Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination

Prévost, Chantal; Takahashi, Masayuki

doi:10.1017/s0033583504003956

Cited by 43 publications

(44 citation statements)

References 113 publications

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“…Thus, transposition will predominantly affect certain areas of the phytoplasma genomes, and hence, the synteny in the rest of the genome can be maintained. Second, because of the absence of recA, ruvA, and ruvB, rearrangements between PMUs through homologous recombination are likely to occur at lower frequencies than in genomes with RecA-dependent homologous recombination machineries (78,79).…”

Section: Discussionmentioning

confidence: 99%

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Bai

Zhang

Ewing³

et al. 2006

J Bacteriol

350

447

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Phytoplasmas ("CandidatusPhytoplasmaThe phylogenetic tree of mollicutes is composed of two major clades that diverged early in evolution (51). One clade contains the orders Acholeplasmatales and Anaeroplasmatales (AAA clade mollicutes), and the other clade contains the orders Mycoplasmatales and Entomoplasmatales (SEM clade mollicutes) (9). Phytoplasmas, formerly known as mycoplasma-like organisms of plants, form a monophyletic group in the order Acholeplasmatales (51) and were recently assigned to a novel genus, "Candidatus Phytoplasma" (41). Approximately 20 phytoplasma phylogenetic groups have been proposed based on 16S rRNA gene sequences, and new branches are continuously being discovered (69,85). Members of the order Acholeplasmatales are distinct from other mollicutes in several ways. For instance, whereas most mollicutes use UGA as a tryptophan codon instead of a stop codon, a feature they share with mitochondria, the acholeplasmas and phytoplasmas retained UGA as a stop codon (80).

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Section: Discussionmentioning

confidence: 99%

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Bai

Zhang

Ewing³

et al. 2006

J Bacteriol

350

447

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“…Many research groups have shown that if a force of approximately 65 pN is applied to the ends of a long dsDNA, the molecule will undergo an abrupt overstretching transition into a structure having a length-per-base pair that is approximately 1.7 times the length of B-DNA (1)(2)(3)(4)(5)(6)(7)(8)(9)(10). It has been proposed that the structure of overstretched DNA plays an important role in the function of proteins whose interaction with dsDNA involves a change in length (11)(12)(13)(14).…”

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confidence: 99%

The structure of DNA overstretched from the 5′5′ ends differs from the structure of DNA overstretched from the 3′3′ ends

Danilowicz¹,

Limouse²,

Hatch³

et al. 2009

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

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It has been suggested that the structure that results when doublestranded DNA (dsDNA) is pulled from the 3 3 ends differs from that which results when it is pulled from the 5 5 ends. In this work, we demonstrate, using phage dsDNA, that the overstretched states do indeed show different properties, suggesting that they correspond to different structures. For 3 3 pulling versus 5 5 pulling, the following differences are observed: (i) the forces at which half of the molecules in the ensemble have made a complete force-induced transition to single stranded DNA are 141 ؎ 3 pN and 122 ؎ 4 pN, respectively; (ii) the extension vs. force curve for overstretched DNA has a marked change in slope at 127 ؎ 3 pN for 3 3 and 110 ؎ 3 pN for 5 5 ; (iii) the hysteresis (H) in the extension vs. force curves at 150 mM NaCl is 0.3 ؎ 0.8 pN m for 3 3 versus 13 ؎ 8 pN for 5 5 ; and (iv) 3 3 and 5 5 molecules show different changes in hysteresis due to interactions with ␤-cyclodextrin, a molecule that is known to form stable host-guest complexes with rotated base pairs, and glyoxal that is known to bind stably to unpaired bases. These differences and additional findings are well-accommodated by the corresponding structures predicted on theoretical grounds.

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“…In eukaryotes, from yeast to human, Rad51 is involved in homology search and DNA strand-exchange, central processes for recombination (1,2). The mechanism of DNA strand-exchange appears evolutionarily conserved (3), and has been extensively studied with the bacterial RecA as a model protein (4)(5)(6)(7)(8). The nucleo-protein filament structures appear similar among the RecA and RecA-like proteins, including Rad51 (3,9,10).…”

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confidence: 99%

Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy

Reymer

Frykholm

Morimatsu

et al. 2009

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

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To get mechanistic insight into the DNA strand-exchange reaction of homologous recombination, we solved a filament structure of a human Rad51 protein, combining molecular modeling with experimental data. We build our structure on reported structures for central and N-terminal parts of pure (uncomplexed) Rad51 protein by aid of linear dichroism spectroscopy, providing angular orientations of substituted tyrosine residues of Rad51-dsDNA filaments in solution. The structure, validated by comparison with an electron microscopy density map and results from mutation analysis, is proposed to represent an active solution structure of the nucleoprotein complex. An inhomogeneously stretched double-stranded DNA fitted into the filament emphasizes the strategic positioning of 2 putative DNA-binding loops in a way that allows us speculate about their possibly distinct roles in nucleo-protein filament assembly and DNA strand-exchange reaction. The model suggests that the extension of a single-stranded DNA molecule upon binding of Rad51 is ensured by intercalation of Tyr-232 of the L1 loop, which might act as a docking tool, aligning protein monomers along the DNA strand upon filament assembly. Arg-235, also sitting on L1, is in the right position to make electrostatic contact with the phosphate backbone of the other DNA strand. The L2 loop position and its more ordered compact conformation makes us propose that this loop has another role, as a binding site for an incoming double-stranded DNA. Our filament structure and spectroscopic approach open the possibility of analyzing details along the multistep path of the strand-exchange reaction.homologous recombination ͉ HsRad51 H omologous recombination, the process of exchanging DNA strands of homologous sequences, is important for both the repair of damaged DNA and the maintenance of genomic diversity. In eukaryotes, from yeast to human, Rad51 is involved in homology search and DNA strand-exchange, central processes for recombination (1, 2). The mechanism of DNA strand-exchange appears evolutionarily conserved (3), and has been extensively studied with the bacterial RecA as a model protein (4-8). The nucleo-protein filament structures appear similar among the RecA and RecA-like proteins, including Rad51 (3, 9, 10). The first structure of a RecA filament was solved Ͼ15 years ago (11) and more recently structures of Rad51 proteins have been reported (12)(13)(14). Despite these efforts, though, no detailed filamentous structure of the human Rad51 protein has been reported and only the principal steps of the recombination process are known.RecA and Rad51 protein filaments formed in presence of DNA and ATP, or a nonhydrolysable ATP analogue, all show an extended conformation with a helical pitch of Ϸ90-100 Å. The RecA and Rad51 filament structures vary significantly depending on the presence of DNA and type of nucleotide cofactor (10,(15)(16)(17)(18)(19) suggesting that the filament structure may change during the strand-exchange reaction, possibly related to its function. Thus, a st...

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Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination

Cited by 43 publications

References 113 publications

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

The structure of DNA overstretched from the 5′5′ ends differs from the structure of DNA overstretched from the 3′3′ ends

Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy

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