Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective.

Production of public goods in biological systems is often a collaborative effort that may be detrimental to the producers. It is therefore sustainable only if a small fraction of the population shoulders the cost while the majority reap the benefits. We modelled this scenario using Escherichia coli populations producing colicins, an antibiotic that kills producer cells' close relatives. Colicin expression is a costly trait, and it has been proposed that only a small fraction of the population actively expresses the antibiotic. Colicinogenic populations were followed at the single-cell level using time-lapse microscopy, and showed two distinct, albeit dynamic, subpopulations: the majority silenced colicin expression, while a small fraction of elongated, slow-growing cells formed colicin-expressing hotspots, placing a significant burden on expressers. Moreover, monitoring lineages of individual colicinogenic cells showed stochastic switching between expressers and non-expressers. Hence, colicin expressers may be engaged in risk-reducing strategies-or bet-hedging-as they balance the cost of colicin production with the need to repel competitors. To test the bet-hedging strategy in colicin-mediated interactions, competitions between colicin-sensitive and producer cells were simulated using a numerical model, demonstrating a finely balanced expression range that is essential to sustaining the colicinogenic population.

Redesign of high-affinity nonspecific nucleases with altered sequence preference.

It is of crucial importance to elucidate the underlying principles that govern the binding affinity and selectivity between proteins and DNA. Here we use the nuclease domain of Colicin E7 (nColE7) as a model system to generate redesigned nucleases with improved DNA-binding affinities. ColE7 is a bacterial toxin, bearing a nonspecific endonuclease domain with a preference for hydrolyzing DNA phosphodiester bonds at the 3'O-side after thymine and adenine; i.e., it prefers Thy and Ade at the -1 site. Using systematic computational screening, six nColE7 mutants were predicted to bind DNA with high affinity. Five of the redesigned single-point mutants were constructed and purified, and four mutants had a 3- to 5-fold higher DNA binding affinity than wild-type nColE7 as measured by fluorescence kinetic assays. Moreover, three of the designed mutants, D493N, D493Q, and D493R, digested DNA with an increased preference for guanine at +3 sites compared to the wild-type enzyme, as shown by DNA footprint assays. X-ray structure determination of the ColE7 mutant D493Q-DNA complex in conjunction with structural and free energy decomposition analyses provides a physical basis for the improved protein-DNA interactions: Replacing D493 at the protein-DNA interface with an amino acid residue that can maintain the native hydrogen bonds removes the unfavorable electrostatic repulsion between the negatively charged carboxylate and DNA phosphate groups. These results show that computational screening combined with biochemical, structural, and free energy analyses provide a useful means for generating redesigned nucleases with a higher DNA-binding affinity and altered sequence preferences in DNA cleavage.

The presence of pMRC01 promotes greater cell permeability and autolysis in lactococcal starter cultures.

Conjugative transfer of plasmid-associated properties is routinely used to generate food-grade derivatives of lactococcal starter strains with improved technological traits. However, the introduction of one or more plasmids in a single strain is likely to impose a burden on regular cell metabolism and may affect the growth characteristics of the transconjugant culture. The aim of this study was to evaluate the impact of the 60.2-kb plasmid pMRC01 (encoding for an abortive infection bacteriophage resistance system and production of the anti-microbial, lacticin 3147) on starter performance. Five lactococcal strains (L. lactis HP, 255A, SK1, 712 and IL1403) and their pMRC01-containing derivatives were compared in terms of technological properties, including analysis of growth, acidification and autolysis rates. The transconjugants exhibited lower specific growth rates and higher generation times compared to the parental strains when grown at 30 degrees C in glucose-M17, but the presence of pMRC01 did not significantly affect the acidification capacity of strains in 11% reconstituted skimmed milk and synthetic media. Levels of lactate dehydrogenase were two-fold higher in supernatants of transconjugants than in those of parental strains, after 24 and 72 h of growth at 30 degrees C in glucose-M17, suggesting that the presence of pMRC01 somehow accelerates and promotes cellular autolysis. Analysis by flow cytometry following live/dead staining confirmed this result by showing larger populations of injured and dead cells in pMRC01-carrying cultures compared to the parental strains. The results of this study reveal that the plasmid pMRC01 places a burden on lactococcal host metabolism, which is associated with an increased cell permeability and autolysis, without significantly affecting the acidification capacity of the starter. While the magnitude of these effects appears to be strain dependent, the production of the bacteriocin lacticin 3147 may not be involved.

Evolution of colicin BM plasmids: the loss of the colicin B activity gene.

Colicins, a class of antimicrobial compounds produced by bacteria, are thought to be important mediators of intra- and interspecific interactions, and are a significant factor in maintaining microbial diversity. Colicins B and M are among the most common colicins produced by Escherichia coli, and are usually encoded adjacently on the same plasmid. In this study, the characterization of a collection of E. coli isolated from Australian vertebrates revealed that a significant fraction of colicin BM strains lack an intact colicin B activity gene. The colicin B and M gene region was sequenced in 60 strains and it was found (with one exception) that all plasmids lacking an intact colicin B activity gene have an identical colicin gene structure, possessing a complete colicin B immunity gene and a 130 bp remnant of the B activity gene. A phylogenetic analysis of the colicin M and B operons and characterization of the plasmids suggested that ColBM plasmids with a truncated B activity gene have evolved on at least three separate occasions. Colicin B immunity was found to be non-functional in strains that have lost colicin B activity, and colicin M was still produced despite the absence of the SOS box believed to regulate its production in colicin BM strains. The presence of a remnant of the microcin V operon next to the truncated colicin B activity gene indicated that these plasmids evolved as a consequence of gene transfer between colicin BM and microcin V plasmids. We suggest that these transfer events most likely involved the transfer of some microcin V genes and associated virulence factors onto ColBM plasmids.

Heterologous expression of enterocin AS-48 in several strains of lactic acid bacteria.

AIMS: Enterococcus faecalis produces a cationic and circular enterocin, AS-48, of 7149 Da, the genetic determinants of which are located within the pMB2 plasmid. We have compared enterocin AS-48 production by different enterococci species with that of other 'safe' lactic acid bacteris (LAB) (GRAS status) and looked into the subsequent application of this enterocin in food production. METHODS AND RESULTS: In an effort to exploit this system for the heterologous expression of enterocin AS-48, a number of vectors containing the as-48 cluster were constructed and used to transform several LAB strains (genera Enterococcus, Lactococcus and Lactobacillus) CONCLUSION: Heterologous production of enterocin AS-48 failed when bacteria other than those belonging to the genus Enterococcus were used as hosts, although expression of a partial level of resistance against AS-48 were always detected, ruling out the possibility of a lack of recognition of the enterococcal promoters. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results reveal the special capacity of species from the genus Enterococcus to produce AS-48, an enterocin that requires a post-transcriptional modification to generate a circular peptide with a wide range of inhibitory activity against pathogenic and spoilage bacteria. Preliminary experiments in foodstuffs using nonvirulent enterococci with interesting functional properties reveal the possibility of a biotechnological application of these transformants.

Distinct functions of the two specificity determinants in replication initiation of plasmids ColE2-P9 and ColE3-CA38.

The plasmid ColE2-P9 Rep protein specifically binds to the cognate replication origin to initiate DNA replication. The replicons of the plasmids ColE2-P9 and ColE3-CA38 are closely related, although the actions of the Rep proteins on the origins are specific to the plasmids. The previous chimera analysis identified two regions, regions A and B, in the Rep proteins and two sites, alpha and beta, in the origins as specificity determinants and showed that when each component of the region A-site alpha pair and the region B-site beta pair is derived from the same plasmid, plasmid DNA replication is efficient. It is also indicated that the replication specificity is mainly determined by region A and site alpha. By using an electrophoretic mobility shift assay, we demonstrated that region B and site beta play a critical role for stable Rep protein-origin binding and, furthermore, that 284-Thr in this region of the ColE2 Rep protein and the corresponding 293-Trp of the ColE3 Rep protein mainly determine the Rep-origin binding specificity. On the other hand, region A and site alpha were involved in the efficient unwinding of several nucleotide residues around site alpha, although they were not involved in the stable binding of the Rep protein to the origin. Finally, we discussed how the action of the Rep protein on the origin involving these specificity determinants leads to the plasmid-specific replication initiation.

High-level gene expression in Lactobacillus plantarum using a pheromone-regulated bacteriocin promoter.

AIMS: To use promoters and regulatory genes involved in the production of the bacteriocin sakacin P to obtain high-level regulated gene expression in Lactobacillus plantarum. METHODS AND RESULTS: In a plasmid containing all three operons naturally involved in sakacin P production, the genes encoding sakacin P and its immunity protein were replaced by the aminopeptidase N gene from Lactococcus lactis (pepN) or the beta-glucuronidase gene from Escherichia coli (gusA). The new genes were precisely fused to the start codon of the sakacin P gene and the stop codon of the immunity gene. This set-up permitted regulated (external pheromone controlled) overexpression of both reporter genes in L. plantarum NC8. For PepN, production levels amounted to as much as 40% of total cellular protein. CONCLUSIONS: Promoters and regulatory genes involved in production of sakacin P are suitable for establishing inducible high-level gene expression in L. plantarum. SIGNIFICANCE AND IMPACT OF THE STUDY: This study describes a system for controllable gene expression in lactobacilli, giving some of the highest expression levels reported so far in this genus.

Escherichia coli CoIV plasmid pRK100: genetic organization, stability and conjugal transfer.

Uropathogenic Escherichia coli strains express chromosomal and plasmid-encoded virulence-associated factors such as specific adhesins, toxins and iron-uptake systems. A CoIV plasmid (pRK100) of a uropathogenic strain and its host KS533 were studied. The host strain encodes the K1 capsule, and P and S fimbriae, but neither haemolysin nor the cytotoxic-necrotic factor CNF1, indicating that this strain does not harbour a larger pathogenicity island. A restriction map of pRK100 was constructed on the basis of hybridization experiments and nucleotide sequencing. pRK100 harbours CoIV, the conserved replication region RepFIB, the aerobactin-uptake system, a RepFIC replicon and additionally Colla as well as transposon Tn5431. The location of the RepFIC replicon was similar to that in plasmid F. CoIV plasmids and F thus share a region spanning more than half the length of plasmid F. Even though their replication and transfer regions are homologous, CoIV plasmids are found only in E. coli strains. Among the four other species tested, conjugal transfer of pRK100 was demonstrated, with low frequency, only to Klebsiella pneumoniae, suggesting that a natural barrier effectively bars transfer. In vitro stability of the plasmid with integration into the chromosome to ensure maintenance in the presence of an incompatible plasmid was demonstrated.

Specificity determinants in interaction of the initiator (Rep) proteins with the origins in the plasmids ColE2-P9 and ColE3-CA38 identified by chimera analysis.

The ColE2-P9 rep protein specifically binds to the orgin and initiates DNA synthesis. Interaction of the Rep protein with the origins of plasmids ColE2-P9 and ColE-3-CA38 (one of the close relatives of ColE2-P9) is plasmid-specific. By using chimeric rep genes and chimeric origins we showed that the two region, A and B, in the C-terminal regions of the Rep proteins and the two sites alpha and beta, in the origins are important for the determination of specificity. When each of the A/alpha and B/beta pairs is from the same plasmids, the plasmid replication is efficient. On the other hand, if only the A/alpha pair is from the same plasmids, the plasmid replication is inefficient. For the region A, the plasmid-specificity is mainly determined by the presence or absence of a nine-amino acid sequence. For the region B, the specificity is probably determined by several amino acids. The region B, contains a segment of amino acid sequence which shows significant homology with the DNA recognition helices of various DNA binding proteins. At the site alpha, the single additional base-pair in the ColE3-CA38 origin can be either A/T or T/A. At the site beta, however, the single additional base-pair in the ColE2-P9 origin must be G/C. Among other possibilities we propose that the region A is a linker connecting the two domains in the Rep protein involved in DNA-binding and that the region B is a part of the sequence-specific DNA-binding domain.

Assessment of quantitative models for plasmid ColE1 copy number control.

Two quantitative models of plasmid ColE1 copy number control are compared with respect to mathematical logic of derivation and application to experimental observations. Explanatory background material and clarifications are supplied for selected aspects of each model. Contrasting features are emphasized and experiments are suggested to distinguish between predictions of the models.

Structure of the ColE1 DNA molecule before segregation to daughter molecules.

The segregation of daughter DNA molecules at the end stage of replication of plasmid ColE1 was examined. When circular ColE1 DNA replicates in a cell extract at a high KCl concentration (140 mM), a unique class of molecules accumulates. When the molecule is cleaved by a restriction enzyme that cuts the ColE1 DNA at a single site, an X-shaped molecule in which two linear components are held together around the origin of DNA replication is made. For a large fraction of these molecules, the 5' end of the leading strand remains at the origin and the 3' end of the strand is about 30 nucleotides upstream of the origin. The 3' end of the lagging strand is located at the terH site (17 nucleotides upstream of the origin) and the 5' end of the strand is a few hundred nucleotides upstream of the terH site. Thus the parental strands of the molecule intertwine with each other only once. When the KCl concentration is lowered to 70 mM, practically all of these molecules are converted to daughter circular monomers or to catenanes consisting of two singly interlocked circular units.