User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2008/10/10: Difference between revisions

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==Classification==
==Classification==
Keywords for classification, which can be overlapped
Keywords for classification, which can be overlapped
*Tyrosine recombinase
*By Structure
*Serine recombinase
**Tyrosine recombinase
*Large Serine recombinase
**Serine recombinase
*Integrase
**Large Serine recombinase
*Excisionase
*By Function
*Invertase
**Integrase
*Resolvase
**Excisionase
*Transposase
**Invertase
*Integron
**Resolvase
**Transposase
*other stuffs
**Integron


==Site Specific recombinases==
==Site Specific recombinases==

Revision as of 18:56, 21 October 2008

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Summary Note on site-specific recombinase system

  • Insert content here...

Classification

Keywords for classification, which can be overlapped

  • By Structure
    • Tyrosine recombinase
    • Serine recombinase
    • Large Serine recombinase
  • By Function
    • Integrase
    • Excisionase
    • Invertase
    • Resolvase
    • Transposase
  • other stuffs
    • Integron

Site Specific recombinases

Name: lambda, Host: Escherichia Coli

  • Action: tyrosine integrase
  • Structure:

length:: 356 aa. N-terminal 1-64 aa binds to arm-type site. C-terminal 65-169 aa binds to low affinity core-type site. 170-356 aa is the minimal catalytic domain which include catalytic tyrosine and RKHRK pentad crystal structure of C-terminal catalytic domain is known

attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type) is about 9-13 bps. The overlap region is about 6-8 bps and shares sequence with attP. Here is where crossing over occur. attP is more complicated, with arm-type sites flanking core-type site. overlap-region::TTTATAC

  • Change specificity:

Mutation could change specificity to HK022's site

  • Mechanism: high affinity binding at arm-region of attP, low affinity binding at core-region. Integration

host factor (IHF, from HimA and hip genes) is required for sharp bending in DNA, allowing the integrase bound at arm-type site to also bind at the low affinity core-type sites.

  • Exision: Excision is mediated by viral Xis excisionase and enhanced by host FIS.
  • Usage:

the mutant works in mammalian cell (see more experiment detail)



Name: HK022, Host: Escherichia Coli

  • Action: tyrosine integrase
  • Structure: length:: 357 aa
  • Target sequence:

attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type). The overlap region shares sequence with attP. Crossing over occurs at the overlap region. overlap-region::AGGTGAA attP has arm-type sites flanking core-type site.

  • Mechanism:

Integrases from lambda and HK022 recognize the same arm-type site. However, the integrases notice the difference in core-type site. IHF is required.




Name: P22, Host Salmonella tryphimurium

  • Action: tyrosine integrase
  • Structure: length:: 387 aa
  • Target sequence:

attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type). The overlap region shares sequence with attP. Crossing over occurs at the overlap region. overlap-region::TTCGTAA attP has arm-type sites flanking core-type site.

  • Mechanism:

IHF is required.


Name: HP1, Host: Haemophilus influenzae

  • Action: tyrosine integrase
  • Structure:

length:: 337 aa crystal structure of C-terminal catalytic domain is known

  • Target sequence:

attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type). The overlap region shares sequence with attP. Crossing over occurs at the overlap region. overlap-region::TTTTAAA attP has arm-type sites flanking core-type site.

  • Mechanism:



Name: L5, Host: Mycobacterium smegmatis



Name: PhiC31, Host: Streptomyces lividans

  • Action: tyrosine integrase
  • Structure:

length:: 613 aa crystal structure is unknown.

  • Target sequence: attB:: has two inverted repeated sequence (core-type) flanking an overlap region (TTG). Minimal attB is 34 bps while minimal attP is 39 bp for e.coli intramolecular integration.

attP:: has core-type sites and overlap region, without an arm-type site

  • Change specificity:

Mutation/directed evolution could change specificity to pseudo attP site (HpsA, 44% identity)

  • Mechanism:
  • Excision:

Excisionase has not yet been found.

  • Usage:

Integration works in E.coli, mammalian and in vitro


Name: R4, Host: Streptomyces

  • Action: tyrosine integrase
  • Structure:

length:: 469 aa crystal structure is unknown.

  • Target sequence: attB:: has two inverted repeated sequence (core-type) flanking an overlap region .

attP:: has core-type sites and overlap region, without an arm-type site. Minimal attB and attP site is <56 bps.

  • Excision:

Excisionase has not yet been found.

  • Usage:

Integration works in mammalian cell.



Name: TP901, Host: Lactococcus lactis

  • Action: tyrosine integrase
  • Structure:

length:: 485 aa. crystal structure is unknown.

  • Target sequence: attB:: has two inverted repeated sequence (core-type) flanking an overlap region.

attP:: has core-type sites and overlap region, without an arm-type site. Minimal attB and attP site is <56 bps

  • Mechanism:
  • Excision: Excisionase has already been indentified.
  • Usage:

Integration works in E.coli, mammalian cell and in vitro.



Name: Cre (P1), Host: Escherichia coli

  • Action: recombinase
  • Target sequence: two identical simple sequence < 50 bp



Name: FLP, Host: Saccharomyces cerevisiae

  • Action: invertase
  • Target sequence: two identical simple sequence < 50 bp



Name: XerC, Host: Escherichia coli


Name: Gamma-Delta, Host: Escherichia coli Action: resolvase

  • Structure:

length:: 183 aa some crystal structure with res target have been identified.

  • Target sequence: TATTATAAAT
  • Usage:

Integration works in mammalian cell.


Name: Tn3, Host: Klebsiella pneumoniae Action: resolvase


Name: gin (Phage Mu), Host: Escherichia coli Action: invertase

questions/notes

  • ask Michele about site-specific recombinase database
  • read Allan's paper on site-specificity of lambda integrase..esp 2002 paper

Database

Reference

  1. Groth AC & Calos MP (2004), Phage Integrases: Biology and Applications. J.Mol.Biol.

335:667-678

  1. Sclimenti CR, Thyagarajan B & Calos MP, Directed evolution of a recombinase for

improved genomic integration at a native human sequence. Nucl Acids Res, 29 5044-5051


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