Colicin Research Articles

Characterization of a Cyanobacterial Outer Membrane Protein: An E. Coli Tolc Homologue from Synechocystis Sp. Pcc 6803

E. coli TolC (tolerance to colicins) represents an interesting class of outer membrane (OM) proteins, as it has an α-helical periplasmic tunnel and β-barrel membrane region, providing a conduit for export of metabolites and xenobiotics from cell interior to exterior, and import of colicin E1 (1). A TolC homologue, Slr1270 from Synechocystis 6803, cloned and expressed in E. coli, has > 40% similarity and ∼16% identity to E. coli and Pseudomonas counterparts, and has a similar domain organization. Homology modeling using Pseudomonas OprM as template modeled 93% of Slr1270 sequence. The 1581bp slr1270 gene was cloned and overexpressed in E. coli. Protein from inclusion bodies, refolded through step-wise dialysis showed major bands at ∼55kDa and >150 kDa on SDS-PAGE corresponding to the monomer and trimer respectively and ∼300 kDa on CN-PAGE. Purified protein displays a far-UV CD spectrum characteristic of E. coli TolC with > 50% α-helix, and formed channels in planar lipid bilayers with a characteristic single channel conductance of ∼50 pS in 0.1M NaCl. The intact protein mass spectrum (LC-MS) with a major peak at 54,489 probably represents a mixture of two species, the TolC product with 1-40 removed and an intact 6-His tag (calculated mass 54,457.1 Da), and a product with 1-38 removed and a 5-His tag (calculated mass 54,490.2 Da) after a single carboxypeptidase event. The small peak at 54,638 Da probably corresponds to TolC product with 1-38 removed and an intact 6-His tag (calculated mass 54,627.3 Da). Peptides 39-76 and 41-76 were recovered from trypsin digests confirming N-terminal heterogeneity. (1) Zakharov, S. D. et al. 2012. Pathways of Colicin Import: Utilization of BtuB, OmpF Porin, and the TolC Drug Export Protein, Biochem. Soc. Trans., 40, 1463-1468.

Blind prediction of interfacial water positions in CAPRI

We report the first assessment of blind predictions of water positions at protein-protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to predict the positions of interfacial water molecules using the method of their choice. The predictions-20 groups submitted a total of 195 models-were assessed by measuring the recall fraction of water-mediated protein contacts. Of the 176 high- or medium-quality docking models-a very good docking performance per se-only 44% had a recall fraction above 0.3, and a mere 6% above 0.5. The actual water positions were in general predicted to an accuracy level no better than 1.5 Å, and even in good models about half of the contacts represented false positives. This notwithstanding, three hotspot interface water positions were quite well predicted, and so was one of the water positions that is believed to stabilize the loop that confers specificity in these complexes. Overall the best interface water predictions was achieved by groups that also produced high-quality docking models, indicating that accurate modelling of the protein portion is a determinant factor. The use of established molecular mechanics force fields, coupled to sampling and optimization procedures also seemed to confer an advantage. Insights gained from this analysis should help improve the prediction of protein-water interactions and their role in stabilizing protein complexes.

High Variation of Fluorescence Protein Maturation Times in Closely Related Escherichia coli Strains

Fluorescent proteins (FPs) are widely used in biochemistry, biology and biophysics. For quantitative analysis of gene expression FPs are often used as marking molecules. Therefore, sufficient knowledge of maturation times and their affecting factors is of high interest. Here, we investigate the maturation process of the FPs GFP and mCherry expressed by the three closely related Escherichia coli strains of the Colicin E2 system, a model system for colicinogenic interaction. One strain, the C strain produces Colicin, a toxin to which the S strain is sensitive, and against which the R strain is resistant. Under the growth conditions used in this study, the S and R strain have similar growth rates, as opposed to the C strain whose growth rate is significantly reduced due to the toxin production. In combination with theoretical modelling we studied the maturation kinetics of the two FPs in these strains and could confirm an exponential and sigmoidal maturation kinetic for GFP and mCherry, respectively. Our subsequent quantitative experimental analysis revealed a high variance in maturation times independent of the strain studied. In addition, we determined strain dependent maturation times and maturation behaviour. Firstly, FPs expressed by the S and R strain mature on similar average time-scales as opposed to FPs expressed by the C strain. Secondly, dependencies of maturation time with growth conditions are most pronounced in the GFP expressing C strain: Doubling the growth rate of this C strain results in an increased maturation time by a factor of 1.4. As maturation times can vary even between closely related strains, our data emphasize the importance of profound knowledge of individual strains' maturation times for accurate interpretation of gene expression data.

Engineered genetic selection links in vivo protein folding and stability with asparagine‐linked glycosylation

Predicting the structural consequences of site-specific glycosylation remains a major challenge due in part to the lack of convenient experimental tools for rapidly determining how glycosylation influences protein folding. To address this shortcoming, we developed a genetic selection that directly links the in vivo folding of asparagine-linked (N-linked) glycoproteins with antibiotic resistance. Using this assay, we identified three known or putative glycoproteins from Campylobacter jejuni (Peb3, CjaA, and Cj0610c) whose folding was significantly affected by N-glycosylation. We also used the genetic selection to isolate a glycoengineered variant of the Escherichia coli colicin E7 immunity protein (Im7) whose intracellular folding and stability were enhanced as a result of N-glycosylation. In addition to monitoring the effect of glycan attachment on protein folding in living cells, this strategy could easily be extended for optimizing protein folding in vivo and engineering glycosylation enzymes, pathways, and hosts for optimal performance.

Immunity protein release from a cell‐bound nuclease colicin complex requires global conformational rearrangement

Nuclease colicins bind their target receptor BtuB in the outer membrane of sensitive Escherichia coli cells in the form of a high-affinity complex with their cognate immunity proteins. The release of the immunity protein from the colicin complex is a prerequisite for cell entry of the colicin and occurs via a process that is still relatively poorly understood. We have previously shown that an energy input in the form of the cytoplasmic membrane proton motive force is required to promote immunity protein (Im9) release from the colicin E9/Im9 complex and colicin cell entry. We report here that engineering rigidity in the structured part of the colicin translocation domain via the introduction of disulfide bonds prevents immunity protein release from the colicin complex. Reduction of the disulfide bond by the addition of DTT leads to immunity protein release and resumption of activity. Similarly, the introduction of a disulfide bond in the DNase domain previously shown to abolish channel formation in planar bilayers also prevented immunity protein release. Importantly, all disulfide bonds, in the translocation as well as the DNase domain, also abolished the biological activity of the Im9-free colicin E9, the reduction of which led to a resumption of activity. Our results show, for the first time, that conformational flexibility in the structured translocation and DNase domains of a nuclease colicin is essential for immunity protein release, providing further evidence for the hypothesis that global structural rearrangement of the colicin molecule is required for disassembly of this high-affinity toxin-immunity protein complex prior to outer membrane translocation.

Genetically Programmable Pathogen Sense and Destroy

Pseudomonas aeruginosa (P. aeruginosa) is a major cause of urinary tract and nosocomial infections. Here, we propose and demonstrate proof-of-principle for a potential cell therapy approach against P. aeruginosa. Using principles of synthetic biology, we genetically modified E. coli to specifically detect wild type P. aeruginosa (PAO1) via its quorum sensing (QS) molecule, 3OC 12 HSL. Engineered E. coli sentinels respond to the presence of 3OC 12 HSL by secreting CoPy, a novel pathogen-specific engineered chimeric bacteriocin, into the extracellular medium using the flagellar secretion tag FlgM. Extracellular FlgM-CoPy is designed to kill PAO1 specifically. CoPy was constructed by replacing the receptor and translocase domain of Colicin E3 with that of Pyocin S3. We show that CoPy toxicity is PAO1 specific, not affecting sentinel E. coli or the other bacterial strains tested. In order to define the system's basic requirements and PAO1-killing capabilities, we further determined the growth rates of PAO1 under different conditions and concentrations of purified and secreted FlgM-CoPy. The integrated system was tested by co-culturing PAO1 cells, on semisolid agar plates, together with engineered sentinel E. coli, capable of secreting FlgM-CoPy when induced by 3OC 12 HSL. Optical microscopy results show that the engineered E. coli sentinels successfully inhibit PAO1 growth.

Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF.

Porins are β-barrel outer-membrane proteins through which small solutes and metabolites diffuse that are also exploited during cell death. We have studied how the bacteriocin colicin E9 (ColE9) assembles a cytotoxic translocon at the surface of Escherichia coli that incorporates the trimeric porin OmpF. Formation of the translocon involved ColE9's unstructured N-terminal domain threading in opposite directions through two OmpF subunits, capturing its target TolB on the other side of the membrane in a fixed orientation that triggers colicin import. Thus, an intrinsically disordered protein can tunnel through the narrow pores of an oligomeric porin to deliver an epitope signal to the cell to initiate cell death.

Pattern of induction of colicin E9 synthesis by sub MIC of Norfloxacin antibiotic

The presence of dual SOS boxes in the regulatory region of the most of colicin operons confines synthesis of colicin to times of stress, presumably to reduce the cost of its production. However, in presence of certain inducing agents, such as antibiotics, this tight control of colicin operon is usually lost. Although synthesis of most of colicins is known to be regulated by SOS response of host cell, different patterns of induction from distinct colicins against various inducing agents have been shown in recent years. In this study, we investigated the induction pattern of enzymatic colicin E9 (ColE9) synthesis following treatment with various concentrations (sub MICs) of the Norfloxacin (NOR) using pSBM23 construct which carries transcriptional fusion of SOS inducible promoter of pColE9 (ColE9p) and a fluorescent reporter gene (gfpmut2) into kanamycin resistant pColE9-J plasmid. Flow cytomtry analysis of the Escherichia coli cells containing pSBM23, following treatment with various concentrations showed that the SOS response mediated induction of the synthesis of ColE9 happens in a dose-dependent manner. In summary, our results suggest that the presence, even in a minute amount, of SOS response inducing agents such as fluoroquinolone antibiotic in natural habitat of colicinogenic population can promote such a costly antagonistic behaviour of microbes.

Crystallization and preliminary crystallographic analysis of anEscherichia coli-selected mutant of the nuclease domain of the metallonuclease colicin E7

The metallonuclease colicin E7 is a member of the HNH family of endonucleases. It serves as a bacterial toxin in Escherichia coli, protecting the host cell from other related bacteria and bacteriophages by degradation of their chromosomal DNA under environmental stress. Its cell-killing activity is attributed to the nonspecific nuclease domain (NColE7), which possesses the catalytic ββα-type metal ion-binding HNH motif at its C-terminus. Mutations affecting the positively charged amino acids at the N-terminus of NColE7 (444-576) surprisingly showed no or significantly reduced endonuclease activity [Czene et al. (2013), J. Biol. Inorg. Chem. 18, 309-321]. The necessity of the N-terminal amino acids for the function of the C-terminal catalytic centre poses the possibility of allosteric activation within the enzyme. Precise knowledge of the intramolecular interactions of these residues that affect the catalytic activity could turn NColE7 into a novel platform for artificial nuclease design. In this study, the N-terminal deletion mutant ΔN4-NColE7-C* of the nuclease domain of colicin E7 selected by E. coli was overexpressed and crystallized at room temperature by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 1.6 Å resolution and could be indexed and averaged in the trigonal space group P3121 or P3221, with unit-cell parameters a=b=55.4, c=73.1 Å. Structure determination by molecular replacement is in progress.

Cloning, purification and metal binding of the HNH motif from colicin E7

The HNH family of endonucleases is characterized by a ββα metal-finger structural motif. Colicin E7 is a representative member of this family containing the strictly conserved HNH motif at its C-terminus. Structural and biochemical studies suggested that the HNH motif could contain all the residues necessary for metal ion binding and nuclease activity. In this work a 43 amino acid peptide extending from V534 to K576 of colicin E7 and encompassing the HNH motif was cloned and expressed in Escherichia coli as a ubiquitin fusion protein. The N-terminal fusion tag was cleaved off by a specific protease, and the HNH peptide was purified free of ubiquitin. Circular dichroism, fluorescence and mass spectrometry showed that the zinc-ion binding affinity of the purified HNH peptide was much weaker than that of the intact nuclease domain suggesting that the N-terminal part of the nuclease domain is essential for stabilizing the structure of the HNH motif. The coordination sphere of the metal ion was found to be not fully equipped by the ligand – leaving a free coordination site for the substrate. Neither DNA binding nor DNAse activity of the purified HNH peptide was detected. Comparison of the glutathion-S-transferase-fused N-terminal deletion mutants of the colicin E7 nuclease domain suggested that the presence of the DNA-binding site is still not sufficient for the catalytic activity.

Monomeric TonB and the Ton Box Are Required for the Formation of a High-Affinity Transporter–TonB Complex

The energy-dependent uptake of trace nutrients by Gram-negative bacteria involves the coupling of an outer membrane transport protein to the transperiplasmic protein TonB. In this study, a soluble construct of Escherichia coli TonB (residues 33-239) was used to determine the affinity of TonB for outer membrane transporters BtuB, FecA, and FhuA. Using fluorescence anisotropy, TonB(33-239) was found to bind with high affinity (tens of nanomolar) to both BtuB and FhuA; however, no high-affinity binding to FecA was observed. In BtuB, the high-affinity binding of TonB(33-239) was eliminated by mutations in the Ton box, which yield transport-defective protein, or by the addition of a Colicin E3 fragment, which stabilizes the Ton box in a folded state. These results indicate that transport requires a high-affinity transporter-TonB interaction that is mediated by the Ton box. Characterization of TonB(33-239) using double electron-electron resonance (DEER) demonstrates that a significant population of TonB(33-239) exists as a dimer; moreover, interspin distances are in approximate agreement with interlocked dimers observed previously by crystallography for shorter TonB fragments. When the TonB(33-239) dimer is bound to the outer membrane transporter, DEER shows that the TonB(33-239) dimer is converted to a monomeric form, suggesting that a dimer-monomer conversion takes place at the outer membrane during the TonB-dependent transport cycle.

Designing a synthetic genetic circuit that enables cell density-dependent auto-regulatory lysis for macromolecule release

Escherichia coli is widely used as a host cell for synthesis of valuable macromolecular products such as recombinant proteins. However, E. coli has limited ability to secrete such macromolecules so that product harvest from the cells frequently requires chemical, enzymatic, and/or mechanical lysis, thus increasing production costs. In this study, we aimed to enable cell density-dependent auto-regulatory lysis in E. coli to directly aid in extraction of macromolecule products and simplify product harvest processes. Towards this aim, we designed and constructed a lysis genetic circuit based on a transducer-switch scheme by harnessing the characteristics of the stationary phase-operated carbon starvation promoter csiDp, the las quorum sensing regulatory unit, and the lytic protein colicin E7. Our transducer-switch lysis genetic circuit enabled: (i) lysis to be activated exclusively at stationary phase coupled with carbon starvation, which ensured that maximum cell growth was reached before product extraction; (ii) lysis-activating cell density to be controllable by varying input glucose amounts; and (iii) lysis performance to remain consistent independent of the amount of input glucose. Finally, we demonstrated the applicability of the lysis circuit to biotechnological applications by employing plasmid DNA extraction as a testbed. We envision that our novel genetic circuit, which conferred cell density-dependent auto-regulatory lysis, would serve as an economical, simplistic and environmentally friendly means for extraction of valuable macromolecules produced in E. coli.

A Force-Activated Trip Switch Triggers Rapid Dissociation of a Colicin from Its Immunity Protein

Author SummaryMany proteins interact with other proteins as part of their function. One method of modulating the activity of protein complexes is to break them apart. Some complexes, however, are extremely kinetically stable and it is unclear how these can dissociate on a biologically relevant timescale. In this study we address this question using protein complexes between colicin E9 (a bacterial toxin) and its immunity protein Im9. These highly avid complexes (with a lifetime of days) must be broken apart for colicin to be activated. By using single-molecule force methods we show that pulling on one end of colicin E9 drastically destabilises the complex so that it dissociates a million-fold faster than its intrinsic rate. We then show that preventing this destabilisation (by the insertion of cross-links that pin the N-terminus of E9 in place) yields a kinetically stable complex. It has previously been postulated that force can destabilise a protein complex by partially unfolding one or more binding partners. Our work provides new experimental evidence that shows this is the case and provides a mechanism for this phenomenon, which we term a trip bond. For the E9:Im9 complex, trip bond behaviour allows a stable complex to be rapidly dissociated by application of a surprisingly small force.

The Sulfur Carrier Protein TusA Has a Pleiotropic Role in Escherichia coli That Also Affects Molybdenum Cofactor Biosynthesis*

The Escherichia coli L-cysteine desulfurase IscS mobilizes sulfur from L-cysteine for the synthesis of several biomolecules such as iron-sulfur (FeS) clusters, molybdopterin, thiamin, lipoic acid, biotin, and the thiolation of tRNAs. The sulfur transfer from IscS to various biomolecules is mediated by different interaction partners (e.g. TusA for thiomodification of tRNAs, IscU for FeS cluster biogenesis, and ThiI for thiamine biosynthesis/tRNA thiolation), which bind at different sites of IscS. Transcriptomic and proteomic studies of a ΔtusA strain showed that the expression of genes of the moaABCDE operon coding for proteins involved in molybdenum cofactor biosynthesis is increased under aerobic and anaerobic conditions. Additionally, under anaerobic conditions the expression of genes encoding hydrogenase 3 and several molybdoenzymes such as nitrate reductase were also increased. On the contrary, the activity of all molydoenzymes analyzed was significantly reduced in the ΔtusA mutant. Characterization of the ΔtusA strain under aerobic conditions showed an overall low molybdopterin content and an accumulation of cyclic pyranopterin monophosphate. Under anaerobic conditions the activity of nitrate reductase was reduced by only 50%, showing that TusA is not essential for molybdenum cofactor biosynthesis. We present a model in which we propose that the direction of sulfur transfer for each sulfur-containing biomolecule is regulated by the availability of the interaction partner of IscS. We propose that in the absence of TusA, more IscS is available for FeS cluster biosynthesis and that the overproduction of FeS clusters leads to a modified expression of several genes.

Harmonic Analysis of the Fluorescence Response of Bimane Adducts of Colicin E1 at Helices 6, 7, and 10

The pre-channel state of helices 6, 7, and 10 (Val(447)-Gly(475) and Ile(508)-Ile(522)) of colicin E1 was investigated by a site-directed fluorescence labeling technique. A total of 44 cysteine variants were purified and covalently labeled with monobromobimane fluorescent probe. A variety of fluorescence properties of the bimane fluorophore were measured for both the soluble and membrane-bound states of the channel peptide, including the fluorescence emission maximum, fluorescence anisotropy, and membrane bilayer penetration depth. Using site-directed fluorescence labeling combined with our novel helical periodicity analysis method, the data revealed that helices 6, 7, and 10 are separate amphipathic α-helices with a calculated periodicity of T = 3.34 ± 0.08 for helix 6, T = 3.56 ± 0.03 for helix 7, and T = 2.99 ± 0.12 for helix 10 in the soluble state. In the membrane-bound state, the helical periodicity was determined to be T = 3.00 ± 0.15 for helix 6, T = 3.68 ± 0.03 for helix 7, and T = 3.47 ± 0.04 for helix 10. Dual fluorescence quencher analysis showed that both helices 6 and 7 adopt a tilted topology that correlates well with the analysis based on the fluorescence anisotropy profile. These data provide further support for the umbrella model of the colicin E1 channel domain.

The role of the N-terminal loop in the function of the colicin E7 nuclease domain

Colicin E7 (ColE7) is a metallonuclease toxin of Escherichia coli belonging to the HNH superfamily of nucleases. It contains highly conserved amino acids in its HHX(14)NX(8)HX(3)H ββα-type metal ion binding C-terminal active centre. However, the proximity of the arginine at the N-terminus of the nuclease domain of ColE7 (NColE7, 446-576) is necessary for the hydrolytic activity. This poses a possibility of allosteric activation control in this protein. To obtain more information on this phenomenon, two protein mutants were expressed, i.e. four and 25 N-terminal amino acids were removed from NColE7. The effect of the N-terminal truncation on the Zn(2+) ion and DNA binding as well as on the activity was investigated in this study by mass spectrometry, synchrotron-radiation circular dichroism and fluorescence spectroscopy and agarose gel mobility shift assays. The dynamics of protein backbone movement was simulated by molecular dynamics. Semiempirical quantum chemical calculations were performed to obtain better insight into the structure of the active centre. The longer protein interacted with both Zn(2+) ion and DNA more strongly than its shorter counterpart. The results were explained by the structural stabilization effect of the N-terminal amino acids on the catalytic centre. In agreement with this, the absence of the N-terminal sequences resulted in significantly increased movement of the backbone atoms compared with that in the native NColE7: in ΔN25-NColE7 the amino acid strings between residues 485-487, 511-515 and 570-571, and in ΔN4-NColE7 those between residues 467-468, 530-535 and 570-571.

Force Triggered Dissociation of the Highly Avid E9:Im9 Complex

Colicin E9 is a nuclease antibiotic produced by E.coli to target and kill competing bacteria in times of stress. Immunity protein 9 (Im9) is expressed co-translationally and binds strongly to E9, inactivating the nuclease to protect the producing cell from the cytotoxic effects of E9. The affinity between E9:Im9 is highly avid with an off-rate of the order of days. However, upon binding to an outer membrane protein of a competing cell, a complex set of protein:protein interactions coupled to protein remodelling results in rapid Im9 release allowing E9 translocation into the cytoplasm and cell death on a timescale of minutes.In order to investigate the molecular basis for such an extreme switch in complex avidity we have used an atomic force microscope to perform dynamic force spectroscopy (DFS) measurements on E9:Im9. We observe a force-induced switching mechanism from the long lived complex (koff ∼ 1x10−5 s−1) in the absence of force to a much shorter lived state (koff ∼ 5 s−1) under the application of small biologically relevant forces. The decrease in complex lifetime under force can be abrogated by introduction of disulfide cross cross-links. This suggests that protein dynamics lie at the heart of the bipartite function of the complex switching from a highly stable complex protective to host, to one where rapid dissociation facilitates competitor death.

Translocation of TonB Dependent Colicins

Colicins are protein toxins produced by E. coli to kill closely related competitor E. coli. Colicins initially attach to target bacteria by binding to outer membrane receptors, most of which are TonB-dependent nutrient transporters—22-stranded -barrels plugged by their amino-terminal domains. One group of colicins, which use the Tol proteins, TolA,B,Q,R, for uptake, have been shown to use OmpF or TolC as their translocators after the initial step when the colicin binds to its receptor. The N-terminal translocation domain of the colicin actually threads into the translocator (Housden et al. (2010) PNAS: 107: 20412).Until recently, no translocator or “second receptor” had been identified for the other family of colicins, those that use TonB and ExbB and D for uptake. Recently, colicin Ia was shown to use a second copy of its primary receptor, Cir, as its translocator (Jakes, K.S. and Finkelstein, A. (2010) Mol. Micro.: 75: 567). In an attempt to determine whether other TonB-dependent colicins also use a second copy of their primary receptor as a translocator, I have made chimera constructs with colicin M, substituting the receptor-binding domain of colicin E3 for that of colicin M, and also deleting the entire receptor-binding domain. These constructs were insoluble and went into inclusion bodies. Dissolving the inclusion bodies in 8M urea, renaturing by dilution and dialysis, and purifying by nickel chelation yielded a small amount of pure protein that had no in vivo killing activity. However, the chimera blocks killing by colicin E3, demonstrating that it binds the E3 receptor, BtuB. Osmotic shock to bypass receptor binding and translocation showed that the enzymatic moiety of the chimera is also active.These results suggest that colicin M translocates differently than colicin Ia and may not normally use a translocator remote from its primary binding site.

A Novel Endogenous Induction of ColE7 Expression in a csrA Mutant of Escherichia coli

Carbon storage regulator A (CsrA) is an important regulator that controls central metabolic pathways and a variety of physiological functions. We found that disruption of csrA in cells containing the ColE7 operon caused a 12-fold increase in colicin E7 production. Moreover, real-time RT-PCR demonstrated a decrease of around 50 % in the lexA mRNA of the csrA mutant. However, the cellular level of RecA protein and its mRNA were not significantly different from the wild type strain. Our results suggest that a novel induction mechanism might exist in E. coli that allows the expression of ColE7 operon in response to a metabolic shift. Proteomic analysis suggested that csrA deficient mutant may adapt PEP-glyoxylate cycle for energy production. Thus, the physiological changes in the csrA mutant may be similar to carbon source limitation for initiating the expression of ColE7 operon in response to stringent environmental conditions.

Pathways of colicin import: utilization of BtuB, OmpF porin and the TolC drug-export protein

Pathway I. Group A nuclease colicins parasitize and bind tightly (Kd ≤ 10(-9) M) to the vitamin B12 receptor on which they diffuse laterally in the OM (outer membrane) and use their long (≥100 Å; 1 Å=0.1 nm) receptor-binding domain as a 'fishing pole' to locate the OmpF porin channel for translocation. Crystal structures of OmpF imply that a disordered N-terminal segment of the colicin T-domain initiates insertion. Pathway II. Colicin N does not possess a 'fishing pole' receptor-binding domain. Instead, it uses OmpF as the Omp (outer membrane protein) for reception and translocation, processes in which LPS (lipopolysaccharide) may also serve. Keio collection experiments defined the LPS core that is used. Pathway III. Colicin E1 utilizes the drug-export protein TolC for import. CD spectra and thermal-melting analysis predict: (i) N-terminal translocation (T) and central receptor (BtuB) -binding (R) domains are predominantly α-helical; and (ii) helical coiled-coil conformation of the R-domain is similar to that of colicins E3 and Ia. Recombinant colicin peptides spanning the N-terminal translocation domain defined TolC-binding site(s). The N-terminal 40-residue segment lacks the ordered secondary structure. Peptide 41-190 is helical (78%), co-elutes with TolC and occluded TolC channels. Driven by a trans-negative potential, peptides 82-140 and 141-190 occluded TolC channels. The use of TolC for colicin E1 import implies that the interaction of this colicin with the other Tol proteins does not occur in the periplasmic space, but rather through Tol domains in the cytoplasmic membrane, thus explaining colicin E1 cytotoxicity towards a strain in which a 234 residue periplasmic TolA segment is deleted.