Synthesis and functioning of the colicin E1 lysis protein: comparison with the colicin A lysis protein

Systematic approach to Escherichia coli cell population control using a genetic lysis circuit

BACKGROUND

Cell population control allows for the maintenance of a specific cell population density. In this study, we use lysis gene BBa_K117000 from the Registry of Standard Biological Parts, formed by MIT, to lyse Escherichia coli (E. coli). The lysis gene is regulated by a synthetic genetic lysis circuit, using an inducer-regulated promoter-RBS component. To make the design more easily, it is necessary to provide a systematic approach for a genetic lysis circuit to achieve control of cell population density.

RESULTS

Firstly, the lytic ability of the constructed genetic lysis circuit is described by the relationship between the promoter-RBS components and inducer concentration in a steady state model. Then, three types of promoter-RBS libraries are established. Finally, according to design specifications, a systematic design approach is proposed to provide synthetic biologists with a prescribed I/O response by selecting proper promoter-RBS component set in combination with suitable inducer concentrations, within a feasible range.

CONCLUSION

This study provides an important systematic design method for the development of next-generation synthetic gene circuits, from component library construction to genetic circuit assembly. In future, when libraries are more complete, more precise cell density control can be achieved.

Efficient specific release of periplasmic proteins from Escherichia coli using temperature induction of cloned kil gene of pMB9

We have cloned the kil gene of pMB9 under control of the tightly regulated leftward promoter (pL) of coliphage lambda. Three types of plasmids were constructed. In all cases the activity of the lambda promoter is controlled by a thermosensitive cl repressor (product of the c/857 gene) supplied form a resident defective prophage or cloned onto a compatible p 15A-derived plasmid. Induction of the kil protein is brought about by a temperature shift of the culture from 28 degrees C to 42 degrees C. Plasmid pPLc28K1 contains the kil gene including its natural ribosome-binding site and preceded by a transcription termination site. Using a bacterial strain with antitermination properties (e.g., M5219), periplasmic proteins can upon induction be gradually the growth of the host strain. The second plasmid pPLc321K1, contains the kil-coding sequence preceded by an engineered ribosome binding site derived from the attenuator of the Escherichia coli tryptophan operon. With this plasmid induction of the Kil protein is very rapid and specific release of the periplasmic proteins in essentially complete within 30 min after induction. In a third construct, pcl857K1, the pL-kil cassette together with c/857 allele are present on the same replicon, which is compatible with ColE1-derived expression vectors. This configuration allows accumulation in the periplasm of cloned gene products, induced by, e.g., tac or trp promoters at low temperature and subsequent release into the medium following increase of the temperature of the culture. Under repressed conditions (growth at low temperature) all plasmids are perfectly stable in a large number of E. coli strains tested, also when cultivated on a 20-L fermentor scale. Controlled, heat-induced release of periplasmic proteins is highly specific and applicable at relatively high cell densities. The method therefore is an attractive alternative to cumbersome osmotic shock procedures for large-scale cultures.

Induction of membrane permeability in Escherichia coli mediated by lysis protein of the ColE7 operon

A glycogen nonpolyphosphate-accumulating organism (GAO) enrichment culture dominated by the Alphaproteobacteria cluster 1 Defluviicoccus was investigated to determine the metabolic pathways involved in the anaerobic formation of polyhydroxyalkanoates, carbon storage polymers important for the proliferation of microorganisms in enhanced biological phosphorus removal processes. FISH-microautoradiography and post-FISH fluorescent chemical staining confirmed acetate assimilation as polyhydroxyalkanoates in cluster 1 Defluviicoccus under anaerobic conditions. Chemical inhibition of glycolysis using iodoacetate, and of isocitrate lyase by 3-nitropropionate and itaconate, indicated that carbon is likely to be channelled through both glycolysis and the glyoxylate cycle in cluster 1 Defluviicoccus. The effect of metabolic inhibitors of aconitase (monofluoroacetate) and succinate dehydrogenase (malonate) suggested that aconitase, but not succinate dehydrogenase, was active, providing further support for the role of the glyoxylate cycle in these GAOs. Metabolic inhibition of fumarate reductase using oxantel decreased polyhydroxyalkanoate production. This indicated reduction of fumarate to succinate and the operation of the reductive branch of the tricarboxylic acid cycle, which is possibly important in the production of the polyhydroxyvalerate component of polyhydroxyalkanoates observed in cluster 1 Defluviicoccus enrichment cultures. These findings were integrated with previous metabolic models for GAOs and enabled an anaerobic central metabolic pathway model for polyhydroxyalkanoate formation in cluster 1 Defluviicoccus to be proposed.

Structure and function of colicin S4, a colicin with a duplicated receptor-binding domain

Colicins are plasmid-encoded toxic proteins produced by Escherichia coli strains to kill other E. coli strains that lack the corresponding immunity protein. Colicins intrude into the host cell by exploiting existing transport, diffusion, or efflux systems. We have traced the way colicin S4 takes to execute its function and show that it interacts specifically with OmpW, OmpF, and the Tol system before it inserts its pore-forming domain into the cytoplasmic membrane. The common structural architecture of colicins comprises a translocation, a receptor-binding, and an activity domain. We have solved the crystal structure of colicin S4 to a resolution of 2.5 A, which shows a remarkably compact domain arrangement of four independent domains, including a unique domain duplication of the receptor-binding domain. Finally, we have determined the residues responsible for binding to the receptor OmpW by mutating exposed charged residues in one or both receptor-binding domains.

Increasing the secretion ability of the kil gene for recombinant proteins in Escherichia coli by using a strong stationary-phase promoter

By using a beta-glucanase from Bacillus as a model protein, we investigated whether the secretion competence based on the action of the kil gene can be improved using stronger promoters for the expression of the kil gene. Since the production of extracellular target proteins also depends on the promoter strengths of the target gene, we constructed four expression vectors with all possible combinations of a weak and a strong stationary-phase promoter for the kil gene, and a weak and a strong constitutive promoter, respectively, for the beta-glucanase gene. The results of batch fermentations showed that the use of stronger promoters generally decreased the cell density. However, a drastic increase of productivity of the cells to produce and secrete beta-glucanase resulted in a significantly higher activity of extracellular beta-glucanase. The yield of extracellular beta-glucanase can be increased (to 168 %) by using a strong promoter for the beta-glucanase alone. However, the increase was much higher when the weak promoter of the kil gene was replaced by a strong stationary-phase promoter (to 221 %). An even higher yield of extracellular beta-glucanase was reached when beta-glucanase was expressed by a strong promoter in addition indicating a combinatorial effect. This shows that the extracellular production of a recombinant target gene can be optimized by tuning the promoter strengths of components, the kil gene and the target gene.

Colicin biology

Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic determinants for colicin synthesis, immunity, and release. Insights gained into each fundamental aspect of their biology are presented: their synthesis, which is under SOS regulation; their release into the extracellular medium, which involves the colicin lysis protein; and their uptake mechanisms and modes of action. Colicins are organized into three domains, each one involved in a different step of the process of killing sensitive bacteria. The structures of some colicins are known at the atomic level and are discussed. Colicins exert their lethal action by first binding to specific receptors, which are outer membrane proteins used for the entry of specific nutrients. They are then translocated through the outer membrane and transit through the periplasm by either the Tol or the TonB system. The components of each system are known, and their implication in the functioning of the system is described. Colicins then reach their lethal target and act either by forming a voltage-dependent channel into the inner membrane or by using their endonuclease activity on DNA, rRNA, or tRNA. The mechanisms of inhibition by specific and cognate immunity proteins are presented. Finally, the use of colicins as laboratory or biotechnological tools and their mode of evolution are discussed.

Role of Cal, the colicin A lysis protein, in two steps of colicin A release and in the interaction with colicin A–porin complexes

Release of colicin A was studied inEscherichia colicells that differed in expressing thecolicinAlysis protein (Cal). Pools of released and unreleased colicin A were harvested throughout colicin A induction. The amount of colicin A in each pool varied with the time of induction, allowing the definition of two sequential steps in colicin A release, one of which was dependent on Cal. Each step of colicin A release was differently affected in cells containing Cal mutants in which the N-terminal cysteine residue was substituted by either proline or threonine, preventing them from being acylated and matured. These Cal mutants were only observed indegPcells, indicating that the DegP protease cleaved the unacylated precursor of Cal. Cal was found in the insoluble fraction of the pools of released and unreleased colicin A together with the hetero-oligomers of colicin A and porins (colicins Au). The biogenesis of colicins Au was studied in temperature-sensitivesecAandsecYstrains and found to be Sec-independent, indicating that they are formed by newly synthesized colicin A binding to mature porins already incorporated in the outer membrane. Cal is a lipoprotein similar to VirB7, a constituent of the type IV secretion system. It would interact with colicins Au to constitute the colicin A export machinery.

Assembly of colicin A in the outer membrane of producing Escherichia coli cells requires both phospholipase A and one porin, but phospholipase A is sufficient for secretion

Three oligomeric forms of colicin A with apparent molecular masses of about 95 to 98 kDa were detected on sodium dodecyl sulfate (SDS)-polyacrylamide gels loaded with unheated samples from colicin A-producing cells of Escherichia coli. These heat-labile forms, called colicins Au, were visualized both on immunoblots probed with monoclonal antibodies against colicin A and by radiolabeling. Cell fractionation studies show that these forms of colicin A were localized in the outer membrane whether or not the producing cells contained the cal gene, which encodes the colicin A lysis protein responsible for colicin A release in the medium. Pulse-chase experiments indicated that their assembly into the outer membrane, as measured by their heat modifiable migration in SDS gels, was an efficient process. Colicins Au were produced in various null mutant strains, each devoid of one major outer membrane protein, except in a mutant devoid of both OmpC and OmpF porins. In cells devoid of outer membrane phospholipase A (OMPLA), colicin A was not expressed. Colicins Au were detected on immunoblots of induced cells probed with either polyclonal antibodies to OmpF or monoclonal antibodies to OMPLA, indicating that they were associated with both OmpF and OMPLA. Similar heat-labile forms were obtained with various colicin A derivatives, demonstrating that the C-terminal domain of colicin A, but not the hydrophobic hairpin present in this domain, was involved in their formation.

Bacteriocin release proteins: mode of action, structure, and biotechnological application

The mechanism by which Gram-negative bacteria like Escherichia coli secrete bacteriocins into the culture medium is unique and quite different from the mechanism by which other proteins are translocated across the two bacterial membranes, namely through the known branches of the general secretory pathway. The release of bacteriocins requires the expression and activity of a so-called bacteriocin release protein and the presence of the detergent-resistant phospholipase A in the outer membrane. The bacteriocin release proteins are highly expressed small lipoproteins which are synthesized with a signal peptide that remains stable and which accumulates in the cytoplasmic membrane after cleavage. The combined action of these stable, accumulated signal peptides, the lipid-modified mature bacteriocin release proteins (BRPs) and phospholipase A cause the release of bacteriocins. The structure and mode of action of these BRPs as well as their application in the release of heterologous proteins by E. coli is described in this review.

Role of DegP protease on levels of various forms of colicin A lysis protein

The total amount of the colicin A lysis protein produced by cells grown in rich medium was analysed by immunoblotting. The intermediate forms of synthesis of this small lipoprotein were present in the cells at any time of induction, confirming that processing and maturation of colicin A lysis protein are slow and incomplete processes. The level of these various forms varied according to the time of induction, the growth conditions, the producing strain and the plasmid carrying the cal gene. It depended mainly on the presence in the producing strain of a degP gene which encodes the DegP protease. According to growth conditions, the DegP protease hydrolysed either a part or the total amount of the acylated precursor form. In some cases, a protease(s) other than DegP seemed to act on either form(s) of the colicin A lysis protein.

Truncated mutants of the colicin A lysis protein are acylated and processed when overproduced

The lipid modification and processing of truncated mutants of the colicin A lysis protein were observed after overproduction by Escherichia coli bacteria, but at a rate far slower than that of the wild-type. The unmodified precursor form of the mutants was stable over hour(s). The truncated mutants provoked lethality, but neither caused protein release nor quasi-lysis.

Colicin A and colicin E1 lysis proteins differ in their dependence on secA and secY gene products

The export of colicin A and of colicin E1 is not equally affected in both secA and secY mutants of Escherichia coli: release of colicin A occurs slowly while that of colicin E1 is blocked. Processing and functioning of Cal, the colicin A lysis protein, seem to be slightly or not at all modified in these mutants, whereas synthesis and assembly of CelA, the colicin E1 lysis protein, are highly inhibited. These variations observed in the dependence of the two lysis proteins on secA and secY gene products are interpreted as being either the cause or the consequence of the differences observed in their rate of biogenesis.