Methods of developing terpene synthase variants   

Abstract: The present disclosure relates to methods of developing terpene synthase variants through engineered host cells. Particularly, the disclosure provides methods of developing terpene synthase variants with improved in vivo performance that are useful in the commercial production of terpene products. Further encompassed in the present disclosure are superior terpene synthase variants and host cells comprising such terpene synthase variants.

This application is a continuation of U.S. patent application Ser. No. 13/363,588, filed Feb. 2, 2012, which claims the benefit of priority under 35 U.S.C. §119(e) to U.S. Provisional Patent Application No. 61/438,948, filed Feb. 2, 2011. Each of these priority documents are incorporated herein by reference, in their entirety.

FIELD OF THE INVENTION

The present disclosure relates to methods of developing terpene synthase variants through engineered host cells. Particularly, the disclosure provides methods of developing terpene synthase variants with improved in vivo performance that are useful in the commercial production of terpene products. Further encompassed in the present disclosure are superior terpene synthase variants, and host cells comprising such terpene synthase variants.

Terpenes are a large class of hydrocarbons that are produced in many organisms. They are derived by linking units of isoprene (C5H8), and are classified by the number of isoprene units present. Hemiterpenes consist of a single isoprene unit. Isoprene itself is considered the only hemiterpene. Monoterpenes are made of two isoprene units, and have the molecular formula C10H16. Examples of monoterpenes are geraniol, limonene, and terpineol. Sesquiterpenes are composed of three isoprene units, and have the molecular formula C15H24. Examples of sesquiterpenes are farnesenes, farnesol and patchoulol. Diterpenes are made of four isoprene units, and have the molecular formula C20H32. Examples of diterpenes are cafestol, kahweol, cembrene, and taxadiene. Sesterterpenes are made of five isoprene units, and have the molecular formula C25H40. An example of a sesterterpenes is geranylfarnesol. Triterpenes consist of six isoprene units, and have the molecular formula C30H48. Tetraterpenes contain eight isoprene units, and have the molecular formula C40H64. Biologically important tetraterpenes include the acyclic lycopene, the monocyclic gamma-carotene, and the bicyclic alpha- and beta-carotenes. Polyterpenes consist of long chains of many isoprene units. Natural rubber consists of polyisoprene in which the double bonds are cis.

When terpenes are chemically modified (e.g., via oxidation or rearrangement of the carbon skeleton) the resulting compounds are generally referred to as terpenoids, which are also known as isoprenoids. Isoprenoids play many important biological roles, for example, as quinones in electron transport chains, as components of membranes, in subcellular targeting and regulation via protein prenylation, as photosynthetic pigments including carotenoids, chlorophyll, as hormones and cofactors, and as plant defense compounds with various monoterpenes, sesquiterpenes, and diterpenes. They are industrially useful as antibiotics, hormones, anticancer drugs, insecticides, and chemicals.

Terpenes are biosynthesized through condensations of isopentenyl pyrophosphate (isopentenyl diphosphate or IPP) and its isomer dimethylallyl pyrophosphate (dimethylallyl diphosphate or DMAPP). Two pathways are known to generate IPP and DMAPP, namely the mevalonate-dependent (MEV) pathway of eukaryotes, and the mevalonate-independent or deoxyxylulose-5-phosphate (DXP) pathway of prokaryotes. Plants use both the MEV pathway and the DXP pathway. IPP and DMAPP in turn are condensed to polyprenyl diphosphates (e.g., geranyl disphosphate or GPP, farnesyl diphosphate or FPP, and geranylgeranyl diphosphate or GGPP) through the action of prenyl disphosphate synthases (e.g., GPP synthase, FPP synthase, and GGPP synthase, respectively).

The polyprenyl diphosphate intermediates are converted to more complex isoprenoid structures by terpene synthases. Terpene synthases are organized into large gene families that form multiple products. Examples of terpene synthases include sesquiterpene synthases, which convert FPP into sesquiterpenes. An example of a sesquiterpene synthase is farnesene synthase, which converts FPP to farnesene. The reaction mechanism of terpene synthases has been extensively investigated and is well understood. Overall, three steps are required to convert a diphosphate substrate such as FPP to its isoprenoid product: a) formation of enzyme-substrate complex (ES), b) formation of an enzyme-bound reactive carbocation intermediate, subsequent rearrangements, and the formation of product (EP), and c) release of product from the enzyme-product complex. In vitro kinetic and pre-steady state kinetic studies on terpene synthase catalyzed reactions have shown that the overall rate-limiting step for the reactions is the release of product (Cane et al. (1997) Biochemistry, 36(27):8332-9, and Mathis et al. (1997) Biochemistry 36(27):8340-8). The turnover rates of terpene synthases are low, generally measured at less than 0.5 per second (Cane, D. C. (1990) Chem. Rev. 90:1089-1103).

Terpene synthases are important in the regulation of pathway flux to an isoprenoid because they operate at metabolic branch points and often compete with other metabolic enzymes for a prenyl diphosphate pool. For example, FPP is the precursor to many cellular molecules including squalene, dolichols, and the cofactor heme. In engineered microbes where the production of sesquiterpenes such as farnesene is desired, the terpene synthases hold the key to high yield production of such terpenes. However, because they are slow enzymes, terpene synthases are often the bottlenecks in the metabolic pathways. In addition, they can suffer from other shortcomings such as substrate inhibition that limit the kinetic capacity required for efficient production of terpenes in engineered microbial hosts (Crock et al. (1997) Proc. Natl. Acad. Sci. USA 94:12833-12838).

Hence, there are potentially enormous benefits to improving the catalytic efficiency of terpene synthases so that these enzymes would no longer limit the overall metabolic flux to an isoprenoid. Attempts to engineer terpene synthases for altered product specificity as well as the use of rational approaches such as those based on structural guidance or adaptive evolution have been described previously (Greenhagen et al. (2006) Proc. Natl. Acad. Sci. USA 103:9826-9831; O\'Maille et al. (2008) Nat. Chem. Biol. 4:617-623; Yoshikuni et al. (2006) Nature 440:1078-1082; Yoshikuni et al. (2008) Chem. Biol. 15:607-618). However, these studies have fallen short of improving the kinetic capacity of terpene synthases while also maintaining their product specificity. In addition, the application of conventional protein engineering strategies, such as directed evolution, has been devoid for terpene synthases primarily because of the lack of available and effective high throughput screening methods (Yoshikuni et al. (2008) (supra)). There thus remains a need for reliable and high throughput methods for improving the catalytic efficiency of terpene synthases, and for terpene synthase variants that have such improved catalytic efficiency.

SUMMARY

The present disclosure relates to methods of developing terpene synthase variants through engineered host cells. Particularly, the disclosure provides methods of developing terpene synthase variants with improved in vivo performance. The methods also allow for the continued improvement of the in vivo performance of these enzymes.

In one aspect, the present invention provides a screening method for a sesquiterpene synthase variant with improved in vivo performance, comprising the steps of: a) engineering a host cell expressing a control sesquiterpene synthase to comprise an elevated level of FPP, wherein the elevated level of FPP reduces the viability of the host cell compared to a parent cell not comprising the elevated level of FPP; b) expressing in the host cell a test sesquiterpene synthase instead of the control sesquiterpene synthase, wherein the test sesquiterpene synthase is a variant of the control sesquiterpene synthase; and c) identifying the test sesquiterpene synthase as having improved in vivo performance compared to the control sesquiterpene synthase by an increase in viability of the host cell expressing the test sesquiterpene synthase compared to the host cell expressing the control terpene synthase.

In some embodiments, the host cell is plated on an agar plate, and a host cell comprising a test terpene synthase variant with improved in vivo performance is identified by colony growth. In some embodiments, the method further comprises selecting and/or isolating the test sesquiterpene synthase having improved in vivo performance.

In some embodiments, a collection of sesquiterpene synthase variants is expressed in a collection of host cells. In some embodiments, the collection of sesquiterpene synthase variants comprises from 2 to 5, from 5 to 10, from 10 to 50, from 50 to 100, from 100 to 500, from 500 to 1,000, from 1,000 to 10,000, from 10,000 to 100,000, from 100,000 to 1,000,000, and more, sesquiterpene synthase variants.

In some embodiments, the screening method is used in an iterative fashion, wherein the test sesquiterpene synthase identified in an iteration is used as the control sesquiterpene synthase of the next iteration, and wherein the host cell in an iteration comprises such elevated level of FPP that it has reduced viability in the presence of the test sesquiterpene synthase identified in the previous iteration compared to a parent cell not comprising the elevated level of FPP.

In another aspect, provided herein is a composition comprising two cell subpopulations derived from a common population of host cells comprising an elevated level of FPP, wherein: a) the first subpopulation comprises a control sesquiterpene synthase, wherein the elevated level of FPP reduces the viability of cells of the first subpopulation compared to the viability of a parent cell not comprising the elevated level of FPP; and b) the second subpopulation comprises a test sesquiterpene synthase, wherein the test sesquiterpene synthase is a variant of the control sesquiterpene synthase.

In some embodiments, the viability of the cells of the second subpopulation is greater than the viability of the cells of the first subpopulation.

In another aspect, the present invention provides a second screening method for identifying terpene synthase variants with improved in vivo performance, comprising the steps of: a) providing a host cell expressing a control terpene synthase and having a growth rate; b) expressing in the host cell a test terpene synthase instead of the control terpene synthase, wherein the test terpene synthase is a variant of the control terpene synthase; and d) identifying the test terpene synthase as having improved in vivo performance compared to the control terpene synthase by a decreased growth rate of the host cell expressing the test terpene synthase compared to the growth rate of the host cell expressing the control terpene synthase.

In yet another aspect, the present invention provides a competition method for identifying and/or ranking the in vivo performance of terpene synthase variants, comprising the steps of: a) dividing a population of host cells into a control population and a test population; b) expressing in the control population a control terpene synthase and a comparison terpene synthase, wherein the control terpene synthase can convert a polyprenyl diphosphate to a first terpene, and wherein the comparison terpene synthase can convert a polyprenyl diphosphate to a second terpene; c) expressing in the test population the comparison terpene synthase and a test terpene synthase, wherein the test terpene synthase is a variant of the control terpene synthase, and wherein the comparison terpene synthase is expressed at similar levels in the test population and in the control population; and d) measuring a ratio of the first terpene over the second terpene in the test population and in the control population.

In separate embodiments, the competition method is applied to identify and/or to rank terpene synthases selected from the group consisting of monoterpene synthases, diterpene synthases, sesquiterpene synthases, sesterterpene synthases, triterpene synthases, tetraterpene synthases, and polyterpene synthases.

In some embodiments, the competition method is used to screen a library of mutant terpene synthases on the basis that compared to the control terpene synthase, a terpene synthase variant with improved in vivo performance is capable of diverting more flux from a polyprenyl diphosphate substrate to its terpene product, thus, giving a higher ratio of terpene of interest/comparison terpene (i.e., first terpene/second terpene). In such embodiments, it is important that the test terpene synthase is expressed at a similar level in the test population as the control terpene synthase is expressed in the control population.

In other embodiments, the competition method is used to identify a promoter of a desired strength. In such embodiments, the control terpene synthase and the test terpene synthase are identical, and the control population and test population differ in the expression level of the control terpene synthase.

In another aspect, provided herein is a composition comprising two cell subpopulations derived from a common population of host cells, wherein: a) the first subpopulation comprises a control terpene synthase and a comparison terpene synthase, wherein the control terpene synthase converts a polyprenyl diphosphate to a first terpene, and wherein the comparison sesquiterpene synthase converts the polyprenyl diphosphate to a second terpene; and b) the second subpopulation comprises a test terpene synthase and the comparison terpene synthase, wherein the control terpene synthase converts the polyprenyl diphosphate to the first terpene, and wherein the test terpene synthase is a variant of the control terpene synthase.

In some embodiments, the ratio of the first terpene over the second terpene is greater in the second subpopulation compared to that in the first subpopulation.

In yet another aspect, provided herein are isolated β-farnesene synthase variants, and isolated nucleic acids comprising a nucleotide sequence encoding such β-farnesene synthase variants, having an amino acid sequence as given in SEQ ID NO: 111 but comprising one or more amino acid substitutions at positions selected from the group consisting of positions 2, 3, 4, 6, 9, 11, 18, 20, 24, 35, 38, 50, 61, 72, 80, 89, 105, 115, 144, 196, 211, 251, 280, 288, 319, 348, 357, 359, 369, 371, 385, 398, 423, 433, 434, 442, 444, 446, 460, 467, 488, 495, 505, 526, 531, 556, 572, and 575 of SEQ ID NO: 111.

In yet another aspect, the present invention provides a genetically modified host cell that comprises: (a) a heterologous β-farnesene synthase, wherein the heterologous β-farnesene synthase is a variant of a β-farnesene synthase encoded by SEQ ID NO: 111; and (b) a MEV pathway or DXP pathway enzyme; wherein the host cell makes at least 15% more of a β-farnesene compared to a parent cell that comprises the MEV pathway or DXP pathway enzyme and the β-farnesene synthase encoded by SEQ ID NO: 111.

In yet another aspect, provided herein is a method of producing β-farnesene comprising the steps of: (a) obtaining a plurality of genetically modified host cells comprising: i) a first heterologous nucleotide sequence encoding a variant of a β-farnesene synthase encoded by SEQ ID NO: 111; and ii) a second heterologous nucleotide sequence encoding a MEV pathway or DXP pathway enzyme; (b) culturing said genetically modified host cells in a medium comprising a carbon source under conditions suitable for making the β-farnesene; and (c) recovering the β-farnesene from the medium.

The present disclosure is best understood when read in conjunction with the accompanying figures, which serve to illustrate the preferred embodiments. It is understood, however, that the disclosure is not limited to the specific embodiments disclosed in the figures.

FIG. 1A-Z provides maps of several chromosomal integration constructs used in the generation of host cells of the invention.

FIG. 2 provides an image of several agar plates on which were plated Escherichia coli host cells comprising active and inactive sesquiterpene synthases for FPP starvation-based selection.

FIG. 3 provides an image of two agar plates on which were plated Escherichia coli host cells comprising active and inactive sesquiterpene synthases for FPP toxicity-based growth selection.

FIG. 4 provides farnesene titers obtained by GC analysis of Escherichia coli host cells comprising various farnesene synthase coding sequences.

FIG. 5 provides an image of agar plates on which were plated Saccharomyces cerevisiae host cells comprising active and inactive sesquiterpene synthases for FPP toxicity-based growth selection.

FIG. 6 provides farnesene titers obtained by Nile Red fluorescence analysis of Saccharomyces cerevisiae host cells comprising either chromosomally intergrated or extrachromosomally maintained farnesene synthase coding sequences.

FIG. 7 provides farnesene titers obtained by GC analysis of Saccharomyces cerevisiae host cells ranked by sesquiterpene synthase competition.

FIG. 8 provides farnesene/trichodiene titer ratios obtained by GC analysis of Saccharomyces cerevisiae host cells comprising increasing copy numbers of farnesene synthase coding sequences.

FIG. 9 provides a comparison of farnesene titers obtained by GC analysis versus Nile Red fluorescence analysis of Escherichia coli host cells of a sesquiterpene synthase library.

FIG. 10 provides farnesene titers obtained by GC analysis of Escherichia coli host strains identified from a library of FS variants screened by Nile Red fluorescence.

FIG. 11 provides farnesene titers obtained by Nile Red fluoresence (A) and GC analysis (B) of Saccharomyces cerevisiae host strains identified from a library of FS variants screened by FPP toxicity based growth selection.

FIG. 12 provides farnesene titers obtained by Nile Red fluourescence analysis of Saccharomyces cerevisiae host strains identified from a library of FS variants by FPP toxicity-based growth selection.

FIG. 13 provides maps of various expression plasmids used in the generation of host cells of the invention.

FIG. 14 provides farnesene titers obtained by GC analysis of Saccharomyces cerevisiae host strains comprising single chromosomally integrated copies of FS variant coding sequences.

FIG. 15 provides a schematic representation of the MEV pathway for the production of IPP and DMAPP.

FIG. 16 provides a schematic representation of the DXP pathway for the production of IPP and DMAPP.

FIG. 17 provides amorphadiene/trichodiene titer ratios obtained by GC analysis of Saccharomyces cerevisiae host cells comprising coding sequences for amorphadiene synthase variants.

FIG. 18 provides limonene/myrcene titer ratios obtained by GC analysis of Saccharomyces cerevisiae host cells comprising coding sequences for limonene synthase variants.

DETAILED DESCRIPTION

The following terms used herein shall have the meanings as indicated below.

As used herein, the term “terpene synthase variant” refers to a terpene synthase that compared to a selected terpene synthase has a different nucleotide or amino acid sequence. For example, compared to the wild-type sequence of the selected terpene synthase, the terpene synthase variant may comprise nucleotide additions, deletions, and/or substitutions that may or may not result in changes to the corresponding amino acid sequence. In some embodiments where nucleotide changes do not result in changes to the amino acid sequence, the changes may nonetheless effect improved activity of the synthase, for example, through codon optimization. In other embodiments, the terpene synthase variant comprises amino acid additions, deletions, and/or substitutions. Accordingly, as used herein, the term “sesquiterpene synthase variant” refers to a sesquiterpene synthase that compared to a selected sesquiterpene synthase has a different nucleotide or amino acid sequence. For example, compared to the selected sesquiterpene synthase, the sesquiterpene synthase variant may comprise nucleotide additions, deletions, and/or substitutions that may or may not result in changes to the corresponding amino acid sequence. In other embodiments, the terpene synthase variant comprises amino acid additions, deletions and/or substitutions.

As used herein, the term “engineered host cell” refers to a host cell that is generated by genetically modifying a parent cell using genetic engineering techniques (i.e., recombinant technology). The engineered host cell may comprise additions, deletions, and/or modifications of nucleotide sequences to the genome of the parent cell.

As used herein, the term “heterologous” refers to what is not normally found in nature. The term “heterologous nucleotide sequence” refers to a nucleotide sequence not normally found in a given cell in nature. As such, a heterologous nucleotide sequence may be: (a) foreign to its host cell (i.e., is “exogenous” to the cell); (b) naturally found in the host cell (i.e., “endogenous”) but present at an unnatural quantity in the cell (i.e., greater or lesser quantity than naturally found in the host cell); or (c) be naturally found in the host cell but positioned outside of its natural locus.

As used herein, the term “naturally occurring” refers to what is found in nature. For example, a terpene synthase that is present in an organism that can be isolated from a source in nature and that has not been intentionally modified by a human in the laboratory is a naturally occurring terpene synthase. Conversely, as used herein, the term “naturally not occurring” refers to what is not found in nature but is created by human intervention.

As used herein, the term “biosynthetic enzyme” refers to an enzyme that functions in a biosynthetic pathway leading to the production of a naturally occurring molecule.

As used herein, the term “in vivo performance” refers to the ability of a terpene synthase to convert a polyprenyl diphosphate substrate to a terpene when expressed in a host cell. Accordingly, the term “improved in vivo performance” refers to an increased ability of a terpene synthase to convert a polyprenyl diphosphate substrate to a terpene when expressed in a host cell.

As used herein, the term “parent cell” refers to a cell that has an identical genetic background as a host cell disclosed herein except that it does not comprise the elevated intracellular level of FPP or does not comprise a particular heterologous nucleotide sequence, and that serves as the starting point for introducing said elevated intracellular level of FPP or said heterologous nucleotide sequence leading to the generation of a host cell disclosed herein.

The present disclosure relates to methods of developing terpene synthase variants through engineered host cells. Particularly, the disclosure provides methods of developing terpene synthase variants with improved in vivo performance. The methods also allow for the continued improvement of the in vivo performance of these enzymes.

In one aspect, the present invention provides a screening method for terpene synthase variants with improved in vivo performance. In some embodiments, terpene synthase variants with improved in vivo performance are identified by their ability to rescue engineered host cells from cell death. The engineered host cells comprise genetic modifications that cause elevated intracellular levels of FPP. Because FPP is highly toxic to cells and thus reduces cell viability (Withers et al. (2007) Appl. Environ. Microbiol. 73:6277-6283), to achieve a viability that is comparable to that of a parent cell that does not comprise the elevated level of intracellular FPP, the engineered host cells require a sufficiently active sesquiterpene synthase to reduce the intracellular levels of FPP.

The presently provided screening method thus comprises the following steps:

a) engineering a host cell expressing a control sesquiterpene synthase to comprise an elevated level of FPP, wherein the elevated level of FPP reduces the viability of the host cell compared to a parent cell not comprising the elevated level of FPP;

b) expressing in the host cell a test sesquiterpene synthase instead of the control sesquiterpene synthase, wherein the test sesquiterpene synthase is a variant of the control sesquiterpene synthase; and

c) identifying the test sesquiterpene synthase as having improved in vivo performance compared to the control sesquiterpene synthase by an increase in viability of the host cell expressing the test sesquiterpene synthase compared to the host cell expressing the control sesquiterpene synthase.

In some embodiments, the method further comprises selecting and/or isolating the test sesquiterpene synthase having improved in vivo performance.

It is most convenient if the elevated level of FPP in the host cell is inducible. Induction may occur in response to an inducing agent or specific growth conditions such as, for example, temperature. The elevated level of FPP in the host cell may range from about 10% to at least about 1,000-fold, or more, higher than the level of FPP of the parent cell.

The reduced viability of the host cell expressing the control sesquiterpene synthase compared to the parent cell may range from decreased cell growth to lethality. Thus, in some embodiments, the host cell expressing the control sesquiterpene synthase produces a reduced number of progeny cells in a liquid culture or on an agar plate compared to the parent cell. In other embodiments, the host cell expressing the control sesquiterpene synthase produces no progeny cells in a liquid culture or on an agar plate compared to the parent cell. Accordingly, the increase in viability of the host cell expressing the test sesquiterpene synthase instead of the control sesquiterpene synthase may be apparent in liquid culture by a higher number of progeny cells, or on an agar plate by a larger colony size, compared to the number of progeny cells or colony size produced by the host cell expressing the control sesquiterpene synthase.

The elevated level of FPP in the host cell may be effected by modifying the expression and/or activity of an enzyme involved in the production of FPP or its precursors in the host cell. In some such embodiments, the expression and/or activity of an enzyme of the MEV or DXP pathway is modified. In some such embodiments, the expression and/or activity of a HMG-CoA reductase and/or a mevalonate kinase is modified. Alternatively, the elevated level of FPP in the host cell may be effected by modifying the expression and/or activity of an enzyme involved in the utilization of FPP or its precursors in the host cell. In some such embodiments, the expression and/or activity of a squalene synthase is modified.

The control sesquiterpene synthase may be a naturally occurring sesquiterpene synthase or a naturally not occurring sesquiterpene synthase. The test sequiterpene synthase may differ from the control sesquiterpene synthase by comprising one or more amino acid substitutions, deletions, and/or additions. In addition or alternatively, the test sequiterpene synthase may comprise identical amino acids as the control sesquiterpene synthase but the codons encoding these amino acids may differ between the test sesquiterpene synthase and the control sesquiterpene synthase. In some such embodiments, the codons are optimized for usage in the host cell.

In some embodiments, the control sesquiterpene synthase is selected from the group consisting of a β-farnesene synthase, an α-farnesene synthase, a trichodiene synthase, a patchoulol synthase, an amorphadiene synthase, a valencene synthase, a farnesol synthase, a nerolidol synthase, and a nootkatone synthase. In some such embodiments, the control sesquiterpene synthase is a β-farnesene synthase of Artemisia annua. In some such embodiments, the control sesquiterpene synthase has an amino acid sequence as given in SEQ ID NO: 111.

To be able to compare the viability of the host cell in the presence of the test sesquiterpene synthase to that of the host cell in the presence of the control sesquiterpene synthase, it is necessary to ensure similar expression levels of the control sesquiterpene synthase and the test sesquiterpene synthase in the host cell. This can be accomplished by placing the nucleotide sequences encoding the sesquiterpene synthases in the two host cells under the control of the same regulatory elements.

To prevent a competitive growth situation in which fast growing false positive host cells comprising a growth promoting mutation rather than an improved sesquiterpene synthase variant take over a host cell culture, one embodiment of the screening method involves an agar-plate based selection system. In this embodiment, the host cell is plated on an agar plate, and a host cell comprising a test sesquiterpene synthase variant with improved in vivo performance is identified by colony growth.

One major advantage of the presently disclosed screening method is its continued capacity to select for better and better sesquiterpene synthase variants in an iterative fashion, wherein a test sesquiterpene synthase identified in an iteration is used as the control sesquiterpene synthase in a subsequent iteration. Thus, this method can be distinguished from other assays known in the art that aim to identify only whether a particular sesquiterpene synthase may be active in a biosynthetic pathway, and do not seek to identify synthases having improved activity over a control, e.g., parent synthase. In some embodiments, the FPP level in the host cell is checked and potentially increased at each iteration (e.g., by increasing or decreasing expression levels of enzymes, adding or subtracting enzymes, increasing or decreasing copy numbers of genes, replacing promoters controlling expression of enzymes, or altering enzymes by genetic mutation) to a level that causes reduced viability when the host cell expresses the new control sesquiterpene synthase (i.e., the test sesquiterpene synthase of the previous iteration). Alternatively, or in addition, at each iteration, the expression of the control sesquiterpene synthase can be reduced (e.g., by decreasing expression of or by using weaker promoters or by reducing the stability of the control sesquiterpene synthase transcript or polypeptide) to provide reduced control sesquiterpene synthase activity. In the next iteration, a test sequiterpene synthase can then be identified that has yet increased in vivo performance compared to the test sequiterpene synthase of the previous iteration.

Another major advantage of the presently disclosed screening method is its simplicity and capacity for high-throughput implementation. Sesquiterpene synthase variants that can reduce the intracellular FPP levels in the engineered host cell to non-toxic levels are identified simply based on cell viability, making other costly and time consuming screening methods virtually unnecessary. Thus, in one embodiment, the method is used to screen a collection of sesquiterpene synthase variants (e.g., a library of mutant sesquiterpene synthases) for sesquiterpene synthase variants with improved in vivo performance. In such an embodiment, not a single test sesquiterpene synthase is expressed in a host cell but a collection of test sesquiterpene synthases are expressed in a collection of host cells. The host cells can then be grown on agar plates, and host cells expressing sesquiterpene synthase variants with improved in vivo performance can be identified based on colony growth. In some embodiments, the collection of sesquiterpene synthase variants comprises from 2 to 5, from 5 to 10, from 10 to 50, from 50 to 100, from 100 to 500, from 500 to 1,000, from 1,000 to 10,000, from 10,000 to 100,000, from 100,000 to 1,000,000, and more, sesquiterpene synthase variants.

Another major advantage of the presently disclosed screening method is that selection for improved sesquiterpene synthases occurs in vivo rather than in vitro. As a result, improvements of multiple enzyme properties that enhance the in vivo performance of the sesquiterpene synthase variant can be obtained.

In another aspect, the present invention provides a second screening method for identifying terpene synthase variants with improved in vivo performance. In this second screening method, terpene synthase variants with improved in vivo performance are identified by their ability to starve host cells of a polyprenyl diphosphate (e.g., FPP). In the presence of a highly active terpene synthase variant, the intracellular pool of its polyprenyl diphosphate substrate in a host cell may be depleted, causing the cell to not be able to maintain basic cellular processes required for cell survival.

The presently provided second screening method thus comprises the following steps:

a) providing a host cell expressing a control terpene synthase and having a growth rate;

b) expressing in the host cell a test terpene synthase instead of the control terpene synthase, wherein the test terpene synthase is a variant of the control terpene synthase; and

d) identifying the test terpene synthase as having improved in vivo performance compared to the control terpene synthase by a decreased growth rate of the host cell expressing the test terpene synthase compared to the host cell expressing the control terpene synthase.

The control terpene synthase may be a monoterpene synthase, a sesquiterpene synthase, a diterpene synthase, a sesterterpene synthase, a triterpene synthase, a tetraterpene synthase, or a polyterpene synthase. In some embodiments, the control terpene synthase is a sesquiterpene synthase. In some such embodiments, the control terpene synthase is a β-farnesene synthase. In some such embodiments, the control terpene synthase is a β-farnesene synthase of Artemisia annua. In some such embodiments, the control terpene synthase has an amino acid sequence as given in SEQ ID NO: 111.

The polyprenyl diphosphate substrate that becomes depleted in the host cell in the presence of the test terpene synthase may be FPP. Aside from sesquiterpenes, a number of other compounds are synthesized from FPP that are essential for the viability and growth of the host cell. Such compounds include but are not limited to squalene, lanosterol, ergosterol, cycloartenol, cholesterol, steroid hormones, and vitamin D. Thus, in some embodiments, a host cell expressing the test terpene synthase may comprise reduced amounts of cholesterol or ergosterol in its cell membrane. Methods for the quantification of cholesterol or ergosterol in cells are known in the art (e.g., Crockett and Hazel (2005) J. Experimental Zoology, 271(3): 190-195; Arthington-Skaggs et al. (1999) J Clin Microbiol. 37(10): 3332-3337; Seitz et al. (1979) Physiol. Biochem. 69: 1202-1203). In some embodiments, the basic cellular process required for cell survival that cannot be maintained in the host cell in the presence of the test terpene synthase is the production and/or maintenance of a cell membrane. In other embodiments, the polyprenyl diphosphate substrate that becomes depleted in the host cell in the presence of the test terpene synthase is GPP or GGPP.

In yet another aspect, the present invention provides a competition method for identifying and/or ranking the in vivo performance of terpene synthase variants. The competition method employs a known terpene synthase as the comparison enzyme against which the terpene synthase variants are compared. Both the comparison terpene synthase and each of the terpene synthase variants are co-expressed in a host cell in which they then compete for the same polyprenyl diphosphate substrate (e.g., GPP, FPP, or GGPP) to produce their corresponding terpenes. Since the performance of the comparison enzyme remains constant in the host cells, any changes in the ratios of titers of the terpene products produced by the comparison terpene synthase and the terpene synthase variants are the direct result of the activities of the terpene synthase variants. Consequently, such ratios can be used to identify terpene synthase variants with improved in vivo performance, and/or to rank or quantitatively compare the terpene synthase variants for their in vivo kinetic capacities in diverting polyprenyl diphosphate substrates to the production of terpenes.

The presently provided competition method thus comprises the following steps:

a) dividing a population of host cells into a control population and a test population;

b) expressing in the control population a control terpene synthase and a comparison terpene synthase, wherein the control terpene synthase can convert a polyprenyl diphosphate to a first terpene, and wherein the comparison terpene synthase can convert a polyprenyl diphosphate to a second terpene;

c) expressing in the test population the comparison terpene synthase and a test terpene synthase, wherein the test terpene synthase is a variant of the control terpene synthase, and wherein the comparison terpene synthase is expressed at similar levels in the test population and in the control population; and

d) measuring a ratio of the first terpene over the second terpene in the test population and in the control population.

Notably, the presently disclosed competition method can be applied to a wide variety of terpene synthases. Thus, in separate embodiments, the competition method is applied to identify and/or rank terpene synthases selected from the group consisting of monoterpene synthases, diterpene synthases, sesquiterpene synthases, sesterterpene synthases, triterpene synthases, tetraterpene synthases, and polyterpene synthases. Accordingly, in separate embodiments, the first terpene and the second terpene are selected from the group consisting of monoterpenes, sesquiterpenes, diterpenes, sesterterpenes, triterpenes, tetraterpenes, and polyterpenes. In some such embodiments, the first terpene or the second terpene is selected from the group consisting of a β-farnesene, an α-farnesene, a trichodiene, a patchoulol, an amorphadiene, a valencene, a farnesol, a nerolidol, a limonene, a myrcene, and a nootkatone.

The control terpene synthase may be a naturally occurring terpene synthase or a naturally not occurring synthase. The test terpene synthase may comprise amino acid substitutions, deletions, or additions compared to the control terpene synthase, or comprise identical amino acids encoded by different codons in the nucleotide sequences encoding the control terpene synthase and test terpene synthase. In some embodiments, the control terpene synthase is a sesquiterpene synthase. In some such embodiments, the sesquiterpene synthase is selected from the group consisting of a β-farnesene synthase, an α-farnesene synthase, a trichodiene synthase, a patchoulol synthase, an amorphadiene synthase, a valencene synthase, a farnesol synthase, a nerolidol synthase, and a nootkatone synthase. In some such embodiments, the control sesquiterpene synthase is a β-farnesene synthase of Artemisia annua. In some such embodiments, the control sesquiterpene synthase has an amino acid sequence as given in SEQ ID NO: 111.

To be able to compare the ratios of first terpene/second terpene of the control population and the test population, it is necessary to ensure similar expression levels of the comparison terpene synthase. This can be accomplished by placing the nucleotide sequences encoding the comparison terpene synthase in the two host cell populations under the control of the same regulatory elements. In embodiments in which the competition method is used to identify a terpene synthase variant, the expression levels of the control terpene synthase and the test terpene synthase in the two cell populations must also be similar. In other embodiments in which the competition method is used, for example, to identify regulatory elements (e.g., promoters) that provide a desired expression level, the test terpene synthase differs from the control terpene synthase not in nucleotide or amino acid sequence but in expression level. In such embodiments, different regulatory elements are used for the expression of the control terpene synthase and the test terpene synthase.

There are numerous utilities for the presently disclosed competition method. In some embodiments, the method is used to screen for terpene synthase variants with improved in vivo performance (e.g., from a library of mutant terpene synthases) on the basis that compared to the control terpene synthase, a terpene synthase variant with improved in vivo performance is capable of diverting more flux from a polyprenyl diphosphate substrate to its terpene product, thus, giving a higher ratio of terpene of interest/comparison terpene (i.e., first terpene/second terpene). In such embodiments, it is important that the test terpene synthase is expressed at a similar level in the test population as the control terpene synthase is expressed in the control population.

A similar assay can be used to rank the strength of a series of promoters (see Example 16, for example, in which such an assay was used to identify promoters suitable for use in expressing the control sesquiterpene synthase in the first screening method disclosed herein). In such an embodiment, the control terpene synthase and the test terpene synthase are actually identical, but they are under regulatory control of different prometers such that the control population and the test population do not differ in the type of test terpene synthase they comprise but in the level of expression of the test terpene synthase. In such an embodiment, comparing the ratio of the first terpene over the second terpene in the test population and in the control population provides information not about the activity of the test terpene synthase but about the strength of the promoter driving the expression of the test terpene synthase.

In addition, this system can be used to modulate the ratio of two or more terpene products made by various cells so that the combined mixture of the various cells with a defined ratio possesses the desired properties of a commercially useful product.

Major advantages of the presently disclosed competition method are that it eliminates cell-to-cell variations in enzyme expression and activity, that it is robust, and that it can be used even when the overall pathway flux to the polyprenyl diphosphate substrate is limiting in the host cell. The latter is important because assays that are based on absolute terpene titer measurements may mask improvements in enzyme activities when terpene titers are capped by the overall pathway flux to the polyprenyl disphosphate substrate.

Enzymes developed using the presently disclosed screening method and/or competition method can be subjected to additional means of optional screening including, but not limited to, a fluorescent screen and/or a direct quantitation of terpene product by gas chromatography. More specifically, this includes a Nile Red-based high throughput fluorescent assay for measuring production of a sesquiterpene such as farnesene, and a gas chromatography (GC)-based direct quantitation method for measuring the titer of a sesquiterpene such as farnesene. The improved enzymes can also be further improved by genetic engineering methods such as induced mutations and the like. As a result, improvements of multiple enzyme properties that enhance the final enzyme performance are successively accomplished, and the most effective enzyme variants are identified.

The present disclosure also pertains to superior farnesene synthase variants, and host cells comprising such farnesene synthase variants. The farnesene synthase variants were developed using the methods disclosed herein, and show more than a 200% improvement in in vivo performance. The farnesene synthase variants have improved catalytic efficiency, i.e., they are able to catalyze their reaction at a faster rate. As such, they are more suitable for commercial production of sesquiterpene products such as farnesene where high yield production is of major importance.

Thus, in yet another aspect, provided herein are isolated β-farnesene synthase variants, and isolated nucleic acids comprising a nucleotide sequence encoding such β-farnesene synthase variants, having an amino acid sequence as given in SEQ ID NO: 111 but comprising one or more amino acid substitutions at positions selected from the group consisting of positions 2, 3, 4, 6, 9, 11, 18, 20, 24, 35, 38, 50, 61, 72, 80, 89, 105, 115, 144, 196, 211, 251, 280, 288, 319, 348, 357, 359, 369, 371, 385, 398, 423, 433, 434, 442, 444, 446, 460, 467, 488, 495, 505, 526, 531, 556, 572, and 575 of SEQ ID NO: 111.

In yet another aspect, the present invention provides a genetically modified host cell that comprises:

(a) a heterologous β-farnesene synthase, wherein the heterologous β-farnesene synthase is a variant of a β-farnesene synthase encoded by SEQ ID NO: 111; and

(b) a MEV pathway or DXP pathway enzyme;

wherein the host cell makes at least 15% more of a β-farnesene compared to a parent cell that comprises the MEV pathway or DXP pathway enzyme and the β-farnesene synthase encoded by SEQ ID NO: 111.

In some embodiments, the heterologous β-farnesene synthase comprises one or more amino acid substitutions at positions selected from the group consisting of positions 2, 3, 4, 6, 9, 11, 18, 20, 24, 35, 38, 50, 61, 72, 80, 89, 105, 115, 144, 196, 211, 251, 280, 288, 319, 348, 357, 359, 369, 371, 385, 398, 423, 433, 434, 442, 444, 446, 460, 467, 488, 495, 505, 526, 531, 556, 572, and 575 of SEQ ID NO: 111.

In some embodiments, the MEV pathway enzyme is a HMG-CoA reductase. In some embodiments, the MEV pathway enzyme is a mevalonate kinase. Additional exemplary enzymes of the MEV pathway are provided in Section 5.4 below.

In yet another aspect, provided herein is a method of producing a β-farnesene comprising the steps of:

(a) obtaining a plurality of genetically modified host cells comprising: i) a first heterologous nucleotide sequence encoding a variant of a β-farnesene synthase encoded by SEQ ID NO: 111; and ii) a second heterologous nucleotide sequence encoding a MEV pathway or DXP pathway enzyme;

(b) culturing said genetically modified host cells in a medium comprising a carbon source under conditions suitable for making the β-farnesene; and

(c) recovering the β-farnesene from the medium.

In some embodiments, the MEV pathway enzyme is a HMG-CoA reductase. In some embodiments, the MEV pathway enzyme is a mevalonate kinase. Additional exemplary enzymes of the MEV pathway are provided in Section 5.4 below.

Host cells useful in the practice of the present invention include archae, prokaryotic, or eukaryotic cells.

Suitable prokaryotic hosts include but are not limited to any of a variety of gram-positive, gram-negative, or gram-variable bacteria. Examples include but are not limited to cells belonging to the genera: Agrobacterium, Alicyclobacillus, Anabaena, Anacystis, Arthrobacter, Azobacter, Bacillus, Brevibacterium, Chromatium, Clostridium, Corynebacterium, Enterobacter, Erwinia, Escherichia, Lactobacillus, Lactococcus, Mesorhizobium, Methylobacterium, Microbacterium, Phormidium, Pseudomonas, Rhodobacter, Rhodopseudomonas, Rhodospirillum, Rhodococcus, Salmonella, Scenedesmun, Serratia, Shigella, Staphlococcus, Strepromyces, Synnecoccus, and Zymomonas. Examples of prokaryotic strains include but are not limited to: Bacillus subtilis, Bacillus amyloliquefacines, Brevibacterium ammoniagenes, Brevibacterium immariophilum, Clostridium beigerinckii, Enterobacter sakazakii, Escherichia coli, Lactococcus lactis, Mesorhizobium loti, Pseudomonas aeruginosa, Pseudomonas mevalonii, Pseudomonas pudica, Rhodobacter capsulatus, Rhodobacter sphaeroides, Rhodospirillum rubrum, Salmonella enterica, Salmonella typhi, Salmonella typhimurium, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, and Staphylococcus aureus.

Suitable archae hosts include but are not limited to cells belonging to the genera: Aeropyrum, Archaeglobus, Halobacterium, Methanococcus, Methanobacterium, Pyrococcus, Sulfolobus, and Thermoplasma. Examples of archae strains include but are not limited to: Archaeoglobus fulgidus, Halobacterium sp., Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Thermoplasma acidophilum, Thermoplasma volcanium, Pyrococcus horikoshii, Pyrococcus abyssi, and Aeropyrum pernix.

Suitable eukaryotic hosts include but are not limited to fungal cells, algal cells, insect cells, and plant cells. Examples include but are not limited to cells belonging to the genera: Aspergillus, Candida, Chrysosporium, Cryotococcus, Fusarium, Kluyveromyces, Neotyphodium, Neurospora, Penicillium, Pichia, Saccharomyces, Trichoderma, Ascomycota, Basidiomycota, Dothideomycetes, and Xanthophyllomyces (formerly Phaffia). Examples of eukaryotic strains include but are not limited to: Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia quercuum, Pichia pijperi, Pichia stiptis, Pichia methanolica, Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Schizosaccharomyces pombe, Hansenula polymorphs, Kluyveromyces sp., Kluyveromyces lactis, Candida albicans, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, Chrysosporium lucknowense, Fusarium sp., Fusarium gramineum, Fusarium venenatum, Neurospora crassa, and Chlamydomonas reinhardtii.

In a particular embodiment, the host cell is an Escherichia coli cell. In another particular embodiment, the host cell is a Saccharomyces cerevisiae cell. In some embodiments, the host cell is a Saccharomyces cerevisiae cell selected from the group consisting of Baker\'s yeast, CBS 7959, CBS 7960, CBS 7961, CBS 7962, CBS 7963, CBS 7964, IZ-1904, TA, BG-1, CR-1, SA-1, M-26, Y-904, PE-2, PE-5, VR-1, BR-1, BR-2, ME-2, VR-2, MA-3, MA-4, CAT-1, CB-1, NR-1, BT-1, and AL-1. In some embodiments, the host cell is a Saccharomyces cerevisiae cell selected from the group consisting of PE-2, CAT-1, VR-1, BG-1, CR-1, and SA-1. In a particular embodiment, the host cell is a Saccharomyces cerevisiae of strain PE-2. In another particular embodiment, the host cell is a Saccharomyces cerevisiae of strain CAT-1. In another particular embodiment, the host cell is a Saccharomyces cerevisiae of strain BG-1.

In some embodiments, the host cell is a cell that is suitable for industrial fermentation, e.g., bioethanol fermentation. In particular embodiments, the host cell is conditioned to subsist under high solvent concentration, high temperature, expanded substrate utilization, nutrient limitation, osmotic stress, acidity, sulfite and bacterial contamination, or combinations thereof, which are recognized stress conditions of the industrial fermentation environment.

In some embodiments, compared to a parent cell, a host cell comprises an elevated intracellular level of FPP, wherein the elevated intracellular level of FPP decreases the viability of the host cell.

In some embodiments, the host cell comprises an intracellular level of FPP that is at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 2-fold, at least about 2. 5-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 75-fold, at least about 100-fold, at least about 200-fold, at least about 300-fold, at least about 400-fold, at least about 500-fold, or at least about 1,000-fold, or more, higher than the intracellular level of FPP of the parent cell, on a per unit volume of cell culture basis.

In some embodiments, the host cell comprises an intracellular level of FPP that is at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 2-fold, at least about 2. 5-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 75-fold, at least about 100-fold, at least about 200-fold, at least about 300-fold, at least about 400-fold, at least about 500-fold, or at least about 1,000-fold, or more, higher than the intracellular level of FPP of the parent cell, on a per unit dry cell weight basis.

In some embodiments, the host cell comprises an intracellular level of FPP that is at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 2-fold, at least about 2. 5-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 75-fold, at least about 100-fold, at least about 200-fold, at least about 300-fold, at least about 400-fold, at least about 500-fold, or at least about 1,000-fold, or more, higher than the intracellular level of FPP of the parent cell, on a per unit volume of cell culture per unit time basis.

In some embodiments, the host cell comprises an intracellular level of FPP that is at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 2-fold, at least about 2. 5-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 75-fold, at least about 100-fold, at least about 200-fold, at least about 300-fold, at least about 400-fold, at least about 500-fold, or at least about 1,000-fold, or more, higher than the intracellular level of FPP of the parent cell, on a per unit dry cell weight per unit time basis.

In most embodiments, the elevated intracellular level of FPP in the host cell is inducible by an inducing compound. Such a host cell can be manipulated with ease in the absence of the inducing compound. The inducing compound is then added to induce the elevated level of FPP in the host cell. In other embodiments, the elevated intracellular level of FPP in the host cell is inducible by changing culture conditions, such as, for example, the growth temperature. The inducible elevation of intracellular FPP level thus provides a molecular on and off switch for the reduced viability phenotype of the host cell.

The elevation of intracellular FPP level can be effected through targeted genetic engineering of the host cell. A number of enzymes are known to function in the production or utilization of FPP and its precursors, and any one of these enzymes can be manipulated to change the level of FPP in a host cell.

In some embodiments, the production of FPP in the host cell is increased by increasing production of cellular acetyl-CoA in the host cell.

In some embodiments, the production of FPP in the host cell is increased by increasing the production of IPP and/or DMAPP in the host cell. In some such embodiments, the production of IPP and DMAPP in the host cell is increased by increasing the activity of one or more enzymes of the MEV pathway. A schematic representation of the MEV pathway is described in FIG. 15. In general, the pathway comprises six steps:

In the first step, two molecules of acetyl-coenzyme A are enzymatically combined to form acetoacetyl-CoA. An enzyme known to catalyze this step is, for example, acetyl-CoA thiolase. Illustrative examples of nucleotide sequences include but are not limited to the following GenBank accession numbers and the organism from which the sequences derived: (NC—000913 REGION: 2324131 . . . 2325315; Escherichia coli), (D49362; Paracoccus denitrificans), and (L20428; Saccharomyces cerevisiae).

In the second step of the MEV pathway, acetoacetyl-CoA is enzymatically condensed with another molecule of acetyl-CoA to form 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). An enzyme known to catalyze this step is, for example, HMG-CoA synthase. Illustrative examples of nucleotide sequences include but are not limited to: (NC—001145. complement 19061 . . . 20536; Saccharomyces cerevisiae), (X96617; Saccharomyces cerevisiae), (X83882; Arabidopsis thaliana), (AB037907; Kitasatospora griseola), (BT007302; Homo sapiens), and (NC—002758, Locus tag SAV2546, GeneID 1122571; Staphylococcus aureus).

In the third step, HMG-CoA is enzymatically converted to mevalonate. An enzyme known to catalyze this step is, for example, HMG-CoA reductase. Illustrative examples of nucleotide sequences include but are not limited to: (NM—206548; Drosophila melanogaster), (NC—002758, Locus tag SAV2545, GeneID 1122570; Staphylococcus aureus), (NM 204485; Gallus gallus), (AB015627; Streptomyces sp. KO 3988), (AF542543; Nicotiana attenuata), (AB037907; Kitasatospora griseola), (AX128213, providing the sequence encoding a truncated HMGR; Saccharomyces cerevisiae), and (NC—001145: complement (115734 . . . 118898; Saccharomyces cerevisiae).

In the fourth step, mevalonate is enzymatically phosphorylated to form mevalonate 5-phosphate. An enzyme known to catalyze this step is, for example, mevalonate kinase. Illustrative examples of nucleotide sequences include but are not limited to: (L77688; Arabidopsis thaliana), and (X55875; Saccharomyces cerevisiae).

In the fifth step, a second phosphate group is enzymatically added to mevalonate 5-phosphate to form mevalonate 5-pyrophosphate. An enzyme known to catalyze this step is, for example, phosphomevalonate kinase. Illustrative examples of nucleotide sequences include but are not limited to: (AF429385; Hevea brasiliensis), (NM—006556; Homo sapiens), and (NC—001145. complement 712315 . . . 713670; Saccharomyces cerevisiae).

In the sixth step, mevalonate 5-pyrophosphate is enzymatically converted into IPP. An enzyme known to catalyze this step is, for example, mevalonate pyrophosphate decarboxylase. Illustrative examples of nucleotide sequences include but are not limited to: (X97557; Saccharomyces cerevisiae), (AF290095; Enterococcus faecium), and (U49260; Homo sapiens).

In other such embodiments, the production of IPP and DMAPP in the host cell is increased by increasing the activity of one or more enzymes of the DXP pathway. A schematic representation of the DXP pathway is described in FIG. 16. In general, the DXP pathway comprises seven steps:

In the first step, pyruvate is condensed with D-glyceraldehyde 3-phosphate to make 1-deoxy-D-xylulose-5-phosphate. An enzyme known to catalyze this step is, for example, 1-deoxy-D-xylulose-5-phosphate synthase. Illustrative examples of nucleotide sequences include but are not limited to: (AF035440; Escherichia coli), (NC—002947, locus tag PP0527; Pseudomonas putida KT2440), (CP000026, locus tag SPA2301; Salmonella enterica Paratyphi, see ATCC 9150), (NC—007493, locus tag RSP—0254; Rhodobacter sphaeroides 2. 4. 1), (NC—005296, locus tag RPA0952; Rhodopseudomonas palustris CGA009), (NC—004556, locus tag PD1293; Xylella fastidiosa Temecula1), and (NC—003076, locus tag AT5G11380; Arabidopsis thaliana).

In the second step, 1-deoxy-D-xylulose-5-phosphate is converted to 2C-methyl-D-erythritol-4-phosphate. An enzyme known to catalyze this step is, for example, 1-deoxy-D-xylulose-5-phosphate reductoisomerase. Illustrative examples of nucleotide sequences include but are not limited to: (AB013300; Escherichia coli), (AF148852; Arabidopsis thaliana), (NC—002947, locus tag PP1597; Pseudomonas putida KT2440), (AL939124, locus tag SCO5694; Streptomyces coelicolor A3(2)), (NC—007493, locus tag RSP 2709; Rhodobacter sphaeroides 2. 4. 1), and (NC—007492, locus tag Pfl—1107; Pseudomonas fluorescens NO-1).

In the third step, 2C-methyl-D-erythritol-4-phosphate is converted to 4-diphosphocytidyl-2C-methyl-D-erythritol. An enzyme known to catalyze this step is, for example, 4-diphosphocytidyl-2C-methyl-D-erythritol synthase. Illustrative examples of nucleotide sequences include but are not limited to: (AF230736; Escherichia coli), (NC—007493, locus_tag RSP 2835; Rhodobacter sphaeroides 2. 4. 1), (NC—003071, locus_tag AT2G02500; Arabidopsis thaliana), and (NC—002947, locus_tag PP1614; Pseudomonas putida KT2440).

In the fourth step, 4-diphosphocytidyl-2C-methyl-D-erythritol is converted to 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate. An enzyme known to catalyze this step is, for example, 4-diphosphocytidyl-2C-methyl-D-erythritol kinase. Illustrative examples of nucleotide sequences include but are not limited to: (AF216300; Escherichia coli) and (NC—007493, locus_tag RSP—1779; Rhodobacter sphaeroides 2. 4. 1).

In the fifth step, 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate is converted to 2C-methyl-D-erythritol 2,4-cyclodiphosphate. An enzyme known to catalyze this step is, for example, 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Illustrative examples of nucleotide sequences include but are not limited to: (AF230738; Escherichia coli), (NC—007493, locus_tag RSP 6071; Rhodobacter sphaeroides 2. 4. 1), and (NC—002947, locus tag PP1618; Pseudomonas putida KT2440).

In the sixth step, 2C-methyl-D-erythritol 2,4-cyclodiphosphate is converted to 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate. An enzyme known to catalyze this step is, for example, 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase. Illustrative examples of nucleotide sequences include but are not limited to: (AY033515; Escherichia coli), (NC—002947, locus_tag PP0853; Pseudomonas putida KT2440), and (NC—007493, locus_tag RSP 2982; Rhodobacter sphaeroides 2. 4. 1).

In the seventh step, 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate is converted into either IPP or its isomer, DMAPP. An enzyme known to catalyze this step is, for example, isopentyl/dimethylallyl diphosphate synthase. Illustrative examples of nucleotide sequences include but are not limited to: (AY062212; Escherichia coli) and (NC—002947, locus_tag PP0606; Pseudomonas putida KT2440).

In some embodiments, the production of FPP in the host cell is increased by increasing the isomerization of IPP to DMAPP. In some such embodiments, the isomerization of IPP to DMAPP is increased by increasing the activity of an IPP isomerase. Illustrative examples of nucleotide sequences encoding IPP isomerases include but are not limited to: (NC—000913, 3031087 . . . 3031635; Escherichia coli), and (AF082326; Haematococcus pluvialis).

In some embodiments, the production of FPP in the host cell is increased by increasing the condensation of IPP and DMAPP to FPP. In some such embodiments, the condensation of IPP and DMAPP or of IPP and geranyl pyrophosphate (“GPP”) to FPP is increased by increasing the activity of a FPP synthase. Illustrative examples of nucleotide sequences that encode FPP synthases include but are not limited to: (ATU80605; Arabidopsis thaliana), (ATHFPS2R; Arabidopsis thaliana), (AAU36376; Artemisia annua), (AF461050; Bos taurus), (D00694; Escherichia coli K-12), (AE009951, Locus AAL95523; Fusobacterium nucleatum subsp. nucleatum ATCC 25586), (GFFPPSGEN; Gibberella fujikuroi), (CP000009, Locus AAW60034; Gluconobacter oxydans 621H), (AF019892; Helianthus annuus), (HUMFAPS; Homo sapiens), (KLPFPSQCR; Kluyveromyces lactis), (LAU15777; Lupinus albus), (LAU20771; Lupinus albus), (AF309508; Mus musculus), (NCFPPSGEN; Neurospora crassa), (PAFPS1; Parthenium argentatum), (PAFPS2; Parthenium argentatum), (RATFAPS; Rattus norvegicus), (YSCFPP; Saccharomyces cerevisiae), (D89104; Schizosaccharomyces pombe), (CP000003, Locus AAT87386; Streptococcus pyogenes), (CP000017, Locus AAZ51849; Streptococcus pyogenes), (NC—008022, Locus YP—598856; Streptococcus pyogenes MGAS10270), (NC—008023, Locus YP—600845; Streptococcus pyogenes MGAS2096), (NC—008024, Locus YP—602832; Streptococcus pyogenes MGAS10750), (MZEFPS; Zea mays), (AE000657, Locus AAC06913; Aquifex aeolicus VF5), (NM 202836; Arabidopsis thaliana), (D84432, Locus BAA12575; Bacillus subtilis), (U12678, Locus AAC28894; Bradyrhizobium japonicum USDA 110), (BACFDPS; Geobacillus stearothermophilus), (NC—002940, Locus NP—873754; Haemophilus ducreyi 35000HP), (L42023, Locus AAC23087; Haemophilus influenzae Rd KW20), (J05262; Homo sapiens), (YP—395294; Lactobacillus sakei subsp. sakei 23K), (NC—005823, Locus YP—000273; Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130), (AB003187; Micrococcus luteus), (NC—002946, Locus YP—208768; Neisseria gonorrhoeae FA 1090), (U00090, Locus AAB91752; Rhizobium sp. NGR234), (J05091; Saccharomyces cerevisae), (CP000031, Locus AAV93568; Silicibacter pomeroyi DSS-3), (AE008481, Locus AAK99890; Streptococcus pneumoniae R6), and (NC—004556, Locus NP 779706; Xylella fastidiosa Temecula1).

In some embodiments, the production of FPP in the host cell is increased by inhibiting reactions that divert intermediates from productive steps towards formation of FPP. Such reactions include but are not limited to side reactions of the TCA cycle that lead to fatty acid biosynthesis, alanine biosynthesis, the aspartate superpathway, gluconeogenesis, heme biosynthesis, glutamate biosynthesis, and conversion of acetyl-CoA to acetate via the action of phosphotransacetylase.

In some embodiments, a host cell that comprises an elevated intracellular level of FPP is obtained by decreasing the consumption of FPP in the host cell. In some such embodiments, the consumption of FPP in the host cell is decreased by decreasing the activity of a farnesyl-diphosphate farnesyl transferase or squalene synthase that can convert FPP to squalene. In other such embodiments, the consumption of FPP in the host cell is decreased by decreasing the activity of a sesquiterpene synthase in the host cell.

A host cell comprising an elevated intracellular level of FPP can be generated by genetically modifying a parent cell using genetic engineering techniques (i.e., recombinant technology), classical microbiological techniques, or a combination of such techniques. The host cell may also be a naturally occurring genetic variant that is non-viable under certain growth conditions due to an elevated intracellular level of FPP.

A host cell that comprises such an elevated intracellular level of FPP that it has reduced cell viability can be identified by comparing the growth of the host cell on a solid medium with that of a parent cell that does not comprise the elevated intracellular level of FPP. A host cell that comprises an elevated level of intracellular FPP should produce fewer or smaller colonies on the solid agar medium compared to its parent cell. A host cell that comprises the elevated intracellular level of FPP only under certain growth conditions can be identified by first growing the host cell under conditions under which the host cell does not comprise an elevated intracellular level of FPP and under which it has the same viability as its parent cell (“permissive growth conditions”), and then replica-plating the host cell and growing it under conditions under which the host cell does comprise the elevated intracellular level of FPP (“restrictive growth condition”) to identify host cells that has reduced viability only under restrictive growth conditions but that does not have reduced viability under permissive growth conditions. Such restrictive growth conditions can include but are not limited to the presence of a specific nutrient in the culture medium, the presence of a specific nutrient at a specific level in the culture medium, the presence of an inducing compound in the culture medium, the presence of a repressing compound in the culture medium, and a specific growth temperature.

The methods provided herein are focused on developing terpene synthase variants with improved in vivo performance.

In some embodiments, the terpene synthase variant is a variant of a naturally occurring terpene synthase. In other embodiments, the terpene synthase variant is a variant of a naturally not occurring terpene synthase.

In some such embodiments, the terpene synthase variant differs from a naturally occurring terpene synthase or from a naturally not occurring terpene synthase by one or more amino acid substitutions, deletions, and/or additions. In some embodiments, the terpene synthase differs from a naturally occurring terpene synthase or from a naturally not occurring terpene synthase by comprising one, two, three, four, five, six, seven, eight, nine, ten, or more additional amino acids. In some embodiments, the terpene synthase variant differs from a naturally occurring terpene synthase or from a naturally not occurring terpene synthase by comprising one, two, three, four, five, six, seven, eight, nine, ten, or more amino acid substitutions. In some embodiments, the terpene synthase variant differs from a naturally occurring terpene synthase or from a naturally not occurring terpene synthase by lacking one, two, three, four, five, six, seven, eight, nine, ten, or more amino acids.

In some embodiments, the terpene synthase variant has from about 50% to about 55%, from about 55% to about 60%, from about 60% to about 65%, from about 65% to about 70%, from about 70% to about 75%, from about 75% to about 80%, from about 80% to about 85%, from about 85% to about 90%, from about 90% to about 95%, or from about 95% to 99% amino acid sequence identity to the amino acid sequence of a naturally occurring terpene synthase or of a naturally not occurring terpene synthase.

In some embodiments, the terpene synthase variant comprises a consensus amino acid sequence. A consensus amino acid sequence is derived by aligning three or more amino acid sequences, and identifying amino acids that are shared by at least two of the sequences. In some embodiments, the terpene synthase variant comprises a consensus sequence derived from two or more naturally occurring terpene synthases.

In some embodiments, the terpene synthase variant is a hybrid terpene synthase. Hybrid terpene synthases comprise stretches of contiguous amino acids from two or more different terpene synthases. Hybrid terpene synthases can be generated using any known method, including but not limited to exon shuffling, domain swapping, and the like (e.g., Nixon et al. (1997) Proc. Natl. Acad. Sci. USA 94:1069-1073; Fisch et al. (1996) Proc Natl Acad Sci USA 93(15):7761-7766).

In some embodiments, a nucleic acid comprising a nucleotide sequence encoding a terpene synthase variant hybridizes under stringent hybridization conditions to a nucleic acid encoding a naturally occurring terpene synthase. In another embodiment, a nucleic acid comprising a nucleotide sequence encoding a terpene synthase variant hybridizes under moderate hybridization conditions to a nucleic acid encoding a naturally occurring terpene synthase. In yet another embodiment, a nucleic acid comprising a nucleotide sequence encoding a terpene synthase variant hybridizes under low stringency hybridization conditions to a nucleic acid encoding a naturally occurring terpene synthase.

In some embodiments, the nucleotide sequence encoding the terpene synthase variant is altered from the nucleotide sequence encoding a naturally occurring terpene synthase to reflect the codon preferences for a particular host cell (i.e., is codon-optimized for expression in a particular host cell). The use of preferred codons for a particular host cell generally increases the likelihood of translation, and hence expression, of the nucleotide sequence. Codon usage tables that summarize the percentage of time a specific organism uses a specific codon to code a specific amino acid are available for many organisms, and can be used as a reference in designing suitable nucleotide sequences. In some embodiments, the nucleotide sequence encoding the terpene synthase is altered to reflect the codon preferences of Saccharomyces cerevisiae (see, e.g., Bennetzen and Hall (1982) J. Biol. Chem. 257(6): 3026-3031). In some embodiments, the nucleotide sequence encoding the terpene synthase is altered to reflect the codon preferences for Escherichia coli (see, e.g., Gouy and Gautier (1982) Nucleic Acids Res. 10(22):7055-7074; Eyre-Walker (1996) Mol. Biol. Evol. 13(6):864-872; Nakamura et al. (2000) Nucleic Acids Res. 28(1):292).

A nucleic acid comprising a nucleotide sequence encoding a terpene synthase can be obtained using any of a variety of known recombinant techniques and synthetic procedures. The nucleic acid can be prepared from genomic DNA, cDNA, or RNA, all of which can be extracted directly from a cell or can be recombinantly produced by various amplification processes including but not limited to PCR and rt-PCR. Direct chemical synthesis methods are also well known in the art.

A nucleic acid comprising a nucleotide sequence encoding a terpene synthase variant can be obtained using any of a variety of known methods. For example, nucleic acids can be isolated from cells that were treated with chemical mutagens or radiation, or from cells that have deficiencies in DNA repair. Suitable chemical mutagens include, but are not limited to, ethyl methanesulfonate (EMS), methyl methanesulfonate (MMS), N-nitroso urea (ENU), N-methyl-N-nitro-N′-nitrosoguanidine, 4-nitroquino line N-oxide, diethylsulfate, benzopyrene, cyclophosphamide, bleomycin, triethylmelamine, acrylamide monomer, nitrogen mustard, vincristine, diepoxyalkanes (for example, diepoxybutane), ICR-170, formaldehyde, procarbazine hydrochloride, ethylene oxide, dimethylnitrosamine, 7,12 dimethylbenz(a)anthracene, chlorambucil, hexamethylphosphoramide, bisulfan, and acridine dyes (see, for example Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., or Deshpande Mukund V., Appl. Biochem. Biotechnol. 36, 227 (1992)). Suitable radiation exposures include but are not limited to ultraviolet radiation (optionally in combination with exposure to chemical agents such as, for example, trimethylpsoralen), γ-irradiation, X-rays, and fast neutron bombardment. A suitable method for introducing deficiencies in DNA repair in a cell includes but is not limited to the expression of a mutant DNA repair enzyme that generates a high frequency of mutations in the genome of the cell (on the order of about 1 mutation/100 genes to about 1 mutation/10,000 genes). Examples of genes encoding DNA repair enzymes include but are not limited to Mut H, Mut S, Mut L, and Mut U, and the homologs thereof in other species (for example, MSH 1-6, PMS 1-2, MLH 1, GTBP, and ERCC-1). Other methods for obtaining a nucleic acid comprising a nucleotide sequence encoding a terpene synthase variant include manipulation of cell-free in vitro systems (e.g., using error-prone PCR for the amplification of a nucleic acid), random or targeted insertion in the genome of a cell of a mobile DNA element (e.g., a transposable element), or in vitro DNA shuffling (e.g., exon shuffling, domain swapping, and the like; see, for example, Ausubel et al., Current Protocols In Molecular Biology, John Wiley and Sons, New York (current edition); and Sambrook et al., Molecular Cloning, A Laboratory Manual, 3d. ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001)).

In some embodiments, the terpene synthase variants are variants of a sesquiterpene synthase selected from the group consisting of a β-farnesene synthase, an α-farnesene synthase, a trichodiene synthase, a patchoulol synthase, an amorphadiene synthase, a valencene synthase, a farnesol synthase, a nerolidol synthase, and a nootkatone synthase.

In some embodiments, the terpene synthase variant is a β-farnesene synthase variant. In some such embodiments, the β-farnesene synthase variant is derived from a β-farnesene synthase of Artemisia annua. The sequence of the β-farnesene synthase of Artemisia annua has been previously described (Picaud, et al, (2005) Phytochemistry 66 (9):961-967). The nucleotide sequence of the β-farnesene synthase of Artemisia annua is deposited under GenBank accession number AY835398, and SEQ ID NO: 112 as provided herein. The amino acid sequence of the β-farnesene synthase of Artemisia annua is deposited under GenBank accession number AAX39387, and SEQ ID NO: 111 as provided herein.

In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 2 from serine to aspartate (S2D mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 3 from threonine to asparagine (T3N mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 4 from leucine to serine (L4S mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 6 from isoleucine to threonine (16T mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 9 from valine to aspartic acid (V9D mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 11 from phenylalanine to serine (F11S mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 20 from valine to glutamic acid (V20E mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 24 from valine to aspartic acid (V24D mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 35 from methionine to threonine (M35T mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 38 from asparagine to serine (N38S mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 50 from aspartic acid to asparagine (D50N mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 61 from leucine to glutamine (L61Q mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 72 from glutamic acid to lysine (E72K mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 72 from glutamic acid to valine (E72V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 80 from asparagine to aspartic acid (N80D mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 89 from isoleucine to valine (189V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 105 from glutamic acid to aspartic acid (E105D mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 115 from isoleucine to methionine (I115M mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 115 from isoleucine to valine (I115V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 144 from phenylalanine to tyrosine (F144Y mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 196 from threonine to serine (T196S mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 211 from serine to threonine (S211T mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 251 from leucine to methionine (L251M mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 280 from leucine to glutamine (L280Q mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 288 from tyrosine to phenylalanine (Y288F mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 319 from threonine to serine (T319S mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 357 from glutamic acid to valine (E357V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 359 from glutamic acid to threonine (E359T mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 369 from valine to leucine (V369L mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 371 from leucine to methionine (L371M mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 385 from threonine to alanine (T385A mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 398 from isoleucine to valine (I398V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 423 from valine to isoleucine (V423I mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 433 from methionine to isoleucine (M433I mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 434 from isoleucine to threonine (1434T mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 442 from glycine to alanine (G442A mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 442 from glycine to aspartic acid (G442D mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 444 from isoleucine to leucine (I444L mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 446 from threonine to asparagine (T446N mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 460 from isoleucine to valine (I460V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 467 from valine to isoleucine (V467I mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 488 from serine to phenylalanine (S488F mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 495 from glutamic acid to glycine (E495G mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 505 from glutamic acid to valine (E505V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 526 from threonine to serine (T526S mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 531 from proline to serine (P531S mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 556 from alanine to valine (A556V mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 572 from methionine to lysine (M572K mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 575 from a stop codon to lysine (stop575K mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 348 from arginine to lysine (R348K mutation). In some embodiments, the β-farnesene synthase variant has an amino acid sequence as given in SEQ ID NO: 111 but comprising an amino acid substitution at position 18 from leucine to isoleucine (L18I mutation).

The methods provided herein include obtaining a host cell that is genetically engineered to comprise an elevated intracellular FPP level or to express a terpene synthase or a terpene synthase variant. Such a genetically engineered host cell may comprise insertions, deletions, or modifications of nucleotides in such a manner as to provide the desired effect of elevating the intracellular level of FPP or of expressing the terpene synthase or the terpene synthase variant. Such genetic modifications may result in a decrease or increase or modification in copy number or activity of a specific enzyme.

For example, the copy number of an enzyme in a host cell may be altered by modifying the transcription of the gene that encodes the enzyme. This can be achieved for example by modifying the copy number of the nucleotide sequence encoding the enzyme (e.g., by using a higher or lower copy number expression vector comprising the nucleotide sequence, or by introducing additional copies of the nucleotide sequence into the genome of the host cell or by deleting or disrupting the nucleotide sequence in the genome of the host cell), by changing the order of coding sequences on a polycistronic mRNA of an operon or breaking up an operon into individual genes each with its own control elements, or by increasing the strength of the promoter or operator to which the nucleotide sequence is operably linked. Alternatively or in addition, the copy number of an enzyme in a host cell may be altered by modifying the level of translation of an mRNA that encodes the enzyme. This can be achieved for example by modifying the stability of the mRNA, modifying the sequence of the ribosome binding site, modifying the distance or sequence between the ribosome binding site and the start codon of the enzyme coding sequence, modifying the entire intercistronic region located “upstream of” or adjacent to the 5′ side of the start codon of the enzyme coding region, stabilizing the 3′-end of the mRNA transcript using hairpins and specialized sequences, modifying the codon usage of enzyme, altering expression of rare codon tRNAs used in the biosynthesis of the enzyme, and/or increasing the stability of the enzyme, as, for example, via mutation of its coding sequence.

The activity of an enzyme in a host cell can be altered in a number of ways, including, but not limited to, expressing a modified form of the enzyme that exhibits increased or decreased solubility in the host cell, expressing an altered form of the enzyme that lacks a domain through which the activity of the enzyme is inhibited, expressing a modified form of the enzyme that has a higher or lower Kcat or a lower or higher Km for the substrate, or expressing an altered form of the enzyme that is more or less affected by feed-back or feed-forward regulation by another molecule in the pathway.

The methods provided herein further include steps of expressing a terpene synthase or a terpene synthase variant in a host cell that does not naturally express such terpene synthase or terpene synthase variant. Expression of a terpene synthase or a terpene synthase variant in a host cell can be accomplished by introducing into the host cells a nucleic acid comprising a nucleotide sequence encoding the terpene synthase or terpene synthase variant under the control of regulatory elements that permit expression in the host cell. In some embodiments, the nucleic acid is an extrachromosomal plasmid. In other embodiments, the nucleic acid is a chromosomal integration vector that can integrate the nucleotide sequence into the chromosome of the host cell.

In some embodiments, it is essential that expression levels of terpene synthases or terpene synthase variants in two or more host cells are similar. This can be accomplished using nucleic acids comprising nucleotide sequences encoding the terpene synthase or terpene synthase variant under the control of the same regulatory elements. Such nucleic acids can be used as extrachromosomal expression vectors or to integrate the nucleotide sequences encoding the terpene synthase or the terpene synthase variant and the regulatory elements into the chromosome of the host cell. Comparable expression levels can also be accomplished by targeting nucleic acids comprising nucleotide sequences encoding the terpene synthase or terpene synthase variant to identical locations in the two or more host cells, thus placing the nucleotide sequences under the control of the same endogenous regulatory elements. In addition to the use of similar regulatory elements, comparable expression levels may also depend on similar copy numbers of the nucleotide sequences in the two or more host cells. Copy numbers can be controlled by the use of similar or identical origins of replications in extrachromosomal expression vectors, or by the use of similar types and numbers of chromosomal integration constructs for the integration of the nucleotide sequences into the chromosome of the two or more host cells. A number of additional features of the nucleic acids can affect the expression level of the encoded terpene synthases or terpene synthase variants (e.g., protein or mRNA stability, sequence of the ribosome binding site, distance between the ribosome binding site and start codon, nature of the upstream and downstream sequences, hairpins and other specialized sequences, and codon usage), and all of these can be modified to ensure similar expression levels when required in the provided methods.

Nucleic acids can be introduced into microorganisms by any method known to one of skill in the art without limitation (see, for example, Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75:1292-3; Cregg et al. (1985) Mol. Cell. Biol. 5:3376-3385; Goeddel et al., eds, 1990, Methods in Enzymology, vol. 185, Academic Press, Inc., CA; Krieger, 1990, Gene Transfer and Expression—A Laboratory Manual, Stockton Press, NY; Sambrook et al., 1989, Molecular Cloning—A Laboratory Manual, Cold Spring Harbor Laboratory, NY; and Ausubel et al., eds., Current Edition, Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley Interscience, NY). Exemplary techniques include but are not limited to spheroplasting, electroporation, PEG 1000 mediated transformation, and lithium acetate or lithium chloride mediated transformation.

In some embodiments, a nucleic acid used to genetically modify a host cell comprises one or more selectable markers useful for the selection of transformed host cells and for placing selective pressure on the host cell to maintain the foreign DNA.

In some embodiments, the selectable marker is an antibiotic resistance marker. Illustrative examples of antibiotic resistance markers include but are not limited to the BLA, NAT1, PAT, AUR1-C, PDR4, SMR1, CAT, mouse dhfr, HPH, DSDA, KANR, and SH BLE gene products. The BLA gene product from E. coli confers resistance to beta-lactam antibiotics (e.g., narrow-spectrum cephalosporins, cephamycins, and carbapenems (ertapenem), cefamandole, and cefoperazone) and to all the anti-gram-negative-bacterium penicillins except temocillin; the NAT1 gene product from S. noursei confers resistance to nourseothricin; the PAT gene product from S. viridochromogenes Tu94 confers resistance to bialophos; the AUR1-C gene product from Saccharomyces cerevisiae confers resistance to Auerobasidin A (AbA); the PDR4 gene product confers resistance to cerulenin; the SMR1 gene product confers resistance to sulfometuron methyl; the CAT gene product from Tn9 transposon confers resistance to chloramphenicol; the mouse dhfr gene product confers resistance to methotrexate; the HPH gene product of Klebsiella pneumonia confers resistance to Hygromycin B; the DSDA gene product of E. coli allows cells to grow on plates with D-serine as the sole nitrogen source; the KANR gene of the Tn903 transposon confers resistance to G418; and the SH BLE gene product from Streptoalloteichus hindustanus confers resistance to Zeocin (bleomycin). In some embodiments, these antibiotic resistance marker is deleted after the genetically modified host cell disclosed herein is isolated.

In some embodiments, the selectable marker rescues an auxotrophy (e.g., a nutritional auxotrophy) in the genetically modified microorganism. In such embodiments, a parent microorganism comprises a functional disruption in one or more gene products that function in an amino acid or nucleotide biosynthetic pathway and that when non-functional rende a parent cell incapable of growing in media without supplementation with one or more nutrients. Such gene products include but are not limited to the HIS3, LEU2, LYS1, LYS2, MET15, TRP1, ADE2, and URA3 gene products in yeast. The auxotrophic phenotype can then be rescued by transforming the parent cell with an expression vector or chromosomal integration construct encoding a functional copy of the disrupted gene product, and the genetically modified host cell generated can be selected for based on the loss of the auxotrophic phenotype of the parent cell. Utilization of the URA3, TRP1, and LYS2 genes as selectable markers has a marked advantage because both positive and negative selections are possible. Positive selection is carried out by auxotrophic complementation of the URA3, TRP1, and LYS2 mutations, whereas negative selection is based on specific inhibitors, i.e., 5-fluoro-orotic acid (FOA), 5-fluoroanthranilic acid, and α-aminoadipic acid (aAA), respectively, that prevent growth of the prototrophic strains but allows growth of the URA3, TRP1, and LYS2 mutants, respectively.

In other embodiments, the selectable marker rescues other non-lethal deficiencies or phenotypes that can be identified by a known selection method.

The present invention provides methods for developing terpene synthase variants with improved in vivo performance, and for producing terpenes. The methods generally involve growing a host cell under suitable conditions in a suitable medium comprising a carbon source.

Suitable conditions and suitable media for growing microorganisms are well known in the art. In some embodiments, the suitable medium is supplemented with one or more additional agents, such as, for example, an inducing compound (e.g., when one or more nucleotide sequences encoding a gene product are under the control of an inducible promoter), a repressing compound (e.g., when one or more nucleotide sequences encoding a gene product are under the control of a repressible promoter), or a selection agent (e.g., an antibiotic to select for microorganisms comprising the genetic modifications).

In some embodiments, the carbon source is a monosaccharide (simple sugar), a disaccharide, a polysaccharide, a non-fermentable carbon source, or one or more combinations thereof. Non-limiting examples of suitable monosaccharides include glucose, galactose, mannose, fructose, ribose, and combinations thereof. Non-limiting examples of suitable disaccharides include sucrose, lactose, maltose, trehalose, cellobiose, and combinations thereof. Non-limiting examples of suitable polysaccharides include starch, glycogen, cellulose, chitin, and combinations thereof. Non-limiting examples of suitable non-fermentable carbon sources include acetate and glycerol.

In one aspect, the present invention provides a method for identifying a terpene synthase with improved in vivo performance based on the growth rate of a host cell comprising a test terpene synthase. The growth rate of a host cell can be determined, for example, by growing the host cell in liquid medium for a defined period of time, then plating all or an aliquot of the culture on an agar plate, and finally scoring the number of colonies that arise on the agar plate. Alternatively, the growth rate of a host cell is determined by measuring the biomass of a culture after a defined period of time. Biomass can be measured by determining the density of the liquid culture, e.g. by UV spectrometry, or by quantifying biomass index molecules such as hexoseamine and ergosterol (Frey et al. (1992) Biol. Fertil. Soils 13: 229-234; Newell (1992) p. 521-561. In G. C. Carroll and D. T. Wicklow (ed.), The fungal community: its organization and role in the ecosystem, 2nd ed. Marcel Dekker Inc., New York).

The present invention provides methods for producing terpenes.

In some embodiments, the terpene is produced in an amount greater than about 10 grams per liter of fermentation medium. In some such embodiments, the terpene is produced in an amount from about 10 to about 50 grams, more than about 15 grams, more than about 20 grams, more than about 25 grams, or more than about 30 grams per liter of cell culture.

In some embodiments, the terpene is produced in an amount greater than about 50 milligrams per gram of dry cell weight. In some such embodiments, the terpene is produced in an amount from about 50 to about 1500 milligrams, more than about 100 milligrams, more than about 150 milligrams, more than about 200 milligrams, more than about 250 milligrams, more than about 500 milligrams, more than about 750 milligrams, or more than about 1000 milligrams per gram of dry cell weight.

In some embodiments, the terpene is produced in an amount that is at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 2-fold, at least about 2. 5-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 75-fold, at least about 100-fold, at least about 200-fold, at least about 300-fold, at least about 400-fold, at least about 500-fold, or at least about 1,000-fold, or more, higher than the amount of the terpene produced by a host cell that does not comprise the first heterologous nucleotide sequence, on a per unit volume of cell culture basis.