Identification of a Basal System for Unwinding a Bacterial Chromosome Origin

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2019 Jul 4

PMID 31267560

Citations 17

Authors

Tomas T Richardson

Daniel Stevens

Simone Pelliciari

Omar Harran

Theodor Sperlea

Heath Murray

Affiliations

Soon will be listed here.

Abstract

Genome duplication is essential for cell proliferation, and DNA synthesis is generally initiated by dedicated replication proteins at specific loci termed origins. In bacteria, the master initiator DnaA binds the chromosome origin (oriC) and unwinds the DNA duplex to permit helicase loading. However, despite decades of research it remained unclear how the information encoded within oriC guides DnaA-dependent strand separation. To address this fundamental question, we took a systematic genetic approach in vivo and identified the core set of essential sequence elements within the Bacillus subtilis chromosome origin unwinding region. Using this information, we then show in vitro that the minimal replication origin sequence elements are necessary and sufficient to promote the mechanical functions of DNA duplex unwinding by DnaA. Because the basal DNA unwinding system characterized here appears to be conserved throughout the bacterial domain, this discovery provides a framework for understanding oriC architecture, activity, regulation and diversity.

Citing Articles

remains translationally active after CRISPRi-mediated replication initiation arrest.

Munoz-Gutierrez V, Cornejo F, Schmidt K, Frese C, Halte M, Erhardt M mSystems. 2024; 9(4):e0022124.

PMID: 38546227 PMC: 11019786. DOI: 10.1128/msystems.00221-24.

Toward an understanding of the DNA replication initiation in bacteria.

Wegrzyn K, Konieczny I Front Microbiol. 2024; 14:1328842.

PMID: 38249469 PMC: 10797057. DOI: 10.3389/fmicb.2023.1328842.

The bacterial replication origin BUS promotes nucleobase capture.

Pelliciari S, Bodet-Lefevre S, Fenyk S, Stevens D, Winterhalter C, Schramm F Nat Commun. 2023; 14(1):8339.

PMID: 38097584 PMC: 10721633. DOI: 10.1038/s41467-023-43823-w.

Dynamics of chromosome organization in a minimal bacterial cell.

Gilbert B, Thornburg Z, Brier T, Stevens J, Grunewald F, Stone J Front Cell Dev Biol. 2023; 11:1214962.

PMID: 37621774 PMC: 10445541. DOI: 10.3389/fcell.2023.1214962.

IHF and Fis as Cell Cycle Regulators: Activation of the Replication Origin and the Regulatory Cycle of the DnaA Initiator.

Kasho K, Ozaki S, Katayama T Int J Mol Sci. 2023; 24(14).

PMID: 37511331 PMC: 10380432. DOI: 10.3390/ijms241411572.

References

Wolanski M, Donczew R, Zawilak-Pawlik A, Zakrzewska-Czerwinska J . oriC-encoded instructions for the initiation of bacterial chromosome replication. Front Microbiol. 2015; 5:735. PMC: 4285127. DOI: 10.3389/fmicb.2014.00735. View

Mott M, Erzberger J, Coons M, Berger J . Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell. 2008; 135(4):623-34. PMC: 2610854. DOI: 10.1016/j.cell.2008.09.058. View

Sutton M, Carr K, Vicente M, Kaguni J . Escherichia coli DnaA protein. The N-terminal domain and loading of DnaB helicase at the E. coli chromosomal origin. J Biol Chem. 1998; 273(51):34255-62. DOI: 10.1074/jbc.273.51.34255. View

Zawilak-Pawlik A, Kois A, Stingl K, Boneca I, Skrobuk P, Piotr J . HobA--a novel protein involved in initiation of chromosomal replication in Helicobacter pylori. Mol Microbiol. 2007; 65(4):979-94. DOI: 10.1111/j.1365-2958.2007.05853.x. View

Duderstadt K, Chuang K, Berger J . DNA stretching by bacterial initiators promotes replication origin opening. Nature. 2011; 478(7368):209-13. PMC: 3192921. DOI: 10.1038/nature10455. View

Krause M, Ruckert B, Lurz R, Messer W . Complexes at the replication origin of Bacillus subtilis with homologous and heterologous DnaA protein. J Mol Biol. 1998; 274(3):365-80. DOI: 10.1006/jmbi.1997.1404. View

Lenhart J, Schroeder J, Walsh B, Simmons L . DNA repair and genome maintenance in Bacillus subtilis. Microbiol Mol Biol Rev. 2012; 76(3):530-64. PMC: 3429619. DOI: 10.1128/MMBR.05020-11. View

Moriya S, Fukuoka T, Ogasawara N, Yoshikawa H . Regulation of initiation of the chromosomal replication by DnaA-boxes in the origin region of the Bacillus subtilis chromosome. EMBO J. 1988; 7(9):2911-7. PMC: 457086. DOI: 10.1002/j.1460-2075.1988.tb03149.x. View

Langer U, Richter S, Roth A, Weigel C, Messer W . A comprehensive set of DnaA-box mutations in the replication origin, oriC, of Escherichia coli. Mol Microbiol. 1996; 21(2):301-11. DOI: 10.1046/j.1365-2958.1996.6481362.x. View

10.

Woelker B, Messer W . The structure of the initiation complex at the replication origin, oriC, of Escherichia coli. Nucleic Acids Res. 1993; 21(22):5025-33. PMC: 310613. DOI: 10.1093/nar/21.22.5025. View

11.

Fuller R, Funnell B, Kornberg A . The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell. 1984; 38(3):889-900. DOI: 10.1016/0092-8674(84)90284-8. View

12.

Luo H, Quan C, Peng C, Gao F . Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform. 2018; 20(4):1114-1124. DOI: 10.1093/bib/bbx174. View

13.

Kaur G, Vora M, Czerwonka C, Rozgaja T, Grimwade J, Leonard A . Building the bacterial orisome: high-affinity DnaA recognition plays a role in setting the conformation of oriC DNA. Mol Microbiol. 2014; 91(6):1148-63. PMC: 3992943. DOI: 10.1111/mmi.12525. View

14.

Zorman S, Seitz H, Sclavi B, Strick T . Topological characterization of the DnaA-oriC complex using single-molecule nanomanipuation. Nucleic Acids Res. 2012; 40(15):7375-83. PMC: 3424547. DOI: 10.1093/nar/gks371. View

15.

Bellomy G, Mossing M, Record Jr M . Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process. Biochemistry. 1988; 27(11):3900-6. DOI: 10.1021/bi00411a002. View

16.

Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T . Structural basis of replication origin recognition by the DnaA protein. Nucleic Acids Res. 2003; 31(8):2077-86. PMC: 153737. DOI: 10.1093/nar/gkg309. View

17.

Natrajan G, Hall D, Thompson A, Gutsche I, Terradot L . Structural similarity between the DnaA-binding proteins HobA (HP1230) from Helicobacter pylori and DiaA from Escherichia coli. Mol Microbiol. 2007; 65(4):995-1005. DOI: 10.1111/j.1365-2958.2007.05843.x. View

18.

Schneider S, Zhang W, Soultanas P, Paoli M . Structure of the N-terminal oligomerization domain of DnaD reveals a unique tetramerization motif and provides insights into scaffold formation. J Mol Biol. 2008; 376(5):1237-50. PMC: 3034642. DOI: 10.1016/j.jmb.2007.12.045. View

19.

Weigel C, Schmidt A, Seitz H, Tungler D, Welzeck M, Messer W . The N-terminus promotes oligomerization of the Escherichia coli initiator protein DnaA. Mol Microbiol. 1999; 34(1):53-66. DOI: 10.1046/j.1365-2958.1999.01568.x. View

20.

Ogura Y, Imai Y, Ogasawara N, Moriya S . Autoregulation of the dnaA-dnaN operon and effects of DnaA protein levels on replication initiation in Bacillus subtilis. J Bacteriol. 2001; 183(13):3833-41. PMC: 95264. DOI: 10.1128/JB.183.13.3833-3841.2001. View