SeqA Protein Stimulates the Relaxing and Decatenating Activities of Topoisomerase IV

Kang, Sung-Myung; Han, Joo Seok; Park, Jong Hoon; Skarstad, Kirsten; Hwang, Deog Su

doi:10.1074/jbc.m308843200

Cited by 50 publications

(46 citation statements)

References 46 publications

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“…Results from bacterial two-hybrid assays indicated that the CTD of E. coli ParC can interact with SeqA protein, a DNA binding modulator of chromosome replication (51). As SeqA was found to preferentially bind hemimethylated DNA and thus localize primarily behind the replication fork, E. coli Topo IV was proposed to be recruited to this general area by SeqA to disentangle precatenanes caused by replication.…”

Section: Resultsmentioning

confidence: 99%

Structure of the Topoisomerase IV C-terminal Domain

Hsieh

Farh

Huang

et al. 2004

Journal of Biological Chemistry

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Bacteria possess two closely related yet functionally distinct essential type IIA topoisomerases (Topos). DNA gyrase supports replication and transcription with its unique supercoiling activity, whereas Topo IV preferentially relaxes (؉) supercoils and is a decatenating enzyme required for chromosome segregation. Here we report the crystal structure of the C-terminal domain of Topo IV ParC subunit (ParC-CTD) from Bacillus stearothermophilus and provide a structure-based explanation for how Topo IV and DNA gyrase execute distinct activities. Although the topological connectivity of ParC-CTD is similar to the recently determined CTD structure of DNA gyrase GyrA subunit (GyrA-CTD), ParC-CTD surprisingly folds as a previously unseen broken form of a six-bladed ␤-propeller. Propeller breakage is due to the absence of a DNA gyrase-specific GyrA box motif, resulting in the reduction of curvature of the proposed DNA binding region, which explains why ParC-CTD is less efficient than GyrA-CTD in mediating DNA bending, a difference that leads to divergent activities of the two homologous enzymes. Moreover, we found that the topology of the propeller blades observed in ParC-CTD and GyrA-CTD can be achieved from a concerted ␤-hairpin invasion-induced fold change event of a canonical six-bladed ␤-propeller; hence, we proposed to name this new fold as "hairpininvaded ␤-propeller" to highlight the high degree of similarity and a potential evolutionary linkage between them. The possible role of ParC-CTD as a geometry facilitator during various catalytic events and the evolutionary relationships between prokaryotic type IIA Topos have also been discussed according to these new structural insights.

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Section: Resultsmentioning

confidence: 99%

Structure of the Topoisomerase IV C-terminal Domain

Hsieh

Farh

Huang

et al. 2004

Journal of Biological Chemistry

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“…In contrast to MukB, numerous examples of proteins with physical and/or functional interactions with ParC have been reported, including the DNA polymerase III holoenzyme, FtsK, MreB, and SeqA (61)(62)(63)(64). Marians and co-workers have clearly shown functional significance for the interactions of Topo IV with the first of these three binding partners (61,62,64).…”

Section: Discussionmentioning

confidence: 99%

Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction

Stewart

Berger

et al. 2010

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

139

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In contrast to the current state of knowledge in the field of eukaryotic chromosome segregation, relatively little is known about the mechanisms coordinating the appropriate segregation of bacterial chromosomes. In Escherichia coli , the MukB/E/F complex and topoisomerase IV (Topo IV) are both crucial players in this process. Topo IV removes DNA entanglements following the replication of the chromosome, whereas MukB, a member of the structural maintenance of chromosomes protein family, serves as a bacterial condensin. We demonstrate here a direct physical interaction between the dimerization domain of MukB and the C-terminal domain of the ParC subunit of Topo IV. In addition, we find that MukB alters the activity of Topo IV in vitro. Finally, we isolate a MukB mutant, D692A, that is deficient in its interaction with ParC and show that this mutant fails to rescue the temperature-sensitive growth phenotype of a mukB - strain. These results show that MukB and Topo IV are linked physically and functionally and indicate that the activities of these proteins are not limited to chromosome segregation but likely also play a key role in the control of higher-order bacterial chromosome structure.

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“…We suggest that the association of NDP reductase within this hyperstructure could be a requirement not only for the synthesis of precursors for replication but also for the correct conformation of the hyperstructure required for the location of the replication fork and for chromosome segregation. In this sense it is interesting to mention the connection of topoisomerase IV (required for decatenation of sister chromosomes and segregation) with SeqA (a hemimethylated DNA-binding protein located at initiation and at the replication fork [21]), and with FtsK (a translocase required to facilitate chromosome dimer resolution, to clear DNA from the closing septum, and to form septa), and with DnaX (which codes for the γ and τ  subunits of DNA polymerase III holoenzyme [22]). Studies on B. subtilis support the idea that the replication factory, for most of the replication cycle with a fixed mid-cell location [23], is likely to be co-…”

Section: Discussionmentioning

confidence: 99%

Differences in the degree of inhibition of NDP reductase by chemical inactivation and by the thermosensitive mutation nrdA101 in Escherichia coli suggest an effect on chromosome segregation

Riola

Guarino

Guzmán

et al. 2007

Cellular and Molecular Biology Letters

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NDP reductase activity can be inhibited either by treatment with hydroxyurea or by incubation of an nrdA ts mutant strain at the non-permissive temperature. Both methods inhibit replication, but experiments on these two types of inhibition yielded very different results. The chemical treatment immediately inhibited DNA synthesis but did not affect the cell and nucleoid appearance, while the incubation of an nrdA101 mutant strain at the nonpermissive temperature inhibited DNA synthesis after more than 50 min, and resulted in aberrant chromosome segregation, long filaments, and a high frequency of anucleate cells. These phenotypes are not induced by SOS. In view of these results, we suggest there is an indirect relationship between NDP reductase and the chromosome segregation machinery through the maintenance of the proposed replication hyperstructure.

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SeqA Protein Stimulates the Relaxing and Decatenating Activities of Topoisomerase IV

Cited by 50 publications

References 46 publications

Structure of the Topoisomerase IV C-terminal Domain

Structure of the Topoisomerase IV C-terminal Domain

Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction

Differences in the degree of inhibition of NDP reductase by chemical inactivation and by the thermosensitive mutation nrdA101 in Escherichia coli suggest an effect on chromosome segregation

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