the-multifaceted-benefits-of-protein-co-expression-in-escherichia-coli

The Multifaceted Benefits of Protein Co-expression in <em>Escherichia coli</em>

We report here that the expression of protein complexes in vivo in Escherichia coli can be more convenient than traditional reconstitution experiments in ...

University of Bologna

University of Firenze

Extremely stable water-in-oil macroemulsions have been obtained by dispersing water in isooctane in the presence of lecithin. Either prokaryotic (Escherichia coli) and eukaryotic (Saccharomyces cerevisiae and Rhodotorula minuta) cells hosted in these water-in-oil macroemulsions are viable for weeks despite the consistent excess of organic solvent (ranging from 70 to 84%, v/v) in these ternary systems. Conjugation occurs upon mixing macroemulsions containing F(+) or F(-) Escherichia coli strains, indicating consistent mass transfer between the water droplets. Populations of yeasts hosted in water-in-oil macroemulsion feature a higher frequency of cells aggregation when compared with the corresponding populations suspended in homogeneous aqueous media.

Water-in-oil macroemulsions sustain long-term viability of microbial cells in organic solvents.

Chromosome replication in Escherichia coli is accomplished by the multimeric enzyme DNA polymerase III; the relevance, in vivo, of the epsilon subunit (encoded by dnaQ) for processivity and fidelity of DNA polymerase III has been evaluated. To this aim, dnaQ has been conditionally silenced by means of in vivo expression of different antisense RNAs. Unexpectedly, the presence of the Shine-Dalgarno sequence is essential for the effectiveness of antisense constructs. Silencing of dnaQ induces a severe decrease in growth rate not paralleled by high mutation frequencies, suggesting that the epsilon subunit primarily affects the processivity of DNA polymerase III.

Silencing of the gene coding for the epsilon subunit of DNA polymerase III slows down the growth rate of Escherichia coli populations.

The Escherichia coli gene dnaQ coding for the epsilon subunit of DNA polymerase III was suppressed in vivo via antisense RNAs. To this aim, different fragments of dnaQ were cloned in reverse orientation into the pBAD-HisB vector or into pT3T7, and the corresponding antisense RNAs were conditionally expressed in vivo. Antisense transcripts featuring fast hybridization in vitro with dnaQ mRNA but lacking stability in vivo did not suppress the target gene. Moreover, the in vivo concentration of an antisense transcript was positively correlated to its silencing effectiveness.

Efficient silencing of the gene coding for the epsilon subunit of DNA polymerase III in Escherichia coli is triggered by antisense RNAs featuring stability in vivo.

Antisense RNA molecules are powerful tools for controlling the expression of specific genes but their use in prokaryotes has been limited by their unpredictable antisense effectiveness. Moreover, appreciation of the molecular mechanisms associated with silencing in bacteria is still restricted. Here we report our attempts to define an effective antisense strategy in E. coli, and to dissect the observed silencing process. Antisense constructs complementary to different regions of lacZ were investigated, and silencing was observed exclusively upon expression of antisense RNA hybridising the 5'UTR of lac messenger. The level of lacZ mRNA was reduced upon expression of this antisense construct, and the silencing competence was found to be closely associated with its stability. These observations may help in the design of antisense molecules directed against prokaryotic genes.

Artificial antisense RNAs silence lacZ in E. coli by decreasing target mRNA concentration.

The C-terminal region of the proofreading subunit (epsilon) of Escherichia coli DNA polymerase III is shown here to be labile and to contain the residues (identified between F187 and R213) responsible for association with the polymerase subunit (alpha). We also identify two alpha-helices of the polymerase subunit (comprising the residues E311-M335 and G339-D353, respectively) as the determinants of binding to epsilon. The C-terminal region of epsilon is degraded by the ClpP protease assisted by the GroL molecular chaperone, while other factors control the overall concentration in vivo of epsilon. Among these factors, the chaperone DnaK is of primary importance for preserving the integrity of epsilon. Remarkably, inactivation of DnaK confers to Escherichia coli inviable phenotype at 42 degrees C, and viability can be restored over-expressing epsilon. Altogether, our observations indicate that the association between epsilon and alpha subunits of DNA polymerase III depends on small portions of both proteins, the association of which is controlled by proteolysis of epsilon. Accordingly, the factors catalysing (ClpP, GroL) or preventing (DnaK) this proteolysis exert a crucial checkpoint of the assembly of Escherichia coli DNA polymerase III core.

Proteolysis of the proofreading subunit controls the assembly of Escherichia coli DNA polymerase III catalytic core.

The mustard trypsin inhibitor 2, MTI2, was expressed in Escherichia coli. A specific procedure for its production and purification is described. The recombinant protein was recovered by protein extraction from the insoluble fraction, then renatured and purified by ion exchange and gel filtration chromatography. Finally, the inhibitory activity against trypsin was also determined.

Expression and purification of the recombinant mustard trypsin inhibitor 2 (MTI2) in Escherichia coli.

The overexpression of four different interferons, i.e., murine interferon alpha1 and human interferons alpha1, alpha 8, and alpha 21 was challenged in Escherichia coli. Synthetic genes coding for these interferons were designed, assembled, and cloned into the vector pET9a (using the NdeI and BamHI sites), placing interferon expression under the control of phage T7 promoter. Despite an intensive screening for optimal culture conditions, no interferon synthesis was observed using overexpression systems based on the regulatory elements of lac operon (e.g., in E. coli BL21DE3). On the contrary, high levels of interferon expression were detected in E. coli BL21AI, which chromosome contains the gene coding for phage T7 RNA polymerase under the control of the araBAD promoter. To analyze the reasons of this striking difference, the molecular events associated with the lack of interferon expression in E. coli BL21DE3 were studied, and murine interferon alpha1 was chosen as a model system. Surprisingly, it was observed that this interferon represses the synthesis of T7 RNA polymerase in E. coli BL21DE3 and, in particular, the expression of lac operon. In fact, by determining beta-galactosidase activity in E. coli BL21AI, a significantly lower LacZ activity was observed in cells induced to interferon synthesis.

The regulatory elements of araBAD operon, contrary to lac-based expression systems, afford hypersynthesis of murine, and human interferons in Escherichia coli.

Silencing of the lacZ gene in Escherichia coli was attempted by means of the expression of antisense RNAs (asRNAs) in vivo. A short fragment of lacZ was cloned into the pBAD expression vector, in reverse orientation, using the EcoRI and PstI restriction sites. This construct (pBAD-Zcal1) was used to transform E. coli cells, and the antisense transcription was induced simply by adding arabinose to the culture medium. We demonstrated that the Zcal1 asRNA effectively silenced lacZ using β-galactosidase activity determinations, SDS-PAGE, and Western blotting. Because the concentration of the lac mRNA was always high in cells that expressed Zcal1, we hypothesize that this antisense acts by inhibiting messenger translation. Similar analyses, performed with a series of site-specific Zcal1 mutants, showed that the Shine-Dalgarno sequence, which is conferred by the pBAD vector, is an essential requisite for silencing competence. Indeed, the presence of the intact Shine-Dalgarno sequence positively affects asRNA stability and, hence, silencing effectiveness. Our observations will contribute to the understanding of the main determinants of silencing as exerted by asRNAs as well as provide useful support for the design of robust and efficient prokaryotic gene silencers.

Shine-Dalgarno sequence enhances the efficiency of lacZ repression by artificial anti-lac antisense RNAs in Escherichia coli.

Two systems for the co-expression of proteins in Escherichia coli were designed and constructed. The first system relies on the new vector, pGOOD, which is compatible with ColE1-type plasmids and sustains efficient co-expression of soluble protein complexes. The second system is based on the pGOOD1 vector (a derivative of pGOOD), useful for the production of toxic proteins, whose synthesis can be regulated by the co-expressed LacI repressor.

pGOODs: new plasmids for the co-expression of proteins in Escherichia coli.

The expression of the recombinant diphtheria toxin mutant CRM197 in bacteria other than Corynebacterium diphtheriae has proven to be difficult. Here we propose a new and alternative procedure for the production of full-length CRM197 in Escherichia coli. The present study relates specifically to the expression of an artificial sequence and to a method for the isolation and purification of the corresponding protein. In particular, a synthetic gene coding for CRM197, bearing a short histidine tag and optimized for E. coli codon usage, was cloned in the pET9a vector. Accordingly, the over-expression of the protein was simply induced with arabinose in E. coli BL21AI. The recombinant protein was insoluble and always found inside protein aggregates, which were solubilised using urea. Surprisingly, the expression of CRM197, devoid of the short tag, always failed. Following a refolding step, the his-tagged CRM197 was purified by affinity and gel-filtration chromatography and the purity of the final preparation reached 95%. Interestingly, the recombinant protein features DNase activity, indicating that the presence of the tag is not affecting its biochemical properties. However, the removal of the synthetic tag could be easily obtained by incubating the target protein with a proper quantity of a commercial enterokinase.

Overexpression and purification of the recombinant diphtheria toxin variant CRM197 in Escherichia coli.

Escherichia coli DNA polymerase III holoenzyme (HE) contains a core polymerase consisting of three subunits: α (polymerase), ε (3'-5' exonuclease), and θ. Genetic experiments suggested that θ subunit stabilizes the intrinsically labile ε subunit and, furthermore, that θ might affect the cellular amounts of Pol III core and HE. Here, we provide biochemical evidence supporting this model by analyzing the amounts of the relevant proteins. First, we show that a ΔholE strain (lacking θ subunit) displays reduced amounts of free ε. We also demonstrate the existence of a dimer of ε, which may be involved in the stabilization of the protein. Second, θ, when overexpressed, dissociates the ε dimer and significantly increases the amount of Pol III core. The stability of ε also depends on cellular chaperones, including DnaK. Here, we report that: (i) temperature shift-up of ΔdnaK strains leads to rapid depletion of ε, and (ii) overproduction of θ overcomes both the depletion of ε and the temperature sensitivity of the strain. Overall, our data suggest that ε is a critical factor in the assembly of Pol III core, and that this is role is strongly influenced by the θ subunit through its prevention of ε degradation.

Stabilization of the Escherichia coli DNA polymerase III ε subunit by the θ subunit favors in vivo assembly of the Pol III catalytic core.

A coupled enzyme assay able to monitor the kinetics of reactions catalyzed by phosphate- or pyrophosphate-releasing enzymes is presented here. The assay is based on the concerted action of inorganic pyrophosphatase (PPase), purine nucleoside phosphorylase (PNPase), and xanthine oxidase (XOD). In the presence of phosphate, PNPase catalyzes the phosphorolysis of inosine, generating hypoxanthine, which is oxidized to uric acid by XOD. The uric acid accordingly formed can be spectrophotometrically monitored at 293 nm, taking advantage of a molar extinction coefficient which is independent of pH between 6 and 9. The coupled assay was tested using DNA polymerases as a model system. The activity of Klenow enzyme was quantitatively determined, and it was found in agreement with the corresponding activity determined by traditional methods. Moreover, the continuous coupled assay was used to determine Km and Vmax of Klenow enzyme, yielding values in good agreement with previous observations. Finally, the coupled assay was also used to determine the activity of partially purified DNA polymerases, revealing its potential use to monitor purification of phosphate- or pyrophosphate-releasing enzymes.

Continuous enzyme-coupled assay of phosphate- or pyrophosphate-releasing enzymes.

The assembly from modular parts is an efficient approach for creating new devices in Synthetic Biology. In the "bottom-up" designing strategy, modular parts are characterized in advance, and then mathematical modeling is used to predict the outcome of the final device. A prerequisite for bottom-up design is that the biological parts behave in a modular way when assembled together. We designed a new synthetic device for post-transcriptional regulation of gene expression and tested if the outcome of the device could be described from the features of its components. Modular parts showed unpredictable behavior when assembled in different complex circuits. This prevented a modular description of the device that was possible only under specific conditions. Our findings shed doubts into the feasibility of a pure bottom-up approach in synthetic biology, highlighting the urgency for new strategies for the rational design of synthetic devices.

Article	Year
Water-in-oil macroemulsions sustain long-term viability of microbial cells in organic solvents. Biotechnology and bioengineering\| PubMed ID: 12474255	2003
Silencing of the gene coding for the epsilon subunit of DNA polymerase III slows down the growth rate of Escherichia coli populations. FEBS letters\| PubMed ID: 12832057	2003
Efficient silencing of the gene coding for the epsilon subunit of DNA polymerase III in Escherichia coli is triggered by antisense RNAs featuring stability in vivo. FEMS microbiology letters\| PubMed ID: 17343677	2007
Artificial antisense RNAs silence lacZ in E. coli by decreasing target mRNA concentration. BMB reports\| PubMed ID: 18755071	2008
Proteolysis of the proofreading subunit controls the assembly of Escherichia coli DNA polymerase III catalytic core. Biochimica et biophysica acta\| PubMed ID: 19635595	2009
Expression and purification of the recombinant mustard trypsin inhibitor 2 (MTI2) in Escherichia coli. Journal of bioscience and bioengineering\| PubMed ID: 19716515	2009
The regulatory elements of araBAD operon, contrary to lac-based expression systems, afford hypersynthesis of murine, and human interferons in Escherichia coli. Biotechnology progress\| PubMed ID: 19731316	2009
Shine-Dalgarno sequence enhances the efficiency of lacZ repression by artificial anti-lac antisense RNAs in Escherichia coli. Journal of bioscience and bioengineering\| PubMed ID: 20646957	2010
pGOODs: new plasmids for the co-expression of proteins in Escherichia coli. Biotechnology letters\| PubMed ID: 21516313	2011
Overexpression and purification of the recombinant diphtheria toxin variant CRM197 in Escherichia coli. Journal of biotechnology\| PubMed ID: 21889551	2010
Stabilization of the Escherichia coli DNA polymerase III ε subunit by the θ subunit favors in vivo assembly of the Pol III catalytic core. Archives of biochemistry and biophysics\| PubMed ID: 22546509	2012
Continuous enzyme-coupled assay of phosphate- or pyrophosphate-releasing enzymes. BioTechniques\| PubMed ID: 23030062	2012
A synthetic post-transcriptional controller to explore the modular design of gene circuits. ACS synthetic biology\| PubMed ID: 23651154	2012

Alessandra Stefan

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