scholarly journals A simplified mathematical model of directional DNA site-specific recombination by serine integrases

2017 ◽  
Vol 14 (126) ◽  
pp. 20160618 ◽  
Author(s):  
Alexandra Pokhilko ◽  
Jia Zhao ◽  
W. Marshall Stark ◽  
Sean D. Colloms ◽  
Oliver Ebenhöh
Keyword(s):  
Mathematical Model ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Thermodynamic Driving Force ◽  
Necessary And Sufficient ◽  
Kinetics Of ◽  
Inactive Protein ◽  
Core Features ◽  
Good Agreement

Serine integrases catalyse site-specific recombination to integrate and excise bacteriophage genomes into and out of their host's genome. These enzymes exhibit remarkable directionality; in the presence of the integrase alone, recombination between attP and attB DNA sites is efficient and irreversible, giving attL and attR products which do not recombine further. However, in the presence of the bacteriophage-encoded recombination directionality factor (RDF), integrase efficiently promotes recombination between attL and attR to re-form attP and attB . The DNA substrates and products of both reactions are approximately isoenergetic, and no cofactors (such as adenosine triphosphate) are required for recombination. The thermodynamic driving force for directionality of these reactions is thus enigmatic. Here, we present a minimal mathematical model which can explain the directionality and regulation of both ‘forward’ and ‘reverse’ reactions. In this model, the substrates of the ‘forbidden’ reactions (between attL and attR in the absence of RDF, attP and attB in the presence of RDF) are trapped as inactive protein–DNA complexes, ensuring that these ‘forbidden’ reactions are extremely slow. The model is in good agreement with the observed in vitro kinetics of recombination by ϕC31 integrase, and defines core features of the system necessary and sufficient for directionality.

Site-Specific Recombination Promoted in Vitro by the FLP Protein of the Yeast Two-Micron Plasmid

1986 ◽  
pp. 397-405
Author(s):  
Julie F. Senecoff ◽  
Robert C. Bruckner ◽  
Leslie Meyer-Leon ◽  
Cynthia A. Gates ◽  
Elizabeth Wood ◽  
...  
Keyword(s):  
Site Specific ◽  
Site Specific Recombination

The response of the centrosome to heat shock and related stresses in a Drosophila cell line

1990 ◽  
Vol 96 (3) ◽  
pp. 403-412
Author(s):  
A. Debec ◽  
A.M. Courgeon ◽  
M. Maingourd ◽  
C. Maisonhaute
Keyword(s):  
Heat Shock ◽  
Microtubule Assembly ◽  
Close Link ◽  
Drosophila Cell ◽  
Shock Response ◽  
Kinetics Of ◽  
Drosophila Cell Line ◽  
Good Agreement ◽  
Cell Division Control

The centrosome of Drosophila melanogaster cells cultured in vitro has been followed by immunofluorescence techniques with the Bx63 antibody of Frasch and Saumweber. After a heat shock, the centrosome labelling becomes very small and finally disappears after 30 min. Other heat-shock protein (hsp) inducers such as ethanol, arsenite and ecdysterone lead to the same disappearance. Moreover, the functional ability of centrosomes to nucleate microtubule assembly is inhibited by these treatments, particularly by heat shock, ethanol and ecdysterone. Two other hsp inducers, cadmium chloride and hydrogen peroxide, do not affect the centrosome seriously. With the exception of cadmium, the rapidity and the intensity of hsp induction are in good agreement with the kinetics of alteration of the organelle. We propose that a close link exists between the heat-shock response and the centrosome and that the physiological induction of hsps could be reinterpreted in terms of cell division control.

scholarly journals Characterization of the Chromosome Dimer Resolution Site in Caulobacter crescentus

2019 ◽  
Vol 201 (24) ◽  
Author(s):  
Ali Farrokhi ◽  
Hua Liu ◽  
George Szatmari
Keyword(s):  
Cell Division ◽  
Caulobacter Crescentus ◽  
Consensus Sequence ◽  
Markov Modeling ◽  
Control Of Gene Expression ◽  
Site Specific ◽  
Content Type ◽  
Site Specific Recombination ◽  
Resolution System

ABSTRACT Chromosome dimers occur in bacterial cells as a result of the recombinational repair of DNA. In most bacteria, chromosome dimers are resolved by XerCD site-specific recombination at the dif (deletion-induced filamentation) site located in the terminus region of the chromosome. Caulobacter crescentus, a Gram-negative oligotrophic bacterium, also possesses Xer recombinases, called CcXerC and CcXerD, which have been shown to interact with the Escherichia coli dif site in vitro. Previous studies on Caulobacter have suggested the presence of a dif site (referred to in this paper as dif1CC), but no in vitro data have shown any association with this site and the CcXer proteins. Using recursive hidden Markov modeling, another group has proposed a second dif site, which we call dif2CC, which shows more similarity to the dif consensus sequence. Here, by using a combination of in vitro experiments, we compare the affinities and the cleavage abilities of CcXerCD recombinases for both dif sites. Our results show that dif2CC displays a higher affinity for CcXerC and CcXerD and is bound cooperatively by these proteins, which is not the case for the original dif1CC site. Furthermore, dif2CC nicked substrates are more efficiently cleaved by CcXerCD, and deletion of the site results in about 5 to 10% of cells showing an altered cellular morphology. IMPORTANCE Bacteria utilize site-specific recombination for a variety of purposes, including the control of gene expression, acquisition of genetic elements, and the resolution of dimeric chromosomes. Failure to resolve dimeric chromosomes can lead to cell division defects in a percentage of the cell population. The work presented here shows the existence of a chromosomal resolution system in C. crescentus. Defects in this resolution system result in the formation of chains of cells. Further understanding of how these cells remain linked together will help in the understanding of how chromosome segregation and cell division are linked in C. crescentus.

scholarly journals Xer-mediated site-specific recombination in vitro.

1996 ◽  
Vol 15 (5) ◽  
pp. 1172-1181 ◽  
Author(s):  
S. D. Colloms ◽  
R. McCulloch ◽  
K. Grant ◽  
L. Neilson ◽  
D. J. Sherratt
Keyword(s):  
Site Specific ◽  
Site Specific Recombination

scholarly journals Gin-mediated site-specific recombination in bacteriophage Mu DNA: overproduction of the protein and inversion in vitro

1984 ◽  
Vol 3 (10) ◽  
pp. 2415-2421 ◽  
Author(s):  
Gabriele Mertens ◽  
Andrea Hoffmann ◽  
Helmut Blöcker ◽  
Ronald Frank ◽  
Regine Kahmann
Keyword(s):  
Bacteriophage Mu ◽  
Site Specific ◽  
Site Specific Recombination ◽  
And Inversion

A comparison of the suitability of different models for describing the gas production kinetics of whole-crop wheat

1998 ◽  
Vol 22 ◽  
pp. 215-216
Author(s):  
A. T. Adesogan ◽  
E. Owen ◽  
D. I. Givens
Keyword(s):  
Mathematical Model ◽  
Time Course ◽  
Rumen Fluid ◽  
Gas Production ◽  
Ruminal Fermentation ◽  
Production Kinetics ◽  
Fermentation Profile ◽  
Kinetics Of

Menkeet al. (1979), Beuvinket al. (1992) and Theodorouet al. (1994) developed techniques for measuring the time course of gas production of foods fermentedin vitrowith rumen fluid. These techniques require description of the fermentation profile with an appropriate mathematical model. Although several authors have used these techniques to study the ruminal fermentation of foods, little information is available on the suitability of the model chosen for describing the fermentation profile of the food under study. In this study, the models of Ørskov and McDonald (1979), Franceet al. (1993) and Beuvink and Kogut (1993) were fitted to thein vitrogas production profiles of 10 whole-crop wheat (WCW) forages (cv.Slepjner) to determine the model most suited to describing the data.

scholarly journals Site-specific recombination of yeast 2-micron DNA in vitro.

1983 ◽  
Vol 80 (23) ◽  
pp. 7284-7288 ◽  
Author(s):  
D. Vetter ◽  
B. J. Andrews ◽  
L. Roberts-Beatty ◽  
P. D. Sadowski
Keyword(s):  
Site Specific ◽  
Site Specific Recombination

scholarly journals The Escherichia coli Fis Protein Stimulates Bacteriophage λ Integrative Recombination In Vitro

2003 ◽  
Vol 185 (10) ◽  
pp. 3076-3080 ◽  
Author(s):  
Dominic Esposito ◽  
Gary F. Gerard
Keyword(s):  
Escherichia Coli ◽  
Host Cell ◽  
Essential Role ◽  
Bacteriophage Λ ◽  
Site Specific ◽  
Site Specific Recombination ◽  
E Coli ◽  
In Vivo Recombination

ABSTRACT The Escherichia coli nucleoid-associated protein Fis was previously shown to be involved in bacteriophage lambda site-specific recombination in vivo, enhancing the levels of both integrative recombination and excisive recombination. While purified Fis protein was shown to stimulate in vitro excision, Fis appeared to have no effect on in vitro integration reactions even though a 15-fold drop in lysogenization frequency had previously been observed in fis mutants. We demonstrate here that E. coli Fis protein does stimulate integrative lambda recombination in vitro but only under specific conditions which likely mimic natural in vivo recombination more closely than the standard conditions used in vitro. In the presence of suboptimal concentrations of Int protein, Fis stimulates the rate of integrative recombination significantly. In addition, Fis enhances the recombination of substrates with nonstandard topologies which may be more relevant to the process of in vivo phage lambda recombination. These data support the hypothesis that Fis may play an essential role in lambda recombination in the host cell.

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