Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Regulating DNA Replication in Bacteria Kirsten Skarstad1 and Tsutomu Katayama2 1Department of Cell Biology, Institute for Cancer Research, The Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway 2Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan Correspondence: [email protected] The replication origin and the initiator protein DnaA are the main targets for regulation of chromosome replication in bacteria. The origin bears multiple DnaA binding sites, while DnaA contains ATP/ADP-binding and DNA-binding domains. When enough ATP-DnaAhas accumulated in the cell, an active initiation complex can be formed at the origin resulting in strand opening and recruitment of the replicative helicase. In Escherichia coli, oriC activity is directly regulated by DNA methylation and specific oriC-binding proteins. DnaA activity is regulated by proteins that stimulate ATP-DnaA hydrolysis, yielding inactive ADP-DnaA in a replication-coupled negative-feedback manner, and by DnaA-binding DNA elements that control the subcellular localization of DnaA or stimulate the ADP-to-ATP exchange of the DnaA-bound nucleotide. Regulation of dnaA gene expression is also important for initiation. The principle of replication-coupled negative regulation of DnaA found in E. coli is con- served in eukaryotes as well as in bacteria. Regulations by oriC-binding proteins and dnaA gene expression are also conserved in bacteria. acteria typically contain few chromosomes, tion timing is maintained such that initiation Beach carrying a defined origin of replication occurs simultaneously at all origins once per (Messer 2002). The model bacteria referred to in generation (Skarstad et al. 1986). this work (Escherichia coli, Bacillus subtilis, Cau- The key protein responsible for DNA strand lobacter crescentus, and Helicobacter pylori) all opening at the origin and for the recruitment of have a single circular chromosome that is repli- replisome components is the initiator protein, cated bidirectionally from the origin. Some bac- DnaA (Kornberg and Baker 1992; Messer 2002; teria, for instance E. coli and B. subtilis, grow Duderstadt and Berger 2008; Ozaki and Ka- with overlapping replication cycles in rich media tayama 2009; Kaguni 2011; Leonard and Grim- (Fig. 1) (Kornberg and Baker 1992; Helmstetter wade 2011). DnaA is an AAAþ type protein that 1996). This allows for cell doubling times that binds ATP and ADP with high affinity. DnaA are shorter than the replication phase, and re- binds to high- and low-affinity sites in oriC quires replication initiation to occur at 2, 4, or 8 and forms an oligomeric structure (Fig. 2) origins, depending on the growth rate. Replica- (Grimwade et al. 2000; Kawakami et al. 2005; Editors: Stephen D. Bell, Marcel Me´chali, and Melvin L. DePamphilis Additional Perspectives on DNA Replication available at www.cshperspectives.org Copyright # 2013 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a012922 Cite this article as Cold Spring Harb Perspect Biol 2013;5:a012922 1 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press K. Skarstad and T. Katayama Initiation Replication of the whole chromosome takes 40–50 min Replication Cell division τ = 80 min Initiation at two origins Initiation at four origins Replication Replication τ = 35 min τ = 25 min Cell division Cell division Figure 1. The replication cycle of the E. coli chromosome in slowly and rapidly growing cells. The chromosomal replication cycle and the cell division cycle in E. coli are shown. When cells are growing slowly (in this example, the doubling time t is 80 min), cell division occurs after replication of the sister chromosomes is completed. When cells are growing rapidly (i.e., t is 35 or 25 min), replication initiation simultaneously occurs at each oriC on the partially replicated chromosomes, and cell division occurs after the previous round of replication has been completed. Closed circles, oriC. Erzberger et al. 2006; Kawakami and Katayama itive regulator of initiation, to oriC induces a 2010) that involves two types of DnaA–DNA 180 degree bend in the DNA (Dillon and Dor- interactions, one with double-stranded and man 2010) and plays an important role in form- one with single-stranded DNA (Speck and ing an optimal initiation complex (Hwang and Messer 2001; Fujikawa et al. 2003; Ozaki et al. Kornberg 1992; Hiasa and Marians 1994; Cass- 2008; Duderstadt et al. 2011; Ozaki and Ka- ler et al. 1995; Grimwade et al. 2000; Ryan et al. tayama 2012). Only the ATP-bound form of 2002; Leonard and Grimwade 2005; Ozaki and DnaA is capable of binding to low-affinity sites Katayama 2012). Other nucleoid-associated (Fig. 2), which is supported by specific inter- proteins (HU and Fis) also affect formation of DnaA interaction mediated through its AAAþ the initiation complex (Fig. 3) (Gille et al. 1991; domain, resulting in the nucleoprotein struc- Hwang and Kornberg 1992; Hiasa and Marians tures required for initiation activity (McGarry 1994; Cassler et al. 1995; Wold et al. 1996; Mar- et al. 2004; Kawakami et al. 2005). Like ATP- gulies and Kaguni 1998; Ryan et al. 2002, 2004). DnaA, ADP-DnaA binds to high-affinity 9- Transcription by RNA polymerase is required mer DnaA boxes through its carboxy-terminal for replication initiation (Kornberg and Baker dsDNA binding domain, but forms multimers 1992), though the mechanism by which this on oriC that are structurally distinct from those occurs remains unclear. Transcription in or of ATP-DnaA. The binding of IHF,another pos- around oriC is thought to facilitate opening of 2 Cite this article as Cold Spring Harb Perspect Biol 2013;5:a012922 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Regulating DNA Replication in Bacteria A datA oriC dnaA DARS1 E. coli genome (4.64 Mb, 100 min) DARS2 terC B gidAp mioC p oriC (245 bp) ** ** ** *** * * L M R R1 IHF R5ττ 21 I2 R2 R3I3FIS R4 datA (1 kb) 1 2 IHF 3 4 5 DARS1 (103 bp) DARS2 (455 bp) Figure 2. Structures of oriC, datA, and DARSs. (A) The E. coli chromosome is shown as a circle and the locations of oriC (at the genome map position of 84.6 min), dnaA (at 83.6 min), datA (at 94.6 min), DARS1 (at 17.5 min), DARS2 (at 64.0 min), and terC (around 36 min) are indicated. (B) Basic structures of oriC, datA, and DARSs are schematically shown. Closed triangle, DnaA box (9-nucleotide sequence). Gray triangle, I-sites, and t-sites (both 6-nucleotide sequence). As for datA, DnaA boxes 2 and 3 are most crucial in repression of initiation (Ogawa et al. 2002). For details on low-affinity DnaA binding sites in datA, see Hansen et al. (2007). Open triangle, 13-mer AT-rich motif within DUE. IHF, IHF-binding site; FIS, FIS-binding site; Ã, GATC sequence within oriC. the DNA strands, and may be a prerequisite oriC complex and is influenced by the DiaA for initiation in vivo under certain conditions, protein (Fig. 3) (Keyamura et al. 2009). DiaA for instance, when nucleoid-associated proteins binds to the amino terminus of DnaA and pro- partially restrain negative superhelicity, thereby motes initiation (Ishida et al. 2004; Keyamura impeding strand opening (Baker and Kornberg et al. 2007). DiaA may also have a modulating 1988; Skarstad et al. 1990; Bates et al. 1997). In effect on DnaB loading, because it binds to some circumstances, transcription through oriC DnaA in the same place as DnaB, and inhibits mayalsobeinhibitory(Su’etsuguetal.2003)and loading of DnaB in vitro (Keyamura et al. 2009). for such transcription, the DnaA protein func- Regulation of initiation must fulfill two re- tions as a transcriptional regulator (Weigel and quirements. It must prevent extra initiation Messer 1997; Fla˚tten et al. 2009). Thus, DnaA events, and it must ensure sufficient initiation has two roles at oriC, one as an initiator and the so that one initiation event occurs per genera- other as a transcription regulator. tion per origin. Several mechanisms ensure that After the DNA strands at oriC are separated, extra initiation events do not occur (described the DnaB helicase, bound to the helicase loader below), but less is known about the timing DnaC, is recruited to the initiation complex via of replication initiation, i.e., the rate-limiting interactions with oriC-bound DnaA (Sutton steps, and whether the same factor(s) are re- et al. 1998; Seitz et al. 2000; Messer 2002; Abe quired under all conditions. The frequency of et al. 2007; Duderstadt and Berger 2008; Leo- replication must match the growth rate, other- nard and Grimwade 2010; Kaguni 2011). This wise the cellular DNA concentration will be stage may involve a reorganization of the DnaA- altered. The cellular concentration of DnaA Cite this article as Cold Spring Harb Perspect Biol 2013;5:a012922 3 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press K. Skarstad and T. Katayama Cell cycle organizer? The dnaA gene ? ?? ATP-DnaA Fis IHF, DiaA Nucleotide exchange oriC Replication DARS SeqA binding to oriC (temporal) SeqA binding to dnaA (temporal) DNA-loaded clamps DnaA-ATP hydrolysis by the ADP-Hda- clamp-DNA complex (RIDA) ADP-DnaA Figure 3. The DnaA cycle and regulation of oriC initiation. Transcription of the dnaA gene is autoregulated. ATP- DnaA is more active in inhibiting dnaA transcription than ADP-DnaA. Also, dnaA transcription increases before replication initiation and is repressed after it in a SeqA-dependent manner. Newly synthesized DnaA molecules adopt the ATPform. ATP-DnaA molecules are also generated by nucleotide exchange of ADP-DnaA in a DARS- dependent manner, though the cell cycle-dependent regulation of DARS remains unclear.