Regulating DNA Replication in Bacteria

Skarstad, Kirsten; Katayama, Tsutomu

doi:10.1101/cshperspect.a012922

Cited by 181 publications

(202 citation statements)

References 161 publications

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“…In bacteria and eukaryotic viruses such as SV40 T antigen and papillomavirus E1, the helicase is loaded in an active form; thus, initiation is controlled at the level of initial DNA unwinding (Schuck and Stenlund 2005;Skarstad and Katayama 2013). In eukaryotes, helicase loading cumulates in a Mcm2-7 double-hexamer formation, which represents an intrinsically inactive form of the replicative helicase, which only becomes activated during S phase (Tanaka and Araki 2013).…”

Section: Multiple Mechanisms Inhibit the Helicase Activity In The MCMmentioning

confidence: 99%

Structural and mechanistic insights into Mcm2–7 double-hexamer assembly and function

et al. 2014

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Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2-7 (minichromosome maintenance proteins 2-7) double hexamer. During S phase, each Mcm2-7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC-Cdc6 function to recruit a single Cdt1-Mcm2-7 heptamer to replication origins prior to Cdt1 release and ORC-Cdc6-Mcm2-7 complex formation, but how the second Mcm2-7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC-Cdc6-Mcm2-7 complex and an ORC-Cdc6-Mcm2-7-Mcm2-7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2-7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2-7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.

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Section: Multiple Mechanisms Inhibit the Helicase Activity In The MCMmentioning

confidence: 99%

Structural and mechanistic insights into Mcm2–7 double-hexamer assembly and function

et al. 2014

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“…Unlike eukaryotes, in which chromosomes are fully replicated and organized into higher order structures before segregation (1), most bacteria segregate their chromosomes progressively during replication (2). DnaA is a conserved bacterial protein responsible for the initiation of DNA synthesis at the chromosomal origin of replication (ori) (3,4). The mechanism by which chromosome segregation is initiated in bacteria is less well understood.…”

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confidence: 99%

Replication initiator DnaA binds at the Caulobacter centromere and enables chromosome segregation

Mera

Kalogeraki

Shapiro

2014

Proc. Natl. Acad. Sci. U.S.A.

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Significance DnaA is an essential and conserved bacterial protein that enables the initiation of DNA replication. Although it is commonly held that the onset of bacterial chromosome segregation depends on the initiation of DNA replication, we have found that in Caulobacter crescentus , chromosome segregation can be induced in a DnaA-dependent, yet replication-independent manner. The chromosome replication origin, containing essential DnaA binding motifs, resides 8 kb from the centromere parS region that also contains DnaA binding motifs. The centromere parS region bound to the ParB partition protein initiates movement across the cell followed by the origin region. Mutations in a centromere DnaA motif that alter DnaA–centromere interaction exhibit aberrant patterns of ParB/ parS translocation, implicating DnaA in the process of chromosome segregation.

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“…SeqA protein binds to hemi-methylated oriC DNA, blocking DnaA polymerization over it and thus preventing premature initiation (reviewed in Waldminghaus and Skarstad 2009). Eventually, all the multiple GATC sites in oriC are fully methylated by the Dam methyltransferase, resulting in SeqA/oriC disassociation and making oriC initiation-proficient again (initiation itself may not happen for another hour due to operation of other regulatory circuits) (reviewed in Skarstad and Katayama 2013). In the seqA mutants, initiations are less regulated and also less synchronized compared to SeqA+ cells, leading to initial overinitiation in rapidly growing cells .…”

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Static and Dynamic Factors Limit Chromosomal Replication Complexity inEscherichia coli, Avoiding Dangers of Runaway Overreplication

Khan¹,

Mahaseth²,

Kouzminova³

et al. 2016

Genetics

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We define chromosomal replication complexity (CRC) as the ratio of the copy number of the most replicated regions to that of unreplicated regions on the same chromosome. Although a typical CRC of eukaryotic or bacterial chromosomes is 2, rapidly growing Escherichia coli cells induce an extra round of replication in their chromosomes (CRC = 4). There are also E. coli mutants with stable CRC6. We have investigated the limits and consequences of elevated CRC in E. coli and found three limits: the "natural" CRC limit of 8 (cells divide more slowly); the "functional" CRC limit of 22 (cells divide extremely slowly); and the "tolerance" CRC limit of 64 (cells stop dividing). While the natural limit is likely maintained by the eclipse system spacing replication initiations, the functional limit might reflect the capacity of the chromosome segregation system, rather than dedicated mechanisms, and the tolerance limit may result from titration of limiting replication factors. Whereas recombinational repair is beneficial for cells at the natural and functional CRC limits, we show that it becomes detrimental at the tolerance CRC limit, suggesting recombinational misrepair during the runaway overreplication and giving a rationale for avoidance of the latter. KEYWORDS overinitiation; hydroxyurea; seqA; rep; recA E UKARYOTIC and prokaryotic chromosomes differ in many important aspects (Kuzminov 2014), and one key difference lies in the spatio-temporal organization of chromosomal replication. In contrast to eukaryotes, which perform multibubble replication (Masai et al. 2010), most bacteria replicate their singular chromosome in the unibubble format by initiating bidirectional replication from a designated replication origin (oriC) (Sernova and Gelfand 2008;Leonard and Méchali 2013) and finishing replication within a broad termination zone (ter) (Mirkin and Mirkin 2007;Duggin et al. 2008). Eukaryotes always perform a single replication round in their chromosomes (Masai et al. 2010;Diffley 2011), keeping the ratio of maximally replicated to unreplicated DNA in the same chromosome (the "replication complexity index") strictly at 2 ( Figure 1A). Due to the defined origin and terminus of prokaryotic chromosomes, chromosomal replication complexity in bacteria can be simply expressed as the ori/ter ratio ( Figure 1B). Even though unique cell cycles in some bacteria, such as Caulobacter, also maintain a strict CRC = 2 (Collier 2012), bacterial cells are generally recognized for their ability to support multiple concurrent replication rounds within the same chromosome (Morigen et al. 2009).In reality, under typical growth conditions the ori/ter ratio in exponentially growing bacterial cells is still 2 (Bird et al. 1972;Bipatnath et al. 1998;Wang et al. 2007;Murray and Errington 2008;Rotman et al. 2009;Stokke et al. 2011), showing that bacterial cells, like eukaryotes, also prefer to deal with a single replication round in their chromosomes. However, due to the peculiarity of the prokaryotic chromosome cycle (Kuzminov 2013), whe...

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Regulating DNA Replication in Bacteria

Cited by 181 publications

References 161 publications

Structural and mechanistic insights into Mcm2–7 double-hexamer assembly and function

Structural and mechanistic insights into Mcm2–7 double-hexamer assembly and function

Replication initiator DnaA binds at the Caulobacter centromere and enables chromosome segregation

Static and Dynamic Factors Limit Chromosomal Replication Complexity inEscherichia coli, Avoiding Dangers of Runaway Overreplication

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