pOSEX: vectors for osmotically controlled and finely tuned gene expression in Escherichia coli

Thermoinducible E. coli for Recombinant Protein Production in Inclusion Bodies

The temperature-inducible λpL/pR-cI857 expression system has been widely used to produce recombinant proteins (RPs), especially when it is necessary to avoid the addition of exogenous materials to induce the expression of recombinant genes, preventing contamination of bioprocesses. The temperature increase favors the formation of inclusion bodies (IBs). The temperature upshift could change the metabolism, productivities, cell viability, IBs architecture, and the host cell proteins inside IBs, affecting downstream to obtain the final product. In this contribution, we focus on the relationship between the bioprocesses using temperature increase as inducer, the heat shock response associated with temperature up-shift, the RP accumulation, and the formation of IBs. Here, we describe how to produce IBs and how culture conditions can modulate the composition and architecture of IBs by modifying the induction temperature in RP production.

Thermoinducible expression system for producing recombinant proteins in Escherichia coli: advances and insights

Recombinant protein (RP) production from Escherichia coli has been extensively studied to find strategies for increasing product yields. The thermoinducible expression system is commonly employed at the industrial level to produce various RPs which avoids the addition of chemical inducers, thus minimizing contamination risks. Multiple aspects of the molecular origin and biotechnological uses of its regulatory elements (pL/pR promoters and cI857 thermolabile repressor) derived from bacteriophage λ provide knowledge to improve the bioprocesses using this system. Here, we discuss the main aspects of the potential use of the λpL/pR-cI857 thermoinducible system for RP production in E. coli, focusing on the approaches of investigations that have contributed to the advancement of this expression system. Metabolic and physiological changes that occur in the host cells caused by heat stress and by RP overproduction are also described. Therefore, the current scenario and the future applications of systems that use heat to induce RP production is discussed to understand the relationship between the activation of the bacterial heat shock response, RP accumulation, and its possible aggregation to form inclusion bodies.

Expression of Cloned Genes in E. coli Using IPTG-Inducible Promoters

Many Escherichia coli expression vectors make use of the lac operon. In general, the lac operator (lacO) is located downstream from the promoter of the target gene, so that binding of the lac repressor blocks transcription initiation until lactose or the isopropyl-β-d-thiogalactopyranoside (IPTG) analog is added. The protocol given here is intended for use with IPTG-inducible vectors. l-Arabinose-inducible systems derived from the ara operon offer an alternative to expression systems based on the lac operon; guidance for their use is also provided.

Tunable recombinant protein expression in E. coli: promoter systems and genetic constraints

Tuning of transcription is a promising strategy to overcome challenges associated with a non-suitable expression rate like outgrowth of segregants, inclusion body formation, metabolic burden and inefficient translocation. By adjusting the expression rate-even on line-to purposeful levels higher product titres and more cost-efficient production processes can be achieved by enabling culture long-term stability and constant product quality. Some tunable systems are registered for patents or already commercially available. Within this contribution, we discuss the induction mechanisms of various Escherichia coli inherent promoter systems with respect to their tunability and review studies using these systems for expression tuning. According to the current level of knowledge, some promoter systems were successfully used for expression tuning, and in some cases, analytical evidence on single-cell level is still pending. However, only a few studies using tunable strains apply a suitable process control strategy. So far, expression tuning has only gathered little attention, but we anticipate that expression tuning harbours great potential for enabling and optimizing the production of a broad spectrum of products in E. coli.

A tightly regulated expression system for E. coli using supersaturated silicic acid

OBJECTIVE

To develop a new expression system regulated by a ferric uptake regulator in which silicic acid is used as an inducer.

RESULTS

Fur box (binding site for Fur) was substituted for the lac operator to regulate the expression of GFP with the lac promoter. Since the addition of supersaturated silicic acid invokes iron deficiency, supersaturated silicic acids were used as an inducer. GFP expression was dependent on silica concentration, and the expression level without silica was negligible. Basal expression level of this lac-Fur system was extremely low and, hence, lytic enzyme gene E from bacteriophage ϕX174 could be retained in this system. Furthermore, the expression of genes of interest was spontaneously initiated as the cell density increased and the costs of the inducer are considerably less than IPTG.

CONCLUSION

The combination of lac promoter and Ferric uptake repressor allowed the protein expression by supersaturated silicic acid as an inducer in an easy and cost-effective way.

Micro-scale water potential gradients visualized in soil around plant root tips using microbiosensors

Water availability and movement in soil are critical determinants of resource availability to, and interactions among, members of the soil community. However, it has been impossible to observe gradients in soil water potential empirically at millimetre spatial scales. Here we describe progress towards that goal using output from two microbial biosensors, Pantoea agglomerans BRT98/pPProGreen and Pseudomonas putida KT2442/pPProGreen, engineered with a reporter system based on the osmotically sensitive proU promoter from Escherichia coli. The proU-GFP construct in both microbiosensors produced green fluorescent protein (GFP) as a function total water potential in nonsterile soil. Controlled experiments in liquid culture showed that dramatically different microbiosensor growth rates (resulting from exposure to different salts as osmolytes) did not alter the GFP output as a function of water potential in either sensor, but P. agglomerans' GFP levels at a given water potential were strongly influenced by the type of carbon (energy) source available to the microbes. In non-sterile rhizosphere soil along Zea mays L. roots, though GFP expression was quite variable, microbiosensors reported statistically significantly more negative soil water potentials as a function of axial distance from root tips, reflecting the gradient in soil water potential hypothesized to develop during transpiration.

A rapid reporter system using GFP as a reporter protein for identification and screening of synthetic stationary-phase promoters in Escherichia coli

To develop a rapid reporter system for the screening of stationary-phase promoters in Escherichia coli, the expression pattern of the green fluorescent protein (GFP) during bacterial cultivation was compared with that of the commonly used beta-galactosidase. Using GFP with enhanced fluorescence, the expression pattern of both reporter systems GFP and beta-galactosidase were similar and showed a typical induction of gene activity of the reporter genes, i.e. increase of expression at the transition from exponential to stationary phase. The expression was affected by the culture medium, i.e. in contrast to the complex medium (LB medium), the stationary-phase specific induction was only observed in synthetic medium (M9) when amino acids were added, whereas there was generally no induction in MOPS medium. To develop a rapid screening method on agar plates for stationary-phase promoters, a photographic approach was used, continued with computational image treatment. A screening method is presented which enables an on-line monitoring of gene activity.

Libraries of synthetic stationary-phase and stress promoters as a tool for fine-tuning of expression of recombinant proteins in Escherichia coli

Due to their induction characteristics stationary-phase promoters have a great potential in biotechnological processes for the production of heterologous proteins on a large-scale. In order to broaden the utility of stationary-phase promoters in bacterial expression systems and to create novel promoters induced by metabolic conditions, a library of synthetic stationary-phase/stress promoters for Escherichia coli was constructed. For designing the promoters the known -10 consensus sequence as well as the extended -10 region and an A/T-rich region downstream of the -10 region were kept constant, while sequences from -37 to -14 were partially or completely randomized. For detection and selection of stationary-phase promoters GFP with enhanced fluorescence was used. The expression pattern of the GFP reporter system was compared with that of the LacZ reporter system. To screen and characterize colonies containing stationary-phase/stress promoters a bioinformatic approach was developed. In total, 33 promoters were selected which cover a broad range of promoter activities and induction times indicating that the strength of promoters can be modulated by partially randomizing the sequence upstream of the -10 region. The induction ratio of synthetic promoters at the transition from exponential to stationary-phase was from 4 to over 6000 and the induction time relative to the entrance into stationary-phase from -1.4 to 2.7 h. Ninety-one percentage of the promoters had no or only low background activity during exponential growth. The broad variability of the promoters offers good possibilities for fine-tuning of gene expression and for applications in industrial bioprocesses.

A truncated H-NS-like protein from enteropathogenic Escherichia coli acts as an H-NS antagonist

The H-NS nucleoid-associated protein of Escherichia coli is the founder member of a widespread family of gene regulatory proteins which have a bipartite structure, consisting of an N-terminal coiled-coil oligomerization domain and a C-terminal DNA-binding domain. Here we characterize a family of naturally occurring truncated H-NS derivatives lacking the DNA-binding domain, which we term the H-NST family. H-NST proteins are found in large genomic islands in pathogenic E. coli strains, which are absent from the corresponding positions in the E. coli K-12 genome. Detailed analysis of the H-NST proteins from enteropathogenic E. coli (EPEC) and uropathogenic E. coli (UPEC) shows that the EPEC protein (H-NST(EPEC)) has a potent anti-H-NS function at the classical H-NS-repressed operon proU. This correlates with the ability of H-NST(EPEC) to co-purify with H-NS in vitro, and can be abolished by a mutation of leucine 30 to proline which is predicted to prevent the N-terminal region from forming a coiled-coil structure. In contrast, despite being 90% identical to H-NST(EPEC) at the protein level, the UPEC homologue (H-NST(UPEC)) has only a weak anti-H-NS activity, correlating with a much-reduced ability to interact with H-NS during column chromatography. A single amino acid difference at residue 16 appears to account for these different properties. The hnsT(EPEC) gene is transcribed monocistronically and expressed throughout the exponential growth phase in DMEM medium. Our data suggest that a truncated derivative of H-NS encoded by an ancestral mobile DNA element can interact with the endogenous H-NS regulatory network of a bacterial pathogen.

Pseudomonas syringae pv. tomato cells encounter inhibitory levels of water stress during the hypersensitive response of Arabidopsis thaliana

During plant defense against bacterial pathogens, the hypersensitive response (HR) functions to restrict pathogen growth and spread. The mechanisms driving this growth restriction are poorly understood. We used a water stress-responsive transcriptional fusion to quantify the water potential sensed by individual Pseudomonas syringae pv. tomato DC3000 cells during infection of Arabidopsis thaliana leaves. A nonpathogenic DC3000 hrcC mutant defective in type III secretion, as well as the saprophyte Pseudomonas fluorescens A506, sensed water potentials of -0.3 to -0.4 MPa at 48 h postinfiltration (hpi). During pathogenesis, DC3000 sensed lower water potentials (-0.4 to -0.9 MPa), demonstrating that it can modify the intercellular environment, and these water potentials were associated with optimal DC3000 growth in culture. During the HR, DC3000 cells sensed water potentials (-1.6 to -2.2 MPa) that were low enough to prevent cell division in the majority of cells in culture. This water potential decrease occurred within only 4 hpi and was influenced by avirulence gene expression, with avrRpm1 expression associated with lower water potentials than avrRpt2 or avrB expression at 48 hpi. The population sizes of the DC3000 variants tested were significantly correlated with the apoplastic water potential at 48 hpi, with a decrease of -0.9 MPa associated with a 10-fold decrease in cells per gram of leaf. These results suggest that the apoplastic water potential is a determinant of endophytic bacterial population size, and water stress, resulting from high osmolarity or tissue desiccation, is at least one factor restricting bacterial growth during the HR.

Construction and characterization of a proU-gfp transcriptional fusion that measures water availability in a microbial habitat

We constructed and characterized a transcriptional fusion that measures the availability of water to a bacterial cell. This fusion between the proU promoter from Escherichia coli and the reporter gene gfp was introduced into strains of E. coli, Pantoea agglomerans, and Pseudomonas syringae. The proU-gfp fusion in these bacterial biosensor strains responded in a quantitative manner to water deprivation caused by the presence of NaCl, Na(2)SO(4), KCl, or polyethylene glycol (molecular weight, 8000). The fusion was induced to a detectable level by NaCl concentrations of as low as 10 mM in all three bacterial species. Water deprivation induced proU-gfp expression in both planktonic and surface-associated cells; however, it induced a higher level of expression in the surface-associated cells. Following the introduction of P. agglomerans biosensor cells onto bean leaves, the cells detected a significant decrease in water availability within only 5 min. After 30 min, the populations were exposed, on average, to a water potential equivalent to that imposed by approximately 55 mM NaCl. These results demonstrate the effectiveness of a proU-gfp-based biosensor for evaluating water availability on leaves. Furthermore, the inducibility of proU-gfp in multiple bacterial species illustrates the potential for tailoring proU-gfp-based biosensors to specific habitats.

Monitoring of genes that respond to process-related stress in large-scale bioprocesses

In large-scale aerobic fed-batch processes, cells are exposed to local zones of high glucose concentrations that can also cause local oxygen limitations at high cell densities. The mRNA levels of four stress genes (clpB, dnaK, uspA, and proU) and three genes responding to oxygen limitation or glucose excess (pfl, frd, and ackA) were investigated in an industrial 20-m(3) Escherichia coli process and in a scale-down reactor with defined high-glucose and low-oxygen zones. The mRNA levels of ackA and proU were high during the batch growth phase, but declined drastically when glucose became limited, whereas the mRNA levels of the other stress genes were relatively constant throughout the process. In the industrial-scale reactor, the stress gene mRNA levels were, in most cases, highest in the middle part and at the top of the reactor, where the substrate was fed. Cells passing through the high glucose zone of the scale-down reactor had elevated mRNA levels for the oxygen limitation genes and had also elevated heat-shock gene mRNA levels. Both responses to stress occurred within seconds. The approach presented in this study offers a tool for monitoring process-related changes in the transcriptional regulation of genes.

An Escherichia coli host strain useful for efficient overproduction of cloned gene products with NaCl as the inducer

Salt-induced overexpression of genes cloned downstream of the phage T7 phi10 promoter was demonstrated in an Escherichia coli strain (GJ1158) which carries a single chromosomally integrated copy of the gene for phage T7 RNA polymerase under transcriptional control of the cis-regulatory elements of the osmoresponsive proU operon. Plasmids that have been constructed to obtain overproduction of individual target gene products in strain BL21(DE3) (by addition of isopropyl-beta-D-thiogalactopyranoside as an inducer) can directly be transformed into GJ1158. The NaCl induction regimen was also shown to be associated with a decreased propensity for sequestration of overexpressed target proteins within insoluble inclusion bodies.

Purification of active Escherichia coli ribosome recycling factor (RRF) from an osmo-regulated expression system

Ribosome release factor (RRF) from Escherichia coli was overproduced from an osmo-expression vector. More than 40% of cell protein was RRF after 6 h of induction. A purification scheme is described that produced 50 mg of RRF from an initial culture of 2 L. The recycling time for ribosomes synthesising the tripeptide fMet-Phe-Leu in vitro in the absence of RF3 was reduced from 40 to 15 s by the addition of purified 1.5 microM RRF.

Strategies for achieving high-level expression of genes in Escherichia coli

Progress in our understanding of several biological processes promises to broaden the usefulness of Escherichia coli as a tool for gene expression. There is an expanding choice of tightly regulated prokaryotic promoters suitable for achieving high-level gene expression. New host strains facilitate the formation of disulfide bonds in the reducing environment of the cytoplasm and offer higher protein yields by minimizing proteolytic degradation. Insights into the process of protein translocation across the bacterial membranes may eventually make it possible to achieve robust secretion of specific proteins into the culture medium. Studies involving molecular chaperones have shown that in specific cases, chaperones can be very effective for improved protein folding, solubility, and membrane transport. Negative results derived from such studies are also instructive in formulating different strategies. The remarkable increase in the availability of fusion partners offers a wide range of tools for improved protein folding, solubility, protection from proteases, yield, and secretion into the culture medium, as well as for detection and purification of recombinant proteins. Codon usage is known to present a potential impediment to high-level gene expression in E. coli. Although we still do not understand all the rules governing this phenomenon, it is apparent that "rare" codons, depending on their frequency and context, can have an adverse effect on protein levels. Usually, this problem can be alleviated by modification of the relevant codons or by coexpression of the cognate tRNA genes. Finally, the elucidation of specific determinants of protein degradation, a plethora of protease-deficient host strains, and methods to stabilize proteins afford new strategies to minimize proteolytic susceptibility of recombinant proteins in E. coli.

Formation of recombinant proteins in Escherichia coli under control of a nitrogen regulated promoter at low and high cell densities

The use of a modified Escherichia coli glnAP2 promoter results in the formation of both homologous and heterologous, cytoplasmic and periplasmic recombinant proteins in a nitrogen concentration dependent manner. As in the E. coli nitrogen regulatory system, glnAP2 controlled gene expression is induced when ammonium concentration in the growth medium is below 1 mM (nitrogen limitation), otherwise only extremely low expression of recombinant genes is observed. Both high cell density cultivations (HCDC) and low cell density cultivations (LCDC) gave similar results for inducibility and formation of the following recombinant proteins: chloramphenicol-acetyltransferase, phosphorylcholine binding mini-antibodies (scFv-dhlx of McPC603) and K1-streptokinase. Recombinant proteins were formed in quantities of about 2-3% of total cellular protein. At low cell densities, slightly higher quantities resulted under partial nitrogen limitations than under total nitrogen limitation. In contrast, high cell density cultivations resulted in lower product concentrations at partial nitrogen limitation compared with total nitrogen limitation. These lowered product concentrations were probably due to the very high amounts of K+ or Na+ ions which accumulated during pH-regulation, thereby disturbing growth. HCDC under partial nitrogen limitation decreased proteolysis of recombinant proteins, therefore reduced amounts of proteases are considered to be responsible.

Osmo-expression and fast two-step purification of Escherichia coli translation termination factor RF-3

The gene for the translation termination factor RF-3 in Escherichia coli has recently been cloned and sequenced. Only small amounts of the protein have been purified until now, not sufficient for detailed investigation of the structure and function of this factor. For such studies, we have developed an overexpression system and a purification procedure suitable for large quantities of RF-3. The gene prfC was cloned into the osmo-inducible plasmid pOSEX3 and subsequently transformed into the E. coli strain MKH13. The expression of prfC in this plasmid, which is under the control of the osmotic pressure in the growth medium, leads to a level of RF-3 more than 100-times higher than that in wild-type cells. Using a new two-step FPLC protein purification procedure consisting of ion-exchange chromatography on Q-Sepharose FF and S-Sepharose HP, we obtain 220 mg pure RF-3 from 10 g overproducing cells, corresponding to 55 mg RF-3/l medium. The identity of the purified protein was confirmed by matrix-assisted laser desorption/ionisation mass spectrometry of tryptolytic fragments and by N-terminal amino acid sequencing. The activity of the purified factor was tested in vitro by measuring the stimulation of RF-2 dependent formylmethionine release from a ribosomal termination complex and the binding capacity of GTP and GDP. All assays showed that the purified RF-3 was highly active with a specific activity of approximately 2000 units/mg.