Cellular factors couple recombination with growth phase: Characterization of a new component in the λ site-specific recombination pathway

Thompson, John F.; Vargas, Lina; Koch, Christian A.; Kahmann, Regine; Landy, Arthur

doi:10.1016/0092-8674(87)90516-2

Cited by 206 publications

(202 citation statements)

References 33 publications

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“…This activity might play an important role in governing the global dynamics of chromatin reshaping in bacteria. Fis was, however, also identified as a pleiotropic regulator of gene expression [Bosch et al, 1990;Schneider et al, 1999;Hirvonen et al, 2001;Kelly et al, 2004] and site-specific recombination [Koch and Kahmann, 1986;Thompson et al, 1987]. It is thought to act as a topological homeostat that modulates local supercoiling in selected promoter regions in order to maintain conditions that are favorable for transcription.…”

Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 99%

The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler

Wang

Shapiro

2005

J of Cellular Biochemistry

115

100

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Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.

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Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 99%

The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler

Wang

Shapiro

2005

J of Cellular Biochemistry

115

100

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“…During the growth phase, the level of FIS drops, presumably because of the dilution of protein in the course of successive cellular divisions without degradation of the protein produced (Ball et al, 1992). It is conceivable that the sequential dissociation of FIS during the growth cycle from chromosomal sites with binding constants varying from micromolar to nanomolar range (Pan et al, 1996) could allow for correct timing of occupation by regulatory proteins of biologically important DNA loci, such as promoters, replication origins or recombination sequences (see for example Thompson et al, 1987;Cassler et al, 1995). Indeed, there is evidence that the effects of FIS on the initiation of DNA replication at oriC may depend on binding to secondary FIS-binding sites in addition to specific binding at a high-affinity site (Wold et al, 1996).…”

Section: Biological Implicationsmentioning

confidence: 99%

FIS modulates growth phase‐dependent topological transitions of DNA in Escherichia coli

Schneider

Travers

Muskhelishvili

1997

Molecular Microbiology

113

104

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SummaryThe Escherichia coli DNA-binding protein FIS serves as a DNA architectural factor in two unrelated enzymatic reactions, the site-specific inversion of DNA and transcriptional activation of stable RNA promoters. In both these processes, FIS facilitates the assembly and dynamic transitions of two structurally distinct nucleoprotein complexes. We have proposed previously that, in these systems, FIS stabilizes writhed DNA microloops by binding at multiple helically phased sites in DNA. However, FIS also binds and bends DNA at many non-specific sites and, at its maximum levels in the early exponential phase, FIS could potentially occupy a considerable part of the E. coli chromosome. Here, we show that fis affects growth phase-specific alterations in the supercoiling level of DNA. Expression of fis accelerates the accumulation of moderately supercoiled plasmids in stationary phase, which are stabilized by FIS after nutritional shift-up. In accordance with such a function, FIS modulates the relaxing and supercoiling activities of topoisomerases in vitro in a way that keeps DNA in a moderately supercoiled state. Our results suggest that the primary role of FIS is to modulate chromosomal dynamics during bacterial growth.

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“…Studies of these systems have provided detailed information about the architecture of the recombination sites, protein-DNA interactions, juxtaposition of two recombination sites, and key reaction intermediates (1,(10)(11)(12)(13)(14). A potentially useful .approach to many questions that remain is the application of classical enzyme kinetic methods.…”

mentioning

confidence: 99%

“…A number of site-specific recombination systems have been characterized in vitro. These include the bacteriophage A integration system (2), the resolvases derived from the Tn3 class of bacterial transposons (3, 4), the bacterial invertases (5, 6), the Cre-lox system of bacteriophage P1 (7), and the FLP system of the 2-gm plasmid of Saccharomyces cerevisiae (8, 9).Studies of these systems have provided detailed information about the architecture of the recombination sites, protein-DNA interactions, juxtaposition of two recombination sites, and key reaction intermediates (1,(10)(11)(12)(13)(14). A potentially useful .approach to many questions that remain is the application of classical enzyme kinetic methods.…”

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confidence: 99%

FLP recombinase is an enzyme.

Gates

Cox²

1988

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

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The FLP protein of the yeast 2-jum plasmid catalyzes intermolecular site-specific recombination with a turnover number of 0.12 min-(per FLP monomer) for relaxed DNA substrates. Under conditions that enhance its stability, the protein can be used in catalytic rather than stoichiometric amounts. The reaction rate exhibits a strong dependence on FLP protein concentration even when the protein is present in excess relative to available recombination sites.Site-specific recombination events play crucial roles in DNA transposition, partitioning of extrachromosomal elements, gene regulation, and generation of genetic diversity (1). A number of site-specific recombination systems have been characterized in vitro. These include the bacteriophage A integration system (2), the resolvases derived from the Tn3 class of bacterial transposons (3, 4), the bacterial invertases (5, 6), the Cre-lox system of bacteriophage P1 (7), and the FLP system of the 2-gm plasmid of Saccharomyces cerevisiae (8, 9).Studies of these systems have provided detailed information about the architecture of the recombination sites, protein-DNA interactions, juxtaposition of two recombination sites, and key reaction intermediates (1,(10)(11)(12)(13)(14). A potentially useful .approach to many questions that remain is the application of classical enzyme kinetic methods. No detailed kinetic description of a site-specific recombination reaction has appeared. A number of factors contribute to the lack of information about kinetic parameters in these systems. The assays are often tedious, instability of some recombinases may affect reproducibility, and the reactions themselves are complex. Perhaps most important is the fact that it is not clear that these proteins are enzymes. The "recombinase" in each system appears to be required in stoichiometric rather than catalytic amounts (1,3,(15)(16)(17). Enzymatic turnover has not been demonstrated in any case. The focus of this report is turnover in the yeast FLP recombination system.The yeast 2-,um plasmid encodes a site-specific recombination system (FLP) that inverts the two unique regions of the plasmid (18). This inversion event is central to the strategy by which the plasmid amplifies its copy number (19-21). The only protein required is the plasmid-encoded FLP protein (22), which has recently been purified to near homogeneity (23,24). The relatively small recombination site (FLP recombination target or FRT) has been characterized extensively. The FLP protein will promote inversions, deletions, or intermolecular recombination efficiently if appropriate substrates are provided. Supercoiled and relaxed substrates react efficiently in vitro.The minimal FRT site consists of two 13-base-pair (bp) repeats separated by an 8-bp spacer (Fig. 1) (31)(32)(33). The alignment of two sites during recombination is also mediated by asymmetry in the spacer. FRT sites with symmetrical spacers remain functional but permit either of the two possible alignments of two sites during recombination (32). Several of the prop...

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Cellular factors couple recombination with growth phase: Characterization of a new component in the λ site-specific recombination pathway

Cited by 206 publications

References 33 publications

The bacterial nucleoid: A highly organized and dynamic structure

The bacterial nucleoid: A highly organized and dynamic structure

FIS modulates growth phase‐dependent topological transitions of DNA in Escherichia coli

FLP recombinase is an enzyme.

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