Colicin E9

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Colicin E9 is a type of Colicin, an approximately 60kDa[1] bacteriocin made by E. coli which acts against other nearby E. coli to kill them with its DNase activity; it digests the host's genome at specific locations, ultimately leading to the death of the cell.

Contents

Synthesis and release

PDB ID 1emv

1emv, resolution 1.70Å ()
Ligands:
Activity: Deoxyribonuclease I, with EC number 3.1.21.1
Related: 1bxi
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml


Colicin E9 in solution, ie in the cytoplasm after synthesis, is monomeric, and forms a high affinity complex with its immunity protein, Im9. The immunity protein does not directly bind to the active site, but instead to an exosite. This is bound while in the producing cell to protect it from the activity[2]. The structure shown is that of the of colicin E9 bound to [3].

Mechanism of uptake

PDB ID 2ivz

2ivz, resolution 2.00Å ()
Ligands:
Related: 1bxi, 1c5k, 1crz, 1emv, 1fr2, 1fsj, 1v13, 1v14, 1v15
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



The primary receptor for colicin E9 is the vitamin B12 receptor, BtuB. It then requires the outer membrane porin OmpF - either the two form the functional receptor, or OmpF is recruited for subsequent translocation. The OmpF association with the BtuB-colicin complex is weak and transient. After the interaction with OmpF, colicin E9 requires the TolB system to pass across the periplasm[4]. The interaction with is governed by a pentapeptide region in the N terminus called the , where ColE9 folds into a distorted hairpin within the six-bladed β-propeller of TolB[5]. The residues surrounding these (from 34 to 46) are unstructured and highly flexible, but the TolB box of 5 residues (DGSGW) is organised within this disordered domain[6]. Within this pentapeptide sequence, the 3 essential resides are D35, S37 and W39. Mutations in all but one of these residues leads to a reduced affinity of binding to TolB[7]. Some regions in the entire site have reduced mobility relative to other regions, that form local hydrophobic clusters[8].

OmpF acts synergistically with BtuB to protect bacteria against the action of colicin E9. This could indicate that OmpF is a component of the receptor apparatus. Alternatively the role of OmpF could be more to do with translocation rather than receptor recognition [9].

Once bound to the BtuB receptor, it is suggested that the coiled-coil receptor binding domain of the colicin unfolds to lose the immunity protein, Im9, and trigger translocation. This flexibility is crucial for translocation, and therefore the cytotoxicity, as shown by the addition of disulphide bonds. This reduces the flexibility and lowers the activity[10].

The endonuclease domain of colicin E9 is able to form ion channels in planar lipid bilayers. The E9 DNase mediates its own translocation across the cytoplasmic membrane, and the formation of ion channels is essential to this process. The association of colicin E9 with negative phospholipids results in a destabilisation of the DNase. This is protected by the colE9 immunity protein, Im9, but not by the binding of zinc to the active site. Formation of this destabilising complex preempts channel formation by the DNase, and makes up the first step in the translocation of colE9 across the E. coli inner membrane. The channels are then assumed to reseal themselves once the cytotoxic domain of the colicin has entered the cytoplasm.

The destabilisation of the DNase domain upon interaction with negative phospholipids increases its susceptibility to proteolysis and to thermal and chemical denaturation. Once associated, there is a massive disruption of protein tertiary structure, and the secondary structure instead interacts with the lipid bilayer - similar to the interaction between domains involved in Pore Formation in other colicins and the membranes that they disrupt.

The formation of a disulphide bond at D20C/E66C abolishes its channel forming ability, and its cytotoxicity (as it cannot penetrate cells) but has no effect on its DNase activity. It is still able to bind to the phospholipids, but not translocate across the membrane[11].

This uptake is highly similar to the uptake of Colicin E3.

Killing Activities

PDB ID 1fsj

1fsj, resolution 1.80Å ()
Ligands: ,
Activity: Deoxyribonuclease I, with EC number 3.1.21.1
Related: 1bxi, 1emv, 1fr2
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



The cytotoxic activity of colE9 is DNase activity in the 15kDa C terminal domain, where it hydrolyses the DNA[12] [13]. However, it is also able to form ion channels in planar lipid bilayers, similar to the pore-forming colicins. These channels do not cause cell death, instead they are related to the ability of the E9 DNase domain to translocate across the inner membrane. The structure shows the crystal structure of the DNase domain.

The DNase domain nicks dsDNA at thymine bases[14].

The catalytic centre of the DNase domain contains the H-N-H motif, a site for DNA and metal binding. ColE9 binds Mg2+ as its cofactor[15]. Binding the magnesium ion stabilises the protein[16], and regulates the binding of phosphate ions to the active site. Upon binding to the ion, the conformation of the DNase alters. This diagram shows the HNH motif found in ColE9[17].

Image:HNH domain of colE9 17516660.png

In response to the DNA damage by colE9, the E. coli cell initiates an SOS response, prior to cell death[18]. This involves the strong induction of 28 genes of the LexA-regulated SOS response[19].

References

  1. van den Bremer ET, Keeble AH, Kleanthous C, Heck AJ. Metal induced selectivity in phosphate ion binding in E9 DNase. Chem Commun (Camb). 2005 Mar 7;(9):1137-9. Epub 2005 Jan 13. PMID:15726170 doi:10.1039/b415709e
  2. Mosbahi K, Walker D, Lea E, Moore GR, James R, Kleanthous C. Destabilization of the colicin E9 Endonuclease domain by interaction with negatively charged phospholipids: implications for colicin translocation into bacteria. J Biol Chem. 2004 May 21;279(21):22145-51. Epub 2004 Mar 23. PMID:15044477 doi:10.1074/jbc.M400402200
  3. Kuhlmann UC, Pommer AJ, Moore GR, James R, Kleanthous C. Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. J Mol Biol. 2000 Sep 1;301(5):1163-78. PMID:10966813 doi:http://dx.doi.org/10.1006/jmbi.2000.3945
  4. Law CJ, Penfold CN, Walker DC, Moore GR, James R, Kleanthous C. OmpF enhances the ability of BtuB to protect susceptible Escherichia coli cells from colicin E9 cytotoxicity. FEBS Lett. 2003 Jun 19;545(2-3):127-32. PMID:12804762
  5. Loftus SR, Walker D, Mate MJ, Bonsor DA, James R, Moore GR, Kleanthous C. Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12353-8. Epub 2006 Aug 7. PMID:16894158
  6. Macdonald CJ, Tozawa K, Collins ES, Penfold CN, James R, Kleanthous C, Clayden NJ, Moore GR. Characterisation of a mobile protein-binding epitope in the translocation domain of colicin E9. J Biomol NMR. 2004 Sep;30(1):81-96. PMID:15452437 doi:10.1023/B:JNMR.0000042963.71790.19
  7. Hands SL, Holland LE, Vankemmelbeke M, Fraser L, Macdonald CJ, Moore GR, James R, Penfold CN. Interactions of TolB with the translocation domain of colicin E9 require an extended TolB box. J Bacteriol. 2005 Oct;187(19):6733-41. PMID:16166536 doi:10.1128/JB.187.19.6733-6741.2005
  8. Macdonald CJ, Tozawa K, Collins ES, Penfold CN, James R, Kleanthous C, Clayden NJ, Moore GR. Characterisation of a mobile protein-binding epitope in the translocation domain of colicin E9. J Biomol NMR. 2004 Sep;30(1):81-96. PMID:15452437 doi:10.1023/B:JNMR.0000042963.71790.19
  9. Law CJ, Penfold CN, Walker DC, Moore GR, James R, Kleanthous C. OmpF enhances the ability of BtuB to protect susceptible Escherichia coli cells from colicin E9 cytotoxicity. FEBS Lett. 2003 Jun 19;545(2-3):127-32. PMID:12804762
  10. Penfold CN, Healy B, Housden NG, Boetzel R, Vankemmelbeke M, Moore GR, Kleanthous C, James R. Flexibility in the receptor-binding domain of the enzymatic colicin E9 is required for toxicity against Escherichia coli cells. J Bacteriol. 2004 Jul;186(14):4520-7. PMID:15231784 doi:10.1128/JB.186.14.4520-4527.2004
  11. Mosbahi K, Walker D, Lea E, Moore GR, James R, Kleanthous C. Destabilization of the colicin E9 Endonuclease domain by interaction with negatively charged phospholipids: implications for colicin translocation into bacteria. J Biol Chem. 2004 May 21;279(21):22145-51. Epub 2004 Mar 23. PMID:15044477 doi:10.1074/jbc.M400402200
  12. Law CJ, Penfold CN, Walker DC, Moore GR, James R, Kleanthous C. OmpF enhances the ability of BtuB to protect susceptible Escherichia coli cells from colicin E9 cytotoxicity. FEBS Lett. 2003 Jun 19;545(2-3):127-32. PMID:12804762
  13. Macdonald CJ, Tozawa K, Collins ES, Penfold CN, James R, Kleanthous C, Clayden NJ, Moore GR. Characterisation of a mobile protein-binding epitope in the translocation domain of colicin E9. J Biomol NMR. 2004 Sep;30(1):81-96. PMID:15452437 doi:10.1023/B:JNMR.0000042963.71790.19
  14. Vankemmelbeke M, Healy B, Moore GR, Kleanthous C, Penfold CN, James R. Rapid detection of colicin E9-induced DNA damage using Escherichia coli cells carrying SOS promoter-lux fusions. J Bacteriol. 2005 Jul;187(14):4900-7. PMID:15995205 doi:10.1128/JB.187.14.4900-4907.2005
  15. Walker DC, Georgiou T, Pommer AJ, Walker D, Moore GR, Kleanthous C, James R. Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases. Nucleic Acids Res. 2002 Jul 15;30(14):3225-34. PMID:12136104
  16. Mosbahi K, Walker D, Lea E, Moore GR, James R, Kleanthous C. Destabilization of the colicin E9 Endonuclease domain by interaction with negatively charged phospholipids: implications for colicin translocation into bacteria. J Biol Chem. 2004 May 21;279(21):22145-51. Epub 2004 Mar 23. PMID:15044477 doi:10.1074/jbc.M400402200
  17. Eastberg JH, Eklund J, Monnat R Jr, Stoddard BL. Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism. Biochemistry. 2007 Jun 19;46(24):7215-25. Epub 2007 May 22. PMID:17516660 doi:10.1021/bi700418d
  18. Mosbahi K, Walker D, Lea E, Moore GR, James R, Kleanthous C. Destabilization of the colicin E9 Endonuclease domain by interaction with negatively charged phospholipids: implications for colicin translocation into bacteria. J Biol Chem. 2004 May 21;279(21):22145-51. Epub 2004 Mar 23. PMID:15044477 doi:10.1074/jbc.M400402200
  19. Vankemmelbeke M, Healy B, Moore GR, Kleanthous C, Penfold CN, James R. Rapid detection of colicin E9-induced DNA damage using Escherichia coli cells carrying SOS promoter-lux fusions. J Bacteriol. 2005 Jul;187(14):4900-7. PMID:15995205 doi:10.1128/JB.187.14.4900-4907.2005

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