1. CROSS REFERENCE TO RELATED APPLICATION
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
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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.
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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.
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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. 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.