# Patent

## Title
Methods of generating protein variants

## Abstract

The present invention provides methods of designing and generating polypeptide variants that have altered properties compared to a parent polypeptide. The present invention further provides a computer program product for carrying out the design of a variant polypeptide. The present invention further provides nucleic acids encoding enzyme variants, as well as vectors and host cells comprising the nucleic acids. The present invention further provides variant enzymes; methods of producing the variant enzymes; and methods of producing compounds using the enzymes.

## Background
CROSS-REFERENCE
This application claims the benefit of U.S. Provisional Patent Application No. 60/918,417, filed Mar. 16, 2007, which application is incorporated herein by reference in its entirety.


GOVERNMENT GRANT SUPPORT
This invention was made with government support under Grant Number 2001-52104-11228 awarded by the U.S. Department of Agriculture, CSREES. The government has certain rights in the invention.


BACKGROUND
The in vivo enzyme properties attributable to their intracellular activity and concentration are important determinants of the efficiencies of metabolic pathways. It is well known that many enzymes are able to catalyze very specific chemical reactions with surprising accuracy and efficiency. These enzymes, each catalyzing different but a series of chemical reactions, often cooperate to act and minimize the unnecessary accumulation of metabolic intermediates, and thus form highly integrated metabolic pathways. It is thought that the evolution of enzymes and metabolic pathways are driven in large part by the recruitment of enzymes from other metabolic pathways; enzymes with promiscuous function initially shared by a few distinctive pathways may divergently and cooperatively evolve through gene duplications and subsequent functional specialization depending on the importance of each metabolite, resulting in a mosaic or patchwork of homologous enzymes in two distinct pathways8. Since natural evolution is known to be a highly accomplished designer for in vivo enzyme properties and the efficiencies of metabolic pathways, understanding the mechanisms for molecular evolution might allow for the development of a methodology to redesign efficiencies of constructed synthetic metabolic pathways.
In molecular evolution, the fixation probability of mutations is simply determined by their fitness effects: deleterious (opposed by purifying selection and likely discarded from a population), neutral or nearly neutral (genetic drift), or advantageous (supposed by positive selection and likely fixed to a population)9. However, detailed mechanisms for the molecular basis of adaptations of enzymes and pathways are still largely unclear, as the fitness effects are highly dependent on genotypic and/or phenotypic backgrounds of host organisms. Additionally, impacted by changes in the environment, the fitness effects could also vary even in a population in the same environment due to biological noise10,11. Since it is assumed that the large diversity in protein sequences with orthologous relations are created based on the contributions of mutations to fitness effects, it is thought that changes that are kept to a minimum during the course of evolution may be very essential to maintain in vivo enzyme functions.
Directed evolution, modifying a parent protein such that the modified protein exhibits a desirable property, can be achieved by mutagenizing one or more parent proteins and screening the mutants to identify those having a desired property. A variety of directed evolution methods are currently available for generating protein variants that exhibit altered function, compared to a parent polypeptide. However, currently available methods involve generation of tens of thousands to a million or more mutants, which must be screened to find a few critical mutations. Thus, application of currently available methods is limited by inefficiency of screening the enormous number of mutants that are generated.
There is a need in the art for efficient methods of designing and generating protein variants that exhibit altered properties, without the need for generating and screening large numbers of variants.
LITERATURE


    WO 06/133013; Martin et al. (2003) Nat. Biotech. 21(7):796-802; U.S. Pat. No. 7,172,886.


SUMMARY OF THE INVENTION
The present invention provides methods of designing and generating polypeptide variants that have altered properties compared to a parent polypeptide. The present invention further provides a computer program product for carrying out the design of a variant polypeptide. The present invention further provides nucleic acids encoding enzyme variants, as well as vectors and host cells comprising the nucleic acids. The present invention further provides variant enzymes; methods of producing the variant enzymes; and methods of producing compounds using the enzymes.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-Y present an alignment of amino acid sequences (SEQ ID NOs:1-48) of sesquiterpene synthases, monoterpene synthases, and diterpene synthases.
FIGS. 2A-M present an alignment of amino acid sequences (SEQ ID NOs:49-71) of a truncated form of yeast HMGR, and various archaeal HMGR.
FIGS. 3A-D present a schematic depiction of constructs used for production of terpenoids.
FIGS. 4A-E depict an evolutionary study of the relative stability of each amino acid.
FIGS. 5A-D depict the relevance between evolutionary relations and the fitness effects of Gly and Pro distribution in gamma-humulene synthase (HUM).
FIGS. 6A-D depict co-integration of designed HUM and tHMGR into a synthetic biological system for production of terpenoids and resulting sesquiterpene production.
FIGS. 7A-D depict the relevance between evolutionary relations and functional consequences of Gly and Pro distributions in tHMGR.
FIGS. 8A and 8B depict integration of redesigned tHMGR and resulting mevalonate production.
FIGS. 9A-D depict the effect of Gly and Pro mutations at various temperatures.
FIGS. 10 A, C, and D depict the amino acid sequences of γ-humulene synthase and variant γ-humulene synthases; and FIG. 10B depicts the nucleotide sequence encoding the γ-humulene synthase depicted in FIG. 10A.
FIGS. 11A-C depict the amino acid sequences of a truncated HMGR (tHMGR) and variant tHMGR.
FIGS. 12A-O provide a list of exemplary proteins analyzed using a subject method.
FIGS. 13A-C provide the primer sequences used for site directed mutagenesis of humulene synthase (HUM).
FIGS. 14A-D provide the primer sequences used for site directed mutagenesis of tHMGR.



DEFINITIONS
The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, this term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.
The terms “peptide,” “polypeptide,” and “protein” are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.
The term “conservative amino acid substitution” refers to the interchangeability in proteins of amino acid residues having similar side chains. For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide-containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains consists of cysteine and methionine. Exemplary conservative amino acids substitution groups are: valine-leucine-isoleucine, serine-threonine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartate-glutamate, and asparagine-glutamine.
“Recombinant,” as used herein, means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. Generally, DNA sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Such sequences can be provided in the form of an open reading frame uninterrupted by internal non-translated sequences, or introns, which are typically present in eukaryotic genes. Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5′ or 3′ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “DNA regulatory sequences”, below).
Thus, e.g., the term “recombinant” polynucleotide or nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such is usually done to replace a codon with a redundant codon encoding the same or a conservative amino acid, while typically introducing or removing a sequence recognition site. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.
By “construct” is meant a recombinant nucleic acid, generally recombinant DNA, which has been generated for the purpose of the expression of a specific nucleotide sequence(s), or is to be used in the construction of other recombinant nucleotide sequences.
The terms “DNA regulatory sequences,” “control elements,” and “regulatory elements,” used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate expression of a coding sequence and/or production of an encoded polypeptide in a host cell.
The term “transformation” is used interchangeably herein with “genetic modification” and refers to a permanent or transient genetic change induced in a cell following introduction of new nucleic acid (i.e., DNA exogenous to the cell). Genetic change (“modification”) can be accomplished either by incorporation of the new DNA into the genome of the host cell, or by transient or stable maintenance of the new DNA as an episomal element. Where the cell is a eukaryotic cell, a permanent genetic change is generally achieved by introduction of the DNA into the genome of the cell. In prokaryotic cells, permanent changes can be introduced into the chromosome or via extrachromosomal elements such as plasmids and expression vectors, which may contain one or more selectable markers to aid in their maintenance in the recombinant host cell.
“Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. As used herein, the terms “heterologous promoter” and “heterologous control regions” refer to promoters and other control regions that are not normally associated with a particular nucleic acid in nature. For example, a “transcriptional control region heterologous to a coding region” is a transcriptional control region that is not normally associated with the coding region in nature.
A “host cell,” as used herein, denotes an in vivo or in vitro eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells can be, or have been, used as recipients for a nucleic acid (e.g., an expression vector that comprises a nucleotide sequence encoding one or more biosynthetic pathway gene products such as mevalonate pathway gene products), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector. For example, a subject prokaryotic host cell is a genetically modified prokaryotic host cell (e.g., a bacterium), by virtue of introduction into a suitable prokaryotic host cell a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to (not normally found in nature in) the prokaryotic host cell, or a recombinant nucleic acid that is not normally found in the prokaryotic host cell; and a subject eukaryotic host cell is a genetically modified eukaryotic host cell, by virtue of introduction into a suitable eukaryotic host cell a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to the eukaryotic host cell, or a recombinant nucleic acid that is not normally found in the eukaryotic host cell.
Expression cassettes may be prepared comprising a transcription initiation or transcriptional control region(s) (e.g., a promoter), the coding region for the protein of interest, and a transcriptional termination region. Transcriptional control regions include those that provide for over-expression of the protein of interest in the genetically modified host cell; those that provide for inducible expression, such that when an inducing agent is added to the culture medium, transcription of the coding region of the protein of interest is induced or increased to a higher level than prior to induction.
“Synthetic nucleic acids” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments which are then enzymatically assembled to construct the entire gene. “Chemically synthesized,” as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well-established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. The nucleotide sequence of the nucleic acids can be modified for optimal expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.
A polynucleotide or polypeptide has a certain percent “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity can be determined in a number of different manners. To determine sequence identity, sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al. (1990), J. Mol. Biol. 215:403-10. Another alignment algorithm is FASTA, available in the Genetics Computing Group (GCG) package, from Madison, Wis., USA, a wholly owned subsidiary of Oxford Molecular Group, Inc. Other techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, Calif., USA. Of particular interest are alignment programs that permit gaps in the sequence. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments. See Meth. Mol. Biol. 70: 173-187 (1997). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. See J. Mol. Biol. 48: 443-453 (1970).
As used herein the term “isolated” is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs. An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells.
The terms “isoprenoid,” “isoprenoid compound,” “terpene,” “terpene compound,” “terpenoid,” and “terpenoid compound” are used interchangeably herein. Isoprenoid compounds are made up various numbers of so-called isoprene (C5) units. The number of C-atoms present in the isoprenoids is typically evenly divisible by five (e.g., C5, C10, C15, C20, C25, C30 and C40). Irregular isoprenoids and polyterpenes have been reported, and are also included in the definition of “isoprenoid.” Isoprenoid compounds include, but are not limited to, monoterpenes, sesquiterpenes, diterpenes, triterpenes, and polyterpenes.
As used herein, the term “prenyl diphosphate” is used interchangeably with “prenyl pyrophosphate,” and includes monoprenyl diphosphates having a single prenyl group (e.g., IPP and DMAPP), as well as polyprenyl diphosphates that include 2 or more prenyl groups. Monoprenyl diphosphates include isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP).
As used herein, the term “terpene synthase” or “isoprenoid synthase” refers to any enzyme that enzymatically modifies IPP, DMAPP, or a polyprenyl pyrophosphate, such that a terpenoid compound is produced. The term “terpene synthase” includes enzymes that catalyze the conversion of a prenyl diphosphate into an isoprenoid.
As used herein, the term “prenyl transferase” is used interchangeably with the terms “isoprenyl diphosphate synthase” and “polyprenyl synthase” (e.g., “GPP synthase,” “FPP synthase,” “OPP synthase,” etc.) to refer to an enzyme that catalyzes the consecutive 1′-4 condensation of isopentenyl diphosphate with allylic primer substrates, resulting in the formation of prenyl diphosphates of various chain lengths.
The word “pyrophosphate” is used interchangeably herein with “diphosphate.” Thus, e.g., the terms “prenyl diphosphate” and “prenyl pyrophosphate” are interchangeable; the terms “isopentenyl pyrophosphate” and “isopentenyl diphosphate” are interchangeable; the terms farnesyl diphosphate” and farnesyl pyrophosphate” are interchangeable; etc.
The term “mevalonate pathway” or “MEV pathway” is used herein to refer to the biosynthetic pathway that converts acetyl-CoA to IPP. The mevalonate pathway comprises enzymes that catalyze the following steps: (a) condensing two molecules of acetyl-CoA to acetoacetyl-CoA; (b) condensing acetoacetyl-CoA with acetyl-CoA to form HMG-CoA; (c) converting HMG-CoA to mevalonate; (d) phosphorylating mevalonate to mevalonate 5-phosphate; (e) converting mevalonate 5-phosphate to mevalonate 5-pyrophosphate; and (f) converting mevalonate 5-pyrophosphate to isopentenyl pyrophosphate.
The term “1-deoxy-D-xylulose 5-diphosphate pathway” or “DXP pathway” is used herein to refer to the pathway that converts glyceraldehyde-3-phosphate and pyruvate to IPP and DMAPP through a DXP pathway intermediate.
A “computer-based system” refers to the hardware means, software means, and data storage means used to analyze the information of the present invention. The minimum hardware of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based system are suitable for use in the present invention. The data storage means may comprise any manufacture comprising a recording of the present information as described above, or a memory access means that can access such a manufacture.
To “record” data, programming or other information on a computer readable medium refers to a process for storing information, using any such methods as known in the art. Any convenient data storage structure may be chosen, based on the means used to access the stored information. A variety of data processor programs and formats can be used for storage, e.g. word processing text file, database format, etc.
A “processor” references any hardware and/or software combination that will perform the functions required of it. For example, any processor herein may be a programmable digital microprocessor such as available in the form of a electronic controller, mainframe, server or personal computer (desktop or portable). Where the processor is programmable, suitable programming can be communicated from a remote location to the processor, or previously saved in a computer program product (such as a portable or fixed computer readable storage medium, whether magnetic, optical or solid state device based). For example, a magnetic medium or optical disk may carry the programming, and can be read by a suitable reader communicating with each processor at its corresponding station.
Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an enzyme variant” includes a plurality of such variants and reference to “the algorithm” includes reference to one or more algorithms and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.
DETAILED DESCRIPTION
The present invention provides methods of designing and generating polypeptide variants that have altered properties compared to a parent polypeptide. The present invention further provides a computer program product for carrying out the design of a variant polypeptide. The present invention further provides nucleic acids encoding enzyme variants, as well as vectors and host cells comprising the nucleic acids. The present invention further provides variant enzymes; methods of producing the variant enzymes; and methods of producing compounds using the enzymes.
Methods of Designing and Generating Polypeptide Variants
The present invention provides methods of designing and generating polypeptide variants that have altered properties (e.g., altered functional and/or physical properties) compared to a parent polypeptide. The methods generally involve: a) identifying one or more conserved amino acid residues in a family of polypeptides, where the parent polypeptide is a member of the family of polypeptides; b) calculating a conservation probability PiX for an amino acid (X) (where X corresponds to the identified, conserved amino acid residue) at an amino acid position (i) for a parent polypeptide; and c) where the conservation probability for the amino acid sequence at the amino acid position is above a threshold value, modifying the amino acid sequence of the parent polypeptide to include amino acid X at position i; or where the conservation probability for an amino acid is below the threshold value, modifying the amino acid sequence of the parent polypeptide to include an amino acid other than amino acid X at the amino acid position, thereby generating a polypeptide variant with altered functional and/or physical properties. Conserved amino acid residues can be identified using a method as described in Example 1, below.
The conservation probability is calculated by aligning amino acid sequences of polypeptide members of a polypeptide family, e.g., polypeptides sharing a function, e.g., an enzymatic activity or similar enzymatic activities; etc., to generate a multiple sequence alignment (MSA). P1X is calculated as follows:




  
    P
    i
    X
  
  =
  
    
      N
      i
      X
    
    
      N
      i
    
  




where NiX and Ni denote the number of amino acid X (e.g., Gly or Pro) and the total number of aligned amino acids at position i in each column of a multiple sequence alignment, respectively.
For example, in some embodiments, the conservation probabilities for glycine (Gly) and proline (Pro) for a given polypeptide are calculated. The conservation probability for Gly (PiG) and Pro (PiP) at column i in a given MSA is calculated based on the composition of Gly and Pro at column i as follows:




  
    P
    i
    X
  
  =
  
    
      N
      i
      X
    
    
      N
      i
    
  




where NiX and Ni denote the number of amino acid X (Gly or Pro) and the total number of aligned amino acids at position i in each column of MSA, respectively. The fitness effects contributed by mutations of these residues are predicted dependent on the value of Pi; when PiX≦0, the mutation to amino acid X likely shows neutral, nearly neutral, or positive fitness effects, and when PiX≦0 the mutations to amino acid X likely shows neutral, nearly neutral, or negative fitness effects. PiX=0.4 can be used as a threshold; and the PiX compared; and the fitness effects resulting from single mutations evaluated.
As an example, where the PiG value is greater than 0.4 and the amino acid at position i is other than Gly, the amino acid sequence of the parent polypeptide is modified to include a Gly at position i. As another example, where the PiG value is less than 0.4, and the amino acid at position i is a Gly, the amino acid sequence of the parent polypeptide is modified to include an amino acid other than Gly at position i. As another example, where the PiP value is less than 0.4 and the amino acid at position i is other than Pro, the amino acid sequence of the parent polypeptide is modified to include a Pro at position i. As another example, where the Pip value is less than 0.4 and the amino acid at position i is a Pro, the amino acid sequence of the parent polypeptide is modified to include an amino acid other than Pro at position i. In some embodiments, where the conservation probability for a Pro or a Gly at a position i is below a threshold (e.g., below 0.4), the Pro or the Gly at position i is substituted with an Ala.
Using a subject method, polypeptide variants can be generated based on a wide variety of parent polypeptides, where parent polypeptides include, but are not limited to, enzymes, antibodies, transcription factors, receptors for ligands, polypeptide ligands for receptors, signal proteins, a fluorescent protein, a carrier protein, a small molecule binding protein, a large molecule binding protein, and the like. A “parent” polypeptide is any polypeptide that serves as a reference for generating a variant polypeptide, where a variant polypeptide comprises one or more amino acid substitutions compared to the amino acid sequence of the parent polypeptide. A “parent” polypeptide is in some embodiments a wild-type polypeptide, e.g., a polypeptide found in nature.
As noted above, a subject method for generating a protein variant provides for generating a protein variant that has one or more altered properties compared to a parent polypeptide. As used herein, the term “altered property(ies)” refers to one or more characteristics present in a parent polypeptide that is altered in a variant of the parent polypeptide. Altered properties (e.g., altered functional and/or physical properties) exhibited by a variant polypeptide include, but are not limited to, increased enzymatic activity; increased substrate affinity; increased ligand binding affinity; increased solubility (e.g., increased solubility in the cytosol of a prokaryotic host cell; etc.); increased stability (e.g., increased in vivo and/or in vitro half life); and the like, where the one or more functional and/or physical properties are altered compared to a parent polypeptide.
Altered properties include altered intracellular properties, e.g., increased intracellular solubility in a host cell (e.g., increased solubility in the cytosol or cytoplasm of a host cell); reduced likelihood that a variant protein produced by a prokaryotic host cell will be sequestered in an inclusion body; improved folding (e.g., increased degree of native folding; e.g., an increased proportion of protein that exhibits native folding) such that activity of the polypeptide is maintained; and the like. For example, where a variant polypeptide is produced recombinantly in a host cell (e.g., a prokaryotic host cell), the variant polypeptide will exhibit one or more of: a) increased solubility in the cytosol or cytoplasm of the host cell, compared to the solubility of the parent polypeptide when produced recombinantly in the host cell; increased proportion of the recombinantly produced variant that is soluble in the cytosol compared to the proportion of the parent polypeptide that is soluble in the cytosol when produced recombinantly in the host cell; reduced proportion of the recombinantly produced variant that is insoluble, e.g., sequestered in an inclusion body compared to the proportion of the parent polypeptide that is insoluble when produced recombinantly in the host cell; reduced proportion of the recombinantly produced variant that is present in an aggregate (e.g., an insoluble aggregate) compared to the proportion of the parent polypeptide that is present in an aggregate when produced recombinantly in the host cell; and increased native folding, e.g., the proportion of recombinantly produced variant protein that exhibits native folding is increased, compared to the proportion of the parent polypeptide that exhibits native folding when produced recombinantly in the host cell.
In some embodiments, the parent polypeptide is an enzyme; and the variant enzyme exhibits enhanced enzymatic activity level compared to the parent polypeptide. For example, in some embodiments, the variant enzyme exhibits an at least about 5%, at least about 10%, at least about 25%, at least about 50%, at least about 75%, at least about 10% (or two-fold), at least about 2.5-fold, at least about 5-fold, at least about 7.5-fold, at least about 10-fold, at least about 25-fold, at least about 50-fold, or at least about 100-fold, or greater than 100-fold, higher enzymatic activity level compared to the parent polypeptide. In some embodiments, e.g., where the enzyme is produced recombinantly in a host cell (e.g., a prokaryotic host cell), a property such as increased solubility, improved folding, and the like, can result in increased enzymatic activity level, compared to the activity level of a parent polypeptide produced recombinantly in the host cell.
In some embodiments, the parent polypeptide is an enzyme that is part of a biosynthetic pathway (a “biosynthetic pathway enzyme”) having and end product and/or intermediate products, and the variant polypeptide provides for increased production of the intermediate and/or end product when integrated into the biosynthetic pathway. For example, in some embodiments, the variant biosynthetic pathway enzyme, when integrated into a biosynthetic pathway, provides for production of an intermediate and/or an end product at a level that is at least about 5%, at least about 10%, at least about 25%, at least about 50%, at least about 75%, at least about 10% (or two-fold), at least about 2.5-fold, at least about 5-fold, at least about 7.5-fold, at least about 10-fold, at least about 25-fold, at least about 50-fold, or at least about 100-fold, or greater than 100-fold, higher than the level produced by the parent biosynthetic pathway enzyme when integrated into the biosynthetic pathway.
In some embodiments, the parent polypeptide is an antibody, where “antibody” includes single chain antibodies, monoclonal antibodies, antibody fragments that retain antigen-binding (e.g., Fv, F(ab′)2 and Fab fragments), and the like. In some embodiments, the parent antibody binds specifically to an antigen (or epitope); and the variant antibody binds with altered (greater or less) affinity to the antigen (or epitope). The term “specific binding,” in the context of antibody binding to an antigen, is a term well understood in the art and refers to binding of an antibody to the antigen to which the antibody was raised, but not other, unrelated antigens. Specific binding typically refers to binding with an affinity of at least about 10−6 M, at least about 10−7 M, at least about 10−8 M, or at least about 10−9 M, or greater.
In some embodiments, the parent polypeptide is a receptor, e.g., a cell surface receptor, a nuclear receptor, a cytoplasmic receptor, etc., that binds to a ligand; and the variant polypeptide is a receptor that binds to the ligand with altered affinity.
In some embodiments, the parent polypeptide is a fluorescent protein. Fluorescent proteins are proteins that, following excitation at a first wavelength of light, will emit light at a second wavelength. For example, the excitation spectra of fluorescent proteins typically ranges from about 300 to 700, while the emission spectra of typically ranges from about 400 to 800. Fluorescent proteins are known in the art, and include green fluorescent proteins (GFP) from Aequoria victoria; derivatives of GFP that are known in the art; and any of a variety of fluorescent proteins from Anthozoan species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973. In some embodiments, following excitation at an excitation wavelength of light, the parent fluorescent protein emits light at a first emission wavelength, and the variant polypeptide emits light at second emission wavelength.
Functions or properties that may be altered include, but are not limited to, enzymatic activity (where the parent polypeptide and the corresponding variant polypeptide are enzymes), where enzymatic activity includes specific activity, substrate specificity, and product profile (where “product profile” refers to the product(s) generated using a given substrate); antigen-binding properties (where the parent polypeptide and the corresponding variant polypeptide are antibodies or antigen-binding fragments of antibodies), where antigen-binding properties include antigen specificity, antigen binding affinity, etc.; ligand binding properties (e.g., where the parent polypeptide and the corresponding variant polypeptide are ligand receptors), where ligand binding properties include ligand specificity, ligand affinity, etc.; substrate binding properties, e.g., where the parent polypeptide and the corresponding variant polypeptide are transcription factors, the function being altered is in some embodiments specificity for a particular nucleotide sequence; protein stability; protein solubility; fluorescent properties (e.g., where the parent polypeptide is a fluorescent protein); signal transduction properties (e.g., where the parent polypeptide is a signal transduction protein such as a receptor); binding specificity and/or affinity to a small molecule; binding specificity and/or affinity to a large molecule; and the like.
Computer Program Product and Computational Analysis System
The present invention provides a computer program product for carrying out a subject method for designing a variant polypeptide. The present invention also includes an algorithm for performing the subject methods, where the algorithm is recorded on a computer readable medium. The present invention further provides computational analysis systems that include a subject computer program product. The present invention further provides a kit for identifying a polypeptide variant.
One or more aspects of the above methodology may be in the form of computer readable media having programming stored thereon for implementing the subject methods. In other words, the subject methodology may be provided in the form of programming (a computer program product) or an algorithm recorded onto a computer readable medium. The computer readable media may be, for example, in the form of a computer disk or CD (compact disc), a floppy disc, a magnetic “hard card”, a server, or any other computer readable media capable of containing data or the like, stored electronically, magnetically, optically or by other means. Accordingly, stored programming embodying steps for carrying-out the subject methods may be transferred to a computer such as a personal computer (PC), (i.e., accessible by a researcher or the like), by physical transfer of a CD, floppy disk, or like medium, or may be transferred using a computer network, server, or other interface connection, e.g., the Internet.
In some embodiments, a subject computer-readable medium has recorded thereon a program (a computer program product) that: a) identifies one or more conserved amino acid residues in a family of polypeptides, wherein the parent polypeptide is a member of the family of polypeptides; b) assigns a conservation probability to an amino acid (e.g., a Gly; a Pro; etc.) at an amino acid position of a parent polypeptide, where the amino acid is at a position corresponding to the position of an identified conserved amino acid; and c) based on the conservation probability, identifies at least one amino acid sequence modification that provides for a variant polypeptide that exhibits one or more altered properties as compared to the parent polypeptide.
The present invention provides a computational analysis system comprising a subject computer-readable medium or a subject computer program product. In one embodiment of the subject invention, a system of the invention may include a single computer or the like with a stored algorithm capable of carrying out a subject method, i.e., a computational analysis system. In certain embodiments, the system is further characterized in that it provides a user interface, where the user interface presents to a user the option of selecting among one or more different, including multiple different, inputs, e.g., various parameter values for the algorithm, as described above, such as an omega value, etc. Computational systems that may be readily modified to become systems of the subject invention include those described in U.S. Pat. No. 6,251,588; the disclosure of which is herein incorporated by reference.
The present invention provides a kit for generating a polypeptide variant exhibiting one or more altered properties as compared to a parent polypeptide. A subject kit comprises a computer readable medium, as described above, which computer readable medium has an algorithm stored or recorded thereon, as described above; and instructions for using the algorithm to identify candidate mutant sequences, where a polypeptide comprising such a mutant sequence exhibits one or more altered properties as compared to a parent polypeptide.
Polypeptide Variants
The present invention provides polypeptide variants that exhibit one or more altered properties compared to a parent polypeptide. As noted above, a subject method for generating a protein variant provides for generating a protein variant that has one or more altered properties compared to a parent polypeptide. As used herein, the term “altered property(ies)” refers to one or more characteristics present in a parent polypeptide that is altered in a variant of the parent polypeptide. Altered properties (e.g., altered functional and/or physical properties) exhibited by a variant polypeptide include, but are not limited to, increased enzymatic activity; increased substrate affinity; increased ligand binding affinity; increased solubility (e.g., increased solubility in the cytosol of a prokaryotic host cell; etc.); increased stability (e.g., increased in vivo and/or in vitro half life); and the like, where the one or more functional and/or physical properties are altered compared to a parent polypeptide.
Altered properties include altered intracellular properties, e.g., increased intracellular solubility in a host cell (e.g., increased solubility in the cytosol or cytoplasm of a host cell); reduced likelihood that a variant protein produced by a prokaryotic host cell will be sequestered in an inclusion body; improved folding (e.g., increased degree of native folding; e.g., an increased proportion of protein that exhibits native folding) such that activity of the polypeptide is maintained; and the like. For example, where a variant polypeptide is produced recombinantly in a host cell (e.g., a prokaryotic host cell), the variant polypeptide will exhibit one or more of: a) increased solubility in the cytosol or cytoplasm of the host cell, compared to the solubility of the parent polypeptide when produced recombinantly in the host cell; increased proportion of the recombinantly produced variant that is soluble in the cytosol compared to the proportion of the parent polypeptide that is soluble in the cytosol when produced recombinantly in the host cell; reduced proportion of the recombinantly produced variant that is insoluble, e.g., sequestered in an inclusion body compared to the proportion of the parent polypeptide that is insoluble when produced recombinantly in the host cell; reduced proportion of the recombinantly produced variant that is present in an aggregate (e.g., an insoluble aggregate) compared to the proportion of the parent polypeptide that is present in an aggregate when produced recombinantly in the host cell; and increased native folding, e.g., the proportion of recombinantly produced variant protein that exhibits native folding is increased, compared to the proportion of the parent polypeptide that exhibits native folding when produced recombinantly in the host cell.
In addition to altered properties such as increased intracellular solubility, increased native folding, etc., a subject variant protein can have one or more additional altered features, including, but not limited to, altered substrate specificity, and the like.
The present invention provides variant biosynthetic pathway enzymes. In some embodiments, a subject variant biosynthetic pathway enzyme is a variant isoprenoid synthase (also referred to herein as a variant terpene cyclase). In other embodiments, a subject variant biosynthetic pathway enzyme is a variant mevalonate biosynthetic pathway enzyme.
A subject variant terpene cyclase catalyzes an enzymatic reaction, using a polyprenyl diphosphate as substrate. Polyprenyl diphosphate substrates that can serve as substrate for a subject variant terpene cyclase include, but are not limited to, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), geranylgeranyl diphosphate (GGPP), hexaprenyl diphosphate (HexPP), heptaprenyl diphosphate (HepPP), octaprenyl diphosphate (OPP), solanesyl diphosphate (SPP), decaprenyl diphosphate (DPP), nonaprenyl diphosphate (NPP), and undecaprenyl diphosphate (UPP) In some embodiments, the substrate of a subject variant terpene cyclase is GPP. In other embodiments, the substrate of a subject variant terpene cyclase is FPP. In other embodiments, the substrate of a subject variant terpene cyclase is GGPP.
Variant Sesquiterpene Synthases
In some embodiments, a subject variant terpene cyclase is a sesquiterpene synthase. The present invention provides variant sesquiterpene synthases; and methods of producing the variant sesquiterpene synthases. The present invention further provides compositions comprising a subject variant sesquiterpene synthases. The present invention further provides methods of producing an isoprenoid compound, the method involving culturing a genetically modified host cell in a suitable medium, where the genetically modified host cell comprises a nucleic acid comprising a nucleotide sequence encoding a subject variant sesquiterpene synthase.
In some embodiments, a subject variant sesquiterpene synthase, when integrated into a biosynthetic pathway (e.g., a mevalonate pathway) provides for production of a sesquiterpene at a level that is at least about 5%, at least about 10%, at least about 25%, at least about 50%, at least about 75%, at least about 10% (or two-fold), at least about 2.5-fold, at least about 5-fold, at least about 7.5-fold, at least about 10-fold, at least about 25-fold, at least about 50-fold, or at least about 100-fold, or greater than 100-fold, higher than the level produced by a parent sesquiterpene synthase when integrated into the same biosynthetic pathway.
For example, in some embodiments, a subject variant sesquiterpene synthase comprises at least one amino acid substitution compared to the amino acid sequence set forth in FIG. 10A (GenBank Accession No. AAC05728; SEQ ID NO:1). In some embodiments, a subject variant sesquiterpene synthase comprises from one amino acid substitution to about 50 amino acid substitutions compared to the amino acid sequence set forth in FIG. 10A and in SEQ ID NO:1; e.g., in some embodiments, a subject variant sesquiterpene synthase comprises one, two, three, four, five, six, seven, eight, nine, or 10 amino acid substitutions, from about 10 amino acid substitutions to about 12 amino acid substitutions, from about 12 amino acid substitutions to about 15 amino acid substitutions, from about 15 amino acid substitutions to about 20 amino acid substitutions, from about 20 amino acid substitutions to about 25 amino acid substitutions, or from about 25 amino acid substitutions to about 50 amino acid substitutions compared to the amino acid sequence set forth in FIG. 10A.
In some embodiments, a subject variant sesquiterpene synthase comprises at least the amino acid substitutions K126P, R142G, and G227A, compared to the amino acid sequence set forth in FIG. 10A and in SEQ ID NO:1, or a variant thereof. In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; and comprising the amino acid substitutions K126P, R142G, and G227A.
In some embodiments, a subject variant sesquiterpene synthase comprises at least the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A compared to the amino acid sequence set forth in FIG. 10A, or a variant thereof. In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; and comprising the amino acid substitutions amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A, and further comprises amino acid substitutions as set forth in Table 1.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A, and further comprises amino acid substitutions as set forth in Table 1.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A, and further comprises the amino acid substitutions F312Q, M339A, and M447F.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A, and further comprises the amino acid substitutions M339N, S484C, and M565I.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A, and further comprises the amino acid substitutions A317N, A336S, S484C, and I562V.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A, and further comprises the amino acid substitutions A336C, T445C, S484C, I562L, and M565L.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A, and further comprises the amino acid substitutions A336V, M447H, and I562T.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A, and further comprises the amino acid substitutions S484A and Y566F.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A, and further comprises the amino acid substitutions F312Q, M339A, and M447F.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A, and further comprises the amino acid substitutions M339N, S484C, and M565I.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A, and further comprises the amino acid substitutions A317N, A336S, S484C, and I562V.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A, and further comprises the amino acid substitutions A336C, T445C, S484C, I562L, and M565L.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A, and further comprises the amino acid substitutions A336V, M447H, and I562T.
In some embodiments, a subject variant sesquiterpene synthase comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A, and further comprises the amino acid substitutions S484A and Y566F.
Amino acid sequences of exemplary variant sesquiterpene synthases are depicted in FIGS. 10C and 10D.
Variant Mevalonate Biosynthetic Pathway Enzyme
In some embodiments, a subject variant enzyme is a variant mevalonate biosynthetic pathway enzyme, e.g., a variant of an enzyme selected from an acetoacetyl-CoA thiolase, a hydroxymethyl glutaryl-CoA synthase (HMGS), a hydroxymethyl glutaryl-CoA reductase (HMGR), a mevalonate kinase (MK), a phosphomevalonate kinase (PMK), a mevalonate pyrophosphate decarboxylase (MPD), and an isopentenyl pyrophosphate (IPP) isomerase.
In some embodiments, a subject variant mevalonate biosynthetic pathway enzyme, when integrated into a mevalonate pathway, provides for production of a sesquiterpene at a level that is at least about 5%, at least about 10%, at least about 25%, at least about 50%, at least about 75%, at least about 10% (or two-fold), at least about 2.5-fold, at least about 5-fold, at least about 7.5-fold, at least about 10-fold, at least about 25-fold, at least about 50-fold, or at least about 100-fold, or greater than 100-fold, higher than the level produced by a parent mevalonate biosynthetic pathway enzyme integrated into a mevalonate pathway.
As one non-limiting example, a subject variant enzyme is a variant HMGR. In some embodiments, a subject variant HMGR comprises one or more amino acid substitutions compared to the amino acid sequence set forth in FIG. 11A and in SEQ ID NO:49.
In some embodiments, a subject variant HMGR comprises from one amino acid substitution to about 50 amino acid substitutions compared to the amino acid sequence set forth in FIG. 11A and in SEQ ID NO:49; e.g., in some embodiments, a subject variant sesquiterpene synthase comprises one, two, three, four, five, six, seven, eight, nine, or 10 amino acid substitutions, from about 10 amino acid substitutions to about 12 amino acid substitutions, from about 12 amino acid substitutions to about 15 amino acid substitutions, from about 15 amino acid substitutions to about 20 amino acid substitutions, from about 20 amino acid substitutions to about 25 amino acid substitutions, or from about 25 amino acid substitutions to about 50 amino acid substitutions compared to the amino acid sequence set forth in FIG. 11A.
In some embodiments, a subject variant HMGR comprises at least the amino acid substitutions G206A, G319A, G352A, G417A, and G495A, compared to the amino acid sequence set forth in FIG. 10A, or a variant thereof. In some embodiments, a subject variant HMGR comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 11A; where the variant HMGR comprises the amino acid substitutions G206A, G319A, G352A, G417A, and G495A.
In some embodiments, a subject variant HMGR comprises at least the amino acid substitutions P200A, G206A, T239P, G319A, G352A, G417A, P428G, K474G, and G495A, compared to the amino acid sequence set forth in FIG. 11A, or a variant thereof. In some embodiments, a subject variant HMGR comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 11A; where the variant HMGR comprises the amino acid substitutions P200A, G206A, T239P, G319A, G352A, G417A, P428G, K474G, and G495A.
Amino acid sequences of exemplary variant HMGR are depicted in FIGS. 11B and 11C.
Production of a Subject Variant Enzyme
A subject variant enzyme is readily generated using well-established methods. A subject variant enzyme can be produced synthetically, or can be produced recombinantly, i.e., a subject variant enzyme-coding region can be inserted into an expression vector, and the coding region transcribed and translated, either in a living cell or in an in vitro transcription/translation system. One may employ solid phase peptide synthesis techniques, where such techniques are known to those of skill in the art. See Jones, The Chemical Synthesis of Peptides (Clarendon Press, Oxford)(1994). Generally, in such methods a peptide is produced through the sequential additional of activated monomeric units to a solid phase bound growing peptide chain.
A subject variant enzyme can be produced recombinantly, e.g., a subject variant enzyme-coding region can be inserted into an expression vector, and the coding region transcribed and translated, either in a living cell or in an in vitro transcription/translation system. For expression, an expression cassette may be employed. The expression vector will provide a transcriptional and translational initiation region, which may be inducible or constitutive, where the coding region is operably linked under the transcriptional control of the transcriptional initiation region, and a transcriptional and translational termination region. These control regions may be native to the subject gene, or may be derived from exogenous sources. Expression vectors generally have convenient restriction sites located near the promoter sequence to provide for the insertion of nucleic acid sequences encoding heterologous proteins. A selectable marker operative in the expression host may be present.
A subject variant enzyme may be produced in prokaryotes or eukaryotes in accordance with conventional ways, depending upon the purpose for expression. For large scale production of the variant terpene cyclase, a unicellular organism, such as E. coli, B. subtilis, S. cerevisiae, insect cells in combination with baculovirus vectors, or cells of a higher organism such as vertebrates, particularly mammals, e.g. COS 7 cells, may be used as the expression host cells. In some situations, it is desirable to produce the variant enzyme in eukaryotic cells, where the protein will benefit from native folding and post-translational modifications. In other situations, it is desirable to produce the variant enzyme in a prokaryotic cell, e.g., for production of an isoprenoid compound generated by action of the enzyme on a substrate in a mevalonate pathway or in an isoprenoid biosynthetic pathway.
With the availability of a subject enzyme in large amounts, e.g., by employing an expression host, the variant enzyme may be isolated and purified in accordance with conventional ways. A lysate may be prepared of the expression host, and the lysate purified using high performance liquid chromatography, size exclusion chromatography, gel electrophoresis, affinity chromatography, or other purification technique.
The present invention further provides compositions comprising a subject variant enzyme. Compositions comprising a subject variant enzyme will in many embodiments include one or more of: a salt, e.g., NaCl, MgCl, KCl, MgSO4, etc.; a buffering agent, e.g., a Tris buffer, N-(2-Hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid) (HEPES), 2-(N-Morpholino)ethanesulfonic acid (MES), 2-(N-Morpholino)ethanesulfonic acid sodium salt (MES), 3-(N-Morpholino)propanesulfonic acid (MOPS), N-tris[Hydroxymethyl]methyl-3-aminopropanesulfonic acid (TAPS), etc.; a solubilizing agent; a detergent, e.g., a non-ionic detergent such as Tween-20, etc.; a protease inhibitor; and the like.
Nucleic Acids, Vectors, and Host Cells
The present invention provides nucleic acids encoding a subject polypeptide variant (e.g., a subject variant biosynthetic pathway enzyme, a subject variant mevalonate pathway enzyme, a subject variant isoprenoid biosynthetic pathway enzyme), as well as recombinant vectors and recombinant host cells comprising the nucleic acids or recombinant vectors. In many embodiments, a subject nucleic acid is isolated, and is can be synthetic. In some embodiments, a subject nucleic acid is pure, e.g., at least about 50% pure, at least about 60% pure, at least about 70% pure, at least about 80% pure, at least about 90%, or at least about 95% or more pure. In many embodiments, a subject host cell is isolated. In some embodiments, a subject host cell is part of a multicellular organism. In other embodiments, a subject host cell is in vitro and is cultured as a unicellular entity.
A subject nucleic acid comprises a nucleotide sequence encoding a subject variant enzyme. A subject recombinant vector comprises a subject nucleic acid. In many embodiments, a subject recombinant vector comprises a subject nucleic acid operably linked to one or more control elements, such as a promoter, a transcription terminator, and the like. A subject recombinant vector in some embodiments provides for amplification of the copy number of a subject nucleic acid. A subject recombinant vector is in some embodiments an expression vector that provides for synthesis of a subject variant terpene cyclase in a host cell, e.g., a prokaryotic host cell or a eukaryotic host cell.
Nucleic Acids Encoding Variant Sesquiterpene Synthase
In some embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence encoding a subject variant sesquiterpene synthase and having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A and in SEQ ID NO:1; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A.
In some embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence encoding a subject variant sesquiterpene synthase and having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A.
In some embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence encoding a subject variant sesquiterpene synthase and having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions K126P, R142G, and G227A; and where the variant sesquiterpene synthase further comprises one or more additional amino acid sequences as set forth in Table 1, as described above.
In some embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence encoding a subject variant sesquiterpene synthase and having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 10A; where the variant sesquiterpene synthase comprises the amino acid substitutions amino acid substitutions K126P, R142G, G148A, G227A, G327A, and G361A; and where the variant sesquiterpene synthase further comprises one or more additional amino acid sequences as set forth in Table 1, as described above.
Nucleic Acids Encoding Variant HMGR
In some embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence encoding a subject variant HMGR and having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 11A and in SEQ ID NO:49; where the variant HMGR comprises the amino acid substitutions G206A, G319A, G352A, G417A, and G495A.
In some embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence encoding a subject variant HMGR and having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in FIG. 11A; where the variant HMGR comprises the amino acid substitutions P200A, G206A, T239P, G319A, G352A, G417A, P428G, K474G, and G495A.
Expression Vectors
In some embodiments, a subject nucleic acid is an expression vector that includes a nucleic acid comprising a nucleotide sequence that encodes a subject variant enzyme. Suitable expression vectors include, but are not limited to, baculovirus vectors, bacteriophage vectors, plasmids, phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral vectors (e.g. viral vectors based on vaccinia virus, poliovirus, adenovirus, adeno-associated virus, SV40, herpes simplex virus, and the like), P1-based artificial chromosomes, yeast plasmids, yeast artificial chromosomes, and any other vectors specific for specific hosts of interest (such as E. coli and yeast). Thus, for example, a nucleic acid encoding a subject variant terpene cyclase is included in any one of a variety of expression vectors for expressing the variant terpene cyclase. Such vectors include chromosomal, nonchromosomal and synthetic DNA sequences.
Numerous suitable expression vectors are known to those of skill in the art, and many are commercially available. The following vectors are provided by way of example; for bacterial host cells: pQE vectors (Qiagen), pBluescript plasmids, pNH vectors, lambda-ZAP vectors (Stratagene); pTrc99a, pKK223-3, pDR540, and pRIT2T (Pharmacia); for eukaryotic host cells: pXT1, pSG5 (Stratagene), pSVK3, pBPV, pMSG, and pSVLSV40 (Pharmacia). However, any other plasmid or other vector may be used so long as it is compatible with the host cell.
The variant enzyme-encoding nucleotide sequence in the expression vector is operably linked to an appropriate expression control sequence(s) (promoter) to direct synthesis of the encoded variant enzyme. Depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. may be used in the expression vector (see e.g., Bitter et al. (1987) Methods in Enzymology, 153:516-544).
Suitable promoters for use in prokaryotic host cells include, but are not limited to, a bacteriophage T7 RNA polymerase promoter; a trp promoter; a lac operon promoter; a hybrid promoter, e.g., a lac/tac hybrid promoter, a tac/trc hybrid promoter, a trp/lac promoter, a T7/lac promoter; a trc promoter; a tac promoter, and the like; an araBAD promoter; in vivo regulated promoters, such as an ssaG promoter or a related promoter (see, e.g., U.S. Patent Publication No. 20040131637), a pagC promoter (Pulkkinen and Miller, J. Bacteriol., 1991: 173(1): 86-93; Alpuche-Aranda et al., PNAS, 1992; 89(21): 10079-83), a nirB promoter (Harborne et al. (1992) Mol. Micro. 6:2805-2813), and the like (see, e.g., Dunstan et al. (1999) Infect. Immun. 67:5133-5141; McKelvie et al. (2004) Vaccine 22:3243-3255; and Chatfield et al. (1992) Biotechnol. 10:888-892); a sigma70 promoter, e.g., a consensus sigma70 promoter (see, e.g., GenBank Accession Nos. AX798980, AX798961, and AX798183); a stationary phase promoter, e.g., a dps promoter, an spv promoter, and the like; a promoter derived from the pathogenicity island SPI-2 (see, e.g., WO96/17951); an actA promoter (see, e.g., Shetron-Rama et al. (2002) Infect. Immun. 70:1087-1096); an rpsM promoter (see, e.g., Valdivia and Falkow (1996). Mol. Microbiol. 22:367-378); a tet promoter (see, e.g., Hillen, W. and Wissmann, A. (1989) In Saenger, W. and Heinemann, U. (eds), Topics in Molecular and Structural Biology, Protein-Nucleic Acid Interaction. Macmillan, London, UK, Vol. 10, pp. 143-162); an SP6 promoter (see, e.g., Melton et al. (1984) Nucl. Acids Res. 12:7035-7056); and the like.
Non-limiting examples of suitable eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector may also contain a ribosome binding site for translation initiation and a transcription terminator. The expression vector may also include appropriate sequences for amplifying expression.
In addition, the expression vectors will in many embodiments contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in prokaryotic host cells such as E. coli. 
Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli, the S. cerevisiae TRP1 gene, etc.; and a promoter derived from a highly-expressed gene to direct transcription of the variant terpene cyclase-encoding sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), α-factor, acid phosphatase, or heat shock proteins, among others.
In many embodiments, a subject nucleic acid includes a nucleotide sequence encoding a subject variant enzyme, where the nucleotide sequence encoding the variant enzyme is operably linked to an inducible promoter. Inducible promoters are well known in the art. Suitable inducible promoters include, but are not limited to, the pL of bacteriophage λ; Placo; Ptrp; Ptac (Ptrp-lac hybrid promoter); an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible promoter, e.g., a lacZ promoter; a tetracycline-inducible promoter; an arabinose inducible promoter, e.g., PBAD (see, e.g., Guzman et al. (1995) J. Bacteriol. 177:4121-4130); a xylose-inducible promoter, e.g., Pxyl (see, e.g., Kim et al. (1996) Gene 181:71-76); a GAL1 promoter; a tryptophan promoter; a lac promoter; an alcohol-inducible promoter, e.g., a methanol-inducible promoter, an ethanol-inducible promoter; a raffinose-inducible promoter; a heat-inducible promoter, e.g., heat inducible lambda PL promoter, a promoter controlled by a heat-sensitive repressor (e.g., C1857-repressed lambda-based expression vectors; see, e.g., Hoffmann et al. (1999) FEMS Microbiol Lett. 177(2):327-34); and the like.
In many embodiments, a subject nucleic acid includes a nucleotide sequence encoding a subject variant enzyme, where the nucleotide sequence encoding the variant enzyme is operably linked to a constitutive promoter. Suitable constitutive promoters for use in prokaryotic cells are known in the art and include, but are not limited to, a sigma70 promoter, e.g., a consensus sigma70 promoter.
In yeast, a number of vectors containing constitutive or inducible promoters may be used. For a review see, Current Protocols in Molecular Biology, Vol. 2, 1988, Ed. Ausubel, et al., Greene Publish. Assoc. & Wiley Interscience, Ch. 13; Grant, et al., 1987, Expression and Secretion Vectors for Yeast, in Methods in Enzymology, Eds. Wu & Grossman, 31987, Acad. Press, N.Y., Vol. 153, pp. 516-544; Glover, 1986, DNA Cloning, Vol. II, IRL Press, Wash., D.C., Ch. 3; and Bitter, 1987, Heterologous Gene Expression in Yeast, Methods in Enzymology, Eds. Berger & Kimmel, Acad. Press, N.Y., Vol. 152, pp. 673-684; and The Molecular Biology of the Yeast Saccharomyces, 1982, Eds. Strathern et al., Cold Spring Harbor Press, Vols. I and II. A constitutive yeast promoter such as ADH or LEU2 or an inducible promoter such as GAL may be used (Cloning in Yeast, Ch. 3, R. Rothstein In: DNA Cloning Vol. 11, A Practical Approach, Ed. D M Glover, 1986, IRL Press, Wash., D.C.). Alternatively, vectors may be used which promote integration of foreign DNA sequences into the yeast chromosome.
The present invention provides genetically modified host cells, where a subject genetically modified host cell comprises a subject nucleic acid or a subject recombinant vector. Genetically modified host cells are in many embodiments unicellular organisms, or are grown in culture as single cells. In some embodiments, the host cell is a eukaryotic cell. Suitable eukaryotic host cells include, but are not limited to, yeast cells, insect cells, plant cells, fungal cells, and algal cells. Suitable eukaryotic host cells include, but are not limited to, Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia guercuum, Pichia pijperi, Pichia stiptis, Pichia methanolica, Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Hansenula polymorpha, Kluyveromyces sp., Kluyveromyces lactis, Candida albicans, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, Chrysosporium lucknowense, Fusarium sp., Fusarium gramineum, Fusarium venenatum, Neurospora crassa, Chlamydomonas reinhardtii, and the like.
In other embodiments, the genetically modified host cell is a prokaryotic cell. Suitable prokaryotic cells include, but are not limited to, any of a variety of laboratory strains of Escherichia coli, Lactobacillus sp., Salmonella sp., Shigella sp., and the like. See, e.g., Carrier et al. (1992) J. Immunol. 148:1176-1181; U.S. Pat. No. 6,447,784; and Sizemore et al. (1995) Science 270:299-302. Examples of Salmonella strains which can be employed in the present invention include, but are not limited to, Salmonella typhi and S. typhimurium. Suitable Shigella strains include, but are not limited to, Shigella flexneri, Shigella sonnei, and Shigella disenteriae. Typically, the laboratory strain is one that is non-pathogenic. Non-limiting examples of other suitable bacteria include, but are not limited to, Pseudomonas pudita, Pseudomonas aeruginosa, Pseudomonas mevalonii, Rhodobacter sphaeroides, Rhodobacter capsulatus, Rhodospirillum rubrum, Rhodococcus sp., and the like.
To generate a genetically modified host cell, a subject nucleic acid or a subject recombinant vector is introduced stably or transiently into a host cell, using established techniques, including, but not limited to, electroporation, calcium phosphate precipitation, DEAE-dextran mediated transfection, liposome-mediated transfection, and the like. For stable transformation, a nucleic acid will generally further include a selectable marker, e.g., any of several well-known selectable markers such as neomycin resistance, ampicillin resistance, tetracycline resistance, chloramphenicol resistance, kanamycin resistance, and the like.
The present invention further provides compositions comprising a subject genetically modified host cell. A subject composition comprises a subject genetically modified host cell; and will in some embodiments comprise one or more further components, which components are selected based in part on the intended use of the genetically modified host cell. Suitable components include, but are not limited to, salts; buffers; stabilizers; protease-inhibiting agents; cell membrane- and/or cell wall-preserving compounds, e.g., glycerol, dimethylsulfoxide, etc.; nutritional media appropriate to the cell; and the like.
A subject genetically modified host cell is useful for producing isoprenoid or isoprenoid precursor compound, as described below. For the production of an isoprenoid or isoprenoid precursor compound, a host cell is one that produces, or has been genetically modified to produce, one or more enzymes in a mevalonate pathway and/or an isoprenoid biosynthetic pathway. In some embodiments, the host cell is one that produces a substrate of a subject variant sesquiterpene synthase via a mevalonate pathway. In other embodiments, the host cell is one that produces a substrate of a subject variant sesquiterpene synthase via a DXP pathway. In some embodiments, the host cell is one that produces one or more mevalonate pathway enzymes.
In some embodiments, a genetically modified host cell is a host cell that comprises an endogenous mevalonate pathway. In other embodiments, a genetically modified host cell is a host cell that does not normally produce mevalonate or IPP via a mevalonate pathway, but has been genetically modified with one or more nucleic acids comprising nucleotide sequences encoding one or more mevalonate pathway enzymes. See, e.g., U.S. Patent Publication No. 2004/005678; U.S. Patent Publication No. 2003/0148479; Martin et al. (2003) Nat. Biotech. 21(7):796-802.
In some embodiments, a suitable host cell is a host cell that does not normally produce mevalonate or IPP via a mevalonate pathway, but has been genetically modified to produce mevalonate, or IPP, via a mevalonate pathway, e.g., has been genetically modified with one or more nucleic acids comprising nucleotide sequences encoding acetoacetyl-CoA thiolase; hydroxymethylglutaryl-CoA (HMG-CoA) synthase; and a subject variant HMGR. In some embodiments, a suitable host cell is a host cell that does not normally produce mevalonate or IPP via a mevalonate pathway, but has been genetically modified to produce mevalonate, or IPP, via a mevalonate pathway, e.g., has been genetically modified with one or more nucleic acids comprising nucleotide sequences encoding acetoacetyl-CoA thiolase; HMG-CoA synthase; HMG-CoA reductase; mevalonate kinase; phosphomevalonate kinase; and mevalonate pyrophosphate decarboxylase. In some embodiments, a suitable host cell is a host cell that does not normally produce mevalonate or IPP via a mevalonate pathway, but has been genetically modified to produce mevalonate, or IPP, via a mevalonate pathway, e.g., has been genetically modified with one or more nucleic acids comprising nucleotide sequences encoding mevalonate kinase; phosphomevalonate kinase; and mevalonate pyrophosphate decarboxylase. In some of these embodiments, the host cell has been further genetically modified with a nucleic acid comprising a nucleotide sequence encoding a polyprenyl diphosphate synthase, e.g., FPP synthase, GPP synthase, GGPP synthase, and the like. In some embodiments, the DXP pathway of the host cell has been functionally disabled.
The present invention further provides compositions comprising a subject nucleic acid. Compositions comprising a subject nucleic acid will in many embodiments include one or more of: a salt, e.g., NaCl, MgCl, KCl, MgSO4, etc.; a buffering agent, e.g., a Tris buffer, N-(2-Hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid) (HEPES), 2-(N-Morpholino)ethanesulfonic acid (MES), 2-(N-Morpholino)ethanesulfonic acid sodium salt (MES), 3-(N-Morpholino)propanesulfonic acid (MOPS), N-tris[Hydroxymethyl]methyl-3-aminopropanesulfonic acid (TAPS), etc.; a solubilizing agent; a detergent, e.g., a non-ionic detergent such as Tween-20, etc.; a nuclease inhibitor; and the like.
The present invention further provides compositions comprising a subject genetically modified host cell. A subject composition comprises a subject genetically modified host cell; and will in some embodiments comprise one or more further components, which components are selected based in part on the intended use of the genetically modified host cell. Suitable components include, but are not limited to, salts; buffers; stabilizers; protease-inhibiting agents; cell membrane- and/or cell wall-preserving compounds, e.g., glycerol, dimethylsulfoxide, etc.; nutritional media appropriate to the cell; and the like.
Methods of Producing Isoprenoid Compounds
The present invention provides methods of producing an isoprenoid or isoprenoid precursor compound in a host cell. The methods generally involve culturing a subject genetically modified host cell in a suitable culture medium under conditions that promote synthesis of an isoprenoid compound or isoprenoid precursor compound, where the isoprenoid compound is generated by action of a subject variant enzyme(s), which enzyme is produced in the genetically modified host cell, on a substrate present in the host cell. In some embodiments, a subject method further comprises isolating the isoprenoid compound from the cell and/or from the culture medium.
In some embodiments, the isoprenoid or isoprenoid compound is produced in a subject genetically modified host cell at a level that is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 25-fold, at least about 50-fold, at least about 100-fold, at least about 500-fold, at least about 1000-fold, at least about 2000-fold, at least about 3000-fold, at least about 4000-fold, at least about 5000-fold, or at least about 10,000-fold, or more, higher than the level of the isoprenoid or isoprenoid precursor compound produced in a host cell that produces the isoprenoid or isoprenoid precursor compound via the same biosynthetic pathway having integrated therein a parent isoprenoid biosynthetic pathway enzyme and/or a parent mevalonate pathway enzyme.
In some embodiments, a subject genetically modified host cell is cultured in a suitable medium (e.g., Luria-Bertoni broth, optionally supplemented with one or more additional agents, such as an inducer (e.g., where the variant terpene cyclase is under the control of an inducible promoter), etc.); and the culture medium is overlaid with an organic solvent, e.g. dodecane, forming an organic layer. The isoprenoid compound produced by the genetically modified host cell partitions into the organic layer, from which it can be purified. In some embodiments, where the variant terpene cyclase-encoding nucleotide sequence is operably linked to an inducible promoter, an inducer is added to the culture medium; and, after a suitable time, the isoprenoid compound is isolated from the organic layer overlaid on the culture medium.
In some embodiments, the isoprenoid compound will be separated from other products which may be present in the organic layer. Separation of the isoprenoid compound from other products that may be present in the organic layer is readily achieved using, e.g., standard chromatographic techniques.
In some embodiments, the isoprenoid compound is pure, e.g., at least about 40% pure, at least about 50% pure, at least about 60% pure, at least about 70% pure, at least about 80% pure, at least about 90% pure, at least about 95% pure, at least about 98%, or more than 98% pure, where “pure” in the context of an isoprenoid compound refers to an isoprenoid compound that is free from other isoprenoid compounds, contaminants, etc.
EXAMPLES
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pl, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c., subcutaneous(ly); and the like.
Example 1
Design and Generation of Variant Enzymes
Redesigning in vivo enzyme properties and thereby efficiencies of metabolic pathways based on their evolutionary relations allows us to test our current understandings for the molecular basis of adaptation, and has many important practical applications in synthetic biology1-5. Here, we demonstrate a strategy to redesign functionalities of enzymes using evolutionary relations as the sole guide. An analysis of over 10,000 sequences in 209 different enzyme families involved in central metabolism indicated that Gly and Pro were significantly more immutable; hence each enzyme family may have a preference for Gly and Pro distributions in its primary sequence. To investigate how these residues contribute to the evolution of enzymes and metabolic pathways, and thereby formulate redesign methodology, Gly and Pro distributions in several enzymes catalyzing the rate-limiting-steps (γ-humulene synthase (HUM)1,6 specific mutant variants of HUM1, and truncated hydroxy-3-methylglutaryl-CoA reductase (tHMGR)7) in a previously constructed synthetic metabolic pathway for mass-production of terpenoids3 were probed. Approximately 80-90% of the fitness effects for those substitutions were accurately predicted, and multiple substitutions significantly improved the in vivo properties of these enzymes. Co-integration of these enzymes into the system dramatically improved host (E. coli) viability (3-4-fold) and the specific sesquiterpene production ( ̃3,500-fold). Creation of these enzymes demonstrated that fitness effects contributed by the appropriate Gly and Pro distributions are important for in vivo properties of enzymes, may have been evolutionary acquired and maintained, and are therefore essential for the construction of novel metabolic pathways both in nature and a laboratory.
Methods
Analysis of amino acid composition changes in proteins across multiple species. To examine the relative importance of each of twenty different amino acids (X: Ala, Cys, Asp . . . ), we examined the average free energy difference for each amino acid in 209 different protein families against mutations (gain and loss by substitutions, deletions, and insertions) (−ΔGMutX). These protein families are all involved in central metabolism, including: glycolysis, citric acid cycle, pentose phosphate pathway, oxidative phosphorylation, fatty acid metabolism, amino acid metabolism, and nucleic acid metabolism (FIGS. 12A-O). Because of their essential roles in maintaining the viability of every organism, if any of these proteins had suboptimal in vivo functions, that enzyme would be a major bottleneck in the particular metabolic pathway and cause a severe competitive growth disadvantage for the host organisms. Consequently, these proteins are expected to have better in vivo properties across multiple species in order to maintain the efficiencies of biological systems and viabilities of organisms. In this analysis, we compared protein sequences derived from E. coli to their orthologous counterparts derived from other organisms, because our primary objective was to redesign heterologous enzymes adaptable to expression in E. coli. 
In each protein family (F), orthologous protein sequences (O) were searched using the basic local alignment search tool for proteins (BLASTP: on the world wide web at www(dot)ncbi(dot)nih(dot)gov). In pair-wise alignment between a particular E. coli protein sequence and its orthologous protein sequence derived from a particular species, the probability of mutations (PMut,O,FX) for each amino acid (X) was calculated based on the composition of each mutated amino acid between the two sequences. The pair-wise alignments used herein covered more than eighty-percent and less than hundred twenty-percent of the corresponding E. coli protein sequences. If proteins evolved without any constraint, the PMut,O,FX should be identical to that for all amino acids (PMut,O,F). PMut,O,FX was then plotted against PMut,O,FX. Interestingly, in many cases, PMut,O,FX and PMut,O,F were linearly correlated. On average, 490 (S.D. 265) plots (pair-wise sequence alignments) were made for each protein family. PMut,FX/PMut,F is defined as the slope for the linear regression of the data in the plot. The free energy of each amino acid X for the mutations in each protein family F (−ΔGMut,FX) was then calculated according to Boltzmann statistics as follows:




  
    
      P
      
        Mut
        ,
        F
      
      X
    
    
      P
      
        Mut
        ,
        F
      
    
  
  =
  
    exp
    (
    
      
        
          -
          Δ
        
        ⁢
        
          
        
        ⁢
        
          G
          
            Mut
            ,
            F
          
          X
        
      
      
        kT
        *
      
    
    )
  




where kT* denotes an arbitrary constant. In this analysis, we calculated ΔGMut,FX only when the R2 of the PMut,FX/PMUt,F plot was greater than 0.5.
Design methodology to improve in vivo properties of enzymes using MSA as a guide. To predict where to distribute Gly, Pro, and Xaa (Xaa denotes any amino acid residues other than Gly, and Pro), we first created an MSA for both γ-humulene synthase (HUM) and truncated hydroxymethyl glutaryl-CoA reductase (tHMGR) using MUSCLE (on the internet at phylogenomics(dot)berkeley(dot)edu/cgi-bin/muscle/inpu_muscle(dot)py). The primary sequence of HUM from Abies grandis was aligned with other mono-, sesqui-, and diterpene synthases derived from gymnosperms (MSA 1; FIGS. 1A-Y). Although many sesquiterpene synthases have been isolated from angiosperms, mono- and diterpene synthases from gymnosperms are more closely correlated to HUM at the primary sequence level. The primary sequence of tHMGR derived from yeast was aligned with other orthologous sequences derived from archaeal species, as the archaeal HMGR is produced in a soluble form as opposed to the membrane bound form found in most eukaryotes (MSA 2; FIGS. 2A-M). The conservation probability for Gly (PiG) and Pro (PiP) at column i in a given MSA was calculated based on the composition of Gly and Pro at column i as follows:




  
    P
    i
    X
  
  =
  
    
      N
      i
      X
    
    
      N
      i
    
  




where NiX and Ni denote the number of amino acid X (Gly or Pro) and the total number of aligned amino acids at position i in each column of MSA, respectively. The fitness effects contributed by these mutations were predicted dependent on the value of Pi; when PiX≧0, the mutation to amino acid X likely shows neutral, nearly neutral, or positive fitness effects, and when PiX≧0, the mutations to amino acid X likely shows neutral, nearly neutral, or negative fitness effects. We used PiX=0.4 as a threshold and compared PiX and the fitness effects resulting from single mutations.
Reagents and equipments. All enzymes and chemicals were purchased from New England Biolabs and Sigma-Aldrich Co, respectively, unless otherwise stated. An HP6890 gas chromatograph equipped with a 5973 mass selective detector (Hewlett Packard) or flame ionization detector, a CyclosilB capillary column (30 m×250 μm i.d.×0.25 μm thickness, Agilent Technologies) or DB5-MS capillary column (30 m×250 μm i.d.×0.25 μm thickness, Agilent Technologies), and a Combi PAL auto sample-injector (LEAP Technologies) were used for analysis. An LS6500 multi-purpose scintillation counter (Beckman coulter) was used for enzyme kinetics.
Strains and Plasmids. Escherichia coli strain DH10B and DH1 was used for both mevalonate and sesquiterpene productions, and BL21(DE3) was used for protein over-expression and purification. Plasmids pBADMevT1,2 and their mutant variants were used for mevalonate production. A plasmid pBBRMBIS1 was used for FPP production. Plasmids pTrcHUM3, pTrcHUM15, and their mutant variants were used for sesquiterpene productions (FIG. 3). Plasmids pTrcSHUM15 and its mutant variants were used for quantification of protein concentrations in vivo. Plasmids pETHUM3 and its mutant variants were used for protein over-expression and purification.
FIGS. 3A-D. Synthetic biological system for mass-production of terpenoids. The plasmids contained in our system are shown. (A) pBADMevT, an artificial operon of atoB (acetoacetyl-CoA synthase from E. coli), HMGS (HMG-CoA synthase from yeast), and tHMGR (HMG-CoA reductase I from yeast with its membraning-spanning region truncated) under control of PBAD. (B) pBBRMBIS, an artificial operon of ERG12 (mevalonate kinase (MK) from yeast), ERG8 (phosphomevalonate kinase (PMK) from yeast), MVD (mevalonate diphosphate decarboxylase from yeast), idi (isopentenyldiphosphate (IPP) isomerase from E. coli), and ispA (farnesyldiophosphate (FPP) synthase from E. coli) under control of PLac, (C) pTrcHUM15, containing modified ribosome-binding-site (mRBS). (D) pTrcHUM.
Since reduced expression of HUM slightly improved sesquiterpene production, an extra seven base pairs were introduced between the ribosome-binding-site (RBS) and the start codon at the NcoI site of pTrcHUM. The RBS region were amplified by polymerase chain reaction (PCR): 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward (5′-GCGCGTTGGTGCGGATATC-3′; SEQ ID NO:77) and reverse (5′-CATGCCATGGAGCTTATTCTGTTTCCTGTGTGAAATTG-3′; SEQ ID NO:78) primers, 2.5 U Phusion DNA polymerase (Finezyme), and 50 ng pTrcHUM as a template in a total volume of 100 μl. The amplified fragments were then digested with EcoRV/NcoI and inserted into the corresponding site of pTrcHUM to form pTrcHUM15.
pTrcSHUM15 was constructed based on pTrcHUM15 backbone. S-tag was fused to the N-terminal of HUM. The RBS region in pTrcHUM15 was amplified by PCR: 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated for 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward (5′-GCGCGTTGGTGCGGATATC-3′; SEQ ID NO:79) and reverse (5′-GCAGCAGCGGTTTCTTTCATGGAGCTTATTCTGTTTC-3′; SEQ ID NO:80) primers, 2.5 U Phusion DNA polymerase (Finezyme), and 50 ng pTrcHUM15 as a template in total volume of 100 μl. The S-tag was amplified by PCR: 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated for 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward (5′-GAAACAGAATAAGCTCCATGAAAGAAACCGCTGCTGC-3′; SEQ ID NO:81) and reverse (5′-CATGCCATGGAACCGCGTGGC-3′; SEQ ID NO:82) primers, 2.5 U Phusion DNA polymerase (Finezyme), and 50 ng pET29 (Novagen) as a template in a total volume of 100 μl. These two amplified fragments were spliced by over-lap PCR: 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated for 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward (5′-GCGCGTTGGTGCGGATATC-3′; SEQ ID NO:83) and reverse (5′-CATGCCATGGAACCGCGTGGC-3′; SEQ ID NO:84) primers, 2.5 U Phusion DNA polymerase (Finezyme), and the abovementioned fragments as a template in a total volume of 100 μl. The spliced fragment was then digested with EcoRV/NcoI and inserted into the corresponding site of pTrcHUM to form pTrcSHUM15.
GC-FID and GC-MS analysis for in vivo sesquiterpene production. To screen the single mutation library, a single colony harboring pTrcHUM (wild type HUM or its mutant variants) and pBBRMBIS was inoculated into Luria Bertani (LB) medium containing 50 μg/ml carbenicillin (Cb50) and 50 μg/ml kanamycin (Km50) and grown overnight at 37° C. An aliquot (50 μl) of this seed culture was inoculated into fresh LB medium (5 ml) containing 10 mM D/L-mevalonate, Cb50, and Km50, overlaid with 500 μl dodecane, and grown for 24 hours at 37° C. An aliquot of dodecane (50 μl) was diluted into 200 μl of ethyl acetate, and the mixture was analyzed by GC-MS or GC-FID using a GC oven temperature program of 80° C. for 1 min, then ramping 30° C./min to 110° C., 5° C./min to 160° C., and 130° C./min to 250° C. for CyclosilB capillary column analysis and of 80° C. for 3 min, then ramping 5° C./min to 160° C., and 120° C./min to 300° C. for DB-5MS capillary column analysis. Camphor was used as an internal standard. Sesquiterpenes were identified from their mass spectra and GC retention times by comparison to available authentic standards and spectra in libraries previously reported in the literature.
As for the final sesquiterpene production assay, a bacterial system containing three plasmids was used1. A single colony harboring pTrcHUM15 or pTrcSHUM15 (wild type HUM or its mutant variants), pBBRMBIS, and pBADMevT (wild type tHMGR4 or its mutant variants) was inoculated into LB medium containing Cb50, Km50, and chloramphenicol (Cm50) and grown for overnight at 37° C. An aliquot of this seed culture was inoculated into fresh modified m9 medium (pH 7, M9 salt, 75 mM MOPS, 3% glycerol, 5 g/L yeast extract, 2 mM MgSO4, 1 mg/L thiamine, 10 μM FeSO4, 0.01 mM CaCl2, and micronutrient) (50 ml) to the final OD600nm of 0.05 containing Cb50, Km50, and Cm50, overlaid with 10 ml of dodecane. Two hours after the inoculation, isopropyl-β-D-thiogalactopyranosid (IPTG) and (+)-L-arabinose were added to the final concentrations of 1 mM and 13.3 mM, respectively. Sesquiterpene production was analyzed as mentioned above.
GC-MS analysis for in vivo mevalonate production. As for screening the single mutation library, a single colony harboring pBADMevT (wild type tHMGR or its mutant variants) was inoculated into LB medium containing Cm50 and grown overnight at 37° C. An aliquot (50 μl) of this seed culture was inoculated into fresh LB medium (5 ml) containing Cm50 and 13.3 mM (+)-L-arabinose, and grown for 24 hours at 37° C. An aliquot of culture (560 μl) was mixed with 140 μl of 0.5 M HC1 to dehydrate the mevalonate to form mevalonolactone, and 700 μl of ethyl acetate was then added to the sample. The mixture was vortexed for 5 minutes, and the ethyl acetate was analyzed by GC-MS using a GC oven temperature program of 90° C. for 1 min, then ramping 30° C./min to 250° C. for CyclosilB capillary column analysis. Mevalonolactone was identified from its mass spectra and retention time by comparison to an authentic standard.
As for the final mevalonate production assay, a single colony harboring pBADMevT (wild type tHMGR or its mutant variants) was inoculated into LB medium containing Cm50 and grown overnight at 37° C. An aliquot (500 μl) of this seed culture was inoculated into fresh modified m9 medium (50 ml, see above formulation) containing Cm50. Two hours after the inoculation (+)-L-arabinose was added to the final concentration of 13.3 mM. Mevalonate production was analyzed as mentioned above.
Site directed mutagenesis of HUM by overlap PCR. Site directed mutagenesis for HUM was carried out using over-lap PCR (FIGS. 13A-C provide the primer sequences used for site directed mutagenesis of HUM).
DNA fragments encoding the N- and C-terminus of the mutation were amplified by PCR: 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward and reverse primers, 2.5 U Phusion DNA polymerase (Finezyme), and 50 ng pTrcHUM in 100 μl as a template for γ-humulene synthase. Amplified DNA was gel purified using a gel purification kit (Qiagen) or treated with DpnI and purified using a PCR purification kit (Qiagen). These two amplified DNA fragments were spliced via over-lap PCR: 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated for 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward and reverse primers, 2.5 U Phusion DNA polymerase (Finezyme), and 50 ng of the abovementioned DNA fragments as a template in a total volume of 100 μl. The fully amplified HUM fragment was digested with NcoI/XbaI and cloned into the corresponding site in pTrcHUM.
Site directed mutagenesis of tHMGR by overlap PCR. Site directed mutagenesis for tHMGR was carried out using overlap PCR (FIGS. 14A-D provide the primer sequences used for site directed mutagenesis of tHMGR).
DNA fragments encoding the N- and C-terminus of the mutation were amplified by PCR: 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated for 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward and reverse primers, 2.5 U Phusion DNA polymerase (Finezyme), and 50 ng pBADMevT as a template for tHMGR in a total volume of 100 μl. The amplified DNA fragment was gel purified using a gel purification kit (Qiagen) or treated with DpnI and purified using a PCR purification kit (Qiagen). These two amplified DNA fragments were spliced via over-lap PCR: 98° C. for 30 sec, 55° C. for 30 sec, and 72° C. for 30 sec, repeated for 30 times. The reaction mixture contained 1× Phusion buffer, 2 mM dNTP, 0.5 μM forward and reverse primers, 2.5 U Phusion DNA polymerase (Finezyme), and 50 ng abovementioned DNA fragments as a template in a total volume of 100 μl. The fully amplified HMGR fragment was digested with SpeI/HindIII and inserted into the corresponding site of pBADMevT.
Quantification of in vivo HUM concentrations. A single colony harboring pTrcSHUM15 (wild type or its mutant variant), pBBRMBIS, and pBADMevT was inoculated into LB medium containing Cb50, Km50, and Cm50 was grown overnight at 37° C. An aliquot of this seed culture was inoculated into fresh modified m9 medium (50 ml, see above formulation) containing Cb50, Km50, and Cm50 to the final OD600nm of 0.05 and was grown at 37° C. Two hours after the inoculation, IPTG and (+)-L-arabinose was added to the final concentrations of 1 mM and 13.3 mM, respectively. The cultures were then grown at 20° C., 30° C., and 37° C. An aliquot of culture (1 ml) was taken and centrifuged at 14,000×g. The resulting pellet was resuspended into Bugbuster containing recommended amount of Lysonase (Novagen) to the final OD600nm of 20, and it was incubated for half an hour at room temperature. This lysis solution was centrifuged for 10 min at 14,000×g. 24 μl of whole lysis solution (both soluble and insoluble fractions) and supernatant of lysis solution (soluble fraction) were mixed with 75 μl of 8 M guanidium hydrochloride and 1 μl of 4 M dithiothreitol. These solutions were incubated for another hour at room temperature. The concentration of HUM was determined by FRET Works S-tag assay kit following the recommended protocols (Novagen). In vivo sesquiterpene production from each culture was measured as described above.
Protein expression and purification of HUM. Wild type HUM and its variants were cloned into pET29 and transformed into BL21 (DE3). Each transformant was inoculated into LB medium (5 ml) containing Km50 and was grown overnight at 30° C. An aliquot (2 ml) of this seed culture was inoculated into fresh terrific broth (TB) medium containing Km50 (500 ml), and the culture was grown at 30° C. When the culture reached OD600nm of 0.6-0.8, 0.1 mM of IPTG was added, and it was grown at 20° C. for another 16 hours. Cells were harvested by centrifugation at 6,000×g for 15 min. The pellet was suspended in 50 ml of BugBuster (Novagen) containing 20 U DNaseI and bacterial protease inhibitor cocktail II (Novagen), and was incubated for an hour at 4° C. The solution was then centrifuged at 20,000×g for 30 min, and then filtered through a 0.45-μm filter. S-tagTM Thrombin purification kit (Novagen) was used for the purification following the protocol recommended by Novagen. All purifications were done at half scale. The eluted protein solution was dialyzed twice (PIERCE, MW 3,000 Da) against 1 L of buffer containing 10 mM Tes (pH 7.0), 10 mM MgCl2, 1 mM DTT and 5% glycerol overnight. The protein concentration was measured using the Bradford method. We obtained approximately 3 ml of 25-500 μg/ml of protein solution with about 95% purity (confirmed by SDS-PAGE gel).
Enzyme kinetics. The kinetics studies of HUM and its variants were carried out following a slightly modified protocol from that previously reported by Little et. al. Kinetics for each enzyme was measured in a 40 μl reaction containing 0.15-0.4 μM enzyme, in buffer described in the previous section and overlaid with dodecane. The concentration of FPP was varied from 0.229 to 58.6 μM with a fixed ratio of [3H]FPP. Seven to nine different concentrations of FPP were used for each enzyme (n=3). The reaction mixture was incubated for 20 minutes at 31° C. To stop the reaction, 40 μL of a solution containing 4 M NaOH and 1 M EDTA was added and mixed. To extract sesquiterpene products, the reaction mixture was vortexed for 2 min, and 400 μL of dodecane was taken from the solution and mixed with 15 mL of scintillation fluid. Radioactivity was measured by scintillation counting. kcat, Km and kcat/Km were calculated using Enzyme Kinetics!Pro (ChemSW).
Results
In this analysis, we primarily considered enzymes involved in central metabolism. Because of their essential roles in maintaining the viability of host organisms and their practical applications to many different industries12, the in vivo properties of these enzymes and the efficiencies of these metabolic pathways are expected to be very high. Since our objective is to redesign in vivo enzyme properties adaptable to an E. coli environment, protein sequences derived from E. coli were compared to each of their orthologous counterparts derived from other organisms. We analyzed over 10,000 protein sequences in 209 different protein families involved in central metabolism across multiple species (see Methods section for detail) spanning a wide range of different lifestyles and environments (FIGS. 12A-O). The probability of mutations to each amino acid between two sequences was plotted against that for all amino acids. The plots for Ala, Gln, Gly, and Pro of the glutamate synthase large subunit are shown as examples (FIG. 4A-D, respectively). The stability of each amino acid (X) to mutations (−ΔGMutX) was then calculated (FIG. 4E). It clearly shows that Gly and Pro are significantly more immutable compared to other amino acids; hence, it is likely that each protein family has its own preference in Gly and Pro distributions in its primary sequence, and satisfaction of this preference might be very important for in vivo enzyme function.
FIGS. 4A-E. Evolutionary study of the relative stability for each amino acid. A relative stability (−ΔGMutX; kT* denotes arbitrary unit) for each amino acid to mutations (gain and loss by substitutions, insertions, and deletions) was calculated by comparing E. coli proteins involved in central metabolism and each of their orthologous counterparts. A probability of mutation to each amino acid (PMutX) is plotted against that for all amino acids (PMut); plots for alanine (PMutA/PMut=1)(A), glutamine (PMutQ/PMut>1)(B), glycine (PMutG/PMut<1)(C), and proline (PMutP/PMut<1)(D) using the glutamate synthase large subunit protein family are shown. The average of the relative stability for each amino acid to mutations obtained from analyses of 209 different protein families is shown (E: Mean±S.E.) (N=4042; ANOVA: P=0, F=234.43, d.f.=19). The result clearly indicates that Gly and Pro were significantly more immutable during the course of evolution.
To investigate the contributions of Gly and Pro distributions to in vivo enzyme properties, we chose HUM as a model enzyme. HUM is a sesquiterpene synthase from Abies grandis that is known to produce 52 different sesquiterpenes from a sole substrate, farnesyl diphosphate, through wide varieties of cyclization mechanisms6. We previously explored the evolvability of this enzyme, and successfully constructed, based on the theory of divergent molecular evolution, several specific sesquiterpene synthases that produce a single product13. However, integration of HUM and its specific mutant variants into our synthetic biological system3 resulted in very poor sesquiterpene production (approximately 1 mg/L). Thus, redesigning HUM should allow us to explore the mechanisms of divergent molecular evolution even further. In addition, it will allow us to redesign any terpene synthase useful for the mass production of single terpenes that have found use as drugs, flavors, fragrances, neutraceuticals and in many other applications.
First, multiple sequence alignment (MSA) for HUM was constructed (see Methods section for detail). Since few sesquiterpene synthases derived from gymnosperms have been discovered, mono- and diterpene synthases derived from gymnosperms were also used for MSA construction (MSA 1; FIGS. 1A-Y). Although a number of sesquiterpene synthases have been cloned from angiosperms, mono- and diterpene synthases derived from gymnosperms are more closely related to HUM14. The probability of conservation for both Gly (PiG) and Pro (PiP) at ith residue of HUM was calculated (FIGS. 5A and C). Substitutions involving Gly and Pro were then introduced to HUM according to the calculated profile, and the fitness effects of these mutations were monitored by the level of in vivo sesquiterpene production (FIGS. 5B and D). Although MSA was constructed primarily from various terpene synthases sharing neither substrate specificity nor product selectivity, approximately 80-90% of the fitness effects for these mutations were accurately predicted (Pi=0.4 as a threshold); the exceptions were the residues predominantly conserved in mono- and diterpene synthases (green and purple bars in FIG. 5A-D respectively). In particular, mutations that most significantly affected the in vivo enzyme functions (R142G and G227A) were accurately predicted. Although saturation mutagenesis was carried out on G148, G227, G327, and G361, Ala substitution was appeared to be the best in terms of in vivo sesquiterpene production and steady state kinetics.
FIGS. 5A-D. Relevance between evolutionary relations and the fitness effects of Gly and Pro distributions in HUM. Distributions for Gly (A) and Pro (C) were predicted based on an MSA constructed using the primary sequences of mono-, sesqui-, and diterpene synthases derived from gymnosperms as a guide. According to this profile, Gly→Ala, Xaa→Gly, Pro→Ala, and Xaa→Pro substitutions were introduced into HUM, and fitness effects for these substitutions were monitored by in vivo sesquiterpene production (B: Gly→Ala and Xaa→Gly, D: Pro→Ala, and Xaa→Pro; Mean±S.D. of triplicate measurements is shown). The results show that 80-90% of fitness effects were well predicted from the value of Pi (Pi=0.4 as a threshold; see Methods section) except for the residues unaligned (orange), aligned only in monoterpene synthases (green), and aligned only in diterpene synthases (purple). The sequences aligned only in sesquiterpene synthases are shown in light blue.
Mutations that improved the in vivo properties of HUM were subsequently recombined. The effects of many of selected mutations were cumulative. As a result, we obtained the HUM-G6 mutant containing the changes K126P/R142G/G148A/G227A/G327A/G361A, resulting in significantly higher sesquiterpene production ( ̃80-fold) (FIG. 6A, 6B, and FIG. 3). Interestingly, none of the single mutations to HUM-G6 predicted as false negative (G350A, G441A, and G500A) improved sesquiterpene production further. Some single mutations that demonstrated positive fitness effect as they were predicted to HUM-G6 (Q242P, S298G, and P443A) did not improve sesquiterpene production either. Overall, all of the mutations introduced into HUM-G6 were well predicted using the methodology formulated herein. Interestingly, product selectivity for HUM-G6 was comparable to that of the HUM (Table 1), even though the enzymes are known to be very plastic (single mutations have been known to significantly alter product selectivity1).







TABLE 1







Product selectivity of HUM and its mutant variants









Products*2*3














Name*1
Mutations
1
2
3
4
5
6

















WT
None
8.3
7.2
14.9
26.1
34.0
9.5


G3
K126P, 142G, G227A
7.2
6.3
16.5
27.9
31.7
10.4


G6
K126P, 142G, G148A, G227A, G327A G361A
7.1
6.8
15.2
27.4
32.8
10.7


SIB
K126P, 142G, G148A, G227A, G327A G361A
0.2
2.8
2.2
80.1
13.8
0.9



F312Q, M339A, M447F


HUM
K126P, 142G, G148A, G227A, G327A G361A
5.6
11.7
5.9
0.7
75.6
0.6



M339N, S484C, M565I


LFN
K126P, 142G, G148A, G227A, G327A G361A
12.8
3.4
62.1
1.6
11.9
8.1



A317N*4, A336S, S484C, I562V


ALP
K126P, 142G, G148A, G227A, G327A, G361A
60.2
4.6
13.7
0.4
14.6
6.5



A336C, T445C, S484C, I562L, M565L


BBA
K126P, 142G, G148A, G227A, G327A, G361A
1.6
0.2
3.9
0.5
4.7
89.1



A336V, M447H, I562T


AYG
K126P, 142G, G148A, G227A, G327A, G361A
14.6
27.5
0.5
0.6
47.1
9.6



S484A, Y566F





*1WT: wild type γ-humulene synthase, G3: third generation of mutant γ-humulene synthase, G6: sixth generation of mutant γ-humulene synthase, SIB: sibirene synthase, HUM: new γ-humulene synthase, LFN: longifolene synthase, ALP: α-longipinene synthase, BBA: β-bisabolene synthase, AYG: α-ylangene synthase


*21: α-longipinene, 2: α-ylangene, 3: longifolene 4: sibirene, 5: γ-humulene, 6: β-bisabolene


*3All product distributions were represented for 1-6 as 100%; these are corresponding to more than 85-95% and to 75% of total products in mutants and wild type (including G3 and G6), respectively.


*4A317N occurred during recombination, and improved in vivo terpene production without a change in product distribution






In addition, both kcat and Km decreased in HUM-G6, resulting in a similar kcat/Km to that of HUM (Table 2).







TABLE 2







Steady state kinetics for HUM and some of its mutant variants.













kcat
Km
kcat/Km



Enzymes
(10−3s−1)
(μM)
(103M−1s−1)







WT
12.00 ± 0.34 
2.01 ± 0.17
5.96



G3
7.62 ± 0.21
4.66 ± 0.39
1.64



G6
1.71 ± 0.17
0.69 ± 0.13
2.47










Using the same methodology, we also redesigned the in vivo properties of tHMGR (ERG12) (FIGS. 7A-D; and FIGS. 8A and 8B), which has been identified as another enzyme catalyzing a rate-limiting-step in our synthetic biological system15. Integration of pBADMevT containing tHMGR-G9 (P200A/G206A/T239P/G319A/G352A/G417A/P428G/K474G/G495A) improved both growth ( ̃3-fold) and mevalonate production ( ̃3-fold). Co-integration of both tHMGR-G9 and HUM-G6 into the system dramatically improved growth (3-4-fold) and sesquiterpene production (800-fold) (FIGS. 6A and B), such that the production reached approximately 1 g/L 48 hours after inoculation. The same mutations were also introduced to specific mutant variants of HUM previously constructed in our laboratory1, and the specific terpene productivities were also dramatically improved (400-3500-fold: FIGS. 6C and D). Since these enzymes are divergently evolved from HUM and these predictions were made based on other terpene synthases as guides, these results implied that appropriate Gly and Pro distributions are essential for proper enzyme function in vivo. Additionally, similar mutations may improve the in vivo properties of other terpene synthases including mono-, sesqui-, and diterpene synthases.
FIGS. 6A-D. Co-integration of redesigned HUM and tHMGR into a synthetic biological system for mass-production of terpenoids and the resulting in vivo sesquiterpene production. Escherichia coli DH1 harboring pBADMevT (containing tHMGR-WT, tHMGR-G3 (G206A/G319A/G352A/G417A/G495A), or tHMGR-G6 (P200A/G206A/T239P/G319A/G352A/G417A/P428G/K474G/G495A)), pBBRMBIS, and pTrcHUM (containing HUM-WT, HUM-G3 (K126P/R142G/G227A), or HUM-G6 (K126P/R142G/G148A/G227A/G327A/G361A)) was used for in vivo sesquiterpene production. The growth curve (A) and sesquiterpene production at 24 hours after inoculation (B) are shown. HUM-WT, HUM-G3, and HUM-G6 co-integrated with tHMGR are shown in light blue, medium blue, and blue, respectively, and those with tHMGR-G9 are shown in orange, light green, and green, respectively. The strain containing tHMGR-G9 grew 3-fold higher and produced 3-fold more mevalonate (FIGS. 8A and 8B), resulting in synergistic improvement in overall sesquiterpene production. The mutations in HUM-G6 were also applied to specific mutant variants of HUM previously constructed in our laboratory (SIB, sibirene synthase; sHUM, specific γ-humulene synthase; LFN, longifolene synthase; ALP, α-longipinene synthase; BBA, β-bisabolene synthase; and AYG, α-ylangene synthase). The resulting specific terpene production was also dramatically improved in each case (400-3500-fold). All data represent mean±S.D. of triplicate measurements.
FIGS. 7A-D. Relevance between evolutionary relations and functional consequences of Gly and Pro distributes in tHMGR. Proper distributes of Gly (A) and Pro (C) for tHMGR were predicted based on an MSA constructed using the primary sequences of HMGR derived from archaea as a guide (sharing 30-40% sequence identity). HMGR derived from archaea is produced in a soluble form rather than membrane bound form as is generally found in eukaryotes; thus, it is more appropriate to use an MSA derived from archaea. According to this profile, Gly→Ala, Xaa→Gly, Pro→Ala, and Xaa→Pro substitutions were introduced into tHMGR, and functional consequences for these substitutions were monitored by in vivo mevalonate production (B: Gly→Ala and Xaa→Gly, D: Pro→Ala, and Xaa→Pro). The results show that 80-90% of mutations were well predicted from these profiles with Pi=0.4 as a threshold except for the unaligned residues (orange).
FIGS. 8A and 8B Integration of redesigned tHMGR to E. coli and resulting mevalonate production. The growth (A) and mevalonate production (B) for strains harboring pBADMevT containing tHMGR-WT (wild type HMGR1 of its membrane binding domain truncated), tHMGR-G5 (G206A/G319A/G352A/G417A/G495A) and tHMGR-G9 (P200A/G206A/T239P/G319A/G352A/G417A/P428G/K474G/G495A) were measured. Interestingly, both growth level and mevalonate production improved approximately 2.5-3-fold, and the increase in growth level accounts for the increase in mevalonate production. We previously proposed that accumulation of HMG-CoA inhibits cell growth5. Thus, improvement of the in vivo properties of tHMGR allowed E. coli to alleviate the toxicity derived from HMG-CoA. Three days after inoculation, both growth and mevalonate production from strains harboring pBADMevT containing any tHMGR variant reached an almost identical level of mevalonate (approximately 10 in OD600nm and 40 mM in mevalonate production).
To understand how Gly and Pro redistributions contributed to this enormous improvement in sesquiterpene production, sesquiterpene production from S-tagged versions of HUM, HUM-G3 (K126P/R142G/G227A), and HUM-G6 were examined at different temperatures (FIGS. 9A and 9B). Interestingly, in vivo sesquiterpene production from S-tagged HUM-G6 increased approximately two-fold over the non-S-tagged HUM-G6 ( ̃1350-fold). HUM showed the highest sesquiterpene production at 30° C. In contrast, HUM-G6 showed the highest production at 37° C. The differences in sesquiterpene production between HUM and HUM-G6 increased with temperature (3.3-fold at 20° C., 10-fold at 30° C., and 220-fold at 37° C.: FIG. 9B), suggesting that HUM does not fold properly at higher temperatures, and Gly and Pro redistributions made HUM more adaptable in the E. coli growth environment. Quantification of in vivo enzyme concentrations in both the soluble fraction and crude lysate revealed that increases in sesquiterpene production were primarily attributable to increases in overall protein production at the lower temperature, and large increases in sesquiterpene production at higher temperatures were due to increased solubility (or foldability) (FIGS. 9C and 9D).
FIGS. 9A-D. Investigation of the effects for Gly and Pro mutations at different temperatures. S-tagged HUM-WT (orange), HUM-G3 (light green), and HUM-G6 (green) were co-integrated with tHMGR-G9 into the synthetic biological system for mass-production of terpenoids to see the temperature effects of accumulated Gly and Pro mutations. The growth (A), fold increases in sesquiterpene production over that of the strain harboring tHMGR-WT and HUM-WT (B), soluble enzyme concentration (C), and total enzyme concentration (D) at 24 hours after inoculation are shown. Interestingly, sesquiterpene productivity of HUM-G6 was improved almost 2-fold with an N-terminal S-tag ( ̃1.350-fold). The higher the temperature becomes, the more HUM proteins were produced. At 37° C., HUM-G6 in the soluble fraction was significantly higher than that of HUM-WT. Thus, Gly and Pro redistributions likely improved foldability of HUM-G6. All data represent mean±S.D. of triplicate measurements.
Although we were unable to quantify the free energies of folding and unfolding for the effects of those mutations (due to irreversibility of HUM folding), several studies have considered the physicochemical roles of Gly and Pro in protein structure16,17. Substitutions of Gly→Xaa and Xaa→Pro (Xaa denotes any amino acids other than Gly and Pro) could reduce the conformational entropy of unfolding, and thereby stabilize the native states of proteins by  ̃1 kcal/mol (entropic stabilization)18. In addition, substitutions of Gly→Ala (or Xaa) can reduce the conformational complexity (accessible conformations during protein folding) by approximately 3.4-fold, and hence the protein can fold to its native state faster19. However, substitutions of Xaa→Gly and Pro→Xaa at some local positions are known to be favorable, because the more rigid or bulky residues at some positions can introduce unfavorable kinetic barriers to their folding and/or strain energy to their native states; for example, Gly is more favorable at the C-terminal cap of α-helices20. Thus, Gly and Pro redistributions for both HUM and tHMGR might be similarly affected.
More recently, it has been proposed that amino acid substitutions were asymmetric rather than symmetric as was often assumed 2. All amino acids with declining frequencies were thought to be incorporated into the genetic code at earlier stages in evolution, and vice versa (R=0.55)21,22. Interestingly, Gly and Pro were shown to be among the strong ‘loosers’. Thought to over-represent primordial protein sequences and to be gradually diluted upon recruitment of new amino acids, Gly and Pro might have been longer exposed to natural selection and have had higher chance to be properly distributed, resulting in higher immutability. Although the general tendency is likely affected by the genetic drift of each amino acid depending on codon biases and degree of differences in chemical properties from other amino acids, the stability of amino acids to mutations was relatively well correlated to both a rate of recent gain and loss of amino acids (R=0.60)21, and the consensus order of amino acid recruitment into the genetic code (R=0.59)22. In addition to the unique physicochemical roles of Gly and Pro in protein structure, this may explain why these two residues are relatively more conserved in proteins that are evolutionary related. Therefore, it is reasonable to consider the proper distributions of these amino acids to redesign protein function.
On the basis of the evolutionary relationship, we successfully redesigned the enzymes of a heterologous metabolic pathway to improve its efficiency. Although the methodology developed herein focused only on Gly and Pro, the results showed that it was very powerful and effective, and might be generally applied to improve the function of any other proteins. In addition, the methodology required neither the structural information nor the high-throughput screening generally required for conventional protein engineering strategies: rational design23, computational design24, and directed evolution25,26. These results also provide evidence that proper Gly and Pro distributions are very important for enzyme function and therefore metabolic pathways. Since proper distributions of these residues can largely be predicted from their evolutionary relations, it is likely that there exists proper distributions innate to each protein scaffold, and this can be achieved mainly as a result of adaptation in earlier stages of evolution.
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While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

## Claims

1. A variant biosynthetic pathway enzyme that exhibits one or more of increased intracellular solubility, increased native folding, and reduced aggregate formation when produced recombinantly in a host cell, compared to a parent biosynthetic pathway enzyme when produced recombinantly in the host cell, wherein the parent biosynthetic pathway enzyme is
a γ-humulene synthase, and wherein said variant biosynthetic pathway enzyme is a variant γ-humulene synthase comprising an amino acid sequence having at least about 95% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1, wherein the variant γ-humulene synthase comprises K126P, R142G, and G227A amino acid substitutions.

2. The variant biosynthetic pathway enzyme of claim 1, wherein said variant γ-humulene synthase comprises the amino acid sequence set forth in SEQ ID NO:73.

3. The variant biosynthetic pathway enzyme of claim 1, wherein said variant γ-humulene synthase comprises the amino acid sequence set forth in SEQ ID NO:74.

4. The variant biosynthetic pathway enzyme of claim 1, wherein said variant γ-humulene synthase further comprises a set of amino acid substitutions selected from set A (G148A, G327A, and G361A), set B (F312Q, M339A, M447F), set C (M339N, S484C, and M5651), set D (A317N, A336S, S484C, and I562V), set E (A336C, T445C, S484C, 1562L, and M565L), set F (A336V, M447H, and I562T), and set G (S484A and Y566F).

5. A nucleic acid comprising a nucleotide sequence encoding the variant biosynthetic pathway enzyme of claim 1.

6. A recombinant vector comprising the nucleic acid of claim 5.

7. A recombinant host cell comprising the nucleic acid of claim 5 or the recombinant vector of claim 6.

8. The recombinant host cell of claim 7, wherein said recombinant host cell is a prokaryotic cell.

9. A method of producing an isoprenoid or isoprenoid precursor compound, the method comprising culturing the host cell of claim 8 in a suitable culture medium.

10. The method of claim 9, further comprising isolating the isoprenoid or isoprenoid precursor compound from an organic layer overlaid on the culture medium.

11. A variant biosynthetic pathway enzyme that exhibits one or more of increased intracellular solubility, increased native folding, and reduced aggregate formation when produced recombinantly in a host cell, compared to a parent biosynthetic pathway enzyme when produced recombinantly in the host cell, wherein the parent biosynthetic pathway enzyme is a truncated hydroxymethyl glutaryl-CoA reductase (tHMGR), and the variant biosynthetic pathway enzyme is a variant tHMGR comprising an amino acid sequence having at least about 95% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:49, wherein said variant tHMGR comprises G206A, G319A, G352A, G417A, and G495A amino acid substitutions.

12. The variant biosynthetic pathway enzyme of claim 11, wherein said variant tHMGR comprises the amino acid sequence set forth in SEQ ID NO:75.

13. The variant biosynthetic pathway enzyme of claim 11, wherein said variant tHMGR comprises the amino acid sequence set forth in SEQ ID NO:76.

14. The variant biosynthetic pathway enzyme of claim 11, further comprising P200A, T239P, P428G, and K474G amino acid substitutions.

15. A nucleic acid comprising a nucleotide sequence encoding the variant biosynthetic pathway enzyme of claim 11.

16. A recombinant vector comprising the nucleic acid of claim 15.

17. A recombinant host cell comprising the nucleic acid of claim 15.

18. The recombinant host cell of claim 17, wherein said recombinant host cell is a prokaryotic cell.

19. A recombinant host cell comprising the recombinant vector of claim 16.

20. The recombinant host cell of claim 19, wherein said recombinant host cell is a prokaryotic cell.