# Patent

## Title
Carotenoid ketolase genes with improved ketocarotenoid yield

## Abstract

Protein engineered CrtO ketolases isolated from Rhodococcus erythropolis AN12 are provided having increased carotenoid ketolase activity. Methods using the present CrtO ketolases are also provided for increasing ketocarotenoid production in suitable production hosts.

## Background
This application claims the benefit of U.S. Provisional Application No. 60/577,970, filed Jun. 8, 2004.


FIELD OF THE INVENTION
This invention is in the field of microbiology and molecular biology. More specifically, nucleic acid molecules encoding CrtO carotenoid ketolases characterized by improved ketocarotenoid production are provided. Methods for microbial production of ketocarotenoid compounds using the present CrtO ketolases are also provided.
BACKGROUND OF THE INVENTION
Carotenoids are pigments that are ubiquitous throughout nature and synthesized by all photosynthetic organisms, and in some heterotrophic growing bacteria and fungi. Carotenoids provide color for flowers, vegetables, insects, fish and birds. Colors of carotenoid range from yellow to red with variations of brown and purple. As precursors of vitamin A, carotenoids are fundamental components in our diet and they play additional important role in human health. Industrial uses of carotenoids include pharmaceuticals, food supplements, animal feed additives and colorants in cosmetics to mention a few.
Because animals are unable to synthesize carotenoids de novo, they must obtain them by dietary means. Thus, manipulation of carotenoid production and composition in plants or bacteria can provide new or improved source for carotenoids.
Carotenoids come in many different forms and chemical structures. Most naturally occurring carotenoids are hydrophobic tetraterpenoids containing a C40 methyl-branched hydrocarbon backbone derived from successive condensation of eight C5 isoprene units (IPP). In addition, rare carotenoids with longer or shorter backbones occur in some species of nonphotosynthetic bacteria. The term “carotenoid” actually include both carotenes and xanthophylls. A “carotene” refers to a hydrocarbon carotenoid. Carotene derivatives that contain one or more oxygen atoms, in the form of hydroxy-, methoxy-, oxo-, epoxy-, carboxy-, or aldehydic functional groups, or within glycosides, glycoside esters, or sulfates, are collectively known as “xanthophylls”. Carotenoids are furthermore described as being acyclic, monocyclic, or bicyclic depending on whether the ends of the hydrocarbon backbones have been cyclized to yield aliphatic or cyclic ring structures (G. Armstrong, (1999) In Comprehensive Natural Products Chemistry, Elsevier Press, volume 2, pp 321-352).
Carotenoid biosynthesis starts with the isoprenoid pathway and the generation of a C5 isoprene unit, isopentenyl pyrophosphate (IPP). IPP is condensed with its isomer dimethylallyl pyrophophate (DMAPP) to form the C10, geranyl pyrophosphate (GPP), and elongated to the C15, farnesyl pyrophosphate (FPP). FPP synthesis is common to both carotenogenic and non-carotenogenic bacteria. Enzymes in subsequent carotenoid pathways generate carotenoid pigments from the FPP precursor and can be divided into two categories: carotene backbone synthesis enzymes and subsequent modification enzymes. The backbone synthesis enzymes include geranyl geranyl pyrophosphate synthase, phytoene synthase, phytoene dehydrogenase and lycopene cyclase, etc. The modification enzymes include ketolases, hydroxylases, dehydratases, glycosylases, etc.
Carotenoid ketolases are enzymes that introduce keto groups to the β-ionone ring of the cyclic carotenoids, such as β-carotene and zeaxanthin, to produce ketocarotenoids. Examples of ketocarotenoids include astaxanthin, canthaxanthin, adonixanthin, adonirubin, echinenone, 3-hydroxyechinenone, 3′-hydroxyechinenone, 4-keto-gamma-carotene, 4-keto-rubixanthin, 4-keto-torulene, 3-hydroxy-4-keto-torulene, deoxyflexixanthin, and myxobactone. Unlike genes in the upstream isoprenoid pathway that are common in many organisms, the downstream carotenoid modifying enzymes are less common.
Several classes of carotenoid ketolase have been reported (Hannibal et al., J. Bacteriol. 182: 3850-3853 (2000)). These include CrtW ketolases from Agrobacterium aurantiacum (Misawa et al., J. Bacteriol. 177(22): 6575-6584 (1995); WO 99/07867), Bradyrhizobium sp. ORS278 (Hannibal et al., supra), Brevundimonas aurantiaca (De Souza et al., WO 02/79395), Paracoccus marcusii (Yao et al., CN1380415); Bkt ketolases from Haematococcus pluvialis (Sun et al., Proc. Natl. Acad. Sci. USA, 95(19): 11482-11488 (1998); Linde, H. and Sandmann, G., EP1173579; Breitenbach et al., FEMS Microbiol. Lett., 404(2-3): 241-246 (1996)); and CrtO ketolases from Synechocystis sp. (Lagarde et al., Appl. Environ. Microbiol., 66(1): 64-72 (2000); Masamoto et al., Plant Cell Physiol., 39(5): 560-564 (2000); FR 2792335; Cheng et al., U.S. Ser. No. 10/209,372, hereby incorporated by reference)), Rhodococcus erythropolis (Cheng et al., supra), Deinococcus radiodurans (Cheng et al., supra), and Gloeobacter violaceus (Nakamura et al., DNA Res., 10: 181-201 (2003)). It should be noted that the CrtO ketolase reported in Haematococcus pluvialis (Harker, M. and Hirschberg, J., FEBS Lett., 404(2-3): 129-134 (1997); U.S. Pat. No. 5,965,795; U.S. Pat. No. 5,916,791; and U.S. Pat. No. 6,218,599) appears to be a CrtW/Bkt ketolasd based on its size and homology to other CrtW/Bkt ketolases. Sequence comparison between the Bkt ketolase from Haematococcus pluvialis to publicly available sequences mostly closely matched to other CrtW ketolases. Bkt ketolases appear to be closely related to CrtW ketolases, sharing very little structural similarity to the CrtO ketolases (Cheng, et al, supra). For example, reported CrtW/Bkt ketolases are generally encoded by nucleic acid fragments about 800-1000 bp in length while CrtO ketolases are normally encoded by a nucleic acid fragments of about 1.6 kb in size. Cheng et al. defines CrtO ketolases based on the presence of six conserved motifs considered diagnostic for all CrtO ketolases. The reported CrtO ketolases from Rhodococcus erythropolis, Deinococcus radiodurans, and Synechocystis sp. PCC6803 are comprised of these diagnostic motifs (U.S. Ser. No. 10/209,372).
The CrtO ketolases reported by Cheng et al. generally exhibit much lower activity when producing ketocarotenoids (i.e. canthaxanthin) from β-carotene in comparison to the reported CrtW ketolases (see Tables 2 and 3 in U.S. Ser. No. 10/209,372). In vitro experiments using recombinantly expressed R. erythropolis AN12 CrtO ketolase showed that after 20 hours only 30% of the initial β-carotene substrate was converted into canthaxanthin (35% of the initial β-carotene was converted to echinenone with the remaining 35% remaining as β-carotene).
There is a need for CrtO carotenoid ketolases having improved activity for ketocarotenoid production. Improvements in ketocarotenoid production will enable use of CrtO ketolases for industrial production of commercially useful ketocarotenoids, such as canthaxanthin and astaxanthin. Additionally, commercially useful CrtO ketolases can be recombinantly coexpressed with one or more structurally unrelated CrtW/Bkt ketolases to increase carotenoid titer. Coexpressing divergent ketocarotenoids should improve ketocarotenoid titer without adding instability to the host expression system.
The problem to be solved therefore is to provide nucleic acid molecules encoding CrtO ketolases useful for ketocarotenoid production.
SUMMARY OF THE INVENTION
Applicants have solved the stated problem by creating several mutant CrtO ketolases exhibiting improved ketocarotenoid production in comparison to the wild type CrtO from Rhodococcus erythropolis AN12. The CrtO ketolase from R. erythropolis AN12 was protein engineered using a combination of error-prone PCR and gene shuffling techniques to create a series of ketolases with significantly improved activity.
In one aspect, the invention provides an isolated nucleic acid molecule encoding a mutant carotenoid ketolase having the amino acid sequence, as set forth in SEQ ID NO:2 and comprising at least selected from the group consisting of:

    
    
        a) a replacement of threonine at amino acid position 121 with alanine;
        b) a replacement of methionine at amino acid position 142 with leucine;
        c) a replacement of alanine at amino acid position 164 with valine;
        d) a replacement of isoleucine at amino acid position 283 with valine;
        e) a replacement of threonine at amino acid position 304 with lysine;
        f) a replacement of arginine at amino acid position 339 with glutamine;
        g) a replacement of arginine at amino acid position 519 with tryptophan; and
        h) a replacement of glutamine at amino acid position 524 with leucine or arginine.
    
    


In another embodiment the invention provides an isolated nucleic acid molecule encoding a carotenoid ketolase enzyme having an amino acid sequence selected from the group consisting SEQ ID NO: 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, and 52. Additionally the invention provides polypeptides encoded by the isolated nucleic molecules of the invention and genetic chimera and host cells comprising the same.
In another embodiment the invention provides a method for the production of cyclic ketocarotenoid compounds comprising:

    
    
        a) providing a host cell which produces monocyclic or bicyclic carotenoids;
        b) transforming the host cell with the isolated nucleic acid molecule of the invention encoding a carotenoid ketolase enzyme;
        c) growing the transformed host cell of (b) under conditions whereby a cyclic ketocarotenoid is produced; and
        d) optionally isolating the ketocarotenoid produced in step c).
    
    


In another embodiment the invention provides a method of altering cyclic ketocarotenoid biosynthesis in an organism comprising,

    
    
        (a) introducing into a host cell the isolated nucleic acid molecule of the invention encoding a carotenoid ketolase; and
        (b) growing the host cell of (a) under conditions whereby the carotenoid ketolase gene is expressed and cyclic ketocarotenoid biosynthesis is altered.
    
    





BRIEF DESCRIPTION OF THE FIGURES AND SEQUENCE DESCRIPTIONS
FIG. 1 illustrates common carotenoid products produced by a ketolase in conjunction with an hydroxylase enzyme.
FIG. 2 illustrates the phylogenetic relationship of the carotenoid ketolases.



The invention can be more fully understood from the following detailed description, biological deposits, and the accompanying sequence descriptions, which form a part of this application.
The following sequences comply with 37 C.F.R. 1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the European Patent Convention (EPC) and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.
SEQ ID NO:1 is the nucleotide sequence of the wild type crtO ketolase coding sequence from Rhodococcus erythropolis AN12. SEQ ID NO:2 is deduced amino acid sequence of the wild type crtO ketolase from Rhodococcus erythropolis AN12.
SEQ ID NO: 3 is the nucleotide sequence encoding the codon optimized crtO319 gene in pDCQ319.
SEQ ID NO: 4 is the nucleotide sequence encoding the codon optimized crtO303 gene in pDCQ303.
SEQ ID NO: 5 is the deduced amino acid sequence of the polypeptide encoded by the crtO303 gene.
SEQ ID NO: 6 is the nucleotide sequence encoding the codon optimized crtO320 gene in pDCQ320.
SEQ ID NO: 7 is the nucleotide sequence of primer crtO-For.
SEQ ID NO: 8 is the nucleotide sequence of primer crtO-Rev.
SEQ ID NO: 9 is the nucleotide sequence of primer crtO900-For.
SEQ ID NO: 10 is the nucleotide sequence of primer crtO303-Rev.
SEQ ID NO: 11 is the nucleotide sequence of primer 320-F1.
SEQ ID NO: 12 is the nucleotide sequence of primer 320-R1.
SEQ ID NO: 13 is the nucleotide sequence of 319M3022.
SEQ ID NO: 14 is the deduced amino acid sequence of 319M3022.
SEQ ID NO: 15 is the nucleotide sequence of 303M3044.
SEQ ID NO: 16 is the deduced amino acid sequence of 303M3044.
SEQ ID NO: 17 is the nucleotide sequence of 320M4006.
SEQ ID NO: 18 is the deduced amino acid sequence of 320M4006.
SEQ ID NO: 19 is the nucleotide sequence of 320M4007.
SEQ ID NO: 20 is the deduced amino acid sequence of 320M4007.
SEQ ID NO: 21 is the nucleotide sequence of 320M4009.
SEQ ID NO: 22 is the deduced amino acid sequence of 320M4009.
SEQ ID NO: 23 is the nucleotide sequence of 320M4018.
SEQ ID NO: 24 is the deduced amino acid sequence of 320M4018.
SEQ ID NO: 25 is the nucleotide sequence of 320M4019.
SEQ ID NO: 26 is the deduced amino acid sequence of 320M4019.
SEQ ID NO: 27 is the nucleotide sequence of 320M4020.
SEQ ID NO: 28 is the deduced amino acid sequence of 320M4020.
SEQ ID NO: 29 is the nucleotide sequence of 320M4023.
SEQ ID NO: 30 is the deduced amino acid sequence of 320M4023 SEQ ID NO: 31 is the nucleotide sequence of 320M4027.
SEQ ID NO: 32 is the deduced amino acid sequence of 320M4027.
SEQ ID NO: 33 is the nucleotide sequence of 320M4032.
SEQ ID NO: 34 is the deduced amino acid sequence of 320M4032.
SEQ ID NO: 35 is the nucleotide sequence of 320M4036.
SEQ ID NO: 36 is the deduced amino acid sequence of 320M4036.
SEQ ID NO: 37 is the nucleotide sequence of 320SHU001.
SEQ ID NO: 38 is the deduced amino acid sequence of 320SHU001.
SEQ ID NO: 39 is the nucleotide sequence of 320SHU004.
SEQ ID NO: 40 is the deduced amino acid sequence of 320SHU004.
SEQ ID NO: 41 is the nucleotide sequence of 320SHU008.
SEQ ID NO: 42 is the deduced amino acid sequence of 320SHU008.
SEQ ID NO: 43 is the nucleotide sequence of 320SHU015.
SEQ ID NO: 44 is the deduced amino acid sequence of 320SHU015.
SEQ ID NO: 45 is the nucleotide sequence of 320SHU016.
SEQ ID NO: 46 is the deduced amino acid sequence of 320SHU016.
SEQ ID NO: 47 is the nucleotide sequence of 320SHU017.
SEQ ID NO: 48 is the deduced amino acid sequence of 320SHU017.
SEQ ID NO: 49 is the nucleotide sequence of 320SHU019.
SEQ ID NO: 50 is the deduced amino acid sequence of 320SHU019.
SEQ ID NO: 51 is the nucleotide sequence of 320SHU022.
SEQ ID NO: 52 is the deduced amino acid sequence of 320SHU022.
BRIEF DESCRIPTION OF BIOLOGICAL DEPOSITS
The following biological deposits have been made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the purposes of patent Procedure:












Depositor Identification
Int'l. Depository



Reference
Designation
Date of Deposit







Methylomonas 16a
ATCC# PTA-2402
Aug. 22, 2000


WS#208 E. coli
ATCC# PTA-4823
Nov. 26, 2002


strain PT5-dxs PT5-idi PT5-


ygbBP PT5-ispB, pDCQ108









As used herein, “ATCC” refers to the American Type Culture Collection International Depository Authority located at ATCC, 10801 University Blvd., Manassas, Va. 20110-2209, USA. The “International Depository Designation” is the accession number to the culture on deposit with ATCC.
The listed deposits will be maintained in the indicated international depository for at least thirty (30) years and will be made available to the public upon the grant of a patent disclosing it. The availability of a deposit does not constitute a license to practice the subject invention in derogation of patent rights granted by government action.
DETAILED DESCRIPTION OF THE INVENTION
The invention relates to engineered CrtO ketolases with improved catalytic efficiency (i.e. improved ketocarotenoid production) for use in commercial ketocarotenoid production. All of the ketolases were characterized as having an improved ability to produce ketocarotenoids when compared to a corresponding codon optimized version of the wild-type enzyme from which they were created.
The present mutant crtO genes and their expression products, CrtO carotenoid ketolases, are useful for the creation of recombinant organisms having the ability to produce ketocarotenoid compounds. Additionally, the present CrtO ketolases can be coexpressed with well-known CrtW ketolases since they share no structural similarity, creating stable recombinant organisms capable of increased ketocarotenoid production.
The present crtO ketolase genes described herein enable the production of ketocarotenoids in a recombinant host cell. Incorporation and expression of these genes in an industrially-suitable production host enables cost effective production of ketocarotenoids. The ketocarotenoid produced can be used for a variety of applications including, but not limited to, dietary supplements, fish and poultry pigmentation, and electro-optic applications. For example, salmon and shrimp aquacultures are particularly useful applications for this invention as carotenoid pigmentation is critically important for the value of these organisms (Shahidi, F. and Brown, J. A., Crit. Rev Food Sci 38(1): 1-67 (1998)). Additionally, the ketocarotenoid astaxanthin is a powerful antioxidant and has been reported to boost immune functions and reduce carcinogenesis in humans (Jyonouchi et al., Nutr. Cancer 23: 171-183 (1995); Tanaka et al., Cancer Res. 55: 4059-4064 (1995)).
In this disclosure, a number of terms and abbreviations are used. The following definitions are provided.
“Open reading frame” is abbreviated ORF.
“Polymerase chain reaction” is abbreviated PCR.
As used herein, an “isolated nucleic acid fragment” is a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.
As used herein, the term “isoprenoid” or “terpenoid” refers to the compounds are any molecule derived from the isoprenoid pathway including 10 carbon terpenoids and their derivatives, such as carotenoids and xanthophylls.
As used herein, the terms “Rhodococcus erythropolis AN12”, “Rhodococcus erythropolis strain AN12” or “AN12” will be used interchangeably and refer to the Rhodococcus erythropolis AN12 strain (U.S. Ser. No. 10/209,372).
As used herein, the term “carotenoid” refers to a compound composed of a polyene backbone which is condensed from five-carbon isoprene unit. Carotenoids can be acyclic or terminated with one (monocyclic) or two (bicyclic) cyclic end groups. The term “carotenoid” may include both carotenes and xanthophylls. A “carotene” refers to a hydrocarbon carotenoid. Carotene derivatives that contain one or more oxygen atoms, in the form of hydroxy-, methoxy-, oxo-, epoxy-, carboxy-, or aldehydic functional groups, or within glycosides, glycoside esters, or sulfates, are collectively known as “xanthophylls”. Carotenoids that are particularly suitable in the present invention are monocyclic and bicyclic carotenoids.
As used herein, the term “carotenoid ketolase” or “ketolase” or “cyclic carotenoid ketolase” refers to an enzyme that can add keto groups to the ionone ring of either monocyclic or bicyclic carotenoids. Two distinct classes of carotenoid ketolase have been reported. The first class is CrtW/Bkt ketolases that typically exhibit homology to one another and are generally encoded by a nucleotide sequence of approximately 800-1000 bp in length. The second class of ketolase, and the object of the present application, are CrtO ketolases. These ketolases are normally encoded by nucleotide sequence of approximately 1.6 kb in length and exhibit no structural similarity to the CrtW/Bkt ketolases. A phylogentic analysis illustrating the differences between CrtO and CrtW ketolases is provided in FIG. 2 (WO 10/209,372).
As used herein, the term “motif” refers to short conserved amino acid sequences found in a group of protein sequences. Motifs frequently form a recognition sequence or are highly conserved parts of domains. Motif may also refer to all localized homology regions, independent of their size. A motif descriptor could be used to describe the short sequence motifs, consisting of amino acid characters and other characters represent ambiguities and length insertions. CrtO ketolases are known to possess six diagnostic conserved motifs (U.S. Ser. No. 10/209,372) not found in CrW/Bkt ketolases.
As used herein, the terms “diagnostic conserved motifs”, “conserved amino acid motifs”, and “diagnostic motif” refers to amino acid sequences that are common among CrtO ketolase enzymes and the presence of which is diagnostic for cyclic carotenoid ketolase functionality.
As used herein, the term “keto group” or “ketone group” will be used interchangeably and refers to a group in which a carbonyl group is bonded to two carbon atoms: R2C═O (neither R may be H).
As used herein the term “β-ionone ring” or “β-ionone group” is defined as C9H15.
The term “complementary” is used to describe the relationship between nucleotide bases that are capable to hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing.
The term “percent identity”, as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, NY (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, NY (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, NJ (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, NY (1991). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp, CABIOS 5: 151-153 (1989)) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
“Codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment that encodes all or a substantial portion of the amino acid sequence encoding the instant microbial polypeptides as set forth in SEQ ID NOs: 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, and 52. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
“Synthetic genes” 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 that 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. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene 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. In the present application, the coding sequence of several genes was either partially or completely codon optimized to match the codon usage found in a Methylomonas sp. 16a (Table 1).
As used herein, the term “gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.
“Coding sequence” refers to a DNA sequence that codes for a specific amino acid sequence. As used herein, the term “suitable regulatory sequences” refers to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site and stem-loop structure.
“Promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters that cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
The “3′ non-coding sequences” refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal (normally limited to eurkaryotes) is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor.
As used herein, the term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.
The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide.
“Transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic”, “recombinant” or “transformed” organisms.
As used herein, the term “recombination” will refer to a process whereby genetic combinations are formed which were not present in parental template molecules, by the processes of crossing over or independent assortment. Thus, recombination includes all combinations of genetic sequences that can be obtained from the parental template molecules (whereby each nucleotide position of the newly generated “recombinogenic product(s)” can be derived from any of the parental templates at that particular nucleotide position); and additionally, recombination includes the introduction of new mutations (i.e. deletions, substitutions, or insertions).
As used herein, the term “recombined polypeptide” means a polypeptide encoded by recombined genes or DNA. Recombined polypeptides will often have altered or enhanced properties. The term “Entner-Douderoff pathway” refers to a series of biochemical reactions for conversion of hexoses such as glucose or fructose to the important 3-carbon cellular intermediates pyruvate and glyceraldehyde 3-phosphate without any net production of biochemically useful energy. The key enzymes unique to the Entner-Douderoff pathway are the 6-phosphogluconate dehydratase and a ketodeoxyphospho-gluconate aldolase.
The term “Embden-Meyerhof pathway” refers to the series of biochemical reactions for conversion of hexoses such as glucose and fructose to important cellular 3-carbon intermediates such as glyceraldehyde 3 phosphate, dihydroxyacetone phosphate, phosphoenol pyruvate and pyruvate. These reactions typically proceed with net yield of biochemically useful energy in the form of ATP. The key enzymes unique to the Embden-Meyerhof pathway are the phosphofructokinase and fructose 1,6 bisphosphate aldolase.
As used herein, the term “carbon substrate” refers to a carbon source capable of being metabolized by host organisms of the present invention and particularly carbon sources selected from the group consisting of monosaccharides, disaccharides, polysaccharides, and single carbon substrates (C1 carbon substrates) or mixtures thereof.
The term “C1 carbon substrate” or “single carbon substrate” refers to any carbon-containing molecule that lacks a carbon-carbon bond. Examples are methane, methanol, formaldehyde, formic acid, formate, methylated amines (e.g., mono-, di-, and tri-methyl amine), methylated thiols, and carbon dioxide. In one aspect, the C1 carbon substrate is methane and/or methanol.
The term “C1 metabolizer” refers to a microorganism that has the ability to use a single carbon substrate as its sole source of energy and biomass. C1 metabolizers will typically be methylotrophs and/or methanotrophs.
The term “methylotroph” means an organism capable of oxidizing organic compounds that do not contain carbon-carbon bonds. Where the methylotroph is able to oxidize CH4, the methylotroph is also a methanotroph. In one aspect, the methylotroph is a methylotrophic bacteria. In another aspect, the methylotrophic bacteria grown on methane and/or methanol.
The term “methanotroph” or “methanotrophic bacteria” means a methylotrophic bacteria capable of utilizing methane as its primary source of carbon and energy. Complete oxidation of methane to carbon dioxide occurs by aerobic degradation pathways. Typical examples of methanotrophs useful in the present invention include (but are not limited to) the genera Methylomonas, Methylobacter, Methylococcus, and Methylosinus. In one aspect, the methanotroph is grown on methane and/or methanol.
As used herein, the term “high growth methanotrophic bacterial strain” refers to a bacterium capable of growth with methane or methanol as the sole carbon and energy source and which possesses a functional Embden-Meyerof carbon flux pathway resulting in a high rate of growth and yield of cell mass per gram of C1 substrate metabolized. The specific “high growth methanotrophic bacterial strain” described herein is referred to as “Methylomonas 16a”, “16a” or “Methylomonas sp. 16a”, which terms are used interchangeably and which refer to the Methylomonas sp. 16a (ATCC PTA-2402) strain (U.S. Pat. No. 6,689,601; hereby incorporated by reference).
The terms “plasmid”, “vector” and “cassette” refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA fragments. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell. “Transformation cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitates transformation of a particular host cell. “Expression cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.
As used herein, the term “altered biological activity” or “altered activity” will refer to an activity associated with a protein encoded by a microbial nucleotide sequence which can be measured by an assay method, where that activity is either greater than or less than the activity associated with the native microbial sequence. As used herein, “enhanced biological activity” refers to an altered activity that is greater than that associated with the native sequence. As used herein, “diminished biological activity” refers to an altered activity that is less than that associated with the native sequence. In the present application, protein engineered CrtO ketolases are provided which have improved ketolase activity when compared to a codon optimized version of the wild type gene from which they were developed (endogenous crtO gene from Rhodococcus erythropolis AN12; U.S. Ser. No. 10/209,372). Increases in ketolase activity were measured by the amount of β-carotene converted into canthaxanthin (reported as percentage yield) under similar reaction conditions. The expression system used to evaluate each mutant and the corresponding control was essentially identical. The recombinant protein expression level of each mutant CrtO ketolase was essentially identical. Improvements in the percentage yield of ketocarotenoid production were therefore attributed to structural differences associated with each of the present CrtO ketolases. The structural differences are represented by the nucleotide and amino acid sequences provided for each of the present CrtO ketolases.
As used herein, the terms “recombinogenic extension method using unpaired primers” and “the unpaired primers method” are used interchangeably to refer to the method disclosed in WO 03/072743 (corresponding to U.S. Ser. No. 10/374,366; hereby incorporated by reference) wherein recombinogenic products are created from template molecules using a method based on unpaired primers.
As used herein, the term “paired primers” will refer to a pair of primers, consisting of a forward and reverse primer, which are designed to anneal to a single template molecule and permit synthesis of an exact copy of that template by a primer directed nucleic acid amplification process. In the case of a double-stranded template molecule, the forward and reverse primers enable the synthesis of an exact copy of the double-stranded template since the forward primer produces an exact copy of the antisense strand (that is, a complementary copy of the sense strand which it is using as a template) and the reverse primer produces an exact copy of the sense strand (that is, a complementary copy of the antisense strand which it is using as a template). In contrast, when the template molecule is single-stranded, an exact copy of that template is produced using a primer directed nucleic acid amplification process.
As used herein, the term “unpaired primers” will refer to a pair of primers, consisting of a forward and a reverse primer, which are not designed to anneal to a single template molecule and permit synthesis of an exact copy of that template by a primer directed nucleic acid amplification process. Instead, the forward primer will anneal to a first template molecule, but will not be able to anneal to a second template molecule. The reverse primer will anneal to a second template molecule that is different in sequence from the first template molecule, and yet will not be able to anneal to the first template molecule. This unique design of unpaired primers ensures that a single-or double-stranded template molecule can not be amplified by a primer directed nucleic acid amplification process, unless recombination occurs during replication via template switching.
As used herein, the term “template(s)” or “parent template(s)” refers to a nucleic acid molecule that is copied by a DNA or RNA polymerase according to the rules of Watson-Crick base pairing to produce a new strand of DNA or RNA. The sequence information in the template (or “model”) is preserved, since the first copy produced from that template molecule has a complementary sequence. Template molecules may be single or double-stranded and derived from any source.
The “5′ region” and “3′ region” of a nucleic acid will be used as relative terms, in reference to the region of nucleotides wherein it is desirable for recombination to occur. These regions may be within a template molecule or within a flanking DNA sequence that is attached to the template molecules. Unpaired primers will anneal to a portion of these 5′ and 3′ regions.
As used herein, the term “flanking sequence” or “flanking DNA fragment” will refer to a short segment of DNA that is attached to either the 5′ or 3′ region of a template molecule, in order to provide a unique nucleotide sequence (with respect to the template molecule) to which an unpaired primer may anneal.
As used herein, a “full length extension product” is a nucleotide sequence produced by primer-directed replication that has a length very similar (within about 100 bases) to that contained between the 5′ and 3′ region of the parent templates.
As used herein, the term “amplification” is used to describe the process in which replication is repeated in cyclic manner such that the number of copies of the “template nucleic acid” is increased in either a linear or logarithmic fashion.
As used herein, the term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software will include, but is not limited to: 1.) the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.); 2.) BLASTP, BLASTN, BLASTX (Altschul et al., J. Mol. Biol. 215: 403-410 (1990)); 3.) DNASTAR (DNASTAR, Inc. Madison, Wis.); 4.) the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Plenum: New York, N.Y.); and 5.) the Vector NTI version 7.0 programs (Informax, Inc., Bethesda, Md.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default values” will mean any set of values or parameters (set by the manufacturer) which originally load with the software when first initialized.
Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Cold Press Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987).
As used herein, the term “improved ketolase activity” or “significantly improved ketolase activity” refers to the present crtO genes encoding mutant CrtO ketolases having improved ketolase activity when compared to the ketolase activity of the Rhodococcus erythropolis AN12 wild type CrtO ketolase (SEQ ID NO: 2). Improvements in ketolase activity were determined by measuring the percentage yield of canthaxanthin produced in recombinant hosts previously engineered to produce excess amounts of the ketolase substrate, β-carotene, when grown under similar conditions.
In one embodiment, mutant CrtO ketolases of the present invention are those having an increase in the percentage yield of canthaxanthin of at least a 5% when compared to the percentage yield of canthaxanthin from a codon optimized version (crtO320; SEQ ID NO: 6) of the Rhodococcus erythropolis AN12 crtO gene encoding the wild type CrtO amino acid sequence (SEQ ID NO: 2) grown under similar reaction conditions. As used herein, “similar reaction conditions” will be used to described reactions conditions that are essentially identical when assaying ketocarotenoid yield. In another embodiment, mutant CrtO ketolases of the present invention are those having at least a 10% increase in the percentage yield of canthaxanin. In yet another embodiment, preferred ketolases are those having at least a 25% increase in the percentage yield of canthaxanthin. Most preferred ketolases are those exhibiting at least a 50% increase in the percentage yield of canthaxanthin. Comparisons in ketolase activity can be conducted under a variety of reaction conditions depending upon the selected host organism. Suitable comparisons are those conducted between the engineered ketolase of interest and a suitable control under similar reaction conditions. Recombinant expression levels of the present ketolases were essentially identical, indicating that improvement in canthaxanthin yield were attributed to structural modifications resulting increased ketolase activity.
The present CrtO ketolases may be used in vitro or in vivo in for the production of ketocarotenoids from carotenoid compounds having at least one β-ionone ring.
Recombinant Expression—Microbial
The genes and gene products of the instant sequences may be produced in heterologous host cells, particularly in the cells of microbial hosts. Expression in recombinant microbial hosts may be useful for the expression of various pathway intermediates, for the modulation of pathways already existing in the host, or for the synthesis of new products heretofore not possible using the host.
Preferred heterologous host cells for expression of the present genes are microbial hosts that can be found broadly within the fungal or bacterial families and which grow over a wide range of temperature, pH values, and solvent tolerances. For example, it is contemplated that any of bacteria, yeast, and filamentous fungi will be suitable hosts for expression of the present nucleic acid fragments. Because of transcription, translation and the protein biosynthetic apparatus is the same irrespective of the cellular feedstock, functional genes are expressed irrespective of carbon feedstock used to generate cellular biomass. Large-scale microbial growth and functional gene expression may utilize a wide range of simple or complex carbohydrates, organic acids and alcohols, saturated hydrocarbons such as methane or carbon dioxide in the case of photosynthetic or chemoautotrophic hosts. However, the functional genes may be regulated, repressed or depressed by specific growth conditions, which may include the form and amount of nitrogen, phosphorous, sulfur, oxygen, carbon or any trace micronutrient including small inorganic ions. In addition, the regulation of functional genes may be achieved by the presence or absence of specific regulatory molecules that are added to the culture and are not typically considered nutrient or energy sources. Growth rate may also be an important regulatory factor in gene expression. Examples of host strains include, but are not limited to bacterial, fungal or yeast species such as Aspergillus, Trichoderma, Saccharomyces, Pichia, Phaffia, Candida, Hansenula, or bacterial species such as Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus. Preferred bacterial species include Escherichia coli, Methylomonas sp. 16a, and derivatives thereof.
Microbial expression systems and expression vectors containing regulatory sequences that direct high-level expression of foreign proteins are well known to those skilled in the art. Any of these can be used to construct chimeric genes for expression of present ketolases. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide high-level expression of the present ketolases.
Accordingly, it is expected that introduction of chimeric genes encoding the instant bacterial enzymes under the control of the appropriate promoters will demonstrate increased or altered ketocarotenoid production. It is contemplated that it will be useful to express the instant genes both in natural host cells as well as heterologous hosts. Introduction of the present mutant crtO genes into native host will result in altered levels of existing carotenoid production. Additionally, the instant genes may also be introduced into non-native host bacteria where the existing carotenoid pathway may be manipulated.
Specific ketocarotenoids that will be produced by the present invention include but are not limited to, canthaxanthin, astaxanthin, adonixanthin, adonirubin, echinenone, 3-hydroxyechinenone, 3′-hydroxyechinenone, 4-keto-gamma-carotene, 4-keto-rubixanthin, 4-keto-torulene, 3-hydroxy-4-keto-torulene, deoxyflexixanthin, and myxobactone. Of particular interest is the production of canthaxanthin, astaxanthin, 4-keto-γ-carotene, and 4-keto-rubixanthin (FIG. 1). The specific substrate for the present CrtO enzyme is a carotenoid having at least one β-ionone ring. Cyclic carotenoids are well known in the art and available commercially. Preferred substrates in the present invention are cyclic carotenoids that include, but are not limited to, β-carotene, γ-carotene, zeaxanthin, rubixanthin, echinenone, and torulene. In the present examples, an E. coli strain (WS210) containing chromosomal modifications for enhanced carotenoid production previously engineered to produce elevated levels of β-carotene (up to 6000 ppm) was used to monitor ketolase activity (E. coli strain WS210 contains the same chromosomal modifications as E. coli strain WS208; ATCC PTA-4823; U.S. Ser. No. 10/735,442; hereby incorporated by reference). WS210 is identical to WS208 except for the fact that WS208 is comprised of plasmid (pDCQ108) expressing the β-carotene synthesis genes (crtEXYIB) from Pantoea stewartii (ATCC No. 8199).
Vectors or cassettes useful for the transformation of suitable host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.
Initiation control regions or promoters which are useful to drive expression of the instant ORF's in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the present invention including, but not limited to: CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (e.g., useful for expression in Saccharomyces); AOX1 (e.g., useful for expression in Pichia); and lac, ara, tet, trp, IPL, IPR, T7, tac, and trc (e.g., useful for expression in Escherichia coli) as well as the amy, apr, npr promoters and various phage promoters useful for expression in, e.g., Bacillus. Additionally, the deoxy-xylulose phosphate synthase or methanol dehydrogenase operon promoter (Springer et al., FEMS Microbiol Lett 160: 119-124 (1998)), the promoter for polyhydroxyalkanoic acid synthesis (Foellner et al., Appl. Microbiol. Biotechnol. 40: 284-291 (1993)), promoters identified from native plasmids in methylotrophs (EP 296484), Plac (Toyama et al., Microbiology 143: 595-602 (1997); EP 62971), Ptrc (Brosius et al., Gene 27: 161-172 (1984)), promoters identified from methanotrophs (PCT/US03/33698), and promoters associated with antibiotic resistance [e.g., kanamycin (Springer et al., supra; Ueda et al., Appl. Environ. Microbiol. 57: 924-926 (1991)) or tetracycline (U.S. Pat. No. 4,824,786)] are suitable for expression in C1 metabolizers.
It may be necessary to include an artificial ribosomal binding site (“RBS”) upstream of a gene to be expressed, when the RBS is not provided by the vector. This is frequently required for the second, third, etc. gene(s) of an operon to be expressed, when a single promoter is driving the expression of a first, second, third, etc. group of genes. Methodology to determine the preferred sequence of a RBS in a particular host organism will be familiar to one of skill in the art, as are means for creation of this synthetic site.
Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included.
Merely inserting a gene into a cloning vector does not ensure that it will be successfully expressed at the level needed. In response to the need for a high expression rate, many specialized expression vectors have been created by manipulating a number of different genetic elements that control aspects of transcription, translation, protein stability, oxygen limitation, and secretion from the host cell. More specifically, the molecular features that have been manipulated to control gene expression include: 1.) the nature of the relevant transcriptional promoter and terminator sequences; 2.) the strength of the ribosome binding site; 3.) the number of copies of the cloned gene and whether the gene is plasmid-borne or integrated into the genome of the host cell; 4.) the final cellular location of the synthesized foreign protein; 5.) the efficiency of translation in the host organism; 6.) the intrinsic stability of the cloned gene protein within the host cell; and 7.) the codon usage within the cloned gene, such that its frequency approaches the frequency of preferred codon usage of the host cell. Each of these types of modifications are encompassed in the present invention, as means to further optimize expression of the present mutant CrtO ketolases.
Finally, to promote accumulation of ketocarotenoids, it may be necessary to reduce or eliminate the expression of certain genes in the target pathway or in competing pathways that may serve as sinks for energy or carbon. Alternatively, it may be useful to over-express various genes upstream of desired carotenoid intermediates to enhance production. Methods of manipulating genetic pathways for the purposes described above are common and well known in the art.
For example, once a key genetic pathway has been identified and sequenced, specific genes may be up-regulated to increase the output of the pathway. For example, additional copies of the targeted genes may be introduced into the host cell on multicopy plasmids such as pBR322. Alternatively the target genes may be modified so as to be under the control of non-native promoters. Where it is desired that a pathway operate at a particular point in a cell cycle or during a fermentation run, regulated or inducible promoters may used to replace the native promoter of the target gene. Similarly, in some cases the native or endogenous promoter may be modified to increase gene expression. For example, endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (U.S. Pat. No. 5,565,350; Zarling et al., PCT/US93/03868).
In another aspect, where the sequence of the gene to be disrupted is known, one of the most effective methods for gene down-regulation is targeted gene disruption, where foreign DNA is inserted into a structural gene so as to disrupt transcription. This can be affected by the creation of genetic cassettes comprising the DNA to be inserted (often a genetic marker) flanked by sequences having a high degree of homology to a portion of the gene to be disrupted. Introduction of the cassette into the host cell results in insertion of the foreign DNA into the structural gene via the native DNA replication mechanisms of the cell. (See for example Hamilton et al., J. Bacteriol. 171: 4617-4622 (1989); Balbas et al., Gene 136: 211-213 (1993); Gueldener et al., Nucleic Acids Res. 24: 2519-2524 (1996); and Smith et al., Methods Mol. Cell. Biol. 5: 270-277 (1996)).
Antisense technology is another method of down-regulating genes where the sequence of the target gene is known. To accomplish this, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. This construct is then introduced into the host cell and the antisense strand of RNA is produced. Antisense RNA inhibits gene expression by preventing the accumulation of mRNA encoding the protein of interest. The person skilled in the art will know that special considerations are associated with the use of antisense technologies in order to reduce expression of particular genes. For example, the proper level of expression of antisense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan.
Although targeted gene disruption and antisense technology offer effective means of down-regulating genes where the sequence is known, other less specific methodologies have been developed that are not sequence-based. For example, cells may be exposed to UV radiation and then screened for the desired phenotype. Mutagenesis with chemical agents is also effective for generating mutants and commonly used substances include chemicals that affect nonreplicating DNA (e.g., HNO2 and NH2OH), as well as agents that affect replicating DNA (e.g., acridine dyes, notable for causing frameshift mutations). Specific methods for creating mutants using radiation or chemical agents are well documented in the art. See, for example: Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, 2nd ed., (1989) Sinauer Associates: Sunderland, M A; or Deshpande, Mukund V., Appl. Biochem. Biotechnol. 36: 227-234 (1992).
Another non-specific method of gene disruption is the use of transposable elements or transposons. Transposons are genetic elements that insert randomly in DNA but can be later retrieved on the basis of sequence to determine where the insertion has occurred. Both in vivo and in vitro transposition methods are known. Both methods involve the use of a transposable element in combination with a transposase enzyme. When the transposable element or transposon is contacted with a nucleic acid fragment in the presence of the transposase, the transposable element will randomly insert into the nucleic acid fragment. The technique is useful for random mutagenesis and for gene isolation, since the disrupted gene may be identified on the basis of the sequence of the transposable element. Kits for in vitro transposition are commercially available (see, for example: The Primer Island Transposition Kit, available from Perkin Elmer Applied Biosystems, Branchburg, N.J., based upon the yeast Ty1 element; The Genome Priming System, available from New England Biolabs, Beverly, Mass., based upon the bacterial transposon Tn7; and the EZ::TN Transposon Insertion Systems, available from Epicentre Technologies, Madison, Wis., based upon the Tn5 bacterial transposable element).
Within the context of the present invention, it may be useful to modulate the expression of the carotenoid biosynthetic pathway by any one of the methods described above. For example, a number of genes encoding enzymes in the carotenoid pathway (crtE, crtX, crtY, crtI, crtB, crtZ, crtN, crtM, crtN1, crtN2, ald, sqs, etc.) are known, leading to the production of carotenoid. Thus, it may also be useful to up-regulate the initial condensation of 3-carbon compounds (pyruvate and D-glyceraldehyde 3-phosphate) to increase the yield of the 5-carbon compound D-1-deoxyxylulose-5-phosphate (mediated by the dxs gene). This would increase the flux of carbon entering the carotenoid biosynthetic pathway and permit increased production of ketocarotenoids. Alternatively (or in addition to), it may be desirable to knockout the crtM/crtN genes leading to the synthesis of C30 carotenoids, if the microbial host is capable of synthesizing these types of compounds. For example, an optimized Methylomonas sp. 16a strain has been created containing a knockout of the native C30 pathway, creating a non-pigmented strain suitable for engineering C40 carotenoid production (U.S. Ser. No. 10/997,844; hereby incorporated by reference). Or, in systems having native functional crtE, crtX, crtY, crtI, crtB, and crtZ genes, the accumulation of β-carotene or zeaxanthin may be effected by the disruption of down-stream genes (e.g., crtZ or crtX) by any one of the methods described above.
In another embodiment, the present CrtO ketolases can be coexpressed with one or more structurally unrelated CrtW/Bkt ketolases for increased production of ketocarotenoids. As used herein, “structurally unrelated” refers to differences in the gene's nucleic acid sequence. The absence of highly homologous regions between crtW/bkt and crtO ketolase genes permits stable expression as the probably of homologous recombination decreases. Cheng et al. (10/209,372) have previously shown that CrtW/Bkt ketolases are structurally unrelated CrtO ketolases based on a phylogenetic analysis (FIG. 2). Preferred structurally unreladed CrtW/Bkt ketolases useful for coexpression have less than 60% nucleic acid sequence identity based on BLASTN analysis when compared to the coding sequence of the present ketolases. More preferred structurally unrelated CrtW/Bkt ketolases share less than 50% identity with the present CrtO ketolases. Most preferred structurally unrelated CrtW/Bkt ketolases share less than 40% identify with the present CrtO ketolases.
Methods of manipulating genetic pathways are common and well known in the art. Selected genes in a particularly pathway may be upregulated or down regulated by variety of methods. Additionally, competing pathways organism may be eliminated or sublimated by gene disruption and similar techniques.
Industrial Production using Recombinant Microorganisms
Where commercial production of ketocarotenoid compounds is desired using the present crtO genes, a variety of culture methodologies may be applied. For example, large-scale production of a specific gene product overexpressed from a recombinant microbial host may be produced by both batch and continuous culture methodologies.
A classical batch culturing method is a closed system where the composition of the media is set at the beginning of the culture and not subject to artificial alterations during the culturing process. Thus, at the beginning of the culturing process the media is inoculated with the desired organism or organisms and growth or metabolic activity is permitted to occur adding nothing to the system. Typically, however, a “batch” culture is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase are often responsible for the bulk of production of end product or intermediate in some systems. Stationary or post-exponential phase production can be obtained in other systems.
A variation on the standard batch system is the fed-batch system. Fed-batch culture processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the culture progresses. Fed-batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in fed-batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO2. Batch and fed-batch culturing methods are common and well known in the art and examples may be found in Brock (supra) or Deshpande (supra).
Commercial production of cyclic ketocarotenoids may also be accomplished with a continuous culture. Continuous cultures are an open system where a defined culture media is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous cultures generally maintain the cells at a constant high liquid phase density where cells are primarily in log phase growth. Alternatively, continuous culture may be practiced with immobilized cells where carbon and nutrients are continuously added, and valuable products, by-products or waste products are continuously removed from the cell mass. Cell immobilization may be performed using a wide range of solid supports composed of natural and/or synthetic materials.
Continuous or semi-continuous culture allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to media being drawn off must be balanced against the cell growth rate in the culture. Methods of modulating nutrients and growth factors for continuous culture processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.
Fermentation media in the present invention must contain suitable carbon substrates. Suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, disaccharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpurified mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt. Additionally, the carbon substrate may also be one-carbon substrates such as carbon dioxide, methane or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In one aspect, the host cell is a methylotrophic microorganism grown on methane and/or methanol. In addition to one and two carbon substrates methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity. For example, methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., Microb. Growth C1-Compd., [Int. Symp.], 7th (1993), 415-32. Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK). Similarly, various species of Candida will metabolize alanine or oleic acid (Sulter et al., Arch. Microbiol. 153: 485-489 (1990)). Hence it is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism.
Methylotrophs and Methylomonas sp. 16a as Microbial Hosts
Although a number of carotenoids have been produced from recombinant microbial sources [e.g., E. coli and Candida utilis for production of lycopene (Farmer, W. R. and Liao, J. C., Biotechnol. Prog. 17: 57-61 (2001); Wang et al., Biotechnol Prog. 16: 922-926 (2000); Misawa, N. and Shimada, H., J. Biotechnol. 59: 169-181 (1998); Shimada et al., Appl. Environm. Microbiol. 64: 2676-2680 (1998)]; E. coli, Candida utilis and Pfaffia rhodozyma for production of β-carotene (Albrecht et al., Biotechnol. Lett. 21: 791-795 (1999); Miura et al., Appl. Environm. Microbiol. 64: 1226-1229 (1998); U.S. Pat. No. 5,691,190); E. coli and Candida utilis for production of zeaxanthin (Albrecht et al., supra; Miura et al., supra; E. Coli and Phaffia rhodozyma for production of astaxanthin (U.S. Pat. No. 5,466,599; U.S. Pat. No. 6,015,684; U.S. Pat. No. 5,182,208; U.S. Pat. No. 5,972,642); see also: U.S. Pat. No. 5,656,472, U.S. Pat. No. 5,545,816, U.S. Pat. No. 5,530,189, U.S. Pat. No. 5,530,188, U.S. Pat. No. 5,429,939, and U.S. Pat. No. 6,124,113), these methods of producing carotenoids using various combinations of different crt genes suffer from low yields and reliance on relatively expensive feedstocks. Thus, it is desirable to use a method that produces higher yields of carotenoids in a microbial host from an inexpensive feedstock.
There are a number of microorganisms that utilize single carbon substrates as their sole energy source. Such microorganisms are referred to herein as “C1 metabolizers”. These organisms are characterized by the ability to use carbon substrates lacking carbon to carbon bonds as a sole source of energy and biomass. These carbon substrates include, but are not limited to: methane, methanol, formate, formaldehyde, formic acid, methylated amines (e.g., mono-, di- and tri-methyl amine), methylated thiols, carbon dioxide, and various other reduced carbon compounds which lack any carbon-carbon bonds.
All C1 metabolizing microorganisms are generally classified as methylotrophs. Methylotrophs may be defined as any organism capable of oxidizing organic compounds that do not contain carbon-carbon bonds. However, facultative methylotrophs, obligate methylotrophs, and obligate methanotrophs are all various subsets of methylotrophs. Specifically:

    
    
        Facultative methylotrophs have the ability to oxidize organic compounds which do not contain carbon-carbon bonds, but may also use other carbon substrates such as sugars and complex carbohydrates for energy and biomass. Facultative methylotrophic bacteria are found in many environments, but are isolated most commonly from soil, landfill and waste treatment sites. Many facultative methylotrophs are members of the β and γ subgroups of the Proteobacteria (Hanson et al., Microb. Growth C1 Compounds., [Int. Symp.], 7th (1993), pp 285-302. Murrell, J. Collin and Don P. Kelly, eds. Intercept: Andover, UK; Madigan et al., Brock Biology of Microorganisms, 8th ed., Prentice Hall: Upper Saddle River, N.J. (1997)).
        Obligate methylotrophs are those organisms that are limited to the use of organic compounds that do not contain carbon-carbon bonds for the generation of energy.
        Obligate methanotrophs are those obligate methylotrophs that have the distinct ability to oxidize methane.
    
    


Additionally, the ability to utilize single carbon substrates is not limited to bacteria but extends also to yeasts and fungi. A number of yeast genera are able to use single carbon substrates as energy sources in addition to more complex materials (i.e., the methylotrophic yeasts).
Although a large number of these methylotrophic organisms are known, few of these microbes have been successfully harnessed in industrial processes for the synthesis of materials. And, although single carbon substrates are cost-effective energy sources, difficulty in genetic manipulation of these microorganisms as well as a dearth of information about their genetic machinery has limited their use primarily to the synthesis of native products.
Despite these hardships, many methanotrophs contain an inherent isoprenoid pathway which enables these organisms to synthesize pigments and provides the potential for one to envision engineering these microorganisms for production of other non-endogenous isoprenoid compounds. Since methanotrophs can use single carbon substrates (i.e., methane and/or methanol) as an energy source, it could be possible to produce carotenoids at low cost in these organisms. Examples wherein a methanotroph was engineered for production of β-carotene are described in U.S. Ser. No. 09/941,947 and U.S. Ser. No. 10/997,844; each hereby incorporated by reference.
In the present invention, methods are provided for the expression of genes involved in the biosynthesis of carotenoid compounds in microorganisms that are able to use single carbon substrates as a sole energy source. The host microorganism may be any C1 metabolizer that has the ability to synthesize farnesyl pyrophosphate (FPP) as a metabolic precursor for carotenoids. More specifically, facultative methylotrophic bacteria suitable in the present invention include, but are not limited to: Methylophilus, Methylobacillus, Methylobacterium, Hyphomicrobium, Xanthobacter, Bacillus, Paracoccus, Nocardia, Arthrobacter, Rhodopseudomonas, and Pseudomonas. Specific methylotrophic yeasts useful in the present invention include, but are not limited to: Candida, Hansenula, Pichia, Torulopsis, and Rhodotorula. And, exemplary methanotrophs are included in, but are not limited to, the genera Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylocyctis, Methylomicrobium, and Methanomonas. 
Of particular interest in the present invention are high growth obligate methanotrophs having an energetically favorable carbon flux pathway. For example, a specific strain of methanotroph has been reported having several pathway features that makes it particularly useful for carbon flux manipulation. This strain is known as Methylomonas sp. 16a (ATCC PTA 2402) (U.S. Pat. No. 6,689,601); and, this particular strain and other related methylotrophs are preferred microbial hosts for expression of the gene products of this invention, useful for the production of C40 carotenoids.
Methylomonas sp. 16a naturally produces C30 carotenoids. Odom et al. have reported that expression of C40 carotenoid genes in Methylomonas 16a produced a mixture of C30 and C40 carotenoids (U.S. Ser. No. 09/941,947). Several of the genes involved in C30 carotenoid production in this strain have been identified including (but not limited to) the crtN1, ald, crtN2, and crtN3 genes. Disruption of the crtN1/ald genes or the promoter driving expression of the crtN1/ald/crtN2 gene cluster created various non-pigmented mutants (“white mutants”) more suitable for C40 carotenoid production (U.S. Ser. No. 10/997,844).
Transformation of C1 Metabolizing Bacteria
Electroporation has been used successfully for the transformation of: Methylobacterium extorquens AM1 (Toyama, H., et al., FEMS Microbiol. Lett. 166: 1-7 (1998)), Methylophilus methylotrophus AS1 (Kim, C. S., and Wood, T. K., Appl. Microbiol. Biotechnol. 48: 105-108 (1997)), and Methylobacillus sp. strain 12S (Yoshida, T., et al., Biotechnol. Lett., 23: 787-791 (2001)). Extrapolation of specific electroporation parameters from one specific C1 metabolizing utilizing organism to another may be difficult, however, as is well to known to those of skill in the art.
Bacterial conjugation, relying on the direct contact of donor and recipient cells, is frequently more readily amenable for the transfer of genes into C1 metabolizing bacteria. Simplistically, this bacterial conjugation process involves mixing together “donor” and “recipient” cells in close contact with one another. Conjugation occurs by formation of cytoplasmic connections between donor and recipient bacteria, with direct transfer of newly synthesized donor DNA into the recipient cells. As is well known in the art, the recipient in a conjugation is defined as any cell that can accept DNA through horizontal transfer from a donor bacterium. The donor in conjugative transfer is a bacterium that contains a conjugative plasmid, conjugative transposon, or mobilizable plasmid. The physical transfer of the donor plasmid can occur in one of two fashions, as described below:

    
    
        In some cases, only a donor and recipient are required for conjugation. This occurs when the plasmid to be transferred is a self-transmissible plasmid that is both conjugative and mobilizable (i.e., carrying both tra genes and genes encoding the Mob proteins). In general, the process involves the following steps: 1.) Double-strand plasmid DNA is nicked at a specific site in oriT; 2.) A single-strand DNA is released to the recipient through a pore or pilus structure; 3.) A DNA relaxase enzyme cleaves the double-strand DNA at oriT and binds to a release 5′ end (forming a relaxosome as the intermediate structure); and 4.) Subsequently, a complex of auxiliary proteins assemble at oriT to facilitate the process of DNA transfer.
        Alternatively, a “triparental” conjugation is required for transfer of the donor plasmid to the recipient. In this type of conjugation, donor cells, recipient cells, and a “helper” plasmid participate. The donor cells carry a mobilizable plasmid or conjugative transposon. Mobilizable vectors contain an oriT, a gene encoding a nickase, and have genes encoding the Mob proteins; however, the Mob proteins alone are not sufficient to achieve the transfer of the genome. Thus, mobilizable plasmids are not able to promote their own transfer unless an appropriate conjugation system is provided by a helper plasmid (located within the donor or within a “helper” cell). The conjugative plasmid is needed for the formation of the mating pair and DNA transfer, since the plasmid encodes proteins for transfer (Tra) that are involved in the formation of the pore or pilus.
    
    


Examples of successful conjugations involving C1 metabolizing bacteria include the work of: Stolyar et al. (Mikrobiologiya 64(5): 686-691 (1995)); Motoyama et al. (Appl. Micro. Biotech. 42(1): 67-72 (1994)); Lloyd et al. (Archives of Microbiology 171(6): 364-370 (1999)); and Odom et al. (U.S. Ser. No. 09/941,947).
Recombinant Expression—Plants
Plants and algae are also known to produce carotenoid compounds. The nucleic acid fragments of the instant invention may be used to create transgenic plants having the ability to express the microbial protein. Preferred plant hosts will be any variety that will support a high production level of the instant proteins. Suitable green plants will include but are not limited to soybean, rapeseed (Brassica napus, B. campestris), pepper, sunflower (Helianthus annus), cotton (Gossypium hirsutum), corn, tobacco (Nicotiana tabacum), alfalfa (Medicago sativa), wheat (Triticum sp), barley (Hordeum vulgare), oats (Avena sativa, L), sorghum (Sorghum bicolor), rice (Oryza sativa), Arabidopsis, cruciferous vegetables (broccoli, cauliflower, cabbage, parsnips, etc.), melons, carrots, celery, parsley, tomatoes, potatoes, strawberries, peanuts, grapes, grass seed crops, sugar beets, sugar cane, beans, peas, rye, flax, hardwood trees, softwood trees, and forage grasses. Algal species include but not limited to commercially significant hosts such as Spirulina, Haemotacoccus, and Dunalliela. Production of the carotenoid compounds may be accomplished by first constructing chimeric genes of present invention in which the coding regions are operably linked to promoters capable of directing expression of a gene in the desired tissues at the desired stage of development. For reasons of convenience, the chimeric genes may comprise promoter sequences and translation leader sequences derived from the same genes. 3′ Non-coding sequences encoding transcription termination signals must also be provided. The instant chimeric genes may also comprise one or more introns in order to facilitate gene expression.
Any combination of any promoter and any terminator capable of inducing expression of a coding region may be used in the chimeric genetic sequence. Some suitable examples of promoters and terminators include those from nopaline synthase (nos), octopine synthase (ocs) and cauliflower mosaic virus (CaMV) genes. One type of efficient plant promoter that may be used is a high level plant promoter. Such promoters, in operable linkage with the genetic sequences or the present invention should be capable of promoting expression of the present gene product. High level plant promoters that may be used in this invention include the promoter of the small subunit (ss) of the ribulose-1,5-bisphosphate carboxylase from example from soybean (Berry-Lowe et al., J. Molecular and App. Gen., 1: 483-498 1982)), and the promoter of the chlorophyll a/b binding protein. These two promoters are known to be light-induced in plant cells (see, for example, Genetic Engineering of Plants, an Agricultural Perspective, A. Cashmore, Plenum, N.Y. (1983), pages 29-38; Coruzzi, G. et al., The Journal of Biological Chemistry, 258: 1399 (1983), and Dunsmuir, P. et al., Journal of Molecular and Applied Genetics, 2: 285 (1983)).
Plasmid vectors comprising the instant chimeric genes can then constructed. The choice of plasmid vector depends upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., EMBO J. 4: 2411-2418 (1985); De Almeida et al., Mol. Gen. Genetics 218: 78-86 (1989)), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA blots (Southern, J. Mol. Biol. 98, 503, (1975)), Northern analysis of mRNA expression (Kroczek, R. A., J. Chromatogr. Biomed. Appl., 618 (1-2): 133-145 (1993)), Western analysis of protein expression, or phenotypic analysis.
For some applications it will be useful to direct the instant proteins to different cellular compartments. It is thus envisioned that the chimeric genes described above may be further supplemented by altering the coding sequences to encode enzymes with appropriate intracellular targeting sequences such as transit sequences (Keegstra, K., Cell 56: 247-253 (1989)), signal sequences or sequences encoding endoplasmic reticulum localization (Chrispeels, J. J., Ann. Rev. Plant Phys. Plant Mol. Biol. 42: 21-53 (1991)), or nuclear localization signals (Raikhel, N., Plant Phys. 100: 1627-1632 (1992)) added and/or with targeting sequences that are already present removed. While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of utility may be discovered in the future that are useful in the invention.
In vitro Bio-Conversion of Carotenoids
Alternatively, it is possible to carry out the bioconversions of the present application in vitro. Where substrates for the present CrtO ketolases are not synthesized endogenously by the host cell it will be possible to add the substrate exogenously. In this aspect, the suitable carotenoid substrate may be solubilized with mild detergent (e.g., DMSO) or mixed with phospholipid vesicles. To assist in transport into the cell, the host cell may optionally be permeabilized with a suitable solvent such as toluene. Methods for this type of in vitro bio-conversion of carotenoid substrates has basis in the art (see for example: Hundle, B. S., et al., FEBS, 315: 329-334 (1993); and Bramley, P. M., et al., Phytochemistry, 26: 1935-1939 (1987)).
Protein Engineering CrtO Ketolases
The present CrtO ketolases were protein engineered using a combination of error-prone PCR ((Melnikov et al., Nucleic Acids Research, 27(4): 1056-1062 (1999); Leung et al., Techniques, 1: 11-15 (1989); and Zhou et al., Nucleic Acids Res. 19: 6052-6052 (1991)) and a gene shuffling technique (“recombinogenic extension method using unpaired primers”; (U.S. Ser. No. 10/374,366; hereby incorporated by reference). It is contemplated that the present crtO genes may be further engineered to produce gene products having further enhanced or altered activity. Various methods are known for mutating a native gene sequence to produce a gene product with altered or enhanced activity including, but not limited to: 1.) error-prone PCR; 2.) site-directed mutagenesis (Coombs et al., Proteins (1998), pp 259-311, 1 plate. Angeletti, Ruth Hogue, Ed., Academic: San Diego, Calif.); and 3.) “gene-shuffling” (U.S. Pat. No. 5,605,793; U.S. Pat. No. 5,811,238; U.S. Pat. No. 5,830,721; and U.S. Pat. No. 5,837,458 or any similar means of promoting recombinogenic activity between nucleic acids (U.S. Ser. No. 10/374,366)).
The method of gene shuffling is particularly attractive due to its facile implementation, high rate of mutagenesis, and ease of screening. The process of gene shuffling involves the restriction endonuclease cleavage of a gene of interest into fragments of specific size in the presence of additional populations of DNA fragments having regions of similarity or difference to the gene of interest. This pool of fragments will then be denatured and reannealed to create a mutated gene. The mutated gene is then screened for altered activity.
The instant microbial sequences of the present invention may be mutated and screened for altered or enhanced activity by this method. The sequences should be double-stranded and can be of various lengths ranging from 50 bp to 10 kB. The sequences may be randomly digested into fragments ranging from about 10 bp to 1000 bp, using restriction endonucleases well known in the art (Maniatis, supra). In addition to the instant microbial sequences, populations of fragments that are hybridizable to all or portions of the microbial sequence may be added. Similarly, a population of fragments that are not hybridizable to the instant sequences may also be added. Typically these additional fragment populations are added in about a 10 to 20-fold excess by weight as compared to the total nucleic acid. Generally, if this process is followed, the number of different specific nucleic acid fragments in the mixture will be about 100 to about 1000. The mixed population of random nucleic acid fragments are denatured to form single-stranded nucleic acid fragments and then reannealed. Only those single-stranded nucleic acid fragments having regions of homology with other single-stranded nucleic acid fragments will reanneal. The random nucleic acid fragments may be denatured by heating. One skilled in the art could determine the conditions necessary to completely denature the double-stranded nucleic acid. Preferably the temperature is from about 80° C. to 100° C. The nucleic acid fragments may be reannealed by cooling. Preferably the temperature is from about 20° C. to 75° C. Renaturation can be accelerated by the addition of polyethylene glycol (“PEG”) or salt. A suitable salt concentration may range from 0 mM to 200 mM. The annealed nucleic acid fragments are then incubated in the presence of a nucleic acid polymerase and dNTPs (i.e., dATP, dCTP, dGTP and dTTP). The nucleic acid polymerase may be the Klenow fragment, the Taq polymerase or any other DNA polymerase known in the art. The polymerase may be added to the random nucleic acid fragments prior to annealing, simultaneously with annealing or after annealing. The cycle of denaturation, renaturation and incubation in the presence of polymerase is repeated for a desired number of times. Preferably the cycle is repeated from about 2 to 50 times, more preferably the sequence is repeated from 10 to 40 times. The resulting nucleic acid is a larger double-stranded polynucleotide ranging from about 50 bp to about 100 kB and may be screened for expression and altered activity by standard cloning and expression protocols (Maniatis, supra).
Furthermore, a hybrid protein can be assembled by fusion of functional domains using the gene shuffling (exon shuffling) method (Nixon et al., Proc. Natl. Acad. Sci., 94: 1069-1073 (1997)). The functional domain of the instant gene can be combined with the functional domain of other genes to create novel enzymes with desired catalytic function. A hybrid enzyme may be constructed using PCR overlap extension methods and cloned into various expression vectors using the techniques well known to those skilled in art.
In addition to the methods exemplified above (which are designed to directly mutagenize the genes encoding CrtO ketolases), traditional methods of creating mutants could be utilized for the purposes described herein. For example, wild-type cells having CrtO ketolase activity may be exposed to a variety of agents such as radiation or chemical mutagens and then screened for the desired phenotype. When creating mutations through radiation either ultraviolet (UV) or ionizing radiation may be used. Suitable short wave UV wavelengths for genetic mutations will fall within the range of 200 nm to 300 nm, where 254 nm is preferred. UV radiation in this wavelength principally causes changes within nucleic acid sequence from guanidine and cytosine to adenine and thymidine. Since all cells have DNA repair mechanisms that would repair most UV induced mutations, agents such as caffeine and other inhibitors may be added to interrupt the repair process and maximize the number of effective mutations. Long wave UV mutations using light in the 300 nm to 400 nm range are also possible; but this range is generally not as effective as the short wave UV light, unless used in conjunction with various activators (such as psoralen dyes) that interact with the DNA. Likewise, mutagenesis with chemical agents is also effective for generating mutants and commonly used substances include chemicals that affect nonreplicating DNA (such as HNO2 and NH2OH), as well as agents that affect replicating DNA (such as acridine dyes, notable for causing frameshift mutations). Specific methods for creating mutants using radiation or chemical agents are well documented in the art. See, for example, Brock (supra) or Deshpande (supra).
Irrespective of the method of mutagenesis, a gene may be evolved such that the enzyme has an increase in ketolase activity. The increase in ketolase activity can be measured using a variety of techniques known in the art. In the present invention, a simple measurement of ketocarotenoid production in the presence of excess substrate (i.e. β-carotene) under essentially identical reaction conditions will typically be suitiable to identify enzymes capable of providing a higher percentage yield of a ketocarotenoid.
Preferred Codon Usage Table for Methylomonas sp. 16a
The preferred codon usage for Methylomonas sp. 16a (ATCC PTA-2402) has previously been reported (U.S. Ser. No. 10/997,844). Briefly, the genome of Methylomonas sp. 16a was sequenced and 201 highly-expressed Methylomonas genes, according to microarray analysis, were used to determine the preferred codon usage profile in Methylomonas sp. 16a, which is shown in Table 1. The coding regions of these genes, comprising 164,751 bp, were translated by the Editseq program of DNASTAR to the corresponding 54,917 amino acids. The column titled “Number” refers to the number of times a given codon encodes a particular amino acid in the sample of 54,917 amino acids. The column titled “Fraction” refers to the frequency that a given codon encodes a particular amino acid. The stop codons were not included in the coding regions for tabulation.
TABLE 1
Preferred Codon Usage Table for Methylomonas sp. 16a







TABLE 1







Preferred Codon Usage Table for Methylomonas sp. 16a












Amino Acid
Codon
Number
Fraction
















Gly
GGG
288.00
0.07



Gly
GGA
300.00
0.07



Gly
GGU
1168.00
0.27



Gly
GGC
2541.00
0.59



Glu
GAG
966.00
0.28



Glu
GAA
2514.00
0.72



Asp
GAU
1435.00
0.46



Asp
GAC
1712.00
0.54



Val
GUG
1287.00
0.32



Val
GUA
508.00
0.13



Val
GUU
717.00
0.18



Val
GUC
1450.00
0.37



Ala
GCG
1576.00
0.31



Ala
GCA
607.00
0.12



Ala
GCU
658.00
0.13



Ala
GCC
2279.00
0.45



Lys
AAG
1055.00
0.35



Lys
AAA
1988.00
0.65



Asn
AAU
877.00
0.40



Asn
AAC
1317.00
0.60



Met
AUG
1443.00
1.00



Ile
AUA
301.00
0.09



Ile
AUU
933.00
0.28



Ile
AUC
2122.00
0.63



Thr
ACG
544.00
0.19



Thr
ACA
263.00
0.09



Thr
ACU
380.00
0.13



Thr
ACC
1738.00
0.59



Trp
UGG
600.00
1.00



Cys
UGU
151.00
0.24



Cys
UGC
474.00
0.76



Tyr
UAU
779.00
0.52



Tyr
UAC
723.00
0.48



Phe
UUU
793.00
0.38



Phe
UUC
1308.00
0.62



Ser
AGU
317.00
0.10



Ser
AGC
868.00
0.27



Ser
UCG
733.00
0.23



Ser
UCA
318.00
0.10



Ser
UCU
291.00
0.09



Ser
UCC
701.00
0.22



Arg
AGG
186.00
0.06



Arg
AGA
287.00
0.09



Arg
CGG
411.00
0.13



Arg
CGA
250.00
0.08



Arg
CGU
693.00
0.22



Arg
CGC
1292.00
0.41



Gln
CAG
893.00
0.40



Gln
CAA
1345.00
0.60



His
CAU
635.00
0.51



His
CAC
600.00
0.49



Leu
UUG
1825.00
0.38



Leu
UUA
319.00
0.07



Leu
CUG
1980.00
0.41



Leu
CUA
172.00
0.04



Leu
CUU
221.00
0.05



Leu
CUC
277.00
0.06



Pro
CCG
1104.00
0.44



Pro
CCA
443.00
0.18



Pro
CCU
441.00
0.18



Pro
CCC
520.00
0.21










The preferred codon usage for Methyolmonas was used to codon optimize all (or at least a portion of) the coding sequence of the crtO ketolase genes used for error-prone PCR (crtO303, SEQ ID NO: 4; crtO319, SEQ ID NO: 3; and crtO320 (SEQ ID NO: 6).

Accordingly, using the above described methods a number of mutants of crtO ketolase genes were created and screened for activity. Useful mutants had at least one of the following mutations based on the crtO ketolase from Rhodococcus erythropolis AN12 (SEQ ID NO:2):

    
    
        a) a replacement of threonine at amino acid position 121 with alanine;
        b) a replacement of methionine at amino acid position 142 with leucine;
        c) a replacement of alanine at amino acid position 164 with valine;
        d) a replacement of isoleucine at amino acid position 2 with valine;
        e) a replacement of threonine at amino acid position 304 with lysine;
        f) a replacement of arginine at amino acid position 339 with glutamine;
        g) a replacement of arginine at amino acid position 519 with tryptophan; and
        h) a replacement of glutamine at amino acid position 524 with leucine or arginine.
    
    


A preferred mutant had the following mutations based on the crtO ketolase from Rhodococcus erythropolis AN12 (SEQ ID NO:2):

    
    
        a) a replacement of methionine at amino acid position 142 with leucine; and
        b) a replacement of alanine at amino acid position 164 with valine.
    
    


The specific mutant amino acid sequences corresponding are given here in as SEQ ID NO: 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, and 52.
EXAMPLES
The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions.
General Methods
Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by Maniatis (supra), Silhavy et al. (supra), and Ausubel et al. (supra).
Materials and methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following examples may be found as set out in Manual of Methods for General Bacteriology (Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds), American Society for Microbiology, Washington, D.C. (1994)) or by Brock (supra). All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wis.), DIFCO Laboratories/BD Diagnostics (Sparks, Md.), Promega (Madison, Wis.), New England Biolabs (Beverly, Mass.), GIBCO/BRL Life Technologies (Carlsbad, Calif.), or Sigma Chemical Company (St. Louis, Mo.) unless otherwise specified.
XL1-Blue MRF′ Electroporation-Competent E. coli cells (Catalog No. 200158) were purchased from Stratagene (La Jolla, Calif.).
PCR reactions were run on GeneAMP PCR System 9700 using Amplitaq or Amplitaq Gold enzymes (PE Applied Biosystems, Foster City, Calif.), unless otherwise specified. The cycling conditions and reactions were standardized according to the manufactures' instructions. The meaning of abbreviations is as follows: “min” means minute(s), “h” means hour(s), “μL” means microliter, “mL” means milliliters, “L” means liters, “cm” means centimeters, “nm” means nanometers, “mM” means millimolar, “kb” means kilobases, and “kV” means kilovolts.
Example 1
Making Mutant libraries
Error-Prone PCR
The gene encoding the carotene ketolase enzyme (CrtO) from Rhodococcus erythropolis AN12 was cloned by PCR (U.S. Ser. No. 10/209,372; hereby incorporated by reference). The coding sequence of the wild-type R. erythropolisAN12 crtO is approximately 1600 bp (SEQ ID NO: 1) encoding the amino acid sequence represented by SEQ ID NO: 2. It should be noted that the start codon for all of the present crtO coding sequences was changed from GTG (as found in the wild type R. erythropolis AN12 coding sequence) to ATG to facilitate expression. Three constructs, pDCQ319, pDCQ303 and pDCQ320 were created and used as templates for error-prone PCR.
Briefly, plasmids pDCQ303, pDCQ319, and pDCQ320 were prepared by cloning variants of crtO genes into the unique Mfel site of pDCQ301 downsteam of crtE gene, which contains the crtEYIB genes from Pantoea stewartii (ATCC8199) in the pBHR1 vector (MoBiTec GmbH, Goettingen, Germany) for β-carotene synthesis. The unique Mfel site of pDCQ301 was introduced in the junction of crtE and crtY genes when removing the crtX gene in the original crtEXYIB cluster. The three plasmids pDCQ303, pDCQ319 and pDCQ320 all contain crtEOYIB gene cluster cloned under the Pcat promoter in pBHR1 vector. The crtO gene in each construct was confirmed to be expressed in the same orientation as the crtEYIB genes.
Plasmid pDCQ319 contained a codon modified R. erythropolis AN12 crtO (“crtO319”). The entire codon usage of crtO319 (SEQ ID NOs: 3) was optimized for Methylomonas sp. 16a (Table 1). The crtO319 gene was synthesized by GenScript Corp. (Scotch Plains, N.J.).
Plasmid pDCQ303 also contained a partially codon optimized version of the R. erythropolis AN12 crtO denoted as “crtO303” (SEQ ID NOs: 4 and 5). CrtO303 is different from crtO319 in that only several codons on the 5′- and 3′-ends of crtO303 introduced by PCR primers were optimized for Methylomonas 16a. Compared with natural crtO gene product from Rhodococcus erythropolis AN12, crtO303 contains three additional amino acids (Met-Ala-Leu) at its N-terminus (SEQ ID NO: 5).
Plasmid pDCQ320 contained a partially codon optimized version of R. erythropolis AN12 crtO denoted as “crtO320”. The coding sequence of crtO320 (SEQ ID NO: 6) construct is the same as the coding sequence for crtO303 except that the three additional amino acids (Met-Ala-Leu) have been removed from the N-terminus.
The various crtO genes (crtO303, crtO319, and crtO320) were removed from the construct using MfeI and XbaI digestion. Three random mutant libraries targeting the entire crtO gene were made for all three constructs. The following primers were used to amplify the inserts by error-prone PCR:









for pDCQ319:




crtO-For


(5′-AGCCAATTGAAGGAGGAATAAACCATG-3′)
(SEQ ID NO:7)


crtO-Rev


(5′-GCGAATTCCTCTAGATTAGCTACGGCT-3′)
(SEQ ID NO:8)


 


for pDCQ303:


crtO900-For


5′-TAACAATTGAAGGAGGAATAAACCATGGCC-3′
(SEQ ID NO:9)


crtO303-Rev


5′-GCGAATTCCTCTAGATCACGAGCGGCTCGA-3′
(SEQ ID NO:10)


 


for pDCQ320:


320-F1


5′-GCCATTAGCCAGACCGGCA-3′
(SEQ ID NO:11)


320-R1


5′-GCGCCTGGCCAGTGAACA-3′
(SEQ ID NO:12)






A Clontech mutagenesis kit (Clontech Laboratories, Inc., Palo Alto, Calif.) was used for performing error-prone PCR. The following conditions described in Table 2 were used for preparing the error-prone PCR reaction mixture:








TABLE 2







Condition for Error-prone PCR using Clontech Mutagenesis Kit










Volumes (μL)













Condition-1
Condition-2















PCR grade water
38
37



10x AdvanTaq Plus Buff.
5
5



MnSO4 (8 mM)
2
3



dGTP (2 mM)
1
1



50x Diversify dNTP Mix
1
1



Primer mix
1
1



Template DNA
1
1



AdvanTaq Plus Polym.
1
1










Condition-1 was used for crtO319 and crtO303 libraries, and Condition-2 was for the crtO320 library. The thermal cycling reaction was carried out according to the manufacturer's instructions. The 1.6 kb PCR products were digested with MfeI and XbaI, and ready for ligation. The mutants exhibiting red-orange color found from the crtO320 mutant library were further mutagenezied, and the resulting 1.6 kb DNA fragments were digested with MfeI and XbaI.

Mutant Library Construction

To prepare the vector, the template plasmids (pDCQ303, pDCQ319 and pDCQ320) were digested with MfeI and XbaI to remove the crtO insert. The digested vector was purified from the agarose gel. The Mfe I and XbaI-digested error-prone PCR products were then ligated with the MfeI/XbaI-digested vectors. After ethanol precipitation, the ligation mixture was ready for the transformation.
The ligation mixture was first transformed into XL1-Blue MRF′ Electroporation-Competent E. coli cells (Stratagene, La Jolla, Calif.) by electroporation. After growing the mutant library cells in liquid or Agar LB containing kanamycin, the plasmids were isolated from the library cells.
E. coli strain WS210 was used for the mutant library construction. E. coli strain WS210 contains the same chromsomal modifications found in E. coli strain WS208 (ATCC PTA-4823; U.S. Ser. No. 10/735,442, hereby incorporated by reference), a strain capable of producing up to 6000 ppm β-carotene. WS210 is genetically identical to WS208 except for the fact that the β-carotene expression plasmid found in WS208 (pDCQ108) has been removed.
First, the electroporation-competent WS210 cells were made. Overnight cell culture (2.5 mL) was added to 500 mL of LB broth in a 2-L sterile flask. The culture was incubated at 37° C. on the shaker until the OD600nm reached 0.5 to 0.8. The cells were then incubated on ice for 10 min, followed by the centrifugation at 4° C. for 10 min. After washing the cell pellet once with 500 mL ice-cold water, the cells were resuspended in 1-2 mL of 10% ice-cold glycerol. Aliquots (50 μL) were made in sterile Eppendorf tubes and immediately frozen on dry ice. The competent cells were stored at −80° C. To do the transformation, 1 μL of mutant library plasmids isolated from E. coli XL1-Blue cells was added to 40 μL of competent cells, and the sample was transferred into electroporation cuvette with 0.1 cm gap. The voltage used for electroporation was 1.7 kV/cm. The cells were plated onto LB plates in the presence of kanamycin (50 μg/mL) and incubated overnight at 37° C. The mutant colonies were ready for high throughput screening.
Dna Sequence Analysis of the Mutant Libraries
Ten mutant colonies from each library were randomly picked for DNA sequencing analyses. The mutant genes were sequenced on an ABI 377 automated sequencer (Applied Biosystems, Foster City, Calif.), and the data managed using Vector NTI Version 7.0 program (InforMax, Inc., Bethesda, Md.). Most of the mutations were base substitution. The frequency of deletion and insertion mutations in the mutant libraries was very low. Many types of base substitution were present in these mutants, indicating that there was no bias for the mutation type. The mutation rate was 1-5 point mutations per kb. The enzyme activity distribution was estimated by the color of the mutant colonies (see Example 2). The results showed that about 40-60% of the mutants in the library were active.
Example 2
Screening the Mutant Libraries and Identifying the Hits
Cells producing β-carotene are yellow, and the color of the cells producing canthaxanthin are red-orange. The cells that make different amounts of canthaxanthin show slightly different coloration. Therefore, the mutant colonies that produce different amounts of canthaxanthin can be distinguished by the eye. Approximately 20,000-150,000 mutant colonies from each library were visually screened. The putative “hits” were streaked on Agar plates, and ranked based on their pigmentation.
HPLC analysis was used to confirm the percentage of canthaxanthin produced. Briefly, Cells were grown in LB with 50 μg/mL kanamycin at 37° C. shaking overnight. Cells were pelleted by centrifugation at 4000 g for 15 min, and the cell pellets were extracted with 10 mL acetone. The extraction was dried under nitrogen and redisolved in 1-2 mL of acetone. The extraction was filtered with an Acrodisc® CR25 mm syringe filter (Pall Corporation, Ann Arbor, Mich.). It was then analyzed using an Agilent Series 1100 LC/MSD Si (Agilent, Foster City, Calif.).
Sample (20 μL) was loaded onto a 150 mm×4.6 mm ZORBAX C18 (3.5 μm particles) column (Agilent Technologies, Inc.). The column temperature was kept at 40° C. The flow rate was 1 mL/min, while the solvent running program used was

    
    
        0-2 min: 95% buffer A and 5% buffer B;
        2-10 min: linear gradient from 95% buffer A and 5% buffer B to 60% buffer A and 40% buffer B;
        10-12 min: linear gradient from 60% buffer A and 40% buffer B to 50% buffer A and 50% buffer B;
        12-18 min: 50% buffer A and 50% buffer B; and,
        18-20 min: 95% buffer A and 5% buffer B.
    
    


Buffer A was 95% acetonitrile and 5% dH2O; buffer B was 100% tetrahydrofuran.
The peaks were identified based on comparisons of retention time, absorption spectra and molecular weight with those of the synthetic standards purchased from CaroteNature (Lupsingen, Switzerland). The percentage of canthaxanthin was calculated as the area of the canthaxanthin peak divided by the area of the total carotenoid peaks.
Table 3 summarizes the follow-up assay results for the hits:







TABLE 3







Confirmation results of the hits











Percentage Yield



Strain
of Canthaxanthin














CrtO319(starting gene)
4.05



319M3022
14.9



CrtO303(starting gene)
5.9



303M3044
16.0



CrtO320(starting gene)
20.0



320M4019
46.3



320M4018
44.4



320M4006
43.4



320M4007
43.7



320M4027
39.5



320M4020
43.1



320M4036
41.2



320M4023
40.1



320M4009
45.8



320M4032
36.7



320SHU019
91.4



320SHU001
88.9



320SHU017
88.9



320SHU016
78.4



320SHU015
68.3



320SHU008
59.0



320SHU022
57.7



320SHU004
55.7







The cells were grown for 75 h at 30° C. in LB medium in the presence of kanamycin (50 μg/mL).






Table 3 shows that the percentage yield of canthaxanthin for the mutant gene products has been greatly improved. For example, compared with the starting gene crtO319, the mutant 319M3022 gene product showed a significant increase in percentage yield of canthaxanthin. Similar results were also obtained for the mutant (303M3044) from the crtO303 library. Several mutants from crtO320 library showed more than 40% of canthaxathin yield. Many mutants created using error-prone PCR (“first round mutants”) exhibited a significant improvement in canthaxanthin yield. A second round of mutagenesis was performed using a gene shuffling technique in order to further improve canthaxanthin yield (U.S. Ser. No. 10/374,366). Many of the mutants (320SHU001-320SHU022) made from the improved first round mutants showed a significant improvement for their percentage yield of canthaxanthin. The mutants 320SHU001 and 320SHU019 exhibit an improvement in the percentage of canthaxanthin yield of approximately 90% yield (Table 3). Under the current screening system, the performance of crtO gene product has significantly been improved.
Example 3
DNA Sequence Analysis of the Mutant Genes
The mutant genes were sequenced on an ABI377 automated sequencer (Applied Biosystem, Foster City, Calif.), and the data managed using Vector NTI program (InforMax, Inc., Bethesda, Md.). Analysis of the mutants, followed by comparison with the wild type gene, indicated that the mutant genes contained the following point mutations:







TABLE 4







DNA Sequence Analysis of Mutant Genes









Strain (crtO NT




and AA SEQ ID Nos.)
Mutations











319M3022
GCC(Ala3) to ACC(Thr)


(SEQ ID NOs. 13 and 14)


 


303M3044
AGC(Ser5) to CGC(Arg)


(SEQ ID NOs. 15 and 16)
ACG(Thr498) to ACA(Thr)


 


320M4006
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 17 and 18)
TCG(Ser449) to ACG(Thr)


 


320M4007
CTC(Leu17) to CTT(Leu)


(SEQ ID NOs. 19 and 20)
GCA(Ala24) to GCT(Ala)



TGC(Cys112) to TAC(Tyr)



GCG(Ala252) to ACG(Thr)



CAG(Gln524) to CGG(Arg)


 


320M4009
AGC(Ser2) to AGA(Arg)


(SEQ ID NOs. 21 and 22)
ACG(Thr37) to ATG(Met)



CGA(Arg117) to CGT(Arg)



CCC(Pro444) to CCA(Pro)



AGT(Ser505) to AGC(Ser)


 


320m4018
CGA(Arg117) to CGT(Arg)


(SEQ ID NOs. 23 and 24)
GTC(Val133) to GTA(Val)



ACA(Thr147) to TCA(Ser)



CTG(Leu224) to CTT(Leu)



TCA(Ser464) to ACA(Thr)



CCC(Pro497) to CCT(Pro)


 


320M4019
AGC(Ser2) to AAC(Asn)


(SEQ ID NOs. 25 and 26)
AGT(Ser67) to AAT(Asn)



TTT(Phe145) to TCT(Ser)



CGA(Arg302) to CGG(Arg)



GAC(Asp446) to GGC(Gly)


 


320M4020
ATG(Met142) to TTG(Leu)


(SEQ ID NOs. 27 and 28)
GCG(Ala164) to GTG(Val)



ATC(Ile283) to GTC(Val)


 


320M4023
AGC(Ser2) to AGA(Arg)


(SEQ ID NOs. 29 and 30)
GAC(Asp36) to GAT(Asp)



GAT(Asp293) to GGT(Gly)


 


320M4027
TCC(Ser331) to TCT(Ser)


(SEQ ID NOs. 31 and 32)
CGG(Arg519) to TGG(Trp)


 


320M4031
GAA(Glu208) to GAG(Glu)


(SEQ ID NOs. 33 and 34)
ACG(Thr304) to AAG(Lys)



CCT(Pro369) to CCC(Pro)



GCC(Ala509) to GCT(Ala)



CAG(Gln524) to CTG(Leu)



TCG(Ser529) to TGG(Trp)


 


320M4032
GCG(Ala16) to GGG(Gly)


(SEQ ID NOs. 33 and 34)
TTG(Leu240) to CTG(Leu)



GAA(Glu276) to GAG(Glu)



TTT(Phe428) to TAT(Tyr)


 


320M4036
AGC(Ser2) to AGT(Ser)


(SEQ ID NOs. 35 and 36)
GCA(Ala180) to GCG(Ala)



GCG(Ala252) to ACG(Thr)



TCG(Ser264) to CCG(Pro)



CAT(His407) to CAA(Gln)


 


320SHU001
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 37 and 38)
GCA(Ala24) to GCC(Ala)



ATG(Met142) to TTG(Leu)



GCG(Ala164) to GTG(Val)



ACG(Thr304) to AAG(Lys)



GTG(Leu477) to TTG(Leu)



CGG(Arg519) to TGG(Trp)


 


320SHU004
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 39 and 40)
TCC(Ser331) to TCT(Ser)



CGG(Arg519) to TGG(Trp)


 


320SHU008
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 41 and 42)
GCA(Ala24) to GCC(Ala)



GTC(Val131) to GTT(Val)



ATG(Met142) to TTG(Leu)



GCG(Ala164) to GTG(Val)



ATC(Ile283) to GTC(Val)


 


320SHU015
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 43 and 44)
TCG(Ser152) to TTG(Leu)



TCC(Ser331) to TCT(Ser)



CGG(Arg519) to TGG(Trp)


 


320SHU016
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 45 and 46)
GCA(Ala24) to GCC(Ala)



ACA(Thr121) to GCA(Ala)



ATG(Met142) to TTG(Leu)



GCG(Ala164) to GTG(Val)



ATC(Ile283) to GTC(Val)



GCC(Ala509) to GCT(Ala)



CAG(Gln524) to CTG(Leu)


 


320SHU017
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 47 and 48)
GCA(Ala24) to GCC(Ala)



ATG(Met142) to TTG(Leu)



GCG(Ala164) to GTG(Val)



ATC(Ile283) to GTC(Val)



CGG(Arg519) to TGG(Trp)


 


320SHU019
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 49 and 50)
GCA(Ala24) to GCC(Ala)



ATG(Met142) to TTG(Leu)



CTG(Leu161) to CTA(Leu)



GCG(Ala164) to GTG(Val)



CGG(Arg339) to CAG(Gln)



CCT(Pro369) to CCC(Pro)



CGG(Arg519) to TGG(Trp)


 


320SHU022
GCG(Ala16) to GCA(Ala)


(SEQ ID NOs. 51 and 52)
GCA(Ala24) to GCC(Ala)



ATG(Met142) to TTG(Leu)



GCG(Ala164) to GTG(Val)



ATC(Ile283) to GTC(Val)



CAG(Gln524) to CGG(Arg)









Except for the silent mutations, all the mutations were amino acid substitutions (Table 4). Some of the mutations have been observed in many mutants, such as ATG(Met142) to TTG(Leu), GCG(Ala164) to GTG(Val), ATC(Ile283) to GTC(Val), CGG(Arg519) to TGG(Trp), CAG(Gln524) to CGG(Arg), GCG(Ala16) to GCA(Ala), and GCA(Ala24) to GCC(Ala). In particular, two mutations (Met142 to Leu and Ala164 to Val) were found in many of the mutant exhibiting particularly high yields of ketocarcarotenoids, namely, 320SHU001, 320SHU008, 320SHU016, 320SHU017, 320SHU019, 320SHU022, and 320M4020 (Table 3). This observation suggests that these sites, and possibly the regions around these sites, are important regions for the crtO gene's improvement of bioproduction of canthaxanthin.
Example 4
Performance of Mutant Genes in Methylomonas sp. 16a
Some of the improved crtO mutants have been tested their performance in Methylomonas sp. 16a. The plasmids containing the mutant genes in WS210 host E. coli cells were incorporated into Methylomonas 16a through conjugation as described previously (U.S. 60/527,083; hereby incorporated by reference). Methylomonas sp. 16a (ATCC PTA-2402) cells expressing the mutant crtO genes were then grown in “BTZ-3” medium, and the amounts of canthaxanthin produced were analyzed by HPLC as previously described (Table 7). The standard gas phase for cultivation contains 25% methane in air.
Briefly, Methylomonas 16a strains expressing various crtO mutants on the present invention were grown in serum stoppered Wheaton bottles (Wheaton Scientific, Wheaton Ill.) using a gas/liquid ratio of at least 8:1 (i.e., 20 mL of Nitrate liquid “BTZ-3” media in 160 mL total volume) at 30° C. with constant shaking.
Nitrate liquid medium, also referred to herein as “defined medium” or “BTZ-3” medium was comprised of various salts mixed with Solution 1 as indicated below (Tables 5 and 6) or where specified the nitrate was replaced with 15 mM ammonium chloride. Solution 1 provides the composition for 100-fold concentrated stock solution of trace minerals.







TABLE 5







Solution 1*














Conc.





MW
(mM)
g per L
















Nitriloacetic acid
191.1
66.9
12.8



CuCl2 × 2H2O
170.48
0.15
0.0254



FeCl2 × 4H2O
198.81
1.5
0.3



MnCl2 × 4H2O
197.91
0.5
0.1



CoCl2 × 6H2O
237.9
1.31
0.312



ZnCl2
136.29
0.73
0.1



H3BO3
61.83
0.16
0.01



Na2MoO4 × 2H2O
241.95
0.04
0.01



NiCl2 × 6H2O
237.7
0.77
0.184







*Mix the gram amounts designated above in 900 mL of H2O, adjust to pH = 7, and add H2O to an end volume of 1 L. Keep refrigerated.













TABLE 6







Nitrate liquid medium (BTZ-3)**














Conc.





MW
(mM)
g per L
















NaNO3
84.99
10
 0.85



KH2PO4
136.09
3.67
0.5



Na2SO4
142.04
3.52
0.5



MgCl2 × 6H2O
203.3
0.98
0.2



CaCl2 × 2H2O
147.02
0.68
0.1



1 M HEPES (pH 7)
238.3

50 mL



Solution 1


10 mL







**Dissolve in 900 mL H2O. Adjust to pH = 7, and add H2O to give 1 L.



For agar plates: Add 15 g of agarose in 1 L of medium, autoclave, let cool down to 50° C., mix, and pour plates.






Table 7 summarizes the percentage yield of canthaxanthin in Methylomonas strains expressing the present crtO mutants:







TABLE 7







Percentage Yields of Canthaxanthin in Methylomonas sp. 16a











Percentage yield



Strain
of Canthaxanthin







CrtO319 (starting gene)
3-9%



CrtO303 (starting gene)
 7-15%



CrtO320 (starting gene)
15-21%



320M4019
38-40%



320SHU001
45-53%



320SHU019
44-51%










These results indicate that the performance of the mutant crtO genes of the present invention has been greatly improved when compared with the starting genes. However, the absolute percentage yield of canthaxanthin in Methylomonas 16a was generally less than that in E. coli (Table 3). There could be many reasons for this observation. For example, the fermentation condition was not optimized for these mutant crtO genes; or the microenvironment inside the cell was different between E. coli and Methylomonas 16a. Since the percentage yield of canthaxanthin in E. coli for some of the mutants (e.g. 320SHU001 and 320SHU019) has almost been optimized, the further improvement of these mutant genes should be carried out in Methylomonas 16a.

## Claims

1. An isolated nucleic acid molecule encoding a polypeptide having carotenoid ketolase activity, the polypeptide having the amino acid sequence set forth in SEQ ID NO:2, wherein the polypeptide has an amino acid substitution selected from the group consisting of:
a) a replacement of threonine at amino acid position 121 of SEQ ID NO:2 with alanine;
b) a replacement of methionine at amino acid position 142 of SEQ ID NO:2 with leucine;
c) a replacement of alanine at amino acid position 164 of SEQ ID NO:2 with valine;
d) a replacement of isoleucine at amino acid position 283 of SEQ ID NO:2 with valine;
e) a replacement of threonine at amino acid position 304 of SEQ ID NO:2 with lysine;
f) a replacement of arginine at amino acid position 339 of SEQ ID NO:2 with glutamine;
g) a replacement of arginine at amino acid position 519 of SEQ ID NO:2 with tryptophan;
h) a replacement of glutamine at amino acid position 524 of SEQ ID NO:2 with leucine or arginine; and
i) a combination thereof.

2. An isolated nucleic acid molecule encoding a polypeptide having carotenoid ketolase activity, the polypeptide having the amino acid sequence set forth in SEQ ID NO:2, wherein the polypeptide has an amino acid substitution selected from the group consisting of:
a) a replacement of methionine at amino acid position 142 of SEQ ID NO:2 with leucine;
b) a replacement of alanine at amino acid position 164 of SEQ ID NO:2 with valine; and
c) a combination thereof.

3. An isolated nucleic acid molecule encoding a carotenoid ketolase enzyme having an amino acid sequence selected from the group consisting SEQ ID NO: 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 44, 46, 48, 50, and 52.

4. The isolated nucleic acid molecule of claim 3 selected from the group consisting of SEQ ID NO: 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, and 51.

5. A chimeric gene comprising the isolated nucleic acid molecule of claims 1 or 3 operably linked to suitable regulatory sequences.

6. A transformed host cell comprising the isolated nucleic acid molecule of claims 1 or 3.

7. The transformed host cell of claim 6 wherein the host cell is selected from the group consisting of bacteria, yeast, filamentous fungi, algae, and green plants.

8. The transformed host cell of claim 7 wherein the host cell is selected from the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Phaffia, Candida, Hansenula, Salmonella, Bacillus, Acinectorbacter, Zymomonas, Agrobacterium, Erythrobacter, Chloroborium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Methanomonas, Synechococcus, Anabeana, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus.

9. The transformed host cell of claim 8 wherein the host cell is selected from the group consisting of Escherichia and Methylomonas.

10. The transformed host cell of claim 9 wherein the host cell is selected from the group consisting of Escherichia coli and Methylomonas sp. 16a (ATCC PTA-2402).

11. The transformed host cell of claim 7 where the host cell is selected from the group consisting of soybean, rapeseed, pepper, sunflower, cotton, corn, tobacco, alfalfa, wheat, barley, oats, sorghum, rice, Arabidopsis, cruciferous vegetables, melons, carrots, celery, parsley, tomatoes, potatoes, strawberries, peanuts, grapes, sugar beets, sugar cane, beans, peas, rye, flax, hardwood trees, softwood trees, and forage grasses.

12. A method for the production of cyclic ketocarotenoid compounds comprising:
a) providing a host cell which produces monocyclic or bicyclic carotenoids;
b) transforming the host cell with the isolated nucleic acid molecule of either of claims 1 or 3 encoding a carotenoid ketolase enzyme;
c) growing the transformed host cell of (b) under conditions whereby a cyclic ketocarotenoid is produced; and
d) optionally isolating the ketocarotenoid produced in step c).

13. A method according to claim 12 wherein the cyclic ketocarotenoid compounds are selected from the group consisting of canthaxanthin, astaxanthin, adonixanthin, adonirubin, echinenone, 3-hydroxyechinenone, 3′-hydroxyechinenone, 4-keto-γ-carotene, 4-keto-rubixanthin, 4-keto-torulene, 3-hydroxy-4-keto-torulene, deoxyflexixanthin, and myxobactone.

14. A method according to claim 13 wherein the monocyclic or bicyclic carotenoids are selected from the group consisting of β-carotene, γ-carotene, zeaxanthin, rubixanthin, echinenone, and torulene.

15. A method according to claim 12 wherein the host cell is selected from the group consisting of bacteria, yeast, filamentous fungi, algae, and green plants.

16. A method according to claim 15 wherein the transformed host cell is selected from the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Phaffia, Candida, Hansenula, Salmonella, Bacillus, Acinectorbacter, Zymomonas, Agrobacterium, Erythrobacter, Chloroborium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Methanomonas, Synechococcus, Anabeana, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus.

17. The method according to claim 16 wherein the transformed host cell is selected from the group consisting of Escherichia and Methylomonas.

18. A method according to claim 17 wherein the transformed host cell is selected from the group consisting of Escherichia coli and Methylomonas sp. 16a (ATCC PTA 2402).

19. A method according to claim 15 wherein the host cell is selected from the group consisting of soybean, rapeseed, pepper, sunflower, cotton, corn, tobacco, alfalfa, wheat, barley, oats, sorghum, rice, Arabidopsis, cruciferous vegetables, melons, carrots, celery, parsley, tomatoes, potatoes, strawberries, peanuts, grapes, sugar beets, sugar cane, beans, peas, rye, flax, hardwood trees, softwood trees, and forage grasses.

20. A method of altering cyclic ketocarotenoid biosynthesis in an organism comprising,
(a) introducing into a host cell the isolated nucleic acid molecule of either of claims 1 or 3 encoding a carotenoid ketolase; and
(b) growing the host cell of (a) under conditions whereby the carotenoid ketolase gene is expressed and cyclic ketocarotenoid biosynthesis is altered.

21. A method according to claim 20 wherein the isolated nucleic acid molecule encodes a polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO: 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 44, 46, 48, 50, and 52.

22. A method according to claim 20 wherein the isolated nucleic acid molecule is upregulated.

23. A method according to claim 20 wherein the isolated nucleic acid molecule is over-expressed on a multicopy plasmid.

24. A method according to claim 20 wherein the isolated nucleic acid molecule is operably linked to an inducible or regulated promoter.