parC:Gene: Difference between revisions

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Table edited by Azweifel via TableEdit
Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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**''dnaN'' (β subunit of the DNA polymerase holoenzyme)
**''dnaN'' (β subunit of the DNA polymerase holoenzyme)
**''spcA'' (suppressor of ''parC'' A- will be renamed ''setB'')
**''spcA'' (suppressor of ''parC'' A- will be renamed ''setB'')
==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:52, 24 June 2011

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

parC

Mnemonic

partitioning of the nucleoid Partition

Synonyms

ECK3010, b3019, JW2987[1]

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Notes

Location(s) and DNA 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

68.15 minutes 

MG1655: 3163995..3161737
<gbrowseImage> name=NC_000913:3161737..3163995 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3100145..3097887
<gbrowseImage> name=NC_012967:3097887..3100145 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3048885..3051143
<gbrowseImage> name=NC_012759:3048885..3051143 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3164629..3162371
<gbrowseImage> name=AC_000091:3162371..3164629 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3261740..3259482
<gbrowseImage> name=NC_010473:3259482..3261740 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

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

parC1215

G2199A

G703D

Growth Phenotype

  • ts @ 42
  • Chromosome partitioning phenotype
  • Filamentation

PMID:2170028[2], PMID:2842295[3]

actual nucleotide mapping was referenced in [2]

parC10

Y120H

DNA nicking independent of ATP hydrolysis

PMID:9077455[4]


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Notes

  • The partitioning defect comes from the inability of these cells to partition the nucleoids into daughter cells. This results in filamentous cells with a cluster of nucleoid at the center and subsequent DNA-free cells.
  • The Keio collection[5] lists a deletion of parC, which is an essential gene. There is a duplication of the parC region.[6].
  • Suppressors of the parC1215 mutation when expressed at high-copy[7]:
    • topB
    • dnaN (β subunit of the DNA polymerase holoenzyme)
    • spcA (suppressor of parC A- will be renamed setB)


Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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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

JW2987

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCAGCGATATGGCAGAGCGCCT

Primer 2:CCtTCTTCGCTATCACCGCTGCT

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[9]

est. P1 cotransduction: 67% [10]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[9]

est. P1 cotransduction: 56% [10]

plexBA-parEC

Plasmid Clone

  • IPTG-inducible Topo IV expression plasmid[11]

pLC4-14

Plasmid Clone

plasmid from the Clarke-Carbon collection

PMID:2842295[3]

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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10686

EchoBASE (EcoliWiki Page)

EchoBASE:EB0680

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3019

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3760

EcoGene (EcoliWiki Page)

EcoGene:EG10686

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PARC

CGSC (EcoliWiki Page)

CGSC:33440

ASAP (EcoliWikiPage)

ASAP:ABE-0009916


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Notes

Links

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References

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

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 Kato, J et al. (1990) New topoisomerase essential for chromosome segregation in E. coli. Cell 63 393-404 PubMed
  3. ↑ 3.0 3.1 Kato, J et al. (1988) Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli. J. Bacteriol. 170 3967-77 PubMed
  4. ↑ Yokochi, T et al. (1996) DNA nicking by Escherichia coli topoisomerase IV with a substitution mutation from tyrosine to histidine at the active site. Genes Cells 1 1069-75 PubMed
  5. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  6. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
  7. ↑ Nurse, P et al. (2003) Topoisomerase III can serve as the cellular decatenase in Escherichia coli. J. Biol. Chem. 278 8653-60 PubMed
  8. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  11. ↑ Mossessova, E et al. (2000) Mutational analysis of Escherichia coli topoisomerase IV. I. Selection of dominant-negative parE alleles. J. Biol. Chem. 275 4099-103 PubMed

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