The dimer-dimer interaction surface of the replication terminator protein of Bacillus subtilis and termination of DNA replication.

Manna, A. La; Pai, Karnire S.; Bussiere, Dirksen E.; White, Stephen W.; Bastia, Deepak

doi:10.1073/pnas.93.8.3253

Cited by 21 publications

(50 citation statements)

References 39 publications

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“…This was followed quickly by models for the structures of the complex of the RTP dimer and tetramer with half and full Ter sites, derived from consolidation of the structure of the free protein with an extensive series of biochemical data (115,125,134,135). The structure of the half-site complex determined subsequently by a combination of nuclear magnetic resonance and crystallographic studies (172) was largely in accord with these models.…”

Section: The Crystal Structure Of the Tus-ter Complexmentioning

confidence: 90%

Replication Termination inEscherichia coli: Structure and Antihelicase Activity of the Tus-TerComplex

Neylon

Kralicek

Hill

et al. 2005

Microbiol Mol Biol Rev

134

144

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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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Section: The Crystal Structure Of the Tus-ter Complexmentioning

confidence: 90%

Replication Termination inEscherichia coli: Structure and Antihelicase Activity of the Tus-TerComplex

Neylon

Kralicek

Hill

et al. 2005

Microbiol Mol Biol Rev

134

144

View full text Add to dashboard Cite

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“…The answer comes from the asymmetry of protein-DNA contacts between RTP dimers and core and auxiliary sites (Fig. 1B, right) (27,151,178,252). RTP binds the core site much more strongly than the auxiliary site.…”

Section: Dna Binding Proteinsmentioning

confidence: 99%

Replication Fork Stalling at Natural Impediments

Mirkin

2007

Microbiol Mol Biol Rev

452

466

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SUMMARY Accurate and complete replication of the genome in every cell division is a prerequisite of genomic stability. Thus, both prokaryotic and eukaryotic replication forks are extremely precise and robust molecular machines that have evolved to be up to the task. However, it has recently become clear that the replication fork is more of a hurdler than a runner: it must overcome various obstacles present on its way. Such obstacles can be called natural impediments to DNA replication, as opposed to external and genetic factors. Natural impediments to DNA replication are particular DNA binding proteins, unusual secondary structures in DNA, and transcription complexes that occasionally (in eukaryotes) or constantly (in prokaryotes) operate on replicating templates. This review describes the mechanisms and consequences of replication stalling at various natural impediments, with an emphasis on the role of replication stalling in genomic instability.

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“…Another mutant half-site, named the B* site, was designed to have intrinsically lower affinity for RTP than the B site. It contains sequence features from both the B and A sites and is based on the mutations (bp [17][18][19][20] made previously in the TerI B site (18). Finally, site "Y" was designed so that it would not bind RTP specifically and was used to isolate the various adjacent half-sites, to provide a consistent sequence context for separate measurements of their binding affinities.…”

Section: The Dba Model For Polar Replication Fork Arrest By the Rtp-tmentioning

confidence: 99%

“…A replication fork is arrested only when it approaches the B site side of the complex, although a single RTP dimer bound to an isolated B site cannot cause arrest (16). It is clear that interaction between the two bound RTP dimers (13,17,18), possibly involving direct protein-protein contacts (14), is essential for fork arrest at Ter sites. Structural models of the complete RTP-Ter complex have been developed with the aid of the crystal structures of RTP (15) and an RTP-DNA complex (14), together with other less direct structural studies (13, 18 -20).…”

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confidence: 99%

A Complex Mechanism Determines Polarity of DNA Replication Fork Arrest by the Replication Terminator Complex of Bacillus subtilis

Duggin

Matthews

Dixon

et al. 2005

Journal of Biological Chemistry

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Two dimers of the replication terminator protein (RTP) of Bacillus subtilis bind to a chromosomal DNA terminator site to effect polar replication fork arrest. Cooperative binding of the dimers to overlapping halfsites within the terminator is essential for arrest. It was suggested previously that polarity of fork arrest is the result of the RTP dimer at the blocking (proximal) side within the complex binding very tightly and the permissive-side RTP dimer binding relatively weakly. In order to investigate this "differential binding affinity" model, we have constructed a series of mutant terminators that contain half-sites of widely different RTP binding affinities in various combinations. Although there appeared to be a correlation between binding affinity at the proximal half-site and fork arrest efficiency in vivo for some terminators, several deviated significantly from this correlation. Some terminators exhibited greatly reduced binding cooperativity (and therefore have reduced affinity at each half-site) but were highly efficient in fork arrest, whereas one terminator had normal affinity over the proximal half-site, yet had low fork arrest efficiency. The results show clearly that there is no direct correlation between the RTP binding affinity (either within the full complex or at the proximal half-site within the full complex) and the efficiency of replication fork arrest in vivo. Thus, the differential binding affinity over the proximal and distal half-sites cannot be solely responsible for functional polarity of fork arrest. Furthermore, efficient fork arrest relies on features in addition to the tight binding of RTP to terminator DNA.Replication terminator proteins are a diverse group of DNAbinding proteins that cause DNA replication fork arrest (or pausing) at designated DNA terminator sites. They have roles in a variety of tasks, including the coordination of DNA replication and transcription at eukaryotic rDNA loci (1, 2), regulation of mating-type switching in yeast by strand-specific imprinting during replication (3, 4), and participation in the final stages of bacterial chromosome replication and partitioning (5).These functions require the DNA replication fork to be blocked at the terminator site from only one direction of approach. Thus, a terminator protein-DNA complex exhibits functional polarity. An understanding of the mechanism of polar replication fork arrest has remained elusive.Considerable progress in the characterization of replication termination systems has been made with those from Bacillus subtilis and Escherichia coli (6, 7), and this has recently aided the study of analogous eukaryotic systems (4, 8, 9). In both bacteria, the numerous terminator (Ter) 1 sites are clustered in the terminal region of the chromosome and are arranged so as to control the location of replication fork fusion at the end of a round of replication (for a review see Ref. 10). Despite the same apparent function of these two bacterial systems, the terminator proteins from E. coli and B. subtilis share no sequ...

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The dimer-dimer interaction surface of the replication terminator protein of Bacillus subtilis and termination of DNA replication.

Cited by 21 publications

References 39 publications

Replication Termination inEscherichia coli: Structure and Antihelicase Activity of the Tus-TerComplex

Replication Termination inEscherichia coli: Structure and Antihelicase Activity of the Tus-TerComplex

Replication Fork Stalling at Natural Impediments

A Complex Mechanism Determines Polarity of DNA Replication Fork Arrest by the Replication Terminator Complex of Bacillus subtilis

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