiation complex formation. We reveal a requirement for the tau form of DnaX complex to relieve inhibition by single-stranded DNA binding protein during initiation complex formation. We propose that, after loading beta(2), DnaX complex preserves an SSB-free segment of DNA immediately downstream of the primer terminus and chaperones Pol III into that position, preventing competition by SSB. The C-terminal tail of SSB stimulates reactions catalyzed by tau-containing DnaX complexes through a contact distinct from the contact involving the chi subunit. Chaperoning of Pol III by the DnaX complex provides a molecular explanation for how initiation complexes form when supported by the nonhydrolyzed analog ATPgammaS.
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Affiliation(s)
- Christopher D Downey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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Saxena M, Abhyankar M, Bastia D. Replication initiation at a distance: determination of the cis- and trans-acting elements of replication origin alpha of plasmid R6K. J Biol Chem 2009; 285:5705-12. [PMID: 20018882 DOI: 10.1074/jbc.m109.067348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Plasmid R6K, which contains 3 replication origins called alpha, gamma, and beta, is a favorable system to investigate the molecular mechanism(s) of action at a distance, i.e. replication initiation at a considerable distance from the primary initiator protein binding sites (iterons). The centrally located gamma origin contains 7 iterons that bind to the plasmid-encoded initiator protein, pi. Ori alpha, located at a distance of approximately 4 kb from gamma, contains a single iteron that does not directly bind to pi but is believed to access the protein by pi-mediated alpha-gamma iteron-iteron interaction that loops out the intervening approximately 3.7 kb of DNA. Although the cis-acting components and the trans-acting proteins required for ori gamma function have been analyzed in detail, such information was lacking for ori alpha. Here, we have identified both the sequence elements located at alpha and those at gamma, that together promoted alpha activity. The data support the conclusion that besides the single iteron, a neighboring DNA primase recognition element called G site is essential for alpha-directed plasmid maintenance. Sequences preceding the iteron and immediately following the G site, although not absolutely necessary, appear to play a role in efficient plasmid maintenance. In addition, while both dnaA1 and dnaA2 boxes that bind to DnaA protein and are located at gamma were essential for alpha activity, only dnaA2 was required for initiation at gamma. Mutations in the AT-rich region of gamma also abolished alpha function. These results are consistent with the interpretation that a protein-DNA complex consisting of pi and DnaA forms at gamma and activates alpha at a distance by DNA looping.
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Affiliation(s)
- Mukesh Saxena
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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McInerney P, Johnson A, Katz F, O'Donnell M. Characterization of a triple DNA polymerase replisome. Mol Cell 2007; 27:527-38. [PMID: 17707226 DOI: 10.1016/j.molcel.2007.06.019] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 05/15/2007] [Accepted: 06/12/2007] [Indexed: 11/20/2022]
Abstract
The replicase of all cells is thought to utilize two DNA polymerases for coordinated synthesis of leading and lagging strands. The DNA polymerases are held to DNA by circular sliding clamps. We demonstrate here that the E. coli DNA polymerase III holoenzyme assembles into a particle that contains three DNA polymerases. The three polymerases appear capable of simultaneous activity. Furthermore, the trimeric replicase is fully functional at a replication fork with helicase, primase, and sliding clamps; it produces slightly shorter Okazaki fragments than replisomes containing two DNA polymerases. We propose that two polymerases can function on the lagging strand and that the third DNA polymerase can act as a reserve enzyme to overcome certain types of obstacles to the replication fork.
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Affiliation(s)
- Peter McInerney
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA
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11
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Maul RW, Ponticelli SKS, Duzen JM, Sutton MD. Differential binding of Escherichia coli DNA polymerases to the beta-sliding clamp. Mol Microbiol 2007; 65:811-27. [PMID: 17635192 DOI: 10.1111/j.1365-2958.2007.05828.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli strains expressing the mutant beta159-sliding clamp protein (containing both a G66E and a G174A substitution) are temperature sensitive for growth and display altered DNA polymerase (pol) usage. We selected for suppressors of the dnaN159 allele able to grow at 42 degrees C, and identified four intragenic suppressor alleles. One of these alleles (dnaN780) contained only the G66E substitution, while a second (dnaN781) contained only the G174A substitution. Genetic characterization of isogenic E. coli strains expressing these alleles indicated that certain phenotypes were dependent upon only the G174A substitution, while others required both the G66E and G174A substitutions. In order to understand the individual contributions of the G66E and the G174A substitution to the dnaN159 phenotypes, we utilized biochemical approaches to characterize the purified mutant beta159 (G66E and G174A), beta780 (G66E) and beta781 (G174A) clamp proteins. The G66E substitution conferred a more pronounced effect on pol IV replication than it did pol II or pol III, while the G174A substitution conferred a greater effect on pol III and pol IV than it did pol II. Taken together, these findings indicate that pol II, pol III and pol IV interact with distinct, albeit overlapping surfaces of the beta clamp.
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Affiliation(s)
- Robert W Maul
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, New York 14214, USA
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12
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Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Nucleic Acids Res 2007; 35:2813-24. [PMID: 17355988 PMCID: PMC1888804 DOI: 10.1093/nar/gkm079] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by τC16 derivatives for binding to α gave values of KD of 7 μM for the α−τC16Δ7 complex. Low-level expression of the genes encoding τC16 and τC16▵7, but not τC16Δ11, is lethal to E. coli. Suppression of this lethal phenotype enabled selection of mutations in the 3′ end of the τC16 gene, that led to defects in α binding. The data suggest that the unstructured C-terminus of τ becomes folded into a helix–loop–helix in its complex with α. An N-terminally extended construct, τC24, was found to bind DNA in a salt-sensitive manner while no binding was observed for τC16, suggesting that the processivity switch of the replisome functionally involves Domain IV of τ.
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Affiliation(s)
- Slobodan Jergic
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Kiyoshi Ozawa
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Neal K. Williams
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Xun-Cheng Su
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Daniel D. Scott
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Samir M. Hamdan
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Jeffrey A. Crowther
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Nicholas E. Dixon
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia and Department of Chemistry, University of Wollongong, NSW 2522, Australia
- *To whom correspondence should be addressed. +61 2 42214346+61 2 42214287
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Indiani C, O'Donnell M. The replication clamp-loading machine at work in the three domains of life. Nat Rev Mol Cell Biol 2006; 7:751-61. [PMID: 16955075 DOI: 10.1038/nrm2022] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sliding clamps are ring-shaped proteins that tether DNA polymerases to DNA, which enables the rapid and processive synthesis of both leading and lagging strands at the replication fork. The clamp-loading machinery must repeatedly load sliding-clamp factors onto primed sites at the replication fork. Recent structural and biochemical analyses provide unique insights into how these clamp-loading ATPase machines function to load clamps onto the DNA. Moreover, these studies highlight the evolutionary conservation of the clamp-loading process in the three domains of life.
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Affiliation(s)
- Chiara Indiani
- Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10021, USA
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14
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Jarvis TC, Beaudry AA, Bullard JM, Janjic N, McHenry CS. Reconstitution of a minimal DNA replicase from Pseudomonas aeruginosa and stimulation by non-cognate auxiliary factors. J Biol Chem 2004; 280:7890-900. [PMID: 15611049 DOI: 10.1074/jbc.m412263200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase III holoenzyme is responsible for chromosomal replication in bacteria. The components and functions of Escherichia coli DNA polymerase III holoenzyme have been studied extensively. Here, we report the reconstitution of replicase activity by essential components of DNA polymerase holoenzyme from the pathogen Pseudomonas aeruginosa. We have expressed and purified the processivity factor (beta), single-stranded DNA-binding protein, a complex containing the polymerase (alpha) and exonuclease (epsilon) subunits, and the essential components of the DnaX complex (tau(3)deltadelta'). Efficient primer elongation requires the presence of alphaepsilon, beta, and tau(3)deltadelta'. Pseudomonas aeruginosa alphaepsilon can substitute completely for E. coli polymerase III in E. coli holoenzyme reconstitution assays. Pseudomonas beta and tau(3)deltadelta' exhibit a 10-fold lower activity relative to their E. coli counterparts in E. coli holoenzyme reconstitution assays. Although the Pseudomonas counterpart to the E. coli psi subunit was not apparent in sequence similarity searches, addition of purified E. coli chi and psi (components of the DnaX complex) increases the apparent specific activity of the Pseudomonas tau(3)deltadelta' complex approximately 10-fold and enables the reconstituted enzyme to function better under physiological salt conditions.
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Majka J, Burgers PMJ. The PCNA-RFC families of DNA clamps and clamp loaders. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 78:227-60. [PMID: 15210332 DOI: 10.1016/s0079-6603(04)78006-x] [Citation(s) in RCA: 240] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The proliferating cell nuclear antigen PCNA functions at multiple levels in directing DNA metabolic pathways. Unbound to DNA, PCNA promotes localization of replication factors with a consensus PCNA-binding domain to replication factories. When bound to DNA, PCNA organizes various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modeling. Its modification by ubiquitin directs the cellular response to DNA damage. The ring-like PCNA homotrimer encircles double-stranded DNA and slides spontaneously across it. Loading of PCNA onto DNA at template-primer junctions is performed in an ATP-dependent process by replication factor C (RFC), a heteropentameric AAA+ protein complex consisting of the Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Loading of yeast PCNA (POL30) is mechanistically distinct from analogous processes in E. coli (beta subunit by the gamma complex) and bacteriophage T4 (gp45 by gp44/62). Multiple stepwise ATP-binding events to RFC are required to load PCNA onto primed DNA. This stepwise mechanism should permit editing of this process at individual steps and allow for divergence of the default process into more specialized modes. Indeed, alternative RFC complexes consisting of the small RFC subunits together with an alternative Rfc1-like subunit have been identified. A complex required for the DNA damage checkpoint contains the Rad24 subunit, a complex required for sister chromatid cohesion contains the Ctf18 subunit, and a complex that aids in genome stability contains the Elg1 subunit. Only the RFC-Rad24 complex has a known associated clamp, a heterotrimeric complex consisting of Rad17, Mec3, and Ddc1. The other putative clamp loaders could either act on clamps yet to be identified or act on the two known clamps.
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Affiliation(s)
- Jerzy Majka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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16
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Abhyankar MM, Zzaman S, Bastia D. Reconstitution of R6K DNA replication in vitro using 22 purified proteins. J Biol Chem 2003; 278:45476-84. [PMID: 12970346 DOI: 10.1074/jbc.m308516200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have reconstituted a multiprotein system consisting of 22 purified proteins that catalyzed the initiation of replication specifically at ori gamma of R6K, elongation of the forks, and their termination at specific replication terminators. The initiation was strictly dependent on the plasmid-encoded initiator protein pi and on the host-encoded initiator DnaA. The wild type pi was almost inert, whereas a mutant form containing 3 amino acid substitutions that tended to monomerize the protein was effective in initiating replication. The replication in vitro was primed by DnaG primase, whereas in a crude extract system that had not been fractionated, it was dependent on RNA polymerase. The DNA-bending protein IHF was needed for optimal replication and its substitution by HU, unlike in the oriC system, was less effective in promoting optimal replication. In contrast, wild type pi-mediated replication in vivo requires IHF. Using a template that contained ori gamma flanked by two asymmetrically placed Ter sites in the blocking orientation, replication proceeded in the Cairns type mode and generated the expected types of termination products. A majority of the molecules progressed counterclockwise from the ori, in the same direction that has been observed in vivo. Many features of replication in the reconstituted system appeared to mimic those of in vivo replication. The system developed here is an important milestone in continuing biochemical analysis of this interesting replicon.
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Affiliation(s)
- Mayuresh M Abhyankar
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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Leu FP, O'Donnell M. Interplay of clamp loader subunits in opening the beta sliding clamp of Escherichia coli DNA polymerase III holoenzyme. J Biol Chem 2001; 276:47185-94. [PMID: 11572866 DOI: 10.1074/jbc.m106780200] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli beta dimer is a ring-shaped protein that encircles DNA and acts as a sliding clamp to tether the replicase, DNA polymerase III holoenzyme, to DNA. The gamma complex (gammadeltadelta'chipsi) clamp loader couples ATP to the opening and closing of beta in assembly of the ring onto DNA. These proteins are functionally and structurally conserved in all cells. The eukaryotic equivalents are the replication factor C (RFC) clamp loader and the proliferating cell nuclear antigen (PCNA) clamp. The delta subunit of the E. coli gamma complex clamp loader is known to bind beta and open it by parting one of the dimer interfaces. This study demonstrates that other subunits of gamma complex also bind beta, although weaker than delta. The gamma subunit like delta, affects the opening of beta, but with a lower efficiency than delta. The delta' subunit regulates both gamma and delta ring opening activities in a fashion that is modulated by ATP interaction with gamma. The implications of these actions for the workings of the E. coli clamp loading machinery and for eukaryotic RFC and PCNA are discussed.
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Affiliation(s)
- F P Leu
- Department of Pharmacology, Joan and Sanford I. Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
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18
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Song MS, Dallmann HG, McHenry CS. Carboxyl-terminal domain III of the delta' subunit of the DNA polymerase III holoenzyme binds delta. J Biol Chem 2001; 276:40668-79. [PMID: 11518714 DOI: 10.1074/jbc.m106373200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The delta and delta' subunits are essential components of the DNA polymerase III holoenzyme, required for assembly and function of the DnaX-complex clamp loader (tau2gammadeltadelta'chipsi). The x-ray crystal structure of delta' contains three structural domains (Guenther, B., Onrust, R., Sali, A., O'Donnell, M., and Kuriyan, J. (1997) Cell 91, 335-345). In this study, we localize the delta-binding domain of delta' to a carboxyl-terminal domain III by quantifying the interaction of delta with a series of delta' fusion proteins lacking specific domains. Purification and immobilization of the fusion proteins were facilitated by the inclusion of a tag containing hexahistidine and a short biotinylation sequence. Both NH2- and COOH-terminal-tagged full-length delta' were soluble and had specific activities comparable with that of native delta'. delta and delta' form a 1:1 heterodimer with a dissociation constant (K(D)) of 5 x 10(-7) m determined by equilibrium sedimentation. The K(D) determined by surface plasmon resonance was comparable. Domain III alone bound delta at an affinity comparable to that of wild type delta', whereas proteins lacking domain III did not bind delta. Using a panel of domain-specific anti-delta' monoclonal antibodies, we found that two of the domain III-specific monoclonal antibodies interfered with delta-delta' interaction and abolished the replication activity of DNA polymerase-III holoenzyme.
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Affiliation(s)
- M S Song
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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19
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Song MS, Pham PT, Olson M, Carter JR, Franden MA, Schaaper RM, McHenry CS. The delta and delta ' subunits of the DNA polymerase III holoenzyme are essential for initiation complex formation and processive elongation. J Biol Chem 2001; 276:35165-75. [PMID: 11432857 DOI: 10.1074/jbc.m100389200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
delta and delta' are required for assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. We developed protocols for generating highly purified preparations of delta and delta'. In holoenzyme reconstitution assays, delta' could not be replaced by delta, tau, or gamma, even when either of the latter were present at a 10,000-fold molar excess. Likewise, delta could not be replaced by delta', tau, or gamma. Bacterial strains bearing chromosomal knockouts of either the holA(delta) or holB(delta') genes were not viable, demonstrating that both delta and delta' are essential. Western blots of isolated initiation complexes demonstrated the presence of both delta and delta'. However, in the absence of chipsi and single-stranded DNA-binding protein, a stable initiation complex lacking deltadelta' was isolated by gel filtration. Lack of delta-delta' decreased the rate of elongation about 3-fold, and the extent of processive replication was significantly decreased. Adding back delta-delta' but not chipsi, delta, or delta' alone restored the diminished activity, indicating that in addition to being key components required for the beta loading activity of the DnaX complex, deltadelta' is present in initiation complex and is required for processive elongation.
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Affiliation(s)
- M S Song
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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20
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Pritchard AE, McHenry CS. Assembly of DNA polymerase III holoenzyme: co-assembly of gamma and tau is inhibited by DnaX complex accessory proteins but stimulated by DNA polymerase III core. J Biol Chem 2001; 276:35217-22. [PMID: 11463784 DOI: 10.1074/jbc.m102735200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the two alternative Escherichia coli dnaX gene products, tau and gamma, are found co-assembled in purified DNA polymerase III holoenzyme, the pathway of assembly is not well understood. When the 10 subunits of holoenzyme are simultaneously mixed, they rapidly form a nine-subunit assembly containing tau but not gamma. We developed a new assay based on the binding of complexes containing biotin-tagged tau to streptavidin-coated agarose beads to investigate the effects of various DNA polymerase III holoenzyme subunits on the kinetics of co-assembly of gamma and tau into the same complex. Auxiliary proteins in combination with delta' almost completely blocked co-assembly, whereas chipsi or delta' alone slowed the association only moderately compared with the interaction of tau with gamma alone. In contrast, DNA polymerase III core, in the absence of deltadelta' and chipsi, accelerated the co-assembly of tau and gamma, suggesting a role for DNA polymerase III' [tau(2)(pol III core)(2)] in the assembly pathway of holoenzyme.
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Affiliation(s)
- A E Pritchard
- Department of Biochemistry and Molecular Genetics and the Program in Molecular Biology, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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21
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Gao D, McHenry CS. Tau binds and organizes Escherichia coli replication proteins through distinct domains. Domain III, shared by gamma and tau, binds delta delta ' and chi psi. J Biol Chem 2001; 276:4447-53. [PMID: 11078742 DOI: 10.1074/jbc.m009827200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DnaX complex of the DNA polymerase holoenzyme assembles the beta(2) processivity factor onto the primed template enabling highly processive replication. The key ATPases within this complex are tau and gamma, alternative frameshift products of the dnaX gene. Of the five domains of tau, I-III are shared with gamma In vivo, gamma binds the auxiliary subunits deltadelta' and chipsi (Glover, B. P., and McHenry, C. S. (2000) J. Biol. Chem. 275, 3017-3020). To localize deltadelta' and chipsi binding domains within gamma domains I-III, we measured the binding of purified biotin-tagged DnaX proteins lacking specific domains to deltadelta' and chipsi by surface plasmon resonance. Fusion proteins containing either DnaX domains I-III or domains III-V bound deltadelta' and chipsi subunits. A DnaX protein only containing domains I and II did not bind deltadelta' or chipsi. The binding affinity of chipsi for DnaX domains I-III and domains III-V was the same as that of chipsi for full-length tau, indicating that domain III contained all structural elements required for chipsi binding. Domain III of tau also contained deltadelta' binding sites, although the interaction between deltadelta' and domains III-V of tau was 10-fold weaker than the interaction between deltadelta' and full length tau. The presence of both delta and chipsi strengthened the delta'-C(0)tau interaction by at least 15-fold. Domain III was the only domain common to all of tau fusion proteins whose interaction with delta' was enhanced in the presence of delta and chipsi. Thus, domain III of the DnaX proteins not only contains the deltadelta' and chipsi binding sites but also contains the elements required for the positive cooperative assembly of the DnaX complex.
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Affiliation(s)
- D Gao
- Department of Biochemistry, Program in Molecular Biology, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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22
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Pritchard AE, Dallmann HG, Glover BP, McHenry CS. A novel assembly mechanism for the DNA polymerase III holoenzyme DnaX complex: association of deltadelta' with DnaX(4) forms DnaX(3)deltadelta'. EMBO J 2000; 19:6536-45. [PMID: 11101526 PMCID: PMC305859 DOI: 10.1093/emboj/19.23.6536] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have constructed a plasmid-borne artificial operon that expresses the six subunits of the DnaX complex of Escherichia coli DNA polymerase III holoenzyme: tau, gamma, delta, delta', chi and psi. Induction of this operon followed by assembly in vivo produced two taugamma mixed DnaX complexes with stoichiometries of tau(1)gamma(2)deltadelta'chipsi and tau(2)gamma(1)deltadelta'chipsi rather than the expected gamma(2)tau(2)deltadelta'chipsi. We observed the same heterogeneity when taugamma mixed DnaX complexes were reconstituted in vitro. Re-examination of homomeric DnaX tau and gamma complexes assembled either in vitro or in vivo also revealed a stoichiometry of DnaX(3)deltadelta'chipsi. Equilibrium sedimentation analysis showed that free DnaX is a tetramer in equilibrium with a free monomer. An assembly mechanism, in which the association of heterologous subunits with a homomeric complex alters the stoichiometry of the homomeric assembly, is without precedent. The significance of our findings to the architecture of the holoenzyme and the clamp-assembly apparatus of all other organisms is discussed.
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Affiliation(s)
- A E Pritchard
- Department of Biochemistry and Molecular Genetics and Program in Molecular Biology, University of Colorado Health Sciences Center, Denver, CO 80262, USA
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23
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Walker JR, Hervas C, Ross JD, Blinkova A, Walbridge MJ, Pumarega EJ, Park MO, Neely HR. Escherichia coli DNA polymerase III tau- and gamma-subunit conserved residues required for activity in vivo and in vitro. J Bacteriol 2000; 182:6106-13. [PMID: 11029431 PMCID: PMC94745 DOI: 10.1128/jb.182.21.6106-6113.2000] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli DNA polymerase III tau and gamma subunits are single-strand DNA-dependent ATPases (the latter requires the delta and delta' subunits for significant ATPase activity) involved in loading processivity clamp beta. They are homologous to clamp-loading proteins of many organisms from phages to humans. Alignment of 27 prokaryotic tau/gamma homologs and 1 eukaryotic tau/gamma homolog has refined the sequences of nine previously defined identity and functional motifs. Mutational analysis has defined highly conserved residues required for activity in vivo and in vitro. Specifically, mutations introduced into highly conserved residues within three of those motifs, the P loop, the DExx region, and the SRC region, inactivated complementing activity in vivo and clamp loading in vitro and reduced ATPase catalytic efficiency in vitro. Mutation of a highly conserved residue within a fourth motif, VIc, inactivated clamp-loading activity and reduced ATPase activity in vitro, but the mutant gene, on a multicopy plasmid, retained complementing activity in vivo and the mutant gene also supported apparently normal replication and growth as a haploid, chromosomal allele.
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Affiliation(s)
- J R Walker
- Section of Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.
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24
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Dallmann HG, Kim S, Pritchard AE, Marians KJ, McHenry CS. Characterization of the unique C terminus of the Escherichia coli tau DnaX protein. Monomeric C-tau binds alpha AND DnaB and can partially replace tau in reconstituted replication forks. J Biol Chem 2000; 275:15512-9. [PMID: 10748120 DOI: 10.1074/jbc.m909257199] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A contact between the dimeric tau subunit within the DNA polymerase III holoenzyme and the DnaB helicase is required for replication fork propagation at physiologically-relevant rates (Kim, S., Dallmann, H. G., McHenry, C. S., and Marians, K. J. (1996) Cell 84, 643-650). In this report, we exploit the OmpT protease to generate C-tau, a protein containing only the unique C-terminal sequences of tau, free of the sequences shared with the alternative gamma frameshifting product of dnaX. We have established that C-tau is a monomer by sedimentation equilibrium and sedimentation velocity ultracentrifugation. Monomeric C-tau binds the alpha catalytic subunit of DNA polymerase III with a 1:1 stoichiometry. C-tau also binds DnaB, revealed by a coupled immunoblotting method. C-tau restores the rapid replication rate of inefficient forks reconstituted with only the gamma dnaX gene product. The acceleration of the DnaB helicase can be observed in the absence of primase, when only leading-strand replication occurs. This indicates that C-tau, bound only to the leading-strand polymerase, can trigger the conformational change necessary for DnaB to assume the fast, physiologically relevant form.
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Affiliation(s)
- H G Dallmann
- Department of Biochemistry and Molecular Genetics and Molecular Biology Program, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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25
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Glover BP, McHenry CS. The DnaX-binding subunits delta' and psi are bound to gamma and not tau in the DNA polymerase III holoenzyme. J Biol Chem 2000; 275:3017-20. [PMID: 10652279 DOI: 10.1074/jbc.275.5.3017] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DnaX complex subassembly of the DNA polymerase III holoenzyme is comprised of the DnaX proteins tau and gamma and the auxiliary subunits delta, delta', chi, and psi, which together load the beta processivity factor onto primed DNA in an ATP-dependent reaction. delta' and psi bind directly to DnaX whereas delta and chi bind to delta' and psi, respectively (Onrust, R., Finkelstein, J., Naktinis, V., Turner, J., Fang, L., and O'Donnell, M. (1995) J. Biol. Chem. 270, 13348-13357). Until now, it has been unclear which DnaX protein, tau or gamma, in holoenzyme binds the auxiliary subunits delta, delta', chi,and psi. Treatment of purified holoenzyme with the homobifunctional cross-linker bis(sulfosuccinimidyl)suberate produces covalently cross-linked gamma-delta' and gamma-psi complexes identified by Western blot analysis. Immunodetection of cross-linked species with anti-delta' and anti-psi antibodies revealed that no tau-delta' or tau-psi cross-links had formed, suggesting that the delta' and psi subunits reside only on gamma within holoenzyme.
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Affiliation(s)
- B P Glover
- Department of Biochemistry, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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26
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Matsuo E, Sampei G, Mizobuchi K, Ito K. The plasmid F OmpP protease, a homologue of OmpT, as a potential obstacle to E. coli-based protein production. FEBS Lett 1999; 461:6-8. [PMID: 10561486 DOI: 10.1016/s0014-5793(99)01418-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OmpT, an outer membrane-localized protease of Escherichia coli, cleaves a number of exogenous and endogenous proteins during their purification. SecY, an endogenous membrane protein, is a target of this artificial proteolysis in vitro. Here we report that SecY cleavage occurs even in cell extracts from ompT-disrupted cells, if they carry an F plasmid derivative. A gene, ompP, on the F plasmid was shown to be responsible for this proteolysis. These results indicate that the absence of an F-like plasmid should be checked when choosing a host strain for E. coli-based protein production.
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Affiliation(s)
- E Matsuo
- Institute for Virus Research, Kyoto University, Kyoto, Japan
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27
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Larsen B, Gesteland RF, Atkins JF. Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%. J Mol Biol 1997; 271:47-60. [PMID: 9300054 PMCID: PMC7126992 DOI: 10.1006/jmbi.1997.1162] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three elements are crucial for the programmed frameshifting in translation of dnaX mRNA: a Shine-Dalgarno (SD)-like sequence, a double-shift site, and a 3' structure. The conformation of the mRNA containing these three elements was investigated using chemical and enzymatic probes. The probing data show that the structure is a specific stem-loop. The bottom half of the stem is more stable than the top half of the stem. The function of the stem-loop was further investigated by mutagenic analysis. Reducing the stability of the bottom half of the stem strongly effects frameshifting levels, whereas similar changes in the top half are not as effective. Stabilizing the top half of the stem gives increased frameshifting beyond the WT efficiency. The identity of the primary RNA sequence in the stem-loop is unimportant, provided that the overall structure is maintained. The calculated stabilities of the variant stem-loop structures correlate with frameshifting efficiency. The SD-interaction and the stem-loop element act independently to increase frameshifting in dnaX.
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Key Words
- dnax
- frameshifting
- recoding
- probing
- stem-loop structure
- sd, shine-dalgarno
- dms, dimethylsulfate
- cmct, 1-cyclohexyl-3-(morpholino-ethyl) carbodiimide metho-p-toluenesulfonate
- wt, wild-type
- ibv, infectious bronchitis virus
- mmtv, mouse mammary tumor virus
- hiv, human immunodeficiency virus
- pcr, polymerase chain reaction
- 2d, two-dimensional
- fiv, feline immunodeficiency virus
- htlv-ii, human t-cell leukemia virus type ii
- srv-1, simian retrovirus type 1
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Affiliation(s)
- B Larsen
- Department of Human Genetics, University of Utah, Salt Lake City 84112, USA
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28
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Blinkova A, Burkart MF, Owens TD, Walker JR. Conservation of the Escherichia coli dnaX programmed ribosomal frameshift signal in Salmonella typhimurium. J Bacteriol 1997; 179:4438-42. [PMID: 9209069 PMCID: PMC179275 DOI: 10.1128/jb.179.13.4438-4442.1997] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Escherichia coli DNA polymerase III subunits tau and gamma are produced from one gene, dnaX, by a programmed ribosomal frameshift which generates the C terminal of gamma within the tau reading frame. To help evaluate the role of the dispensable gamma, the distribution of tau and gamma homologs in several other species and the sequence of the Salmonella typhimurium dnaX were determined. All four enterobacteria tested produce tau and gamma homologs. S. typhimurium dnaX is 83% identical to E. coli dnaX, but all four components of the frameshift signal are 100% conserved.
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Affiliation(s)
- A Blinkova
- Microbiology Department, University of Texas at Austin, 78712, USA
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29
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Kim S, Dallmann HG, McHenry CS, Marians KJ. tau couples the leading- and lagging-strand polymerases at the Escherichia coli DNA replication fork. J Biol Chem 1996; 271:21406-12. [PMID: 8702922 DOI: 10.1074/jbc.271.35.21406] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Synthesis of an Okazaki fragment occurs once every 1 or 2 s at the Escherichia coli replication fork. To account for the rapid recycling required of the lagging-strand polymerase, it has been proposed that it is held at the replication fork by protein-protein interactions with the leading-strand polymerase as part of a dimeric polymerase assembly. Solution studies showed that the replicative polymerase, the DNA polymerase III holoenzyme, was indeed a dimer with two catalytic cores held together by the tau subunit. However, the functionality of this arrangement at the replication fork has never been demonstrated. We showed previously that the lagging-strand polymerase acted processively during multiple rounds of Okazaki fragment synthesis, i.e. the same polymerase core assembly synthesized each and every fragment made by the fork. Using extreme dilution of active replication forks and the isolation of protein-DNA complexes capable of supporting coupled leading- and lagging-strand synthesis, we demonstrate here that this coupling of leading- and lagging-strand synthesis is, in fact, mediated by the tau subunit of the holoenzyme acting as a physical bridge between the core assemblies synthesizing the leading and lagging strands.
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Affiliation(s)
- S Kim
- Graduate Program in Molecular Biology Cornell University Graduate School of Medical Sciences, New York, New York 10021, USA
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30
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Kim DR, McHenry CS. Biotin tagging deletion analysis of domain limits involved in protein-macromolecular interactions. Mapping the tau binding domain of the DNA polymerase III alpha subunit. J Biol Chem 1996; 271:20690-8. [PMID: 8702819 DOI: 10.1074/jbc.271.34.20690] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The tau subunit dimerizes DNA polymerase III via interaction with the alpha subunit, allowing DNA polymerase III holoenzyme to synthesize both leading and lagging strands simultaneously at the DNA replication fork. Here, we report a general method to map the limits of domains required for heterologous protein-protein interactions using surface plasmon resonance. The method employs fusion of a short biotinylation sequence at either the NH2 or COOH terminus of the protein to be immobilized on streptavidin-derivatized biosensor chips. Inclusion of a hexahistidine sequence permits rapid purification and separation of the fusion protein from the endogenous Escherichia coli biotin carboxyl carrier protein. Ten deletions of the alpha subunit were constructed and purified by Ni2+-nitrilotriacetic acid chromatography and, when required, monomeric avidin chromatography. Each alpha deletion protein was captured by streptavidin immobilized on a Pharmacia Biosensor BIAcore chip, and the tau binding activity of each alpha deletion was analyzed using surface plasmon resonance. The tau subunit bound very tightly to a full-length amino-terminal fusion of the biotinylation sequence with alpha (KD approximately 70 pm). Four additional NH2-terminal alpha deletion proteins (60, 240, 360, and 542 residues deleted) retained strong binding activity to the tau subunit (KD = 0.19-0.39 nM), whereas deletion of 705 residues or more from the NH2 terminus of the alpha subunit abolished tau binding activity. Full-length alpha that contained a carboxyl-terminal fusion with the biotinylation sequence bound tau strongly (KD = 0.37 nM). However, deletion of 48 amino acids from the COOH terminus totally eliminated tau binding. These results indicate that the COOH-terminal half of the alpha subunit is involved in tau interaction.
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Affiliation(s)
- D R Kim
- Department of Biochemistry, Biophysics, and Genetics, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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