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Journal articles on the topic 'DnaG primase'

Author: Grafiati

Published: 4 March 2024

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1

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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2

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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3

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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4

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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5

Ilic, Stefan, Shira Cohen, Meenakshi Singh, Benjamin Tam, Adi Dayan, and Barak Akabayov. "DnaG Primase—A Target for the Development of Novel Antibacterial Agents." Antibiotics 7, no. 3 (August 13, 2018): 72. http://dx.doi.org/10.3390/antibiotics7030072.

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The bacterial primase—an essential component in the replisome—is a promising but underexploited target for novel antibiotic drugs. Bacterial primases have a markedly different structure than the human primase. Inhibition of primase activity is expected to selectively halt bacterial DNA replication. Evidence is growing that halting DNA replication has a bacteriocidal effect. Therefore, inhibitors of DNA primase could provide antibiotic agents. Compounds that inhibit bacterial DnaG primase have been developed using different approaches. In this paper, we provide an overview of the current literature on DNA primases as novel drug targets and the methods used to find their inhibitors. Although few inhibitors have been identified, there are still challenges to develop inhibitors that can efficiently halt DNA replication and may be applied in a clinical setting.

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6

Koepsell, Scott A., Marilynn A. Larson, Mark A. Griep, and Steven H. Hinrichs. "Staphylococcus aureus Helicase but Not Escherichia coli Helicase Stimulates S. aureus Primase Activity and Maintains Initiation Specificity." Journal of Bacteriology 188, no. 13 (July 1, 2006): 4673–80. http://dx.doi.org/10.1128/jb.00316-06.

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ABSTRACT Bacterial primases are essential for DNA replication due to their role in polymerizing the formation of short RNA primers repeatedly on the lagging-strand template and at least once on the leading-strand template. The ability of recombinant Staphylococcus aureus DnaG primase to utilize different single-stranded DNA templates was tested using oligonucleotides of the sequence 5′-CAGA (CA)5 XYZ (CA)3-3′, where XYZ represented the variable trinucleotide. These experiments demonstrated that S. aureus primase synthesized RNA primers predominately on templates containing 5′-d(CTA)-3′ or TTA and to a much lesser degree on GTA-containing templates, in contrast to results seen with the Escherichia coli DnaG primase recognition sequence 5′-d(CTG)-3′. Primer synthesis was initiated complementarily to the middle nucleotide of the recognition sequence, while the third nucleotide, an adenosine, was required to support primer synthesis but was not copied into the RNA primer. The replicative helicases from both S. aureus and E. coli were tested for their ability to stimulate either S. aureus or E. coli primase. Results showed that each bacterial helicase could only stimulate the cognate bacterial primase. In addition, S. aureus helicase stimulated the production of full-length primers, whereas E. coli helicase increased the synthesis of only short RNA polymers. These studies identified important differences between E. coli and S. aureus related to DNA replication and suggest that each bacterial primase and helicase may have adapted unique properties optimized for replication.

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7

Kuron, Aneta, Malgorzata Korycka-Machala, Anna Brzostek, Marcin Nowosielski, Aidan Doherty, Bozena Dziadek, and Jaroslaw Dziadek. "Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics." Antimicrobial Agents and Chemotherapy 58, no. 3 (December 30, 2013): 1699–706. http://dx.doi.org/10.1128/aac.01721-13.

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ABSTRACTMycobacteria contain genes for several DNA-dependent RNA primases, includingdnaG, which encodes an essential replication enzyme that has been proposed as a target for antituberculosis compounds. Anin silicoanalysis revealed that mycobacteria also possess archaeo-eukaryotic superfamily primases (AEPs) of unknown function. Using a homologous recombination system, we obtained direct evidence that wild-typednaGcannot be deleted from the chromosome ofMycobacterium smegmatiswithout disrupting viability, even in backgrounds in which mycobacterial AEPs are overexpressed. In contrast, single-deletion AEP mutants or mutants defective for all four identifiedM. smegmatisAEP genes did not exhibit growth defects under standard laboratory conditions. Deletion of nativednaGinM. smegmatiswas tolerated only after the integration of an extra intact copy of theM. smegmatisorMycobacterium tuberculosisdnaGgene, under the control of chemically inducible promoters, into theattBsite of the chromosome.M. tuberculosisandM. smegmatisDnaG proteins were overproduced and purified, and their primase activities were confirmed using radioactive RNA synthesis assays. The enzymes appeared to be sensitive to known inhibitors (suramin and doxorubicin) of DnaG. Notably,M. smegmatisbacilli appeared to be sensitive to doxorubicin and resistant to suramin. The growth and survival of conditional mutant mycobacterial strains in which DnaG was significantly depleted were only slightly affected under standard laboratory conditions. Thus, although DnaG is essential for mycobacterial viability, only low levels of protein are required for growth. This suggests that very efficient inhibition of enzyme activity would be required for mycobacterial DnaG to be useful as an antibiotic target.

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8

Britton, Robert A., and James R. Lupski. "Isolation and Characterization of Suppressors of Two Escherichia coli dnaG Mutations, dnaG2903 and parB." Genetics 145, no. 4 (April 1, 1997): 867–75. http://dx.doi.org/10.1093/genetics/145.4.867.

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The dnaG gene of Escherichia coli encodes the primase protein, which synthesizes a short pRNA that is essential for the initiation of both leading and lagging strand DNA synthesis. Two temperature-sensitive mutations in the 3′ end of the dnaG gene, dnaG2903 and parB, cause a defect in chromosome partitioning at the nonpermissive temperature 42°. We have characterized 24 cold-sensitive suppressor mutations of these two dnaG alleles. By genetic mapping and complementation, five different classes of suppressors have been assigned: sdgC, sdgD, sdgE, sdgG and sdgH. The genes responsible for suppression in four of the five classes have been determined. Four of the sdgC suppressor alleles are complemented by the dnaE gene, which encodes the enzymatic subunit of DNA polymerase III. The sdgE class are mutations in era, an essential GTPase of unknown function. The sdgG suppressor is likely a mutation in one of three genes: ubiC, ubiA or yjbI. The sdgH class affects rpsF, which encodes the ribosomal protein S6. Possible mechanisms of suppression by these different classes are discussed.

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9

Paschalis, Vasileios, Emmanuelle Le Chatelier, Matthew Green, François Képès, Panos Soultanas, and Laurent Janniere. "Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity." Open Biology 7, no. 9 (September 2017): 170146. http://dx.doi.org/10.1098/rsob.170146.

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During Bacillus subtilis replication two replicative polymerases function at the replisome to collectively carry out genome replication. In a reconstituted in vitro replication assay, PolC is the main polymerase while the lagging strand DnaE polymerase briefly extends RNA primers synthesized by the primase DnaG prior to handing-off DNA synthesis to PolC. Here, we show in vivo that (i) the polymerase activity of DnaE is essential for both the initiation and elongation stages of DNA replication, (ii) its error rate varies inversely with PolC concentration, and (iii) its misincorporations are corrected by the mismatch repair system post-replication. We also found that the error rates in cells encoding mutator forms of both PolC and DnaE are significantly higher (up to 15-fold) than in PolC mutants. In vitro , we showed that (i) the polymerase activity of DnaE is considerably stimulated by DnaN, SSB and PolC, (ii) its error-prone activity is strongly inhibited by DnaN, and (iii) its errors are proofread by the 3′ > 5′ exonuclease activity of PolC in a stable template-DnaE–PolC complex. Collectively our data show that protein–protein interactions within the replisome modulate the activity and fidelity of DnaE, and confirm the prominent role of DnaE during B. subtilis replication.

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10

Li, Jie, Jingfang Liu, Ligang Zhou, Huadong Pei, Jian Zhou, and Hua Xiang. "Two Distantly Homologous DnaG Primases from Thermoanaerobacter tengcongensis Exhibit Distinct Initiation Specificities and Priming Activities." Journal of Bacteriology 192, no. 11 (March 26, 2010): 2670–81. http://dx.doi.org/10.1128/jb.01511-09.

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ABSTRACT Primase, encoded by dnaG in bacteria, is a specialized DNA-dependent RNA polymerase that synthesizes RNA primers de novo for elongation by DNA polymerase. Genome sequence analysis has revealed two distantly related dnaG genes, TtdnaG and TtdnaG 2, in the thermophilic bacterium Thermoanaerobacter tengcongensis. Both TtDnaG (600 amino acids) and TtDnaG2 (358 amino acids) exhibit primase activities in vitro at a wide range of temperatures. Interestingly, the template recognition specificities of these two primases are quite distinctive. When trinucleotide-specific templates were tested, TtDnaG initiated RNA primer synthesis efficiently only on templates containing the trinucleotide 5′-CCC-3′, not on the other 63 possible trinucleotides. When the 5′-CCC-3′ sequence was flanked by additional cytosines or guanines, the initiation efficiency of TtDnaG increased remarkably. Significantly, TtDnaG could specifically and efficiently initiate RNA primer synthesis on a limited set of tetranucleotides composed entirely of cytosines and guanines, indicating that TtDnaG initiated RNA primer synthesis more preferably on GC-containing tetranucleotides. In contrast, it seemed that TtDnaG2 had no specific initiation nucleotides, as it could efficiently initiate RNA primer synthesis on all templates tested. The DNA binding affinity of TtDnaG2 was usually 10-fold higher than that of TtDnaG, which might correlate with its high activity but low template specificity. These distinct priming activities and specificities of TtDnaG and TtDnaG2 might shed new light on the diversity in the structure and function of the primases.

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11

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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12

Klann, Amy G., Aimee E. Belanger, Angelica Abanes-De Mello, Janice Y. Lee, and Graham F. Hatfull. "Characterization of the dnaG Locus inMycobacterium smegmatis Reveals Linkage of DNA Replication and Cell Division." Journal of Bacteriology 180, no. 1 (January 1, 1998): 65–72. http://dx.doi.org/10.1128/jb.180.1.65-72.1998.

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ABSTRACT We have isolated a UV-induced temperature-sensitive mutant ofMycobacterium smegmatis that fails to grow at 42°C and exhibits a filamentous phenotype following incubation at the nonpermissive temperature, reminiscent of a defect in cell division. Complementation of this mutant with an M. smegmatis genomic library and subsequent subcloning reveal that the defect lies within the M. smegmatis dnaG gene encoding DNA primase. Sequence analysis of the mutant dnaG allele reveals a substitution of proline for alanine at position 496. Thus, dnaG is an essential gene in M. smegmatis, and DNA replication and cell division are coupled processes in this species. Characterization of the sequences flanking the M. smegmatis dnaG gene shows that it is not part of the highly conserved macromolecular synthesis operon present in other eubacterial species but is part of an operon with a dgt gene encoding dGTPase. The organization of this operon is conserved in Mycobacterium tuberculosis andMycobacterium leprae, suggesting that regulation of DNA replication, transcription, and translation may be coordinated differently in the mycobacteria than in other bacteria.

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13

Ziegelin, Günter, Nicole Tegtmeyer, Rudi Lurz, Stefan Hertwig, Jens Hammerl, Bernd Appel, and Erich Lanka. "The repA Gene of the Linear Yersinia enterocolitica Prophage PY54 Functions as a Circular Minimal Replicon in Escherichia coli." Journal of Bacteriology 187, no. 10 (May 15, 2005): 3445–54. http://dx.doi.org/10.1128/jb.187.10.3445-3454.2005.

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ABSTRACT The Yersinia enterocolitica prophage PY54 replicates as a linear DNA molecule with covalently closed ends. For replication of a circular PY54 minimal replicon that has been derived from a linear minireplicon, two phage-encoded loci are essential in Escherichia coli: (i) the reading frame of the replication initiation gene repA and (ii) its 212-bp origin located within the 3′ portion of repA. The RepA protein acts in trans on the origin since we have physically separated the PY54 origin and repA onto a two-plasmid origin test system. For this trans action, the repA 3′ end carrying the origin is dispensable. Mutagenesis by alanine scan demonstrated that the motifs for primase and for nucleotide binding present in the protein are essential for RepA activity. The replication initiation functions of RepA are replicon specific. The replication initiation proteins DnaA, DnaG, and DnaB of the host are unable to promote origin replication in the presence of mutant RepA proteins that carry single residue exchanges in these motifs. The proposed origins of the known related hairpin prophages PY54, N15, and PKO2 are all located toward the 3′ end of the corresponding repA genes, where several structure elements are conserved. Origin function depends on the integrity of these elements.

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14

Gajadeera, Chathurada, Melisa J. Willby, Keith D. Green, Pazit Shaul, Micha Fridman, Sylvie Garneau-Tsodikova, James E. Posey, and Oleg V. Tsodikov. "Antimycobacterial activity of DNA intercalator inhibitors of Mycobacterium tuberculosis primase DnaG." Journal of Antibiotics 68, no. 3 (September 24, 2014): 153–57. http://dx.doi.org/10.1038/ja.2014.131.

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15

Maciąg, Monika, Maja Kochanowska, Robert Łyżeń, Grzegorz Węgrzyn, and Agnieszka Szalewska-Pałasz. "ppGpp inhibits the activity of Escherichia coli DnaG primase." Plasmid 63, no. 1 (January 2010): 61–67. http://dx.doi.org/10.1016/j.plasmid.2009.11.002.

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16

Zuo, Zhongfeng, Cory J. Rodgers, Andrey L. Mikheikin, and Michael A. Trakselis. "Characterization of a Functional DnaG-Type Primase in Archaea: Implications for a Dual-Primase System." Journal of Molecular Biology 397, no. 3 (April 2010): 664–76. http://dx.doi.org/10.1016/j.jmb.2010.01.057.

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17

Green, Keith D., Ankita Punetha, Nishad Thamban Chandrika, Caixia Hou, Sylvie Garneau‐Tsodikova, and Oleg V. Tsodikov. "Development of Single‐Stranded DNA Bisintercalating Inhibitors of Primase DnaG as Antibiotics." ChemMedChem 16, no. 12 (March 31, 2021): 1986–95. http://dx.doi.org/10.1002/cmdc.202100001.

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18

Szafranski, Przemyslaw, Cassandra L. Smith, and Charles R. Cantor. "Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1352, no. 3 (June 1997): 243–48. http://dx.doi.org/10.1016/s0167-4781(97)00059-6.

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19

Tocchetti, Arianna, Gloria Galimberti, Gianni Dehò, and Daniela Ghisotti. "Characterization of the oriI andoriII Origins of Replication in Phage-Plasmid P4." Journal of Virology 73, no. 9 (September 1, 1999): 7308–16. http://dx.doi.org/10.1128/jvi.73.9.7308-7316.1999.

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ABSTRACT In the Escherichia coli phage-plasmid P4, two partially overlapping replicons with bipartite ori sites coexist. The essential components of the oriI replicon are the α andcnr genes and the ori1 and crrsites; the oriII replicon is composed of the α gene, with the internal ori2 site, and the crr region. The P4 α protein has primase and helicase activities and specifically binds type I iterons, present in ori1 and crr. Using a complementation test for plasmid replication, we demonstrated that the two replicons depend on both the primase and helicase activities of the α protein. Moreover, neither replicon requires the host DnaA, DnaG, and Rep functions. The bipartite origins of the two replicons share the crr site and differ forori1 and ori2, respectively. By deletion mapping, we defined the minimal ori1 and ori2regions sufficient for replication. The ori1 site was limited to a 123-bp region, which contains six type I iterons spaced regularly close to the helical periodicity, and a 35-bp AT-rich region. Deletion of one or more type I iterons inactivated oriI. Moreover, insertion of 6 or 10 bp within the ori1 region also abolished replication ability, suggesting that the relative arrangement of the iterons is relevant. The ori2 site was limited to a 36-bp P4 region that does not contain type I iterons. In vitro, the α protein did not bind ori2. Thus, the α protein appears to act differently at the two origins of replication.

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20

Versalovic, James, and James R. Lupski. "The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs." Gene 136, no. 1-2 (December 1993): 281–86. http://dx.doi.org/10.1016/0378-1119(93)90480-q.

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21

Syson, Karl, Jenny Thirlway, Andrea M. Hounslow, Panos Soultanas, and Jonathan P. Waltho. "Solution Structure of the Helicase-Interaction Domain of the Primase DnaG." Structure 13, no. 4 (April 2005): 609–16. http://dx.doi.org/10.1016/j.str.2005.01.022.

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22

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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23

Rannou, Olivier, Emmanuelle Le Chatelier, Marilynn A. Larson, Hamid Nouri, Bérengère Dalmais, Charles Laughton, Laurent Jannière, and Panos Soultanas. "Functional interplay of DnaE polymerase, DnaG primase and DnaC helicase within a ternary complex, and primase to polymerase hand-off during lagging strand DNA replication in Bacillus subtilis." Nucleic Acids Research 41, no. 10 (April 5, 2013): 5303–20. http://dx.doi.org/10.1093/nar/gkt207.

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24

Periago, Jessica, Clarissa Mason, and Mark A. Griep. "Theoretical Development of DnaG Primase as a Novel Narrow-Spectrum Antibiotic Target." ACS Omega 7, no. 10 (March 1, 2022): 8420–28. http://dx.doi.org/10.1021/acsomega.1c05928.

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25

Mitkova, Atanaska V., Sujata M. Khopde, and Subhasis B. Biswas. "Mechanism and Stoichiometry of Interaction of DnaG Primase with DnaB Helicase ofEscherichia coliin RNA Primer Synthesis." Journal of Biological Chemistry 278, no. 52 (October 13, 2003): 52253–61. http://dx.doi.org/10.1074/jbc.m308956200.

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26

Su, Xun-Cheng, Patrick M. Schaeffer, Karin V. Loscha, Pamela H. P. Gan, Nicholas E. Dixon, and Gottfried Otting. "Monomeric solution structure of the helicase-binding domain of Escherichia coli DnaG primase." FEBS Journal 273, no. 21 (November 2006): 4997–5009. http://dx.doi.org/10.1111/j.1742-4658.2006.05495.x.

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27

Solteszova, Barbora, Nora Halgasova, and Gabriela Bukovska. "Interaction between phage BFK20 helicase gp41 and its host Brevibacterium flavum primase DnaG." Virus Research 196 (January 2015): 150–56. http://dx.doi.org/10.1016/j.virusres.2014.11.022.

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28

Biswas, Tapan, Esteban Resto-Roldán, Sean K. Sawyer, Irina Artsimovitch, and Oleg V. Tsodikov. "A novel non-radioactive primase–pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG." Nucleic Acids Research 41, no. 4 (December 24, 2012): e56-e56. http://dx.doi.org/10.1093/nar/gks1292.

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Chintakayala, Kiran, Cristina Machón, Anna Haroniti, Marilyn A. Larson, Steven H. Hinrichs, Mark A. Griep, and Panos Soultanas. "Allosteric regulation of the primase (DnaG) activity by the clamp-loader (τ)in vitro." Molecular Microbiology 72, no. 2 (April 2009): 537–49. http://dx.doi.org/10.1111/j.1365-2958.2009.06668.x.

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Bauer, Robert J., Brian W. Graham, and Michael A. Trakselis. "Novel Interaction of the Bacterial-Like DnaG Primase with the MCM Helicase in Archaea." Journal of Molecular Biology 425, no. 8 (April 2013): 1259–73. http://dx.doi.org/10.1016/j.jmb.2013.01.025.

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31

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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32

Hou, Caixia, Tapan Biswas, and Oleg V. Tsodikov. "Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events." Biochemistry 57, no. 14 (March 20, 2018): 2084–93. http://dx.doi.org/10.1021/acs.biochem.8b00036.

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33

Loscha, Karin, Aaron J. Oakley, Bogdan Bancia, Patrick M. Schaeffer, Pavel Prosselkov, Gottfried Otting, Matthew C. J. Wilce, and Nicholas E. Dixon. "Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase." Protein Expression and Purification 33, no. 2 (February 2004): 304–10. http://dx.doi.org/10.1016/j.pep.2003.10.001.

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34

Shortridge, Matthew D., Mark A. Griep, and Robert Powers. "1H, 13C, and 15N NMR assignments for the helicase interaction domain of Staphylococcus aureus DnaG primase." Biomolecular NMR Assignments 6, no. 1 (June 7, 2011): 35–38. http://dx.doi.org/10.1007/s12104-011-9320-7.

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35

Lu, Y. B., P. V. A. L. Ratnakar, B. K. Mohanty, and D. Bastia. "Direct physical interaction between DnaG primase and DnaB helicase of Escherichia coli is necessary for optimal synthesis of primer RNA." Proceedings of the National Academy of Sciences 93, no. 23 (November 12, 1996): 12902–7. http://dx.doi.org/10.1073/pnas.93.23.12902.

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36

SEO, K. H., and R. E. BRACKETT. "Rapid, Specific Detection of Enterobacter sakazakii in Infant Formula Using a Real-Time PCR Assay." Journal of Food Protection 68, no. 1 (January 1, 2005): 59–63. http://dx.doi.org/10.4315/0362-028x-68.1.59.

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Enterobacter sakazakii is a rare cause of invasive infection with high mortality rates in neonates. Powdered milk–based infant formulas have been associated with the E. sakazakii–related outbreaks in premature or other immunocompromised infants. In this study, an assay was developed for the specific detection of E. sakazakii in infant formula using an application of the fluorogenic 5′ nuclease assay (TaqMan). A set of primers and probe was designed using the E. sakazakii partial macromolecular synthesis operon: the rpsU gene 3′ end and the primase (dnaG) gene 5′ end. The specificity of the assay was evaluated using 68 Enterobacter and 55 non-Enterobacter strains. The newly developed assay enables us to detect 100 CFU/ml in pure culture and in reconstituted infant formula in 50 cycles of PCR without enrichment. The assay was specific enough to discriminate E. sakazakii from all other Enterobacter and non-Enterobacter strains tested. The developed real-time PCR assay could save up to 5 days and eliminate the need for plating samples on selective or diagnostic agars and for biochemical confirmation steps. The real-time PCR assay could be used to rapidly screen infant formula samples for E. sakazakii and would be a boon to food industries and regulatory agencies.

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Hakeem, Supriya, Inderpal Singh, Preeti Sharma, V. Verma, and Ratna Chandra. "in silico screening and molecular dynamics simulations study to identify novel potent inhibitors against Mycobacterium tuberculosis DnaG primase." Acta Tropica 199 (November 2019): 105154. http://dx.doi.org/10.1016/j.actatropica.2019.105154.

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38

Gardiennet, Carole, Thomas Wiegand, Alexandre Bazin, Riccardo Cadalbert, Britta Kunert, Denis Lacabanne, Irina Gutsche, Laurent Terradot, Beat H. Meier, and Anja Böckmann. "Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori." Journal of Biomolecular NMR 64, no. 3 (March 2016): 189–95. http://dx.doi.org/10.1007/s10858-016-0018-0.

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39

Naue, Natalie, Monika Beerbaum, Andrea Bogutzki, Peter Schmieder, and Ute Curth. "The helicase-binding domain of Escherichia coli DnaG primase interacts with the highly conserved C-terminal region of single-stranded DNA-binding protein." Nucleic Acids Research 41, no. 8 (February 20, 2013): 4507–17. http://dx.doi.org/10.1093/nar/gkt107.

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40

Versalovic, J., and J. R. Lupski. "Missense mutations in the 3' end of the Escherichia coli dnaG gene do not abolish primase activity but do confer the chromosome-segregation-defective (par) phenotype." Microbiology 143, no. 2 (February 1, 1997): 585–94. http://dx.doi.org/10.1099/00221287-143-2-585.

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41

O’Brien, Elizabeth, Lauren E. Salay, Esther A. Epum, Katherine L. Friedman, Walter J. Chazin, and Jacqueline K. Barton. "Yeast require redox switching in DNA primase." Proceedings of the National Academy of Sciences 115, no. 52 (December 12, 2018): 13186–91. http://dx.doi.org/10.1073/pnas.1810715115.

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Eukaryotic DNA primases contain a [4Fe4S] cluster in the C-terminal domain of the p58 subunit (p58C) that affects substrate affinity but is not required for catalysis. We show that, in yeast primase, the cluster serves as a DNA-mediated redox switch governing DNA binding, just as in human primase. Despite a different structural arrangement of tyrosines to facilitate electron transfer between the DNA substrate and [4Fe4S] cluster, in yeast, mutation of tyrosines Y395 and Y397 alters the same electron transfer chemistry and redox switch. Mutation of conserved tyrosine 395 diminishes the extent of p58C participation in normal redox-switching reactions, whereas mutation of conserved tyrosine 397 causes oxidative cluster degradation to the [3Fe4S]+ species during p58C redox signaling. Switching between oxidized and reduced states in the presence of the Y397 mutations thus puts primase [4Fe4S] cluster integrity and function at risk. Consistent with these observations, we find that yeast tolerate mutations to Y395 in p58C, but the single-residue mutation Y397L in p58C is lethal. Our data thus show that a constellation of tyrosines for protein-DNA electron transfer mediates the redox switch in eukaryotic primases and is required for primase function in vivo.

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Bell, Stephen D. "Initiating DNA replication: a matter of prime importance." Biochemical Society Transactions 47, no. 1 (January 15, 2019): 351–56. http://dx.doi.org/10.1042/bst20180627.

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Abstract It has been known for decades that the principal replicative DNA polymerases that effect genome replication are incapable of starting DNA synthesis de novo. Rather, they require a 3′-OH group from which to extend a DNA chain. Cellular DNA replication systems exploit a dedicated, limited processivity RNA polymerase, termed primase, that synthesizes a short oligoribonucleotide primer which is then extended by a DNA polymerase. Thus, primases can initiate synthesis, proceed with primer elongation for a short distance then transfer the primer to a DNA polymerase. Despite these well-established properties, the mechanistic basis of these dynamic behaviours has only recently been established. In the following, the author will describe recent insights from studies of the related eukaryotic and archaeal DNA primases. Significantly, the general conclusions from these studies likely extend to a broad class of extrachromosomal element-associated primases as well as the human primase-related DNA repair enzyme, PrimPol.

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43

Schneider, C., K. Weisshart, L. A. Guarino, I. Dornreiter, and E. Fanning. "Species-specific functional interactions of DNA polymerase alpha-primase with simian virus 40 (SV40) T antigen require SV40 origin DNA." Molecular and Cellular Biology 14, no. 5 (May 1994): 3176–85. http://dx.doi.org/10.1128/mcb.14.5.3176-3185.1994.

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Physical and functional interactions of simian virus 40 (SV40) and polyomavirus large-T antigens with DNA polymerase alpha-primase were analyzed to elucidate the molecular basis for the species specificity of polymerase alpha-primase in viral DNA replication. SV40 T antigen associated more efficiently with polymerase alpha-primase in crude human extracts than in mouse extracts, while polyomavirus T antigen interacted preferentially with polymerase alpha-primase in mouse extracts. The apparent species specificity of complex formation was not observed when purified polymerase alpha-primases were substituted for the crude extracts. Several functional interactions between T antigen and purified polymerase alpha-primase, including stimulation of primer synthesis and primer elongation on M13 DNA in the presence or absence of the single-stranded DNA binding protein RP-A, also proved to be independent of the species from which polymerase alpha-primase had been purified. However, the human DNA polymerase alpha-primase was specifically required for primosome assembly and primer synthesis on SV40 origin DNA in the presence of T antigen and RP-A.

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44

Schneider, C., K. Weisshart, L. A. Guarino, I. Dornreiter, and E. Fanning. "Species-specific functional interactions of DNA polymerase alpha-primase with simian virus 40 (SV40) T antigen require SV40 origin DNA." Molecular and Cellular Biology 14, no. 5 (May 1994): 3176–85. http://dx.doi.org/10.1128/mcb.14.5.3176.

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Physical and functional interactions of simian virus 40 (SV40) and polyomavirus large-T antigens with DNA polymerase alpha-primase were analyzed to elucidate the molecular basis for the species specificity of polymerase alpha-primase in viral DNA replication. SV40 T antigen associated more efficiently with polymerase alpha-primase in crude human extracts than in mouse extracts, while polyomavirus T antigen interacted preferentially with polymerase alpha-primase in mouse extracts. The apparent species specificity of complex formation was not observed when purified polymerase alpha-primases were substituted for the crude extracts. Several functional interactions between T antigen and purified polymerase alpha-primase, including stimulation of primer synthesis and primer elongation on M13 DNA in the presence or absence of the single-stranded DNA binding protein RP-A, also proved to be independent of the species from which polymerase alpha-primase had been purified. However, the human DNA polymerase alpha-primase was specifically required for primosome assembly and primer synthesis on SV40 origin DNA in the presence of T antigen and RP-A.

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Brückner, A., F. Stadlbauer, L. A. Guarino, A. Brunahl, C. Schneider, C. Rehfuess, C. Previes, E. Fanning, and H. P. Nasheuer. "The mouse DNA polymerase alpha-primase subunit p48 mediates species-specific replication of polyomavirus DNA in vitro." Molecular and Cellular Biology 15, no. 3 (March 1995): 1716–24. http://dx.doi.org/10.1128/mcb.15.3.1716.

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Mouse cell extracts support vigorous replication of polyomavirus (Py) DNA in vitro, while human cell extracts do not. However, the addition of purified mouse DNA polymerase alpha-primase to human cell extracts renders them permissive for Py DNA replication, suggesting that mouse polymerase alpha-primase determines the species specificity of Py DNA replication. We set out to identify the subunit of mouse polymerase alpha-primase that mediates this species specificity. To this end, we cloned and expressed cDNAs encoding all four subunits of mouse and human polymerase alpha-primase. Purified recombinant mouse polymerase alpha-primase and a hybrid DNA polymerase alpha-primase complex composed of human subunits p180 and p68 and mouse subunits p58 and p48 supported Py DNA replication in human cell extracts depleted of polymerase alpha-primase, suggesting that the primase heterodimer or one of its subunits controls host specificity. To determine whether both mouse primase subunits were required, recombinant hybrid polymerase alpha-primases containing only one mouse primase subunit, p48 or p58, together with three human subunits, were assayed for Py replication activity. Only the hybrid containing mouse p48 efficiently replicated Py DNA in depleted human cell extracts. Moreover, in a purified initiation assay containing Py T antigen, replication protein A (RP-A) and topoisomerase I, only the hybrid polymerase alpha-primase containing the mouse p48 subunit initiated primer synthesis on Py origin DNA. Together, these results indicate that the p48 subunit is primarily responsible for the species specificity of Py DNA replication in vitro. Specific physical association of Py T antigen with purified recombinant DNA polymerase alpha-primase, mouse DNA primase heterodimer, and mouse p48 suggested that direct interactions between Py T antigen and primase could play a role in species-specific initiation of Py replication.

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46

Hines, Jane C., and Dan S. Ray. "A Second Mitochondrial DNA Primase Is Essential for Cell Growth and Kinetoplast Minicircle DNA Replication in Trypanosoma brucei." Eukaryotic Cell 10, no. 3 (January 21, 2011): 445–54. http://dx.doi.org/10.1128/ec.00308-10.

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ABSTRACT The mitochondrial DNA of trypanosomes contains two types of circular DNAs, minicircles and maxicircles. Both minicircles and maxicircles replicate from specific replication origins by unidirectional theta-type intermediates. Initiation of the minicircle leading strand and also that of at least the first Okazaki fragment involve RNA priming. The Trypanosoma brucei genome encodes two mitochondrial DNA primases, PRI1 and PRI2, related to the primases of eukaryotic nucleocytoplasmic large DNA viruses. These primases are members of the archeoeukaryotic primase superfamily, and each of them contain an RNA recognition motif and a PriCT-2 motif. In Leishmania species, PRI2 proteins are approximately 61 to 66 kDa in size, whereas in Trypanosoma species, PRI2 proteins have additional long amino-terminal extensions. RNA interference (RNAi) of T. brucei PRI2 resulted in the loss of kinetoplast DNA and accumulation of covalently closed free minicircles. Recombinant PRI2 lacking this extension (PRI2ΔNT) primes poly(dA) synthesis on a poly(dT) template in an ATP-dependent manner. Mutation of two conserved aspartate residues (PRI2ΔNTCS) resulted in loss of enzymatic activity but not loss of DNA binding. We propose that PRI2 is directly involved in initiating kinetoplast minicircle replication.

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47

Stadlbauer, F., C. Voitenleitner, A. Brückner, E. Fanning, and H. P. Nasheuer. "Species-specific replication of simian virus 40 DNA in vitro requires the p180 subunit of human DNA polymerase alpha-primase." Molecular and Cellular Biology 16, no. 1 (January 1996): 94–104. http://dx.doi.org/10.1128/mcb.16.1.94.

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Human cell extracts efficiently support replication of simian virus 40 (SV40) DNA in vitro, while mouse cell extracts do not. Since human DNA polymerase alpha-primase is the major species-specific factor, we set out to determine the subunit(s) of DNA polymerase alpha-primase required for this species specificity. Recombinant human, mouse, and hybrid human-mouse DNA polymerase alpha-primase complexes were expressed with baculovirus vectors and purified. All of the recombinant DNA polymerase alpha-primases showed enzymatic activity and efficiently synthesized the complementary strand on an M13 single-stranded DNA template. The human DNA polymerase alpha-primase (four subunits [HHHH]) and the hybrid DNA polymerase alpha-primase HHMM (two human subunits and two mouse subunits), containing human p180 and p68 and mouse primase, initiated SV40 DNA replication in a purified system. The human and the HHMM complex efficiently replicated SV40 DNA in mouse extracts from which DNA polymerase alpha-primase was deleted, while MMMM and the MMHH complex did not. To determine whether the human p180 or p68 subunit was required for SV40 DNA replication, hybrid complexes containing only one human subunit, p180 or p68, together with three mouse subunits (HMMM and MHMM) or three human subunits and one mouse subunit (MHHH and HMHH) were tested for SV40 DNA replication activity. The hybrid complexes HMMM and HMHH synthesized oligoribonucleotides in the SV40 initiation assay with purified proteins and replicated SV40 DNA in depleted mouse extracts. In contrast, the hybrid complexes containing mouse p180 were inactive in both assays. We conclude that the human p180 subunit determines host-specific replication of SV40 DNA in vitro.

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Rechkoblit, Olga, Yogesh K. Gupta, Radhika Malik, Kanagalaghatta R. Rajashankar, Robert E. Johnson, Louise Prakash, Satya Prakash, and Aneel K. Aggarwal. "Structure and mechanism of human PrimPol, a DNA polymerase with primase activity." Science Advances 2, no. 10 (October 2016): e1601317. http://dx.doi.org/10.1126/sciadv.1601317.

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PrimPol is a novel human enzyme that contains both DNA primase and DNA polymerase activities. We present the first structure of human PrimPol in ternary complex with a DNA template-primer and an incoming deoxynucleoside triphosphate (dNTP). The ability of PrimPol to function as a DNA primase stems from a simple but remarkable feature—almost complete lack of contacts to the DNA primer strand. This, in turn, allows two dNTPs to bind initiation and elongation sites on the enzyme for the formation of the first dinucleotide. PrimPol shows the ability to synthesize DNA opposite ultraviolet (UV) lesions; however, unexpectedly, the active-site cleft of the enzyme is constrained, which precludes the bypass of UV-induced DNA lesions by conventional translesion synthesis. Together, the structure addresses long-standing questions about how DNA primases actually initiate synthesis and how primase and polymerase activities combine in a single enzyme to carry out DNA synthesis.

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Díaz-Talavera, Alberto, Cristina Montero-Conde, Luis Javier Leandro-García, and Mercedes Robledo. "PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy." Biomolecules 12, no. 2 (February 3, 2022): 248. http://dx.doi.org/10.3390/biom12020248.

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DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out this task. PrimPol is a primase that operates in both the nucleus and mitochondria. In contrast with convectional primases, PrimPol is a DNA primase able to initiate DNA synthesis de novo using deoxynucleotides, discriminating against ribonucleotides. In vitro, PrimPol can act as a translesion synthesis (TLS) DNA primase, elongating primers that PrimPol itself sythesizes, or as TLS DNA polymerase, elongating pre-existing primers across lesions. However, the lack of evidence for PrimPol polymerase activity in vivo suggests that PrimPol only uses its TLS abilities to facilitate priming across lesions in cells, thus acting as a TLS DNA primase. Here, we provide a comprehensive review of human PrimPol covering its biochemical properties and structure, in vivo function and regulation, and the processes that take place to fill the gap-containing lesion that PrimPol leaves behind. Finally, we explore the available data on human PrimPol expression in different tissues in physiological conditions and its role in cancer.

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Makowska-Grzyska, Magdalena, and Jon M. Kaguni. "Primase Directs the Release of DnaC from DnaB." Molecular Cell 37, no. 1 (January 2010): 90–101. http://dx.doi.org/10.1016/j.molcel.2009.12.031.

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