WO2019035955A1 - High-throughput system using a cell-free expression system and in situ sequencing - Google Patents

Abstract

A method for high throughput screening of biosynthetic pathways using a cell free system is provided.

Description

HIGH-THROUGHPUT SYSTEM USING A

CELL-FREE EXPRESSION SYSTEM AND IN SITU SEQUENCING

RELATED APPLICATION DATA

This application claims priority to U.S. Provisional Application No. 62/545,600 filed on August 15, 2017, which is hereby incorporated herein by reference in its entirety for all purposes.

STATEMENT OF GOVERNMENT INTERESTS

This invention was made with government support under Grant No. GM1 10714 awarded by National Institutes of Health. The government has certain rights in the invention.

BACKGROUND

The in vitro production and screening of biomolecules is desirable for a range of applications, including the discovery of high-value therapeutics and other biologies, expression of membrane proteins and viral particles, directed protein evolution and prototyping synthetic gene circuits or biosynthesis pathways. See Carlson, E.D. et al., 2012. Cell-free protein synthesis: applications come of age. Biotechnology advances, 30(5), pp.1 185-1 194.

SUMMARY

Embodiments of the present disclosure are directed to a method of screening a plurality of template nucleic acid sequences for small molecule or protein production including adding a template nucleic acid sequence from the plurality to each reaction volume within a plurality of reaction volumes, wherein each reaction volume includes a cell-free expression system under conditions of transcription and translation; detecting generation of a small molecule in a target reaction volume; and sequencing of the template nucleic acid sequence of the target reaction volume.

It is noted that in this disclosure and particularly in the claims and/or paragraphs, terms such as "comprises", "comprised", "comprising" and the like can have the meaning attributed to it in U.S. Patent law; e.g., they can mean "includes", "included", "including", and the like; and that terms such as "consisting essentially of and "consists essentially of have the meaning ascribed to them in U.S. Patent law, e.g., they allow for elements not explicitly recited, but exclude elements that are found in the prior art or that affect a basic or novel characteristic of the invention.

Further features and advantages of certain embodiments of the present invention will become more fully apparent in the following description of embodiments and drawings thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. The foregoing and other features and advantages of the present embodiments will be more fully understood from the following detailed description of illustrative embodiments taken in conjunction with the accompanying drawings in which:

Figs. 1A-1C are directed to optimization of cell extract assay. Fig 1A: The Mg- glutamate concentration was optimized for the S. lividans cell extract used to produce sfGFP in a cell free reaction vessel. The optimal final concentration of Mg-glutamate was found to be 4 mM, however each concentration produced GFP over the course of 4 hours in comparison to the blank (35% cell extract and no energy buffer). Fig I B: A non-denaturing 16% Tris-Glycine protein gel was used to verify the weight of the GFP produced from the in vitro reactions. Fig. 1C: The K-Glutamate concentration was calibrated to the S. lividans cell extract after determining the optimal Mg-Glutamate concentration of 4 niM. The 140 mM K- Glutamate sample produced the most sfGFP at 41 ng/uL +/- 1 ng/uL, n = 3. This concentration was determined using a recombinant GFP standard curve that was made up in 35% cell extract and phosphate buffered saline (PBS) - (dynamic range of this assay was determined to be 250 ug/mL -3.9 ug/mL),

Fig. 2 is a spectral scan of lycopene in 35% cell extract diluted in hexane - blank corrected.

Fig. 3 is a schematic of a screening process using a metagenomic DNA library.

Figs. 4A-4I depict data from various experiments directed to a V. natriegens cell free system.

Figs 5A-5F depict data from various experiments directed to a Pseudomonas aeruginosa cell-free expression system.

Figs 6A-6B depict -data from various experiments directed to temperature calibration of a Pseudomonas aeruginosa cell-free expression system.

Fig. 7 depicts data directed to cyclic voltammetry electrochemical analysis of Pseudomonas aeruginosa cell-free reactions.

Fig. 8 depicts data directed to square wave voltammetry electrochemical analysis of Pseudomonas aeruginosa cell-free reactions.

Figs. 9A-9E depict data directed to square wave voltammetry electrochemical analysis of Streptomyces spps. cell-free reactions.

Figs. 10A-10D depict data directed to square wave voltammetry electrochemical analysis of Vibrio natriegens cell-free reactions (effect of optical density). Figs. 1 1 A-1 1G depict data directed to square wave voltammetry electrochemical analysis of Vibrio natriegens cell-free reactions (effect of growth media).

Fig. 12 depicts data directed to cell-free protein synthesis from mixtures of E. coli and V. natriegens crude extracts.

DETAILED DESCRIPTION

Embodiments of the present disclosure are directed to high throughput screening assays using cell-free systems for the screening of small molecule production. According to one aspect, a plurality of individual reaction volumes of a cell-free expression system is used to screen nucleic acid templates for the production of small molecules. According to one aspect, a single nucleic acid template is provided to or is contained within a single reaction volume of the plurality of reaction volumes of the cell-free expression system under conditions favoring expression of the nucleic acid template into one or more proteins or enzymes. Stated differently, each reaction volume of the plurality of reaction volumes of the cell-free expression system includes a nucleic acid template, such as a single nucleic acid template, under conditions favorable for nucleic acid expression of one or more proteins or enzymes. The reaction volume also includes factors for manufacture of the small molecule by the one or more proteins or enzymes. The reaction volume coordinates in vitro co- expression of multiple enzymes required for synthesis of the small molecule.

Each reaction volume is analyzed to determine whether a small molecule has been generated in the reaction volume using a detection method, such as a color detection method should the small molecule exhibit a color as a feature of the small molecule. Other small molecule detection methods known to those of skill in the art, such as Liquid Chromatography - Mass Spectrometry (LC-MS), Nuclear Magnetic Resonance (NMR), X- Ray Crystallography, electrochemical sensing methods or other small molecule or protein or enzyme detection methods can be used for detection and characterization of the small molecule, protein or enzyme. For a given reaction volume of the cell-free expression system, if small molecule production is detected, then the reaction volume is subjected to nucleic acid sequencing, such as in situ nucleic acid sequencing, to determine the sequence of the template nucleic acid sequence and therefore the identity of the one or more proteins or enzymes used to make the small molecule. The small molecule may be characterized by methods known to those of skill in the art to determine features, such as structure or other characteristics of the small molecule.

Aspects of the present disclosure are directed to a method for high throughput screening of biomolecules, such as proteins, small molecules and natural products, using a cell-free system. Methods described herein enable rapid identification of products in cell-free extracts, such that large libraries of metabolic pathways can be screened, for example metagenomic fragments. According to one aspect, a cell-free system including cell extract is used for expression of proteins and small molecules within a reaction volume. Since the present disclosure contemplate high throughput methods, a plurality of reaction volumes are used. Each reaction volume includes cell extract in an amount, for example, of about 10 uL or less. A nucleic acid template, encoding a single gene or an entire metabolic pathway, is added to the cell extract in the reaction volume to initiate transcription and translation of proteins or enzymes required for production of product. According to one aspect, each reaction volume of the plurality of reaction volumes within the high throughput system includes a different nucleic acid template. Libraries of nucleic acid templates are known and methods of incorporating a single nucleic acid template from a library of nucleic acid templates into an individual reaction volume are known to those of skill in the art, for example, by dilution of pooled libraries or using microfluidic device to compartmentalize single template in single droplet. As a result, an array of cell-free reactions is utilized for high throughput screening of proteins, enzymes or small molecules using detection methods, such as spectrophotometric or fiuorimetric methods or other detection methods known to those of skill in the art.

Aspects of the present disclosure are directed to an in vitro Streptomyces cell-free expression or reaction system capable of producing colored small molecules for detection. Such a system can be used to determine the ability of the in vitro Streptomyces cell-free reaction system to produce a target molecule. Such an in vitro Streptomyces cell-free reaction system capable of producing colored small molecules has utility in methods of high- throughput screening and optimization of biosynthesis of biomolecules. Accordingly, aspects of the present disclosure are directed to a cell-free system including the cellular machinery of Streptomyces or other cell source, such as bacterial, yeast, plant, insect, or mammalian cell extract, for a cell-free transcription and translation system utilized in a high throughput screening system to identify template nucleic acids that produce small molecules.

Embodiments of the present disclosure are directed to a cell-free expression system including cell extract from Streptomyces for the expression of proteins and small molecules. According to one aspect, a reaction volume of cell extract from Streptomyces in the range of from about 1 μΐ to about 10 μΐ is provided or generated in a reaction system. According to one aspect a plurality of a reaction volumes of cell extract from Streptomyces in the range of from about 1 μΐ to about 10 μΐ is provided or generated in a reaction system. According to one aspect, a nucleic acid template is within the reaction volume of cell extract from Streptomyces under conditions to initiate transcription and translation of the nucleic acid template. The nucleic acid template may be a DNA or RNA template, such as a DNA template encoding a single gene, one or more genes or a metabolic pathway. Useful templates are those as are known in the art and can be readily identified by those of skill based on the present disclosure. The template can be linear (PCR product) or circular (plasmid) nucleic acid. The DNA template may be added to the extract to initiate transcription and translation of proteins or enzymes required for production of a target protein or target small molecule. Each reaction volume is analyzed for the small molecule generation. If a small molecule is detected, then the template nucleic acid is sequenced to identify the proteins or enzymes or biosynthetic pathway used to make the small molecule. The small molecule may be identified using characterization methods know to those of skill in the art, such as LC-MS, NMR, X-Ray Crystallography or electrochemical sensing methods.

Aspects of the present disclosure integrate or combine an in vitro cell-free reaction system with a high-throughput screening method. Such a high throughput screening method may utilize traditional well plates, such as a 96- or 384-well plate, or depressions or wells on a slide to form in vitro compartments or may utilize droplets, microdroplets or emulsion microdroplets for the reaction volume which may then sorted based on positive hits, deposition on the surface, or in a gel. See, for example, Zinchenko, A. et al., 2014. One in a million: flow cytometric sorting of single cell-lysate assays in monodisperse picolitre double emulsion droplets for directed evolution. Analytical chemistry, 86(5), pp.2526-2533 and Caschera, F. et al., 2016. Cell-free compartmentalized protein synthesis inside double emulsion templated liposomes with in vitro synthesized and assembled ribosomes. Chemical Communications, 52(31), pp.5467-5469 each of which are hereby incorporated by reference in its entirety. Using UV-Vis spectral scanning and fluorescence excitation, active pathways can be rapidly identified by the production of colored or fluorescent small molecules without the use of expensive equipment or time-consuming protocols. Once color molecules are detected, the desired well / droplet is further analyzed by DNA sequencing in order to identify the corresponding metabolic pathway (for example, by NGS or in situ sequencing). The target molecule can be further analyzed by methods such as LC-MS, NMR or X-Ray Crystallography.

Aspects of the present disclosure are directed to detecting and/or identifying small molecules produced by a template nucleic acid sequence in a cell-free expression system. The system and methods described herein can also be used to screen for regulators of biosynthetic pathways which might enhance expression of cryptic pathways for production of novel molecules. Additional methods include identification of unknown biomolecules in metagenomic or other libraries; screening for in vitro production of synthetic natural products analogs; screening for optimized conditions for cell-free production of natural products; screening for optimized conditions for cell-free production of synthetic biomolecules; or screening for global regulators (transcription factors) that can enhance expression of cryptic pathways in host cell-extract system.

Aspects of the present disclosure utilize emulsion droplet methods for compartmentalization of reaction volumes. Such droplet methods can be scaled up for biosynthetic libraries and desired biomolecules. The emulsion droplet reaction volumes can be integrated into systems for primary readout of the emulsion droplets. FACS and cell sorting methods can be adapted to the emulsion droplet reaction volumes. Embodiments of the present disclosure utilize automated systems and devices for reagent delivery and/or mixing in reagent volumes, reagent volume immobilization such as in a gel (a polyacrylamide gel for example) or three dimensional compartment and in situ sequencing. Screening of library components, such as metagenomic fragments or biosynthetic pathways, can be multiplexed, i.e. massively parallel screening, wherein library components can reach on the order of 10¹⁰ members. CELL-FREE SYSTEMS

According to one aspect, the screening method utilizes a cell-free expression system to screen for expression of a template nucleic acid sequence and production of a small molecule. It is to be understood that one of skill will readily be able to identify useful cell- free expressions known in the art based on the present disclosure. According to one aspect, methods are provided for using an active cell free system to rapidly screen for production of valuable molecules or proteins. According to one aspect, one or more, two or more or a plurality of different genus or species of cells, such as those described herein, can be used for making cell-free systems as described herein. Accordingly, a library of cell free systems is provided to carry out the methods described herein.

Cell-free expression systems are useful in the present embodiments as they greatly reduce the complexity of cellular assays by using cell extract rather than live cells. In a cell- free system, cell lysis is followed by removal of cellular debris and chromosomal DNA. The remaining cell extract is added with energy substrates, such as NTPs, PEP (phosphoenolpyruvic acid) or 3-PGA (3-phosphoglyceric acid) or other energy source, cofactors, salts, amino acids and deoxynucleotides in sufficient amounts and under sufficient conditions to be able to transcribe and translate a temple nucleic acid sequence. The desired template DNA or RNA is added for transcription and translation of desired proteins or biomolecules. See Carlson, E.D. et al., 2012. Cell-free protein synthesis: applications come of age. Biotechnology advances, 30(5), pp.1 185-1 194 hereby incorporated by reference in its entirety.

According to one aspect, a cell for providing or producing a cell free extract is selected based on the number and type of readily detectable natural products, which may be readily detectable, and subsequently, available precursor compounds. Such cells are selected for preparing extracts, crude or otherwise, for cell-free expression as such extracts are advantageous as a host for screening biosynthesis pathways in a high-throughput manner. Furthermore, such extracts and cell-free expression systems can be used in the analysis of the underlying biosynthetic pathways involved in breakdown and/or production of chemical compounds, such as hydrocarbons or other biopolymers, and in resistance studies, such as antibiotic resistance. Exemplary cells may have one or more of clinical relevance, bioenergy relevance, environmental relevance, soil dwelling relevance, natural product relevance, radiation resistance relevance; high temperature relevance, extreme growth conditions relevance, thermostable enzyme relevance and the like.

According to one aspect, cell-free expression systems are based on extracts of the Staphylococcus genus. Exemplary species include Staphylococcus aureus or Staphylococcus epidermidis and the like.

According to one aspect, cell-free expression systems are based on extracts of the Pseudomonas genus. Exemplary species include P. aeruginosa, P. fluorescens, and P. putida.

According to one aspect, cell-free expression systems are based on extracts of the Streptomyces genus. Exemplary species include Streptomyces coelicolor, S. lividans, S. albicans, S. griseus, and S. plicatosporus and the like.

According to one aspect, cell-free expression systems are based on extracts of the Flavobacterium genus. Exemplary species include F. columnare, F. psychrophilum, F. branchiophilum, F. aquatile; F. ferrugineum; F. johnsoniae; F. limicola; F. micromati; and F. psychrolimnae and the like.

According to one aspect, cell-free expression systems are based on extracts of the Bacillus genus. Exemplary species include Bacillus cereus, Bacillus halodurans, Bacillus insolitus, Bacillus pumilis, and Bacillus subtilis and the like. According to one aspect, cell-free expression systems are based on extracts of the Deinococcus genus. Exemplary species include D. geothermalis, D. grandis, D. indicus, D. murrayi, D. p oteolyticus, and D. radiodurans and the like.

According to one aspect, cell-free expression systems are based on extracts of the Thermus genus. Exemplary species include T. antranikianii, T. aquaticus, T. brockianus, T. caldophilus, T. filiformis, T. igniterrae, T. kawarayuensis, T. nonproteolyticus, T. oshimai, T. rehai, T. scotoductus, and T. thermophilus and the like.

According to one aspect, cell-free expression systems are based on extracts of the Escherichia genus. Exemplary species include E. coli and the like.

According to one aspect, cell-free expression systems are based on extracts of the Vibrio genus. Exemplary species include V. cholerae, V. natriegens, V. parahaemolyticus and the like.

According to one aspect, cell-free expression systems are based on extracts of plants. Exemplary species include Nicotiana tabacum, Arabidopsis thaliana, Artemisia annua, and the like.

According to one aspect, cell-free expression systems are based on extracts of fungal cells. Exemplary species include Aspergillus oryzae, Saccharomyces rouxii, Aspergillus terreus, Aspergillus griseus, Penicillium notatum, S. cerevisiae, S. pombe and the like.

According to certain aspects, methods are provided that utilize mixtures of various cell-free crude extracts to express template nucleic acids such as in a method to screen biosynthesis pathways that may be active in the presence of the respective combination or mixture. For example, a mixture of Streptomyces violaceruber and Pseudomonas aeruginosa is contemplated to yield natural products from otherwise inaccessible pathways not common naturally. Any mixture of cell-free extracts from different genus or species of cells is contemplated. According to one aspect, cell-free expression systems are based on extracts of one or more, two or more or a plurality of cells of the following genera: Staphylococcus, Pseudomonas, Streptomyces, Flavobacterium, Bacillus, Deinococcus, Thermus, Escherichia or Vibrio. According to one aspect, cell-free expression systems are based on extracts of two or more different genus of cells, such as is described herein. According to one aspect, cell- free expression systems are based on extracts of two or more different species of cells, such as is described herein. According to one aspect, cell-free expression systems are based on a combination of extracts from two or more different genera or species of cells. According to one aspect, cell-free expression systems are based on a combination of extracts from two or more different genus or species of cells, for example, cells selected from two or more genera among Staphylococcus, Pseudomonas, Streptomyces, Flavobacterium, Bacillus, Deinococcus, Thermus, Escherichia or Vibrio or the species described herein.

Cell-free expression systems have been based on extracts of E. coli. See Dudley, Q.M., Karim, A.S. & Jewett, M.C., 2015. Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnology journal, 10(1), pp.69-82 and Dudley, Q.M., Anderson, K.C. & Jewett, M.C., 2016. Cell-Free Mixing of Escherichia coli Crude Extracts to Prototype and Rationally Engineer High-Titer Mevalonate Synthesis. ACS synthetic biology, 5(12), pp.1578-1588 each of which is hereby incorporated by reference in its entirety. Cell-free expression systems have been based on yeast, plant and several eukaryotic cell systems. See Carlson, E.D. et al., 2012. Cell-free protein synthesis: applications come of age. Biotechnology advances, 30(5), pp.1 185-1 194 hereby incorporated by reference in its entirety. Exemplary cell-free expression systems are based on extracts of Streptomyces, Escherichia or Bacillus. See Kelwick, R. et al., 2016. Development of a Bacillus subtilis cell-free transcription-translation system for prototyping regulatory elements. Metabolic engineering, 38, pp.370-381 hereby incorporated by reference in its entirety. Cell-free systems are also commercially available such as Thermo-fisher Ί -step IVT kits' (product AM1200: Rabbit reticulocyte, product 88881 : Human HeLa cell lysate, product 88893: CHO (chinese hamster ovary) lysate), New England biolabs E.coli IVT system (product E6800S), Promega Wheat germ extract (L4330). Exemplary cell free systems for protein synthesis include those a cell free system in E. coli (see Kim H-C, Kim T-W, Kim D-M. Prolonged production of proteins in a cell-free protein synthesis system using polymeric carbohydrates as an energy source. Process Biochem. 201 1 ;46: 1366-1369; Zawada JF, Yin G, Steiner AR, Yang J, Naresh A, Roy SM, et al. Microscale to manufacturing scale-up of cell-free cytokine production— a new approach for shortening protein production development timelines. Biotechnol Bioeng. Wiley Online Library; 201 1 ;108: 1570-1578; Boyer ME, Stapleton JA, Kuchenreuther JM, Wang C-W, Swartz JR. Cell-free synthesis and maturation of [FeFe] hydrogenases. Biotechnol Bioeng. 2008;99: 59-67 each of which are hereby incorporated by reference in its entirety), Wheat germ (see Madin K, Sawasaki T, Ogasawara T, Endo Y. A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes. Proc Natl Acad Sci U S A. 2000;97: 559-564 hereby incorporated by reference in its entirety), Insect cells (see Tarui H, Murata M, Tani I, Imanishi S, Nishikawa S, Hara T. Establishment and characterization of cell-free translation/glycosylation in insect cell (Spodoptera frugiperda 21) extract prepared with high pressure treatment. Appl Microbiol Biotechnol. 2001 ;55: 446—453 hereby incorporated by reference in its entirety), Rabbit reticulocyte (see Hancock JF. [7] Reticulocyte lysate assay for in Vitro translation and posttranslational modification of Ras proteins. Methods Enzymol. 1995;255: 60-65; Gibbs PE, Zouzias DC, Freedberg IM. Differential post-translational modification of human type I keratins synthesized in a rabbit reticulocyte cell-free system. Biochim Biophys Acta. 1985;824: 247-255 each of which is hereby incorporated by reference in its entirety), Yeast (see Wang X, Liu J, Zheng Y, Li J, Wang H, Zhou Y, et al. An optimized yeast cell-free system: sufficient for translation of human papillomavirus 58 LI mRNA and assembly of virus-like particles. J Biosci Bioeng. 2008; 106: 8-15 hereby incorporated by reference in its entirety), and Hybridoma (see Mikami S, Kobayashi T, Yokoyama S, Imataka H. A hybridoma-based in vitro translation system that efficiently synthesizes glycoproteins. J Biotechnol. 2006; 127: 65-78 hereby incorporated by reference in its entirety).

Embodiments of the present disclosure are directed to a cell-free expression system based on the Streptomyces genus. According to one aspect, Streptomyces includes the genetic components and cellular machinery to produce antibiotics such as Streptomycin and Tetracyclin. See Kieser, T. et al., Practical Streptomyces Genetics. 2000. Norwich: John Innes Foundation Google Scholar hereby incorporated by reference in its entirety. Streptomyces also includes the genetic components and cellular machinery to produce bioactive compounds for immunosuppression, antifungal agents, antiparasitic drugs, and antitumoral medications. See Avignone-Rossa, C, Kierzek, A.M. & Bushell, M.E., 2013. Secondary Metabolite Production in Streptomyces. In W. Dubitzky et al., eds. Encyclopedia of Systems Biology. Springer New York, pp. 1903-1913 hereby incorporated by reference in its entirety. Certain species of Streptomyces have been genome sequenced and metabolic pathways are known to those of skill in the art. See, for example, the complete genome sequencing of S. coelicolor A3(2) and other species as described in Bentley, S.D. et al., 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature, 417(6885), pp.141— 147 hereby incorporated by reference in its entirety.

Certain cell-free protein expression systems based on Streptomyces find use in the present disclosure. See for example Streptomyces species S. lividans (Li, J. et al., 2017. Establishing a high yielding streptomyces-based cell-free protein synthesis system. Biotechnology and bioengineering, 1 14(6), pp.1343— 1353 hereby incorporated by reference in its entirety) and S. venezuelae (Moore, S.J. et al., 2017. Streptomyces venezuelae TX-TL - a next generation cell-free synthetic biology tool. Biotechnology journal, 12(4). Available at: world wide website dx.doi.org/10.1002/biot.201600678 hereby incorporated by reference in its entirety), achieving overexpression of GFP protein and metabolic enzymes. See for example synthesis of nonribosomal peptide ε-Poly-l-lysine (ε-PL) in cell-free system of S. albulus (Kawai, T. et al., 2003. Biosynthesis of epsilon-poly-L-lysine in a cell-free system of Streptomyces albulus. Biochemical and biophysical research communications, 31 1(3), pp.635-640 hereby incorporated by reference in its entirety), and synthesis of the antibiotic cefrninox by cell-free extracts of S. clavuligerus (Kim, J.K. et al., 2000. Synthesis of cefrninox by cell-free extracts of Streptomyces clavuligerus. FEMS microbiology letters, 182(2), pp.313-317 hereby incorporated by reference in its entirety). See for example, synthesis of antibiotics in cell-free extracts of S. clavuligerus (Jensen, S.E., Westlake, D. W. & Wolfe, S., 1982. Cyclization of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine to penicillins by cell-free extracts of Streptomyces clavuligerus. The Journal of antibiotics, 35(4), pp.483-490 hereby incorporated by reference in its entirety). Additional useful systems and pathways of Streptomyces include those described in Moore et al. 2007 and Kang, H.-S. & Brady, S.F., 2014. Mining soil metagenomes to better understand the evolution of natural product structural diversity: pentangular polyphenols as a case study. Journal of the American Chemical Society, 136(52), pp.181 1 1-181 19 each of which are hereby incorporated by reference in its entirety. Exemplary species include S. albus, S. lividans, S. coelicolor, S. albovinaceus and S. violaceoruber and the like.

Certain cell-free protein expression systems based on the genus Pseudomonas find use in the present disclosure. A particularly exemplary species includes Pseudomonas aeruginosa which is known to produce naturally occurring products such as the phenazines class of compounds, which are primarily utilized by Pseudomonas aeruginosa in quorum sensing, virulence, and other important biological processes. Important phenazine compounds produced by Pseudomonas aeruginosa include, but are not limited to: pyocyanin, pyoverdine, pyorubin, pyomelanin, fluorescein, 1 -hydroxyphenzaine, phenazine-l-carboxamide, 5- methylphenazine-l-carboxylic acid. A defining characteristic of these compounds is that many are redox-active colored pigments which can be readily detected at low concentrations using high-throughput UV-Vis spectral analysis or electrochemical methods such as cyclic voltammetry, square wave voltammetry, and the like.

Certain cell-free protein expression systems based on the genus Vibrio find use in the present disclosure. A particularly exemplary species includes V. natrigens which can be used for providing extracts, crude or otherwise for use as cell free system for expression of template nucleic acids.

TEMPLATE NUCLEIC ACEPS

Aspects of the present disclosure are directed to the screening of template nucleic acids for the production of a small molecule. Exemplary template nucleic acids include libraries of genes or metabolic pathways, such as libraries generated from genomic fragments, from metagenomic fragments and other genetic source material. Such template nucleic acids may include biosynthetic pathways, fragments containing a biosynthetic pathway, a library of biosynthetic pathways. The source of such biosynthetic pathways may include natural genomic DNA from bacteria, plants, mammals or any other source of natural biosynthetic pathways. The biosynthetic pathways may be synthetic, i.e. engineered, insofar as they do not exist in nature but are created by combining particular genes to create a particular small molecule.

A DNA library for screening can be rationally designed, or can be combinatorial enzyme libraries, or can be derived from natural pathways derived from unknown metagenomic sequences. DNA template for cell-free system can be linear or circular, and prepared from natural or synthetic DNA. In order to identify novel biosynthetic pathways, DNA is extracted from unknown or unculturable environmental organisms to make metagenomic libraries. Natural metagenomic libraries are constructed by extraction and cloning of large DNA fragments into bacterial artificial chromosome (BAC) or other vectors. The pooled library is then maintained and amplified in E.coli for further screening (see for example Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 2000;66: 2541-2547 hereby incorporated by reference in its entirety). Alternatively, synthetic pathways can be constructed by shuffling of natural biosynthetic genes from multiple organisms in a combinatorial fashion, to achieve production of synthetic products and analogs of natural biomolecules (see Martin VJJ, Pitera DJ, Withers ST, Newman JD, Keasling JD. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol. 2003;21 : 796-802; Ro D-K, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 2006;440: 940-943; Keasling JD. Manufacturing molecules through metabolic engineering. Science. 2010;330: 1355-1358 each of which is hereby incorporated by reference in its entirety). In addition, complex genetic circuits can be achieved by adding transcription factors, global regulators, repressors and promoters to affect gene expression (see Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature. 2002;420: 224-230; Sprinzak D, Elowitz MB. Reconstruction of genetic circuits. Nature. 2005;438: 443-448; Guet CC, Elowitz MB, Hsing W, Leibler S. Combinatorial synthesis of genetic networks. Science. 2002;296: 1466-1470 each of which is hereby incorporated by reference in its entirety). Finally, synthetic libraries can also be constructed by mutagenesis of natural genes such that the resulting proteins promote biosynthesis of novel molecules. Methods for producing synthetic genes are known to those of skill in the art and include de novo DNA synthesis, directed evolution, PCR mutagenesis, recombination or chimeragenesis).

It is to be understood that one aspect of the present disclosure is a screening method or assay and so the template nucleic acid within a particular reaction volume is unknown. If small molecule generation is detected, then the template nucleic acid is subject to sequencing to determine its sequence, such as by in situ sequencing.

PROTEINS. ENZYMES OR SMALL MOLECULES

Aspects of the present disclosure are directed to the production of a protein, enzyme or small molecule using a cell-free expression system. It is to be understood that one aspect of the present disclosure is a screening method or assay and so the small molecule that may be generated is unknown. Likewise, the nucleic acid template is unknown.

Small molecules within the scope of the present disclosure include natural products, synthetic products and the like. Important natural product groups include, but are not limited to, terpenoids, anthocyanins, batalains, flavonoids and polyketides (see Delgado- Vargas F, Jimenez AR, Paredes-Lopez O. Natural pigments: carotenoids, anthocyanins, and betalains— characteristics, biosynthesis, processing, and stability. Crit Rev Food Sci Nutr. 2000;40: 173— 289 hereby incorporated by reference in its entirety.) Synthetic products include natural products analogs and synthetic small molecules.

REACTION VOLUMES INCLUDING A TEMPLATE NUCLEIC ACID

Aspects of the present disclosure are directed to a system or method for creating or using a plurality of individual reaction volumes including a cell-free expression system for the screening of small molecule production from a template nucleic acid. Methods and apparatuses for creating a plurality of reaction volumes for high throughput methods are known to those of skill in the art and are adaptable to the present disclosure. For example, cell-free expression systems are advantageous insofar as they utilize a minimal reaction volume which promotes low cost of critical reagents, and are easily integratable into a high- throughput assay scheme using high-capacity well-plates, microarrays, emulsion microdroplets, or mechanical automation. See Sun, Z.Z. et al., 2013. Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. Journal of visualized experiments: JoVE, (79), p.e50762 and Kwon, Y.-C. & Jewett, M.C., 2015. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Scientific reports, 5, p.8663 each of which is hereby incorporated by reference in its entirety.

Methods are known for processing a library of nucleic acid templates such that a single template is present within a single reaction volume. Exemplary reaction volumes may be present within wells of a well plate, on slides, on microarrays, within reaction chambers of a microfluidic device, within microdroplets of an emulsion and the like. See Guo MT, Rotem A, Heyman JA, Weitz DA. Droplet microfluidics for high-throughput biological assays. Lab Chip. 2012; 12: 2146-2155; Zinchenko A, Devenish SRA, Kintses B, Colin P-Y, Fischlechner M, Hollfelder F. One in a million: flow cytometric sorting of single cell-lysate assays in monodisperse picolitre double emulsion droplets for directed evolution. Anal Chem. 2014;86: 2526-2533; Caschera F, Lee JW, Ho KKY, Liu AP, Jewett MC. Cell-free compartmentalized protein synthesis inside double emulsion templated liposomes with in vitro synthesized and assembled ribosomes. Chem Commun . 2016;52: 5467-5469 each of which is hereby incorporated by reference in its entirety. According to one aspect, each reaction volume within a plurality of reaction volumes, for example, for high throughput sequencing, can contain a single nucleic acid template or one or more or multiple or a plurality of nucleic acid templates encoding one or more or a plurality of genes of a biosynthetic pathway for making a small molecule. Accordingly, a single reaction volume can contain one or more or multiple or a plurality of nucleic acid templates. It is to be understood that each reaction volume is not limited to a single nucleic acid template. A single nucleic acid template may be used when the single nucleic acid template encodes all gene form a biosynthetic pathway. However, multiple separate nucleic acid templates can be used which express one or more genes for one or more biosynthetic pathways that together synthesize a small molecule.

Exemplary reaction volumes are within the range of about 1 ul to about 10 ul for high capacity plates, such as a 384-well plate and within the range of approximately 100 pL to 10 nL for microdroplets. Microdroplets are generated using a liquid pump system and microfluidic channels/array from commercial available vendors such as Dolomite Microfluidics, where aqueous droplets containing the reagents for the cell-free reaction are formed within a flowing organic phase. Additional components such as small beads can also be incorporated into this design in order to deliver sensitive payloads like those that could be degraded by endogenous nucleases or proteases as well as to increase temporal control of the cell-free reaction system. Microdroplet formation can be viewed and evaluated for efficiency using a mounted magnifying scope, CCD camera and computer-aided detection software. In one embodiment, microdroplets containing the cell free reaction are singular in nature, however the preferred embodiment would be a double-emulsion in which microdroplets containing the cell-free reaction are again encapsulated in another droplet of larger size formed in a directly connecting channel/array. The double emulsion cell-free system allows for microdroplets to be screened in a high-throughput manner with Fluorescence-activated cell sorting (FACS), general colorimetric based cell sorting, surface deposition on a microarray, or in situ sequencing without prematurely bursting or lose of microdroplet contents. See Caschera F, Lee JW, Ho KKY, Liu AP, Jewett MC. Cell-free compartmentalized protein synthesis inside double emulsion templated liposomes with in vitro synthesized and assembled ribosomes. Chem. Commun. 2016;52: 5467-5469 hereby incorporated by reference in its entirety for further reference for cell-free compartmentalized biosynthesis.

SMALL MOLECULE DETECTION AND IDENTIFICATION

Aspects of the present disclosure are directed to the detection of a small molecule, protein or enzyme using any suitable detection methods, such as detection of color as a feature of the small molecule, protein or enzyme. The screening of desired products can be done by colorimetric, fluorescent or electrochemical methods. Electrochemical screening is exemplary for redox-based detection in several samples.

Exemplary methods for detecting a small molecule exhibiting a color include spectrophotometric methods, fiuorimetric methods and the like. Individual reaction volumes are analyzed to detect whether a small molecule has been produced. Where the reaction volumes are droplets, methods known to those of skill in the art such as FACS or flow cell sorting or other sorting methods may be used to identify the presence of a small molecule in a droplet and then separate out and isolate the droplet for further analysis.

In one embodiment of the methods for small molecule, protein or enzyme detection and identification, the cell-free reactions in 384-well plates are scanned using an instrument with the capacity for scanning the absorbance in the UV and visible wavelengths or an instrument using another detection method. A positive hit, in which a biosynthesis pathway has produced a small molecule, protein or enzyme from a known or unknown pathway from the starting template, is indicated by the formation of distinct peaks on the spectrogram upon the cell-free reaction reaching its termination after a pre-defined number of hours. In order to distinguish between a false-positive, high capacity plates include a set number of wells containing only cell-free extract without template or reaction buffer to be used as a reference blank. These wells do not produce a colorimetric or fluorescent signal beyond background noise. Biomolecules or small molecules extracted from positive hits are then further analyzed using the aforementioned instrumental analysis methods such Liquid Chromatography-Mass Spectrometry (LC-MS), Nuclear Magnetic Resonance (NMR), X-Ray Crystallography to determine molecular structure as well as function with additional assays. The template within the positive hit well is then sequenced with traditional sequencing methods (such as Sanger sequencing), next-generation gene sequencing, or in situ sequencing. This general method for identifying and screening for biomolecules or small molecules can be applied to the aforementioned microdroplet emulsion (singular or double) system established in the previous section in combination with flow cytometry or microarraying methods. For further reference in the instrumental analysis methods for the identification of small molecules discovered from enivionmental/metagenomic sources see Kallifidas, Dimitris, Hahk-Soo Kang, and Sean F. Brady. "Tetarimycin A, an MRSA-Active Antibiotic Identified through Induced Expression of Environmental DNA Gene Clusters." Journal of the American Chemical Society 134.48 (2012): 19552-9555, which is hereby incorporated by reference in its entirety.

According to one aspect, methods are provided for detection of expression products using electrochemical sensing, such as where the expressed product is redox-active. Accordingly, methods are provided for screening redox-active products, such as natural products, in cell-free systems as described herein using electrochemical sensing. For example, methods are provided for the electrochemical detection of natural products in V.natriegens, P. aeruginosa and several Streptomyces spp. IN SITU AMPLIFICATION AND SEQUENCING

According to certain aspects, sequencing is used to identify the coding DNA once a desired product is detected. Sequencing facilitates testing of libraries of unknown metabolic pathways.

The template nucleic acid sequence can be amplified using methods known to those of skill in the art. Methods of amplifying nucleic acids include rolling circle amplification in situ. In certain aspects, methods of amplifying nucleic acids involves the use of PCR, such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241 : 1077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91 :360-364; incorporated herein by reference in their entirety for all purposes). Alternative amplification methods include: self-sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87: 1874, incorporated herein by reference in its entirety for all purposes), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. US. 86: 1 173, incorporated herein by reference in its entirety for all purposes), Q-Beta Replicase (Lizardi et al. (1988) BioTechnology 6: 1 197, incorporated herein by reference in its entirety for all purposes), recursive PCR (Jaffe et al. (2000) J. Biol. Chem. 275:2619; and Williams et al. (2002) J. Biol. Chem. 277:7790; incorporated herein by reference in their entirely for all purposes) or any other nucleic acid amplification method using techniques well known to those of skill in the art. A variety of amplification methods are described in U.S. Patent Nos. 6,391,544, 6,365,375, 6,294,323, 6,261,797, 6, 124,090 and 5,612, 199, incorporated herein by reference in their entirety for all purposes.

The template nucleic acid within a given reaction volume can be sequenced using methods known to those of skill in the art such as in situ sequencing. General sequencing methods known in the art, such as sequencing by extension with reversible terminators, fluorescent in situ sequencing (FISSEQ), pyrosequencing, massively parallel signature sequencing (MPSS) and the like (described in Shendure et al. (2004) Nat. Rev. 5:335, incorporated herein by reference in its entirety), are suitable for use with the matrix in which the nucleic acids are present. Reversible termination methods use step-wise sequencing-by- synthesis biochemistry that coupled with reversible termination and removable fluorescence (Shendure et al. supra and U.S. Patent Nos. 5,750,341 and 6,306,597, incorporated herein by reference. FISSEQ is a method whereby DNA is extended by adding a single type of fluorescently-labelled nucleotide triphosphate to the reaction, washing away unincorporated nucleotide, detecting incorporation of the nucleotide by measuring fluorescence, and repeating the cycle. At each cycle, the fluorescence from previous cycles is bleached or digitally subtracted or the fluorophore is cleaved from the nucleotide and washed away. FISSEQ is described further in Mitra et al. (2003) Anal. Biochem. 320:55, incorporated herein by reference in its entirety for all purposes. Pyrosequencing is a method in which the pyrophosphate (PPi) released during each nucleotide incorporation event (i.e., when a nucleotide is added to a growing polynucleotide sequence). The PPi released in the DNA polymerase-catalyzed reaction is detected by ATP sulfurylase and luciferase in a coupled reaction which can be visibly detected. The added nucleotides are continuously degraded by a nucleotide-degrading enzyme. After the first added nucleotide has been degraded, the next nucleotide can be added. As this procedure is repeated, longer stretches of the template sequence are deduced. Pyrosequencing is described further in Ronaghi et al. (1998) Science 281 :363, incorporated herein by reference in its entirety for all purposes. MPSS utilizes ligation-based DNA sequencing simultaneously on microbeads. A mixture of labelled adaptors comprising all possible overhangs is annealed to a target sequence of four nucleotides. The label is detected upon successful ligation of an adaptor. A restriction enzyme is then used to cleave the DNA template to expose the next four bases. MPSS is described further in Brenner et al. (2000) Nat. Biotech. 18:630, incorporated herein by reference in its entirety for all purposes.

The following examples are set forth as being representative of the present disclosure. These examples are not to be construed as limiting the scope of the present disclosure as these and other equivalent embodiments will be apparent in view of the present disclosure, figures and accompanying claims.

EXAMPLE I

Optimization of Streptomyces Ceil-Free System for the Expression of Superfold sfGFP

A Streptomyces optimized cell free system for in vitro protein expression was developed using an enhanced Transcription-Translation (TX-TL) preparation protocol, based on previously described methods. See Li, J. et al., 2017. Establishing a high yielding streptomyces-based cell-free protein synthesis system. Biotechnology and bioengineering, 114(6), pp.1343— 1353 and Moore, S.J. et al., 2017. Streptomyces venezuelae TX-TL - a next generation cell-free synthetic biology tool. Biotechnology journal, 12(4). Available at: world wide website dx.doi.org/10.1002 biot.201600678 each of which is hereby incorporated by reference in its entirety.

Cell Extract Preparation: S. lividans with strain designation 3213 was purchased from ATCC as a lyophilized spore stock was used to optimize an enhanced TX-TL protocol for expression and quantification of Superfolder GFP (sfGFP). 10 mL of Yeast Extract-Malt Extract (YEME) medium was inoculated in a 100 mL baffled flask with spores from S. lividans lyophilized stock and incubated at 30°C, rotating at 250 RPM for 72 hours. After reaching OD450 of 3.0, cell suspensions were diluted at 1 :500 ratio in 50 mL of fresh YEME medium in a 500 mL baffled flask and incubated for 8 hours under the same conditions. The resulting cell-suspensions were then transferred to 50 mL Falcon tubes and pelleted via centrifugation at 3000 x G for 25 minutes at 4°C. The supernatant of the resulting pellets were suctioned off and the pellets were washed with fresh S30A buffer containing 2 mM DTT twice before being resuspended in 1 mL of S30A buffer in a 2 mL Eppendorf tube for cell lysis via sonication. Concentrated cells-suspensions were then pulse sonicated (Qsonica Sonicator Model CI- 18) for 40 sec with 59 sec stops x4 times in an ice water bath within a cold-room at 4°C. The resulting cell extracts were spun at 15,000 x G for 30 minutes at 4°C and the supernatants were passed through a microcentrifuge column polyethylene filter with a 30 um pore size (Thermo Scientific) at 1000 x G for 5 minutes at 4°C to remove any remaining cell debris. The cell extracts' total protein concentration was quantified with a Qubit Fluorometer Protein Kit (Invitrogen) before being flash frozen in liquid nitrogen and stored until needed at -80°C.

Amino Acid Master Mix: Solutions of each amino acid was obtained from BiotechRabbit (P/N: BR1401801) at a concentration of 168 mM (Lysine at 140 mM). At 4X master mix was made up at a final concentration of 8 mM in this following order: (ALA, ARG, ASN, ASP, GLN, GLU, GLY, HIS, ILE, LYS, MET, PHE, PRO, SER, THR, VAL, TRP, TYR, LEU, CYS) and flash frozen in liquid nitrogen and stored until needed at -80°C.

Energy Solution Master Mix: A 10X master mix of the energy solution was prepared at a total volume of 125 uL. This contained: 500 mM HEPES (pH 8.0 adjusted with 5M KOH), 15 mM ATP, 15 mM GTP, 9 mM CTP, 9 mM UTP, 2 mg/mL E. coli tRNA (MRE100), 2.6 mM CoA, 3.3 mM NAD, 7.5 mM cAMP, 0.70 mM folinic acid, 10 mM Spermidine, and 300 mM 3-Phosphoglyceric Acid (Santa Cruz) added in this order. Energy solutions were aliquoted at 12.5 uL per tube, flash frozen in liquid nitrogen, and stored until needed at -80°C. All reaction components were purchased from Sigma Aldrich unless otherwise specified. Calibration of Critical Components for Optimal Protein Expression: Mg-Glutamate Concentration: The final TX-TL reaction contained 7 mg/mL S. lividans cell extract (volume was 35% of the total), variable Mg-Glutamate (Fig. 1A and IB), 80 mM K-Glutamate, lx Amino Acid Master Mix (1.5 mM each), lx Energy Solution, 500 ng of sfGFP pJLl plasmid (Jewett Lab, Addgene), 2% PEG 8000, 10.5 U of T7 RNA Polymerase (NEB) and 10.5 U of RNase Inhibitor (NEB); the final reaction volume was 10.5 uL and the incubation temperature was 30C. sfGFP signal was measured every 5 minutes over 4 hours on a BioTek Synergy HT plate reader, ex: 485/20 nm & em: 528/20 nm. K-Glutamate Concentration: Using the best results from the Mg-Glutamate concentration calibration (4 mM), the K- Glutamate concentration for TX-TL reactions was also calibrated using the reagents as previously described above, with the exception of variable K-Glutamate.

GFP Quantification: A recombinant GFP (Roche) standard curve was made up in 35% S. lividans cell extract and phosphate buffer saline (PBS) (dynamic range 250 ug/mL - 3.9 ug/mL). After 4 hours of incubation, the TX-TL reaction was stopped by placing plate on ice and then GFP standard curve was added to the 384-well plate. Samples were quantified by comparing their signal at 485/20 nm & em: 528/20 nm to the linear regression generated by the GFP standards. The resulting concentrations were adjusted for background signal with a blank.

It was determined that 4 mM Mg-Glutamate & 140 mM K-Glutamate produced the most GFP at the fastest rate. A GFP concentration was achieved of 42 ng/uL +/- 2 ng/uL, n=3 in 10.5 uL of reaction volume as quantified by the custom GFP plate assay and standard curve described above (see Fig. 1C). EXAMPLE Π

Production of Color Pigments in Streptomyces Cell-Free System

Demonstrate biosynthesis of known biomolecule: To test for cell free production of small molecules, the system of Example I was used for expression of lycopene, an isoprenoid pigment naturally produced in bacteria and plants. The lycopene biosynthetic pathway, previously heterologously expressed in E.coli and S. cerevisiae, is a simple 3-enzyme pathway widely used in microbial metabolic engineering. See Farmer, W.R. & Liao, J.C., 2000. Improving lycopene production in Escherichia coli by engineering metabolic control. Nature biotechnology, 18(5), pp.533-537; Yamano, S. et al., 1994. Metabolic engineering for production of beta-carotene and lycopene in Saccharomyces cerevisiae. Bioscience, biotechnology, and biochemistry, 58(6), pp.1 1 12-1 1 14; and Wang, H.H. et al., 2009. Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460(7257), pp.894-898 each of which are hereby incorporated by reference in its entirety. The CrtE, CrtB and Crtl enzymes necessary for lycopene biosynthesis were expressed under the control of a T7 promoter in transcription-translation reaction conditions calibrated to the S. lividans cell extract used to optimally produce sfGRP in high quantities (Example I).

UV-Vis spectroscopy is used to demonstrate the production of lycopene in the Streptomyces cell-free reaction system by first performing a spectral scan from 300 nm to 700 nm with 10 nm increments and comparing these to a reference standard of lycopene. In order to quantify the concentration of biosynthesized lycopene, a standard curve of lycopene (Sigma) (See Fig. 2) is used to generate a linear regression in which the biosynthesized lycopene can be compared. Using detection methods, the concentration and rate of production of lycopene can be determined. Lycopene further can be characterized with LC-MS, NMR, X-Ray Crystallography or any additional instrumental analysis methods. It is to be understood that the methods described herein for in vitro production and detection of lycopene with instrumental analysis methods can be applied to any other molecule produced in a cell-free reaction environment, for optimization of in vitro conditions and for screening for in vitro production of analogs of natural products.

EXAMPLE ΙΠ

High-Throughput Screen for Rapid Detection of Biosynthesis Pathways Encoding

Biomolecules Exhibiting Color as a Characteristic

Methods described herein allow for previously unexplored biosynthetic pathways encoding novel biomolecules to be produced and identified for further study. In one embodiment, a library of unknown biosynthetic pathways, for example metagenomic fragments, can be screened for production of desired molecules exhibiting color. Extremely small volume (100 pL to 10 nL) transcription - translation reactions can be carried out in 384- well plate or in emulsion droplets generated with a microfluidic chip (t-junction or y- junction) and biphasic (organic/aqueous) pump system. Each microdroplet contains a single barcoded plasmid encoding a biosynthesis pathway of interest. Pathway enzymes can be controlled by T7 promoter or a species-specific promoter, provided the appropriate polymerase is included in the extract. In order to implement sorting of positive hits for small molecule production (as indicated by a color or fluorescent signal change), the emulsion droplets can be encapsulated in a secondary droplet. The mix is screened by flow sorting, or via spectral and fluorescent plate scan.

Exemplary method steps include growing cells and creating cell lysate. The cell lysate is aliquoted (l Oul) in 384-well format with additional assay components. A single template from a DNA library is added to each well to induce small molecule production. High throughput screening is carried out using a plate reader to detect color change. The identity of the small molecule is determined, for example using LC-MS. DNA sequencing is carried out to identify the template nucleic acid sequence for the underlying biosynthetic pathway.

Accordingly, Fig. 3 depicts a schematic of a screening process using a metagenomic DNA library. Cell extracts are produced by optimized protocol (described in Examples I and II). Cell-free extract is aliquoted into array, for example 348-well plate, glass slide or droplets. DNA library is added as template for a transcription-translation system (TX-TL system) (for example metagenomic library carrying unknown or cryptic pathways), such that each reaction mix carries a single template. DNA template initiates transcription and translation of desired pathway, followed by production of biomolecules. The array is then screened for color compounds, for example by UV-vis or fluorimeter. Positive spots are analyzed to detect the product of interest by LC-MS, NMR, X-Ray crystallography and the like and to identify the underlying DNA pathway by NGS (or in situ) sequencing.

Based upon the present disclosure, embodiments include a method of screening a plurality of template nucleic acid sequences for small molecule production including adding a template nucleic acid sequence from the plurality to each reaction volume within a plurality of reaction volumes, wherein each reaction volume includes a cell-free expression system under conditions of transcription and translation; detecting generation of a small molecule in a target reaction volume; and sequencing of the template nucleic acid sequence of the target reaction volume. According to one aspect, the cell-free expression system includes cell lysate from bacterial cells, yeast cells, plant cells, insect cells, or mammalian cells. According to one aspect, the cell-free expression system includes cell lysate from bacterial cells. According to one aspect, the cell-free expression system includes cell lysate from Streptomyces, Escherichia or Bacillus. According to one aspect, the cell-free expression system includes cell lysate from Streptomyces. According to one aspect, the template nucleic acid sequence is a DNA template or an RNA template. According to one aspect, the template nucleic acid sequence is a DNA template encoding one or more genes for making the small molecule. According to one aspect, the template nucleic acid sequence is a DNA template encoding a metabolic pathway for the small molecule. According to one aspect, the template nucleic acid sequence is a linear DNA template or circular DNA template. According to one aspect, each reaction volume includes a single template nucleic acid sequence from the plurality. According to one aspect, the method includes detecting generation of small molecules in a plurality of reaction volumes and sequencing of the template nucleic acid sequence of the plurality of reaction volumes. According to one aspect, detecting generation of the small molecule includes detecting color of the small molecule. According to one aspect, the template nucleic acid sequence is sequenced using in situ sequencing. According to one aspect, the template nucleic acid sequence is sequenced using fluorescent in situ sequencing. According to one aspect, the plurality of reaction volumes is a plurality of wells in a well plate. According to one aspect, the plurality of reaction volumes is a plurality of droplets. According to one aspect, the plurality of reaction volumes is a plurality of droplets within an emulsion. According to one aspect, each reaction volume includes one or more energy substrates, one or more cofactors, one or more salts, one or more amino acids and one or more nucleotides. According to one aspect, the plurality of template nucleic acid sequences is a library of template nucleic acid sequences. According to one aspect, the plurality of template nucleic acid sequences is a subset of a library of template nucleic acid sequences. According to one aspect, the plurality of template nucleic acid sequences is a subset of a library of biosynthetic pathways. According to one aspect, the plurality of template nucleic acid sequences is a subset of a library of fragments comprising a biosynthetic pathway. According to one aspect, the plurality of template nucleic acid sequences comprises natural genomic DNA. According to one aspect, the plurality of template nucleic acid sequences comprises natural biosynthetic pathways. According to one aspect, the plurality of template nucleic acid sequences comprises engineered biosynthetic pathways. According to one aspect, the plurality of template nucleic acid sequences is comprised of metagenomic sequences. According to one aspect, the plurality of template nucleic acid sequences is comprised of unknown metagenomic sequences.

EXAMPLE IV

Establishment of a V. natriegens Cell Free System

The effect V. natriegens culture conditions on extract protein yield was studied. Fig. 4A depicts the effect of culture growth media on cell-free extract protein yield. V. natriegens cells were grown in the indicated media at 30°C to OD₆oo = 1.0. Crude cell extract was prepared and production of sfGFP measured over three hours. (LB3 - LB with 3% (w/v) NaCl; LB-V2 - LB with V2 salts; LBO - LB with Ocean Salts, NBO - Nutrient Broth with Ocean Salts; BHIO - Brain Heart Infusion with Ocean Salts; and MB - Marine Broth). V. natriegens cell-free systems derived from crude extract grown in each of these media diversifies the library of cell-free reactions to perform high-throughput screens.

Fig. 4B depicts the generation time and sfGFP yield for each media type tested. This indicates the general activity level in terms of cell-free protein expression for each of the media types.

Fig. 4C depicts the optical density at the time of cell harvest. Unless otherwise indicated, cell free reactions were incubated at 26°C in a thermocycler using 500 ng of plasmid DNA, 80 mM K-glutamate and 3.5 mM Mg-glutamate. sfGFP yield was measured after 3 hours. The mean and standard deviations are shown (N=3). Optical density of the cells at the time of harvest dictates the state of the cell-free system. Typically, high protein expression is observed in from crude extracts derived from cells in exponential phase of growth, whereas secondary metabolite pathways are active at stationary phase.

Fig. 4D depicts results of a study of cell-free incubation temperature. The temperature of cell-free incubation affects the expression activity of the cell-free system. This can vary depending on the application, for example, 26°C is exemplary for protein expression in V. natriegens cell-free reactions.

Fig. 4E depicts results of a study of supplemented potassium ions in reaction buffer. The concentration of supplemented potassium ions also affects the activity of the cell-free system. This can vary depending on the application, for example, 80 mM K+ is exemplary for protein expression in V. natriegens cell-free reactions.

Fig. 4F depicts results of a study of supplemented magnesium ions in reaction buffer. The concentration of supplemented magnesium ions also affects the activity of the cell-free system. This can vary depending on the application, for example, 3.5 mM Mg²⁺ is exemplary for protein expression in V. nulriegem cell-free reactions.

Fig. 4G depicts percent of cell free extract relative to total reaction volume. Yield and rate of reaction are shown. The percent of cell free extract relative to the total reaction volume affects the activity of the cell-free system.

Fig. 4H depicts the template DNA used for expression of sfGFP. Equimolar amount of circular plasmid (pJLl, grey), linear DNA (PCR product, black solid line) or linear DNA with two phosphorothioated bonds on each end (PCR product, black dotted line) was used. The use of linear template over circular plasmid in cell-free reactions allows for template derived from PCR amplicons to be directly expressed in the cell-free reaction. This increases the accessibility testable sequences for high-throughput screening.

Fig. 41 depicts degradation of linear DNA template. Fluorescence of AlexaFluor 594- 5-dUTP labeled linear template was monitored over two hours. Template with (dotted) or without (solid) two phosphorothioated bonds on each end was used. Unless otherwise indicated, all experiments were performed using V. natriegens crude cell extract incubated at 26°C for three hours, supplemented with 80 mM K-glutamate and 3.5mM Mg-glutamate. The mean and standard deviations are shown (N=3). The use of linear template over circular plasmid in cell-free reactions allows for template derived from PCR amplicons to be directly expressed in the cell-free reaction. This increases the accessibility testable sequences for high-throughput screening. While there is some observed degradation of the linear template, enough is present to produce appreciable amounts of protein in the V. natriegens cell-free system.

EXAMPLE V

Pseudomonas aeruginosa Cell Free System

A Pseudomonas aeruginosa cell-free expression system was provided. Fig. 5A and 5B depict sfGFP production measured at varying potassium and magnesium ion concentrations that was used to perform an initial calibration of T7 RNA Polymerase mediated protein synthesis by the cell-free expression system. Pseudomonas aeruginosa was harvested at (a) OD6oo=1.0 or (b) OD6oo=3.0. Figs. 5C and 5D depict natural product production at varying potassium and magnesium ion concentrations as measuring by UV/Vis analysis. Pseudomonas aeruginosa was harvested at OD6oo⁼1.0 or OD6oo=3.0, respectively. Full spectral analysis of Pseudomonas aeruginosa cell-free expression system from crude extract prepared from cells at OD₆oo=1.0 (Fig. 5E) after 360 minutes of incubation and OD₆oo=3.0 after 360 minutes of incubation (Fig. 5F). These data indicate the results of an exemplary cell-free expression system and its initial optimization for protein expression and natural product synthesis. It was observed that P. aeruginosa cell-free system produced natural products under certain cell-free reaction conditions as detected by UV-Vis spectroscopy.

EXAMPLE VI

Temperature Calibration of Pseudomonas aeruginosa cell-free expression system

Fig. 6A depicts that sfGFP cell-free expression was calibrated for Pseudomonas aeruginosa crude extracts derived from cells harvested at OD6oo=1.0 or OD6oo=3.0. Fig. 6B is a heat-map of full UV-Vis spectral scan of Pseudomonas aeruginosa cell-free reactions with crude extract derived from cells harvested at OD6oo=3.0 from post 360-minute incubation at the indicated temperature. High absorbances at 340-390 nm indicate a natural product accumulating in Pseudomonas aeruginosa cell-free expression system. Please describe the importance of the data. These data indicate the results of an exemplary cell-free expression system and its initial optimization for protein expression and natural product synthesis specially for cell-free reaction temperature. It was observed that P. aeruginosa cell-free system produced natural products under certain cell-free reaction temperatures as detected by UV-Vis spectroscopy.

EXAMPLE VII

Cyclic Voltammetry Electrochemical Analysis of Pseudomonas aeruginosa Cell-free

Reactions

Cyclic voltammetry electrochemical analysis was performed on Pseudomonas aeruginosa cell-free reactions post incubation at 37°C for 360 minutes. As depicted in Fig. 7, black arrows indicate detected peaks corresponding to redox-active molecules in cell-free reactions derived from cells harvested at (lighter) OD6oo=l -0 or (darker) OD6oo=3.0. Cyclic voltammetry was performed on a DropSens μ8ΤΑΤ8000 Potentiostat and analyzed using DropView software. All measurements were baseline corrected. These results indicate that redox-active natural products are detectable by the electrochemical analysis method cyclic voltammetry in P. aeruginosa cell-free reactions. Using cyclic voltammetry for analysis of cell-free reactions is an advantageous application of the method.

EXAMPLE VIII

Square Wave Voltammetry Electrochemical Analysis of Pseudomonas aeruginosa Cell- free Reaction

Square wave voltammetry electrochemical analysis was performed on a Pseudomonas aeruginosa cell-free reaction post incubation at 37°C for 360 minutes. As depicted in Fig. 8, black arrows indicate detected peaks corresponding to redox-active compounds in cell-free reactions derived from cells harvested at OD6oo=3.0. Square wave voltammetry was performed on a DropSens μ8ΤΑΤ8000 Potentiostat and analyzed using DropView software. All measurements were baseline corrected. These results indicate that redox-active natural products are detectable by the electrochemical analysis method square wave voltammetry in P. aeruginosa cell-free reactions. Using square wave voltammetry for analysis of cell-free reactions is an advantageous application of the method.

EXAMPLE IX

Square Wave Voltammetry Electrochemical Analysis of Several Streptomyces spps. Cell- free Reactions

Square wave voltammetry electrochemical analysis was performed on a several Streptomyces spps. cell-free reactions post incubation at 30°C for 360 minutes. As depicted in Figs. 9A-9E, black arrows indicate detected peaks corresponding to redox-active compounds in cell-free reactions derived from cells harvested at OD6oo=1.0. Square wave voltammetry was performed on a DropSens μ8ΤΑΤ8000 Potentiostat and analyzed using DropView software. All measurements were baseline corrected. Fig. 8A: Protein expression in Streptomyces spps. cell-free reactions. Square wave voltammetry analysis of S. violaceoruber (Fig. 9B), S. lividans (Fig. 9C), S. coelicolor (Fig. 9D), and S. albovinaceus (Fig. 9E). All electrochemical measurements were baseline corrected. These results indicate that redox- active natural products are detectable by the electrochemical analysis method square wave voltammetry in Streptomyces spps. cell-free reactions.

EXAMPLE X

Square Wave Voltammetry Electrochemical Analysis of Vibrio natriegens Cell-Free

Reactions (Effect of Optical Density)

Square wave voltammetry electrochemical analysis was performed on a Vibrio natriegens cell-free reactions post incubation at 26°C for 180 minutes. As indicated in Figs. 10A-10D, black arrows indicate detected peaks corresponding to redox-active compounds in cell-free reactions derived from cells harvested at OD₆oo=1.0 (Fig. IOC) and OD6oo=3.0 (Fig. 10D). All electrochemical measurements were baseline corrected. Protein expression was measured concurrently as indicated in a kinetic plot of sfGFP production (Fig. 10A) and rate of sfGFP production at each measured time point for Vibrio natriegens cell-free (Fig. 10B). Please describe the importance of the data. These results indicate that redox-active natural products are detectable by the electrochemical analysis method square wave voltammetry in V. natriegens cell-free reactions. In addition, it was observed that the optical density at the time of harvest affects the production of natural products. As previously described, lower optical densities corresponding to exponential phase of growth are less apt to have biosynthetic pathways active to produce secondary metabolites, whereas optical densities corresponding to stationary phase are likely to have many active biosynthetic pathways. EXAMPLE XI

Square Wave Voltammetry Electrochemical Analysis of Vibrio natriegens Cell-Free

Reactions (Effect of Growth Media)

Square wave voltammetry electrochemical analysis was performed on a Vibrio natriegens cell-free reactions derived from various cells grown in various media types post incubation at 26°C for 180 minutes. Figs. 11A and 11B indicate cell-free reaction activity by plotting kinetic expression of sfGFP. Fig. 1 1C depicts generation time of Vibrio natriegens in several media types. Black arrows indicate detected peaks corresponding to redox-active compounds in cell-free reactions derived from cells grown in LB3 (Fig. 1 1D), Brain Heart Infusion + Ocean Salts (Fig. HE), LB + Ocean Salts (Fig. 1 IF), and Marine Broth (Fig. 1 1G). All electrochemical measurements were baseline corrected. These results indicate that redox-active natural products are detectable by the electrochemical analysis method square wave voltammetry in V. natriegens cell-free reactions. As previously indicated, the growth media affects the overall state of the cell when harvesting for cell-free crude extract production. Cell-free reactions of V. natriegens derived from the various cell growth media produce different redox-active natural products as determined by square voltammetry.

EXAMPLE XII

Cell-free Protein Synthesis from Mixtures of E. coli and V. natriegens crude extracts

Super fold GFP yields from cell-free reactions consisting of 1 :1 mixtures of crude extracts derived from E. coli strain A19 and V. natriegens under varying reaction conditions was determined. Fig. 12 depicts from left to right: optimized control reaction for V. natriegens at the preferred incubation temperature of 26C, optimized control reactions for E. coli strain A19 at the preferred incubation temperature of 37C, mixture of crude extracts incubated at V. natriegens preferred incubation temperature and optimal conditions, mixture of crude extracts at E. coli strain A19 preferred incubation temperature and V. natriegens optimal conditions, mixture of crude extracts at V. natriegens preferred incubation temperature and E. coli strain A19 optimal conditions, mixture of crude extracts incubated at E. coli strain A19 preferred incubation temperature and optimal conditions. (N=3). Mixtures of various cell-free crude extracts are provided in methods herein to further explore biosynthesis pathways that may be active in the presence of the respective combination. For example, a mixture of E. coli and V. natriegens could yield natural products from otherwise inaccessible pathways not common naturally. Here, it was observed that under certain cell- free reaction conditions, protein expression is enhanced in cell-free mixture reaction over the single species cell-free reaction controls.

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Claims

What is claimed is:

1. A method of screening a plurality of template nucleic acid sequences for small molecule production comprising

adding a template nucleic acid sequence from the plurality to each reaction volume within a plurality of reaction volumes, wherein each reaction volume includes a cell-free expression system under conditions of transcription and translation;

detecting generation of a small molecule in a target reaction volume; and

sequencing of the template nucleic acid sequence of the target reaction volume.

2. The method of claim 1 wherein the cell-free expression system comprises cell lysate from bacterial cells, yeast cells, plant cells, insect cells, or mammalian cells.

3. The method of claim 1 wherein the cell-free expression system comprises cell lysate from bacterial cells.

4. The method of claim 1 wherein the cell-free expression system comprises cell lysate from Streptomyces, Escherichia or Bacillus.

5. The method of claim 1 wherein the cell-free expression system comprises cell lysate from Streptomyces.

6. The method of claim 1 wherein the template nucleic acid sequence is a DNA template or an RNA template.

7. The method of claim 1 wherein the template nucleic acid sequence is a DNA template encoding one or more genes for making the small molecule.

8. The method of claim 1 wherein the template nucleic acid sequence is a DNA template encoding a metabolic pathway for the small molecule.

9. The method of claim 1 wherein the template nucleic acid sequence is a linear DNA template or circular DNA template.

10. The method of claim 1 wherein each reaction volume includes a single template nucleic acid sequence from the plurality.

1 1. The method of claim 1 comprising detecting generation of small molecules in a plurality of reaction volumes and sequencing of the template nucleic acid sequence of the plurality of reaction volumes.

12. The method of claim 1 wherein detecting generation of the small molecule includes detecting color of the small molecule.

13. The method of claim 1 wherein the template nucleic acid sequence is sequenced using in situ sequencing.

14. The method of claim 1 wherein the template nucleic acid sequence is sequenced using fluorescent in situ sequencing.

15. The method of claim 1 wherein the plurality of reaction volumes is a plurality of wells in a well plate.

16. The method of claim 1 wherein the plurality of reaction volumes is a plurality of droplets.

17. The method of claim 1 wherein the plurality of reaction volumes is a plurality of droplets within an emulsion.

18. The method of claim 1 wherein each reaction volume includes one or more energy substrates, one or more cofactors, one or more salts, one or more amino acids and one or more nucleotides.

19. The method of claim 1 wherein the plurality of template nucleic acid sequences is a library of template nucleic acid sequences.

20. The method of claim 1 wherein the plurality of template nucleic acid sequences is a subset of a library of template nucleic acid sequences.

21. The method of claim 1 wherein the plurality of template nucleic acid sequences is a subset of a library of biosynthetic pathways.

22. The method of claim 1 wherein the plurality of template nucleic acid sequences is a subset of a library of fragments comprising a biosynthetic pathway.

23. The method of claim 1 wherein the plurality of template nucleic acid sequences comprises natural genomic DNA.

24. The method of claim 1 wherein the plurality of template nucleic acid sequences comprises natural biosynthetic pathways.

25. The method of claim 1 wherein the plurality of template nucleic acid sequences comprises engineered biosynthetic pathways,

26. The method of claim 1 wherein the plurality of template nucleic acid sequences is comprised of metagenomic sequences.

27. The method of claim 1 wherein the plurality of template nucleic acid sequences is comprised of unknown metagenomic sequences.

28. The method of claim 1 wherein detecting generation of the small molecule includes detecting using colorimetric, fluorescent or electrochemical methods.

29. The method of claim 1 wherein the cell-free expression system comprises cell lysate from two or more different genus or species cells.

30. The method of claim 1 wherein the cell-free expression system comprises cell lysate from extracts of one or more, two or more or a plurality of cells of the following, but not limited to, genera: Staphylococcus, Pseudomonas, Streptomyces, Flavobacterium, Bacillus, Deinococcus, Thermus, Escherichia or Vibrio.

31. The method of claim 1 wherein the cell-free expression system comprises cell lysate from two or more or a plurality of cells of the following, but not limited to, genera: Staphylococcus, Pseudomonas, Streptomyces, Flavobacterium, Bacillus, Deinococcus, Thermus, Escherichia or Vibrio.