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Inhibition by toxic substrates enables multiple steady states to arise in biodegradation systems. This phenomenon was investigated for the continuous metabolism of aniline by Pseudomonas sp. CIT1. Differences of various metabolic parameters between the two growth regimes (uninhibited and inhibited) and the transient response to a step-up in dilution rate were determined. Regulatory mechanisms consistent with the experimental evidence are proposed. Aniline is the transcriptional inducer of a metabolic pathway that converts aniline to TCA cycle intermediates. The suite of enzymes is coordinately expressed from a single promoter. We followed the level of the pathway mRNA using a fragment containing the catechol 2,3 dioxygenase gene (andioxB) and monitored the pathway enzyme activity using catechol 2,3 dioxygenase (C23D). The inhibited regime resulted in a 60% lower growth yield, near constant levels of C23D monomer, but a 50% reduction in the specific activity of C23D, increased RNA synthesis rates (total and aniline pathway mRNA), and elevated RNA decay rates. Elucidation of regulatory mechanisms indicates that C23D is noncompetitively inhibited by aniline and subject to feedback inhibition by 2-hydroxymuconic semialdehyde (HMS). During uninhibited growth regime operation, metabolism of HMS is the rate-limiting step; in contrast, conversion of aniline to catechol limits growth in the inhibited regime., (Copyright 1998 John Wiley & Sons, Inc.)

A strain of Pseudomonas putida that harbors plasmids RK2 and pDLB101 was exposed to a pure culture biofilm of Bacillus azotoformans grown in a rotating annular reactor. Transfer of the RK2 mobilizable pDLB101 plasmid to B. azotoformans was monitored over a 4-day period. Experimental results demonstrated that the broad host range, RSF1010 derivative pDLB101 was transferred to and expressed by B. azotoformans. In the companion article to this work, the rate of plasmid transfer was quantified as a function of the limiting nutrient, succinate, and as a function of the mechanism of transfer. A biofilm process simulation program (AQUASIM) was modified to analyze resultant experimental data. Although the AQUASIM package was not designed to simulate or predict genetic events in biofilms, modification of the rate process dynamics allowed successful modeling of plasmid transfer. For the narrow range of substrate concentrations used in these experiments, nutrient level had only a slight effect on the rate and extent of plasmid transfer in biofilms. However, further simulations using AQUASIM revealed that under nutrient poor conditions, the number of transconjugants appearing in the biofilm was limited., (Copyright 1998 John Wiley & Sons, Inc.)

Biofilm formation and plasmid segregational instability in biofilm cultures of Escherichia coli DH5alpha (pMJR1750) were investigated under different medium-carbon-to-nitrogen (C/N) ratios. At C/N ratios of 0.07 and 1, net accumulation of both biofilm plasmid-bearing and plasmid-free cells continued through the entire experiment without attaining any apparent steady state. At C/N ratios of 5 and 10, net biofilm cell accumulation for the two populations reached apparent steady states after 84 and 72 h, respectively. At C/N ratios of 0.07 and 1, polysaccharide production increased slowly and reached about 2g alginate equivalent/cm(2) by the end of both experiments. At a C/N ratio of 5, polysaccharide increase significantly after 84 h, reaching about 7 microg alginate equivalent/cm(2) prior to termination. At a C/N ratio of 10, polysaccharide increased significantly after 72 h and reached 21 microg alginate equivalent/cm(2) at 108 h. At C/N ratios of 0.07 and 1, protein production reached 6.5 and 4 microg/cm(2), respectively. At C/N ratios of 5 and 10, protein production increased slightly for the first 84 h and reached a maximum at 108 h, at 3 and 2 microg/cm(2), respectively, then decreased over the last 12 h of the experiment. Ratios of polysaccharide to protein increased with increasing C/N ratios. At C/N ratios of 0.07 and 1, the ratios between extracellular polysaccharide (EP) and protein were no more than 205 microg polysaccharide/microg protein, whereas those at C/N ratios of 5 and 10 increased to about 7 and 12 microg polysaccharide/microg protein, respectively.Probabilities of plasmid loss in the biofilm cultures increased with increasing C/N ratios. At C/N ratios of 0.07, 1, and 5, the probabilities of plasmid loss were 0.0013 +/- 0.011, 0.020 +/- 0.006 and 0.122 +/- 0.021, respectively. At a C/N ratio of 10, the probability of plasmid loss was significantly higher, reaching 0.38 +/- 0.125. The increase of probability of plasmid loss at higher C/N ratios results from competition between cell replication and extracellular polysaccharide production.

Differences in plasmid retention and expression are studied in both suspended and biofilm cultures of Escherichia coli DH5alpha(PMJR1750). An alternative mathematical model is proposed which allows the determination of plasmid loss probability in both suspended batch and continuously fed biofilm cultures. In our experiments, the average probability of plasmid loss of E. coli DH5alpha(pMJR1750) is 0.0022 in batch culture in the absence of antibiotic selection pressure and inducer. Under the induction of 0.17 MM IPTG, the maximum growth rate of plasmid-bearing cells in suspended batch culture dropped from 0.45 h(-1) to 0.35 h(-1) and the beta-galactosidase concentration reached an experimental maximum of 0.32. pg/cell 4 hours after the initiation of induction. At both 0.34 and 0.51 mM IPTG, growth rates in batch cultures decreased to 0.16 h(-1), about 36% of that without IPTG, and the beta-galactosidase concentration reached an experimental maximum of 0.47 pg/cell 3 hours after induction.In biofilm cultures, both plasmid-bearing and plasmid-free cells in increase with time reaching a plateau after 96 hours n the absence of both the inducer and any antibiotic selection pressure. Average probability of plasmid loss for biofilm-bound E. coli DH5beta(pMJR1750) population was 0.017 without antibiotic selection. Once the inducer IPTG was added, the concentration of plasmid-bearing cells in biofilm dropped dramatically while plasmid-free cell numbers maintained unaffected. The beta-galactosidase concentration reached a maximum in all biofilm experiments 24 hours after induction; they were 0.08, 0.1, and 0.12 pg/cel under 0.17, 0.34, and 0.51 mM IPTG, respectively., ((c) 1993 John Wiley & Sons, Inc.)

An expression system utilizing specialized ribosomes has been constructed with beta-galactosidase as the product. Ribosomes specific for lacZ mRNA are generated due to a mutation within the anti-Shine-Dalgarno region of a plasmidborne 16S rRNA gene that is complementary to a mutation within the ribosome-binding site of lacZ. Hence, a subpopulation of ribsomes specific for translation of the cloned gene mRNA is produced. Transcription of the lacZ gene is regulated by the tac promoter, while transcription of the mutated rrnB locus is controlled by the lambdaP(L) promoter. Batch experiments indicate that full induction of both operons (2 mM IPTG, 42 degrees C) leads to maximal beta-galactosidase activity per cell at levels 35% higher than that obtained using a wild-type ribosome expression system. Using a novel, site-directed mutagenesis technique, construction of the specialized ribosome vector is outlined, and the results of lacZ expression are presented as transcription of both the cloned-gene and the specialized-ribosome locus are induced.

Earlier experiments in our lab investigated the metabolic limitations of cloned-gene expression in bacterial cells (for over-production of beta-lactamase). These experiments showed that the steady-state concentration of ribosomal RNA decreased upon plasmid amplification while both the synthesis rate and steady-state beta-lactamase mRNA level increased significantly. This appeared to indicate substantial limitation exist within the transnational machinery of the bacterial cell at high copy numbers. To establish the generality of this phenomenon, the impact increasing protein expression from pa plasmid by chemically inducing a strong promoter while maintaining constant copy number has been investigated. A plasmid has been constructed which contains the lacZ gene under control of the tac promoter and contains the parB stability locus to maintain plasmid stability. Using this vector, beta-galactosidase expression in chemostat cultures operated at specific growth rates of 0.6 h(-1) was induced with IPTG such that enzyme activity was varied over a 460-fold range. When fully induced beta-galactosidase protein production represented 14 wt % of total cell protein. As transcription was induced, the synthesis rate of the beta-galactosidase mRNA increased 42-fold while the steady-state level of beta-galactosidase mRNA increased only fourfold. This indicates stability may play a larger role for beta-galactosidase expression with a strong promoter than seen with beta-lactamase production in the elevated copy number system. Furthermore, rRNA synthesis rates increased at high expression rates as seen in the copy number experiments. However, unlike the amplified-plasmid system, the steady-state levels of rRNA increased as well. Since the total protein levels closely followed the steady-state level of eRNA, transnational limitations are again suggested for the chemically induced transcription system.

Pronounced spatial nonuniformities in cell density, physiology, and activity frequently arise within densely packed immobilized cell supports. For a more fundamental understanding of immobilized cell phenomena, we have developed high-resolution microfluorimetric procedures to analyze local variations in both immobilized cell loading and growth rate. Fluorescent staining of total cellular DNA provides a measure of local biomass density. Actively growing (DNA synthesizing) cells are marked by pulse-labeling newly synthesized DNA with the thymine analog, bromouracil. An immunofluorescent technique allows subsequent detection of spatial variations in DNA synthesis rates. These procedures enable the influence of mass-transfer limitations and other immobilization effects on cell distribution and activity to be readily quantified. We demonstrate this approach through analysis of the patterns of growth of Escherichia coli entrapped within Sr-alginate gel beads. The experimental techniques are potentially applicable to a variety of other aggregate cell systems.

Recombinant bacterial systems exhibit limited capacities for heterologous protein production. As seen with this and other systems, cloned-gene protein production reaches an upper limit despite further increases in gene dosage. A series of closely related plasmids which contain mutations affecting their copy number has been used to investigate the macromolecular impediments to enhanced recombinant protein production. Within a common host, HB101, the level of the ampicillin resistance gene, bla, was varied using five plasmids which differ solely in their replication machinery. Separate fermentations were conducted in which the plasmid copy number was varied from 0 to over 400 while the specific growth rate was fixed at 0.6 h(-1) for each chemostat cultivation. The effects of constitutive expression of the bla gene as copy number was elevated were then determined using pulse-labelling and RNA-DNA hybridizations. Specifically, the steady-state level, synthesis rate, and stability of beta-lactamase messenger RNA and ribosomal RNA were determined as a function of copy number. The results indicate that as copy number rises, both beta-lactamase mRNA synthesis rates and steady-state mRNA levels increase. Therefore, beta-lactamase production in these strains does not appear to be limited by the level of beta-lactamase mRNA. However, as the copy number was amplified, the stability of rRNA decreased to the point that steady-state levels of rRNA decreased. These data indicate that a limitation develops within the translational capacity of the cell at high levels of cloned-gene expression. The results suggest that strategies designed to enhance recombinant protein expression should include manipulation of translation as well as transcription.

A mechanistically detailed single-cell model E. coli B/r-A was adapted to simulate the effects of vector presence on cell metabolism. Competition for RNA polymerase between chromosome and plasmid DNA is explicitly included. Distribution of active ribosomes among chromosome- and plasmid-derived messenger RNA, another key facet of host-plasmid interactions, is also treated in detail. Simulations of recombinant cell growth rate and cloned-gene productivity as a function of relative plasmid number per cell agree closely with experimental results. Model prediction of the variation of cell cycle parameters C and D with plasmid number are roughly consistent with available data. Models of this class can be used to simulate changes in productivity resulting from specific alterations in the expression vector. The effects of changing cloned-gene promoter and ribosome binding strengths and of augmenting cell transcription or translation capacity have been studied using the recombinant cell model. Results suggest that cloned-gene expression is limited by cellular transcription capacity. These and other parametric studies, conveniently implemented using the computer cell, provide important guidance for future experiments directed at better understanding of host-plasmid interactions and at optimizing recombinant system productivity.

A structured mathematical model for cellular metabolism in Escherichia coli has been extended to encompass the mechanistic structure surrounding the kinetics and control of transcription and translation. The dependence of transcription on RNA polymerase and the mechanism of translation initiation have been explicitly included. This model correctly simulates cell growth, cell composition, and the timing of chromosome synthesis as a function of extracellular substrate concentration for glucose-limited balanced growth. Simulation results for the subpopulation of RNA polymerase engaged in transcription and for the distribution of this subpopulation among different promoter sites agree closely with experimental findings, as do calculated estimates of the active ribosomal fraction. In addition, the existence of an antitermination system for transcription of stable RNA operons is supported by model results. This model should provide a useful framework for investigating metabolic perturbations to E. coli, such as those resulting from insertion of extra-chromosomal vectors into the cells.

Experiments were performed to evaluate, qualitatively and quantitatively, the adaptation of Escherichia coli to plasmid maintenance and cloned gene expression. Experimental findings indicate that the metabolic response to low plasmid levels is an increase of the biosynthetic capacity of both transcription and translation. At high copy number levels the gene-specific transcription rate continues to increase but the stability of plasmid-derived mRNA drops sharply. Protein levels are maintained, but translation efficiency decreases. These results indicate that cellular biosynthetic capacity may not be limiting productivity in recombinant systems. If macromolecular stability is the bottleneck, then current efforts to increase gene expression that focus on enhancing synthesis rates will be ineffective.