Fis Targets Assembly of the Xis Nucleoprotein Filament to Promote Excisive Recombination by Phage Lambda

Papagiannis, Christie V.; Sam, My D.; Abbani, Mohamad A.; Yoo, Daniel; Cascio, Duilio; Clubb, Robert T.; Johnson, Reid C.

doi:10.1016/j.jmb.2006.12.071

Cited by 37 publications

(53 citation statements)

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“…Fis N73S is much less compromised for binding or bending, consistent with the importance of H bonding by the side chain (Pan et al 1996;McLeod et al 1999). A more planar DNA axis would decrease the H-bonding distances between Asn73 Nd2 and T À9 O1P T À9 O1P or T +9b O1P, and increase the distances between Thr75 Og and T À8 O2P or T +8b O2P, which would better fit the severe effect of N73A but mild effect by T75A on binding (Feldman-Cohen et al 2006;Skoko et al 2006;Papagiannis et al 2007). A more planar DNA axis will also increase availability of the Thr75 side chain for cooperative binding with the RNA polymerase s subunit and phage l Xis protein (Papagiannis et al 2007;Typas et al 2007).…”

Section: Dna Conformational Changesmentioning

confidence: 65%

“…A more planar DNA axis would decrease the H-bonding distances between Asn73 Nd2 and T À9 O1P T À9 O1P or T +9b O1P, and increase the distances between Thr75 Og and T À8 O2P or T +8b O2P, which would better fit the severe effect of N73A but mild effect by T75A on binding (Feldman-Cohen et al 2006;Skoko et al 2006;Papagiannis et al 2007). A more planar DNA axis will also increase availability of the Thr75 side chain for cooperative binding with the RNA polymerase s subunit and phage l Xis protein (Papagiannis et al 2007;Typas et al 2007). Elimination of the Arg89 side chain severely decreases nonspecific binding and formation of specific complexes with most Fis-binding sites (Osuna et al 1991;Feldman-Cohen et al 2006;Skoko et al 2006).…”

Section: Dna Conformational Changesmentioning

confidence: 99%

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The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Stella¹,

Cascio²,

Johnson³

2010

Genes Dev.

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181

261

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The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNAdependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high-and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of 65°, and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.[Keywords: DNA structure; protein-DNA recognition; DNA bending; nucleoid protein; X-ray crystallography] Supplemental material is available at http://www.genesdev.org.

show abstract

Section: Dna Conformational Changesmentioning

confidence: 65%

Section: Dna Conformational Changesmentioning

confidence: 99%

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Stella¹,

Cascio²,

Johnson³

2010

Genes Dev.

Self Cite

181

261

View full text Add to dashboard Cite

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“…At H2, the P-arm is directed along the plane of the catalytic domain tetramer. An A-tract sequence that is stabilized by Fis binding (11,28) directs the P-arm upward, toward the Int CB domains. The cooperative Xis filament (10, 11) then redirects the P-arm across the top of the Int CB domains, where the P2 site is bound by the Int subunit bound at the B' core site.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, NMR and/or crystal structures of IHF (9), Xis (10-13), and Fis (11,14,15) have provided structural models for the accessory proteins and their corresponding DNA complexes. When combined with the large body of genetic and biochemical analyses that have been performed in these systems, the structural data have revealed how DNA bending by the accessory proteins could facilitate Int bridging between the Significance Despite a vast array of genetic, biochemical, and structural data, there have not been any panoptic investigations designed to generate structural models for the large complexes responsible for λ Integrase protein (Int)-dependent site-specific recombination.…”

mentioning

confidence: 99%

Nucleoprotein architectures regulating the directionality of viral integration and excision

Seah

Warren

Tong

et al. 2014

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

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The virally encoded site-specific recombinase Int collaborates with its accessory DNA bending proteins IHF, Xis, and Fis to assemble two distinct, very large, nucleoprotein complexes that carry out either integrative or excisive recombination along regulated and essentially unidirectional pathways. The core of each complex consists of a tetramer of Integrase protein (Int), which is a heterobivalent DNA binding protein that binds and bridges a core-type DNA site (where strand cleavage and ligation are executed), and a distal arm-type site, that is brought within range by one or more DNA bending proteins. The recent determination of the patterns of these Int bridges has made it possible to think realistically about the global architecture of the recombinogenic complexes. Here, we combined the previously determined Int bridging patterns with in-gel FRET experiments and in silico modeling to characterize and differentiate the two 400-kDa multiprotein Holiday junction recombination intermediates formed during λ integration and excision. The results lead to architectural models that explain how integration and excision are regulated in λ site-specific recombination. Our confidence in the basic features of these architectures is based on the redundancy and self-consistency of the underlying data from two very different experimental approaches to establish bridging interactions, a set of strategic intracomplex distances from FRET experiments, and the model's ability to explain key aspects of the integrative and excisive recombination pathways, such as topological changes, the mechanism of capturing attB, and the features of asymmetry and flexibility within the complexes.regulation of directionality | topology | recombinogenic architectures | molecular machines H igh-precision DNA transactions responsible for a variety of fundamental processes are typically promoted and modulated by large multiprotein machines that use cooperative interactions and involve DNA bending and/or wrapping. One well-studied example is the tightly regulated and highly directional site-specific recombination by which bacteriophage λ inserts and excises its DNA into and out of the Escherichia coli host chromosome, using the phage attP and the bacterial attB DNA sequences for integration and the resulting junction sequences, attL and attR, for excision. These reactions are catalyzed by the phage-encoded Integrase protein (Int), the founding member of the tyrosine recombinase family of site-specific recombinases (1). In addition to mediating integration and excision of viral genomes, members of this family function in a variety of other cellular processes including chromosome segregation, gene regulation, and conjugative transposition (2).Int has three well-characterized domains: an N-terminal DNA-binding domain (NTD), a central core-binding domain (CB), and a C-terminal catalytic domain (CAT). The CB and CAT domains (referred to here as the CTD) are together responsible for binding to the core-type DNA sequences where strand exchange and ligation t...

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“…The overall organization of the mv4 attP site highlights the absence of binding sites for bending proteins between the Int armtype binding sites and the core region (8); this is unlike what has been found for the attP site in well-characterized phages (3,(10)(11)(12)(13). Analysis of the core region sequence does not reveal any Int core-type binding sites (14), and the Int P2 arm-binding site has a noticeable position close to the left border of the core region (Fig.…”

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confidence: 99%

Bacteriophage mv4 Site-Specific Recombination: the Central Role of the P2 ^mv4 Int-Binding Site

Coddeville¹,

Spinella²,

Cassart³

et al. 2014

J Virol

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bThe contributions of the five mv4 Int-and two mv4 Xis arm-binding sites to the spatial intasome organization of bacteriophage mv4 were found not to be equivalent. The 8-bp overlap region was mapped to the left extremity of the core region and is directly flanked by the P2 Int arm-binding site. These results and the absence of characteristic Int core-binding sites suggest that the P2 site is the determinant for integrase positioning and recognition of the core region. During the establishment of the lysogeny, many temperate bacteriophages integrate their genome into the host bacterial chromosome through a site-specific recombination mechanism. This integration is catalyzed by a phage-encoded recombinase (integrase) and occurs between the attB and attP attachment sites located on the bacterial and phage genomes, respectively. Prophage excision during the induction of lytic growth is also catalyzed by the recombinase: it involves recombination between the attR and attL attachment junctions and requires at least one phage-encoded recombination directionality factor (RDF) in addition to the integrase.In well-characterized site-specific recombination systems, the protein binding sites at the att recombination sites are not all used in the same way for integrative or excisive recombination (1-3). The integrase of phage is a heterobivalent recombinase that binds two different families of DNA sequences: the "arm-type" and the "core-type" binding sites (4). The set of proteins and the number and combination of the binding sites used are different in integrative and excisive recombination reactions. During integrative recombination, in the intasome, Int binds to four arm-type binding sites (P1, P=1, P=2, and P=3) on attP whereas the accessory factor IHF binds to all three of its cognate sites (2). During excisive recombination, Xis binds to the X1, X1.5, and X2 sites on attR and Int to three of the arm-type sites (P2 on attR and P=1 and P=2 on attL) (2). In contrast, in phage KplE1, the same combination of IntS arm-type binding sites is used for both excisive and integra-

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Fis Targets Assembly of the Xis Nucleoprotein Filament to Promote Excisive Recombination by Phage Lambda

Cited by 37 publications

References 50 publications

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Nucleoprotein architectures regulating the directionality of viral integration and excision

Bacteriophage mv4 Site-Specific Recombination: the Central Role of the P2 ^mv4 Int-Binding Site

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Fis Targets Assembly of the Xis Nucleoprotein Filament to Promote Excisive Recombination by Phage Lambda

Cited by 37 publications

References 50 publications

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Nucleoprotein architectures regulating the directionality of viral integration and excision

Bacteriophage mv4 Site-Specific Recombination: the Central Role of the P2 mv4 Int-Binding Site

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Product

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Bacteriophage mv4 Site-Specific Recombination: the Central Role of the P2 ^mv4 Int-Binding Site