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Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour

Integrating artificial with natural cells to translate chemical messages that direct E. coli... ARTICLE Received 4 Jan 2014 | Accepted 30 Apr 2014 | Published 30 May 2014 DOI: 10.1038/ncomms5012 OPEN Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour 1 1,2 1 1 1 Roberta Lentini , Silvia Perez Santero , Fabio Chizzolini , Dario Cecchi , Jason Fontana , 3 1 4,5 1 1 Marta Marchioretto , Cristina Del Bianco , Jessica L. Terrell , Amy C. Spencer , Laura Martini , 1 2 3 4,5 1 Michele Forlin , Michael Assfalg , Mauro Dalla Serra , William E. Bentley & Sheref S. Mansy Previous efforts to control cellular behaviour have largely relied upon various forms of genetic engineering. Once the genetic content of a living cell is modified, the behaviour of that cell typically changes as well. However, other methods of cellular control are possible. All cells sense and respond to their environment. Therefore, artificial, non-living cellular mimics could be engineered to activate or repress already existing natural sensory pathways of living cells through chemical communication. Here we describe the construction of such a system. The artificial cells expand the senses of Escherichia coli by translating a chemical message that E. coli cannot sense on its own to a molecule that activates a natural cellular response. This methodology could open new opportunities in engineering cellular behaviour without exploiting genetically modified organisms. 1 2 CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy. Department of Biotechnology, University of Verona, 37134 Verona, Italy. 3 4 National Research Council—Institute of Biophysics & Bruno Kessler Foundation, Via alla Cascata 56/C, 38123 Trento, Italy. Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA. Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA. Correspondence and requests for materials should be addressed to S.S.M. (email: mansy@science.unitn.it). NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 ynthetic biology thus far has relied upon the engineering of and IPTG does not cross the vesicle membrane of the artificial cell new cellular function through the insertion and deletion of in the absence of the pore. The ability of E. coli to receive the Sgenetic information in living cells. This genetic engineering chemical message sent by the artificial cells is assessed in two based approach has progressed rapidly. There is now available a ways. First, the fluorescence of E. coli carrying a plasmid encoding 1–3 set of well-characterized biological parts that can be used to a fluorescent protein behind an IPTG-responsive, lac operator build complex genetic circuitry within and between the living sequence is evaluated. Second, the gene expression of 4–6 7 8 cells . Further, entire genomes can be edited and synthesized , untransformed E. coli is monitored by reverse transcription suggesting that fully designed organisms with heretofore unseen quantitative PCR (RT–qPCR). To our knowledge, this is the first capabilities are likely in the future. artificial, cell-like system capable of translating unrecognized Despite the wide range of technologies and target pathways signals into a chemical language that natural cells can recognize. exploited, the desire to control microorganisms to date has always The integration of artificial translator cells with natural cells employed direct genetic intervention. The limitations of these represents a new strategy to introduce synthetic features to a prevalent methods are due to the difficulties of engineering living biological system while circumventing the need for direct genetic systems, including evolutionary pressures that may alter engi- manipulation. neered pathways over time and the potential long-term consequences of altering ecosystems with engineered organisms. However, it may not be necessary to genetically modify living Results cells. Extant life is already extremely complex, endowed with The theophylline-sensing device is functional in vitro. To build numerous sensory and metabolic pathways tuned by billions of artificial cells that sense theophylline and in response release years of evolution to be efficiently responsive to changing IPTG (Fig. 1), a theophylline-sensing genetic device was built intracellular and extracellular conditions. A simple change in with a T7 transcriptional promoter, a theophylline riboswitch and pH, for example, results in the up and downregulation of nearly a gene encoding a fusion between aHL and super folder GFP at 1,000 genes in Escherichia coli . In other words, cells are already the carboxy terminus. If functioning properly, this arrangement capable of sensing many different stimuli and capable of should result in the expression of protein and thus green fluor- performing many tasks. Therefore, it should be possible to escence only in the presence of theophylline. However, cell-free exploit these existing cellular pathways to control cellular expression in the presence and absence of theophylline showed behaviour without changing the genetic makeup of the cells. similar levels of fluorescence (Fig. 2a). Since this same riboswitch Here we explore this idea of engineering E. coli through was previously shown to function in vitro , the sequence of the alternative means by targeting the sensory pathways of E. coli.To aHL-GFP gene was more closely examined. Multiple pairs of do so without altering the genetic content of the bacterium, we potential ribosome binding sites (RBS) and start codons were instead construct artificial cells that could interact with natural identified within the aHL portion of the gene that were in-frame cells in order to evoke a behavioural response. The artificial cells with the GFP-encoding region. The theophylline riboswitch in this system function as chemical translators that sense controls translation, meaning that sequences behind the molecules that E. coli alone cannot sense. In response, the theophylline riboswitch are always transcribed. Translation artificial cells release a molecule that E. coli can naturally respond from the RBS within the riboswitch is activated by direct to, thereby translating an unrecognized chemical message into a binding of theophylline to the messenger RNA. Therefore, if recognized chemical message. In this way, the sensory capabilities additional sequences outside of the riboswitch but within the aHL of E. coli are expanded without altering the genetic content of the portion of the gene were recognized by the ribosome, then bacterium. The artificial cell is built with a phospholipid vesicle regardless of the theophylline concentration, the expression of containing isopropyl b-D-1-thiogalactopyranoside (IPTG), DNA, truncated peptide products with fluorescently active GFP would and transcription–translation machinery. The DNA template have been possible. To test if such internal RBSs were present, the codes for a previously selected riboswitch that activates transla- theophylline riboswitch and thus the RBS preceding the aHL- tion in response to the presence of theophylline . The GFP sequence was deleted. In vitro transcription–translation of theophylline riboswitch controls the synthesis of the pore this construct showed the accumulation of fluorescence over time forming protein a-hemolysin (aHL). Therefore, in the presence, similar to the riboswitch containing construct (Fig. 2b). Sequence but not the absence, of theophylline a pore forms that releases analysis revealed three potential RBS-start codon pairs within the entrapped IPTG. E. coli alone does not respond to theophylline, aHL coding portion of the gene. Of these, a putative RBS of O O H H H C H C 3 N 3 N N N N N O N O N CH CH 3 3 CH OH H C 3 OH N O OH O N CH OH Figure 1 | Artificial cells translate chemical signals for E. coli. (a) In the absence of artificial cells (circles), E. coli (oblong) cannot sense theophylline. (b) Artificial cells can be engineered to detect theophylline and in response release IPTG, a chemical signal that induces a response in E. coli. 2 NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 ARTICLE – RBS 8,000 25,000 – Theo + Theo – RBS mutant 4,000 10,000 0 0 0123 4567 0 1 2 3 4567 Time (h) Time (h) 6,000 αHL + Theo 4,000 + Theo – Theo 2,000 – Theo – RBS mutant Negative control 0123 4567 0 5 10 15 20 25 30 Time (h) Time (min) Figure 2 | In vitro characterization of the theophylline-sensing device and aHL. (a) The cell-free expression of aHL–GFP behind a theophylline riboswitch gives rise to similar levels of fluorescence both in the presence ( þ theo) and absence (  theo) of theophylline at 37 C. (b) The removal of the theophylline riboswitch and thus, the RBS preceding the start codon of aHL–GFP shows production of a fluorescent protein product when incubated with transcription– translation machinery (  RBS). The removal of a putative internal RBS within the aHL coding portion of the fusion construct significantly decreases the production of the fluorescent protein product (  RBS mutant). (c) The activity of the theophylline-sensing device is observable by fluorescence when an internal RBS is removed. The top and middle curves are the in vitro expression of aHL–GFP behind the theophylline riboswitch in the presence ( þ theo) and absence of theophylline (  theo), respectively. Background fluorescent protein production is shown with the same construct lacking the theophylline riboswitch (  RBS mutant) used in b.(d) The cell-free expression of theophylline riboswitch-controlled aHL-degraded red blood cells (RBCs) in the presence ( þ theo) but not the absence of theophylline (  theo). Control reactions include the expression of an aHL construct lacking the theophylline riboswitch (aHL) and RBCs alone (negative control). RBC degradation was monitored by attenuance at 22 C. The exploited constructs were SP011A for panel A, SP002A and AS014A for panel B, RL069A and AS014A for c, and RL067A and JF001A for d (Supplementary Table 1). Data are averages of three independent reactions. AAAGAA was selected as the most likely candidate for giving theophylline gave haemolysis levels similar to the negative control fluorescent protein expression based on sequence composition reactions (Fig. 2d), as was expected for a functioning theophylline and spacing . The putative internal RBS was removed by riboswitch that controls the production of aHL. Control reactions mutation to TCTACC, resulting in a carboxy-terminal GFP with commercial aHL-purified protein and in vitro-expressed tagged K30S E31T aHL construct. Fluorescence from this aHL and aHL–GFP all were fully active (Fig. 2d, Supplementary mutated construct was reduced threefold, consistent with the Table 2), whereas aliquots from in vitro-expressed GFP alone removal of an internal RBS (Fig. 2b). Finally, K30S E31T aHL- and aHL with a carboxy-terminal His-tag were inactive GFP was placed behind the theophylline riboswitch to test the (Supplementary Table 2). aHL with a carboxy-terminal His-tag activity of the cell-free sensing device. A clear difference was was previously shown to have reduced activity . Also, observed between protein expression in the presence and absence comparison of the riboswitch activity fluorescence data with the of theophylline (Fig. 2c), and the fluorescence arising in the haemolysis assay data was consistent with the production of GFP absence of theophylline was within 20% of the construct lacking containing protein fragments from an internal RBS without an an RBS upstream of the full gene. The data were consistent with a active aHL domain. For example, the aHL–GFP construct lacking functioning riboswitch sensor with background fluorescent one of the putative internal RBSs failed to produce protein with protein expression arising from internal RBS within aHL. haemolysis activity (Supplementary Table 2), despite giving rise Therefore, the final artificial cellular mimic described below was to fluorescence during in vitro transcription–translation (Fig. 2b). built with aHL lacking a GFP-tag to avoid complications arising from the expression of truncated fluorescent protein product. Artificial cells can translate chemical messages for E. coli. After demonstrating that the riboswitch was able to control the in vitro Active aHL is produced in response to theophylline in vitro.To expression of aHL in response to theophylline and that the ensure that the cell-free expressed aHL was active as a pore, the expressed aHL molecules formed functional pores, the compo- ability of aHL to degrade rabbit red blood cells was assessed nent parts were next assembled inside of phospholipid vesicles to through a standard haemolysis assay . Each construct was build artificial cells. Theophylline is capable of passing through expressed in vitro at 37 C for 6 h after which, an aliquot was the membrane of vesicles . Phospholipid vesicles were generated removed and added to red blood cells. Haemolysis was quantified in the presence of IPTG, transcription–translation machinery and by measuring attenuance at 650 nm. In the presence of DNA encoding aHL under the control of the theophylline theophylline, 90% haemolysis was observed when the genetic riboswitch. The vesicles were then purified by dialysis at 4 Cto construct containing a riboswitch-controlled aHL was expressed. remove unencapsulated molecules. The receiver bacterial cells The cell-free expression of the same construct in the absence of were mid-exponential phase E. coli BL21(DE3) pLysS carrying a NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications 3 & 2014 Macmillan Publishers Limited. All rights reserved. RFU (a.u.) RFU (a.u.) RFU (a.u.) Haemolysis (%) ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 plasmid encoding GFP behind a T7 promoter and a lac operator RT–qPCR was used to measure gene expression from the lac sequence. In this commonly exploited system, IPTG induces the operon of E. coli. The lac operon is one of the most thoroughly expression of a chromosomal copy of T7 RNA polymerase in characterized sensory pathways . The presence of allolactose (or E. coli BL21(DE3) and derepresses the expression of GFP from the non-hydrolyzable analogue IPTG) induces the expression of the plasmid. Background expression is typically low with such an lacZ, lacY and lacA. To facilitate detection of E. coli responding to arrangement because of the presence of constitutively expressed the chemical message sent from the artificial cells, E. coli BL21 lysozyme from pLysS, a natural inhibitor of T7 RNA polymerase. (DE3) pLysS were grown in LB supplemented with glucose to To test if the artificial cells could function as chemical decrease the background expression of the lac operon and then translators for E. coli, the artificial cells were incubated with transferred to M9 minimal media prior to incubation with E. coli BL21(DE3) pLysS carrying the GFP-encoding plasmid at artificial cells. The artificial cells were prepared as described for 37 C, and the fluorescence of E. coli was evaluated by flow the GFP induction experiments above. After incubating together cytometry. A control reaction in which theophylline was directly artificial cells with E. coli in the presence and absence of added to E. coli in the absence of artificial cells failed to show theophylline for 4 h, aliquots were collected for RNA isolation. green fluorescence after 3 h (Fig. 3a). Similarly, IPTG loaded The RNA was then reverse transcribed and lacZ, lacY, and lacA vesicles that did not contain the machinery necessary to form expression quantified by qPCR. The RNA isolated from bacteria pores did not induce fluorescence in E. coli. Therefore, theophyl- incubated with artificial cells plus theophylline showed on average line was not able to induce a detectable response in E. coli, and over 20-fold higher lacZYA expression than samples incubated IPTG could not cross the vesicle membrane in the absence of with artificial cells alone (calculated from AC/(AC þ theo) as aHL, which was consistent with permeability measurements shown in Fig. 3c). Taken together, the data are consistent with the (Supplementary Fig. 1). However, when E. coli was incubated ability of artificial cells to translate chemical messages and induce ± ± with artificial cells and theophylline, 17 10% and 69 3% of the both engineered and natural pathways in E. coli. bacteria fluoresced green after 0.5 and 3 h, respectively. When the same experiment was repeated in the absence of theophylline, ± ± 3 1% and 24 5% of the bacteria were fluorescent after 0.5 and Discussion 3 h, respectively (Fig. 3a,b). Longer incubations resulted in Direct genetic engineering of living cells is not needed to control diminishing differences between the two samples suggesting the cellular behaviour. It is possible, instead, to coerce desired activity presence of low levels of aHL expression in the absence of through communication with artificial cells. The foundation for theophylline. Also, the GFP response was encoded within a such technologies has already been laid by both cell-free and medium copy number plasmid. Therefore, higher background in vivo studies. Engineered communication paths between living levels of GFP were to be expected in comparison with gene cells have been constructed to coordinate cellular activities in 6,16 expression from the chromosome. The flow cytometry experi- response to external stimuli and are being developed for ments were consistent with the ability of artificial cells to translate therapeutic purposes . In these systems, sender cells often can an unrecognized chemical signal (theophylline) into a signal process information and in response release molecules that affect (IPTG) that E. coli could respond to. other cells. What has been shown herein builds on these past Although the artificial cells were capable of communicating efforts but does so by integrating reconstituted, non-living with E. coli, the induction of GFP synthesis, as observed above, systems with living cells. This allows for the genetic engineering exploited an engineered response. To assess whether artificial component of the system to be moved from the living, evolving, cells could elicit a natural, chromosomally encoded response, replicating cells to the more controllable, ephemeral artificial 100 100 Theo Theo AC AC 80 80 AC + theo AC + theo 60 60 IPTG Encapsulated IPTG 40 IPTG 20 20 0 0 3 3 4 5 –10 0 10 10 10 FITC-A Theo AC AC + theo Encapsulated IPTG lacZ lacY lacA Figure 3 | The artificial translator cells are functional. (a) Artificial cells can induce the expression of a plasmid encoded gene within E. coli in response to a molecule that E. coli cannot naturally sense. BL21(DE3) pLysS carrying a plasmid encoding GFP behind a lac operator sequence was incubated with the following components at 37 C for 3 h: theophylline (theo), artificial cells (AC), artificial cells plus theophylline (AC þ theo), IPTG encapsulated inside of vesicles (encapsulated IPTG), and unencapsulated IPTG (IPTG). E. coli fluorescence was quantified by flow cytometry. The reported averages and s.e.m. were calculated from three separate reactions run on three different days from independently assembled artificial cells. (b) A histogram of a subset of the FACS data used in panel a shows a clear shift in the E. coli population in the presence of artificial cells plus theophylline. (c) Artificial cells can induce the expression of chromosomally encoded genes of E. coli. After 4 h of incubation of artificial cells with E. coli at 37 C, the messenger RNA encoding lacZ, lacY and lacA was quantified by RT–qPCR. Data are reported as averages of three measurements and error bars represent s.e.m. 4 NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. Fold change % Green cells Max (%) NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 ARTICLE cells. When the artificial cells degrade, the natural cells go back sequence was from Lynch and Gallivan and was amplified from a previously described construct . All genes were subcloned into pET21b (Novagen) with NdeI to their original state, thereby diminishing the possibility and XhoI restriction sites. Mutagenesis was performed by Phusion site-directed of unintended long-term consequences. For example, rather mutagenesis (Thermo Scientific). All constructs were confirmed by sequencing at than engineering bacteria to search for and clean up Genechron or Eurofins MWG Operon. Sequences of all the exploited constructs are environmental contaminants, artificial cells could be built to listed in Supplementary Table 1. All experiments were repeated at least three times. Data are reported as averages with standard error, or representative runs are sense the contaminant molecules and in response release shown. chemoattractants that bring natural bacteria capable of feeding on the contaminants to the affected site. In vitro characterization of the riboswitch. Plasmids were amplified in E. coli Several recent reports have described the engineering of seek- Novablue (Novagen) and purified with Wizard Plus SV Minipreps DNA Pur- and-destroy bacteria for the eradication of tumours or bacterial ification System (Promega). Plasmid DNA was phenol–chloroform extracted, 19–22 infections . However, these methods ultimately rely on ethanol precipitated and resuspended in deionized and diethyl pyrocarbonate- administering living bacteria to the patient. Artificial cells could treated water. PCR products were purified with Wizard Plus SV Gel and PCR Clean-Up Systems (Promega). Transcription–translation reactions used the be built to carry out similar tasks if the sensor module of the PURExpress In Vitro Protein Synthesis Kit (New England Biolabs) supplemented artificial cell was designed to detect the chemical conditions with 20 units of Human Placenta RNase Inhibitor (New England Biolabs). Reac- associated with the ailment. For instance, rather than spraying tions were monitored by fluorescence with a CFX96 Touch real-time PCR (Bio- engineered bacteria into the lungs of cystic fibrosis patients, Rad) using the SYBR green filter set. artificial cells could be built to detect the presence of Pseudomonas aeruginosa biofilms through the quorum a-hemolysin activity. Each construct was expressed with the PURExpress In Vitro signalling molecules that are naturally secreted by the organism, Protein Synthesis Kit at 37 C in a final volume of 25 ml either in the presence or absence of 1.5 mM theophylline for 6 h. Rabbit red blood cell (RBC) suspensions such as N-(3-oxododecanoyl)-L-homoserine lactone, a molecule (adjusted to D ¼ 0.1 at 650 nm) were added to a microplate where the reaction capable of crossing membranes without the aid of transporters. mixtures were serially diluted. Changes in attenuance of the RBC suspension were Subsequently, the artificial cells could release small molecules, for measured at 650 nm with a microplate reader (UVmax, Molecular Devices) for example, D-amino acids , to disperse the biofilm and thus clear 30 min at 22 C as reported in Laventie et al. The results are reported as percentage of haemolysis or as the time necessary to reach 50% of haemolysis. the infection. Moreover, the use of dispersion rather than killing would decrease the probability of the bacteria developing resistance. Similar strategies with artificial cells could be Preparation of E. coli receiver cells. Mid-exponential E. coli BL21(DE3) pLysS transformed with a plasmid encoding super folder GFP behind a T7 promoter and developed to substitute for engineered probiotics that integrate 24 25,26 a lac operator sequence (CD101A ) were grown in LB supplemented with with gut microbiota and prevent disease . 1  1 100 mgml ampicillin and 34 mgml chloramphenicol to an optical density of There are several limitations to these first generation artificial 0.5 at 600 nm. A quantity of 200 ml aliquots in 10% (vol/vol) glycerol were flash cells. First, heterogeneity in membrane lamellarity and in frozen with liquid nitrogen and stored at  80 C for later use. Aliquots were 27  1 encapsulation efficiency results in a mixture of artificial cells rapidly thawed and mixed with 2 ml LB supplemented with 100 mgml ampicillin and 34 mgml chloramphenicol and incubated for 2 h at 37 C with 220 r.p.m. with varying degrees of activity. Microfluidic-based methods for shaking. Finally, the cells were gently pelleted and resuspended in 1 ml M9 minimal compartment formation and solute encapsulation would likely media. alleviate many of the complications associated with vesicle-to- vesicle and batch-to-batch variability. Also, a system fully 36,37 Preparation of artificial cells. Vesicles were prepared as previously described . dependent upon the permeability properties of the membrane Briefly, 12.5 mg 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and limits the types of molecules that can be sensed and released. 12.5 mg cholesterol (Avanti Polar Lipids) in chloroform were mixed in a round The development of specific membrane-associated sensors and bottom flask. A thin lipid film was made through rotary evaporation with a Buchi Rotovapor R-210 equipped with a Buchi Vacuum Pump V-700 for 5 h. A quantity transporters will likely be necessary as the complexity of artificial of 2 ml DEPC-treated deionized water was then added to the thin lipid film and cells increase. Finally, the simple release of encapsulated vigorously vortexed. The resulting liposome dispersion was homogenized with an molecules means that release could result from compartment IKA T10 basic homogenizer at a power setting of 4 for 1 min. A quantity of 100 ml degradation as opposed to an engineered response to the aliquots were frozen in liquid nitrogen or dry ice and lyophilized overnight in a vacuum concentrator (Centritrap DNA concentrator, Labconco) at 40 C. The detection of a specific molecule. It is, therefore, important to lyophilized empty liposomes were stored at  20 C. A quantity of 100 ml aliquots develop an output that is mediated by synthesis so that of freeze-dried liposomes were hydrated with 25 ml of 100 mM IPTG (Sigma) compartment degradation would only result in the release of dissolved in 50 mM HEPES pH7.6, 25 ml of the PURE system, 500 ng DNA and 20 inactive starting molecules. An example of such a system is the units of human placenta RNase inhibitor (final volume of 50 ml), unless otherwise noted. Solutions were gently mixed for 30 s. biological nanofactory described by Fernandes et al. that To remove extravesicular material, the vesicles were dialyzed following a 0 0 synthesizes a signalling molecule from S-(5 -deoxyadenosin-5 )- method previously described by Zhu and Szostak . The original membranes of L-homocysteine via two enzymatic steps. 500 ml Slide-a-Lyzer dialysis cassettes (Pierce) were exchanged with 25 mm The absence of a living chassis opens up greater opportunities diameter polycarbonate track-etched membranes with a 1 mm pore size (Whatman). A quantity of 50 ml of unpurified vesicles were loaded onto the center to assemble or biofabricate various mechanisms or functions that of the dialysis system with a 100 ml Hamilton syringe and dialyzed against 250 ml of would be difficult to implement with living cells. For example, buffer A (50 mM HEPES, 10 mM MgCl , 100 mM KCl, pH 7.6) with stirring. The chemical systems housed within inorganic and peptide-based first four rounds of dialysis were for 10 min each. Two more rounds of dialysis in compartments are capable of sensing the environment through, which the buffer was changed after 30 min incubations were further performed. All 29,30 in part, the gating behaviour of the non-lipid compartment . dialysis steps were carried out at 4 C. Further, artificial cells can synthesize and release signalling molecules sensed by living cells without exploiting genetically Artificial–natural cell communication. Purified vesicles containing DNA, the 31,32 PURE system, and IPTG were incubated with E. coli BL21(DE3) pLysS trans- encoded parts . The possibility of merging advances with non- formed with CD101A in M9 minimal media supplemented with 1 mg ml of genetically encoded and genetically encoded parts may lead to the Proteinase K and 5 mM theophylline at 37 C in a final volume of 40 ml. Control construction of artificial cells that are better able to imitate reactions did not contain theophylline. At different time points, 1 ml was removed 33,34 natural cellular life . and diluted 1:100 in PBS. The sample was then analysed by flow cytometry with a FACSCanto A (BD Biosciences). The FITC filter was used for the detection of positive cells. The incident light was at 488 nm for forward scatter (FSC), side Methods scatter (SSC) and fluorescence. Detection for SSC and fluorescence was at ± ± Genetic constructs. The gene encoding Staphylococcus aureus aHL was synthe- 488 10 nm and 530 30 nm, respectively. The threshold parameters were 200 for sized by Genscript. Super folder GFP (BBa_I746916) was from the registry of both FSC and SSC. The PMT voltage settings were 525 (FSC), 403 (SSC) and 600 standard biological parts (http://parts.igem.org). The theophylline riboswitch (FITC). The flow rate was set to ‘low’. For each sample 30,000 events were NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications 5 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 collected. Reactions were repeated three times on three separate days. Data were 25. Duan, F. & March, J. C. 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We thank the Armenise-Harvard foundation, the Autonomous Province of Trento 10. Lynch, S. A. & Gallivan, J. P. A flow cytometry-based screen for synthetic (Ecomm), CIBIO, NSF (CBET#1160005, CBET#1264509), and DTRA (HDTRA1-13- riboswitches. Nucleic Acids Res. 37, 184–192 (2009). 0037) for financial support. A.C.S. was supported by the Marie-Curie Trentino COFUND 11. Martini, L. & Mansy, S. S. Cell-like systems with riboswitch controlled gene from the Autonomous Province of Trento. We also thank M. Pizzato, P. Torre and expression. Chem. Commun. 47, 10734–10736 (2011). F. Ausubel for helpful discussions, and H. Bayley for aHL construct suggestions. 12. Lentini, R. et al. Fluorescent proteins and in vitro genetic organization for cell- free synthetic biology. ACS Synth. Biol. 2, 482–489 (2013). 13. Cassidy, P. & Harshman, S. Studies on the binding of staphylococcal 125I- Author contributions labeled alpha-toxin to rabbit erythrocytes. Biochemistry 15, 2348–2355 (1976). 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Emerging biomedical applications of synthetic Supplementary Information accompanies this paper at http://www.nature.com/ biology. Nat. Rev. Genet. 13, 21–35 (2012). naturecommunications 18. Kostka, J. E. et al. Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater Competing financial interests: The authors declare no competing financial interests. horizon oil spill. Appl. Environ. Microbiol. 77, 7962–7974 (2011). 19. Xiang, S., Fruehauf, J. & Li, C. J. Short hairpin RNA-expressing bacteria elicit Reprints and permission information is available online at http://npg.nature.com/ RNA interference in mammals. Nat. Biotechnol. 24, 697–702 (2006). reprintsandpermissions/ 20. Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A. Environmentally How to cite this article: Lentini, R. et al. Integrating artificial with natural cells to controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, translate chemical messages that direct E. coli behaviour. Nat. Commun. 5:4012 619–627 (2006). doi: 10.1038/ncomms5012 (2014). 21. Gupta, S., Bram, E. E. & Weiss, R. Genetically programmable pathogen sense and destroy. ACS Synth. Biol. 12, 715–723 (2013). This work is licensed under a Creative Commons Attribution 3.0 22. Saeidi, N. et al. Engineering microbes to sense and eradicate Pseudomonas Unported License. The images or other third party material in this aeruginosa, a human pathogen. Mol. Syst. Biol. 7, 521 (2011). article are included in the article’s Creative Commons license, unless indicated otherwise 23. Kolodkin-Gal, I. et al. D-amino acids trigger biofilm disassembly. Science 328, in the credit line; if the material is not included under the Creative Commons license, 627–629 (2010). users will need to obtain permission from the license holder to reproduce the material. 24. Kotula, J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl Acad. Sci. USA 111, 4838–4843 (2014). To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ 6 NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Communications Springer Journals

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Copyright © 2014 by The Author(s)
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Science, Humanities and Social Sciences, multidisciplinary; Science, Humanities and Social Sciences, multidisciplinary; Science, multidisciplinary
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Abstract

ARTICLE Received 4 Jan 2014 | Accepted 30 Apr 2014 | Published 30 May 2014 DOI: 10.1038/ncomms5012 OPEN Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour 1 1,2 1 1 1 Roberta Lentini , Silvia Perez Santero , Fabio Chizzolini , Dario Cecchi , Jason Fontana , 3 1 4,5 1 1 Marta Marchioretto , Cristina Del Bianco , Jessica L. Terrell , Amy C. Spencer , Laura Martini , 1 2 3 4,5 1 Michele Forlin , Michael Assfalg , Mauro Dalla Serra , William E. Bentley & Sheref S. Mansy Previous efforts to control cellular behaviour have largely relied upon various forms of genetic engineering. Once the genetic content of a living cell is modified, the behaviour of that cell typically changes as well. However, other methods of cellular control are possible. All cells sense and respond to their environment. Therefore, artificial, non-living cellular mimics could be engineered to activate or repress already existing natural sensory pathways of living cells through chemical communication. Here we describe the construction of such a system. The artificial cells expand the senses of Escherichia coli by translating a chemical message that E. coli cannot sense on its own to a molecule that activates a natural cellular response. This methodology could open new opportunities in engineering cellular behaviour without exploiting genetically modified organisms. 1 2 CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN), Italy. Department of Biotechnology, University of Verona, 37134 Verona, Italy. 3 4 National Research Council—Institute of Biophysics & Bruno Kessler Foundation, Via alla Cascata 56/C, 38123 Trento, Italy. Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA. Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA. Correspondence and requests for materials should be addressed to S.S.M. (email: mansy@science.unitn.it). NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 ynthetic biology thus far has relied upon the engineering of and IPTG does not cross the vesicle membrane of the artificial cell new cellular function through the insertion and deletion of in the absence of the pore. The ability of E. coli to receive the Sgenetic information in living cells. This genetic engineering chemical message sent by the artificial cells is assessed in two based approach has progressed rapidly. There is now available a ways. First, the fluorescence of E. coli carrying a plasmid encoding 1–3 set of well-characterized biological parts that can be used to a fluorescent protein behind an IPTG-responsive, lac operator build complex genetic circuitry within and between the living sequence is evaluated. Second, the gene expression of 4–6 7 8 cells . Further, entire genomes can be edited and synthesized , untransformed E. coli is monitored by reverse transcription suggesting that fully designed organisms with heretofore unseen quantitative PCR (RT–qPCR). To our knowledge, this is the first capabilities are likely in the future. artificial, cell-like system capable of translating unrecognized Despite the wide range of technologies and target pathways signals into a chemical language that natural cells can recognize. exploited, the desire to control microorganisms to date has always The integration of artificial translator cells with natural cells employed direct genetic intervention. The limitations of these represents a new strategy to introduce synthetic features to a prevalent methods are due to the difficulties of engineering living biological system while circumventing the need for direct genetic systems, including evolutionary pressures that may alter engi- manipulation. neered pathways over time and the potential long-term consequences of altering ecosystems with engineered organisms. However, it may not be necessary to genetically modify living Results cells. Extant life is already extremely complex, endowed with The theophylline-sensing device is functional in vitro. To build numerous sensory and metabolic pathways tuned by billions of artificial cells that sense theophylline and in response release years of evolution to be efficiently responsive to changing IPTG (Fig. 1), a theophylline-sensing genetic device was built intracellular and extracellular conditions. A simple change in with a T7 transcriptional promoter, a theophylline riboswitch and pH, for example, results in the up and downregulation of nearly a gene encoding a fusion between aHL and super folder GFP at 1,000 genes in Escherichia coli . In other words, cells are already the carboxy terminus. If functioning properly, this arrangement capable of sensing many different stimuli and capable of should result in the expression of protein and thus green fluor- performing many tasks. Therefore, it should be possible to escence only in the presence of theophylline. However, cell-free exploit these existing cellular pathways to control cellular expression in the presence and absence of theophylline showed behaviour without changing the genetic makeup of the cells. similar levels of fluorescence (Fig. 2a). Since this same riboswitch Here we explore this idea of engineering E. coli through was previously shown to function in vitro , the sequence of the alternative means by targeting the sensory pathways of E. coli.To aHL-GFP gene was more closely examined. Multiple pairs of do so without altering the genetic content of the bacterium, we potential ribosome binding sites (RBS) and start codons were instead construct artificial cells that could interact with natural identified within the aHL portion of the gene that were in-frame cells in order to evoke a behavioural response. The artificial cells with the GFP-encoding region. The theophylline riboswitch in this system function as chemical translators that sense controls translation, meaning that sequences behind the molecules that E. coli alone cannot sense. In response, the theophylline riboswitch are always transcribed. Translation artificial cells release a molecule that E. coli can naturally respond from the RBS within the riboswitch is activated by direct to, thereby translating an unrecognized chemical message into a binding of theophylline to the messenger RNA. Therefore, if recognized chemical message. In this way, the sensory capabilities additional sequences outside of the riboswitch but within the aHL of E. coli are expanded without altering the genetic content of the portion of the gene were recognized by the ribosome, then bacterium. The artificial cell is built with a phospholipid vesicle regardless of the theophylline concentration, the expression of containing isopropyl b-D-1-thiogalactopyranoside (IPTG), DNA, truncated peptide products with fluorescently active GFP would and transcription–translation machinery. The DNA template have been possible. To test if such internal RBSs were present, the codes for a previously selected riboswitch that activates transla- theophylline riboswitch and thus the RBS preceding the aHL- tion in response to the presence of theophylline . The GFP sequence was deleted. In vitro transcription–translation of theophylline riboswitch controls the synthesis of the pore this construct showed the accumulation of fluorescence over time forming protein a-hemolysin (aHL). Therefore, in the presence, similar to the riboswitch containing construct (Fig. 2b). Sequence but not the absence, of theophylline a pore forms that releases analysis revealed three potential RBS-start codon pairs within the entrapped IPTG. E. coli alone does not respond to theophylline, aHL coding portion of the gene. Of these, a putative RBS of O O H H H C H C 3 N 3 N N N N N O N O N CH CH 3 3 CH OH H C 3 OH N O OH O N CH OH Figure 1 | Artificial cells translate chemical signals for E. coli. (a) In the absence of artificial cells (circles), E. coli (oblong) cannot sense theophylline. (b) Artificial cells can be engineered to detect theophylline and in response release IPTG, a chemical signal that induces a response in E. coli. 2 NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 ARTICLE – RBS 8,000 25,000 – Theo + Theo – RBS mutant 4,000 10,000 0 0 0123 4567 0 1 2 3 4567 Time (h) Time (h) 6,000 αHL + Theo 4,000 + Theo – Theo 2,000 – Theo – RBS mutant Negative control 0123 4567 0 5 10 15 20 25 30 Time (h) Time (min) Figure 2 | In vitro characterization of the theophylline-sensing device and aHL. (a) The cell-free expression of aHL–GFP behind a theophylline riboswitch gives rise to similar levels of fluorescence both in the presence ( þ theo) and absence (  theo) of theophylline at 37 C. (b) The removal of the theophylline riboswitch and thus, the RBS preceding the start codon of aHL–GFP shows production of a fluorescent protein product when incubated with transcription– translation machinery (  RBS). The removal of a putative internal RBS within the aHL coding portion of the fusion construct significantly decreases the production of the fluorescent protein product (  RBS mutant). (c) The activity of the theophylline-sensing device is observable by fluorescence when an internal RBS is removed. The top and middle curves are the in vitro expression of aHL–GFP behind the theophylline riboswitch in the presence ( þ theo) and absence of theophylline (  theo), respectively. Background fluorescent protein production is shown with the same construct lacking the theophylline riboswitch (  RBS mutant) used in b.(d) The cell-free expression of theophylline riboswitch-controlled aHL-degraded red blood cells (RBCs) in the presence ( þ theo) but not the absence of theophylline (  theo). Control reactions include the expression of an aHL construct lacking the theophylline riboswitch (aHL) and RBCs alone (negative control). RBC degradation was monitored by attenuance at 22 C. The exploited constructs were SP011A for panel A, SP002A and AS014A for panel B, RL069A and AS014A for c, and RL067A and JF001A for d (Supplementary Table 1). Data are averages of three independent reactions. AAAGAA was selected as the most likely candidate for giving theophylline gave haemolysis levels similar to the negative control fluorescent protein expression based on sequence composition reactions (Fig. 2d), as was expected for a functioning theophylline and spacing . The putative internal RBS was removed by riboswitch that controls the production of aHL. Control reactions mutation to TCTACC, resulting in a carboxy-terminal GFP with commercial aHL-purified protein and in vitro-expressed tagged K30S E31T aHL construct. Fluorescence from this aHL and aHL–GFP all were fully active (Fig. 2d, Supplementary mutated construct was reduced threefold, consistent with the Table 2), whereas aliquots from in vitro-expressed GFP alone removal of an internal RBS (Fig. 2b). Finally, K30S E31T aHL- and aHL with a carboxy-terminal His-tag were inactive GFP was placed behind the theophylline riboswitch to test the (Supplementary Table 2). aHL with a carboxy-terminal His-tag activity of the cell-free sensing device. A clear difference was was previously shown to have reduced activity . Also, observed between protein expression in the presence and absence comparison of the riboswitch activity fluorescence data with the of theophylline (Fig. 2c), and the fluorescence arising in the haemolysis assay data was consistent with the production of GFP absence of theophylline was within 20% of the construct lacking containing protein fragments from an internal RBS without an an RBS upstream of the full gene. The data were consistent with a active aHL domain. For example, the aHL–GFP construct lacking functioning riboswitch sensor with background fluorescent one of the putative internal RBSs failed to produce protein with protein expression arising from internal RBS within aHL. haemolysis activity (Supplementary Table 2), despite giving rise Therefore, the final artificial cellular mimic described below was to fluorescence during in vitro transcription–translation (Fig. 2b). built with aHL lacking a GFP-tag to avoid complications arising from the expression of truncated fluorescent protein product. Artificial cells can translate chemical messages for E. coli. After demonstrating that the riboswitch was able to control the in vitro Active aHL is produced in response to theophylline in vitro.To expression of aHL in response to theophylline and that the ensure that the cell-free expressed aHL was active as a pore, the expressed aHL molecules formed functional pores, the compo- ability of aHL to degrade rabbit red blood cells was assessed nent parts were next assembled inside of phospholipid vesicles to through a standard haemolysis assay . Each construct was build artificial cells. Theophylline is capable of passing through expressed in vitro at 37 C for 6 h after which, an aliquot was the membrane of vesicles . Phospholipid vesicles were generated removed and added to red blood cells. Haemolysis was quantified in the presence of IPTG, transcription–translation machinery and by measuring attenuance at 650 nm. In the presence of DNA encoding aHL under the control of the theophylline theophylline, 90% haemolysis was observed when the genetic riboswitch. The vesicles were then purified by dialysis at 4 Cto construct containing a riboswitch-controlled aHL was expressed. remove unencapsulated molecules. The receiver bacterial cells The cell-free expression of the same construct in the absence of were mid-exponential phase E. coli BL21(DE3) pLysS carrying a NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications 3 & 2014 Macmillan Publishers Limited. All rights reserved. RFU (a.u.) RFU (a.u.) RFU (a.u.) Haemolysis (%) ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 plasmid encoding GFP behind a T7 promoter and a lac operator RT–qPCR was used to measure gene expression from the lac sequence. In this commonly exploited system, IPTG induces the operon of E. coli. The lac operon is one of the most thoroughly expression of a chromosomal copy of T7 RNA polymerase in characterized sensory pathways . The presence of allolactose (or E. coli BL21(DE3) and derepresses the expression of GFP from the non-hydrolyzable analogue IPTG) induces the expression of the plasmid. Background expression is typically low with such an lacZ, lacY and lacA. To facilitate detection of E. coli responding to arrangement because of the presence of constitutively expressed the chemical message sent from the artificial cells, E. coli BL21 lysozyme from pLysS, a natural inhibitor of T7 RNA polymerase. (DE3) pLysS were grown in LB supplemented with glucose to To test if the artificial cells could function as chemical decrease the background expression of the lac operon and then translators for E. coli, the artificial cells were incubated with transferred to M9 minimal media prior to incubation with E. coli BL21(DE3) pLysS carrying the GFP-encoding plasmid at artificial cells. The artificial cells were prepared as described for 37 C, and the fluorescence of E. coli was evaluated by flow the GFP induction experiments above. After incubating together cytometry. A control reaction in which theophylline was directly artificial cells with E. coli in the presence and absence of added to E. coli in the absence of artificial cells failed to show theophylline for 4 h, aliquots were collected for RNA isolation. green fluorescence after 3 h (Fig. 3a). Similarly, IPTG loaded The RNA was then reverse transcribed and lacZ, lacY, and lacA vesicles that did not contain the machinery necessary to form expression quantified by qPCR. The RNA isolated from bacteria pores did not induce fluorescence in E. coli. Therefore, theophyl- incubated with artificial cells plus theophylline showed on average line was not able to induce a detectable response in E. coli, and over 20-fold higher lacZYA expression than samples incubated IPTG could not cross the vesicle membrane in the absence of with artificial cells alone (calculated from AC/(AC þ theo) as aHL, which was consistent with permeability measurements shown in Fig. 3c). Taken together, the data are consistent with the (Supplementary Fig. 1). However, when E. coli was incubated ability of artificial cells to translate chemical messages and induce ± ± with artificial cells and theophylline, 17 10% and 69 3% of the both engineered and natural pathways in E. coli. bacteria fluoresced green after 0.5 and 3 h, respectively. When the same experiment was repeated in the absence of theophylline, ± ± 3 1% and 24 5% of the bacteria were fluorescent after 0.5 and Discussion 3 h, respectively (Fig. 3a,b). Longer incubations resulted in Direct genetic engineering of living cells is not needed to control diminishing differences between the two samples suggesting the cellular behaviour. It is possible, instead, to coerce desired activity presence of low levels of aHL expression in the absence of through communication with artificial cells. The foundation for theophylline. Also, the GFP response was encoded within a such technologies has already been laid by both cell-free and medium copy number plasmid. Therefore, higher background in vivo studies. Engineered communication paths between living levels of GFP were to be expected in comparison with gene cells have been constructed to coordinate cellular activities in 6,16 expression from the chromosome. The flow cytometry experi- response to external stimuli and are being developed for ments were consistent with the ability of artificial cells to translate therapeutic purposes . In these systems, sender cells often can an unrecognized chemical signal (theophylline) into a signal process information and in response release molecules that affect (IPTG) that E. coli could respond to. other cells. What has been shown herein builds on these past Although the artificial cells were capable of communicating efforts but does so by integrating reconstituted, non-living with E. coli, the induction of GFP synthesis, as observed above, systems with living cells. This allows for the genetic engineering exploited an engineered response. To assess whether artificial component of the system to be moved from the living, evolving, cells could elicit a natural, chromosomally encoded response, replicating cells to the more controllable, ephemeral artificial 100 100 Theo Theo AC AC 80 80 AC + theo AC + theo 60 60 IPTG Encapsulated IPTG 40 IPTG 20 20 0 0 3 3 4 5 –10 0 10 10 10 FITC-A Theo AC AC + theo Encapsulated IPTG lacZ lacY lacA Figure 3 | The artificial translator cells are functional. (a) Artificial cells can induce the expression of a plasmid encoded gene within E. coli in response to a molecule that E. coli cannot naturally sense. BL21(DE3) pLysS carrying a plasmid encoding GFP behind a lac operator sequence was incubated with the following components at 37 C for 3 h: theophylline (theo), artificial cells (AC), artificial cells plus theophylline (AC þ theo), IPTG encapsulated inside of vesicles (encapsulated IPTG), and unencapsulated IPTG (IPTG). E. coli fluorescence was quantified by flow cytometry. The reported averages and s.e.m. were calculated from three separate reactions run on three different days from independently assembled artificial cells. (b) A histogram of a subset of the FACS data used in panel a shows a clear shift in the E. coli population in the presence of artificial cells plus theophylline. (c) Artificial cells can induce the expression of chromosomally encoded genes of E. coli. After 4 h of incubation of artificial cells with E. coli at 37 C, the messenger RNA encoding lacZ, lacY and lacA was quantified by RT–qPCR. Data are reported as averages of three measurements and error bars represent s.e.m. 4 NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. Fold change % Green cells Max (%) NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 ARTICLE cells. When the artificial cells degrade, the natural cells go back sequence was from Lynch and Gallivan and was amplified from a previously described construct . All genes were subcloned into pET21b (Novagen) with NdeI to their original state, thereby diminishing the possibility and XhoI restriction sites. Mutagenesis was performed by Phusion site-directed of unintended long-term consequences. For example, rather mutagenesis (Thermo Scientific). All constructs were confirmed by sequencing at than engineering bacteria to search for and clean up Genechron or Eurofins MWG Operon. Sequences of all the exploited constructs are environmental contaminants, artificial cells could be built to listed in Supplementary Table 1. All experiments were repeated at least three times. Data are reported as averages with standard error, or representative runs are sense the contaminant molecules and in response release shown. chemoattractants that bring natural bacteria capable of feeding on the contaminants to the affected site. In vitro characterization of the riboswitch. Plasmids were amplified in E. coli Several recent reports have described the engineering of seek- Novablue (Novagen) and purified with Wizard Plus SV Minipreps DNA Pur- and-destroy bacteria for the eradication of tumours or bacterial ification System (Promega). Plasmid DNA was phenol–chloroform extracted, 19–22 infections . However, these methods ultimately rely on ethanol precipitated and resuspended in deionized and diethyl pyrocarbonate- administering living bacteria to the patient. Artificial cells could treated water. PCR products were purified with Wizard Plus SV Gel and PCR Clean-Up Systems (Promega). Transcription–translation reactions used the be built to carry out similar tasks if the sensor module of the PURExpress In Vitro Protein Synthesis Kit (New England Biolabs) supplemented artificial cell was designed to detect the chemical conditions with 20 units of Human Placenta RNase Inhibitor (New England Biolabs). Reac- associated with the ailment. For instance, rather than spraying tions were monitored by fluorescence with a CFX96 Touch real-time PCR (Bio- engineered bacteria into the lungs of cystic fibrosis patients, Rad) using the SYBR green filter set. artificial cells could be built to detect the presence of Pseudomonas aeruginosa biofilms through the quorum a-hemolysin activity. Each construct was expressed with the PURExpress In Vitro signalling molecules that are naturally secreted by the organism, Protein Synthesis Kit at 37 C in a final volume of 25 ml either in the presence or absence of 1.5 mM theophylline for 6 h. Rabbit red blood cell (RBC) suspensions such as N-(3-oxododecanoyl)-L-homoserine lactone, a molecule (adjusted to D ¼ 0.1 at 650 nm) were added to a microplate where the reaction capable of crossing membranes without the aid of transporters. mixtures were serially diluted. Changes in attenuance of the RBC suspension were Subsequently, the artificial cells could release small molecules, for measured at 650 nm with a microplate reader (UVmax, Molecular Devices) for example, D-amino acids , to disperse the biofilm and thus clear 30 min at 22 C as reported in Laventie et al. The results are reported as percentage of haemolysis or as the time necessary to reach 50% of haemolysis. the infection. Moreover, the use of dispersion rather than killing would decrease the probability of the bacteria developing resistance. Similar strategies with artificial cells could be Preparation of E. coli receiver cells. Mid-exponential E. coli BL21(DE3) pLysS transformed with a plasmid encoding super folder GFP behind a T7 promoter and developed to substitute for engineered probiotics that integrate 24 25,26 a lac operator sequence (CD101A ) were grown in LB supplemented with with gut microbiota and prevent disease . 1  1 100 mgml ampicillin and 34 mgml chloramphenicol to an optical density of There are several limitations to these first generation artificial 0.5 at 600 nm. A quantity of 200 ml aliquots in 10% (vol/vol) glycerol were flash cells. First, heterogeneity in membrane lamellarity and in frozen with liquid nitrogen and stored at  80 C for later use. Aliquots were 27  1 encapsulation efficiency results in a mixture of artificial cells rapidly thawed and mixed with 2 ml LB supplemented with 100 mgml ampicillin and 34 mgml chloramphenicol and incubated for 2 h at 37 C with 220 r.p.m. with varying degrees of activity. Microfluidic-based methods for shaking. Finally, the cells were gently pelleted and resuspended in 1 ml M9 minimal compartment formation and solute encapsulation would likely media. alleviate many of the complications associated with vesicle-to- vesicle and batch-to-batch variability. Also, a system fully 36,37 Preparation of artificial cells. Vesicles were prepared as previously described . dependent upon the permeability properties of the membrane Briefly, 12.5 mg 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and limits the types of molecules that can be sensed and released. 12.5 mg cholesterol (Avanti Polar Lipids) in chloroform were mixed in a round The development of specific membrane-associated sensors and bottom flask. A thin lipid film was made through rotary evaporation with a Buchi Rotovapor R-210 equipped with a Buchi Vacuum Pump V-700 for 5 h. A quantity transporters will likely be necessary as the complexity of artificial of 2 ml DEPC-treated deionized water was then added to the thin lipid film and cells increase. Finally, the simple release of encapsulated vigorously vortexed. The resulting liposome dispersion was homogenized with an molecules means that release could result from compartment IKA T10 basic homogenizer at a power setting of 4 for 1 min. A quantity of 100 ml degradation as opposed to an engineered response to the aliquots were frozen in liquid nitrogen or dry ice and lyophilized overnight in a vacuum concentrator (Centritrap DNA concentrator, Labconco) at 40 C. The detection of a specific molecule. It is, therefore, important to lyophilized empty liposomes were stored at  20 C. A quantity of 100 ml aliquots develop an output that is mediated by synthesis so that of freeze-dried liposomes were hydrated with 25 ml of 100 mM IPTG (Sigma) compartment degradation would only result in the release of dissolved in 50 mM HEPES pH7.6, 25 ml of the PURE system, 500 ng DNA and 20 inactive starting molecules. An example of such a system is the units of human placenta RNase inhibitor (final volume of 50 ml), unless otherwise noted. Solutions were gently mixed for 30 s. biological nanofactory described by Fernandes et al. that To remove extravesicular material, the vesicles were dialyzed following a 0 0 synthesizes a signalling molecule from S-(5 -deoxyadenosin-5 )- method previously described by Zhu and Szostak . The original membranes of L-homocysteine via two enzymatic steps. 500 ml Slide-a-Lyzer dialysis cassettes (Pierce) were exchanged with 25 mm The absence of a living chassis opens up greater opportunities diameter polycarbonate track-etched membranes with a 1 mm pore size (Whatman). A quantity of 50 ml of unpurified vesicles were loaded onto the center to assemble or biofabricate various mechanisms or functions that of the dialysis system with a 100 ml Hamilton syringe and dialyzed against 250 ml of would be difficult to implement with living cells. For example, buffer A (50 mM HEPES, 10 mM MgCl , 100 mM KCl, pH 7.6) with stirring. The chemical systems housed within inorganic and peptide-based first four rounds of dialysis were for 10 min each. Two more rounds of dialysis in compartments are capable of sensing the environment through, which the buffer was changed after 30 min incubations were further performed. All 29,30 in part, the gating behaviour of the non-lipid compartment . dialysis steps were carried out at 4 C. Further, artificial cells can synthesize and release signalling molecules sensed by living cells without exploiting genetically Artificial–natural cell communication. Purified vesicles containing DNA, the 31,32 PURE system, and IPTG were incubated with E. coli BL21(DE3) pLysS trans- encoded parts . The possibility of merging advances with non- formed with CD101A in M9 minimal media supplemented with 1 mg ml of genetically encoded and genetically encoded parts may lead to the Proteinase K and 5 mM theophylline at 37 C in a final volume of 40 ml. Control construction of artificial cells that are better able to imitate reactions did not contain theophylline. At different time points, 1 ml was removed 33,34 natural cellular life . and diluted 1:100 in PBS. The sample was then analysed by flow cytometry with a FACSCanto A (BD Biosciences). The FITC filter was used for the detection of positive cells. The incident light was at 488 nm for forward scatter (FSC), side Methods scatter (SSC) and fluorescence. Detection for SSC and fluorescence was at ± ± Genetic constructs. The gene encoding Staphylococcus aureus aHL was synthe- 488 10 nm and 530 30 nm, respectively. The threshold parameters were 200 for sized by Genscript. Super folder GFP (BBa_I746916) was from the registry of both FSC and SSC. The PMT voltage settings were 525 (FSC), 403 (SSC) and 600 standard biological parts (http://parts.igem.org). The theophylline riboswitch (FITC). The flow rate was set to ‘low’. For each sample 30,000 events were NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications 5 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5012 collected. Reactions were repeated three times on three separate days. Data were 25. Duan, F. & March, J. C. Engineered bacterial communication prevents Vibrio analysed using FlowJo software (TreeStar, USA). cholerae virulence in an infant mouse model. Proc. Natl Acad. Sci. USA 107, Samples were also evaluated by RT–qPCR. Here, the dialyzed vesicles and E. coli 11260–11264 (2010). were incubated as described above for 4 h at 37 C. Subsequently, the total RNA 26. Goh, Y. L., He, H. & March, J. C. Engineering commensal bacteria for was extracted with the RNeasy Mini kit (Qiagen). A quantity of 10 ml of 500 ng of prophylaxis against infection. Curr. Opin. Biotechnol. 23, 924–930 (2012). RNA was reverse transcribed using RevertAid Reverse Transcriptase (Thermo 27. Weitz, M. et al. Diversity in the dynamical behaviour of a compartmentalized Scientific). cDNA was quantified with a CFX96 Touch real-time PCR (Bio-Rad) programmable biochemical oscillator. Nat. Chem. 6, 295–302 (2014). with SYBR green detection. Each sample was diluted to 5 ng and measured in 28. Fernandes, R., Roy, V., Wu, H. 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We thank the Armenise-Harvard foundation, the Autonomous Province of Trento 10. Lynch, S. A. & Gallivan, J. P. A flow cytometry-based screen for synthetic (Ecomm), CIBIO, NSF (CBET#1160005, CBET#1264509), and DTRA (HDTRA1-13- riboswitches. Nucleic Acids Res. 37, 184–192 (2009). 0037) for financial support. A.C.S. was supported by the Marie-Curie Trentino COFUND 11. Martini, L. & Mansy, S. S. Cell-like systems with riboswitch controlled gene from the Autonomous Province of Trento. We also thank M. Pizzato, P. Torre and expression. Chem. Commun. 47, 10734–10736 (2011). F. Ausubel for helpful discussions, and H. Bayley for aHL construct suggestions. 12. Lentini, R. et al. Fluorescent proteins and in vitro genetic organization for cell- free synthetic biology. ACS Synth. Biol. 2, 482–489 (2013). 13. Cassidy, P. & Harshman, S. Studies on the binding of staphylococcal 125I- Author contributions labeled alpha-toxin to rabbit erythrocytes. Biochemistry 15, 2348–2355 (1976). Design, cloning and mutagenesis of genetic constructs were done by R.L., A.C.S., J.F., 14. Mantri, S., Sapra, K. T., Cheley, S., Sharp, T. H. & Bayley, H. An engineered S.P.S., M.F., and C.D.B. In vitro riboswitch activity was investigated by R.L., S.P.S., dimeric protein pore that spans adjacent lipid bilayers. Nat. Commun. 4, 1725 C.D.B., L.M., M.F. and A.C.S. aHL activity was measured by R.L., S.P.S., M.M., and (2013). M.D.S. R.L., J.L.T., D.C., F.C. and S.P.S. ran the cell flow cytometry experiments, and 15. Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of RT–qPCR was performed by R.L. and J.F. S.S.M. supervised the project. All authors proteins. J. Mol. Biol. 3, 318–356 (1961). analysed and interpreted the data and contributed to the writing of the manuscript. 16. Prindle, A. et al. A sensing array of radically coupled genetic ‘biopixels’. Nature 481, 39–44 (2012). Additional information 17. Weber, W. & Fussenegger, M. Emerging biomedical applications of synthetic Supplementary Information accompanies this paper at http://www.nature.com/ biology. Nat. Rev. Genet. 13, 21–35 (2012). naturecommunications 18. Kostka, J. E. et al. Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater Competing financial interests: The authors declare no competing financial interests. horizon oil spill. Appl. Environ. Microbiol. 77, 7962–7974 (2011). 19. Xiang, S., Fruehauf, J. & Li, C. J. Short hairpin RNA-expressing bacteria elicit Reprints and permission information is available online at http://npg.nature.com/ RNA interference in mammals. Nat. Biotechnol. 24, 697–702 (2006). reprintsandpermissions/ 20. Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A. Environmentally How to cite this article: Lentini, R. et al. Integrating artificial with natural cells to controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, translate chemical messages that direct E. coli behaviour. Nat. Commun. 5:4012 619–627 (2006). doi: 10.1038/ncomms5012 (2014). 21. Gupta, S., Bram, E. E. & Weiss, R. Genetically programmable pathogen sense and destroy. ACS Synth. Biol. 12, 715–723 (2013). This work is licensed under a Creative Commons Attribution 3.0 22. Saeidi, N. et al. Engineering microbes to sense and eradicate Pseudomonas Unported License. The images or other third party material in this aeruginosa, a human pathogen. Mol. Syst. Biol. 7, 521 (2011). article are included in the article’s Creative Commons license, unless indicated otherwise 23. Kolodkin-Gal, I. et al. D-amino acids trigger biofilm disassembly. Science 328, in the credit line; if the material is not included under the Creative Commons license, 627–629 (2010). users will need to obtain permission from the license holder to reproduce the material. 24. Kotula, J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl Acad. Sci. USA 111, 4838–4843 (2014). To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ 6 NATURE COMMUNICATIONS | 5:4012 | DOI: 10.1038/ncomms5012 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved.

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Published: May 30, 2014

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