Light-induced gene expression with photocaged IPTG for induction profiling in a high-throughput screening system
© Wandrey et al. 2016
Received: 4 December 2015
Accepted: 13 April 2016
Published: 23 April 2016
Inducible expression systems are frequently used for the production of heterologous proteins. Achieving maximum product concentrations requires induction profiling, namely the optimization of induction time and inducer concentration. However, the respective experiments can be very laborious and time-consuming. In this work, a new approach for induction profiling is presented where induction in a microtiter plate based cultivation system (BioLector) is achieved by light using photocaged isopropyl β-d-1-thiogalactopyranoside (cIPTG).
A flavin mononucleotide-based fluorescent reporter protein (FbFP) was expressed using a T7-RNA-polymerase dependent E. coli expression system which required IPTG as inducer. High power UV-A irradiation was directed into a microtiter plate by light-emitting diodes placed above each well of a 48-well plate. Upon UV irradiation, IPTG is released (uncaged) and induces product formation. IPTG uncaging, formation of the fluorescent reporter protein and biomass growth were monitored simultaneously in up to four 48-well microtiter plates in parallel with an in-house constructed BioLector screening system. The amount of released IPTG can be gradually and individually controlled for each well by duration of UV-A exposure, irradiance and concentration of photocaged IPTG added at the start of the cultivation. A comparison of experiments with either optical or conventional IPTG induction shows that product formation and growth are equivalent. Detailed induction profiles revealed that for the strain and conditions used maximum product formation is reached for very early induction times and with just 6–8 s of UV-A irradiation or 60–80 µM IPTG.
Optical induction and online monitoring were successfully combined in a high-throughput screening system and the effect of optical induction with photocaged IPTG was shown to be equivalent to conventional induction with IPTG. In contrast to conventional induction, optical induction is less costly to parallelize, easy to automate, non-invasive and without risk of contamination. Therefore, light-induced gene expression with photocaged IPTG is a highly advantageous method for the efficient optimization of heterologous protein production and has the potential to replace conventional induction with IPTG.
High productivity in heterologous protein production is achieved by optimization of strains, culture conditions and process related parameters. Inducible expression systems are applied to separate the cultivation into an initial growth phase for unimpeded biomass formation and a subsequent production phase where growth is impeded while metabolic resources are shifted towards product formation. The switch from growth to production phase (induction of target gene expression) can be achieved by addition of small chemical inducer molecules among which isopropyl β-d-1-thiogalactopyranoside (IPTG) is the most popular choice and widely applied, especially in lab scale. The amount of IPTG and the time when it is added during cultivation are crucial parameters for process performance [1, 2]. If induction is performed too early, biomass concentration is insufficient for reasonable protein production; if it is performed too late, not enough substrate is left for product formation. If IPTG concentration is not sufficiently high, cells may not reach their full expression potential; however, if IPTG concentration exceeds a critical limit, a balanced metabolism cannot be maintained and toxic effects might be observed [3–5].
The induction optimum depends on the respective strain, expression plasmid and target gene [2, 6]. Although general recommendations (i.e. ‘induce with 1000 µM IPTG at OD 0.6-1.2′ [1, 2]) commonly yield decent results and mathematical models for induction parameters have been described [5, 7, 8], the optimum parameters for each process still have to be verified in time-consuming experiments. Hence, microtiter plate based screening systems that allow parallelized and cost-effective experiments in small scale have successfully been applied [9, 10]. However, the addition of IPTG solution to small scale cultures is associated with some drawbacks which are usually not discussed in literature. For induction, either cumbersome manual intervention at each time of induction or cost-intensive investment into an automatized liquid handling system is required. Before addition of IPTG, the microtiter plate shaking is usually stopped which can result in an oxygen limitation . Then, the sterile barrier on top of the microtiter plate is pierced or removed which necessitates precautions to avoid contamination . The addition of an IPTG containing solution dilutes the cultures and additional pipetting is required if different amounts of IPTG have to be added to different wells but the dilution effect is to be kept constant. If the sterile barrier is pierced for pipetting, the barrier might not seal the well completely anymore once the pipettes or syringes are retracted. This can result in increased evaporation which affects results. If the sterile barrier is instead removed for pipetting, it has to be replaced either manually or by additional automated equipment, once a pipetting step is completed.
This complex procedure of adding IPTG solution is especially problematic when different clones of a clone library are to be compared regarding heterologous protein production. The clones should not be induced at the same time but when they reach the same optical density. Each time a single clone reaches the induction criterion the invasive induction procedure is activated which interrupts the measurement and affects the growth of all clones . With ever increasing numbers of parallel cultivations individual induction with IPTG solution reaches its limits even with automated pipetting systems. Instead, a parallelized and less invasive induction method for small scale cultivations is highly desirable.
Non-invasive optical measuring techniques have already been applied extensively for online monitoring [11–13]. In this study, it was investigated whether non-invasive optical induction could be practical as well . In 2007, Young and Deiters attached the photo-removable group 6-nitropiperonal to IPTG yielding a photocaged IPTG derivative (cIPTG) which serves as a dormant IPTG reservoir . As long as the photocage is attached, cIPTG cannot bind to the lac repressor and no target gene is expressed. Upon UV-A irradiation IPTG is uncaged and can act as an inducer. Based on this concept, a device for individual optical induction of each well in a microtiter plate was constructed. A high-throughput screening system was then used for detailed induction profiling and to test whether optical induction with cIPTG could replace conventional induction with IPTG.
Results and discussion
LED array for optical induction
Online monitoring with BioLector screening system
The space below the microtiter plate is not affected by the illumination from above. Therefore, non-invasive online fluorescence measurements according to the BioLector design [11, 17] were performed through the transparent bottom using an in-house constructed BioLector prototype. A fluorescence excitation wavelength is chosen from the white spectrum of a xenon lamp by an excitation monochromator inside the fluorescence spectrometer and the light is guided to the microtiter plate through one branch of a Y-shaped optical fibre bundle. Through the other branch the resulting scattered light and fluorescence emission is guided back to the spectrometer where the light passes the emission monochromator and reaches the detector. The optical fibre bundle is moved by a robotic arm which allows measuring each culture in rapid succession without stopping the shaking movement of the well plate. Up to four microtiter plates in parallel can be monitored with an acquisition rate of one to two data points per second. In the most basic setup this device is used to gather quasi-continuous data on biomass growth and fluorescent protein formation by monitoring suitable excitation/emission wavelength combinations.
Identification of additional fluorescence signal
The fluorescence emission spectrum of caged IPTG ester intermediates that were isolated by HPLC and identified by NMR (Additional files 1, 2) are shown in Fig. 3b. The normalized emission spectrum with maximum emission at 417 nm (λex = 330 nm) fits in well with the emission spectrum observed in vivo after photo-cleavage. Besides the ester intermediates the isolated nitropiperonal uncaging product showed a similar emission spectrum. Therefore, the observed fluorescence might be caused by the caged IPTG ester intermediates, the nitropiperonal uncaging product or a combination of both. Fluorescence intensities are not compared directly since the emission spectra were obtained with different devices and the recovery rate of the HPLC method for caged IPTG ester intermediate isolation was not determined. However, the course of the fluorescence intensity during the cultivation can still be valuable to characterize the uncaging reaction.
Characterization of optical induction with cIPTG
Online fluorescence spectroscopy is already a method frequently applied to investigate other uncaging processes . In Fig. 4b the ester intermediate and NP-uncaging product fluorescence measured directly after irradiation is given as a function of duration of exposure (dUV-A = 0–60 s). With longer duration of exposure more cIPTG is uncaged and higher ester intermediate concentrations are detected. Since the substrate of the uncaging reaction (cIPTG) is depleted during the reaction the reaction rate decreases accordingly. The data are in very good accordance with first-order kinetics (equations and solid lines in Fig. 4b, R2 > 0.995). HPLC measurements confirmed the photo-uncaging of cIPTG as a function of UV-A exposure duration (Additional file 4). As to be expected for a photochemical reaction, the reaction rate constant is dependent on irradiance. This is shown by a reduction of irradiance by 75 % from 52 to 13 mW/cm2, resulting in a 66 % slower reaction (black triangles, Fig. 4b). The ester intermediate concentration is also influenced by the amount of cIPTG added at the beginning of the cultivation. A reduction of the initial cIPTG concentration by 87.5 % from 400 µM to 50 µM cIPTG reduces the ester intermediate signal by 63 % (green diamonds, Fig. 4b). These experiments show that three parameters can be used to control the amount of IPTG that is uncaged by optical induction: duration of UV-A exposure, irradiance and initial concentration of cIPTG. In the following experiments only duration of UV-A exposure (dUV-A = 0–60 s) is used to control the amount of released IPTG while irradiance and initial cIPTG concentration are kept constant (52 mW/cm2, 400 µM cIPTG).
The FbFP signal also shows that the rate of product formation can be increased gradually with either increasing duration of UV-A exposure or increasing IPTG concentration. Both induction methods allow fine-tuning the initial product formation rate in the same range and to the same maximum. In this experiment, the maximum initial product formation rate is reached with either about 30 s UV-A or 250 µM IPTG.
A distinct advantage of the constructed UV-A LED array is that optical induction can obviously be achieved within seconds where previously several minutes of irradiation were required for uncaging [15, 19]. The very short induction times are most probably a result of the high irradiance of 52 mW/cm2. Since the strong UV-A irradiation applied in our design could be potentially phototoxic we tested the influence on non-induced cultures. For exposure durations of up to 60 s, no influence on biomass growth was observed during the exponential phase and only minute deviations were detected in the stationary phase (Additional file 5). Therefore, phototoxicity due to UV-A irradiation is of no concern for the short UV-A exposure times (dUV-A = 0–40 s) applied in the subsequent experiments.
Firstly, increasing inducer concentrations reduce growth rates and delay the time to reach final biomass concentration (Fig. 6a, e). For example, a non-induced culture reaches the maximum biomass signal (scattered light intensity) after 18 h while a culture induced with 400 µM IPTG reaches the maximum 19 h later (Fig. 6a, time of induction: 7.5 h). A growth delay of about 17 h is observed when 400 µM of cIPTG are irradiated with UV-A light for 40 s at the same time point (Fig. 6e).
Secondly, a delay in growth is also observed when inductions are performed earlier rather than later (Fig. 6b, f). For example, the highest biomass signal is reached after about 40 h if the induction is performed 1.5 h into the cultivation with either 400 µM IPTG (Fig. 6b) or 400 µM cIPTG and 40 s of UV-A light (Fig. 6f). For later inductions this effect is gradually less pronounced because the cultivation has already progressed further. Decreased growth rates are caused by the drain of metabolites into heterologous protein formation (“metabolic burden”) and models to correlate growth rate and heterologous protein formation have been developed [4, 24, 25].
Thirdly, initial product formation is faster with higher inducer concentrations (Fig. 6c, g; a more detailed view is provided in Additional file 6). However, over the course of the following production phase the rate decreases slightly with more pronounced decreases for higher IPTG concentration (150–1000 µM). This decrease might be attributed to overloading protein synthesis capabilities with gratuitous mRNA coding for the target protein and thereby, in the long run, decreasing synthesis capability. In contrast, cultures induced with less IPTG (25–100 µM) and lower initial product formation rates are less strained and (as visible from the biomass signal) still exhibit growth. Therefore, their production rates can still increase and eventually surpass those of more strongly induced cultures. High product concentrations at the end of the cultivation are not reached with high IPTG concentrations, but rather with moderate values of e.g. 75 to 100 µM (Fig. 6c) or 8–10 s UV-A light (Fig. 6g) (when the induction is preformed 7.5 h after the start of the cultivation).
Fourthly, product formation is also influenced by the time of induction. If, for example, the induction is performed with rather high IPTG concentrations (400 µM, Fig. 6d) or long exposures (40 s, Fig. 6h), product concentration is highest, if the induction is performed 9 h after inoculation. For earlier induction times not enough cells are present to produce high amounts of protein, for later induction times not enough substrate is left.
Figure 7 demonstrates that induction conditions optimized with either method can be applied interchangeably. The transfer of an optimized operation point including time of induction and inducer concentration or duration of UV-A exposure, respectively, is straight-forward: Time of induction is about equivalent and duration of UV-A exposure is, in first approximation, linearly correlated to IPTG concentration with 10 s of UV-A irradiation being equivalent to 100 µM IPTG under the applied conditions (52 mW/cm2, 400 µM cIPTG). HPLC–UV measurements confirmed that 116.2 µM (±29.4 µM) cIPTG were uncaged under these conditions (Additional file 4). However, a direct quantification of the subsequently released IPTG was not possible due the detection being more difficult. Based on the reaction scheme by Young and Deiters the amount of cIPTG uncaged to ester intermediates and the amount of subsequently released IPTG are expected to be equivalent (Fig. 3a). Further experiments are required to independently verify the amount of released IPTG. Fernández et al. developed an HPLC–MS method for the direct quantification of intracellular IPTG in the required µM range . Further experiments would also be required to construct a more detailed model that describes the amount of released IPTG as a function of all optical parameters (UV-A exposure duration, irradiance, cIPTG concentration) and first-order kinetics should be considered for the impact of UV-A exposure duration as presented in the fits in Fig. 4b and Additional file 4.
The presented induction profiles are in accordance with data on a closely related strain (E. coli BL21(DE3)/pRhotHi-2-EcFbFP) cultivated in the same medium, previously published by Huber et al. . Since in this work four microtiter plates were monitored in parallel instead of just one, induction profiles with more data points and higher resolution could be obtained. The importance of detailed induction profiling with high resolution can be exemplified by deviations from the optimum IPTG concentration in the horizontal regime. Inductions with 50 or 150 µM IPTG at 2.5 h yield only 60 % of the protein that is produced after induction with 75 µM IPTG. The still prevalent induction with 1000 µM IPTG in the early exponential growth phase  (in our case after approx. 9–10 h) is also far from ideal to achieve high target protein concentrations with the strain used in this work. The highest protein concentration after an induction with 1000 µM IPTG is achieved when the culture is induced after 10 h. It yields only 70 % of the target protein that is achieved when the culture is induced with 75 µM IPTG after 2.5 h. Thus, overinduction with too much IPTG not only wastes a cost-intensive chemical but also reduces product concentration. An efficient process with high product concentration can only be reached when induction parameters are optimized for each individual strain and target protein. Light-induced gene expression with photocaged IPTG applied in a high-throughput system allows performing this optimization much more easily than before.
An LED array allowing for individual illumination of each well of a 48-well microtiter plate was constructed and successfully applied for light-induced gene expression based on photocaged IPTG. The fluorescence of the reporter protein FbFP was measured online in up to four microtiter plates in parallel. Irradiating photocaged IPTG resulted in an additional distinct fluorescence signal which could be assigned to photocaged IPTG ester intermediates and the nitropiperonal uncaging product. This signal was subsequently applied to characterize the uncaging reaction. In the future, it might also be utilized to control more advanced induction strategies. As an example, the IPTG concentration profile over time which usually follows a step function (addition or release at one time point) could be replaced by fine-tuned profiles with continuous inducer release depending on current biomass concentration or growth rate [27–29]. The combination of an LED array and a BioLector screening system could also be used to study gene expression and protein production controlled by chemically distinct photocaged compounds or by photoreceptors [30–32].
In this study, we compared optical induction with photocaged IPTG to conventional induction with manual addition of IPTG solutions and showed that both methods yield essentially equivalent results under the applied conditions. This means that induction parameters which can be optimized easily with optical induction can later be transferred to conventional induction protocols for e.g. stirred tank bioreactors. Optical induction can be parallelized easily as well and it has the distinct advantage of being less invasive as the shaking motion of the microtiter plate is not stopped. This is of great importance since even short oxygen limitation influences expression of genes involved in central metabolism and can lead to a complete loss of productivity in organisms sensitive to sudden oxygen limitation [33, 34]. Also, optical measurements which are affected by a change in the shaking motion can be continued throughout the induction. Furthermore, the sterile barrier is not compromised by optical induction which might prove very convenient for strictly anaerobic cultivations or cell culture applications . In conclusion, light-induced induction shows several advantages and can readily replace conventional induction for screening purposes in microtiter plates.
Microorganism and target protein
The strain Escherichia coli Tuner(DE3)/pRhotHi-2-LacI-EcFbFP was used for all experiments. Except for the target protein it is identical to a strain previously used to study light-induced gene expression by Binder et al. . It offers several advantageous characteristics for this study: Because of the permease deficiency (lacY −) of E. coli Tuner(DE3) IPTG can only enter the cell via concentration dependent diffusion. Therefore, an unimodal induction response homogenously distributed over the entire population can be expected [19, 36]. The low-copy number plasmid pRhotHi-2 carrying a T7 promoter offers potential for high-level expression . Additional expression of the repressor LacI reduces the basal expression which allows easier quantification at low induction levels . The flavin-based fluorescent protein FbFP was chosen as the target protein because its fluorescence develops immediately after translation and no maturation step depending on intracellular oxygen concentration is required as for proteins of the GFP-family . For better expression, a sequence optimized for E. coli codon bias was used .
The construction of expression vectors and recombinant DNA techniques were carried out in E. coli DH5α  as described by Sambrook et al. . The EcFbFP reporter gene was isolated from pRhotHi-2-EcFbFP [37, 41] and inserted into target vector pRhotHi-2-LacI via NdeI/XhoI restriction, yielding the final construct pRhotHi-2-LacI-EcFbFP.
Prior to induction experiments two sequential precultivation steps were performed. The first precultivation step was done with 10 mL complex TB medium (5 g/L glycerol, 24 g/L yeast extract, 12 g/L tryptone, 12.54 g/L K2HPO4, 2.3 g/L KH2PO4; all ingredients from Roth, Germany) in 250 mL shake flasks. Shake flasks were inoculated to an initial optical density of 0.1 (OD600) from cryogenically preserved cultures and cultivated on an orbital shaker (LS-X, Kuhner, Switzerland) at 350 rpm with a shaking diameter of 50 mm for 5 h at 37 °C. For the second precultivation step 10 mL of a modified Wilms-MOPS minimal medium  (20 g/L glucose, 6.98 g/L (NH4)2SO4, 3 g/L K2HPO4, 2 g/L Na2SO4, 41.85 g/L (N-morpholino)-propanesulfonic acid (MOPS), 0.5 g/L MgSO4·7H2O, 0.01 g/L thiamine hydrochloride, 1 mL/L trace element solution [0.54 g/L ZnSO4·7H2O, 0.48 g/L CuSO4·5H2O, 0.3 g/L MnSO4·H2O, 0.54 g/L CoCl2·6H2O, 41.76 g/L FeCl3·6H2O, 1.98 g/L CaCl2·2H2O, 33.4 g/L Na2EDTA (Titriplex III)]) were used. The pH-value was adjusted to 7.5 with NaOH. Shake flasks were again inoculated to an initial optical density of 0.1 (OD600) and placed on an orbital shaker at 350 rpm with a shaking diameter of 50 mm. After cultivation for 9 h at 30 °C the second precultures reached the early exponential growth phase and the main culture in microtiter plates was inoculated. In all cultivation steps 50 µg/mL kanamycin sulfate was added.
Microtiter plate cultivations
Microtiter plate cultivations for induction experiments were conducted in 48-well FlowerPlates (MTP-48-B, lot 1404 & 1509, m2p-labs, Germany). As in the second precultivation step Wilms-MOPS mineral medium was used. Wilms-MOPS medium is suited to achieve high cell densities and high heterologous protein concentrations . As demonstrated elsewhere, optical induction with cIPTG is not restricted to mineral media and can also be performed in complex media like LB [15, 19]. LB medium was not used here because it is restricted to low cell densities since its nitrogen-containing complex compounds are used as energy source which results in the formation of ammonium and alkalization . Other complex media like TB were not used because lot-to-lot variations in raw materials have been reported to effect reproducibility in induced cultures . Each well was filled with 800 µL Wilms-MOPS medium from a master mix inoculated to an initial optical density of 0.1 (OD600). Plates were sealed with an autoclaved self-adhesive transparent polyolefin sealing foil (900371, HJ-Bioanalytik, Germany) as sterile barrier. The foil reduces evaporation while still allowing sufficient gas transfer. Up to four microtiter plates in parallel were placed on an orbital shaker (ES-X, Kuhner, Switzerland) with a shaking frequency of 1000 rpm and a shaking diameter of 3 mm at 30 °C.
Optical induction with LED array
Nitropiperonal-photocaged IPTG (cIPTG) was synthesized from IPTG and 6-nitropiperonal as previously described . At the beginning of microtiter plate cultivations for optical induction 400 µM cIPTG was added from a 40 mM stock solution in DMSO stored in the dark at −20 °C. An in-house constructed array of 48 high-power UV-A LEDs (LZ1-3x, LED Engin, USA) attached to a heat sink was mounted on top of a microtiter plate resulting in one LED per well to be positioned at a distance of 14 mm in coaxial position (Fig. 1). A mask with cylindrical holes with 11 mm diameter ensures that only the corresponding well is illuminated and no stray light can enter adjacent wells. No induction was observed in wells that were adjacent to illuminated wells but not illuminated themselves. Between heat sink and mask a 3 mm gap is left to allow sufficient gas transfer to and from the wells. When an LED is switched on, UV-A irradiation passes the transparent sterile barrier and reaches the culture where IPTG is uncaged. LEDs are wired in a matrix layout and switched using 14 metal oxide semiconductor field-effect transistors on a driver stage fixed onto the shaking tray next to the microtiter plate. The driver stage is connected to a microcontroller (Arduino Uno R3, Arduino LLC, USA) and controlled via a PC running LabVIEW (LabVIEW v14, National Instruments, USA). LEDs are operated at 700 mA resulting in a high irradiance of at the well bottom (52.7 mW/cm2, λmax = 368 nm) with low well-to-well deviation (SD 3.2 mW/cm2). Irradiance at the position of the well bottom was determined on bottomless microtiter plates with a thermal power sensor (S302C, Thorlabs, Germany). For optical induction experiments cultures were irradiated for 2–60 s. During irradiation a temperature increase of 0.7 K/min occurred which was measured using a rhodamin-based fluorescence method [45, 46] (data not shown). Since uncaging was achieved within 1 min, the temporary temperature increase (<0.7 K) was considered to be within acceptable limits. For one of the experiments performed to characterize photo-uncaging a lower effective irradiance (13 mW/cm2) was used. This was achieved by placing a strip of diffuser foil (White Diffusion LEE216, LEE Filters, USA) directly below the LEDs.
Fluorescence measurements were performed through the transparent bottom of the microtiter plates during cultivation, according to the established BioLector setup [11, 17]. A quartz/quartz multi-mode fiber (LUV 105 µM, LEONI, Germany) is moved sequentially below the wells of four microtiter plates by a Cartesian motion system (CMS, Bosch Rexroth, Germany) to allow quasi-continuous fluorescence measurements on all wells without stopping the shaking movement which might otherwise result in cell sedimentation or oxygen limitation. In contrast to commercially available designs, a spectrofluorometer with excitation/emission monochromators (Fluoromax-4, HORIBA Jobin–Yvon GmbH, Germany) was applied. It enables variation and optimization of excitation/emission wavelength in a range of 200–950 nm. During cultivation cIPTG ester intermediates were excited at a wavelength of λEx = 326 nm and therefore below the maximum excitation wavelength of λEx.max = 335 nm to reduce NADH fluorescence crosstalk. cIPTG ester intermediate fluorescence was measured at λEm = 407 nm. FbFP fluorescence (λEx = 450 nm, λEm = 495 nm) and biomass formation (scattered light at 650 nm) were monitored as well. When measuring the cIPTG ester intermediate fluorescence the excitation and emission slits were set to a bandwidth of 8 nm. The raw intensities measured for FbFP fluorescence and biomass (scattered light) were higher and therefore the slit bandwidth could be reduced to 4 nm. Integration time was set to 600 ms for fluorescence signals and 900 ms for scattered light (biomass). 2D fluorescence spectra of cultures before and after uncaging with UV-A irradiation were obtained by scanning the excitation wavelength from 300 to 600 nm and the emission wavelength from 320 to 600 nm (stepsize: 5 nm) according to a previously published setup . As reference, cIPTG ester intermediates and the nitropiperonal-uncaging product were isolated by HPLC (Additional file 1), identified by NMR (Additional file 2) and fluorescence spectra from 360 to 500 nm were obtained with a plate reader (λEx = 330 nm, Infinite M1000 Pro, Tecan, Switzerland).
Conventional induction with IPTG and optical induction with uncaging of cIPTG were compared in induction experiments. A culture well was either conventionally induced by manually adding IPTG solution with a pipette or optically induced by illumination with the LED array. The two parameters varied were time of induction (in relation to the start of the cultivation, 0.5–16 h) and either IPTG concentration (0–1000 µM) in case of conventional induction or duration of UV-A exposure (0–40 s) in case of optical induction. Conventional induction was achieved by pausing the measurement, stopping the shaker, removing the sealing foil and manually adding 20 µL IPTG solution from a set of sterile stock solutions with a multichannel pipette (Eppendorf, Germany). Then, the sealing foil was replaced and the shaker was started again. For optical induction a cIPTG concentration of 400 µM and a high irradiance of 52.7 mW/cm2 were used. No manual interference was required at all since the LED array was automatically controlled by a LabVIEW script during shaking.
During the induction profiling experiments the microtiter plate supplier (m2p-labs, Germany) changed the manufacturing of the plates’ transparent bottom. According to the supplier, for FlowerPlates with lot numbers 14xx and earlier a 150 µM thin polystyrene foil (158 K, BASF, Germany) was used. In contrast, a 700 µM thick polystyrene foil (Styron 678E, Dow Chemical, USA) was used for plates with lot number 15xx and later. The thicker foil reduced fluorescence and scattered light intensities. Also, the plates with higher lot numbers feature two small opaque spots (intended to take up pH- and oxygen sensor dyes) which increase the scattered light baseline. To allow comparison of cultures on different microtiter plates, data was normalized to the biomass signal (scattered light) of non-induced reference cultures (Additional file 7).
IPTG: isopropyl β-d-1-thiogalactopyranoside; cIPTG: 6-nitropiperonal-photocaged isopropyl β-d-1-thiogalactopyranoside; FbFP: flavin-mononucleotide-based fluorescent reporter protein; T7-RNA-polymerase: ribonucleic acid polymerase from bacteriophage T7; E. coli: Escherichia coli; UV-A: ultraviolet A radiation with a wavelength of 315–400 nm; LED: light-emitting diode; 2D: two-dimensional; EcFbFP: E. coli codon bias-optimized FbFP; HPLC: high-performance liquid chromatography; NMR: nuclear magnetic resonance spectroscopy; GFP: green fluorescent protein; DNA: deoxyribonucleic acid; TB: terrific broth; MOPS: (N-morpholino)-propanesulfonic acid; EDTA: ethylenediaminetetraacetic acid; DMSO: dimethyl sulfoxide; SD: standard deviation; NADH: reduced form of nicotinamide adenine dinucleotide; NP: 6-nitropiperonal; cIPTGe: ester intermediate in the cIPTG photouncaging reaction.
List of symbols
λmax: wavelength with maximum intensity; OD600: optical density at a wavelength of 600 nm; λex,max: excitation wavelength resulting in maximum fluorescence emission; λem,max: wavelength with maximum fluorescence emission; λex, λem: fluorescence excitation and emission wavelength; t1/2: half-life; dUV-A: duration of UV-A exposure; I: irradiance; tinduction: time of induction; cIPTG: IPTG concentration.
GW designed the study, constructed the LED array and BioLector, performed the cultivation experiments and data analysis and drafted the manuscript. CB synthesized the cIPTG, performed the HPLC and NMR experiments and analysis and participated in drafting the manuscript. DB performed the cloning as well as some of the offline fluorescence emission scans and participated in data analysis and drafting the manuscript. KH participated in the cultivation experiments and data analysis. KEJ, JP, TD and JB supervised the study, participated in data interpretation and assisted in drafting the manuscript. All authors read and approved the final manuscript.
The Federal Ministry of Education and Research is gratefully acknowledged for financial support (031A167A-C).
The authors declare that they have no competing interests.
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- Donovan RS, Robinson CW, Glick BR. Review: optimizing inducer and culture conditions for expression of foreign proteins under the control of the lac promoter. J Ind Microbiol. 1996;16:145–54.View ArticleGoogle Scholar
- Berrow NS, Büssow K, Coutard B, Diprose J, Ekberg M, Folkers GE, Levy N, Lieu V, Owens RJ, Peleg Y, et al. Recombinant protein expression and solubility screening in Escherichia coli: a comparative study. Acta Crystallogr D Biol Crystallogr. 2006;62:1218–26.View ArticleGoogle Scholar
- Shitu JO, Woodley JM, Wnek R, Chartrain M, Hewitt CJ. Induction studies with Escherichia coli expressing recombinant interleukin-13 using multi-parameter flow cytometry. Biotechnol Lett. 2009;31:577–84.View ArticleGoogle Scholar
- Bentley WE, Mirjalili N, Andersen DC, Davis RH, Kompala DS. Plasmid-encoded protein—the principal factor in the metabolic burden associated with recombinant bacteria. Biotechnol Bioeng. 1990;35:668–81.View ArticleGoogle Scholar
- Miao F, Kompala DS. Overexpression of cloned genes using recombinant Escherichia coli regulated by a T7-promoter. 1. Batch cultures and kinetic modeling. Biotechnol Bioeng. 1992;40:787–96.View ArticleGoogle Scholar
- Rahmen N, Fulton A, Ihling N, Magni M, Jaeger KE, Büchs J. Exchange of single amino acids at different positions of a recombinant protein affects metabolic burden in Escherichia coli. Microb Cell Fact. 2015;14:10.View ArticleGoogle Scholar
- Dreisigmeyer DW, Stajic J, Nemenman I, Hlavacek WS, Wall ME. Determinants of bistability in induction of the Escherichia coli lac operon. IET Syst Biol. 2008;2:293–303.View ArticleGoogle Scholar
- Noel JT, Pilyugin SS, Narang A. The diffusive influx and carrier efflux have a strong effect on the bistability of the lac operon in Escherichia coli. J Theor Biol. 2009;256:14–28.View ArticleGoogle Scholar
- Huber R, Ritter D, Hering T, Hillmer AK, Kensy F, Müller C, Wang L, Büchs J. Robo-Lector—a novel platform for automated high-throughput cultivations in microtiter plates with high information content. Microb Cell Fact. 2009;8:42.View ArticleGoogle Scholar
- Rohe P, Venkanna D, Kleine B, Freudl R, Oldiges M. An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform. Microb Cell Fact. 2012;11:144.View ArticleGoogle Scholar
- Samorski M, Müller-Newen G, Büchs J. Quasi-continuous combined scattered light and fluorescence measurements: a novel measurement technique for shaken microtiter plates. Biotechnol Bioeng. 2005;92:61–8.View ArticleGoogle Scholar
- Baumann P, Bluthardt N, Renner S, Burghardt H, Osberghaus A, Hubbuch J. Integrated development of up- and downstream processes supported by the cherry-tag (TM) for real-time tracking of stability and solubility of proteins. J Biotechnol. 2015;200:27–37.View ArticleGoogle Scholar
- Höpfner T, Bluma A, Rudolph G, Lindner P, Scheper T. A review of non-invasive optical-based image analysis systems for continuous bioprocess monitoring. Bioprocess Biosyst Eng. 2010;33:247–56.View ArticleGoogle Scholar
- Drepper T, Krauss U, Berstenhorst SMZ, Pietruszka J, Jaeger KE. Lights on and action! controlling microbial gene expression by light. Appl Microbiol Biotechnol. 2011;90:23–40.View ArticleGoogle Scholar
- Young DD, Deiters A. Photochemical activation of protein expression in bacterial cells. Angewandte Chemie. 2007;46:4290–2.View ArticleGoogle Scholar
- Funke M, Diederichs S, Kensy F, Müller C, Büchs J. The baffled microtiter plate: increased oxygen transfer and improved online monitoring in small scale fermentations. Biotechnol Bioeng. 2009;103:1118–28.View ArticleGoogle Scholar
- Kensy F, Zang E, Faulhammer C, Tan RK, Büchs J. Validation of a high-throughput fermentation system based on online monitoring of biomass and fluorescence in continuously shaken microtiter plates. Microb Cell Fact. 2009;8:31.View ArticleGoogle Scholar
- Siepert EM, Gartz E, Tur MK, Delbruck H, Barth S, Buchs J. Short-chain fluorescent tryptophan tags for on-line detection of functional recombinant proteins. BMC Biotechnol. 2012;12:65.View ArticleGoogle Scholar
- Binder D, Grünberger A, Loeschcke A, Probst C, Bier C, Pietruszka J, Wiechert W, Kohlheyer D, Jaeger KE, Drepper T. Light-responsive control of bacterial gene expression: precise triggering of the lac promoter activity using photocaged IPTG. Integr Biol. 2014;6:755–65.View ArticleGoogle Scholar
- Drepper T, Eggert T, Circolone F, Heck A, Krauss U, Guterl JK, Wendorff M, Losi A, Gärtner W, Jaeger KE. Reporter proteins for in vivo fluorescence without oxygen. Nat Biotechnol. 2007;25:443–5.View ArticleGoogle Scholar
- Bley F, Schaper K, Gorner H. Photoprocesses of molecules with 2-nitrobenzyl protecting groups and caged organic acids. Photochem Photobiol. 2008;84:162–71.Google Scholar
- Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev. 2013;113:119–91.View ArticleGoogle Scholar
- Binder D, Bier C, Grünberger A, Drobietz D, Hage-Hülsmann J, Wandrey G, Büchs J, Kohlheyer D, Loeschcke A, Wiechert W et al. Photocaged arabinose—a novel optogenetic switch for rapid and gradual control of microbial gene expression. ChemBioChem. 2015;. doi:10.1002/cbic.201500609.Google Scholar
- Bienick MS, Young KW, Klesmith JR, Detwiler EE, Tomek KJ, Whitehead TA. The interrelationship between promoter strength, gene expression, and growth rate. PLoS One. 2014;9:e109105.View ArticleGoogle Scholar
- Perfeito L, Ghozzi S, Berg J, Schnetz K, Lässig M. Nonlinear fitness landscape of a molecular pathway. PLoS Genet. 2011;7:e1002160.View ArticleGoogle Scholar
- Fernández A, Ruiz J, Caminal G, López-Santín J. Development and validation of a liquid chromatography–mass spectrometry assay for the quantitation of IPTG in E. Coli fed-batch cultures. Anal Chem. 2010;82:5728–34.View ArticleGoogle Scholar
- Striedner G, Cserjan-Puschmann M, Pötschacher F, Bayer K. Tuning the transcription rate of recombinant protein in strong Escherichia coli expression systems through repressor titration. Biotechnol Prog. 2003;19:1427–32.View ArticleGoogle Scholar
- Pinsach J, de Mas C, Lopez-Santín J. Induction strategies in fed-batch cultures for recombinant protein in Escherichia coli: application to rhamnulose 1-phosphate aldolase. Biochem Eng J. 2008;41:181–7.View ArticleGoogle Scholar
- Altenbach-Rehm J, Nell C, Arnold M, Weuster-Botz D. Parallel bubble columns with fed-batch technique for microbial process development on a small scale. Chem Eng Technol. 1999;22:1051–8.View ArticleGoogle Scholar
- Ziegler T, Möglich A. Photoreceptor engineering. Front Mol Biosci. 2015;2:30.View ArticleGoogle Scholar
- Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-Controlled Tools. Angewandte Chemie. 2012;51:8446–76.View ArticleGoogle Scholar
- Heo J, Cho D-H, Ramanan R, Oh H-M, Kim H-S. PhotoBiobox: a tablet sized, low-cost, high throughput photobioreactor for microalgal screening and culture optimization for growth, lipid content and CO2 sequestration. Biochem Eng J. 2015;103:193–7.View ArticleGoogle Scholar
- Gyamerah MH. Oxygen requirement and energy relations of itaconic acid fermentation by Aspergillus terreus NRRL 1960. Appl Microbiol Biotechnol. 1995;44:20–6.View ArticleGoogle Scholar
- Tolla DA, Savageau MA. Regulation of aerobic-to-anaerobic transitions by the FNR cycle in Escherichia coli. J Mol Biol. 2010;397:893–905.View ArticleGoogle Scholar
- Duetz WA. Microtiter plates as mini-bioreactors: miniaturization of fermentation methods. Trends Microbiol. 2007;15:469–75.View ArticleGoogle Scholar
- Marbach A, Bettenbrock K. lac operon induction in Escherichia coli: systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. J Biotechnol. 2012;157:82–8.View ArticleGoogle Scholar
- Katzke N, Arvani S, Bergmann R, Circolone F, Markert A, Svensson V, Jaeger KE, Heck A, Drepper T. A novel T7 RNA polymerase dependent expression system for high-level protein production in the phototrophic bacterium Rhodobacter capsulatus. Protein Expr Purif. 2010;69:137–46.View ArticleGoogle Scholar
- Drepper T, Huber R, Heck A, Circolone F, Hillmer AK, Büchs J, Jaeger KE. Flavin mononucleotide-based fluorescent reporter proteins outperform green fluorescent protein-like proteins as quantitative in vivo real-time reporters. Appl Environ Microbiol. 2010;76:5990–4.View ArticleGoogle Scholar
- Hanahan D. Studies on transformation of Escherichia-Coli with plasmids. J Mol Biol. 1983;166:557–80.View ArticleGoogle Scholar
- Sambrook J, Fritsch EF, Maniatis T, Laboratory CS. Molecular cloning: a laboratory manual. 2nd ed. New York: Cold Spring Harbor Laboratory Press; 1989.Google Scholar
- Wingen M, Potzkei J, Endres S, Casini G, Rupprecht C, Fahlke C, Krauss U, Jaeger KE, Drepper T, Gensch T. The photophysics of LOV-based fluorescent proteins–new tools for cell biology. Photochem Photobiol Sci. 2014;13:875–83.View ArticleGoogle Scholar
- Wilms B, Hauck A, Reuss M, Syldatk C, Mattes R, Siemann M, Altenbuchner J. High-cell-density fermentation for production of l-N-carbamoylase using an expression system based on the Escherichia coli rhaBAD promoter. Biotechnol Bioeng. 2001;73:95–103.View ArticleGoogle Scholar
- Losen M, Frolich B, Pohl M, Buchs J. Effect of oxygen limitation and medium composition on Escherichia coli fermentation in shake-flask cultures. Biotechnol Prog. 2004;20:1062–8.View ArticleGoogle Scholar
- Diederichs S, Korona A, Staaden A, Kroutil W, Honda K, Ohtake H, Buchs J. Phenotyping the quality of complex medium components by simple online-monitored shake flask experiments. Microb Cell Fact. 2014;13(1):1.View ArticleGoogle Scholar
- Sakakibara J, Adrian RJ. Whole field measurement of temperature in water using two-color laser induced fluorescence. Exp Fluids. 1999;26:7–15.View ArticleGoogle Scholar
- Kunze M, Lattermann C, Diederichs S, Kroutil W, Büchs J. Minireactor-based high-throughput temperature profiling for the optimization of microbial and enzymatic processes. J Biol Eng. 2014;8:22.View ArticleGoogle Scholar