Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/52—Genes encoding for enzymes or proenzymes
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
  • C12N9/10—Transferases (2.)
  • C12N9/1025—Acyltransferases (2.3)
  • C12N9/1029—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
  • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
  • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
  • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
  • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
  • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
  • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
  • C12N15/8247—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving modified lipid metabolism, e.g. seed oil composition

Definitions

• the present invention is directed to plant acyltransferase-like nucleic acid and amino acid sequences and constructs, and methods related to their use in altering sterol composition and/or content, and oil composition and/or content in host cells and plants.
• Sterol biosynthesis branches from the farnesyl diphosphate intermediate in the isoprenoid pathway. Sterol biosynthesis occurs via a mevalonate dependent pathway in mammals and higher plants (Goodwin,(1981) Biosynthesis oflsoprenoid Compounds, vol
• Sterol O-acyltransferase enzymes such as acyl CoA:cholesterol acyltransferase (ACAT) and lecithinxholesterol acyltransferase (LCAT) catalyze the formation of cholesterol esters, and thus are key to controlling the intracellular cholesterol storage.
• ACAT acyl CoA:cholesterol acyltransferase
• LCAT lecithinxholesterol acyltransferase
• acyltransferase proteins The characterization of various acyltransferase proteins is useful for the further study of plant sterol synthesis systems and for the development of novel and/or alternative sterol sources. Studies of plant mechanisms may provide means to further enhance, control, modify, or otherwise alter the sterol composition of plant cells. Furthermore, such alterations in sterol content and/or composition may provide a means for obtaining tolerance to stress and insect damage. Of particular interest are the nucleic acid sequences of genes encoding proteins which may be useful for applications in genetic engineering.
• the present invention is directed to lecithinxholesterol acyltransferase-like polypeptides (also referred to herein as LCAT) and acyl CoAxholesterol acyltransferase- like polypeptides (also referred to herein as ACAT).
• LCAT lecithinxholesterol acyltransferase-like polypeptides
• ACAT acyl CoAxholesterol acyltransferase- like polypeptides
• the invention is related to polynucleotides encoding such sterohacyltransferases, polypeptides encoded by such polynucleotides, and the use of such polynucleotides to alter sterol composition and oil production.
• the polynucleotides ofthe present invention include those derived from plant sources.
• One aspect ofthe invention is an isolated nucleic acid sequence encoding a plant lecithinxholesterol acyltransferase-like polypeptide, a fragment of a plant lecithinxholesterol acyltransferase-like polypeptide, a plant acyl CoAxholesterol acyltransferase-like polypeptide or a fragment of a plant acyl CoAxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence consisting essentially of SEQ ID NO: 2, 4, 6, 8, 10-29, 43-51, 73 or 75. Also provided is an isolated nucleic acid sequence consisting of SEQ ID NO: 2, 4, 6, 8, 10-29, 43-51, 73 or 75.
• Still another aspect provides an isolated nucleic acid sequence comprising a polynucleotide selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO: 3 or SEQ ID NO: 3 with at least one conservative amino acid substitution; SEQ ID NO: 2; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 2; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 2; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 2 and encodes a plant lecithinxholesterol acyltransferase-like polypeptide.
• Still another aspect provides an isolated nucleic acid sequence consisting essentially of a polynucleotide ofthe formula 5' X-(R 1 ) n -(R 2 ) n -(R 3 ) n -Y 3' where X is a hydrogen, Y is a hydrogen or a metal, R, and R 2 are any nucleic acid, n is an integer between 0-3000, and R 2 is selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO: 3 or SEQ ID NO: 3 with at least one conservative amino acid substitution; SEQ ID NO: 2; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 2; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 2; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleot
• Another aspect provides an isolated nucleic acid sequence comprising a polynucleotide selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO:5 or SEQ ID NO: 5 with at least one conservative amino acid substitution; SEQ ID NO: 4; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 4; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 4; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 4 and encodes a plant lecithinxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence consisting essentially of a polynucleotide ofthe formula 5' X-(R 1 ) n -(R 2 ) n -(R 3 ) n -Y 3' where X is a hydrogen, Y is a hydrogen or a metal, R ; and R 2 are any nucleic acid, n is an integer between 0-3000, and R 2 is selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO: 5 or SEQ ID NO: 5 with at least one conservative amino acid substitution; SEQ ID NO: 4; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 4; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 4; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleot
• Another aspect provides an isolated nucleic acid sequence comprising a polynucleotide selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO:7 or SEQ ID NO: 7 with at least one conservative amino acid substitution; SEQ ID NO: 6; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 6; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 6; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 6 and encodes a plant lecithinxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence consisting essentially of a polynucleotide ofthe formula 5' X-(R,) n -(R 2 ) n -(R 3 ) n -Y 3' where X is a hydrogen, Y is a hydrogen or a metal, R j and R 2 are any nucleic acid, n is an integer between 0-3000, and R 2 is selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO: 7 or SEQ ID NO: 7 with at least one conservative amino acid substitution; SEQ ID NO: 6; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 6; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 6; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide
• Another aspect provides an isolated nucleic acid sequence comprising a polynucleotide selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO:9 or SEQ ID NO: 9 with at least one conservative amino acid substitution; SEQ ID NO: 8; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 8; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 8; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 8 and encodes a plant lecithinxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence consisting essentially of a polynucleotide ofthe formula 5' X-(R 1 ) n -(R 2 ) n -(R 3 ) n -Y 3' where X is a hydrogen, Y is a hydrogen or a metal, R, and R 2 are any nucleic acid, n is an integer between 0-3000, and R 2 is selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO: 9 or SEQ ID NO: 9 with at least one conservative amino acid substitution; SEQ ID NO: 8; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95%o sequence identity with SEQ ID NO: 8; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 8; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleot
• Another aspect provides an isolated nucleic acid sequence comprising a polynucleotide selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO:74 or SEQ ID NO: 74 with at least one conservative amino acid substitution; SEQ ID NO: 73; an isolated polynucleotide that has at least 70%, 80%, 90%), or 95%) sequence identity with SEQ ID NO: 73; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 73; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 73 and encodes a plant lecithinxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence consisting essentially of a polynucleotide ofthe formula 5' X-(R,) n -(R 2 ) n -(R 3 ) n -Y 3' where X is a hydrogen, Y is a hydrogen or a metal, R [ and R 2 are any nucleic acid, n is an integer between 0-3000, and
• R 2 is selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO: 74 or SEQ ID NO: 74 with at least one conservative amino acid substitution; SEQ ID NO: 73; an isolated polynucleotide that has at least 70%, 80%, 90%), or 95% sequence identity with SEQ ID NO: 73; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 73; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 73 and encodes a plant lecithinxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence comprising a polynucleotide selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO:76 or SEQ ID NO: 76 with at least one conservative amino acid substitution; SEQ ID NO: 75; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95%o sequence identity with SEQ ID NO: 75; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 75; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 75 and encodes a plant lecithinxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence consisting essentially of a polynucleotide ofthe formula 5' X-(R,) n -(R 2 ) n -(R 3 ) n -Y 3' where X is a hydrogen, Y is a hydrogen or a metal, R, and R 2 are any nucleic acid, n is an integer between 0-3000, and R 2 is selected from the group consisting of an isolated polynucleotide encoding a polypeptide of SEQ ID NO: 76 or SEQ ID NO: 76 with at least one conservative amino acid substitution; SEQ ID NO: 75; an isolated polynucleotide that has at least 70%, 80%, 90%), or 95% sequence identity with SEQ ID NO: 75; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 75; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleot
• Another aspect provides an isolated nucleic acid sequence comprising a polynucleotide selected from the group consisting of SEQ ID NO: 42 or a degenerate variant thereof; an isolated polynucleotide that has at least 70%, 80%, 90%, or 95% sequence identity with SEQ ID NO: 42; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 42; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 42 and encodes an acyl CoAxholesterol acyltransferase-like polypeptide.
• Another aspect provides an isolated nucleic acid sequence consisting essentially of a polynucleotide ofthe formula 5' X-(R 1 ) n -(R 2 ) n -(R 3 ) n -Y 3' where X is a hydrogen, Y is a hydrogen or a metal, Ri and R 2 are any nucleic acid, n is an integer between 0-3000, and R 2 is selected from the group consisting of SEQ ID NO: 42 or a degenerate variant thereof; an isolated polynucleotide that has at least 70%, 80%), 90%, or 95% sequence identity with SEQ ID NO: 42; an isolated polynucleotide of at least 10 amino acids that hybridizes under stringent conditions to SEQ ID NO: 42; an isolated polynucleotide complementary to any ofthe foregoing; and an isolated polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 42 and encodes a acyl CoAxholesterol acyl
• a recombinant nucleic acid construct comprising a regulatory sequence operably linked to a polynucleotide encoding a lecithinxholesterol acyltransferase-like polypeptide and/or an acyl CoAxholesterol acyltransferase-like polypeptide.
• the sterol acyl transferases are plant sterol acyl transferases.
• the recombinant nucleic acid constructs further comprises a termination sequence.
• the regulatory sequence can be a constitutive promoter, an inducible promoter, a developmentally regulated promoter, a tissue specific promoter, an organelle specific promoter, a seed specific promoter or a combination of any ofthe foregoing.
• a plant containing this recombinant nucleic acid construct and the seed and progeny from such a plant can also be introduced into a suitable host cell to provide yet another aspect of the invention. If the host cell is a plant host cell, the cell can be used to generate a plant to provide another aspect ofthe invention. Further aspects include seed and progeny from such a plant.
• Yet another aspect is a purified polypeptide comprising, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 74, SEQ ID NO: 76, or any ofthe preceding sequences with at least one conservative amino acid substitution.
• Still another aspect provides a purified immunogenic polypeptide comprising at least 10 consecutive amino acids from an amino acid sequence selected from the group consisting of SEQ ID NO: 3, 5, 7, 9, 74, 76 and any ofthe preceding sequences containing at least one conservative amino acid substitution. Also provided are antibodies, either polyclonal or monoclonal, that specifically bind the preceding immunogenic polypeptides.
• One aspect provides a method for producing a lecithinxholesterol acyltransferase- like polypeptide or an acyl CoAxholesterol acyltransferase-like polypeptide comprising culturing a host cell containing any recombinant nucleic acid construct ofthe present invention under condition permitting expression of said lecithinxholesterol acyltransferase-like polypeptide or acyl CoAxholesterol acyltransferase-like polypeptide.
• Another aspect provides a method for modifying the sterol content of a host cell, comprising transforming a host cell with a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding a lecithinxholesterol acyltransferase-like polypeptide and culturing said host cell under conditions wherein said host cell expresses a lecithinxholesterol acyltransferase-like polypeptide such that said host cell has a modified sterol composition as compared to host cells without the recombinant construct.
• An additional aspect is a method for modifying the sterol content of a host cell comprising transforming a host cell with a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding an acyl CoAxholesterol acyltransferase-like polypeptide and culturing said host cell under conditions wherein said host cell expresses an acyl CoAxholesterol acyltransferase-like polypeptide such that said host cell has a modified sterol composition as compared to host cells without the recombinant construct.
• a further aspect is a plant comprising a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding a lecithinxholesterol acyltransferase-like polypeptide wherein expression of said recombinant construct results in modified sterol composition of said plant as compared to the same plant without said recombinant construct.
• Another aspect provides a plant comprising a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding an acyl CoAxholesterol acyltransferase-like polypeptide wherein expression of said recombinant construct results in modified sterol composition of said plant as compared to the same plant without said recombinant construct.
• an oil obtained from any ofthe plants or host cells of the present invention.
• a method for producing an oil with a modified sterol composition comprising providing any ofthe plants or host cells ofthe present invention and extracting oil from the plant by any known method. Also provided is an oil produced by the preceding method.
• Still another aspect provides a method for altering oil production by a host cell comprising, transforming a host cell with a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding a lecithinxholesterol acyltransferase-like polypeptide and culturing the host cell under conditions wherein the host cell expresses a lecithinxholesterol acyltransferase-like polypeptide such that the host cell has an altered oil production as compared to host cells without the recombinant construct.
• Another aspect provides a method for altering oil production by a host cell comprising, transforming a host cell with a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding an acyl CoAxholesterol acyltransferase-like polypeptide and culturing the host cell under conditions wherein the host cell expresses an acyl CoAxholesterol acyltransferase-like polypeptide such that the host cell has an altered oil production as compared to host cells without the recombinant construct.
• a plant comprising a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding a lecithinxholesterol acyltransferase-like polypeptide wherein expression of said recombinant construct results in an altered production of oil by said plant as compared to the same plant without said recombinant construct.
• a plant comprising a recombinant construct containing a regulatory sequence operably linked to a polynucleotide encoding an acyl CoAxholesterol acyltransferase-like polypeptide wherein expression of said recombinant construct results in an altered production of oil by said plant as compared to the same plant without said recombinant construct.
• Additional aspects provide a food, food ingredient or food product comprising any oil, plant or host cell ofthe present invention; a nutritional or dietary supplement comprising any oil, plant or host cell ofthe present invention; and a pharmaceutical composition comprising any oil, plant or host cell ofthe present invention along with a suitable diluent, carrier or excipient.
• Figure 1 shows an alignment of yeast, human and rat lecithinxholesterol acyltransferase protein sequences with Arabidopsis LCATl, LCAT2, LCAT3, and LCAT4 deduced amino acid sequences.
• Figure 2 shows the results of NMR sterol ester analysis on T2 seed from plant expressing LCAT4 under the control ofthe napin promoter (pCGN9998).
• Figure 3 shows the results of HPLC/MS sterol analysis on oil extracted from T2 seed from control lines (pCGN8640) and lines expressing LCAT3 (pCGN9968) under the control ofthe napin promoter.
• Figure 4 shows the results of HPLC/MS sterol analysis on oil extracted from T2 seed from control lines (pCGN8640), and plant line expressing LCATl (pCGN9962), LCAT2 (pCGN9983), LCAT3 (pCGN9968), and LCAT4 (pCGN9998) under the control ofthe napin promoter. Additionally, data from 3 lines expressing LCAT4 under the control ofthe 35S promoter (pCGN9996) are shown.
• Figure 5 shows the results of Nir analysis ofthe oil content of T2 seed from control lines (pCGN8640), and plant lines expressing LCATl (pCGN9962), LCAT2
• lecithinxholesterol acyltransferase particularly the isolated nucleic acid sequences encoding lecithinxholesterol-like polypeptides (LCAT) from plant sources and acyl CoAxholesterol: acyltransferase, particularly the isolated nucleic acid sequences encoding acyl CoAxholesterol acyltransferase-like polypeptides (ACAT) from plant sources.
• Lecithinxholesterol acyltransferase-like as used herein includes any nucleic acid sequence encoding an amino acid sequence from a plant source, such as a protein, polypeptide or peptide, obtainable from a cell source, which demonstrates the ability to utilize lecithin (phosphatidyl choline) as an acyl donor for acylation of sterols or glycerides to form esters under enzyme reactive conditions along with such proteins polypeptides and peptides.
• a plant source such as a protein, polypeptide or peptide
• Acyl CoAxholesterol acyltransferase-like as used herein includes any nucleic acid sequence encoding an amino acid sequence from a plant source, such as a protein, polypeptide or peptide, obtainable from a cell source, which demonstrates the ability to utilize acyl CoA as an acyl donor for acylation of sterols or glycerides to form esters under enzyme reactive conditions along with such proteins polypeptides and peptides.
• enzyme reactive conditions is meant that any necessary conditions are available in an environment (i.e., such factors as temperature, pH, lack of inhibiting substances) which will permit the enzyme to function.
• sterol refers to any chiral tetracyclic isopentenoid which may be formed by cyclization of squalene oxide through the transition state possessing stereochemistry similar to the trans-syn-trans-anti-trans-anti configuration, for example, protosteroid cation, and which retains a polar group at C-3 (hydroxyl or keto), an all-trans-anti stereochemistry in the ring system, and a side-chain 20R-conf ⁇ guration (Parker, et al. (1992) In Nes, et al, Eds., Regulation of Isopentenoid Metabolism, ACS Symposium Series No. 497, p. 110; American Chemical Society, Washington, D.C.). Sterols may or may not contain a C-5-C-6 double bond, as this is a feature introduced late in the biosynthetic pathway. Sterols contain a C 8 -C 10 side chain at the C-17 position.
• phytosterol which applies to sterols found uniquely in plants, refers to a sterol containing a C-5, and in some cases a C-22, double bond. Phytosterols are further characterized by alkylation ofthe C-17 side-chain with a methyl or ethyl substituent at the C-24 position.
• Major phytosterols include, but are not limited to, sitosterol, stigmasterol, campesterol, brassicasterol, etc.
• Cholesterol which lacks a C-24 methyl or ethyl side- chain, is found in plants, but is not unique thereto, and is not a "phytosterol.”
• phytostanols are saturated forms of phytosterols wherein the C-5 and, when present, C-22 double bond(s) is (are) reduced, and include, but are not limited to, sitostanol, campestanol, and 22-dihydrobrassicastanol.
• Steps are further characterized by the presence of a fatty acid or phenolic acid moiety rather than a hydroxyl group at the C-3 position.
• sterol includes sterols, phytosterols, phytosterol esters, phytostanols, and phytostanol esters.
• sterol compounds includes sterols, phyotsterols, phytosterol esters, phytostanols, and phytostanol esters.
• phytosterol compound refers to at least one phytosterol, at least one phytosterol ester, or a mixture thereof.
• phytostanol compound refers to at least one phytostanol, at least one phytostanol ester, or a mixture thereof.
• glycolide refers to a fatty acid ester of glycerol and includes mono-, di-, and tri- acylglycerols.
• recombinant construct is defined either by its method of production or its structure. In reference to its method of production, e.g., a product made by a process, the process is use of recombinant nucleic acid techniques, e.g., involving human intervention in the nucleotide sequence, typically selection or production. Alternatively, in terms of structure, it can be a sequence comprising fusion of two or more nucleic acid sequences which are not naturally contiguous or operatively linked to each other
• regulatory sequence means a sequence of DNA concerned with controlling expression of a gene; e.g. promoters, operators and attenuators.
• a "heterologous regulatory sequence” is one which differs from the regulatory sequence naturally associated with a gene.
• polynucleotide and “oligonucleotide” are used interchangeably and mean a polymer of at least two nucleotides joined together by a phosphodiester bond and may consist of either ribonucleotides or deoxynucleotides.
• sequence means the linear order in which monomers appear in a polymer, for example, the order of amino acids in a polypeptide or the order of nucleotides in a polynucleotide.
• polypeptide As used herein, "polypeptide” , “peptide”, and “protein” are used interchangeably and mean a compound that consist of two or more amino acids that are linked by means of peptide bonds.
• the terms “complementary” or “complementarity” refer to the pairing of bases, purines and pyrimidines, that associate through hydrogen bonding in double stranded nucleic acids. For example, the following base pairs are complementary: guanine and cytosine; adenine and thymine; and adenine and uracil. The terms, as used herein, include complete and partial complementarity.
• a first aspect ofthe present invention relates to isolated LCAT polynucleotides.
• the polynucleotide sequences ofthe present invention include isolated polynucleotides that encode the polypeptides ofthe invention having a deduced amino acid sequence selected from the group of sequences set forth in the Sequence Listing and to other polynucleotide sequences closely related to such sequences and variants thereof.
• the invention provides a polynucleotide sequence identical over its entire length to each coding sequence as set forth in the Sequence Listing.
• the invention also provides the coding sequence for the mature polypeptide or a fragment thereof, as well as the coding sequence for the mature polypeptide or a fragment thereof in a reading frame with other coding sequences, such as those encoding a leader or secretory sequence, a pre-, pro-, or prepro- protein sequence.
• the polynucleotide can also include non-coding sequences, including for example, but not limited to, non-coding 5' and 3' sequences, such as the transcribed, untranslated sequences, termination signals, ribosome binding sites, sequences that stabilize mRNA, introns, polyadenylation signals, and additional coding sequence that encodes additional amino acids.
• non-coding sequences including for example, but not limited to, non-coding 5' and 3' sequences, such as the transcribed, untranslated sequences, termination signals, ribosome binding sites, sequences that stabilize mRNA, introns, polyadenylation signals, and additional coding sequence that encodes additional amino acids.
• a marker sequence can be included to facilitate the purification ofthe fused polypeptide.
• Polynucleotides ofthe present invention also include polynucleotides comprising a structural gene and the naturally associated sequences that control gene expression.
• the invention also includes polynucleotides ofthe formula:
• X-(R,) n -(R 2 )-(R 3 ) n -Y wherein, at the 5' end, X is hydrogen, and at the 3' end, Y is hydrogen or a metal, R, and R 3 are any nucleic acid residue, n is an integer between 0 and 3000, preferably between 1 and 1000 and R 2 is a nucleic acid sequence ofthe invention, particularly a nucleic acid sequence selected from the group set forth in the Sequence Listing and preferably SEQ ID
• R 2 is oriented so that its 5' end residue is at the left, bound to R,, and its 3' end residue is at the right, bound to R 3 .
• Any stretch of nucleic acid residues denoted by either R group, where R is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer.
• the invention also relates to variants ofthe polynucleotides described herein that encode for variants ofthe polypeptides ofthe invention. Variants that are fragments ofthe polynucleotides ofthe invention can be used to synthesize full-length polynucleotides of the invention.
• Preferred embodiments are polynucleotides encoding polypeptide variants wherein 5 to 10, 1 to 5, 1 to 3, 2, 1 or no amino acid residues of a polypeptide sequence of the invention are substituted, added or deleted, in any combination. Particularly preferred are substitutions, additions, and deletions that are silent such that they do not alter the properties or activities ofthe polynucleotide or polypeptide.
• polynucleotide encoding a polypeptide ofthe invention and polynucleotides that are complementary to such polynucleotides. More preferable are polynucleotides that comprise a region that is at least 80% identical over its entire length to a polynucleotide encoding a polypeptide ofthe invention and polynucleotides that are complementary thereto.
• polynucleotides at least 90% identical over their entire length are particularly preferred, those at least 95% identical are especially preferred.
• those with at least 97% identity are highly preferred and those with at least 98% and 99% identity are particularly highly preferred, with those at least 99%> being the most highly preferred.
• Preferred embodiments are polynucleotides that encode polypeptides that retain substantially the same biological function or activity as determined by the methods described herein as the mature polypeptides encoded by the polynucleotides set forth in the Sequence Listing.
• the invention further relates to polynucleotides that hybridize to the above- described sequences.
• the invention relates to polynucleotides that hybridize under stringent conditions to the above-described polynucleotides.
• An example of stringent hybridization conditions is overnight incubation at 42°C in a solution comprising 50% formamide, 5x SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt's solution, 10% dextran sulfate, and 20 micrograms/milliliter denatured, sheared salmon sperm DNA, followed by washing the hybridization support in O.lx SSC at approximately 65°C.
• polynucleotides that hybridize under a wash stringency of 0.1X SSC or 0.1X SSPE (at 50°C.
• Other hybridization and wash conditions are well known and are exemplified in Sambrook, et al, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, NY (1989), particularly Chapter 11.
• the invention also provides a polynucleotide consisting essentially of a polynucleotide sequence obtainable by screening an appropriate library containing the complete gene for a polynucleotide sequence set for in the Sequence Listing under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence or a fragment thereof; and isolating said polynucleotide sequence.
• Nucleic acid sequences useful for obtaining such a polynucleotide include, for example, probes and primers as described herein and in particular SEQ ID NO: 2, 4, 6, 8, 10-29, 33, 42-51, 73 and 75.
• sequences are particularly useful in screening libraries obtained from Arabidopsis, soybean and corn for sequences encoding lecithinxholesterol acyltransferase and lecithinxholesterol acyltransferase-like polypeptides and for screening libraries for sequences encoding acyl CoAxholesterol acyl transferase and acyl CoAxholesterol acyl transferase-like polypeptides.
• polynucleotides ofthe invention can be used as a hybridization probe for RNA, cDNA, or genomic DNA to isolate full length cDNAs or genomic clones encoding a polypeptide and to isolate cDNA or genomic clones of other genes that have a high sequence similarity to a polynucleotide set forth in the Sequence Listing and in particular SEQ ED NO: 2, 4, 6, 8, 10-29, 33, 42-51, 73 and 75.
• Such probes will generally comprise at least 15 bases.
• probes will have at least 30 bases and can have at least 50 bases.
• Particularly preferred probes will have between 30 bases and 50 bases, inclusive.
• each gene that comprises or is comprised by a polynucleotide sequence set forth in the Sequence Listing may be isolated by screening using a DNA sequence provided in the Sequence Listing to synthesize an oligonucleotide probe.
• a labeled oligonucleotide having a sequence complementary to that of a gene ofthe invention is then used to screen a library of cDNA, genomic DNA or mRNA to identify members ofthe library which hybridize to the probe.
• synthetic oligonucleotides are prepared which correspond to the LCAT EST sequences.
• the oligonucleotides are used as primers in polymerase chain reaction (PCR) techniques to obtain 5' and 3' terminal sequence of LCAT genes.
• oligonucleotides of low degeneracy can be prepared from particular LCAT peptides
• such probes may be used directly to screen gene libraries for LCAT gene sequences.
• screening of cDNA libraries in phage vectors is useful in such methods due to lower levels of background hybridization.
• a LCAT sequence obtainable from the use of nucleic acid probes will show 60-70% sequence identity between the target LCAT sequence and the encoding sequence used as a probe.
• lengthy sequences with as little as 50-60% sequence identity may also be obtained.
• the nucleic acid probes may be a lengthy fragment ofthe nucleic acid sequence, or may also be a shorter, oligonucleotide probe.
• Oligonucleotide probes can be considerably shorter than the entire nucleic acid sequence encoding an LCAT enzyme, but should be at least about 10, preferably at least about 15, and more preferably at least about 20 nucleotides. A higher degree of sequence identity is desired when shorter regions are used as opposed to longer regions. It may thus be desirable to identify regions of highly conserved amino acid sequence to design oligonucleotide probes for detecting and recovering other related LCAT genes. Shorter probes are often particularly useful for polymerase chain reactions (PCR), especially when highly conserved sequences can be identified. (See, Gould, et al., PNAS USA (1989) 55:1934-1938.).
• PCR polymerase chain reactions
• LCAT polypeptides include isolated polypeptides set forth in the Sequence Listing, as well as polypeptides and fragments thereof, particularly those polypeptides which exhibit LCAT activity and also those polypeptides which have at least 50%, 60% or 70%> identity, * preferably at least 80%> identity, more preferably at least 90%> identity, and most preferably at least 95% identity to a polypeptide sequence selected from the group of sequences set forth in the Sequence Listing, and also include portions of such polypeptides, wherein such portion ofthe polypeptide preferably includes at least 30 amino acids and more preferably includes at least 50 amino acids.
• Identity is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences.
• identity also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as determined by the match between strings of such sequences.
• Identity 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, New York (1988); Biocomputing: Informatics and Genome Projects, Smith, D.W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A.M.
• Computer programs which can be used to determine identity between two sequences include, but are not limited to, GCG (Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984); suite of five BLAST programs, three designed for nucleotide sequences queries (BLASTN, BLASTX, and TBLASTX) and two designed for protein sequence queries (BLASTP and TBLASTN) (Coulson, Trends in Biotechnology, 2: 16- 80 (1994); Birren, et al, Genome Analysis, 1: 543-559 (1997)).
• the BLAST X program is publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al, NCBI NLM NLH, Bethesda, MD 20894; Altschul, S., et al., J. Mol Biol, 215:403-410 (1990)).
• the well known Smith Waterman algorithm can also be used to determine identity.
• Parameters for polypeptide sequence comparison typically include the following: Algorithm: Needleman and Wunsch, J. Mol. Biol. 48:443-453 (1970) Comparison matrix: BLOSSUM62 from Hentikoff and Hentikoff, Proc. Natl. Acad. Sci USA 89:10915-10919 (1992) Gap Penalty: 12 Gap Length Penalty: 4
• the invention also includes polypeptides ofthe formula: X-(R,) n -(R 2 )-(R 3 ) n -Y wherein, at the amino terminus, X is hydrogen, and at the carboxyl terminus, Y is hydrogen or a metal, R, and R 3 are any amino acid residue, n is an integer between 0 and 1000, and R 2 is an amino acid sequence ofthe invention, particularly an amino acid sequence selected from the group set forth in the Sequence Listing and preferably SEQ ID NOs: 3, 5, 7, 9, 74 and 76.
• R 2 is oriented so that its amino terminal residue is at the left, bound to R quarant and its carboxy terminal residue is at the right, bound to R 3 .
• Any stretch of amino acid residues denoted by either R group, where R is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer.
• Polypeptides ofthe present invention include isolated polypeptides encoded by a polynucleotide comprising a sequence selected from the group of a sequence contained in SEQ ID NOs: 2, 4, 6, 8, 73 and 75.
• polypeptides ofthe present invention can be mature protein or can be part of a fusion protein.
• a fragment is a variant polypeptide which has an amino acid sequence that is entirely the same as part but not all ofthe amino acid sequence ofthe previously described polypeptides.
• the fragments can be "free-standing" or comprised within a larger polypeptide of which the fragment forms a part or a region, most preferably as a single continuous region.
• Preferred fragments are biologically active fragments which are those fragments that mediate activities ofthe polypeptides ofthe invention, including those with similar activity or improved activity or with a decreased activity.
• polypeptides and polypeptide fragments that are antigenic or immunogenic in an animal, particularly a human and antibodies, either polyclonal or monoclonal that specifically bind the antigenic fragments.
• antigenic or immunogenic fragments comprise at least 10 consecutive amino acids from the amino acid sequences disclosed herein or such sequences with at least one conservative amino acid substitution.
• such antigenic or immunogenic fragments comprise at least 15, at least 25, at least 50 or at least 100 consecutive amino acids from the amino acid sequences disclosed herein or such sequences with at least one conservative amino acid substitution.
• Variants ofthe polypeptide also include polypeptides that vary from the sequences set forth in the Sequence Listing by conservative amino acid substitutions, substitution of a residue by another with like characteristics.
• modifications in the amino acid sequence of a peptide, polypeptide, or protein can result in equivalent, or possibly improved, second generation peptides, etc., that display equivalent or superior functional characteristics when compared to the original amino acid sequence.
• the present invention accordingly encompasses such modified amino acid sequences. Alterations can include amino acid insertions, deletions, substitutions, truncations, fusions, shuffling of subunit sequences, and the like, provided that the peptide sequences produced by such modifications have substantially the same functional properties as the naturally occurring counterpart sequences disclosed herein.
• hydropathic index of amino acids One factor that can be considered in making such changes is the hydropathic index of amino acids.
• the importance ofthe hydropathic amino acid index in conferring interactive biological function on a protein has been discussed by Kyte and Doolittle ( J. Mol. Biol, 157: 105-132, 1982). It is accepted that the relative hydropathic character of amino acids contributes to the secondary structure ofthe resultant protein. This, in turn, affects the interaction ofthe protein with molecules such as enzymes, substrates, receptors, DNA, antibodies, antigens, etc.
• each amino acid has been assigned a hydropathic index as follows: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (- 0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate/glutamine/aspartate/asparagine (-3.5); lysine (-3.9); and arginine (-4.5).
• amino acids in a peptide or protein can be substituted for other amino acids having a similar hydropathic index or score and produce a resultant peptide or protein having similar biological activity, i.e., which still retains biological functionality.
• amino acids having hydropathic indices within ⁇ 2 are substituted for one another. More preferred substitutions are those wherein the amino acids have hydropathic indices within ⁇ 1. Most preferred substitutions are those wherein the amino acids have hydropathic indices within ⁇ 0.5.
• Like amino acids can also be substituted on the basis of hydrophilicity.
• 4,554,101 discloses that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property ofthe protein.
• the following hydrophilicity values have been assigned to amino acids: arginine/lysine (+3.0); aspartate/glutamate (+3.0 ⁇ 1); serine (+0.3); asparagine/glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 ⁇ 1); alanine/histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine/isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); and tryptophan (-3.4).
• amino acids having hydropathic indices within ⁇ 2 are preferably substituted for one another, those within ⁇ 1 are more preferred, and those within ⁇ 0.5 are most preferred.
• amino acid substitutions in the peptides ofthe present invention can be based on the relative similarity ofthe amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, etc.
• Exemplary substitutions that take various ofthe foregoing characteristics into consideration in order to produce conservative amino acid changes resulting in silent changes within the present peptides, etc. can be selected from other members ofthe class to which the naturally occurring amino acid belongs.
• Amino acids can be divided into the following four groups: (1) acidic amino acids; (2) basic amino acids; (3) neutral polar amino acids; and (4) neutral non- polar amino acids.
• amino acids within these various groups include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, cystine, tyrosine, asparagine, and glutamine; and (4) neutral non-polar amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. It should be noted that changes which are not expected to be advantageous can also be useful if these result in the production of functional sequences.
• variants that are fragments ofthe polypeptides ofthe invention can be used to produce the corresponding full length polypeptide by peptide synthesis. Therefore, these variants can be used as intermediates for producing the full-length polypeptides ofthe invention.
• the polynucleotides and polypeptides ofthe invention can be used, for example, in the transformation of host cells, such as plant cells, animal cells, yeast cells, bacteria, bacteriophage, and viruses, as further discussed herein.
• the invention also provides polynucleotides that encode a polypeptide that is a mature protein plus additional amino or carboxyl-terminal amino acids, or amino acids within the mature polypeptide (for example, when the mature form ofthe protein has more than one polypeptide chain).
• Such sequences can, for example, play a role in the processing of a protein from a precursor to a mature form, allow protein transport, shorten or lengthen protein half-life, or facilitate manipulation ofthe protein in assays or production. It is contemplated that cellular enzymes can be used to remove any additional amino acids from the mature protein.
• a precursor protein, having the mature form ofthe polypeptide fused to one or more prosequences may be an inactive form ofthe polypeptide.
• the inactive precursors generally are activated when the prosequences are removed. Some or all ofthe prosequences may be removed prior to activation.
• Such precursor protein are generally called proproteins.
• nucleotide sequences in recombinant DNA constructs to direct the transcription or transcription and translation (expression) ofthe acyltransferase sequences ofthe present invention in a host cell.
• polynucleotide sequences ofthe present invention in recombinant DNA constructs to direct the transcription or transcription and translation (expression) ofthe acyltransferase sequences ofthe present invention in a host plant cell.
• the expression constructs generally comprise a regulatory sequence functional in a host cell operably linked to a nucleic acid sequence encoding a lecithinxholesterol acyltransferase-like polypeptide or acyl CoAxholesterol acyltransferase-like polypeptide ofthe present invention and a transcriptional termination region functional in a host plant cell.
• promoters also referred to as transcriptional initiation regions
• promoters which are functional in plant cells, and have been described in the literature including constitutive, inducible, tissue specific, organelle specific, developmentally regulated and environmentally regulated promoters. Chloroplast and plastid specific promoters, chloroplast or plastid functional promoters, and chloroplast or plastid operable promoters are also envisioned.
• promoters are constitutive promoters such as the CaMV35S or FMV35S promoters that yield high levels of expression in most plant organs. Enhanced or duplicated versions ofthe CaMV35S and FMV35S promoters are useful in the practice of this invention (Odell, et al. (1985) Nature 313:810-812; Rogers, U.S. Patent Number 5,378, 619).
• Other useful constitutive promoters include, but are not limited to, the mannopine synthase (mas) promoter, the nopaline synthase (nos) promoter, and the octopine synthase (ocs) promoter.
• Useful inducible promoters include heat-shock promoters (Ou-Lee et al. (1986)
• tissue-specific, developmentally-regulated promoters include fruit-specific promoters such as the E4 promoter (Cordes et al. (1989) Plant Cell 1:1025), the E8 promoter (Deikman et al. (1988) EMBO J. 7: 3315), the kiwifruit actinidin promoter (Lin et al. (1993) PNAS 90: 5939), the 2A11 promoter (Houck et al., U.S. Patent 4,943,674), and the tomato pZ130 promoter (U.S. Patents 5,175, 095 and 5,530,185); the ⁇ -conglycinin 7S promoter (Doyle et al. (1986) J. Biol. Chem.
• seed-specific promoters include, but are not limited to, the napin, phaseolin, zein, soybean trypsin inhibitor, 7S, ADR12, ACP, stearoyl-ACP desaturase, oleosin, Lasquerella hydroxylase, and barley aldose reductase promoters (Bartels (1995) Plant J. 1: 809-822), the EA9 promoter (U.S. Patent 5,420,034), and the Bce4 promoter (U.S. Patent 5,530,194).
• Useful embryo-specific promoters include the corn globulin 1 and oleosin promoters.
• Useful endosperm-specific promoters include the rice glutelin-1 promoter, the promoters for the low-pi ⁇ amylase gene (Amy32b) (Rogers et al. (1984) J. Biol. Chem. 259: 12234), the high-pi ⁇ amylase gene (Amy 64) (Khurseed et al. (1988) J. Biol. Chem. 263: 18953), and the promoter for a barley thiol protease gene ("Aleurain”) (Whittier et al. (1987) Nucleic Acids Res. 15 : 2515).
• nucleic acid sequences ofthe present invention from transcription initiation regions which are preferentially expressed in a plant seed tissue.
• seed preferential transcription initiation sequences include those sequences derived from sequences encoding plant storage protein genes or from genes involved in fatty acid biosynthesis in oilseeds.
• promoters include the 5' regulatory regions from such genes as napin (Kridl et al, Seed Sci. Res. 7:209:219 (1991)), phaseolin, zein, soybean trypsin inhibitor, ACP, stearoyl-ACP desaturase, soybean ⁇ ' subunit of ⁇ -conglycinin (soy 7s, (Chen et al, Proc. Natl. Acad.
• Promoter hybrids can also be constructed to enhance transcriptional activity (Hoffman, U.S. Patent No. 5,106,739), or to combine desired transcriptional activity and tissue specificity.
• CTP chloroplast transit peptides
• PTP plastid transit peptides
• the expression construct will additionally contain a gene encoding a transit peptide to direct the gene of interest to the plastid.
• the chloroplast transit peptides may be derived from the gene of interest, or may be derived from a heterologous sequence having a CTP.
• Such transit peptides are known in the art. See, for example, Von Heijne et al. (1991) Plant Mol. Biol. Rep. 9:104-126; Clark et al. (1989) J. Biol. Chem. 264:11544-11550; della-Cioppa et al. (1987) Plant Physiol. 84:965-968; Romer et al. (1993) Biochem. Biophys. Res Commun. 79(5:1414-1421; and, Shah et al. (1986) Science 253:478-481.
• the constructs may contain the nucleic acid sequence which encodes the entire LCAT protein, a portion ofthe LCAT protein, the entire ACAT protein, or a portion ofthe ACAT protein.
• the entire sequence is not required.
• LCAT or ACAT sequences used in constructs are intended for use as probes, it may be advantageous to prepare constructs containing only a particular portion of a LCAT or ACAT encoding sequence, for example a sequence which is discovered to encode a highly conserved region.
• Transcript termination regions may be provided by the DNA sequence encoding the diacylglycerol acyltransferase or a convenient transcription termination region derived from a different gene source, for example, the transcript termination region which is naturally associated with the transcript initiation region. The skilled artisan will recognize that any convenient transcript termination region which is capable of terminating transcription in a plant cell may be employed in the constructs ofthe present invention.
• constructs may be prepared to direct the expression ofthe LCAT or ACAT sequences directly from the host plant cell plastid.
• Such constructs and methods are known in the art and are generally described, for example, in Svab, et al. (1990) Proc.
• a plant cell, tissue, organ, or plant into which the recombinant DNA constructs containing the expression constructs have been introduced is considered transformed, transfected, or transgenic.
• a transgenic or transformed cell or plant also includes progeny ofthe cell or plant and progeny produced from a breeding program employing such a transgenic plant as a parent in a cross and exhibiting an altered phenotype resulting from the presence of a LCAT nucleic acid sequence.
• Plant expression or transcription constructs having a plant LCAT as the DNA sequence of interest for increased or decreased expression thereof may be employed with a wide variety of plant life, particularly, plant life involved in the production of vegetable oils for edible and industrial uses. Most especially preferred are temperate oilseed crops.
• Plants of interest include, but are not limited to, rapeseed (Canola and High Erucic Acid varieties), sunflower, safflower, cotton, soybean, peanut, coconut and oil palms, and corn.
• rapeseed Canola and High Erucic Acid varieties
• sunflower safflower
• cotton cotton
• soybean peanut
• coconut peanut
• coconut safflower
• cotton cotton
• soybean peanut
• coconut peanut
• coconut safflower
• corn Depending on the method for introducing the recombinant constructs into the host cell
• this invention is applicable to dicotyledyons and monocotyledons species alike and will be readily applicable to new and/or improved transformation and regulation techniques.
• plant LCAT and ACAT constructs in plants to produce plants or plant parts, including, but not limited to leaves, stems, roots, reproductive, and seed, with a modified content of lipid and/or sterol esters and to alter the oil production by such plants.
• ACAT genes in conjunction with the LCAT sequences to increase the sterol content of seeds.
• overexpression of a nucleic acid sequence encoding an ACAT and LCAT in an oilseed crop may find use in the present invention to increase sterol levels in plant tissues and/or increase oil production.
• the gene sequences may be synthesized, either completely or in part, especially where it is desirable to provide plant-preferred sequences.
• all or a portion ofthe desired structural gene may be synthesized using codons preferred by a selected host. Host- preferred codons may be determined, for example, from the codons used most frequently in the proteins expressed in a desired host species.
• antibody preparations, nucleic acid probes (DNA and RNA) and the like may be prepared and used to screen and recover "homologous" or "related" sequences from a variety of plant sources.
• Homologous sequences are found when there is an identity of sequence, which may be determined upon comparison of sequence information, nucleic acid or amino acid, or through hybridization reactions between a known LCAT and a candidate source. Conservative changes, such as Glu/Asp, Val/Ile, Ser/Thr, Arg/Lys and Gin/ Asn may also be considered in determining sequence homology. Amino acid sequences are considered homologous by as little as 25%) sequence identity between the two complete mature proteins. (See generally, Doolittle, R.F., OF URFS and ORES (University Science Books, C A, 1986.)
• LCATs may be obtained from the specific sequences provided herein.
• synthetic sequences including modified amino acid sequences and starting materials for synthetic-protein modeling from the exemplified LCAT and ACAT sequences and from sequences which are obtained through the use of such exemplified sequences.
• Modified amino acid sequences include sequences which have been mutated, truncated, increased and the like, whether such sequences were partially or wholly synthesized. Sequences which are actually purified from plant preparations or are identical or encode identical proteins thereto, regardless ofthe method used to obtain the protein or sequence, are equally considered naturally derived.
• antibodies to the protein can be prepared by injecting rabbits or mice with the purified protein or portion thereof, such methods of preparing antibodies being well known to those in the art. Either monoclonal or polyclonal antibodies can be produced, although typically polyclonal antibodies are more useful for gene isolation.
• Western analysis may be conducted to determine that a related protein is present in a crude extract ofthe desired plant species, as determined by cross- reaction with the antibodies to the encoded proteins. When cross-reactivity is observed, genes encoding the related proteins are isolated by screening expression libraries representing the desired plant species. Expression libraries can be constructed in a variety of commercially available vectors, including lambda gtl 1, as described in Sambrook, et al.
• in vitro assays are performed in insect cell cultures using baculovirus expression systems.
• baculovirus expression systems are known in the art and are described by Lee, et al U.S. Patent Number 5,348,886, the entirety of which is herein incorporated by reference.
• expression constructs may be prepared to assay for protein activity utilizing different expression systems. Such expression constructs are transformed into yeast or prokaryotic host and assayed for acyltransferase activity. Such expression systems are known in the art and are readily available through commercial sources.
• the method of transformation in obtaining such transgenic plants is not critical to the instant invention, and various methods of plant transformation are currently available. Furthermore, as newer methods become available to transform crops, they may also be directly applied hereunder. For example, many plant species naturally susceptible to Agrobacterium infection may be successfully transformed via tripartite or binary vector methods of Agrobacterium mediated transformation. In many instances, it will be desirable to have the construct bordered on one or both sides by T-DNA, particularly having the left and right borders, more particularly the right border. This is particularly useful when the construct uses A. tumefaciens or A. rhizogenes as a mode for transformation, although the T-DNA borders may find use with other modes of transformation. In addition, techniques of microinjection, DNA particle bombardment, and electroporation have been developed which allow for the transformation of various monocot and dicot plant species.
• included with the DNA construct will be a structural gene having the necessary regulatory regions for expression in a host and providing for selection of transformant cells.
• the gene may provide for resistance to a cytotoxic agent, e.g. antibiotic, heavy metal, toxin, etc., complementation providing prototrophy to an auxotrophic host, viral immunity or the like.
• a cytotoxic agent e.g. antibiotic, heavy metal, toxin, etc.
• complementation providing prototrophy to an auxotrophic host, viral immunity or the like.
• one or more markers may be employed, where different conditions for selection are used for the different hosts.
• Non-limiting examples of suitable selection markers include genes that confer resistance to bleomycin, gentamycin, glyphosate, hygromycin, kanamycin, methotrexate, phleomycin, phosphinotricin, spectinomycin, streptomycin, sulfonamide and sulfonylureas. Maliga et al., Methods in Plant Molecular Biology, Cold Spring Harbor Laboratory Press, 1995, p. 39.
• markers include, but are not limited to, alkaline phosphatase (AP), myc, hemagglutinin (HA), ⁇ glucuronidase (GUS), luciferase, and green fluorescent protein (GFP).
• a vector may be used which may be introduced into the Agrobacterium host for homologous recombination with T-DNA or the Ti- or Ri-plasmid present in the Agrobacterium host.
• the Ti- or Ri-plasmid containing the T-DNA for recombination may be armed (capable of causing gall formation) or disarmed (incapable of causing gall formation), the latter being permissible, so long as the vtr genes are present in the transformed Agrobacterium host.
• the armed plasmid can give a mixture of normal plant cells and gall.
• the expression or transcription construct bordered by the T-DNA border region(s) will be inserted into a broad host range vector capable of replication in E. coli and Agrobacterium, there being broad host range vectors described in the literature.
• pRK2 or derivatives thereof. See, for example, Ditta, et al., (Proc. Nat. Acad. Sci., U.S.A. (1980) 77:7347-7351) and ⁇ PA 0 120 515, which are inco ⁇ orated herein by reference.
• a vector containing separate replication sequences one of which stabilizes the vector in E. coli, and the other in Agrobacterium.
• McBride and Summerfelt Plant Mol. Biol. (1990) 14:269-216
• the pRiHRI Jouanin, et al, Mol. Gen. Genet. (1985) 201:370-374
• origin of replication is utilized and provides for added stability of the plant expression vectors in host Agrobacterium cells.
• the expression construct and the T-DNA can be one or more markers, which allow for selection of transformed Agrobacterium and transformed plant cells.
• markers include resistance to chloramphenicol, kanamycin, the aminoglycoside G418, hygromycin, or the like.
• the particular marker employed is not essential to this invention, one or another marker being preferred depending on the particular host and the manner of construction.
• explants may be combined and incubated with the transformed Agrobacterium for sufficient time for transformation, the bacteria killed, and the plant cells cultured in an appropriate selective medium. Once callus forms, shoot formation can be encouraged by employing the appropriate plant hormones in accordance with known methods and the shoots transferred to rooting medium for regeneration of plants. The plants may then be grown to seed and the seed used to establish repetitive generations and for isolation of vegetable oils.
• methods for modifying the sterol and/or stanol composition of a host cell are also interest.
• the methods for modifying the sterol and/or stanol composition of a host plant cell involve either increasing the levels of sterol ester compounds as a proportion ofthe total sterol compounds.
• the method generally comprises the use of expression constructs to direct the expression ofthe polynucleotides ofthe present invention in a host cell.
• the method generally comprises the use of expression constructs to direct the suppression of endogenous acyltransferase proteins in a host cell.
• expression constructs to modify the levels of sterol compounds in a host plant cell.
• the methods find use in modifying the levels of sterol compounds in seed oils obtained from plant seeds.
• expression constructs ofthe present invention to alter oil production in a host cell and in particular to increase oil production.
• expression constructs containing nucleic acid sequences encoding LCAT and/or ACAT polypeptides to transform host plant cells and to use these host cells to regenerate whole plants having increase oil production as compared to the same plant not containing the expression construct.
• oils obtained from transgenic plants having modified sterol compound content find use in a wide variety of applications.
• Of particular interest in the present invention is the use ofthe oils containing modified levels of sterol compounds in applications involved in improving human nutrition and cardiovascular health.
• phytostanols are beneficial for lowering serum cholesterol (Ling, et al. (1995) Life Sciences 57:195-206).
• Cholesterol-lowering compositions comprise the oils and sterol ester compound compositions obtained using the methods ofthe present invention.
• Such cholesterol lowering compositions include, but are not limited to foods, food products, processed foods, food ingredients, food additive compositions, or dietary/nutritional supplements that contain oils and/or fats.
• Non-limiting examples include margarines; butters; shortenings; cooking oils; frying oils; dressings, such as salad dressings; spreads; mayonnaises; and vitamin mineral supplements.
• Patent documents relating to such compositions include, U.S. Patents 4,588,717 and 5,244,887, and PCT International Publication Nos. WO 96/38047, WO 97/42830, WO 98/06405, and WO 98/06714.
• toppings dairy products such as cheese and processed cheese; processed meat; pastas; sauces; cereals; desserts, including frozen and shelf-stable desserts; dips; chips; baked goods; pastries; cookies; snack bars; confections; chocolates; beverages; unextracted seed; and unextracted seed that has been ground, cracked, milled, rolled, extruded, pelleted, defatted, dehydrated, or otherwise processed, but which still contains the oils, etc., disclosed herein.
• the cholesterol-lowering compositions can also take the form of pharmaceutical compositions comprising a cholesterol-lowering effective amount ofthe oils or sterol compound compositions obtained using the methods ofthe present invention, along with a pharmaceutically acceptable carrier, excipient, or diluent.
• These pharmaceutical compositions can be in the form of a liquid or a solid.
• Liquids can be solutions or suspensions; solids can be in the form of a powder, a granule, a pill, a tablet, a gel, or an extrudate.
• U.S. Patent 5,270,041 relates to sterol-containing pharmaceutical compositions.
• nucleic acid sequences encoding acyltransferase-like sequences ofthe present invention in a host cell, it is possible to modify the lipid content and/or composition as well as the sterol content and/or composition ofthe host cell.
• RNA from the inflorescence and developing seeds of Arabidopsis thaliana was isolated for use in construction of complementary (cDNA) libraries.
• the procedure was an adaptation ofthe DNA isolation protocol of Webb and Rnapp (D.M. Webb and S.J. Knapp, (1990) Plant Molec. Reporter, 8, 180-185).
• the following description assumes the use of lg fresh weight of tissue. Frozen seed tissue was powdered by grinding under liquid nitrogen. The powder was added to 10ml REC buffer (50mM Tris-HCl, pH 9, 0.8M NaCl, lOmM EDTA, 0.5%> w/v CTAB (cetyltrimethyl-ammonium bromide)) along with
• RNA pellet was redissolved in 0.4 ml of 1M NaCl. The RNA pellet was redissolved in water and extracted with phenol chloroform.
• total RNA may be obtained using TRIzol reagent (BRL- Lifetechnologies, Gaithersburg, MD) following the manufacturer's protocol. The RNA precipitate was dissolved in water and stored frozen.
• the program used to query protein databases was profilesearch. This is a search where the query is not a single sequence but a profile based on a multiple alignment of amino acid or nucleic acid sequences.
• the profile was used to query a sequence data set, i.e., a sequence database.
• the profile contained all the pertinent information for scoring each position in a sequence, in effect replacing the "scoring matrix" used for the standard query searches.
• the program used to query nucleotide databases with a protein profile was tprofilesearch.
• Tprofilesearch searches nucleic acid databases using an amino acid profile query. As the search is running, sequences in the database are translated to amino acid sequences in six reading frames.
• the output file for tprofilesearch is identical to the output file for profilesearch except for an additional column that indicates the frame in which the best alignment occurred.
• Lecithin cholesterol acyltransferase from human (McLean j, et al (1986) Nucleic Acids Res. 14(23):9397-406 SEQ ID NO:l)) was used to search the NCBI non-redundant protein database using BLAST.
• Three sequences were identified from Arabidopsis, GenBank accessions AC004557 ( referred to herein as LCATl, SEQ DD NO:2), AC003027 (referred to herein as LCAT2, SEQ ID NO:4), and AL024486 (referred to herein as LCAT3, SEQ ID NO: 6).
• LCATl GenBank accessions AC004557
• LCAT2 AC003027
• AL024486 referred to herein as LCAT3, SEQ ID NO: 6
• the deduced amino acid sequences are provided in SEQ ID NOs: 3, 5, and 7, respectively.
• the profile generated from the queries using PSI-BLAST was excised from the hyper text markup language (html) file.
• the worldwide web (www)/html interface to psiblast at ncbi stores the current generated profile matrix in a hidden field in the html file that is returned after each iteration of psiblast.
• this matrix has been encoded into string62 (s62) format for ease of transport through html.
• String62 format is a simple conversion ofthe values ofthe matrix into html legal ascii characters.
• the encoded matrix width (x axis) is 26 characters, and comprise the consensus characters, the probabilities of each amino acid in the order A,B,C,D,E,F,G,H,I,K,L,M,N, P,Q,R,S,T,V,W,X,Y,Z (where B represents D and N, and Z represents Q and E, and X represents any amino acid), gap creation value, and gap extension value.
• the length (y axis) ofthe matrix corresponds to the length ofthe sequences identified by PSI-BLAST.
• the order ofthe amino acids corresponds to the conserved amino acid sequence ofthe sequences identified using PSI-BLAST, with the N-terminal end at the top ofthe matrix.
• the probabilities of other amino acids at that position are represented for each amino acid along the x axis, below the respective single letter amino acid abbreviation.
• each row ofthe profile consists ofthe highest scoring (consensus) amino acid, followed by the scores for each possible amino acid at that position in sequence matrix, the score for opening a gap that that position, and the score for continuing a gap at that position.
• the string62 file is converted back into a profile for use in subsequent searches.
• the gap open field is set to 11 and the gap extension field is set to 1 along the x axis.
• the gap creation and gap extension values are known, based on the settings given to the PSIBLAST algorithm.
• the matrix is exported to the standard GCG profile form. This format can be read by Gen Web.
• ALL B positions are set to min of D and N amino acids at that row in sequence matrix
• ALL X positions are set to min of all amino acids at that row in sequence matrix
• LCAT4 The protein sequences of LCATl, LCAT2, and LCAT3 as well as the PSI-BLAST profile were used to search public and proprietary databases for additional LCAT sequences. Two EST sequences were identified which appear to be identical to LCATl and LCAT3, respectively. One additional Arabidopsis sequence was identified from the proprietary databases, LCAT4 (SEQ ID NO: 8). The deduced protein sequence of LCAT4 is provided in SEQ ID NO:9. Two additional genomic sequences were identified using the PSI-BLAST profile from libraries of Arabidopsis ecotypes Columbia and Landsberg, LCAT7 (SEQ ID NO:10) and LCAT8 (SEQ LO NO:l 1). The LCAT7 sequence was present in both the Columbia and Landsberg genomic libraries, while the LCAT8 sequence was only present in the Columbia library.
• LCAT5 An open reading frame was predicted from the genomic sequence of LCAT7 in the Arabidopsis public database and this sequence was called MSH12 (referred to herein as LCAT5, SEQ ID NO: 73).
• the deduced protein sequence of LCAT5 is provided in SEQ ID NO: 74.
• the PSI-BLAST profile and the LCAT sequences were used to query the public yeast database and proprietary libraries containing corn and soy EST sequences.
• the yeast genome contains only one gene, LROl (LCAT Related Open reading frame, YNR008W, Figure 1) with distinct similarity to the human LCAT.
• LROl LCAT Related Open reading frame, YNR008W, Figure 1
• the DNA sequence of LROl is provided in SEQ LD NO: 75 and the protein sequence is provided in SEQ ID NO: 76. Seven EST sequences were identified from soybean libraries as being LCAT sequences.
• SEQ ID NOs: 12 and 13 Two sequences from soy (SEQ ID NOs: 12 and 13) are most closely related to the Arabidopsis LCATl sequence, a single sequence was identified as being most closely related to LCAT2 (SEQ ID NO: 14) , three were closely related to LCAT3 (SEQ ID NOs: 15-17), and an additional single sequence was identified (SEQ LD NO: 18). A total of 11 corn EST sequences were identified as being related to the Arabidopsis LCAT sequences.
• a public database containing mouse Expressed Sequence Tag (EST) sequences (dBEST) was searched for ACAT-like sequences.
• the search identified two sequences (SEQ ID 30 and 31) which were related (approximately 20% identical), but divergent, to known ACAT sequences.
• the two mouse ACAT sequences were used to search public and proprietary databases containing EST sequences from human and rat tissues. Results ofthe search identified several sequences from the human database and from the rat database which were closely related to the mouse sequences.
• the human and rat ACAT-like EST sequences were assembled, using the GCG assembly program, to construct a complete inferred cDNA sequence by identifying overlapping sequences (SEQ LD NOs: 32 and 33, respectively).
• the protein sequence ofthe human ACAT-like sequence was aligned with known ACAT sequences from human (Chang, et al (1993) J. Biol. Chem. 268:20747-20755,
• the protein sequence ofthe human sterol O-acyltransferase (ACAT, Acyl CoA:Cholesterol acyltransferase, Accession number A48026) related sequence was used to search protein and nucleic acid Genbank databases.
• a single plant homologue was identified in the public Arabidopsis EST database (Accession A042298, SEQ ID NO:38).
• the protein sequence (SEQ ID NO:39) was translated from the EST sequence, and was found to contain a peptide sequence conserved in both mammalian and yeast ACATs (Chang et al, (1997) Ann. Rev. Biochem., 66:613-638). To obtain the entire coding region corresponding to the Arabidopsis ACAT-like
• EST synthetic oligo-nucleotide primers were designed to amplify the 5' and 3' ends of partial cDNA clones containing ACAT-like sequences. Primers were designed according to the Arabidopsis ACAT-like EST sequence and were used in Rapid Amplification of cDNA Ends (RACE) reactions (Frohman et al. (1988) Proc. Natl. Acad. Sci. USA 85:8998-9002).
• RACE Rapid Amplification of cDNA Ends
• Primers were designed (5'-TGCAAATTGACGAGCACACCAACCCCTTC-3' (SEQ ID NO:40) and 5'-AAGGATGCTTTGAGTTCCTGACAATAGG-3' (SEQ ID NO:41)) to amplify the 5' end from the Arabidopsis ACAT EST sequence.
• Amplification of flanking sequences from cDNA clones were performed using the Marathon cDNA Amplification kit (Clontech, CA).
• the sequence derived from the 5 '-RACE amplification was used to search proprietary Arabidopsis EST libraries.
• a single EST accession, LIB25-088-C7 (SEQ LD NO:42), was identified which contained a sequence identical to the 5'-RACE sequence.
• LIB25-088-C7 was found to contain the complete putative coding sequence for the Arabidopsis ACAT-like product.
• nucleic acid as well as the putative translation product sequences of A042298 were used to search public and proprietary databases.
• Four EST sequences were identified in both soybean (SEQ ID NOs:43-46) and maize (SEQ ID NOs:47-50) proprietary databases, and a single ACAT-like sequence was identified from Mortierrella alpina EST sequences (SEQ ID NO:51).
• Sequence alignments between ACAT sequences from several different sources were compared to identify the similarity between the sequences.
• Nucleotide sequences from known human and mouse ACATs, as well as nucleotide sequences from known yeast ACATs were compared to the ACAT-like EST sequences from human and Arabidopsis. Analysis ofthe sequence alignments revealed several classes of ACATs based on sequence similarity. The known human and mouse ACATs, being 88% similar in the nucleotide sequence, formed one class of ACATs. Another class of ACATs included the yeast ACATs which are less than 20% similar to the known human and mouse class ACATs.
• the final class of ACATs included the Arabidopsis and human sequences disclosed in the present invention. This class is approximately 22%> similar to the known human and mouse ACAT class and approximately 23% similar to the yeast class of ACATs. Thus, the ACAT sequences disclosed in the present invention represent a novel class of ACAT enzymes. Partial mouse sequences of this class are also provided.
• LCAT2 LCAT2, LCAT3, LCAT4, LCAT5 and the yeast LROl sequences in plants and cultured insect cells.
• the entire coding region of each LCAT was amplified from the appropriate EST clone or an Arabidopsis genomic cDNA library using the following oligonucleotide primers in a polymerase chain reactions (PCR).
• the LCATl coding sequence was amplified from the EST clone Lib25-082-Ql-El-G4 using the primers 5'-GGATCCGCGGCCGCACAATGAAAAAAATATCTTCACATTATTCGG-3' (SEQ ID NO:52) and 5 '-GGATCCCCTGCAGGTCATTCATTGACGGCATTAACATTGG-3 ' (SEQ ID NO:53).
• the LCAT2 coding sequence was amplified from an Arabidopsis genomic cDNA library using the synthetic oligo nucleotide primers 5 '-GGATCCGCGGCCGCACAATGGGAGCGAATTCGAAATCAGTAACG-3 ' (SEQ ID NO:54) and 5'-GGATCCCCTGCAGGTTAATACCCACTTTTATCAAGCTCCC-3' (SEQ ID NO:55).
• the LCAT3 coding sequence was amplified from the EST clone
• the LCAT4 coding sequence was amplified from the EST clone LIB23-007-Q1-E1-B5 using the synthetic oligo nucleotide primers
• the LCAT5 coding sequence was amplified from LIB23-053-Q1-E1-E3 using the synthetic oligo nucleotide primers 5'-GGATCCGCGGCCGCACAATGCCCCTTATTCATCGG-3' (SEQ LDNO:77) and 5'- GGATCCCCTGCAGGTCACAGCTTCAGGTCAATACG-3' (SEQ IDNO:78).
• the yeast LROl coding sequence was amplified from genomic yeast DNA using the synthetic oligo nucleotide primers 5 'GGATCCGCGGCCGCACAATGGGCACACTGTTTCGAAG3 ' (SEQ ID NO:79) and 5'GGATCCCCTGCAGGTTACATTGGGAAGGGCATCTGAG3' (SEQ ID NO: 80).
• the entire coding region ofthe Arabidopsis ACAT sequence (SEQ ID NO: 42) was amplified from the EST clone LIB25-088-C7 using oligonucleotide primers 5'-TCGACCTGCAGGAAGCTTAGAAATGGCGATTTTGGATTC-3' (SEQ ID NO: 60) and 5'-GGATCCGCGGCCGCTCATGACATCGATCCTTTTCGG-3' (SEQ ID NO: 61) in a polymerase chain reaction (PCR).
• PCR product was subcloned into pCR2.1Topo (Invitrogen) and labeled pCGN9964 (LCATl), pCGN9985 (LCAT2), pCGN9965 (LCAT3), pCGN9995 (LCAT4), pCGN10964 (LCAT5), pCGN10963 (LROl), and pCGN8626 (ACAT).
• Double stranded DNA sequence was obtained to verify that no errors were introduced by the PCR amplification.
• Constructs are prepared to direct the expression ofthe Arabidopsis LCAT and yeast LCAT sequences in cultured insect cells.
• the entire coding region ofthe LCAT proteins was removed from the respective constructs by digestion with Notl and &e8387I, followed by gel electrophoresis and gel purification.
• the fragments containing the LCAT coding sequences were cloned into Notl and Pst digested baculovirus expression vector pFastBacl (Gibco-BRL, Gaithersburg, MD).
• the resulting baculovirus expression constructs were referred to as pCG ⁇ 9992 (LCATl), pCGN9993 (LCAT2), pCGN9994
• LCAT3 pCGN10900
• LCAT5 pCGN10967
• LCAT5 pCGN10962
• a plasmid containing the napin cassette derived from pCGN3223 (described in U.S. Patent No. 5,639,790, the entirety of which is incorporated herein by reference) was modified to make it more useful for cloning large DNA fragments containing multiple restriction sites, and to allow the cloning of multiple napin fusion genes into plant binary transformation vectors.
• An adapter comprised ofthe self annealed oligonucleotide of sequence 5'- CGCGATTTAAATGGCGCGCCCTGCAGGCGGCCGCCTGCAGGGCGCGCCATTTA AAT-3' (SEQ ID NO:62) was ligated into the cloning vector pBC SK+ (Stratagene) after digestion with the restriction endonuclease BssHII to construct vector pCGN7765. Plamids pCGN3223 and pCGN7765 were digested with Notl and ligated together. The resultant vector, pCGN7770, contained the pCGN7765 backbone with the napin seed specific expression cassette from pCGN3223.
• the cloning cassette, pCGN7787 contained essentially the same regulatory elements as pCGN7770, with the exception ofthe napin regulatory regions of pCGN7770 have been replaced with the double CAMV 35S promoter and the tml polyadenylation and transcriptional termination region.
• pCGN5139 A binary vector for plant transformation, pCGN5139, was constructed from pCGN1558 (McBride and Summerfelt, (1990) Plant Molecular Biology, 14:269-276).
• the polylinker of pCGN1558 was replaced as a HindIII/Asp718 fragment with a polylinker containing unique restriction endonuclease sites, Ascl, Pad, Xbal, Swal, BamHI,and Notl.
• Asp718 and Hindlll restriction endonuclease sites are retained in pCGN5139.
• turbo binary vectors A series of turbo binary vectors was constructed to allow for the rapid cloning of DNA sequences into binary vectors containing transcriptional initiation regions (promoters) and transcriptional termination regions.
• the plasmid pCGN8618 was constructed by ligating oligonucleotides
• a plasmid containing the insert oriented so that the napin promoter was closest to the blunted Asp718I site of pCGN5139 and the napin 3' was closest to the blunted Hindlll site was subjected to sequence analysis to confirm both the insert orientation and the integrity of cloning junctions.
• the resulting plasmid was designated pCGN8622.
• the plasmid pCGN8619 was constructed by ligating oligonucleotides 5'-TCGACCTGCAGGAAGCTTGCGGCCGCGGATCC-3' (SEQ ID NO:65) and 5'-TCGAGGATCCGCGGCCGCAAGCTTCCTGCAGG-3' (SEQ ID NO:66) into Sall/XhoI-digested pCGN7770.
• a fragment containing the napin promoter, polylinker and napin 3' region was removed from pCGN8619 by digestion with Asp718I; the fragment was blunt-ended by filling in the 5' overhangs with Klenow fragment then ligated into pCGN5139 that had been digested with Asp7181 and Hindlll and blunt-ended by filling in the 5' overhangs with Klenow fragment.
• a plasmid containing the insert oriented so that the napin promoter was closest to the blunted Asp718I site of pCGN5139 and the napin 3' was closest to the blunted Hindlll site was subjected to sequence analysis to confirm both the insert orientation and the integrity of cloning junctions. The resulting plasmid was designated pCGN8623.
• the plasmid pCGN8620 was constructed by ligating oligonucleotides 5'-TCGAGGATCCGCGGCCGCAAGCTTCCTGCAGGAGCT -3' (SEQ ID NO:67) and 5'-CCTGCAGGAAGCTTGCGGCCGCGGATCC-3' (SEQ ID NO:68) into Sall/Sacl- digested pCGN7787.
• a fragment containing the d35S promoter, polylinker and tml 3' region was removed from pCGN8620 by complete digestion with Asp7181 and partial digestion with Notl.
• the fragment was blunt-ended by filling in the 5' overhangs with Klenow fragment then ligated into pCGN5139 that had been digested with Asp718I and Hindlll and blunt-ended by filling in the 5' overhangs with Klenow fragment.
• a plasmid containing the insert oriented so that the d35S promoter was closest to the blunted Asp7181 site of pCGN5139 and the tml 3 ' was closest to the blunted Hindlll site was subjected to sequence analysis to confirm both the insert orientation and the integrity of cloning junctions.
• the resulting plasmid was designated pCGN8624.
• the plasmid pCGN8621 was constructed by ligating oligonucleotides 5'-TCGACCTGCAGGAAGCTTGCGGCCGCGGATCCAGCT -3' (SEQ ID NO:69) and 5 '-GGATCCGCGGCCGCAAGCTTCCTGCAGG-3 ' (SEQ ID NO:70) into Sall/Sacl- digested pCGN7787.
• a fragment containing the d35S promoter, polylinker and tml 3' region was removed from pCGN8621 by complete digestion with Asp718I and partial digestion with Notl.
• the fragment was blunt-ended by filling in the 5' overhangs with Klenow fragment then ligated into pCGN5139 that had been digested with Asp718I and Hindlll and blunt-ended by filling in the 5' overhangs with Klenow fragment.
• a plasmid containing the insert oriented so that the d35S promoter was closest to the blunted Asp718I site of pCGN5139 and the tml 3' was closest to the blunted Hindlll site was subjected to sequence analysis to confirm both the insert orientation and the integrity of cloning junctions.
• the resulting plasmid was designated pCGN8625.
• the plasmid construct pCGN8640 is a modification of pCGN8624 described above.
• a 938bp Pstl fragment isolated from transposon Tn7 which encodes bacterial spectinomycin and streptomycin resistance (Fling et al. (1985), Nucleic Acids Research 13(19):7095-7106), a determinant for E. coli and Agrobacterium selection, was blunt ended with Pfu polymerase.
• the blunt ended fragment was ligated into pCGN8624 that had been digested with Spel and blunt ended with Pfu polymerase.
• the region containing the Pstl fragment was sequenced to confirm both the insert orientation and the integrity of cloning junctions.
• the spectinomycin resistance marker was introduced into pCGN8622 and pCGN8623 as follows.
• a 7.7 Kbp Avrll-SnaBI fragment from pCGN8640 was ligated to a 10.9 Kbp Avrll-SnaBI fragment from pCGN8623 or ⁇ CGN8622, described above.
• the resulting plasmids were pCGN8641 and pCGN8643, respectively.
• the plasmid pCGN8644 was constructed by ligating oligonucleotides 5'-GATCACCTGCAGGAAGCTTGCGGCCGCGGATCCAATGCA-3' (SEQ ID NO:71) and 5 '-TTGGATCCGCGGCCGCAAGCTTCCTGCAGGT-3 ' (SEQ ID NO:72) into BamHI-Pstl digested pCGN8640.
• the coding sequence of LCATl was cloned from pCGN9964 as a Notl/ &e8387I fragment into pCG ⁇ 8640, pCGN8641, pCGN8643, and pCGN8644 to create the expression constructs pCGN9960, pCGN9961, pCGN9962, and pCGN9963, respectively.
• the construct pCGN9960 was designed to express the LCATl coding sequence in the sense orientation from the constitutive promoter CaMV 35S.
• the construct pCGN9961 was designed to express the LCATl coding sequence in the antisense orientation from the napin promoter.
• the construct pCGN9962 was designed to express the LCATl coding sequence in the sense orientation from the napin promoter.
• the construct pCGN9963 was designed to express the LCATl coding sequence in the antisense orientation from the constitutive promoter CaMV 35S.
• the coding sequence of LCAT2 was cloned from ⁇ CGN9985 as a Notl/ Sse8381l fragment into pCGN8640, pCGN8641 , pCGN8643, and pCGN8644 to create the expression constructs pCGN9981, pCGN9982, pCGN9983, and pCGN9984, respectively.
• the construct pCGN9981 was designed to express the LCAT2 coding sequence in the sense orientation from the constitutive promoter CaMV 35S.
• the construct pCGN9982 was designed to express the LCAT2 coding sequence in the antisense orientation from the napin promoter.
• the construct pCGN9983 was designed to express the LCAT2 coding sequence in the sense orientation from the napin promoter.
• the construct pCGN9984 was designed to express the LCAT2 coding sequence in the antisense orientation from the constitutive promoter CaMV 35S.
• the coding sequence of LCAT3 was cloned from pCGN9965 as a Notl/ Sse8387I fragment into pCG ⁇ 8640, ⁇ CGN8641, pCGN8643, and pCGN8644 to create the expression constructs pCGN9966, pCGN9967, pCGN9968, and ⁇ CGN9969, respectively.
• the construct pCGN9966 was designed to express the LCAT3 coding sequence in the sense orientation from the constitutive promoter CaMV 35S.
• the construct pCGN9967 was designed to express the LCAT3 coding sequence in the antisense orientation from the napin promoter.
• the construct pCGN9968 was designed to express the LCAT3 coding sequence in the sense orientation from the napin promoter.
• the construct pCGN9969 was designed to express the LCAT3 coding sequence in the antisense orientation from the constitutive promoter CaMV 35S.
• the coding sequence of LCAT4 was cloned from pCGN9995 as a Notl/ Sse8387I fragment into pCG ⁇ 8640, ⁇ CGN8641, pCGN8643, and pCGN8644 to create the expression constructs pCGN9996, pCGN9997, pCGN9998, and pCGN9999, respectively.
• the construct pCGN9996 was designed to express the LCAT4 coding sequence in the sense orientation from the constitutive promoter CaMV 35S.
• the construct pCGN9997 was designed to express the LCAT4 coding sequence in the antisense orientation from the napin promoter.
• the construct pCGN9998 was designed to express the LCAT4 coding sequence in the sense orientation from the napin promoter.
• the construct pCGN9999 was designed to express the LCAT4 coding sequence in the antisense orientation from the constitutive promoter CaMV 35S.
• the coding sequence of LCAT5 was cloned from pCGN10964 as a Notl/ Sse8387I fragment into pCG ⁇ 9977 and pCGN9979, to create the expression constructs ⁇ CGN10965, and ⁇ CGN10966, respectively.
• the construct pCGN10965 was designed to express the LCAT5 coding sequence in the sense orientation from the constitutive promoter CaMV 35S.
• the construct pCGN10966 was designed to express the LCAT5 coding sequence in the sense orientation from the napin promoter.
• the coding sequence of LROl was cloned from pCGN10963 as a Notl Sse8387I fragment into pCGN9977 and pCGN9979, to create the expression constructs pCGN10960, and pCGN10961, respectively.
• the construct pCGN10960 was designed to express the LROl coding sequence in the sense orientation from the constitutive promoter CaMV 35S.
• the construct pCGN10961 was designed to express the LROl coding sequence in the sense orientation from the napin promoter.
• Plant ACAT Expression Construct Preparation A fragment containing the Arabidopsis ACAT-like coding region was removed from pCGN8626 by digestion with Sse8387I and Not I. The fragment containing the ACAT-like sequence was ligated into Pstl-Not I digested pCGN8622. The resulting plasmid was designated pCGN8627. DNA sequence analysis confirmed the integrity of the cloning junctions. A fragment containing the Arabidopsis ACAT-like coding region (SEQ ID NO:
• a fragment containing the Arabidopsis ACAT-like coding region was removed from pCGN8626 by digestion with Sse8387 and Not I. The fragment was ligated into Pstl-Not I digested ⁇ CGN8625. The resulting plasmid was designated pCGN8630. DNA sequence analysis confirmed the integrity ofthe cloning junctions.
• the construct pCGN8660 was constructed by cloning approximately 1 Kb ofthe Arabidopsis ACAT-like coding region from pCGN8626 in the sense orientation, and the full-length Arabidopsis ACAT-like coding region in the antisense orientation under the regulatory control ofthe napin transcription initiation sequence.
• the NotI-Sse8387I fragment of pCGN8592 was cloned into Notl-Pstl digested binary vectors pCGN8621, pCGN8622, and pCGN8624 to yield plasmids, pCGN 9700, pCGN9701 , and pCGN9702, respectively.
• Plasmid pCGN9700 expresses a sense transcript ofthe rat ACAT-like cDNA under control of a napin promoter
• plasmid pCGN9701 expresses an antisense transcript of the rat ACAT-like cDNA under control of a napin promoter
• plasmid pCGN9702 expresses a sense transcript ofthe rat ACAT-like cDNA under control of a double 35S promoter.
• Plasmids pCGN 9700, ⁇ CGN9701, and pCGN9702 were introduced in Agrobacterium tumefaciens EHA101.
• Constructs were prepared to direct the expression ofthe rat ACAT-like sequence in the seed embryo of soybean and the endosperm of corn.
• a 1.5 kb NotI/Sse8387I fragment from pCG ⁇ 8592 containing the coding sequence ofthe rat ACAT-like sequence was blunt ended using Mung bean nuclease, and ligated into the Smal site ofthe turbo 7S binary/cloning vector pCGN8809 to create the vector pCGN8817 for transformation into soybean by particle bombardment.
• the vector pCGN8817 contained the operably linked components ofthe promoter region ofthe soybean ⁇ ' subunit of ⁇ -conglycinin (7S promoter, (Chen et al, (1986), Proc. Natl. Acad. Sci., 83:8560-8564), the DNA sequence coding for the entire rat ACAT-like protein, and the transcriptional termination region of pea RuBisCo small subunit, referred to as E9 3' (Coruzzi, et al. (1984) EMBOJ. 3:1671-1679 and Morelli, et al (1985) Nature 315:200-204).
• This construct further contained sequences for the selection of positive transformed plants by screening for resistance to glyphosate using the CP4 EPSPS (U.S. Patent 5,633,435) expressed under the control ofthe figwort mosaic virus (FMV) promoter (U.S. Patent Number 5,378,619) and the transcriptional termination region of E9.
• CP4 EPSPS U.S. Patent 5,633,435
• FMV figwort mosaic virus
• a 1.5 kb NotL &e8387I fragment from pCG ⁇ 8592 containing the coding sequence ofthe rat ACAT-like sequence was blunt ended using Mung bean nuclease, and ligated into the BamHI site ofthe rice pGtl expression cassette pCGN8592 for expression from the pGtl promoter (Leisy, D.J. et al., Plant Mol. Biol. 14 (1989) 41-50) and the HSP70 intron sequence (U.S. Patent Number 5,593,874).
• This cassette also included the transcriptional termination region downstream ofthe cloning site of nopaline synthase, nos 3' (Depicker et al., J. Molec. Appl Genet. (1982) 1: 562-573).
• a 7.5 kb fragment containing the pGtl promoter, the DNA sequence encoding the rat ACAT-like protein, and the nos transcriptional termination sequence was cloned into the binary vector pCGN8816 to create the vector pCGN8818 for transformation into corn.
• This construct also contained sequences for the selection of positive transformants with kanamycin using the kanamycin resistance gene from Tn5 bacteria under the control ofthe CAMV 35S promoter and tml transcriptional termination regions.
• Example 5 Expression in Insect Cell Culture
• a baculovirus expression system was used to express the LCAT cDNAs in cultured insect cells.
• the baculovirus expression constructs pCGN9992, pCGN9993, pCGN9994, pCGN10900, pCGN10962, and pCGN10967 were transformed and expressed using the BAC-to-BAC Baculovirus Expression System (Gibco-BRL, Gaithersburg, MD) according to the manufacturer's directions.
• the transformed insect cells were used to assay for acyltransferase activities using methods known in the art (see Example 8).
• Phytosterol 13C assignments were based on model samples composed of triolein, ⁇ -sitosterol and cholesterol oleate. Triacylglycerol 13C assignments were made from comparison with literature assignments or with shifts computed from a 13C NMR database (Advanced Chemical Development, Inc., version 3.50, Toronto Canada).
• Seed oil from T2 plants expressing LCATl through 4 under the control ofthe napin promoter was extracted using an accelerated solvent extractor (ASE) method. Seed samples were ground, using a mortar and pestle, to achieve a fine homogeneous meal. Oil was obtained using a Dionex Accelerated Solvent Extractor (ASE). Clean ground seed was added to an equal amount of diatomaceous earth. The ground seed sample and the diatomaceous earth were thoroughly mixed until a homogeneous texture was achieved. The sample was then loaded into the instrument and oil extraction was achieved using hexane under validated laboratory protocols.
• ASE accelerated solvent extractor
• Oil from these seed samples was then analyzed for sterol ester analysis using HPLC/MS for free campesterol, stigmasterol, and sitosterol and their fatty acid esters.
• To the autosampler vial containing approximately 0.1 grams oil was added 0.3 mLs CDC1 3 .
• One-hundred micro liters of this solution was added to 900 micro liters CHC1 3 .
• Five micro liters of this diluted sample was subsequently injected into an HPLC/MS with positive ion atmospheric pressure ionization.
• the individual components in the oils were separated using two 4.6 x 50 mm C 8 Zorbax columns in series and a gradient using acetonitrile and acetonitrile with 40% CHC1 3 .
• Baculovirus expression construct pCGN9992, pCGN9993, pCGN9994 and pCGN10900 were transformed and expressed using the BAC-TOBAC Baculovirus Expression System (Gibco-BRL, Gaithersburg, MD) according to the manufacturer's instructions except harvesting of recombinant viruses was done 5 days post-transfection. The supernatant from the transfection mixture was used for generating virus stock which in turn was used for infecting Sf9 cells used in the assay.
• the transformed cells were assayed for lecithin: sterol acyltransferase activities using the method described herein. Insect cells were centrifuged and the resulting cell pellet was either used immediately or stored at -70 C for later analysis. Cells were resuspended in Medium A (100 mM Tricine/NaOH, pH 7.8, 10% (w/v) glycerol, 280 mM
• Lecithin sterol acyltransferase activity was assayed in a 0.1 ml reaction mixture containing 100 mM Tris/HCl, pH 7, 28 mM NaCl, 0.03% Triton X-100, 0.1 mM sitosterol, 20 ⁇ M l,2-[ 14 C]-palmitoyl-phosphatidyl choline (246420 dpm nmole), and 0.05-20 mg of membrane protein. After 15 minutes at 30 °C, the reaction was terminated by addition of a 0.5 ml solution of methylene chloride:methanol (4:1, v/v ) containing 100 ⁇ g cholesterol and cholesterol ester as cold carriers.
• the LCAT 4 protein from pCGN10900 in baculovirus membranes showed a radioactive spot in the region ofthe TLC plate where cholesterol ester migrates indicating that LCAT 4 has the ability to catalyze the transfer of an acyl group from lecithin (PC) to sitosterol to make a sitosterol ester.
• PC lecithin
• Example 9 Plant Assay for Modified Lipid Content Nir (near infrared spectroscopy spectral scanning) can be used to determine the total oil content of Arabidopsis seeds in a non-destructive way provided that a spectral calibration curve has been developed and validated for seed oil content. A seed oil spectral calibartion curve was developed using seed samples from 85 Arabidopsis plants. Seed was cleaned and scanned using a Foss NIR model 6500 (Foss-Nirs Systems, Inc.).
• Oil Content 100%> x (vial plus extracted oil wt - initial vial wt) / (sample wt)
• the analytical data generated by ASE were used to perform spectral calibrations.
• Nir calibration equations were generated using the built-in statistical package within the NirSytems winisi software.
• the spectral calibration portion ofthe software is capable of calibration and self-validation. From a total of 85 samples, 57 samples were used to generate the total percent oil calibration. The remaining samples were used to validate the oil calibrations. Optimized smoothing, derivative size, and mathematical treatment (modified partial least square) was utilized to generate the calibration. The samples that were not used in building respective calibrations were used as a validation set.
• Statistical tools such as correlation coefficient ( R ), coefficient of determination (R 2 ), standard error of prediction ( SEP ), and the standard error of prediction corrected for bias (SEPC) were used to evaluate the calibration equations.
• T2 seeds from plants that had been transformed with the LCAT genes were cleaned and scanned using a Foss NIR model 6500 (Foss-Nirs Systems, Inc.). Approximately 50 to 100 milligrams of whole seeds, per sample, were packed in a mini sample ring cup with quartz lens [ LH-0307 ] consisting a mini-insert [ IH-0337 ] and scanned in reflectance mode to obtain the spectral data. Oil percentage in each seed sample was determined using the seed oil spectral calibration curve detailed above.

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