Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 759-774 ◽  
Author(s):  
Guillaume Pavlovic ◽  
Vincent Burrus ◽  
Brigitte Gintz ◽  
Bernard Decaris ◽  
Gérard Guédon
Keyword(s):  
Streptococcus Thermophilus ◽  
Genomic Islands ◽  
Recombination Site ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Attachment Sites ◽  
Specific Attachment ◽  
Circular Molecule

The 34 734-bp integrative and potentially conjugative element (putative ICE) ICESt1 has been previously found to be site-specifically integrated in the 3′ end of the fda locus of Streptococcus thermophilus CNRZ368. Four types of genomic islands related to ICESt1 are integrated in the same position in seven other strains of S. thermophilus. One of these elements, ICESt3, harbours conjugation and recombination modules closely related to those of ICESt1 and excises by site-specific recombination. Two other types of elements, CIME19258 and CIME302, are flanked by site-specific attachment sites closely related to attL and attR of ICESt1 and ICESt3, whereas ΔCIME308 only possesses a putative attR site; none of these three elements carry complete conjugation and recombination modules. ICESt1 contains a functional internal recombination site, attL′, that is almost identical to attL of CIME19258. The recombination between attL′ and attR of ICESt1 leads to the excision of the expected circular molecule (putative ICE); a cis-mobilizable element (CIME) flanked by an attL site and an attB′ site remains integrated into the 3′ end of fda. Furthermore, sequences that could be truncated att sites were found within ICESt1, ICESt3 and CIME302. All together, these data suggest that these genomic islands evolved by deletion and tandem accretion of ICEs and CIMEs resulting from site-specific recombination. A model for this evolution is proposed and its application to other genomic islands is discussed.

scholarly journals fpr, a Deficient Xer Recombination Site from a Salmonella Plasmid, Fails To Confer Stability by Dimer Resolution: Comparative Studies with the pJHCMW1 mwr Site

2009 ◽  
Vol 192 (3) ◽  
pp. 883-887 ◽  
Author(s):  
Tung Tran ◽  
David J. Sherratt ◽  
Marcelo E. Tolmasky
Keyword(s):  
Central Region ◽  
Comparative Studies ◽  
Recombination Site ◽  
Binding Region ◽  
Site Specific ◽  
Site Specific Recombination ◽  
A Site

ABSTRACT Salmonella plasmid pFPTB1 includes a Tn3-like transposon and a Xer recombination site, fpr, which mediates site-specific recombination at efficiencies lower than those required for stabilizing a plasmid by dimer resolution. Mutagenesis and comparative studies with mwr, a site closely related to fpr, indicate that there is an interdependence of the sequences in the XerC binding region and the central region in Xer site-specific recombination sites.

scholarly journals SeLOX—a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems

2010 ◽  
Vol 38 (suppl_2) ◽  
pp. W293-W298 ◽  
Author(s):  
Vineeth Surendranath ◽  
Janet Chusainow ◽  
Joachim Hauber ◽  
Frank Buchholz ◽  
Bianca H. Habermann
Keyword(s):  
Directed Evolution ◽  
Recombination Site ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Site Search ◽  
Search Tool

scholarly journals Conjugative Transfer of the Integrative Conjugative Elements ICESt1 and ICESt3 from Streptococcus thermophilus

2009 ◽  
Vol 191 (8) ◽  
pp. 2764-2775 ◽  
Author(s):  
Xavier Bellanger ◽  
Adam P. Roberts ◽  
Catherine Morel ◽  
Frédéric Choulet ◽  
Guillaume Pavlovic ◽  
...  
Keyword(s):  
Streptococcus Thermophilus ◽  
Genomic Islands ◽  
Conjugative Transfer ◽  
Integrase Gene ◽  
Site Specific ◽  
Integrative And Conjugative Elements ◽  
Conjugative Transposons ◽  
Site Specific Integration ◽  
The One ◽  
Integrative Conjugative Elements

ABSTRACT Integrative and conjugative elements (ICEs), also called conjugative transposons, are genomic islands that excise, self-transfer by conjugation, and integrate in the genome of the recipient bacterium. The current investigation shows the intraspecies conjugative transfer of the first described ICEs in Streptococcus thermophilus, ICESt1 and ICESt3. Mitomycin C, a DNA-damaging agent, derepresses ICESt3 conjugative transfer almost 25-fold. The ICESt3 host range was determined using various members of the Firmicutes as recipients. Whereas numerous ICESt3 transconjugants of Streptococcus pyogenes and Enterococcus faecalis were recovered, only one transconjugant of Lactococcus lactis was obtained. The newly incoming ICEs, except the one from L. lactis, are site-specifically integrated into the 3′ end of the fda gene and are still able to excise in these transconjugants. Furthermore, ICESt3 was retransferred from E. faecalis to S. thermophilus. Recombinant plasmids carrying different parts of the ICESt1 recombination module were used to show that the integrase gene is required for the site-specific integration and excision of the ICEs, whereas the excisionase gene is required for the site-specific excision only.

scholarly journals Osmoregulation of Dimer Resolution at the Plasmid pJHCMW1 mwr Locus by Escherichia coli XerCD Recombination

2002 ◽  
Vol 184 (6) ◽  
pp. 1607-1616 ◽  
Author(s):  
Huong Pham ◽  
Ken J. Dery ◽  
David J. Sherratt ◽  
Marcelo E. Tolmasky
Keyword(s):  
Escherichia Coli ◽  
Central Region ◽  
High Salt ◽  
Recombination Reaction ◽  
Recombination Site ◽  
Site Specific ◽  
Site Specific Recombination ◽  
E Coli ◽  
Low Salt ◽  
Ionic Effects

ABSTRACT Xer-mediated dimer resolution at the mwr site of plasmid pJHCMW1 is osmoregulated in Escherichia coli. Whereas under low-salt conditions, the site-specific recombination reaction is efficient, under high-salt conditions, it proceeds inefficiently. Regulation of dimer resolution is independent of H-NS and is mediated by changes in osmolarity rather than ionic effects. The low level of recombination at high salt concentrations can be overcome by high levels of PepA or by mutating the ARG box to a sequence closer to the E. coli ARG box consensus. The central region of the mwr core recombination site plays a role in regulation of site-specific recombination by the osmotic pressure of the medium.

scholarly journals New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes forMethanosarcinaspecies

Archaea ◽  
2008 ◽  
Vol 2 (3) ◽  
pp. 193-203 ◽  
Author(s):  
Adam M. Guss ◽  
Michael Rother ◽  
Jun Kai Zhang ◽  
Gargi Kulkkarni ◽  
William W. Metcalf
Keyword(s):  
Chromosomal Integration ◽  
Recombination Site ◽  
Integrase Gene ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Highly Efficient ◽  
Recombination System ◽  
Regulated Gene Expression ◽  
Hybrid Promoters ◽  
Site Specific Recombination System

A highly efficient method for chromosomal integration of cloned DNA intoMethanosarcina spp.was developed utilizing the site-specific recombination system from theStreptomycesphage φC31. Host strains expressing the φC31 integrase gene and carrying an appropriate recombination site can be transformed with non-replicating plasmids carrying the complementary recombination site at efficiencies similar to those obtained with self-replicating vectors. We have also constructed a series of hybrid promoters that combine the highly expressedM. barkeriPmcrBpromoter with binding sites for the tetracycline-responsive, bacterial TetR protein. These promoters are tightly regulated by the presence or absence of tetracycline in strains that express thetetRgene. The hybrid promoters can be used in genetic experiments to test gene essentiality by placing a gene of interest under their control. Thus, growth of strains withtetR-regulated essential genes becomes tetracycline-dependent. A series of plasmid vectors that utilize the site-specific recombination system for construction of reporter gene fusions and for tetracycline regulated expression of cloned genes are reported. These vectors were used to test the efficiency of translation at a variety of start codons. Fusions using an ATG start site were the most active, whereas those using GTG and TTG were approximately one half or one fourth as active, respectively. The CTG fusion was 95% less active than the ATG fusion.

Independent acquisition of site-specific recombination factors by asn tRNA gene-targeting genomic islands

2006 ◽  
Vol 296 (6) ◽  
pp. 341-352 ◽  
Author(s):  
Uladzimir Antonenka ◽  
Christina Nölting ◽  
Jürgen Heesemann ◽  
Alexander Rakin
Keyword(s):  
Gene Targeting ◽  
Trna Gene ◽  
Genomic Islands ◽  
Site Specific ◽  
Site Specific Recombination
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