WO2020118261A2

WO2020118261A2 - Bacillus expression system

Info

Publication number: WO2020118261A2
Application number: PCT/US2019/065080
Authority: WO
Inventors: Jeffrey J. TABOR; Sebastian M. CASTILLO-HAIR
Original assignee: William Marsh Rice University
Current assignee: William Marsh Rice University
Priority date: 2018-12-06
Filing date: 2019-12-06
Publication date: 2020-06-11
Anticipated expiration: 2021-06-06
Also published as: US20250043293A1; US12460215B2; WO2020118261A3

Abstract

An inducible promoter expression system based on the T7 RNA Polymerase (T7 RNAP), lactose repressor (Lad), and a chimeric T7lac promoter (PT7lac), which can be integrated as a single copy into the B. subtilis genome. In the absence of IPTG, Lad strongly represses T7RNAP and PT7lac, and expression of an exemplary ORF — here superfolder green fluorescent protein (sfGFP) reporter protein — is undetectable by flow cytometry. Addition of IPTG de-represses PT7lac, and simultaneously induces expression of T7RNAP, resulting in very high sfGFP levels.

Description

BACILLUS EXPRESSION SYSTEM

PRIOR RELATED APPLICATIONS

[0001] This application claims priority to US Serial No. 62/776,132, filed December

6, 2018, and incorporated by reference in its entirety for all purposes.

FEDERALLY SPONSORED RESEARCH STATEMENT

[0002] This invention was made with government support under Grant Nos:

R21 All 15014 and MCB1616755, awarded by the NIH and NSF, respectively. The government has certain rights in the invention.

FIELD OF THE DISCLOSURE

[0003] This invention provides materials and methods allowing expression of RNA and proteins in Bacillus , especially B. subtilis and similar species, with a new tightly regulated, integrative and inducible expression system.

BACKGROUND OF THE DISCLOSURE

[0004] Bacillus subtilis is a model organism for studies of Gram-positive bacterial biology and systems biology of cellular differentiation, stress responses, and multicellular organization. Additionally, B. subtilis is among the most widely used hosts for protein production in the biotechnology industry due to its ability to secrete proteins into the cell medium, its non-pathogenic GRAS (generally recognized as safe) designation, and its high genetic tractability. For example, B. subtilis is used for large-scale production of lipases, proteases, and amylases, among other industrially- relevant proteins.

[0005] However, B. subtilis work has been limited by a lack of high-quality synthetic biological parts. For example, biotechnology applications require inducible promoters capable of switching between a low production state for early-stage culturing and a high production state that maximizes protein yield during fermentation. Such parts are particularly important when the recombinant protein or metabolic pathway of interest are toxic to the host cells when overproduced. [0006] Typical inducible promoters in B. subtilis have dynamic ranges (ratio of output protein expression in the presence versus absence of inducer) of at most a few hundred. While a B. subtilis bacitracin-inducible promoter with a 1,000-fold range has been reported (13), it requires antibiotic selection to maintain a multicopy plasmid, and its activity is transient and shuts down less than two hours after induction, likely due to an endogenous bacitracin stress response. In contrast, for the Gram-negative bacterium Escherichia coli , inducible promoters have been engineered with dynamic ranges greater than 1,000 or even 10,000.

[0007] Thus, improved B. subtilis inducible promoter systems are greatly needed in the art. The ideal system will be very tightly regulated, result in high levels of protein expression when induced, have 10,000 or even greater fold dynamic range, and ideally be integratable into the genome.

SUMMARY OF THE DISCLOSURE

[0008] Protein expression systems that are activated in response to chemicals such as IPTG, xylose or bacitracin currently exist for B. subtilis. However, their fold- activation values are fairly low, and their active output levels are limited by the B. subtilis endogenous transcription machinery. On the other hand, a few systems based on the exogenous viral T7 RNA Polymerase (T7 RNAP) have been previously built. While these achieve high expression levels, protein production in the inactive state or “leakiness” is fairly high and therefore fold-activation is still low.

[0009] Here, we have engineered an extraordinarily stringent and strongly inducible protein expression system for Bacillus. This system combines the viral T7 RNAP, which produces high amounts of recombinant protein in the active state, with the Lad bacterial transcription factor that inhibits production of both the protein and the viral polymerase, resulting in nearly undetectable output in the inactive state. Our system achieves greater than 10,000-fold or even 20,000-fold activation in response to a chemical inducer. We expect this system to improve yield of existing protein production, especially toxic proteins, or metabolic engineering applications using B. subtilis and possibly other Bacillus species, and enable synthesis of new proteins and chemicals that were previously unfeasible. [0010] Our Lad-T7 inducible system comprises the following elements:

• Transcriptional repressor Lad, expressed constitutively.

• The T7 phage RNA polymerase (T7 RNAP), expressed from the B. subtilis promoter V_hy-spmk, which is normally repressed by Lack

• The hybrid P_T7 iac promoter, normally repressed by Lad as well, under whose control the recombinant protein of interest or ORF is placed.

[0011] For an integrative sequence, these elements should be flanked by first and second portions of a non-essential portion of the Bacillus genome, thereby allowing integration into that genome. The order of parts is typically not critical, but whatever the order, the cassette is flanked by the integrating sequences such that everything there between is integrated into the genome. In addition, sequences to optimize expression of the target ORF can also be included, such as ribosome binding sites, enhancers, terminators, and the like.

[0012] The cassette can be assembled and used as is, or can be formulated as an

expression vector— capable of self-reproduction and ORF expression. For an expression vector, additional vector sequences are added, allowing replication in Bacillus and/or E.coli (e.g., ori), marker genes for selection (e.g., antibiotic resistance), unique restriction endonuclease (RE) sites or the multi-cloning site, shuttle sequences allowing the vector to shuttle e.g., between E. coli and Bacillus (both ori sequences), or between yeast and Bacillus ( Bacillus ori and autonomously replicating sequence (ARS), a yeast centromere (CEN), and a yeast selectable marker), viral packaging sequences, protein degradation tags, and the like. It may also be possible to formulate the cassette described herein as minivectors, such as those described by Twister® (Houston TX).

[0013] La and the V_hy-spanu promoter were obtained from pDRl 11 (ATCC® 53123), a commercially available plasmid for genomic integration in B. subtilis. The P_{T7 lac} promoter sequence is identical to that included in some of the commercially-available E. coli pET plasmids, and was synthesized via oligo annealing and extension. The sequence of the T7 RNAP is identical to that found in the E. coli BL21(DE3) strain, and was obtained from an E. coli plasmid. [0014] DNA coding for these elements was assembled, together with a spectinomycin resistance cassette. Flanking sequences for genome integration were added that were homologous to the B. subtilis amyE genomic locus, but any non-essential loci could be used. The assembled DNA cassette was then integrated into the Bacillus genome via standard Bacillus transformation methods.

[0015] In the inactive state, Lad repression of both T7 RNAP production and P_T7 iac ensures very low production of recombinant protein. Upon addition of chemical inducer IPTG to the cell media, Lacl-repression is relieved and the T7 RNAP is produced. The T7 RNAP can now transcribe the recombinant gene from the now unrepressed P_T7 iac promoter.

[0016] To assess the performance of the Lacl-T7 system, we placed superfolder GFP

(sfGFP) under P_T7 i_ac and measured cell fluorescence in the presence or absence of IPTG. This resulted in high levels of fluorescence in the presence of IPTG, but undetectable levels in its absence. Based on estimates of the limit of detection of our flow cytometer instrument, we placed a lower bound on the fold-activation of this system at 20,000. We have also tested the system with other report

[0017] The invention includes any one or more of the following in any

combination(s) thereof.:

_

[0018] As used herein“recombinant” or“engineered” is relating to, derived from, or containing genetically engineered material. In other words, the genome was intentionally manipulated by humans in some way.

[0019] “Expression vectors” are used in accordance with the art-accepted definition of a plasmid, virus, cosmid, or other propagatable sequence designed for protein expression in cells. There are thousands of such vectors commercially available, and typically each has an origin of replication (ori); a multiple cloning site; a selectable marker; ribosome binding sites; a promoter and often enhancers; and the needed termination sequences. Most expression vectors are inducible, although constitutive expression vectors also exist and either can be used.

[0020] As used herein,“inducible” means that gene expression can be controlled by the hand-of-man, by adding e.g., a ligand to induce expression from an inducible promoter. Exemplary inducible promoters include the lac promoter, inducible by isopropyl thio- -D-galactopyranoside (IPTG), the yeast AOX1 promoter inducible with methanol, the strong LAC4 promoter inducible with lactate, and the like. Low level of constitutive protein synthesis may occur even in expression vectors with tightly controlled promoters. “Constitutive” means there is always expression from that promoter. P_veg is an example of same.

[0021] As used herein,“integrative” or“integratable” means the nucleic acid has the ability to integrate into a B. subtilis or equivalent genome.

[0022] As used herein, an“integrated sequence” means the sequence has been

integrated into the host genome, as opposed to being maintained on an expression vector or as a separate integration cassette. It will still be expressible, either inducibly or consti tutively. Herein, we are more interested in tightly regulated and highly activatable inducible expression vectors and/or cassettes that are integrative or are integrated.

[0023] As used herein,“operatively connected” or“operatively coupled” with respect to DNA sequences means that the oligonucleotide segments are connected in such a way as to allow the DNA (or RNA or protein derived therefrom) to be functional in a cell. Typically, this means e.g., the correct spacing, essential regulatory sequences, and reading frame (if applicable) are maintained.

[0024] As used herein,“homolog” means an enzyme with at least 40% identity to one of the listed sequences and also having the same general catalytic activity, although kinetic parameters of the reactions can of course vary. While higher identity (60%, 70%, 80%) and the like may be preferred, it is typical for bacterial sequences to diverge significantly (40-60% identity), yet still be identifiable as homologs, while mammalian species tend to diverge much less (80-90% identity). Unless specified otherwise, any reference to an enzyme herein also includes its homologs that catalyze the same reaction.

[0025] As used herein, references to cells or bacteria or strains and all such similar designations include progeny thereof. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations that have been added to the parent. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.

[0026] The use of the word“a” or“an” when used in conjunction with the term

“comprising” in the claims or the specification means one or more than one, unless the context dictates otherwise.

[0027] The term“about” means the stated value plus or minus the margin of error of measurement or plus or minus 10% if no method of measurement is indicated.

[0028] The use of the term“or” in the claims is used to mean“and/or” unless

explicitly indicated to refer to alternatives only or if the alternatives are mutually exclusive. [0029] The terms“comprise”,“have”,“include” and“contain” (and their variants) are open-ended linking verbs and allow the addition of other elements when used in a claim.

[0030] The phrase“consisting of’ is closed, and excludes all additional elements.

[0031] The phrase“consisting essentially of’ excludes additional material elements, but allows the inclusions of non-material elements that do not substantially change the nature of the invention.

[0032] The following abbreviations are used herein:

DESCRIPTION OF FIGURES

[0033] FIG 1AF. Lacl-T7 design and performance. [0034] FIG. 1A Genetic device schematic of Lacl-T7 with regulatory interactions shown.

[0035] FIG. IB sfGFP fluorescence from Lacl-T7 and Phy-spank in the absence or presence of IPTG. Fluorescence is shown in calibrated Molecules of Equivalent Fluorescein (MEFL) units. Bars represent the mean of three experimental replicates run on separate days. Dots show the values of the individual replicates.

[0036] FIG. 1C-D Representative flow cytometry histograms of autofluorescence control ( B . subtilis lacking any sfgfp gene), and those with sfgfp under either Lacl-T7 (1C) or P_hy-spank (ID), in the presence or absence of IPTG.

[0037] FIG. IE sfGFP Fluorescence from Lacl-T7 and Phy-spank as a function of IPTG concentration.

[0038] FIG. IF sfGFP fluorescence from Lacl-T7 and Phy-spank after addition of

saturating IPTG. Dots and error bars show the mean and standard deviation, respectively, of three experiments run on separate days. Error bars are, in most cases, smaller than the size of the dots, and thus not visible. Black lines represent model fits.

[0039] FIG. 2: T71ac promoter (PT7 lac) and placing of the gene of interest. PT7 iac is highlighted with underline. Ribosome binding site is highlighted with double underline. The start codon (ATG) of the gene to be expressed is shown in bold. SEQ ID NO 1.

[0040] FIG. 3: Promoter hyper spank SEQ ID NO 2.

[0041] FIG. 4. T7 RNAP SEQ ID NO 3.

[0042] FIG. 5: Promoter _r6hr SEQ ID NO 4.

[0043] FIG. 6. Lacl-T7 -sfgfp. SEQ ID NO 5.

[0044] FIG. 7: Compete expression system sequence SEQ ID NO 6.

[0045] FIG. 8 Complete Vector without sfGFP SEQ ID NO 7.

[0046] FIG. 9. Variant LacI-T7-sfgfp SEQ ID NO 8. [0047] FIG. 10: Compete Vector with sfGFP Variant SEQ ID NO 9.

[0048] FIG. 11. Growth curves of Lacl-T7 strains. Lacl-T7-.s/¾ (A) and Lacl-T7- lacZ (B) strains were grown in the absence or presence of IPTG, and the OD600 of each culture was measured at the indicated timepoints. Dots indicate individual OD600 measurements. Continuous lines indicate best fits to an exponential growth model. Estimated doubling times and uncertainties (standard error) are indicated next to the corresponding growth curves.

[0049] FIG. 12 SDS-PAGE and immunoblot analysis of sfGFP expression from Phy- spank and Lacl-T7. (A) Whole cell extracts of wild-type, Phy-spank-sfgfp and Lacl- ΎΊ- fgfp strains grown in the absence or presence of IPTG were analyzed by SDS- PAGE and stained with Coomassie brilliant-blue . The arrow on the right points to the expected sfGFP location. (B) sfGFP expression was further examined by immunoblot analysis using polyclonal anti-GFP antibodies. (C) As a loading control, expression of the constitutively expressed sA protein was examined by immunoblotting with anti- sA antibodies.

[0050] FIG. 13. Performance of Lacl-T7 measured via b-galactosidase. (A) Device schematic of the Lacl-T7 system expressing lacZ. (B) b-galactosidase activity in the absence or presence of IPTG. Bars show the mean of three experiments run on separate days. Dots show values of individual experimental replicates.

[0051] Table 1. Data.

[0052] Table 2. Various sequences SEQ ID NO 10-22.

PI TA 11 FI) DESCRIPTION

[0053] In more detail, we have engineered a stringent (i.e. non-leaky) and highly- inducible Lacl-T7 promoter system for B. subtilis. Our system utilizes the hybrid P_T7_/OC promoter to express a gene of interest, and the IPTG-inducible promoter P_hy-spank to express the T7 RNA Polymerase (T7 RNAP) (FIG. 1A).

[0054] In the absence of the IPTG inducer, the repressor lacl is active and both T7

RNAP and P_{T7 lac} are thereby repressed. This dual repression minimizes leaky expression of the gene of interest. Thus, the system is very stringent, with little to no detectable leaking. Upon addition of IPTG, Lacl activity is inhibited, and the newly produced T7 RNAP strongly transcribes the gene of interest from the now de- repressed P_T7 iac (FIG. 1A).

[0055] Our Lacl-T7 design is conceptually similar to some variants of the

commercial E. coli pET expression system, where IPTG also induces both expression of T7 RNAP and de-repression of Rt7_/ae. However, our system uses Bacillus or B. subtilis- specific promoters (other than P_T7 i_ac) and ribosome-binding sites (RBSs). Additionally, while a few B. subtilis gene expression systems based on T7 RNAP have been previously reported, they use the Laci-independent P_T7 instead of P-n_/m, resulting in dynamic ranges of less than 50.

[0056] To validate our design, we placed a sfgfp reporter gene²² with a codon- optimized N-terminal fragment {sfgfp*) under control of Lacl-T7, the self-cleaving ribozyme RiboJ, and RBS MF001, and integrated it into the non-essential amyE locus of the B. subtilis genome as a single copy (FIG. 1A).

[0057] We utilized flow cytometry to characterize sfGFP fluorescence levels in the absence and presence of IPTG. We found that, in the absence of inducer, sfGFP fluorescence equals 17.9 ± 4.7 molecules of equivalent fluorescein (MEFL) (FIG. IB and C). In contrast, sfGFP levels in the presence of IPTG are 432,000 ± 20,000 MEFL (FIG. IB and C), resulting in a dynamic range of 25,300 ± 6,900.

Remarkably, only a small growth slowdown was observed under inducing conditions (cell division time: 25.15 ± 0.46 minutes without IPTG, 30.2 ± 1.1 minutes with IPTG) (not shown). Polyacrylamide gel electrophoresis (PAGE) analysis of total cellular protein indicated that sfGFP is the mostly highly expressed protein in the cell in the presence of IPTG (not shown).

[0058] To validate that this high dynamic range is preserved when expressing a

different gene of interest, we placed the lacZ reporter gene under Lacl-T7 (FIG. 13) and measured b-galactosidase activity in the absence and presence of IPTG. This resulted in a dynamic range of 11,000 ± 1,200 (FIG. 11-12). The difference between this value and the one obtained with sfGFP might be explained by uncertainty in reporter measurements under non-inducing conditions, which result in signals that are close to background. Again, we observed only a mild growth slowdown (cell division time: 23.84 ± 0.22 minutes without IPTG, 28.49 ± 0.98 minutes with IPTG). We conclude that Lacl-T7 can regulate expression of several genes with a dynamic range greater than 10,000-fold with little toxicity.

[0059] Phy-spank is a variant of the IPTG-inducible promoter P _spac optimized for higher expression and dynamic range, and is perhaps the most widely used B. subtilis inducible promoter system. We constructed a second B. subtilis strain wherein sfgfp* was expressed under the control of Phy-spank, RiboJ, and RBS MF001 to compare its performance to that of Lacl-T7. We found that Phy-spank exhibits much greater leakiness (565 ± 18 MEFL) and a lower maximal output (160,000 ± 14,000 MEFL) than Lacl-T7, resulting in a dynamic range of only 282 ± 18 (FIG. IB, D).

[0060] Next, we measured the steady state transfer function of both systems by

growing the corresponding strains under different concentrations of IPTG. In both cases, sfGFP fluorescence increases as a function of IPTG concentration in a manner well-approximated by a Hill function (FIG. IE). Remarkably, both systems exhibit similar IPTG detection thresholds (50% activation concentrations: Lacl-T7: 54.1 ±

1.6 mM, Phy-spank: 50.2 ± 1.5 mM). On the other hand, the Hill coefficient of the Lacl- T7 system is larger (3.377 ± 0.051, compared to 2.120 ± 0.033 for Phy-spank), indicating that protein expression is more sensitive to changes in IPTG levels in the responsive range of the system.

[0061] Finally, we characterized the response dynamics of both systems after an instantaneous addition of saturating IPTG (FIG. IF). As expected, both responses show an exponential-like increase until saturation. However, Lacl-T7 responds slightly slower (ti/2 = 82.1 ± 6.5 min for Lacl-T7, 62.1 ± 1.1 min for Phy-spank), consistent with the need to produce an intermediate protein (T7RNAP) before expression of the reporter gene. In conclusion, Lacl-T7 exhibits lower leakiness, higher maximal expression output, similar sensitivity to inducer, and much higher dynamic range than the widely used Phy-spank system, albeit with a slightly slower response time.

[0062] The superior performance of Lacl-T7 appears to arise from its unique design features. First, high maximal expression results from the use of T7 RNAP, a strong viral RNA polymerase which is capable of re-directing all bacterial resources towards expression of a single output gene. In contrast, previous expression systems based on endogenous promoters are limited by the native transcriptional machinery and are subject to competition with other endogenous promoters. Second, leaky expression in the absence of inducer is reduced via the dual repression activity of Lack In E. coli , a similar design has been shown to reduce basal expression by more than an order of magnitude compared to an unmodified P_T7 output promoter.

[0063] Lacl-T7 should be useful in quantitative studies of B. subtilis biology. In particular, its stable single-copy chromosomal location and its low leakiness are desirable for analyses of ultrasensitive or excitable networks where low amounts of excess protein can cause cells to undergo dramatically different differentiation programs.

[0064] We also expect Lacl-T7 to be useful for heterologous protein expression applications. High expression from P_T7 i_ac should enable high yields of both cytoplasmic and secreted proteins. Additionally, low leakiness in the absence of inducer should allow for fast initial cell growth, even with potentially toxic proteins. Furthermore, Lacl-T7 is integrated into the B. subtilis genome, and thus will not suffer from plasmid instability issues or require strong selective pressure to be maintained. Because it relies on the orthogonal T7 polymerase, Lacl-T7 could also be ported to other industrially-relevant Bacillus species or strains with little additional work.

DNA ASSEMBLY AND CLONING

[0065] All cloning and experiments were performed in B. subtilis strain PY79.

Primers were ordered from Integrated DNA Technologies, Inc. P_hy-spank was amplified from integration plasmid pDRl 11. P_T7 iac was constructed via oligo annealing and extension. Synthetic RBS MF001 was obtained from integration plasmid pMF35. Genomic homology fragments required for chromosomal integration were amplified from the purified genome of B. subtilis PY79.

[0066] All systems were built as linear double-stranded integration module (IM) or cassette, as we have previously described. Our IMs contain the DNA of interest and a selection marker flanked by 1.5kb-long sequences homologous to the amyE locus of the B. subtilis genome where chromosomal integration via double crossover occurs. IMs were assembled from PCR-amplified parts using Golden Gate. The resulting Golden Gate product was amplified using NEB Phusion DNA Polymerase and gel purified to obtain the IM. 500 ng was transformed into competent B. subtilis using standard transformation methods.

[0067] The transformants were plated on selective media. Colonies were picked the next day and grown in LB media at 37°C and 250 RPM for a few hours. Finally, freezer stocks were prepared with 700 pL culture and 300 pL 60% glycerol, and stored at -80°C. This method avoids sub-cloning of integration plasmids in E. coli , as long as enough PCR-amplified DNA can be obtained. The complete sequences of all IMs constructed in this study can be found in GenBank via the following accession numbers: P_{h -spank}-y/¾ : MN005205, Lacl-T7-.s/¾ : MN005204, LacI-T7-/acZ: MN005206.

[0068] For DNA sequence verification, an overnight LB culture was grown from a freezer stock, and 2 pL saturated culture was used as template for a 50 pL PCR reaction, either with Taq or Phusion DNA Polymerase. PCR products obtained in this fashion were gel-purified and sent for sequence verification to Genewiz, Inc.

MEDIA AND EXPERIMENTAL PROTOCOLS:

[0069] We used a modified M9 medium for all experiments. 1L 5xM9 salts at pH ~

6.8 were prepared with 64 g Na₂HP0_4.7H₂0, 15 g KH₂P0₄, 2.5 g NaCl, 5 g NH₄C1, 9.2 mL 6M HC1, and up to 1 L dH₂0. For 1 L M9, we used 200 mL 5x M9 salts, 20 mL 10% casamino acids, 6.67 mL 60% glycerol, 1 mL 50 mM FeCL/100 mM CeHsO_? solution, 2 mL 50 mM MnS0₄, 2 mL 1M MgS0₄, 100 pL 1M CaCl₂, and dH₂0 up to 1 L.

[0070] For each experiment, an overnight LB culture was started from the freezer stock of each relevant strain. The next day, saturated cultures (Oϋboo ~ 3) were diluted 10⁵-fold in M9. Media was distributed in culture tubes (3 mL per tube), inoculated with the appropriate inducers (0 pM or 500 pM IPTG), and incubated in a shaker operating at 250 rpm and 37°C, until the ODpoo reached between 0.08 and 0.15 (around 6 hours). Culture tubes were then transferred to ice. 100 pL of each sample was transferred to a flow cytometry tube containing 1 mL PBS for measurement. FLOW CYTOMETRY ANALYSIS

[0071] The sfGFP fluorescence distribution of each culture was measured using a BD

FACScan flow cytometer with an excitation source of 488 nm and an emission window of 510/21 nm. 30,000 events were collected per sample. A suspension of calibration beads (Spherotech® RCP-30-5A) in PBS was measured with each experiment. After data acquisition, raw .fcs flow cytometry files were processed using FlowCal.

[0072] Cell populations were gated by forward scatter/side scatter density (not

shown) retaining 50% of the total number of events. Next, fluorescence of each gated event in arbitrary units was converted into standardized MEFL values using the calibration bead data. The total cellular fluorescence of each culture sample was then obtained by calculating the median MEFL fluorescence of all gated events in that sample. Finally, the reported sfGFP fluorescence values were obtained by subtracting the total cellular fluorescence of a wild-type PY79 sample measured the same day from each sample’s total cellular fluorescence. Numerical sfGFP fluorescence values of every sample and replicate can be found in Table 1.

CODON OPTIMIZATION OF SFGFP

[0073] Codon optimization of the N-terminal sequence of the sfgfp ORF was

performed to decrease secondary structure with the RBS and increase translation efficiency. To do so, for each of the first 15 codons of the original sfgfp sequence, a synonymous codon was chosen to reduce GC and increase AU content, with A preferred over U, with no regard for codon frequency. These changes were confirmed to increase the mRNA secondary structure free energy (and thus decrease secondary structure stability) via Nupack, by using the sequence from the transcription start site up to the 90^th nucleotide residue of the ORF. The complete optimized sfgfp* sequence can be found in Table 2.

[0074] Statistical methods are not reproduced herein, but can be found in Castillo

(2019).

[0075] Each of the following references is incorporated by reference herein in its entirety for all purposes: [0076] Westers, L., Wet al., (2004) Bacillus subtilis as cell factory for pharmaceutical proteins: a biotechnological approach to optimize the host organism. Biochim.

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super-secreting cell factory. Microb. Cell Factories, 12, 3.

[0078] Yansura, D.G. & Henner, D.J. (1984) Use of the Escherichia coli lac repressor and operator to control gene expression in Bacillus subtilis. Proc. Natl. Acad. Sci., 81, 439-443.

[0079] Kim, L., et al., (1996) A xylose-inducible Bacillus subtilis integration vector and its application. Gene, 181, 71-76.

[0080] Conrad, B., et al., (1996) A T7 promoter-specific, inducible protein expression system for Bacillus subtilis. Mol. Gen. Genet. MGG, 250, 230-236.

[0081] Bhavsar, A.P., et al., (2001) Development and Characterization of a Xylose-

Dependent System for Expression of Cloned Genes in Bacillus subtilis: Conditional Complementation of a Teichoic Acid Mutant. Appl Env. Microbiol, 67, 403-410.

[0082] Bongers, R.S., et al., (2005) Development and Characterization of a Subtilin-

Regulated Expression System in Bacillus subtilis: Strict Control of Gene Expression by Addition of Subtilin. Appl Env. Microbiol, 71, 8818-8824.

[0083] Chen, P.T., et al., (2010) Construction of Chromosomally Located T7

Expression System for Production of Heterologous Secreted Proteins in Bacillus subtilis. J. Agric. Food Chem., 58, 5392-5399.

[0084] Toymentseva, A. A., et al., (2012) The LIKE system, a novel protein

expression toolbox for Bacillus subtilis based on the lial promoter. Microb. Cell Factories, 11, 143.

[0085] Dubendorf, J.W. & Studier, F.W. (1991) Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor. J. Mol. Biol., 219, 45-59. [0086] Guzman, L.M., et 1., (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacterid. , 177, 4121-4130.

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[0088] Chen, X., Let al., (2016) An extraordinary stringent and sensitive light- switchable gene expression system for bacterial cells. Cell Res., 10.1038/cr.2016.74.

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Promoter System with over 10 000-Fold Dynamic Range." ACS Synthetic Biology, 8, no. 7 (2019) American Chemical Society: 1673-1678.

Claims

1) A Bacillus promoter system, comprising one or more DNA molecules comprising: a) a Lacl repressor constitutively expressed under a first constitutive promoter; b) a T7 phage RNA polymerase (T7 RNAP) expressed from a second promoter that is normally repressed by Lacl; and c) a third promoter sequence regulated by a T7RNAP that is normally repressed by Lacl.

2) The promoter system of claim 1, further comprising an open reading frame (“ORF”) for a gene of interest inserted after said third promoter sequence, such that said ORF is regulated by said third promoter sequence.

3) The promoter system of claims 1-2, having at least 5,000, 10,000, 15,000 or 20,000 fold activation of expression of said ORF when induced by Isopropyl b-D-l- thiogalactopyranoside (IPTG).

4) The promoter system of claims 1-3, comprising one or more of the following: a) the Lacl is from or is equivalent to the sequences in pDRl 11 or having at least 95% nucleotide identity to SEQ ID NO 11; or b) the first constitutive promoter is a P _penp promoter or a sequence having at least 95% nucleotide identity to SEQ ID NO 15; or c) the second promoter is a Phy-spank promoter or a sequence having at least 95% nucleotide identity to SEQ ID NO 13; or d) the Phy-spank promoter is from or is equivalent to the sequences in pDRl 1 1 ; or e) the hybrid P_{T7 lac} promoter sequence is from or is equivalent to E. coli pET plasmids; or f) the T7 RNAP is from or is equivalent to the E. coli BL21(DE3); or g) the T7RNAP is a sequence having at least 95% nucleotide identity to SEQ ID NO 12 h) the third promoter is a hybrid P_T7i_ac promoter sequence or a sequence having at least 95% nucleotide identity to SEQ ID NO 14; or i) the first constitutive promoter for the Lacl repressor is a promoter from

Bacillus ; or j) the T7RNAP is expressed from a Bacillus Lacl repressed promoter.

5) The promoter system of claims 1-4, further comprising an antibiotic resistance gene.

6) The promoter system of claims 1-4, wherein parts a-c are in a single DNA cassette and further comprising a spectinomycin resistance gene within said cassette.

7) The promoter system of claims 1-6, wherein parts a-c are in a single DNA cassette comprising a 5’ chromosomal sequence from & Bacillus amyE gene at a first end of said cassette and a 3’ chromosomal sequence from said Bacillus amyE gene at a second end of said cassette, thereby allowing homologous recombination into a genome of Bacillus.

8) The promoter system of claims 1-7, further comprising one or more B. subtilis- specific ribosome-binding sites (RBSs) placed to stimulate translation from mRNAs expressed from the first, second or third promoters.

9) The promoter system of claims 1-8, wherein said Bacillus is a Bacillus subtilis.

10) The promoter system of claim 9, further comprising one or more B. subtilis- specific ribosome-binding sites (RBSs) placed to stimulate translation from mRNAs expressed from P_T7 i_ac, Phy-spank, or P_penp promoters, or any combination thereof.

11) The promoter system of claims 1-10, said cassette further comprising a self-cleaving ribozyme placed after P_T7 i_ac to improve output production.

12) The promoter system of claims 1-11, further comprising a multiple cloning site after said third promoter_.

13) The promoter system of claims 1-12, wherein the promoter system is an inducible promoter system.

14) The promoter system of claim 13, wherein said promoter system is inducible by IPTG.

15) An expression system for Bacillus, said system being in a Bacillus and having: a) at least 95% nucleotide identity to the sequence of SEQ ID NO 7, said 95% identity excluding an open reading frame (ORF) added thereto; and b) having at least 5,000, 10,000, 15,000 or 20,000 fold more expression of said ORF with Isopropyl b-D-l-thiogalactopyranoside (IPTG) induction than without IPTG induction.

16) An inducible and integrative expression system for Bacillus subtilis , said system

comprising an expression cassette with the following structure: a) a first portion of a chromosomal sequence from B. subtilis at a 5’ end of said expression cassette; b) a second portion of said chromosomal sequence at a 3’ end of said expression cassette; c) a Lacl repressor constitutively expressed under a B. subtilis P _penp promoter within said expression cassette; d) a lacl-repressible T7 phage RNA polymerase (T7 RNAP) expressed from a B. subtilis P_hy-spank promoter within said expression cassette; e) a hybrid promoter activated by T7RNAP and repressed by Lacl that controls expression of an open reading frame (ORF).

17) The system of claim 16, wherein said ORF encodes an output mRNA, that may or may not encode a protein.

18) The system of claim 16, comprising an ORF for a target protein and being capable of a 10,000 fold increase in expression of said ORF when induced with Isopropyl b-D-l- thiogalactopyranoside (IPTG) as compared to without IPTG.

19) A vector comprising the system of claims 16-18, said vector being self-reproduceable in a Bacillus , Escherichia or yeast.

20) A vector comprising the system of claims 16-18, said vector producing at least 10,000 fold more expression of said ORF in a Bacillus transformed with said vector and induced with IPTG induction, as compared to without IPTG.

21) A recombinant Bacillus, wherein said Bacillus is transformed with the system of

claims 16-18.

22) A recombinant Bacillus, wherein said Bacillus is transformed with the system of

claims 16-18, said expression cassette being integrated into a chromosome of said Bacillus.

23) A method of transforming Bacillus subtilis, comprising introducing the system of claims 16-18 to a population of Bacillus subtilis under conditions that allow

transformation and integration of said system into a chromosome of said Bacillus subtilis , and selecting for transformed and integrated Bacillus subtilis.

24) A method of producing a target protein, comprising introducing the system of claims 16-18 to a population of Bacillus subtilis under conditions that allow integration of said expression cassette into a genome of said Bacillus subtilis , and selecting for integrated Bacillus subtilis, growing said integrated Bacillus subtilis in a growth medium until cells reach near saturation, adding IPTG to said growth medium in an amount sufficient to induce said lac operon, continuing culturing said integrated Bacillus subtilis until said ORF is expressed, and isolating said target protein from said growth medium or said transformed Bacillus subtilis or both.

25) A DNA molecule comprising SEQ ID NO. 7 plus an added open reading frame (ORF).