The topology of plasmid-monomerizing Xer site-specific recombination

2013 ◽  
Vol 41 (2) ◽  
pp. 589-594 ◽  
Author(s):  
Sean D. Colloms
Keyword(s):  
Dna Sequences ◽  
Direct Repeat ◽  
Accessory Proteins ◽  
Site Specific ◽  
Circular Dna ◽  
Site Specific Recombination ◽  
Daughter Cells ◽  
The Core ◽  
Bacterial Plasmid ◽  
Negative Supercoils

Xer site-specific recombination at cer and psi converts bacterial plasmid multimers into monomers so that they can be efficiently segregated to both daughter cells at cell division. Recombination is catalysed by the XerC and XerD recombinases acting at ~30 bp core sites, and is regulated by the action of accessory proteins bound to accessory DNA sequences adjacent to the core sites. Recombination normally occurs only between sites in direct repeat in a negatively supercoiled circular DNA molecule, and yields two circular products linked together in a right-handed four-node catenane with antiparallel sites. These and other topological results are explained by a model in which the accessory DNA sequences are interwrapped around the accessory proteins, trapping three negative supercoils so that strand exchange by the XerC and XerD yields the observed four-node catenane.

Site-specific recombination and circular chromosome segregation

1995 ◽  
Vol 347 (1319) ◽  
pp. 37-42 ◽  
Keyword(s):  
Dna Sequences ◽  
Accessory Proteins ◽  
Circular Chromosome ◽  
Site Specific ◽  
Site Specific Recombination ◽  
E Coli ◽  
Recombination Proteins ◽  
Recombination System ◽  
Insight Into

The Xer site-specific recombination system functions in Escherichia coli to ensure that circular plasmids and chromosomes are in the monomeric state prior to segregation at cell division. Two recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome and to sites present in natural multicopy plasmids. In addition, recombination at the natural plasmid site cer , present in ColE1, requires the function of two additional accessory proteins, ArgR and PepA. These accessory proteins, along with accessory DNA sequences present in the recombination sites of plasmids are used to ensure that recombination is exclusively intramolecular, converting circular multimers to monomers. Wild-type and mutant recombination proteins have been used to analyse the formation of recombinational synapses and the catalysis of strand exchange in vitro . These experiments demonstrate how the same two recombination proteins can act with different outcomes, depending on the organization of DNA sites at which they act. Moreover, insight into the separate roles of the two recombinases is emerging.

scholarly journals A Type Ib ParB Protein Involved in Plasmid Partitioning in a Gram-Positive Bacterium

2006 ◽  
Vol 188 (23) ◽  
pp. 8103-8108 ◽  
Author(s):  
Ping Yin ◽  
Tai-Yuan Li ◽  
Mao-Hua Xie ◽  
Lina Jiang ◽  
Yi Zhang
Keyword(s):  
Dna Sequences ◽  
Plasmid Stability ◽  
Direct Repeat ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Reading Frame ◽  
Plasmid Partition ◽  
Orf4 Protein ◽  
Bacterial Plasmid

ABSTRACT Our current understanding of segregation of prokaryotic plasmids has been derived mainly from the study of the gram-negative bacterial plasmids. We previously reported a replicon of the cryptic plasmid from a gram-positive bacterium, Leifsonia xyli subsp. cynodontis. The replicon contains a putative plasmid partition cassette including a Walker-type ATPase followed by open reading frame 4 without sequence homologue. Here we reported that the orf4 gene was essential for maintaining the plasmid stability in L. xyli subsp. cynodontis. Furthermore, the purified orf4 protein specifically and cooperatively bound to direct repeat sequences located upstream of the parA gene in vitro, indicating that orf4 is a parB gene and that the direct repeat DNA sequences constitute a partition site, parS. The location of parS and the features of ParA and ParB proteins suggest that this plasmid partition cassette belongs to type Ib, representing the first type Ib cassette identified from a gram-positive bacterial plasmid.

Site-Specific Recombination in Bacteriophage λ: Structural Analyses of Reactive DNA Sequences

1980 ◽  
Vol 29 (5_Part_2) ◽  
pp. 1099-1106 ◽  
Author(s):  
Arthur Landy ◽  
Wilma Ross ◽  
Pei-Ling Hsu ◽  
Monika Buraczynska
Keyword(s):  
Dna Sequences ◽  
Bacteriophage Λ ◽  
Site Specific ◽  
Site Specific Recombination

The Interplay between DNA Topology and Accessory Factors in Site-Specific Recombination in Bacteria and their Bacteriophages

2016 ◽  
Vol 99 (4) ◽  
pp. 420-437 ◽  
Author(s):  
Charles J. Dorman ◽  
Marina M. Bogue
Keyword(s):  
Dna Sequences ◽  
Dna Topology ◽  
Life Cycles ◽  
Physiological Status ◽  
Bacterial Cells ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Topological State ◽  
Accessory Factors ◽  
Recombination Reactions

Site-specific recombination is employed widely in bacteria and bacteriophage as a basis for genetic switching events that control phenotypic variation. It plays a vital role in the life cycles of phages and in the replication cycles of chromosomes and plasmids in bacteria. Site-specific recombinases drive these processes using very short segments of identical (or nearly identical) DNA sequences. In some cases, the efficiencies of the recombination reactions are modulated by the topological state of the participating DNA sequences and by the availability of accessory proteins that shape the DNA. These dependencies link the molecular machines that conduct the recombination reactions to the physiological state of the cell. This is because the topological state of bacterial DNA varies constantly during the growth cycle and so does the availability of the accessory factors. In addition, some accessory factors are under allosteric control by metabolic products or second messengers that report the physiological status of the cell. The interplay between DNA topology, accessory factors and site-specific recombination provides a powerful illustration of the connectedness and integration of molecular events in bacterial cells and in viruses that parasitise bacterial cells.

scholarly journals Challenging a Paradigm: the Role of DNA Homology in Tyrosine Recombinase Reactions

2009 ◽  
Vol 73 (2) ◽  
pp. 300-309 ◽  
Author(s):  
Lara Rajeev ◽  
Karolina Malanowska ◽  
Jeffrey F. Gardner
Keyword(s):  
Dna Homology ◽  
Tyrosine Recombinase ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Conjugative Transposons ◽  
The Core ◽  
Sequence Identity ◽  
Tyrosine Recombinases ◽  
Recent Developments

SUMMARY A classical feature of the tyrosine recombinase family of proteins catalyzing site-specific recombination, as exemplified by the phage lambda integrase and the Cre and Flp recombinases, is the ability to recombine substrates sharing very limited DNA sequence identity. Decades of research have established the importance of this short stretch of identity within the core regions of the substrates. Since then, several new enzymes that challenge this paradigm have been discovered and require the role of sequence identity in site-specific recombination to be reconsidered. The integrases of the conjugative transposons such as Tn916, Tn1545, and CTnDOT recombine substrates with heterologous core sequences. The integrase of the mobilizable transposon NBU1 performs recombination more efficiently with certain core mismatches. The integration of CTX phage and capture of gene cassettes by integrons also occur by altered mechanisms. In these systems, recombination occurs between mismatched sequences by a single strand exchange. In this review, we discuss literature that led to the formulation of the current strand-swapping isomerization model for tyrosine recombinases. The review then focuses on recent developments on the recombinases that challenged the paradigm that was derived from the studies of early systems.

scholarly journals Excision of specific DNA-sequences from integrated retroviral vectors via site-specific recombination

1995 ◽  
Vol 23 (21) ◽  
pp. 4451-4454 ◽  
Author(s):  
JörJorg Bergemann ◽  
Klaus K¨hlcke ◽  
Boris Fehse ◽  
IIka Ratz ◽  
Wolfram Ostertag ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Retroviral Vectors ◽  
Site Specific ◽  
Site Specific Recombination

scholarly journals The Streptomyces Genome Contains Multiple Pseudo-attB Sites for the φC31-Encoded Site-Specific Recombination System

2002 ◽  
Vol 184 (20) ◽  
pp. 5746-5752 ◽  
Author(s):  
Patricia Combes ◽  
Rob Till ◽  
Sally Bee ◽  
Margaret C. M. Smith
Keyword(s):  
Dna Sequences ◽  
Southern Blotting ◽  
Streptomyces Coelicolor ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Recombination System ◽  
Crossover Site ◽  
Integration Sites ◽  
Insertion Sites ◽  
Site Specific Recombination System

ABSTRACT The integrase from the Streptomyces phage φC31 is a member of the serine recombinase family of site-specific recombinases and is fundamentally different from that of λ or its relatives. Moreover, φC31 int/attP is used widely as an essential component of integration vectors (such as pSET152) employed in the genetic analysis of Streptomyces species. φC31 or integrating plasmids containing int/attP have been shown previously to integrate at a locus, attB, in the chromosome. The DNA sequences of the attB sites of various Streptomyces species revealed nonconserved positions. In particular, the crossover site was narrowed to the sequence 5′TT present in both attP and attB. Strains of Streptomyces coelicolor and S. lividans were constructed with a deletion of the attB site (ΔattB), and pSET152 was introduced into these strains by conjugation. Thus, secondary or pseudo-attB sites were identified by Southern blotting and after rescue of plasmids containing DNA flanking the insertion sites from the chromosome. The sequences of the integration sites had similarity to those of attB. Analysis of the insertions of pSET152 into both attB+ and ΔattB strains indicated that this plasmid can integrate at several loci via independent recombination events within a transconjugant.

Rearrangement of nif genes during cyanobacterial heterocyst differentiation

1987 ◽  
Vol 317 (1184) ◽  
pp. 173-181 ◽  
Keyword(s):  
Dna Sequences ◽  
Transcription Unit ◽  
Gene Arrangement ◽  
Filamentous Cyanobacterium ◽  
Gene Encoding ◽  
Α Subunit ◽  
Site Specific ◽  
Heterocyst Differentiation ◽  
Site Specific Recombination ◽  
Recombination System

Anabaena is a filamentous cyanobacterium that produces specialized cells, called heterocysts, at regular intervals along each filament when deprived of fixed nitrogen under aerobic conditions. Heterocysts are anaerobic factories for nitrogen fixation. In Anabaena vegetative-cell DNA, the nifD gene, encoding the α subunit of nitrogenase, is interrupted by an 11 000 base pair DNA element. During the differentiation of heterocysts from vegetative cells, this 11 kilobase (kb) element is excised by site-specific recombination between short, directly repeated DNA sequences present at the ends of the element. The excision results in restoration of the nifD coding sequence and of the entire nifHDK transcription unit. A gene has been identified, within the 11 kb element, that is believed to encode the site-specific recombinase responsible for excision of the element during heterocyst differentiation. A second developmentally regulated gene arrangement has also been observed in Anabaena . This event occurs close to the nifS gene and involves a different set of repeated sequences, implying a different site-specific recombination system.

scholarly journals Instability of Pathogenicity Islands in Uropathogenic Escherichia coli 536

2004 ◽  
Vol 186 (10) ◽  
pp. 3086-3096 ◽  
Author(s):  
Barbara Middendorf ◽  
Bianca Hochhut ◽  
Kristina Leipold ◽  
Ulrich Dobrindt ◽  
Gabriele Blum-Oehler ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Direct Repeat ◽  
Pathogenicity Islands ◽  
Site Specific ◽  
Site Specific Recombination ◽  
E Coli ◽  
Specific Pcr ◽  
Specific Pcr Assay ◽  
Derivatives Of ◽  
Specific Sequences

ABSTRACT The uropathogenic Escherichia coli strain 536 carries at least five genetic elements on its chromosome that meet all criteria characteristic of pathogenicity islands (PAIs). One main feature of these distinct DNA regions is their instability. We applied the so-called island-probing approach and individually labeled all five PAIs of E. coli 536 with the counterselectable marker sacB to evaluate the frequency of PAI-negative colonies under the influence of different environmental conditions. Furthermore, we investigated the boundaries of these PAIs. According to our experiments, PAI II536 and PAI III536 were the most unstable islands followed by PAI I536 and PAI V536, whereas PAI IV536 was stable. In addition, we found that deletion of PAI II536 and PAI III536 was induced by several environmental stimuli. Whereas excision of PAI I536, PAI II536, and PAI V536 was based on site-specific recombination between short direct repeat sequences at their boundaries, PAI III536 was deleted either by site-specific recombination or by homologous recombination between two IS100-specific sequences. In all cases, deletion is thought to lead to the formation of nonreplicative circular intermediates. Such extrachromosomal derivatives of PAI II536 and PAI III536 were detected by a specific PCR assay. Our data indicate that the genome content of uropathogenic E. coli can be modulated by deletion of PAIs.

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