Cis Element:dif: Difference between revisions
Table edited by Azweifel via TableEdit |
|||
| Line 111: | Line 111: | ||
===Notes=== | ===Notes=== | ||
Sites where XerCD bind and cleave ''dif'' can be found in Blakely ''et al.'' (1997)<ref name='PMID:8995522'/>. | |||
== Mutant alleles and phenotypes == | == Mutant alleles and phenotypes == | ||
Revision as of 19:21, 29 June 2010
Cis element summary table
| Standard Name |
dif |
|---|---|
| Synonyms |
deletion-induced filamentation |
| Function |
Recombination site in terminus |
| Location |
|
| SO terms |
|
| edit table |
Notes
Location and Sequence
See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.
| Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
|---|---|---|---|---|
|
34.2 minutes |
MG1655: 1588774..1588801 |
|||
| edit table |
Notes
The site is a 28bp sequence located in the "dif activity zone" (DAZ) and is involved in Chromosome Dimer Resolution involving XerCD. dif must be located in the terminus region for proper function and may be functionally replaced by loxP if the Cre recombinase is supplied in trans[2].
Interactions
See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.
| Partner Type | Partner | Notes | References | Evidence |
|---|---|---|---|---|
|
Protein |
XerC |
|||
|
Protein |
XerD |
| ||
| edit table |
Notes
Sites where XerCD bind and cleave dif can be found in Blakely et al. (1997)[4].
Mutant alleles and phenotypes
| Allele | Nt change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
|---|---|---|---|---|---|---|
|
Δdif |
Growth Phenotype |
|
| |||
| edit table |
Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
pSDC124 |
Plasmid Clone |
pUC18-based dif reporter |
|
|
pFC238 |
Plasmid Clone |
pGB2-based dif reporter |
|
|
pFH127 |
Plasmid Clone |
pGB2ts-based dif reporter carrying one dif site |
|
|
NL Strains |
Strain |
This paper lists a variety of different dif deletions and other constructs designed to test the dif locus |
|
|
pUC-dif |
Plasmid Clone |
pUC18-based dif reporter |
|
|
GR35 |
Strain |
AB1157difΔ6 |
|
|
GR47 |
Strain |
AB1157lexA3difΔ6 |
|
| edit table |
Notes
- One way to test the resolution competency at the dif activity zone (DAZ) or individual dif sites is to perform plasmid dimer resolution assays[9], or dif-Km-dif excision assays[10].
Accessions
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
| ||
| edit table |
Notes
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 Kuempel, PL et al. (1991) dif, a recA-independent recombination site in the terminus region of the chromosome of Escherichia coli. New Biol. 3 799-811 PubMed
- ↑ 2.0 2.1 Leslie, NR & Sherratt, DJ (1995) Site-specific recombination in the replication terminus region of Escherichia coli: functional replacement of dif. EMBO J. 14 1561-70 PubMed
- ↑ 3.0 3.1 Barre, FX et al. (2000) FtsK functions in the processing of a Holliday junction intermediate during bacterial chromosome segregation. Genes Dev. 14 2976-88 PubMed
- ↑ Blakely, GW et al. (1997) Binding and cleavage of nicked substrates by site-specific recombinases XerC and XerD. J. Mol. Biol. 265 30-9 PubMed
- ↑ Blakely, G et al. (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol. 3 789-98 PubMed
- ↑ 6.0 6.1 6.2 Recchia, GD et al. (1999) FtsK-dependent and -independent pathways of Xer site-specific recombination. EMBO J. 18 5724-34 PubMed
- ↑ Hayes, F & Sherratt, DJ (1997) Recombinase binding specificity at the chromosome dimer resolution site dif of Escherichia coli. J. Mol. Biol. 266 525-37 PubMed
- ↑ Grainge, I et al. (2007) Unlinking chromosome catenanes in vivo by site-specific recombination. EMBO J. 26 4228-38 PubMed
- ↑ Yates, J et al. (2003) Species specificity in the activation of Xer recombination at dif by FtsK. Mol. Microbiol. 49 241-9 PubMed
- ↑ Pérals, K et al. (2000) Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol. Microbiol. 36 33-43 PubMed