Cis Element:dif: Difference between revisions

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===Notes===
===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''<ref name='PMID:7729430'/>.
The ''dif'' site is a 28bp sequence located within a 30kb region of the terminus known as the "''dif'' activity zone" (DAZ) and is involved in [[Chromosome Dimer Resolution]] involving XerCD<ref name='PMID:7877981'/><ref name='PMID: 8654930 '/><ref name='PMID:8654931'/>.  ''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''<ref name='PMID:7729430'/>. XerC binds the ''dif'' left half site while XerD binds the ''dif'' right half site- these sites are not interchangeable<ref name='PMID:402918'/>.


== Interactions==
== Interactions==
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!|Partner Type!!Partner!!Notes!!References!!Evidence
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PMID:11114887
*PMID:11114887
*PMID:7746851
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PMID:11114887
*PMID:11114887
*PMID:7746851
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===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 ==
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!|Allele!!Nt change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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Δ''dif''
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Growth Phenotype
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Filamentation- >15% of cells
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PMID:15065657
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PMID:1657123
PMID:1657123
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Δ''dif rarA''
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Growth Phenotype
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Filamentation- >15% of cells
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PMID:15065657
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PMID:17805344  
PMID:17805344  
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GR35
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Strain
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AB1157''dif&Delta;6''
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PMID:10523315
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GR47
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Strain
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AB1157''lexA3difΔ6''
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PMID:10523315
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pGB201
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Plasmid Clone
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''dif1-1'' containing plasmid
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PMID:8402918
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pGB102
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Plasmid Clone
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Reporter plasmid with directly repeated''dif1-1'' sites
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PMID:8402918
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pGB204
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Plasmid Clone
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Reporter plasmid containing two right half sites of ''dif1-1'' (''dif1-1''DD)
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PMID:8402918
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pGB103
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Plasmid Clone
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Reporter plasmid with inverted ''dif1-1'' sites
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PMID:8402918
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pGB105
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Plasmid Clone
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Reporter plasmid with inverted ''dif'' sites
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PMID:8402918
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pGB203
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Plasmid Clone
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Reporter plasmid containing two left half sites of ''dif1-1'' (''dif1-1''CC)
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PMID:8402918
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pGB205
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Plasmid Clone
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Reporter plasmid containing isolated right half site of ''dif1-1'' (''dif1-1''D)
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PMID:8402918
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pGB206
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Plasmid Clone
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Reporter plasmid containing isolated left half site of ''dif1-1'' (''dif1-1''C)
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PMID:8402918
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pGB408
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Plasmid Clone
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Reporter plasmid containing two right half sites of ''dif'' (''dif''DD)
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PMID:8402918


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===Notes===
===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<ref name='PMID:12823825'/>, or ''dif''-Km-''dif'' excision assays<ref name='PMID:10760161'/>.
*One way to test the resolution competency at the ''dif'' activity zone (DAZ) or individual ''dif'' sites is to perform plasmid dimer resolution assays<ref name='PMID:12823825'/>, or ''dif''-Km-''dif'' excision assays<ref name='PMID:10760161'/>. Steiner and Kuempel (1998) used a density label assay to analyze ''dif'' recombination<ref name='PMID:9484882'/><ref name='PMID:9829936'/>.


== Accessions ==
== Accessions ==
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[[EcoCyc]]
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EcoCyc:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[RegulonDB]]
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RegulonDB:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 07:17, 27 May 2013

Cis element summary table

Standard Name

dif

Synonyms

deletion-induced filamentation

Function

Recombination site in terminus

Location
  • 34.2 minutes in MG1655
  • 33.6 minutes in AB1157 [1]
SO terms


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Notes

Location and Sequence

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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

MG1655

34.2 minutes

MG1655: 1588774..1588801
gbrowse_img.php?coord=1588774..1588801&genome=ecoli&name=MG1655&trackset=DNA_unlabeled&width=300&.png

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Notes

The dif site is a 28bp sequence located within a 30kb region of the terminus known as the "dif activity zone" (DAZ) and is involved in Chromosome Dimer Resolution involving XerCD[2][3][4]. 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[5]. XerC binds the dif left half site while XerD binds the dif right half site- these sites are not interchangeable[6].

Interactions

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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


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Notes

Sites where XerCD bind and cleave dif can be found in Blakely et al. (1997)[9].

Mutant alleles and phenotypes

[back to top]


Allele Nt change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

Δdif

Growth Phenotype

Filamentation- >15% of cells

PMID:15065657[10]

Δdif

Growth Phenotype

  • subpopulation of filamentous cells with abnormal nucleoids
  • induction of the SOS repair system

PMID:1657123[1]

Δdif rarA

Growth Phenotype

Filamentation- >15% of cells

PMID:15065657[10]


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Notes

Genetic Resources

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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

PMID:1931824[11]

pFC238

Plasmid Clone

pGB2-based dif reporter

PMID:10523315[12]

pFH127

Plasmid Clone

pGB2ts-based dif reporter carrying one dif site

PMID:9067608[13]

NL Strains

Strain

This paper lists a variety of different dif deletions and other constructs designed to test the dif locus

PMID:7729430[5]

pUC-dif

Plasmid Clone

pUC18-based dif reporter

PMID:17805344[14]

GR35

Strain

AB1157difΔ6

PMID:10523315[12]

GR47

Strain

AB1157lexA3difΔ6

PMID:10523315[12]

pGB201

Plasmid Clone

dif1-1 containing plasmid

PMID:8402918[15]

pGB102

Plasmid Clone

Reporter plasmid with directly repeateddif1-1 sites

PMID:8402918[15]

pGB204

Plasmid Clone

Reporter plasmid containing two right half sites of dif1-1 (dif1-1DD)

PMID:8402918[15]

pGB103

Plasmid Clone

Reporter plasmid with inverted dif1-1 sites

PMID:8402918[15]

pGB105

Plasmid Clone

Reporter plasmid with inverted dif sites

PMID:8402918[15]

pGB203

Plasmid Clone

Reporter plasmid containing two left half sites of dif1-1 (dif1-1CC)

PMID:8402918[15]

pGB205

Plasmid Clone

Reporter plasmid containing isolated right half site of dif1-1 (dif1-1D)

PMID:8402918[15]

pGB206

Plasmid Clone

Reporter plasmid containing isolated left half site of dif1-1 (dif1-1C)

PMID:8402918[15]

pGB408

Plasmid Clone

Reporter plasmid containing two right half sites of dif (difDD)

PMID:8402918[15]

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[16], or dif-Km-dif excision assays[17]. Steiner and Kuempel (1998) used a density label assay to analyze dif recombination[18][19].

Accessions

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

eric

dif

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

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Notes

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ Tecklenburg, M et al. (1995) The dif resolvase locus of the Escherichia coli chromosome can be replaced by a 33-bp sequence, but function depends on location. Proc. Natl. Acad. Sci. U.S.A. 92 1352-6 PubMed
  3. ↑ Cornet, F et al. (1996) Restriction of the activity of the recombination site dif to a small zone of the Escherichia coli chromosome. Genes Dev. 10 1152-61 PubMed
  4. ↑ Kuempel, P et al. (1996) Use of a transposon (Tndif) to obtain suppressing and nonsuppressing insertions of the dif resolvase site of Escherichia coli. Genes Dev. 10 1162-71 PubMed
  5. ↑ 5.0 5.1 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
  6. ↑ Smith, MR & Cook, RT (1977) Urea reduces the thermal stability of polyanion-treated chromatin. Biochem. Biophys. Res. Commun. 74 1475-82 PubMed
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 Sherratt, DJ et al. (1995) Site-specific recombination and circular chromosome segregation. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 347 37-42 PubMed
  9. ↑ 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
  10. ↑ 10.0 10.1 Sherratt, DJ et al. (2004) Recombination and chromosome segregation. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 359 61-9 PubMed
  11. ↑ Blakely, G et al. (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol. 3 789-98 PubMed
  12. ↑ 12.0 12.1 12.2 Recchia, GD et al. (1999) FtsK-dependent and -independent pathways of Xer site-specific recombination. EMBO J. 18 5724-34 PubMed
  13. ↑ 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
  14. ↑ Grainge, I et al. (2007) Unlinking chromosome catenanes in vivo by site-specific recombination. EMBO J. 26 4228-38 PubMed
  15. ↑ 15.0 15.1 15.2 15.3 15.4 15.5 15.6 15.7 15.8 Blakely, G et al. (1993) Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell 75 351-61 PubMed
  16. ↑ Yates, J et al. (2003) Species specificity in the activation of Xer recombination at dif by FtsK. Mol. Microbiol. 49 241-9 PubMed
  17. ↑ 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
  18. ↑ Steiner, WW & Kuempel, PL (1998) Cell division is required for resolution of dimer chromosomes at the dif locus of Escherichia coli. Mol. Microbiol. 27 257-68 PubMed
  19. ↑ Steiner, WW & Kuempel, PL (1998) Sister chromatid exchange frequencies in Escherichia coli analyzed by recombination at the dif resolvase site. J. Bacteriol. 180 6269-75 PubMed

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