Статті в журналах: "DnaB helicase"

1

Titok, Marina, Catherine Suski, Bérengère Dalmais, S. Dusko Ehrlich, and Laurent Jannière. "The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72." Microbiology 152, no. 5 (May 1, 2006): 1471–78. http://dx.doi.org/10.1099/mic.0.28693-0.

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Plasmids are the tools of choice for studying bacterial functions involved in DNA maintenance. Here a genetic study on the replication of a novel, low-copy-number, Bacillus subtilis plasmid, pBS72, is reported. The results show that two plasmid elements, the initiator protein RepA and an iteron-containing origin, and at least nine host-encoded replication proteins, the primosomal proteins DnaB, DnaC, DnaD, DnaG and DnaI, the DNA polymerases DnaE and PolC, and the polymerase cofactors DnaN and DnaX, are required for pBS72 replication. On the contrary, the cellular initiators DnaA and PriA, the helicase PcrA and DNA polymerase I are dispensable. From this, it is inferred that pBS72 replication is of the theta type and is initiated by an original mechanism. Indirect evidence suggests that during this process the DnaC helicase might be delivered to the plasmid origin by the weakly active DnaD pathway stimulated by a predicted interaction between DnaC and a domain of RepA homologous to the major DnaC-binding domain of the cellular initiator DnaA. The plasmid pBS72 replication fork appears to require the same functions as the bacterial chromosome and the unrelated plasmid pAMβ1. Most importantly, this replication machinery contains the two type C polymerases, PolC and DnaE. As the mechanism of initiation of the three genomes is substantially different, this suggests that both type C polymerases might be required in any Cairns replication in B. subtilis and presumably in other bacteria encoding PolC and DnaE.

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2

Hayashi, Chihiro, Erika Miyazaki, Shogo Ozaki, Yoshito Abe, and Tsutomu Katayama. "DnaB helicase is recruited to the replication initiation complex via binding of DnaA domain I to the lateral surface of the DnaB N-terminal domain." Journal of Biological Chemistry 295, no. 32 (June 15, 2020): 11131–43. http://dx.doi.org/10.1074/jbc.ra120.014235.

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The DNA replication protein DnaA in Escherichia coli constructs higher-order complexes on the origin, oriC, to unwind this region. DnaB helicase is loaded onto unwound oriC via interactions with the DnaC loader and the DnaA complex. The DnaB–DnaC complex is recruited to the DnaA complex via stable binding of DnaB to DnaA domain I. The DnaB–DnaC complex is then directed to unwound oriC via a weak interaction between DnaB and DnaA domain III. Previously, we showed that Phe46 in DnaA domain I binds to DnaB. Here, we searched for the DnaA domain I–binding site in DnaB. The DnaB L160A variant was impaired in binding to DnaA complex on oriC but retained its DnaC-binding and helicase activities. DnaC binding moderately stimulated DnaA binding of DnaB L160A, and loading of DnaB L160A onto oriC was consistently and moderately inhibited. In a helicase assay with partly single-stranded DNA bearing a DnaA-binding site, DnaA stimulated DnaB loading, which was strongly inhibited in DnaB L160A even in the presence of DnaC. DnaB L160A was functionally impaired in vivo. On the basis of these findings, we propose that DnaB Leu160 interacts with DnaA domain I Phe46. DnaB Leu160 is exposed on the lateral surface of the N-terminal domain, which can explain unobstructed interactions of DnaA domain I–bound DnaB with DnaC, DnaG primase, and DnaA domain III. We propose a probable structure for the DnaA–DnaB–DnaC complex, which could be relevant to the process of DnaB loading onto oriC.

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3

Bazin, Alexandre, Mickaël Cherrier, and Laurent Terradot. "Structural insights into DNA replication initiation in Helicobacter pylori." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1632. http://dx.doi.org/10.1107/s2053273314083673.

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In Gram-negative bacteria, opening of DNA double strand during replication is performed by the replicative helicase DnaB. This protein allows for replication fork elongation by unwinding DNA and interacting with DnaG primase. DnaB is composed of two domains: an N-terminal domain (NTD) and a C-terminal domain (CTD) connected by a flexible linker. The protein forms two-tiered hexamers composed of a NTD-ring and a CTD-ring. In Escherichia coli, the initiator protein DnaA binds to the origin of replication oriC and induces the opening of a AT-rich region. The replicative helicase DnaB is then loaded onto single stranded DNA by interacting with DnaA and with the AAA+ helicase loader DnaC. However, AAA+ loaders are absent in 80% of the bacterial genome, raising the question of how helicases are loaded in these bacteria [1]. In the genome of human pathogen Helicobacter pylori, no AAA+ loader has been identified. Moreover H. pylori DnaB (HpDnaB) has the ability to support replication of an otherwise unviable E. coli strain that bears a defective copy of DnaC by complementation [2]. In order to better understand the properties of HpDnaB we have first shown that HpDnaB forms double hexamers by negative stain electron microscopy [3]. Then, we have then solved the crystal structure of HpDnaB at a resolution of 6.7Å by X-ray crystallography with Rfree/Rfactor of 0.29/0.25. The structure reveals that the protein adopts a new dodecameric arrangement generated by crystallographic three fold symmetry. When compared to hexameric DnaBs, the hexamer of HpDnaB displays an original combination of NTD-ring and CTD-ring symmetries, intermediate between apo and ADP-bound structure. Biochemistry studies of HpDnaB interaction with HpDnaG-CTD and ssDNA provides mechanistic insights into the initial steps of DNA replication in H. pylori. Our results offer an alternative solution of helicase loading and DNA replication initiation in H. pylori and possibly other bacteria that do not employ helicase loaders.

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4

Huang, Yen-Hua, and Cheng-Yang Huang. "Structural Insight into the DNA-Binding Mode of the Primosomal Proteins PriA, PriB, and DnaT." BioMed Research International 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/195162.

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Replication restart primosome is a complex dynamic system that is essential for bacterial survival. This system uses various proteins to reinitiate chromosomal DNA replication to maintain genetic integrity after DNA damage. The replication restart primosome inEscherichia coliis composed of PriA helicase, PriB, PriC, DnaT, DnaC, DnaB helicase, and DnaG primase. The assembly of the protein complexes within the forked DNA responsible for reloading the replicative DnaB helicase anywhere on the chromosome for genome duplication requires the coordination of transient biomolecular interactions. Over the last decade, investigations on the structure and mechanism of these nucleoproteins have provided considerable insight into primosome assembly. In this review, we summarize and discuss our current knowledge and recent advances on the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT.

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5

Sharma, Dhakaram Pangeni, Ramachandran Vijayan, Syed Arif Abdul Rehman, and Samudrala Gourinath. "Structural insights into the interaction of helicase and primase in Mycobacterium tuberculosis." Biochemical Journal 475, no. 21 (November 15, 2018): 3493–509. http://dx.doi.org/10.1042/bcj20180673.

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The helicase–primase interaction is an essential event in DNA replication and is mediated by the highly variable C-terminal domain of primase (DnaG) and N-terminal domain of helicase (DnaB). To understand the functional conservation despite the low sequence homology of the DnaB-binding domains of DnaGs of eubacteria, we determined the crystal structure of the helicase-binding domain of DnaG from Mycobacterium tuberculosis (MtDnaG-CTD) and did so to a resolution of 1.58 Å. We observed the overall structure of MtDnaG-CTD to consist of two subdomains, the N-terminal globular region (GR) and the C-terminal helical hairpin region (HHR), connected by a small loop. Despite differences in some of its helices, the globular region was found to have broadly similar arrangements across the species, whereas the helical hairpins showed different orientations. To gain insights into the crucial helicase–primase interaction in M. tuberculosis, a complex was modeled using the MtDnaG-CTD and MtDnaB-NTD crystal structures. Two nonconserved hydrophobic residues (Ile605 and Phe615) of MtDnaG were identified as potential key residues interacting with MtDnaB. Biosensor-binding studies showed a significant decrease in the binding affinity of MtDnaB-NTD with the Ile605Ala mutant of MtDnaG-CTD compared with native MtDnaG-CTD. The loop, connecting the two helices of the HHR, was concluded to be largely responsible for the stability of the DnaB–DnaG complex. Also, MtDnaB-NTD showed micromolar affinity with DnaG-CTDs from Escherichia coli and Helicobacter pylori and unstable binding with DnaG-CTD from Vibrio cholerae. The interacting domains of both DnaG and DnaB demonstrate the species-specific evolution of the replication initiation system.

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6

Nagata, Koji, Akitoshi Okada, Jun Ohtsuka, Takatoshi Ohkuri, Yusuke Akama, Yukari Sakiyama, Erika Miyazaki, et al. "Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding." Journal of Biochemistry 167, no. 1 (October 30, 2019): 1–14. http://dx.doi.org/10.1093/jb/mvz087.

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Abstract Loading the bacterial replicative helicase DnaB onto DNA requires a specific loader protein, DnaC/DnaI, which creates the loading-competent state by opening the DnaB hexameric ring. To understand the molecular mechanism by which DnaC/DnaI opens the DnaB ring, we solved 3.1-Å co-crystal structure of the interaction domains of Escherichia coli DnaB–DnaC. The structure reveals that one N-terminal domain (NTD) of DnaC interacts with both the linker helix of a DnaB molecule and the C-terminal domain (CTD) of the adjacent DnaB molecule by forming a three α-helix bundle, which fixes the relative orientation of the two adjacent DnaB CTDs. The importance of the intermolecular interface in the crystal structure was supported by the mutational data of DnaB and DnaC. Based on the crystal structure and other available information on DnaB–DnaC structures, we constructed a molecular model of the hexameric DnaB CTDs bound by six DnaC NTDs. This model suggested that the binding of a DnaC would cause a distortion in the hexameric ring of DnaB. This distortion of the DnaB ring might accumulate by the binding of up to six DnaC molecules, resulting in the DnaB ring to open.

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7

Donate, L. E., M. Bárcena, O. Llorca, N. Dixon, and J. M. Carazo. "Quaternary Polymorphism in Helicases and the DnaB.DnaC Complex." Microscopy and Microanalysis 6, S2 (August 2000): 272–73. http://dx.doi.org/10.1017/s1431927600033857.

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Strand separation in double stranded DNA is achieved in vivo by a class of enzymes called helicases in a process fuelled by hydrolysis of nucleoside triphosphates. DnaB is the major replicative helicase in E.coli. For chromosomal replication to initiate, DnaB needs to interact with a partner protein, namely DnaC, which after properly loading DnaB onto the DNA template at the origin of replication is subsequently released from the complex. DnaB turns to be functionally active as a helicase only after DnaC has been released from the complex. The native DnaB is a homohexamer of molecular weight 318 kD. In the presence of ATP and Mg2+, the hexameric DnaB has been shown to form a complex with six molecules of DnaC (total molecular weight of the complex: 480 kD).The reconstructed 3D volume of the DnaB hexamer obtained from frozen-hydrated specimens showed the DnaB oligomer as a particle possessing three-fold rather than six-fold symmetry, despite DnaB being made up by six identical subunits.

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8

Saveson, Catherine J., and Susan T. Lovett. "Enhanced Deletion Formation by Aberrant DNA Replication in Escherichia coli." Genetics 146, no. 2 (June 1, 1997): 457–70. http://dx.doi.org/10.1093/genetics/146.2.457.

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Repeated genes and sequences are prone to genetic rearrangements including deletions. We have investigated deletion formation in Escherichia coli strains mutant for various replication functions. Deletion was selected between 787 base pair tandem repeats carried either on a ColE1-derived plasmid or on the E. coli chromosome. Only mutations in functions associated with DNA Polymerase III elevated deletion rates in our assays. Especially large increases were observed in strains mutant in dnaQ the ϵ editing subunit of Pol III, and dnuB, the replication fork helicase. Mutations in several other functions also altered deletion formation: the α polymerase (dnaE), the γ clamp loader complex (holC, dnaX), and the β clamp (dnaN) subunits of Pol III and the primosomal proteins, dnaC and priA. Aberrant replication stimulated deletions through several pathways. Whereas the elevation in dnaB strains was mostly recA- and lexA-dependent, that in dnaQ strains was mostly recA- and lexA-independent. Deletion product analysis suggested that slipped mispairing, producing monomeric replicon products, may be preferentially increased in a dnaQ mutant and sister-strand exchange, producing dimeric replicon products, may be elevated in dnaE mutants. We conclude that aberrant Polymerase III replication can stimulate deletion events through several mechanisms of deletion and via both recA-dependent and independent pathways.

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9

Odegrip, Richard, Stephan Schoen, Elisabeth Haggård-Ljungquist, Kyusung Park, and Dhruba K. Chattoraj. "The Interaction of Bacteriophage P2 B Protein with Escherichia coli DnaB Helicase." Journal of Virology 74, no. 9 (May 1, 2000): 4057–63. http://dx.doi.org/10.1128/jvi.74.9.4057-4063.2000.

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ABSTRACT Bacteriophage P2 requires several host proteins for lytic replication, including helicase DnaB but not the helicase loader, DnaC. Some genetic studies have suggested that the loading is done by a phage-encoded protein, P2 B. However, a P2 minichromosome containing only the P2 initiator gene A and a marker gene can be established as a plasmid without requiring the P2 B gene. Here we demonstrate that P2 B associates with DnaB. This was done by using the yeast two-hybrid system in vivo and was confirmed in vitro, where 35S-labeled P2 B bound specifically to DnaB adsorbed to Q Sepharose beads and monoclonal antibodies directed against the His-tagged P2 B protein were shown to coprecipitate the DnaB protein. Finally, P2 B was shown to stabilize the opening of a reporter origin, a reaction that is facilitated by the inactivation of DnaB. In this respect, P2 B was comparable to λ P protein, which is known to be capable of binding and inactivating the helicase while acting as a helicase loader. Even though P2 B has little similarity to other known or predicted helicase loaders, we suggest that P2 B is required for efficient loading of DnaB and that this role, although dispensable for P2 plasmid replication, becomes essential for P2 lytic replication.

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10

Spinks, Richard R., Lisanne M. Spenkelink, Sarah A. Stratmann, Zhi-Qiang Xu, N. Patrick J. Stamford, Susan E. Brown, Nicholas E. Dixon, Slobodan Jergic, and Antoine M. van Oijen. "DnaB helicase dynamics in bacterial DNA replication resolved by single-molecule studies." Nucleic Acids Research 49, no. 12 (June 17, 2021): 6804–16. http://dx.doi.org/10.1093/nar/gkab493.

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Abstract In Escherichia coli, the DnaB helicase forms the basis for the assembly of the DNA replication complex. The stability of DnaB at the replication fork is likely important for successful replication initiation and progression. Single-molecule experiments have significantly changed the classical model of highly stable replication machines by showing that components exchange with free molecules from the environment. However, due to technical limitations, accurate assessments of DnaB stability in the context of replication are lacking. Using in vitro fluorescence single-molecule imaging, we visualise DnaB loaded on forked DNA templates. That these helicases are highly stable at replication forks, indicated by their observed dwell time of ∼30 min. Addition of the remaining replication factors results in a single DnaB helicase integrated as part of an active replisome. In contrast to the dynamic behaviour of other replisome components, DnaB is maintained within the replisome for the entirety of the replication process. Interestingly, we observe a transient interaction of additional helicases with the replication fork. This interaction is dependent on the τ subunit of the clamp-loader complex. Collectively, our single-molecule observations solidify the role of the DnaB helicase as the stable anchor of the replisome, but also reveal its capacity for dynamic interactions.

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11

BISWAS, Subhasis B., Stephen FLOWERS, and Esther E. BISWAS-FISS. "Quantitative analysis of nucleotide modulation of DNA binding by DnaC protein of Escherichia coli." Biochemical Journal 379, no. 3 (May 1, 2004): 553–62. http://dx.doi.org/10.1042/bj20031255.

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In this study, we have presented the first report of Escherichia coli DnaC protein binding to ssDNA (single stranded DNA) in an apparent hexameric form. DnaC protein transfers DnaB helicase onto a nascent chromosomal DNA replication fork at oriC, the origin of E. coli DNA replication. In eukaryotes, Cdc6 protein may play a similar role in the DNA helicase loading in the replication fork during replication initiation at the origin. We have analysed the DNA-binding properties of DnaC protein and a quantitative analysis of the nucleotide regulation of DnaC–DNA and DnaC–DnaB interactions using fluorescence anisotropy and affinity sensor analysis. DnaC protein bound to ssDNA with low to moderate affinity and the affinity was strictly modulated by nucleotides. DnaC bound ssDNA in the complete absence of nucleotides. The DNA-binding affinity was significantly increased in the presence of ATP, but not ATP[S]. In the presence of ADP, the binding affinity decreased approximately fifty-fold. Both anisotropy and biosensor analyses demonstrated that with DnaC protein, ATP facilitated ssDNA binding, whereas ADP facilitated its dissociation from ssDNA, which is a characteristic of an ATP/ADP switch. Both ssDNA and nucleotides modulate DnaB6•DnaC6 complex formation, which has significant implications in DnaC protein function. Based on the thermodynamic data provided in this study, we have proposed a mechanism of DnaB loading on to ssDNA by DnaC protein.

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12

Felczak, Magdalena M., Sundari Chodavarapu, and Jon M. Kaguni. "DnaC, the indispensable companion of DnaB helicase, controls the accessibility of DnaB helicase by primase." Journal of Biological Chemistry 292, no. 51 (October 25, 2017): 20871–82. http://dx.doi.org/10.1074/jbc.m117.807644.

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13

Syeda, Aisha H., Adam J. M. Wollman, Alex L. Hargreaves, Jamieson A. L. Howard, Jan-Gert Brüning, Peter McGlynn, and Mark C. Leake. "Single-molecule live cell imaging of Rep reveals the dynamic interplay between an accessory replicative helicase and the replisome." Nucleic Acids Research 47, no. 12 (April 27, 2019): 6287–98. http://dx.doi.org/10.1093/nar/gkz298.

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Abstract DNA replication must cope with nucleoprotein barriers that impair efficient replisome translocation. Biochemical and genetic studies indicate accessory helicases play essential roles in replication in the presence of nucleoprotein barriers, but how they operate inside the cell is unclear. With high-speed single-molecule microscopy we observed genomically-encoded fluorescent constructs of the accessory helicase Rep and core replisome protein DnaQ in live Escherichia coli cells. We demonstrate that Rep colocalizes with 70% of replication forks, with a hexameric stoichiometry, indicating maximal occupancy of the single DnaB hexamer. Rep associates dynamically with the replisome with an average dwell time of 6.5 ms dependent on ATP hydrolysis, indicating rapid binding then translocation away from the fork. We also imaged PriC replication restart factor and observe Rep-replisome association is also dependent on PriC. Our findings suggest two Rep-replisome populations in vivo: one continually associating with DnaB then translocating away to aid nucleoprotein barrier removal ahead of the fork, another assisting PriC-dependent reloading of DnaB if replisome progression fails. These findings reveal how a single helicase at the replisome provides two independent ways of underpinning replication of protein-bound DNA, a problem all organisms face as they replicate their genomes.

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14

Soni, Rajesh K., Parul Mehra, Gauranga Mukhopadhyay, and Suman Kumar Dhar. "Helicobacter pylori DnaB helicase can bypass Escherichia coli DnaC function in vivo." Biochemical Journal 389, no. 2 (July 5, 2005): 541–48. http://dx.doi.org/10.1042/bj20050062.

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In Escherichia coli, DnaC is essential for loading DnaB helicase at oriC (the origin of chromosomal DNA replication). The question arises as to whether this model can be generalized to other species, since many eubacterial species fail to possess dnaC in their genomes. Previously, we have reported the characterization of HpDnaB (Helicobacter pylori DnaB) both in vitro and in vivo. Interestingly, H. pylori does not have a DnaC homologue. Using two different E. coli dnaC (EcdnaC) temperature-sensitive mutant strains, we report here the complementation of EcDnaC function by HpDnaB in vivo. These observations strongly suggest that HpDnaB can bypass EcDnaC activity in vivo.

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15

Cargemel, Claire, Stéphanie Marsin, Magali Noiray, Pierre Legrand, Halil Bounoua, Inès Li de la Sierra-Gallay, Hélène Walbott, and Sophie Quevillon-Cheruel. "The LH–DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders." Acta Crystallographica Section D Structural Biology 79, no. 2 (February 1, 2023): 177–87. http://dx.doi.org/10.1107/s2059798323000281.

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During the initiation step of bacterial genome replication, replicative helicases depend on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, most bacteria do not contain any of these genes, which are domesticated phage elements that have replaced the ancestral and unrelated loader gene dciA several times during evolution. To understand how DciA assists the loading of DnaB, the crystal structure of the complex from Vibrio cholerae was determined, in which two VcDciA molecules interact with a dimer of VcDnaB without changing its canonical structure. The data showed that the VcDciA binding site on VcDnaB is the conserved module formed by the linker helix LH of one monomer and the determinant helix DH of the second monomer. Interestingly, DnaC from Escherichia coli also targets this module onto EcDnaB. Thanks to their common target site, it was shown that VcDciA and EcDnaC could be functionally interchanged in vitro despite sharing no structural similarity. This represents a milestone in understanding the mechanism employed by phage helicase loaders to hijack bacterial replicative helicases during evolution.

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16

Thirlway, Jenny, and Panos Soultanas. "In the Bacillus stearothermophilus DnaB-DnaG Complex, the Activities of the Two Proteins Are Modulated by Distinct but Overlapping Networks of Residues." Journal of Bacteriology 188, no. 4 (February 15, 2006): 1534–39. http://dx.doi.org/10.1128/jb.188.4.1534-1539.2006.

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ABSTRACTWe demonstrate the primase activity ofBacillus stearothermophilusDnaG and show that it initiates at 3′-ATC-5′ and 3′-ATT-5′ sites synthesizing primers that are 22 or 23 nucleotides long. In the presence of the helicase DnaB the size distribution of primers is different, and a range of additional smaller primers are also synthesized. Nine residues from the N- and C-terminal domains of DnaB, as well as its linker region, have been reported previously to affect this interaction. InBacillus stearothermophilusonly three residues from the linker region (I119 and I125) and the N-terminal domain (Y88) of DnaB have been shown previously to have direct structural importance, and I119 and I125 mediate DnaG-induced effects on DnaB activity. The functions of the other residues (L138, T191, E192, R195, and M196) are still a mystery. Here we show that the E15A, Y88A, and E15A Y88A mutants bind DnaG but are not able to modulate primer size, whereas the R195A M196A mutant inhibited the primase activity. Therefore, four of these residues, E15 and Y88 (N-terminal domain) and R195 and M196 (C-terminal domain), mediate DnaB-induced effects on DnaG activity. Overall, the data suggest that the effects of DnaB on DnaG activity and vice versa are mediated by distinct but overlapping networks of residues.

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17

Behrmann, Megan S., Himasha M. Perera, Joy M. Hoang, Trisha A. Venkat, Bryan J. Visser, David Bates, and Michael A. Trakselis. "Targeted chromosomal Escherichia coli:dnaB exterior surface residues regulate DNA helicase behavior to maintain genomic stability and organismal fitness." PLOS Genetics 17, no. 11 (November 12, 2021): e1009886. http://dx.doi.org/10.1371/journal.pgen.1009886.

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Helicase regulation involves modulation of unwinding speed to maintain coordination of DNA replication fork activities and is vital for replisome progression. Currently, mechanisms for helicase regulation that involve interactions with both DNA strands through a steric exclusion and wrapping (SEW) model and conformational shifts between dilated and constricted states have been examined in vitro. To better understand the mechanism and cellular impact of helicase regulation, we used CRISPR-Cas9 genome editing to study four previously identified SEW-deficient mutants of the bacterial replicative helicase DnaB. We discovered that these four SEW mutations stabilize constricted states, with more fully constricted mutants having a generally greater impact on genomic stress, suggesting a dynamic model for helicase regulation that involves both excluded strand interactions and conformational states. These dnaB mutations result in increased chromosome complexities, less stable genomes, and ultimately less viable and fit strains. Specifically, dnaB:mut strains present with increased mutational frequencies without significantly inducing SOS, consistent with leaving single-strand gaps in the genome during replication that are subsequently filled with lower fidelity. This work explores the genomic impacts of helicase dysregulation in vivo, supporting a combined dynamic regulatory mechanism involving a spectrum of DnaB conformational changes and relates current mechanistic understanding to functional helicase behavior at the replication fork.

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18

Arias-Palomo, Ernesto, Valerie L. O’Shea, Iris V. Hood, and James M. Berger. "The Bacterial DnaC Helicase Loader Is a DnaB Ring Breaker." Cell 153, no. 2 (April 2013): 438–48. http://dx.doi.org/10.1016/j.cell.2013.03.006.

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19

Lin, Hsin-Hsien, and Cheng-Yang Huang. "Characterization of Flavonol Inhibition of DnaB Helicase: Real-Time Monitoring, Structural Modeling, and Proposed Mechanism." Journal of Biomedicine and Biotechnology 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/735368.

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DnaB helicases are motor proteins essential for DNA replication, repair, and recombination and may be a promising target for developing new drugs for antibiotic-resistant bacteria. Previously, we established that flavonols significantly decreased the binding ability ofKlebsiella pneumoniaeDnaB helicase (KpDnaB) to dNTP. Here, we further investigated the effect of flavonols on the inhibition of the ssDNA binding, ATPase activity, and dsDNA-unwinding activity ofKpDnaB. The ssDNA-stimulated ATPase activity ofKpDnaB was decreased to 59%, 75%, 65%, and 57%, in the presence of myricetin, quercetin, kaempferol, and galangin, respectively. The ssDNA-binding activity ofKpDnaB was only slightly decreased by flavonols. We used a continuous fluorescence assay, based on fluorescence resonance energy transfer (FRET), for real-time monitoring ofKpDnaB helicase activity in the absence and presence of flavonols. Using this assay, the flavonol-mediated inhibition of the dsDNA-unwinding activity ofKpDnaB was observed. Modeled structures of bound and unbound DNA showed flavonols binding toKpDnaB with distinct poses. In addition, these structural models indicated that L214 is a key residue in binding any flavonol. On the basis of these results, we proposed mechanisms for flavonol inhibition of DNA helicase. The resulting information may be useful in designing compounds that targetK. pneumoniaeand other bacterial DnaB helicases.

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20

Hanada, Katsuhiro, Teruhito Yamashita, Yuko Shobuike, and Hideo Ikeda. "Role of DnaB Helicase in UV-Induced Illegitimate Recombination in Escherichia coli." Journal of Bacteriology 183, no. 17 (September 1, 2001): 4964–69. http://dx.doi.org/10.1128/jb.183.17.4964-4969.2001.

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ABSTRACT To study the involvement of DNA replication in UV-induced illegitimate recombination, we examined the effect of temperature-sensitive dnaB mutations on illegitimate recombination and found that the frequency of illegitimate recombination was reduced by an elongation-deficient mutation,dnaB14, but not by an initiation-deficient mutation,dnaB252. This result indicates that DNA replication is required for UV-induced illegitimate recombination. In addition, thednaB14 mutation also affected spontaneous or UV-induced illegitimate recombination enhanced by the recQmutation. Nucleotide sequence analyses of the recombination junctions showed that DnaB-mediated illegitimate recombination is short homology dependent. Previously, Michel et al. (B. Michel, S. Ehrlich, and M. Uzest, EMBO J. 16:430–438, 1997) showed that thermal treatment of the temperature-sensitive dnaB8 mutant induces double-stranded breaks, implying that induction of illegitimate recombination occurs. To explain the discrepancy between the observations, we propose a model for DnaB function, in which thednaB mutations may exhibit two types of responses, early and late responses, for double-stranded break formation. In the early response, replication forks stall at damaged DNA, resulting in the formation of double-stranded breaks, and the dnaB14mutation reduces the double-stranded breaks shortly after temperature shift-up. On the other hand, in the late response, the arrested replication forks mediated by the dnaB8 mutation may induce double-stranded breaks after prolonged incubation.

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21

Shadrick, William R., Jean Ndjomou, Rajesh Kolli, Sourav Mukherjee, Alicia M. Hanson, and David N. Frick. "Discovering New Medicines Targeting Helicases." Journal of Biomolecular Screening 18, no. 7 (March 27, 2013): 761–81. http://dx.doi.org/10.1177/1087057113482586.

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Helicases are ubiquitous motor proteins that separate and/or rearrange nucleic acid duplexes in reactions fueled by adenosine triphosphate (ATP) hydrolysis. Helicases encoded by bacteria, viruses, and human cells are widely studied targets for new antiviral, antibiotic, and anticancer drugs. This review summarizes the biochemistry of frequently targeted helicases. These proteins include viral enzymes from herpes simplex virus, papillomaviruses, polyomaviruses, coronaviruses, the hepatitis C virus, and various flaviviruses. Bacterial targets examined include DnaB-like and RecBCD-like helicases. The human DEAD-box protein DDX3 is the cellular antiviral target discussed, and cellular anticancer drug targets discussed are the human RecQ-like helicases and eIF4A. We also review assays used for helicase inhibitor discovery and the most promising and common helicase inhibitor chemotypes, such as nucleotide analogues, polyphenyls, metal ion chelators, flavones, polycyclic aromatic polymers, coumarins, and various DNA binding pharmacophores. Also discussed are common complications encountered while searching for potent helicase inhibitors and possible solutions for these problems.

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22

Miller, Christine, and Stanley N. Cohen. "Separate Roles of Escherichia coliReplication Proteins in Synthesis and Partitioning of pSC101 Plasmid DNA." Journal of Bacteriology 181, no. 24 (December 15, 1999): 7552–57. http://dx.doi.org/10.1128/jb.181.24.7552-7557.1999.

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ABSTRACT We report here that the Escherichia coli replication proteins DnaA, which is required to initiate replication of both the chromosome and plasmid pSC101, and DnaB, the helicase that unwinds strands during DNA replication, have effects on plasmid partitioning that are distinct from their functions in promoting plasmid DNA replication. Temperature-sensitive dnaB mutants cultured under conditions permissive for DNA replication failed to partition plasmids normally, and when cultured under conditions that prevent replication, they showed loss of the entire multicopy pool of plasmid replicons from half of the bacterial population during a single cell division. As was observed previously for DnaA, overexpression of the wild-type DnaB protein conversely stabilized the inheritance of partition-defective plasmids while not increasing plasmid copy number. The identification of dnaA mutations that selectively affected either replication or partitioning further demonstrated the separate roles of DnaA in these functions. The partition-related actions of DnaA were localized to a domain (the cell membrane binding domain) that is physically separate from the DnaA domain that interacts with other host replication proteins. Our results identify bacterial replication proteins that participate in partitioning of the pSC101 plasmid and provide evidence that these proteins mediate plasmid partitioning independently of their role in DNA synthesis.

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23

Yamashita, Teruhito, Katsuhiro Hanada, Mihoko Iwasaki, Hirotaka Yamaguchi, and Hideo Ikeda. "Illegitimate Recombination Induced by Overproduction of DnaB Helicase in Escherichia coli." Journal of Bacteriology 181, no. 15 (August 1, 1999): 4549–53. http://dx.doi.org/10.1128/jb.181.15.4549-4553.1999.

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ABSTRACT Illegitimate recombination that usually takes place at a low frequency is greatly enhanced by treatment with DNA-damaging agents. It is thought that DNA double-strand breaks induced by this DNA damage are important for initiation of illegitimate recombination. Here we show that illegitimate recombination is enhanced by overexpression of the DnaB protein in Escherichia coli. The recombination enhanced by DnaB overexpression occurred between short regions of homology. We propose a model for the initiation of illegitimate recombination in which DnaB overexpression may excessively unwind DNA at replication forks and induce double-strand breaks, resulting in illegitimate recombination. The defect in RecQ has a synergistic effect on the increased illegitimate recombination in cells containing the overproduced DnaB protein, implying that DnaB works in the same pathway as RecQ does but that they work at different steps.

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24

Slavcev, Roderick A., and Barbara E. Funnell. "Identification and Characterization of a Novel Allele of Escherichia coli dnaB Helicase That Compromises the Stability of Plasmid P1." Journal of Bacteriology 187, no. 4 (February 15, 2005): 1227–37. http://dx.doi.org/10.1128/jb.187.4.1227-1237.2005.

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ABSTRACT Bacteriophage P1 lysogenizes Escherichia coli cells as a plasmid with approximately the same copy number as the copy number of the host chromosome. Faithful inheritance of the plasmids relies upon proper DNA replication, as well as a partition system that actively segregates plasmids to new daughter cells. We genetically screened for E. coli chromosomal mutations that influenced P1 stability and identified a novel temperature-sensitive allele of the dnaB helicase gene (dnaB277) that replaces serine 277 with a leucine residue (DnaB S277L). This allele conferred a severe temperature-sensitive phenotype to the host; dnaB277 cells were not viable at temperatures above 34°C. Shifting dnaB277 cells to 42°C resulted in an immediate reduction in the rate of DNA synthesis and extensive cell filamentation. The dnaB277 allele destabilized P1 plasmids but had no significant influence on the stability of the F low-copy-number plasmid. This observation suggests that there is a specific requirement for DnaB in P1 plasmid maintenance in addition to the general requirement for DnaB as the replicative helicase during elongation.

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25

Soni, R. K. "Functional characterization of Helicobacter pylori DnaB helicase." Nucleic Acids Research 31, no. 23 (December 1, 2003): 6828–40. http://dx.doi.org/10.1093/nar/gkg895.

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26

Biswas, Esther E., Marjorie H. Barnes, Donald T. Moir, and Subhasis B. Biswas. "An Essential DnaB Helicase of Bacillus anthracis: Identification, Characterization, and Mechanism of Action." Journal of Bacteriology 191, no. 1 (October 17, 2008): 249–60. http://dx.doi.org/10.1128/jb.01259-08.

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ABSTRACT We have described a novel essential replicative DNA helicase from Bacillus anthracis, the identification of its gene, and the elucidation of its enzymatic characteristics. Anthrax DnaB helicase (DnaBBA) is a 453-amino-acid, 50-kDa polypeptide with ATPase and DNA helicase activities. DnaBBA displayed distinct enzymatic and kinetic properties. DnaBBA has low single-stranded DNA (ssDNA)-dependent ATPase activity but possesses a strong 5′→3′ DNA helicase activity. The stimulation of ATPase activity appeared to be a function of the length of the ssDNA template rather than of ssDNA binding alone. The highest specific activity was observed with M13mp19 ssDNA. The results presented here indicated that the ATPase activity of DnaBBA was coupled to its migration on an ssDNA template rather than to DNA binding alone. It did not require nucleotide to bind ssDNA. DnaBBA demonstrated a strong DNA helicase activity that required ATP or dATP. Therefore, DnaBBA has an attenuated ATPase activity and a highly active DNA helicase activity. Based on the ratio of DNA helicase and ATPase activities, DnaBBA is highly efficient in DNA unwinding and its coupling to ATP consumption.

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27

Sandler, Steven J. "Multiple Genetic Pathways for Restarting DNA Replication Forks in Escherichia coli K-12." Genetics 155, no. 2 (June 1, 2000): 487–97. http://dx.doi.org/10.1093/genetics/155.2.487.

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Abstract In Escherichia coli, the primosome assembly proteins, PriA, PriB, PriC, DnaT, DnaC, DnaB, and DnaG, are thought to help to restart DNA replication forks at recombinational intermediates. Redundant functions between priB and priC and synthetic lethality between priA2::kan and rep3 mutations raise the possibility that there may be multiple pathways for restarting replication forks in vivo. Herein, it is shown that priA2::kan causes synthetic lethality when placed in combination with either Δrep::kan or priC303:kan. These determinations were made using a nonselective P1 transduction-based viability assay. Two different priA2::kan suppressors (both dnaC alleles) were tested for their ability to rescue the priA-priC and priA-rep double mutant lethality. Only dnaC809,820 (and not dnaC809) could rescue the lethality in each case. Additionally, it was shown that the absence of the 3′-5′ helicase activity of both PriA and Rep is not the critical missing function that causes the synthetic lethality in the rep-priA double mutant. One model proposes that replication restart at recombinational intermediates occurs by both PriA-dependent and PriA-independent pathways. The PriA-dependent pathways require at least priA and priB or priC, and the PriA-independent pathway requires at least priC and rep. It is further hypothesized that the dnaC809 suppression of priA2::kan requires priC and rep, whereas dnaC809,820 suppression of priA2::kan does not.

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28

Donate, Luis-Enrique, Óscar Llorca, Montserrat Bárcena, Susan E. Brown, Nicholas E. Dixon, and José-Marı́a Carazo. "pH-controlled quaternary states of hexameric DnaB helicase." Journal of Molecular Biology 303, no. 3 (October 2000): 383–93. http://dx.doi.org/10.1006/jmbi.2000.4132.

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29

Carr, Kevin M., and Jon M. Kaguni. "Escherichia coliDnaA Protein Loads a Single DnaB Helicase at a DnaA Box Hairpin." Journal of Biological Chemistry 277, no. 42 (August 2, 2002): 39815–22. http://dx.doi.org/10.1074/jbc.m205031200.

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30

Zhang, Yi, Fude Yang, Yeh-Chih Kao, Michael G. Kurilla, David L. Pompliano, and Ira B. Dicker. "Homogenous Assays for Escherichia coli DnaB-Stimulated DnaG Primase and DnaB Helicase and Their Use in Screening for Chemical Inhibitors." Analytical Biochemistry 304, no. 2 (May 2002): 174–79. http://dx.doi.org/10.1006/abio.2002.5627.

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31

Delagoutte, Emmanuelle, and Peter H. von Hippel. "Helicase mechanisms and the coupling of helicases within macromolecular machines Part II: Integration of helicases into cellular processes." Quarterly Reviews of Biophysics 36, no. 1 (January 27, 2003): 1–69. http://dx.doi.org/10.1017/s0033583502003864.

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1. Helicases as components of macromolecular machines 32. Helicases in replication 72.1 The loading of replicative helicases 72.1.1 Loading Rep helicase at the replication origin of bacteriophage ϕX174 72.1.2 How is a ssDNA strand passed through (and bound in?) the central channel of the hexameric replicative helicases? 82.1.3 Loading of E. coli DnaB helicase in the absence of an auxiliary protein-loading factor 82.1.4 The T7 gp4 primase-helicase is loaded by means of a facilitated ring-opening mechanism 102.1.5 Bacteriophage T4 gp61 primase can be viewed as a loading factor for the homologous gp41 helicase 112.1.6 DnaC serves as the loading factor for E. coli DnaB helicase 112.1.7 The role of bacteriophage T4 gp59 in loading the T4 gp41 helicase 122.1.8 Loading of helicases onto ssDNA covered by ssDNA-binding proteins (SSBPs) 152.2 DNA polymerase and ssDNA-binding proteins can serve as reporters for replicative helicases in their elongation mode 172.2.1 The DNA polymerase, the sliding clamp, and the clamp loader 172.2.2 The role of ssDNA-binding protein 182.2.3 Coupling is achieved by the DNA polymerase and the ssDNA-binding protein 182.3 Arrest of replicative helicases 182.3.1 The Ter sites and termination proteins 192.3.2 Models for orientation-specific fork arrest 203. Helicases in transcription 203.1 Assisted loading of E. coli RNAP by the sigma70 initiation factor 213.1.1 RNAP holoenzyme formation 233.1.2 Formation of closed promoter complexes RPc and RPi 243.1.3 Strand separation and the formation of the open complex 243.1.4 Promoter clearance 243.1.5 Conclusions 253.2 Transcript formation serves as a monitor (reporter) of RNAP helicase activity in the elongation phase of transcription 253.2.1 Structural aspects of transcription complex translocation 263.2.2 Transcript elongation is an approximately isoenergetic process 263.3 Termination of transcription 273.3.1 Intrinsic termination 273.3.2 Termination by transcription-termination helicase Rho 283.3.3 Conclusions 293.4 Loading of the Rho transcription-termination helicase 294. Helicases in nucleotide excision repair (NER) 304.1 The limited strand-separating activity of the UvrAB complex 314.2 UvrB is a DNA helicase adapted for NER 334.2.1 The ATP-binding site of UvrB is similar to that of other helicases 334.2.2 The putative DNA-binding site 334.3 UvrA as a UvrB loader 344.4 Assisted targeting of UvrAB to the transcribed strand of DNA sequences undergoing active transcription 344.4.1 Targeting of UvrAB to damaged DNA sites in the vicinity of promoters is assisted by RNAP 344.4.2 TRCF participates in the assisted targeting of UvrAB to a transcribing RNAP stalled by a DNA lesion 354.4.3 Conclusions 364.5 UvrC endonuclease is the reporter of UvrAB helicase activity in incision 364.6 Post-incision events 364.7 Mechanistic details of the helicase activity of UvrD 374.7.1 Structural organization and conformational changes 374.7.2 Translocation and unwinding activities 384.7.3 Step size of DNA unwinding 384.7.4 Oligomeric state 395. Helicases in recombination 395.1 Role of RecBCD and RecQ in the initiation of recombination 405.1.1 The RecBCD enzyme 405.1.1.1 Loading of RecBCD onto its DNA substrate does not require a separate loading protein 405.1.1.2 The endonuclease activity of RecD, and the binding of SSB protein, serve as reporters of RecBCD helicase activity 405.1.1.3 RecA can also serve as a reporter of RecBCD helicase activity 415.1.1.4 RecBCD step size and unwinding mechanism 415.1.1.5 RecBCD unwinding efficiency 425.1.2 The RecQ protein 435.2 Strand-exchange reaction catalyzed by RecA 435.2.1 The nucleoprotein filament 445.2.2 The strand-exchange reaction 465.2.2.1 A ‘minor-groove’ to ‘major-groove’ triple-helix transition 465.2.2.2 Role of the secondary DNA-binding site of RecA 465.2.2.3 SSB protein stimulates the strand-exchange reaction 465.2.2.4 Cost of the strand-exchange reaction 475.2.3 Conclusion: RecA is a ‘scaffolding’ protein that prepares DNA for a coupled unpairing–reannealing reaction 485.3 Role of the RuvAB helicase in processing recombination intermediates by a branch migration mechanism 485.3.1 A brief description of the RuvA and RuvB proteins 495.3.2 Crystal structures of RuvA and the RuvA–Holliday junction complex 505.3.3 RuvA as a scaffolding protein that prepares the homoduplex for strand separation 515.3.4 Branch migration mechanism 516. RNA unwindases in the spliceosome 526.1 RNA structural rearrangements within the spliceosome: an overview 526.2 The spliceosome consumes chemical free energy 546.3 RNA structural alterations require the concerted (or coupled) action of unwinding and reannealing proteins 546.4 The reannealing proteins of the spliceosome: contribution of the RNA recognition motifs (RRMs) 556.5 The RNA unwindases of the spliceosome 556.6 RNA targets of the RNA unwindases 567. Conclusions and overview 578. Acknowledgments 589. References 59In Part I of this review [Delagoutte & von Hippel, Quarterly Reviews of Biophysics (2002) 35, 431–478] we summarized what is known about the properties, mechanisms, and structures of the various helicases that catalyze the unwinding of double-stranded nucleic acids. Here, in Part II, we consider these helicases as tightly integrated (or coupled) components of the various macromolecular machines within which they operate. The biological processes that are considered explicitly include DNA replication, recombination, and nucleotide excision repair, as well as RNA transcription and splicing. We discuss the activities of the constituent helicases (and their protein partners) in the assembly (or loading) of the relevant complex onto (and into) the specific nucleic acid sites at which the actions of the helicase-containing complexes are to be initiated, the mechanisms by which the helicases (and the complexes) translocate along the nucleic acids in discharging their functions, and the reactions that are used to terminate the translocation of the helicase-containing complexes at specific sites within the nucleic acid ‘substrate’. We emerge with several specific descriptions of how helicases function within the above processes of genetic expression which, we hope, can serve as paradigms for considering how helicases may also be coupled and function within other macromolecular machines.

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32

Weigel, Christoph, and Harald Seitz. "Strand-specific loading of DnaB helicase by DnaA to a substrate mimicking unwound oriC." Molecular Microbiology 46, no. 4 (November 6, 2002): 1149–56. http://dx.doi.org/10.1046/j.1365-2958.2002.03232.x.

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33

Bailey, S., W. K. Eliason, and T. A. Steitz. "Structure of Hexameric DnaB Helicase and Its Complex with a Domain of DnaG Primase." Science 318, no. 5849 (October 19, 2007): 459–63. http://dx.doi.org/10.1126/science.1147353.

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34

Poggi, Silvana, and Sathees Chandra. "Genomics Analysis of Replicative Helicase DnaB Sequences in Proteobacteria." Acta Informatica Medica 22, no. 4 (2014): 249. http://dx.doi.org/10.5455/aim.2014.22.249-254.

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35

Bujalowski, Wlodzimierz. "Expanding the physiological role of the hexameric DnaB helicase." Trends in Biochemical Sciences 28, no. 3 (March 2003): 116–18. http://dx.doi.org/10.1016/s0968-0004(03)00034-3.

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36

Santamarı́a, David, Guillermo de la Cueva, Marı́a Luisa Martı́nez-Robles, Dora B. Krimer, Pablo Hernández, and Jorge B. Schvartzman. "DnaB Helicase Is Unable to Dissociate RNA-DNA Hybrids." Journal of Biological Chemistry 273, no. 50 (December 11, 1998): 33386–96. http://dx.doi.org/10.1074/jbc.273.50.33386.

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37

Griep, Mark A., Sheldon Blood, Marilynn A. Larson, Scott A. Koepsell, and Steven H. Hinrichs. "Myricetin inhibits Escherichia coli DnaB helicase but not primase." Bioorganic & Medicinal Chemistry 15, no. 22 (November 2007): 7203–8. http://dx.doi.org/10.1016/j.bmc.2007.07.057.

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38

Sandler, Steven J., Hardeep S. Samra, and Alvin J. Clark. "Differential Suppression of priA2::kan Phenotypes in Escherichia coli K-12 by Mutations in priA, lexA, and dnaC." Genetics 143, no. 1 (May 1, 1996): 5–13. http://dx.doi.org/10.1093/genetics/143.1.5.

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Abstract First identified as an essential component of the ϕX174 in vitro DNA replication system, PriA has ATPase, helicase, translocase, and primosome-assembly activities. priA1::kan strains of Escherichia coli are sensitive to UV irradiation, deficient in homologous recombination following transduction, and filamentous. priA2::kan strains have eightfold higher levels of uninduced SOS expression than wild type. We show that (1) priA1::kan strains have eightfold higher levels of uninduced SOS expression, (2) priA2::kan strains are UVS and Rec−, (3) lexA3 suppresses the high basal levels of SOS expression of a priA2::kan strain, and (4) plasmid-encoded priA300 (K230R), a mutant allele retaining only the primosome-assembly activity of priA+, restores both UVR and Rec+ phenotypes to a priA2::kan strain. Finally, we have isolated 17 independent UVR Rec+ revertants of priA2::kan strains that carry extragenic suppressors. All 17 map in the C-terminal half of the dnaC gene. DnaC loads the DnaB helicase onto DNA as a prelude for primosome assembly and DNA replication. We conclude that priA's primosome-assembly activity is essential for DNA repair and recombination and that the dnaC suppressor mutations allow these processes to occur in the absence of priA.

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39

Belle, Jerilyn J., Andrew Casey, Charmain T. Courcelle, and Justin Courcelle. "Inactivation of the DnaB Helicase Leads to the Collapse and Degradation of the Replication Fork: a Comparison to UV-Induced Arrest." Journal of Bacteriology 189, no. 15 (May 25, 2007): 5452–62. http://dx.doi.org/10.1128/jb.00408-07.

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ABSTRACT Replication forks face a variety of structurally diverse impediments that can prevent them from completing their task. The mechanism by which cells overcome these hurdles is likely to vary depending on the nature of the obstacle and the strand in which the impediment is encountered. Both UV-induced DNA damage and thermosensitive replication proteins have been used in model systems to inhibit DNA replication and characterize the mechanism by which it recovers. In this study, we examined the molecular events that occur at replication forks following inactivation of a thermosensitive DnaB helicase and found that they are distinct from those that occur following arrest at UV-induced DNA damage. Following UV-induced DNA damage, the integrity of replication forks is maintained and protected from extensive degradation by RecA, RecF, RecO, and RecR until replication can resume. By contrast, inactivation of DnaB results in extensive degradation of the nascent and leading-strand template DNA and a loss of replication fork integrity as monitored by two-dimensional agarose gel analysis. The degradation that occurs following DnaB inactivation partially depends on several genes, including recF, recO, recR, recJ, recG, and xonA. Furthermore, the thermosensitive DnaB allele prevents UV-induced DNA degradation from occurring following arrest even at the permissive temperature, suggesting a role for DnaB prior to loading of the RecFOR proteins. We discuss these observations in relation to potential models for both UV-induced and DnaB(Ts)-mediated replication inhibition.

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40

Bailey, Scott, William K. Eliason, and Thomas A. Steitz. "The crystal structure of the Thermus aquaticus DnaB helicase monomer." Nucleic Acids Research 35, no. 14 (July 2007): 4728–36. http://dx.doi.org/10.1093/nar/gkm507.

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41

Bujalowski, W., M. M. Klonowska, and M. J. Jezewska. "Oligomeric structure of Escherichia coli primary replicative helicase DnaB protein." Journal of Biological Chemistry 269, no. 50 (December 1994): 31350–58. http://dx.doi.org/10.1016/s0021-9258(18)31701-0.

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42

Johnson, Scott K., Saumitri Bhattacharyya, and Mark A. Griep. "DnaB Helicase Stimulates Primer Synthesis Activity on Short Oligonucleotide Templates†." Biochemistry 39, no. 4 (February 2000): 736–44. http://dx.doi.org/10.1021/bi991554l.

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43

Ribeck, Noah, Daniel L. Kaplan, Irina Bruck, and Omar A. Saleh. "DnaB Helicase Activity Is Modulated by DNA Geometry and Force." Biophysical Journal 99, no. 7 (October 2010): 2170–79. http://dx.doi.org/10.1016/j.bpj.2010.07.039.

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44

LeBowitz, J. H., and R. McMacken. "The Escherichia coli dnaB replication protein is a DNA helicase." Journal of Biological Chemistry 261, no. 10 (April 1986): 4738–48. http://dx.doi.org/10.1016/s0021-9258(17)38564-2.

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45

Itsathitphaisarn, Ornchuma, Richard A. Wing, William K. Eliason, Jimin Wang, and Thomas A. Steitz. "The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation." Cell 151, no. 2 (October 2012): 267–77. http://dx.doi.org/10.1016/j.cell.2012.09.014.

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46

Chen, Cheng-Chieh, and Cheng-Yang Huang. "Inhibition of Klebsiella Pneumoniae DnaB Helicase by the Flavonol Galangin." Protein Journal 30, no. 1 (January 2011): 59–65. http://dx.doi.org/10.1007/s10930-010-9302-0.

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47

Neylon, Cameron, Andrew V. Kralicek, Thomas M. Hill, and Nicholas E. Dixon. "Replication Termination in Escherichia coli: Structure and Antihelicase Activity of the Tus-Ter Complex." Microbiology and Molecular Biology Reviews 69, no. 3 (September 2005): 501–26. http://dx.doi.org/10.1128/mmbr.69.3.501-526.2005.

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SUMMARY The arrest of DNA replication in Escherichia coli is triggered by the encounter of a replisome with a Tus protein-Ter DNA complex. A replication fork can pass through a Tus-Ter complex when traveling in one direction but not the other, and the chromosomal Ter sites are oriented so replication forks can enter, but not exit, the terminus region. The Tus-Ter complex acts by blocking the action of the replicative DnaB helicase, but details of the mechanism are uncertain. One proposed mechanism involves a specific interaction between Tus-Ter and the helicase that prevents further DNA unwinding, while another is that the Tus-Ter complex itself is sufficient to block the helicase in a polar manner, without the need for specific protein-protein interactions. This review integrates three decades of experimental information on the action of the Tus-Ter complex with information available from the Tus-TerA crystal structure. We conclude that while it is possible to explain polar fork arrest by a mechanism involving only the Tus-Ter interaction, there are also strong indications of a role for specific Tus-DnaB interactions. The evidence suggests, therefore, that the termination system is more subtle and complex than may have been assumed. We describe some further experiments and insights that may assist in unraveling the details of this fascinating process.

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48

Marsin, Stéphanie, Yazid Adam, Claire Cargemel, Jessica Andreani, Sonia Baconnais, Pierre Legrand, Ines Li de la Sierra-Gallay, et al. "Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase." Nucleic Acids Research 49, no. 11 (June 9, 2021): 6569–86. http://dx.doi.org/10.1093/nar/gkab463.

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Abstract Replicative helicases are essential proteins that unwind DNA in front of replication forks. Their loading depends on accessory proteins and in bacteria, DnaC and DnaI are well characterized loaders. However, most bacteria do not express either of these two proteins. Instead, they are proposed to rely on DciA, an ancestral protein unrelated to DnaC/I. While the DciA structure from Vibrio cholerae shares no homology with DnaC, it reveals similarities with DnaA and DnaX, two proteins involved during replication initiation. As other bacterial replicative helicases, VcDnaB adopts a toroid-shaped homo-hexameric structure, but with a slightly open dynamic conformation in the free state. We show that VcDnaB can load itself on DNA in vitro and that VcDciA stimulates this function, resulting in an increased DNA unwinding. VcDciA interacts with VcDnaB with a 3/6 stoichiometry and we show that a determinant residue, which discriminates DciA- and DnaC/I-helicases, is critical in vivo. Our work is the first step toward the understanding of the ancestral mode of loading of bacterial replicative helicases on DNA. It sheds light on the strategy employed by phage helicase loaders to hijack bacterial replicative helicases and may explain the recurrent domestication of dnaC/I through evolution in bacteria.

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Sakamoto, Y., S. Nakai, S. Moriya, H. Yoshikawa, and N. Ogasawara. "The Bacillus subtilis dnaC gene encodes a protein homologous to the DnaB helicase of Escherichia coli." Microbiology 141, no. 3 (March 1, 1995): 641–44. http://dx.doi.org/10.1099/13500872-141-3-641.

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Allen, G. C., and A. Kornberg. "Fine balance in the regulation of DnaB helicase by DnaC protein in replication in Escherichia coli." Journal of Biological Chemistry 266, no. 33 (November 1991): 22096–101. http://dx.doi.org/10.1016/s0021-9258(18)54538-5.

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