Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability

Popp, David; Narita, Akihiro; Oda, Tatsuya; Fujisawa, Tetsuro; Matsuo, Hiroshi; Nitanai, Yasushi; Iwasa, Mikio; Maéda, Kayo; Onishi, Hiromitsu; Maéda, Yuichiro

doi:10.1038/sj.emboj.7601978

Cited by 82 publications

(149 citation statements)

References 31 publications

(71 reference statements)

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“…Type I systems contain NTPases with deviant Walker A-type ATPase folds, whereas type II systems utilize actin-like NTPases. Interestingly, both types of NTPases form polymers in NTP-dependent manners that are implicated to play a role in plasmid DNA separation (16)(17)(18)(19). The recent discovery of TubZ NTPases has led to the designation of "type III" par systems (13,14).…”

mentioning

confidence: 99%

Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition

Kumaraswami

et al. 2010

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

101

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The segregation of plasmid DNA typically requires three elements: a DNA centromere site, an NTPase, and a centromere-binding protein. Because of their simplicity, plasmid partition systems represent tractable models to study the molecular basis of DNA segregation. Unlike eukaryotes, which utilize the GTPase tubulin to segregate DNA, the most common plasmid-encoded NTPases contain Walker-box and actin-like folds. Recently, a plasmid stability cassette on Bacillus thuringiensis pBtoxis encoding a putative FtsZ/tubulin-like NTPase called TubZ and DNA-binding protein called TubR has been described. How these proteins collaborate to impart plasmid stability, however, is unknown. Here we show that the TubR structure consists of an intertwined dimer with a winged helix-turn-helix (HTH) motif. Strikingly, however, the TubR recognition helices mediate dimerization, making canonical HTH-DNA interactions impossible. Mutagenesis data indicate that a basic patch, encompassing the two wing regions and the N termini of the recognition helices, mediates DNA binding, which indicates an unusual HTH-DNA interaction mode in which the N termini of the recognition helices insert into a single DNA groove and the wings into adjacent DNA grooves. The TubZ structure shows that it is as similar structurally to eukaryotic tubulin as it is to bacterial FtsZ. TubZ forms polymers with guanine nucleotide-binding characteristics and polymer dynamics similar to tubulin. Finally, we show that the exposed TubZ C-terminal region interacts with TubR-DNA, linking the TubR-bound pBtoxis to TubZ polymerization. The combined data suggest a mechanism for TubZ-polymer powered plasmid movement.

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mentioning

confidence: 99%

Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition

Kumaraswami

et al. 2010

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

101

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“…S1 A and B). This value is 2× higher than found for ParM-R1 (14). ParM-R1 concentrations have been shown to be 12-14 μM in the bacterial cell (15), well above the critical concentration.…”

Section: Significancementioning

confidence: 65%

“…The outer diameter of the BtParM filament (∼145 Å; Fig. 2 D and E) is substantially larger than the diameters of the non-supercoiled filaments of F-actin and ParM-R1, which are typically 80-90 Å (6,14).…”

Section: Significancementioning

confidence: 99%

“…However, the appearance of the filaments differed from ParM-R1 or F-actin polymers, in that they appeared twisted. The BtParM filaments were reconstructed following procedures successfully applied in F-actin and ParM-R1 reconstructions (14,17). In brief, an initial 3D structure was produced by helical reconstruction (18) using eight layer lines (∼54-Å resolution; Fig.…”

Section: Significancementioning

confidence: 99%

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Novel actin filaments from Bacillus thuringiensis form nanotubules for plasmid DNA segregation

Jiang

Narita

Popp

et al. 2016

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

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Here we report the discovery of a bacterial DNA-segregating actinlike protein (BtParM) from Bacillus thuringiensis, which forms novel antiparallel, two-stranded, supercoiled, nonpolar helical filaments, as determined by electron microscopy. The BtParM filament features of supercoiling and forming antiparallel double-strands are unique within the actin fold superfamily, and entirely different to the straight, double-stranded, polar helical filaments of all other known ParMs and of eukaryotic F-actin. The BtParM polymers show dynamic assembly and subsequent disassembly in the presence of ATP. BtParR, the DNA-BtParM linking protein, stimulated ATP hydrolysis/phosphate release by BtParM and paired two supercoiled BtParM filaments to form a cylinder, comprised of four strands with inner and outer diameters of 57 Å and 145 Å, respectively. Thus, in this prokaryote, the actin fold has evolved to produce a filament system with comparable features to the eukaryotic chromosomesegregating microtubule.D uring bacterial cell division, equal distribution of replicated plasmids to the two daughter cells ensures their stable inheritance. Type II plasmid segregation systems consist of an actin-like protein (ParM) capable of nucleotide-dependent filament formation and a centrosome-like DNA region (parC), which are linked by an adaptor protein ParR. The model ParCMR system is that of the Escherichia coli R1 plasmid (1). ParM-R1 forms actin-like double-helical straight polar filaments (2), which are paired into randomly oriented bundles. The antiparallel pairing of at least two filaments is required to push apart two R1-ParR/parC complexes (3). All other ParMs, which have been experimentally verified to segregate DNA, including AlfA from Bacillus subtilis (4) and ParM-pSK41 from Staphylococcus aureus (5), have also been shown by electron microscopy to form polar, double-stranded straight filaments with diameters between 80 and 90 Å, similar to eukaryotic F-actin (6).Actins and microtubules have gained dedicated functions during evolution that vary between eukaryotes and prokaryotes. During cell division, the contractile ring in prokaryotes depends on the microtubule-like protein FtsZ, whereas this task relies on actin in eukaryotes. In contrast, DNA segregation in eukaryotes is orchestrated by microtubules, whereas in prokaryotes plasmid DNA segregation depends largely on the actin-like proteins ParMs, although Walker-type ATPase ParA (type I) systems (7) and microtubule-like TubZ (type III) systems have also been found (8). Therefore, a long-standing question has been whether a functional equivalent of the microtubule-like DNA segregating architecture, a hollow cylinder, can be found in bacteria.Using X-ray crystallography, electron microscopy and biochemical assays, we have identified and characterized a novel DNA partitioning ParCMR system from Bacillus thuringiensis (Bt) encoded on the plasmid pBMB67 (9). The filament-forming motor protein, BtParM, proved to be entirely different from all previously studied ParMs; in contrast t...

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“…However, MreB filaments are composed of two parallel strands, while ParM and Factin filaments are helically twisted. In contrast to the right handed actin helix, ParM forms left handed helical filaments [Orlova et al, 2007;Popp et al, 2008]. Unlike actin, MreB from Thermotoga maritima can also polymerise in the presence of GTP [Esue et al, 2006], and ATP appears to be rapidly hydrolysed within the filaments [Bean and Amann, 2008].…”

Section: Mreb Parm and Other Bacterial Actin-like Proteinsmentioning

confidence: 99%

Dynamics of bacterial cytoskeletal elements

Graumann

2009

Cell Motil. Cytoskeleton

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Bacterial cytoskeletal elements are involved in an astonishing spectrum of cellular functions, from cell shape determination to cell division, plasmid segregation, the positioning of membrane-associated proteins and membrane structures, and other aspects of bacterial physiology. Interestingly, these functions are not necessarily conserved, neither between different bacterial species nor between bacteria and eukaryotic cells. The flexibility of cytoskeletal elements in performing different tasks is amazing and emphasises their very early development during evolution. This review focuses on the dynamics of cytoskeletal elements from bacteria. Cell Motil. Cytoskeleton 66: 909-914, 2009. '

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Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability

Cited by 82 publications

References 31 publications

Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition

Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition

Novel actin filaments from Bacillus thuringiensis form nanotubules for plasmid DNA segregation

Dynamics of bacterial cytoskeletal elements

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