Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
  • C12P21/00—Preparation of peptides or proteins
  • C12P21/02—Preparation of peptides or proteins having a known sequence of two or more amino acids, e.g. glutathione
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
  • C12P21/00—Preparation of peptides or proteins
  • C12P21/005—Glycopeptides, glycoproteins
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P3/00—Drugs for disorders of the metabolism
  • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
  • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P37/00—Drugs for immunological or allergic disorders
• • 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
  • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
  • C12N1/14—Fungi; Culture media therefor
• • 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
• • 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
  • C12N15/80—Vectors or expression systems specially adapted for eukaryotic hosts for fungi
• • 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
  • C12N15/80—Vectors or expression systems specially adapted for eukaryotic hosts for fungi
  • C12N15/81—Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts
• • 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.)
  • C12N9/1048—Glycosyltransferases (2.4)
• • 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
  • C12N9/14—Hydrolases (3)
  • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
  • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
  • C12N9/2477—Hemicellulases not provided in a preceding group
  • C12N9/2488—Mannanases
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Y—ENZYMES
  • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
  • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
  • C12Y302/01113—Mannosyl-oligosaccharide 1,2-alpha-mannosidase (3.2.1.113), i.e. alpha-1,2-mannosidase
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
  • C07K2319/04—Fusion polypeptide containing a localisation/targetting motif containing an ER retention signal such as a C-terminal HDEL motif
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
  • C07K2319/05—Fusion polypeptide containing a localisation/targetting motif containing a GOLGI retention signal
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Y—ENZYMES
  • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
  • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)

Definitions

• the present invention is directed to methods and compositions by which fungi or other eukaryotic microorganisms can be genetically modified to produce glycosylated proteins (glycoproteins) having patterns of glycosylation similar to glycoproteins produced by animal cells, especially human cells, which are useful as human or animal therapeutic agents.
• glycosylated proteins glycoproteins
• Glycosylation Pathways De novo synthesized proteins may undergo further processing in cells, known as post-translational modification.
• sugar residues may be added enzymatically, a process known as glycosylation.
• glycosylation The resulting proteins bearing covalently linked oligosaccharide side chains are known as glycosylated proteins or glycoproteins.
• Bacteria typically do not glycosylate proteins; in cases where glycosylation does occur it usually occurs at nonspecific sites in the protein (Moens and Vanderleyden, Arch. Microbiol. 1997 168(3): 169- 175).
• Eukaryotes commonly attach a specific oligosaccharide to the side chain of a protein asparagine residue, particularly an asparagine which occurs in the sequence Asn-Xaa-Ser/Thr/Cys (where Xaa represents any amino acid).
• an N-glycan Following attachment of the saccharide moiety, known as an N-glycan, further modifications may occur in vivo. Typically these modifications occur via an ordered sequence of enzymatic reactions, known as a cascade.
• Different organisms provide different glycosylation enzymes (glycosyltransferases and glycosidases) and different glycosyl substrates, so that the final composition of a sugar side chain may vary markedly depending upon the host.
• microorganisms such as filamentous fungi and yeast
• a complex N-glycan means a structure with typically two to six outer branches with a sialyllactosamine sequence linked to an inner core structure Man 3 Glc ⁇ Ac 2 .
• a complex N- glycan has at least one branch, and preferably at least two, of alternating Glc ⁇ Ac and galactose (Gal) residues that terminate in oligosaccharides such as, for example: ⁇ eu ⁇ Ac-; ⁇ euAc 2-6Gal ⁇ Ac ⁇ l-; NeuAc ⁇ 2-3Gal ⁇ l- 3GalNAc ⁇ l-; NeuAc ⁇ 2-3/6Gal ⁇ l-4GlcNAc ⁇ l-; GlcNAc ⁇ l-4Gal ⁇ l- (mucins only); Fuc ⁇ l-2Gal ⁇ l -(blood group H).
• Glc ⁇ Ac and galactose (Gal) residues that terminate in oligosaccharides such as, for example: ⁇ eu ⁇ Ac-; ⁇ euAc 2-6Gal ⁇ Ac ⁇ l-; NeuAc ⁇ 2-3Gal ⁇ l- 3GalNAc ⁇ l-; NeuAc ⁇ 2-3/6Gal ⁇ l
• Sulfate esters can occur on galactose, GalNAc, and GlcNAc residues, and phosphate esters can occur on mannose residues.
• NeuAc Neuro: neuraminic acid; Ac:acetyl
• NeuGl N-glycolylneuraminic acid
• Complex N- glycans may also have intrachain substitutions of bisecting Glc ⁇ Ac and core fucose (Fuc).
• Human glycosylation begins with a sequential set of reactions in the endoplasmatic reticulum (ER) leading to a core oligosaccharide structure, which is transferred onto de novo synthesized proteins at the asparagine residue in the sequence Asn-Xaa-Ser/Thr (see Figure 1 A). Further processing by glucosidases and mannosidases occurs in the ER before the nascent glycoprotein is transferred to the early Golgi apparatus, where additional mannose residues are removed by Golgi-specific 1,2- mannosidases. Processing continues as the protein proceeds through the Golgi.
• ER endoplasmatic reticulum
• N-acetylglucosamine transferases GnT I, GnT II, GnT III, GnT IV GnT V GnT VI
• mannosidase II fucosyltransferases add and remove specific sugar residues (see Figure IB).
• ST galactosyl tranferases and sialyltransferases
• the protein N-glycans of animal glycoproteins have bi-, tri-, or tetra-antennary structures, and may typically include galactose, fucose, and N-acetylglucosamine. Commonly the terminal residues of the N-glycans consist of sialic acid.
• Figure IB A typical structure of a human N-glycan is shown in Figure IB.
• N-glycans of animal glycoproteins typically include galactose, fucose, and terminal sialic acid. These sugars are not generally found on glycoproteins produced in yeast and filamentous fungi.
• nucleotide sugar precursors e.g. UDP-N-acetylglucosamine, UDP- N-acetylgalactosamine, CMP-N-acetylneuraminic acid, UDP-galactose, GDP-fucose etc.
• UDP-N-acetylglucosamine UDP- N-acetylgalactosamine
• CMP-N-acetylneuraminic acid UDP-galactose
• GDP-fucose etc.
• Glycosyl transfer reactions typically yield a side product which is a nucleoside diphosphate or monophosphate. While monophosphates can be directly exported in exchange for nucleoside triphosphate sugars by an antiport mechanism, diphosphonucleosides (e.g. GDP) have to be cleaved by phosphatases (e.g. GDPase) to yield nucleoside monophosphates and inorganic phosphate prior to being exported.
• phosphatases e.g. GDPase
• UDP is known to be a potent inhibitor of glycosyltransferases and the removal of this glycosylation side product is important in order to prevent glycosyltransferase inhibition in the lumen of the Golgi (Khatara et al.,
• Glycosyltransferases and mannosidases line the inner (luminal) surface of the ER and Golgi apparatus and thereby provide a catalytic surface that allows for the sequential processing of glycoproteins as they proceed through the ER and Golgi network.
• the multiple compartments of the cis, medial, and trans Golgi and the trans Golgi Network (TGN), provide the different localities in which the ordered sequence of glycosylation reactions can take place.
• glycoprotein proceeds from synthesis in the ER to full maturation in the late Golgi or TGN, it is sequentially exposed to different glycosidases, mannosidases and glycosyltransferases such that a specific N-glycan structure may be synthesized.
• the enzymes typically include a catalytic domain, a stem region, a membrane spanning region and an ⁇ - terminal cytoplasmic tail. The latter three structural components are responsible for directing a glycosylation enzyme to the appropriate locus. Localization sequences from one organism may function in other organisms.
• ⁇ -2,6- sialyltransferase ( ⁇ -2,6-ST) from rats, an enzyme known to localize in the rat trans Golgi, was shown to also localize a reporter gene (invertase) in the yeast Golgi (Schwientek, et al., 1995).
• invertase invertase
• yeast Golgi yeast Golgi
• a full length GalT from humans was not even synthesized in yeast, despite demonstrably high transcription levels.
• the transmembrane region of the same human GalT fused to an invertase reporter was able to direct localization to the yeast Golgi, albeit it at low production levels.
• Schwientek and co-workers have shown that fusing 28 amino acids of a yeast mannosyltransferase (Mntl), a region containing an N-terminal cytoplasmic tail, a transmembrane region and eight amino acids of the stem region, to the catalytic domain of human GalT are sufficient for Golgi localization of an active GalT (Schwientek et al. 1995 J. Biol. Chem. 270(10):5483-5489).
• Other galactosyltransferases appear to rely on interactions with enzymes resident in particular organelles since after removal of their transmembrane region they are still able to localize properly.
• Improper localization of a glycosylation enzyme may prevent proper functioning of the enzyme in the pathway.
• Aspergillus nidulans which has numerous ⁇ -l,2-mannosidases (Eades and Hintz, 2000 Gene 255(l):25-34), does not add GlcNAc to Man 5 GlcNAc 2 when transformed with the rabbit GnT I gene, despite a high overall level of GnT I activity (Kalsner et al., 1995).
• GnT I although actively expressed, may be incorrectly localized such that the enzyme is not in contact with both of its substrates: the nascent N-glycan of the glycoprotein and UDP-Glc ⁇ Ac.
• the host organism may not provide an adequate level of UDP- Glc ⁇ Ac in the Golgi.
• glycoproteins are typically immunogenic in humans and show a reduced half-life in vivo after administration (Takeuchi, 1997).
• Specific receptors in humans and animals can recognize terminal mannose residues and promote the rapid clearance of the protein from the bloodstream. Additional adverse effects may include changes in protein folding, solubility, susceptibility to proteases, trafficking, transport, compartmentalization, secretion, recognition by other proteins or factors, antigenicity, or allergenicity. Accordingly, it has been necessary to produce therapeutic glycoproteins in animal host systems, so that the pattern of glycosylation is identical or at least similar to that in humans or in the intended recipient species. In most cases a mammalian host system, such as mammalian cell culture, is used.
• transgenic animals such as goats, sheep, mice and others (Dente Prog. Clin. Biol. 1989 Res. 300:85-98, Ruther et al., 1988 Cell 53(6):847- 856; Ware, J., et al. 1993 Thrombosis and Haemostasis 69(6): 1194-
• Recombinant human proteins expressed in the above-mentioned host systems may still include non-human glycoforms (Raju et al., 2000 Annals Biochem. 283(2):123-132).
• fraction of the N-glycans may lack terminal sialic acid, typically found in human glycoproteins.
• Substantial efforts have been directed to developing processes to obtain glycoproteins that are as close as possible in structure to the human forms, or have other therapeutic advantages.
• Glycoproteins having specific glycoforms may be especially useful, for example in the targeting of therapeutic proteins.
• the addition of one or more sialic acid residues to a glycan side chain may increase the lifetime of a therapeutic glycoprotein in vivo after administration.
• the mammalian host cells may be genetically engineered to increase the extent of terminal sialic acid in glycoproteins expressed in the cells.
• sialic acid may be conjugated to the protein of interest in vitro prior to administration using a sialic acid transferase and an appropriate substrate.
• changes in growth medium composition or the expression of enzymes involved in human glycosylation have been employed to produce glycoproteins more closely resembling the human forms (S. Weikert, et al., Nature Biotechnology, 1999, 17, 1116-1121; Werner, ⁇ oe, et al 1998 Arzneistoffforschung 48(8):870- 880; Weikert, Papac et al., 1999; Andersen and Goochee 1994 Cur. Opin.Biotechnol.5: 546-549; Yang and Butler 2000 Biotechnol.Bioengin.68(4): 370-380).
• cultured human cells may be used.
• the virus or other infectious agent may compromise the growth of the culture, while in other cases the agent may be a human pathogen rendering the therapeutic protein product unfit for its intended use.
• many cell culture processes require the use of complex, temperature-sensitive, animal-derived growth media components, which may carry pathogens such as bovine spongiform encephalopathy (BSE) prions.
• BSE bovine spongiform encephalopathy
• pathogens are difficult to detect and/or difficult to remove or sterilize without compromising the growth medium.
• use of animal cells to produce therapeutic proteins necessitates costly quality controls to assure product safety.
• Transgenic animals may also be used for manufacturing high- volume therapeutic proteins such as human serum albumin, tissue plasminogen activator, monoclonal antibodies, hemoglobin, collagen, f ⁇ brinogen and others.
• transgenic goats and other transgenic animals can be genetically engineered to produce therapeutic proteins at high concentrations in the milk
• the process is costly since every batch has to undergo rigorous quality control.
• Animals may host a variety of animal or human pathogens, including bacteria, viruses, fungi, and prions.
• scrapies and bovine spongiform encephalopathy testing can take about a year to rule out infection.
• the production of therapeutic compounds is thus preferably carried out in a well-controlled sterile environment, e.g. under Good Manufacturing Practice (GMP) conditions.
• GMP Good Manufacturing Practice
• transgenic animal technology relies on different animals and thus is inherently non-uniform.
• external factors such as different food uptake, disease and lack of homogeneity within a herd, may effect glycosylation patterns of the final product. It is known in humans, for example, that different dietary habits result in differing glycosylation patterns.
• Transgenic plants have been developed as a potential source to obtain proteins of therapeutic value.
• high level expression of proteins in plants suffers from gene silencing, a mechanism by which the genes for highly expressed proteins are down-regulated in subsequent plant generations.
• plants add xylose and/or ⁇ - 1,3 -linked fucose to protein N-glycans, resulting in glycoproteins that differ in structure from animals and are immunogenic in mammals (Altmann, Marz et al., 1995 Glycoconj. J. 12(2);150-155).
• it is generally not practical to grow plants in a sterile or GMP environment and the recovery of proteins from plant tissues is more costly than the recovery from fermented microorganisms.
• glycoprotein Production Using Eukarvotic Microorganisms The lack of a suitable expression system is thus a significant obstacle to the low-cost and safe production of recombinant human glycoproteins.
• Production of glycoproteins via the fermentation of microorganisms would offer numerous advantages over the existing systems. For example, fermentation-based processes may offer (a) rapid production of high concentrations of protein; (b) the ability to use sterile, well-controlled production conditions (e.g.
• GMP conditions the ability to use simple, chemically defined growth media; (d) ease of genetic manipulation; (e) the absence of contaminating human or animal pathogens; (f) the ability to express a wide variety of proteins, including those poorly expressed in cell culture owing to toxicity etc.; (g) ease of protein recovery (e.g. via secretion into the medium).
• fermentation facilities are generally far less costly to construct than cell culture facilities.
• bacteria including species such as Escherichia coli commonly used to produce recombinant proteins, do not glycosylate proteins in a specific manner like eukaryotes.
• Various methylotrophic yeasts such as Pichia pastoris, Pichia methanolica, and Hansenula polymorpha, are particularly useful as eukaryotic expression systems, since they are able to grow to high cell densities and/or secrete large quantities of recombinant protein.
• glycoproteins expressed in these eukaryotic microorganisms differ substantially in N-glycan structure from those in animals. This has prevented the use of yeast or filamentous fungi as hosts for the production of many useful glycoproteins.
• glycosyltransferases have been separately cloned and expressed in S. cerevisiae (GalT, GnT I), Aspergillus nidulans (GnT I) and other fungi (Yoshida et al., 1999, Kalsner et al., 1995 Glycoconj. J. 12(3):360-370, Schwientek et al., 1995).
• GalT, GnT I Aspergillus nidulans
• fungi Yoshida et al., 1999, Kalsner et al., 1995 Glycoconj. J. 12(3):360-370, Schwientek et al., 1995.
• N-glycans with human characteristics were not obtained.
• Yeasts produce a variety of mannosyltransferases e.g. 1,3- mannosyltransferases (e.g. M ⁇ 1 in S. cerevisiae) (Graham and Emr, 1991 J. Cell. Biol. 114(2):207-218), 1,2-mannosyltransferases (e.g. KTR/KRE family from S. cerevisiae), 1,6-mannosyltransferases (OCH1 from 5 cerevisiae), mannosylphosphate transferases (M ⁇ 4 and MNN6 from S. cerevisiae) and additional enzymes that are involved in endogenous glycosylation reactions. Many of these genes have been deleted individually, giving rise to viable organisms having altered glycosylation profiles. Examples are shown in Table 1. Table 1. Examples of yeast strains having altered mannosylation
• Japanese Patent Application Public No. 8-336387 discloses an OCH1 mutant strain of Pichia pastoris.
• the OCH1 gene encodes 1,6-mannosyltransferase, which adds a mannose to the glycan structure Man 8 GlcNAc 2 to yield Man 9 GlcNAc 2 .
• the Man 9 GlcNAc 2 structure is then a substrate for further mannosylation in vivo, leading to the hypermannosylated glycoproteins that are characteristic of yeasts and typically may have at least 30-40 mannose residue per N-glycan.
• proteins glycosylated with Man 8 Glc ⁇ Ac are accumulated and hypermannosylation does not occur.
• the structure Man 8 GlcNAc is not a substrate for animal glycosylation enzymes, such as human UDP-GlcNAc transferase I, and accordingly the method is not useful for producing proteins with human glycosylation patterns.
• yeast Saccharomyces cerevisiae 1998 expressed ⁇ -l,2-mannosidase from Asperg ⁇ llus saitoi in the yeast Saccharomyces cerevisiae.
• a signal peptide sequence (His-Asp-Glu-Leu) was engineered into the exogenous mannosidase to promote retention in the endoplasmic reticulum.
• the yeast host was a mutant lacking three enzyme activities associated with hypermannosylation of proteins: l,6-mannosyltransferase (OCH7); 1,3- mannosyltransferase (MNNl); and mannosylphosphatetransferase (MNN4).
• the N-glycans of the triple mutant host thus consisted of the structure Man 8 Glc ⁇ Ac 2 , rather than the high mannose forms found in wild-type S. cerevisiae.
• the N-glycans of a model protein (carboxypeptidase Y) were trimmed to give a mixture consisting of 27 mole % Man 5 Glc ⁇ Ac 2 , 22 mole % Man 6 GlcNAc 2 , 22 mole % Man 7 GlcNAc 2 , 29 mole % Man 8 GlcNAc 2 . Trimming of the endogenous cell wall glycoproteins was less efficient, only 10 mole % of the N-glycans having the desired Man 5 Glc ⁇ Ac 2 structure.
• strains which: do not express certain enzymes which create the undesirable complex structures characteristic of the fungal glycoproteins, which express exogenous enzymes selected either to have optimal activity under the conditions present in the fungi where activity is desired, or which are targeted to an organelle where optimal activity is achieved, and combinations thereof wherein the genetically engineered eukaryote expresses multiple exogenous enzymes required to produce "human-like" glycoproteins.
• the microorganism is engineered to express an exogenous c - 1 ,2-mannosidase enzyme having an optimal pH between 5.1 and 8.0, preferably between 5.9 and 7.5.
• the exogenous enzyme is targeted to the endoplasmic reticulum or Golgi apparatus of the host organism, where it trims N-glycans such as Man 8 Glc ⁇ Ac 2 to yield Man 5 GlcNAc 2 .
• the latter structure is useful because it is identical to a structure formed in mammals, especially humans; it is a substrate for further glycosylation reactions in vivo and/or in vitro that produce a finished N-glycan that is similar or identical to that formed in mammals, especially humans; and it is not a substrate for hypermannosylation reactions that occur in vivo in yeast and other microorganisms and that render a glycoprotein highly irnrnunogenic in animals.
• the glycosylation pathway of an eukaryotic microorganism is modified by (a) constructing a D ⁇ A library including at least two genes encoding exogenous glycosylation enzymes; (b) transforming the microorganism with the library to produce a genetically mixed population expressing at least two distinct exogenous glycosylation enzymes; (c) selecting from the population a microorganism having the desired glycosylation phenotype.
• the D ⁇ A library includes chimeric genes each encoding a protein localization sequence and a catalytic activity related to glycosylation. Organisms modified using the method are useful for producing glycoproteins having a glycosylation pattern similar or identical to mammals, especially humans.
• the glycosylation pathway is modified to express a sugar nucleotide transporter enzyme.
• a nucleotide diphosphatase enzyme is also expressed. The transporter and diphosphatase improve the efficiency of engineered glycosylation steps, by providing the appropriate substrates for the glycosylation enzymes in the appropriate compartments, reducing competitive product inhibition, and promoting the removal of nucleoside diphosphates.
• Figure 1 A is a schematic diagram of typical fungal N-glycosylation pathway.
• Figure IB is a schematic diagram of a typical human N-glycosylation pathway.
• the methods and recombinant lower eukaryotic strains described herein are used to make "humanized glycoproteins".
• the recombinant lower eukaryotes are made by engineering lower eukaryotes which do not express one or more enzymes involved in production of high mannose structures to express the enzymes required to produce human-like sugars.
• a lower eukaryote is a unicellular or filamentous fungus.
• a "humanized glycoprotein” refers to a protein having attached thereto N- glycans including less than four mannose residues, and the synthetic intermediates (which are also useful and can be manipulated further in vitro) having at least five mannose residues.
• the glycoproteins produced in the recombinant lower eukaryotic strains contain at least 27 mole % of the Man5 intermediate. This is achieved by cloning in a better mannosidase, i.e., an enzyme selected to have optimal activity under the conditions present in the organisms at the site where proteins are glycosylated, or by targeting the enzyme to the organelle where activity is desired.
• eukaryotic strains which do not express one or more enzymes involved in the production of high mannose structures are used. These strains can be engineered or one of the many such mutants already described in yeasts, including a hypermannosylation-minus (OCH1) mutant in Pichia pastoris. The strains can be engineered one enzyme at a time, or a library of genes encoding potentially useful enzymes can be created, and those strains having enzymes with optimal activities or producing the most "human-like" glycoproteins, selected.
• N-glycan Man 5 Glc ⁇ Ac 2 are particularly useful since (a) lacking a high degree of mannosylation (e.g. greater than 8 mannoses per N-glycan, or especially 30-40 mannoses), they show reduced immunogenicity in humans; and (b) the N-glycan is a substrate for further glycosylation reactions to form an even more human-like glycoform, e.g. by the action of Glc ⁇ Ac transferase I to form Glc ⁇ AcMan 5 Glc ⁇ Ac 2 .
• a high degree of mannosylation e.g. greater than 8 mannoses per N-glycan, or especially 30-40 mannoses
• the N-glycan is a substrate for further glycosylation reactions to form an even more human-like glycoform, e.g. by the action of Glc ⁇ Ac transferase I to form Glc ⁇ AcMan 5 Glc ⁇ Ac 2 .
• Man 5 GlcNAc 2 must be formed in vivo in a high yield, at least transiently, since all subsequent glycosylation reactions require Man 5 GlcNAc 2 or a derivative thereof. Accordingly, a yield is obtained of greater than 27 mole %, more preferably a yield of 50-100 mole %, glycoproteins in which a high proportion of N-glycans have Man 5 Glc ⁇ Ac2. It is then possible to perform further glycosylation reactions in vitro, using for example the method of U.S. Patent No. 5,834,251 to Maras and Contreras. In a preferred embodiment, at least one further glycosylation reaction is performed in vivo. In a highly preferred embodiment thereof, active forms of glycosylating enzymes are expressed in the endoplasmic reticulum and/or Golgi apparatus. Host Microorganisms
• Yeast and filamentous fungi have both been successfully used for the production of recombinant proteins, both intracellular and secreted (Cereghino, J. L. and J. M. Cregg 2000 FEMS Microbiology Reviews 24(1): 45-66; Harkki, A., et al. 1989 Bio-Technology 7(6): 596; Berka, R. M., et al. 1992 Abstr.Papers Amer. Chem.Soc.203: 121-BIOT; Svetina, M., et al. 2000 J.Biotechnol. 76(2-3): 245-251.
• the first step the transfer of the core oligosaccharide structure to the nascent protein, is highly conserved in all eukaryotes including yeast, fungi, plants and humans (compare Figures 1 A and IB).
• Subsequent processing of the core oligosaccharide differs significantly in yeast and involves the addition of several mannose sugars.
• This step is catalyzed by mannosyltransferases residing in the Golgi (e.g. OCH1, MNT1, MNNl, etc.), which sequentially add mannose sugars to the core oligosaccharide.
• the resulting structure is undesirable for the production of humanoid proteins and it is thus desirable to reduce or eliminate mannosyl transferase activity.
• Mutants of 5. cerevisiae, deficient in mannosyl transferase activity e.g. ochl or mnn9 mutants
• Other oligosacharide processing enzymes, such as mannosylphophate transferase may also have to be eliminated depending on the host's particular endogenous glycosylation pattern.
• After reducing undesired endogenous glycosylation reactions the formation of complex N- glycans has to be engineered into the host system. This requires the stable expression of several enzymes and sugar-nucleotide transporters. Moreover, one has to locate these enzymes in a fashion such that a sequential processing of the maturing glycosylation structure is ensured.
• glycoproteins especially glycoproteins used therapeutically in humans.
• Such therapeutic proteins are typically administered by injection, orally, pulmonary, or other means.
• target glycoproteins include, without limitation: erythropoietin, cytokines such as interferon- ⁇ , interferon- ⁇ , interferon- ⁇ , interferon- ⁇ , and granulocyte-CSF, coagulation factors such as factor VIII, factor IX, and human protein C, soluble IgE receptor -chain, IgG, IgM, urokinase, chymase, and urea trypsin inhibitor, IGF-binding protein, epidermal growth factor, growth hormone-releasing factor, annexin V fusion protein, angiostatin, vascular endothelial growth factor-2, myeloid progenitor inhibitory factor- 1, amd osteoprotegerin.
• cytokines such as interferon- ⁇ , interferon- ⁇ , interferon- ⁇ , interferon- ⁇ , and granulocyte-CSF
• coagulation factors such as factor VIII, factor IX, and human protein C
• soluble IgE receptor -chain IgG
• the first step involves the selection or creation of a lower eukaryote that is able to produce a specific precursor structure of Man 5 GlcNAc 2 , which is able to accept in vivo GlcNAc by the action of a GlcNAc transferase I.
• This step requires the formation of a particular isomeric structure of Man 5 GlcNAc 2 .
• This structure has to be formed within the cell at a high yield (in excess of 30%) since all subsequent manipulations are contingent on the presence of this precursor.
• Man 5 GlcNAc 2 structures are necessary for complex N-glycan formation, however, their presence is by no means sufficient, since Man 5 GlcNAc 2 may occur in different isomeric forms, which may or may not serve as a substrate for GlcNAc transferase I. Most glycosylation reactions are not complete and thus a particular protein generally contains a range of different carbohydrate structures (i.e. glycoforms) on its surface. The mere presence of trace amounts (less than 5%) of a particular structure like Man 5 GlcNAc 2 is of little practical relevance. It is the formation of a particular, GlcNAc transferase I accepting intermediate (Structure I) in high yield (above 30%), which is required. The formation of this intermediate is necessary and subsequently allows for the in vivo synthesis of complex N-glycans.
• the method described herein may be used to engineer the glycosylation pattern of a wide range of lower eukaryotes (e.g. Hansenula polymorpha, Pichia stiptis, Pichia methanolica, Pichia sp, Kluyveromyces sp, Candida albicans, Aspergillus nidulans, Trichoderma reseei etc.).
• Pichia pastoris is used to exemplify the required manipulation steps.
• P.pastoris processes Man 9 GlcNAc 2 structures in the ER with a 1,2- ⁇ - mannosidase to yield Man 8 GlcNAc 2 .
• Mannosyltransferases Through the action of several mannosyltransferases, this structure is then converted to hypermannosylated structures (Man >9 GlcNAc 2 ), also known as mannans.
• Man >9 GlcNAc 2 also known as mannans.
• P. pastoris is able to add non-terminal phosphate groups, through the action of mannosylphosphate transferases to the carbohydrate structure. This is contrary to the reactions found in mammalian cells, which involve the removal of mannose sugars as opposed to their addition. It is of particular importance to eliminate the ability of the fungus to hypermannosylate the existing Man 8 GlcNAc 2 structure. This can be achieved by either selecting for a fungus that does not hypermannosylate, or by genetically engineering such a fungus.
• genes that are involved in this process have been identified in Pichia pastoris and by creating mutations in these genes one is able to reduce the production of "undesirable” glycoforms.
• Such genes can be identified by homology to existing mannosyltransferases (e.g. OCH1, MNN4, MNN6, MNNl), found in other lower eukaryotes such as C. albicans, Pichia angusta or S. cerevisiae or by mutagenizing the host strain and selecting for a phenotype with reduced mannosylation.
• PCR primers examples of which are shown in Table 2
• genes or gene fragments encoding such enzymes as probes to identify homologues in DNA libraries of the target organism.
• one may be able to complement particular phenotypes in related organisms. For example, in order to obtain the gene or genes encoding 1,6- mannosyltransferase activity in P. pastoris, one would carry out the following steps.
• OCH1 mutants of S. cerevisiae are temperature sensitive and are slow growers at elevated temperatures.
• Such mutants of S. cerevisiae may be found at http://genome- www.stanford.edu/Saccharomyces/ and are commercially available at http://www.resgen.com/products/YEASTD.php3. Mutants that display a normal growth phenotype at elevated temperature, after having been transformed with a P. pastoris DNA library, are likely to carry an OCH1 homologue of P. pastoris.
• Such a library can be created by partially digesting chromosomal DNA of P. pastoris with a suitable restriction enzyme and after inactivating the restriction enzyme ligating the digested DNA into a suitable vector, which has been digested with a compatible restriction enzyme.
• Suitable vectors are pRS314, a low copy (CEN6/ARS4) plasmid based on pBluescript containing the Trpl marker (Sikorski, R. S., and Hieter, P., 1989, Genetics 122, pg 19-27) or pFL44S, a high copy (2 ⁇ ) plasmid based on a modified pUC19 containing the URA3 marker (Bonneaud, N., et al., 1991, Yeast 7, pg. 609-615).
• Such vectors are commonly used by academic researchers or similar vectors are available from a number of different vendors such as Invitrogen (Carlsbad, CA), Pharmacia (Piscataway, NJ), New England Biolabs (Beverly, MA). Examples are pYES/GS, 2 ⁇ origin of replication based yeast expression plasmid from Invitrogen, or Yep24 cloning vehicle from New England Biolabs. After ligation of the chromosomal DNA and the vector one may transform the DNA library into strain of S. cerevisiae with a specific mutation and select for the correction of the corresponding phenotype. After sub-cloning and sequencing the DNA fragment that is able to restore the wild-type phenotype, one may use this fragment to eliminate the activity of the gene product encoded by OCH1 in P. pastoris.
• genomic sequence of a particular fungus of interest is known, one may identify such genes simply by searching publicly available DNA databases, which are available from several sources such as NCBI, Swissprot etc. For example by searching a given genomic sequence or data base with a known 1,6 mannosyltransferase gene (OCH1) from S. cerevisiae, one can able to identify genes of high homology in such a genome, which a high degree of certainty encodes a gene that has 1 ,6 mannosyltransferase activity. Homologues to several known mannosyltransferases from S.cerevisiae in P. pastoris have been identified using either one of these approaches.
• OCH1 1,6 mannosyltransferase gene
• genes have similar functions to genes involved in the mannosylation of proteins in S. cerevisiae and thus their deletion may be used to manipulate the glycosylation pattern in P. pastoris or any other fungus with similar glycosylation pathways.
• the creation of gene knock-outsj once a given target gene sequence has been determined, is a well-established technique in the yeast and fungal molecular biology community, and can be carried out by anyone of ordinary skill in the art (R. Rothsteins, (1991) Methods in Enzymology, vol. 194, p. 281). In fact, the choice of a host organism may be influenced by the availability of good transformation and gene disruption techniques for such a host.
• URA3 may be used as a marker to ensure the selection of a transformants that have integrated a construct.
• flanking the URA3 marker with direct repeats one may first select for transformants that have integrated the construct and have thus disrupted the target gene. After isolation of the transformants, and their characterization, one may counter select in a second round for those that are resistant to 5'FOA. Colonies that able to survive on plates containing 5'FOA have lost the URA3 marker again through a crossover event involving the repeats mentioned earlier. This approach thus allows for the repeated use of the same marker and facilitates the disruption of multiple genes without requiring additional markers.
• Eliminating specific mannosyltransferases such as 1,6 mannosyltransferase (OCH1), mannosylphosphate transferases (MNN4, MNN6, or genes complementing lb d mutants) in P. pastoris, allows for the creation of engineered strains of this organism which synthesize primarily Man 8 GlcNAc 2 and thus can be used to further modify the glycosylation pattern to more closely resemble more complex human glycoform structures.
• a preferred embodiment of this method utilizes known DNA sequences, encoding known biochemical glycosylation activities to eliminate similar or identical biochemical functions in P. pastoris, such that the glycosylation structure of the resulting genetically altered P. pastoris strain is modified. Table 2.
• M A or C
• R A or G
• a or T A or T
• S C or G
• a or G or T, B C or G or T,
• N G or A or T or C.
• Mannosidase into the Genetically Engineered Host
• the process described herein enables one to obtain such a structure in high yield for the purpose of modifying it to yield complex N-glycans.
• a successful scheme to obtain suitable Man 5 GlcNAc2 structures must involve two parallel approaches: (1) reducing endogenous mannosyltransferase activity and (2) removing 1,2- ⁇ - mannose by mannosidases to yield high levels of suitable Man 5 GlcNAc 2 structures. What distinguishes this method from the prior art is that it deals directly with those two issues. As the work of Chiba and coworkers demonstrates, one can reduce Man 8 GlcNAc 2 structures to a Man 5 GlcNAc 2 isomer in S.
• a preferred process utilizes an - mannosidase in vivo, where the pH optimum of the mannosidase is within 1.4 pH units of the average pH optimum of other representative marker enzymes localized in the same organelle(s).
• the pH optimum of the enzyme to be targeted to a specific organelle should be matched with the pH optimum of other enzymes found in the same organelle, such that the maximum activity per unit enzyme is obtained.
• Table 3 summarizes the activity of mannosidases from various sources and their respective pH optima.
• Table 4 summarizes their location.
• Man 5 GlcNAc2 structure required to accept subsequent addition of GlcNAc by GnT I Any enzyme or combination of enzymes that has/have shown to generate a structure that can be converted to GlcNAcMan 5 GlcNAc 2 by GnT I in vitro would constitute an appropriate choice.
• This knowledge may be obtained from the scientific literature or experimentally by determining that a potential mannosidase can convert Man 8 GlcNAc 2 -PA to Man 5 GlcNAc 2 -PA and then testing, if the obtained Man 5 GlcNAc 2 -PA structure can serve a substrate for GnT I and UDP-GlcNAc to give GlcNAcMan 5 GlcNAc 2 in vitro.
• mannosidase IA from a human or murine source would be an appropriate choice.
• the ⁇ -l,2-mannosidase enzyme should have optimal activity at a pH between 5.1 and 8.0. In a preferred embodiment, the enzyme has an optimal activity at a pH between 5.9 and 7.5. The optimal pH may be determined under in vitro assay conditions.
• Preferred mannosidases include those listed in Table 3 having appropriate pH optima, e.g. Aspergillus nidulans, Homo sapiens IA(Golgi), Homo sapiens IB (Golgi), Lepidopteran insect cells (IPLB-SF21AE), Homo sapiens, mouse IB (Golgi), and Xanthomonas manihotis.
• a single cloned mannosidase gene is expressed in the host organism.
• the encoded mannosidases should all have pH optima within the preferred range of 5.1 to 8.0, or especially between 5.9 and 7.5.
• mannosidase activity is targeted to the ER or cis Golgi, where the early reactions of glycosylation occur.
• a second step of the process involves the sequential addition of sugars to the nascent carbohydrate structure by engineering the expression of glucosyltransferases into the Golgi apparatus.
• This process first requires the functional expression of GnT I in the early or medial Golgi apparatus as well as ensuring the sufficient supply of UDP-GlcNAc. Integration Sites Since the ultimate goal of this genetic engineering effort is a robust protein production strain that is able to perform well in an industrial fermentation process, the integration of multiple genes into the fungal chromosome involves careful planing. The engineered strain will most likely have to be transformed with a range of different genes, and these genes will have to be transformed in a stable fashion to ensure that the desired activity is maintained throughout the fermentation process.
• any combination of the following enzyme activities will have to be engineered into the fungal protein expression host: sialyltransferases, mannosidases, fucosyltransferases, galactosyltransferases, glucosyltransferases, GlcNAc transferases, ER and Golgi specific transporters (e.g. sym and antiport transporters for UDP-galactose and other precursors), other enzymes involved in the processing of oligosaccharides, and enzymes involved in the synthesis of activated oligosaccharide precursors such as UDP-galactose, CMP-N-acetylneuraminic acid.
• sialyltransferases mannosidases
• fucosyltransferases fucosyltransferases
• galactosyltransferases galactosyltransferases
• glucosyltransferases glucosyltransferases
• Glycosyltransferases and mannosidases line the inner (luminal) surface of the ER and Golgi apparatus and thereby provide a "catalytic" surface that allows for the sequential processing of glycoproteins as they proceed through the ER and Golgi network.
• the multiple compartments of the cis, medial, and trans Golgi and the trans-Golgi Network (TGN) provide the different localities in which the ordered sequence of glycosylation reactions can take place.
• glycoprotein proceeds from synthesis in the ER to full maturation in the late Golgi or TGN, it is sequentially exposed to different glycosidases, mannosidases and glycosyltransferases such that a specific carbohydrate structure may be synthesized.
• Much work has been dedicated to revealing the exact mechanism by which these enzymes are retained and anchored to their respective organelle.
• the evolving picture is complex but evidence suggests that stem region, membrane spanning region and cytoplasmic tail individually or in concert direct enzymes to the membrane of individual organelles and thereby localize the associated catalytic domain to that locus.
• Targeting sequences are well known and described in the scientific literature and public databases, as discussed in more detail below with respect to libraries for selection of targeting sequences and targeted enzymes.
• a library including at least two genes encoding exogeneous glycosylation enzymes is transformed into the host organism, producing a genetically mixed population. Transformants having the desired glycosylation phenotypes are then selected from the mixed population.
• the host organism is a yeast, especially P. pastoris, and the host glycosylation pathway is modified by the operative expression of one or more human or animal glycosylation enzymes, yielding protein N- glycans similar or identical to human glycoforms.
• the D ⁇ A library includes genetic constructs encoding fusions of glycosylation enzymes with targeting sequences for various cellular loci involved in glycosylation especially the ER, cis Golgi, medial Golgi, or trans Golgi.
• modifications to glycosylation which can be effected using method are: (1) engineering an eukaryotic microorganism to trim mannose residues from Man 8 Glc ⁇ Ac2 to yield Man 5 GlcNAc2 as a protein N- glycan; (2) engineering an eukaryotic microorganism to add an N-acetylglucosamine (Glc ⁇ Ac) residue to Man 5 Glc ⁇ Ac 2 by action of GlcNAc transferase I; (3) engineering an eukaryotic microorganism to functionally express an enzyme such as an N-acetylglucosamine transferase (GnT I, GnT II, GnT III, GnT IV, GnT V, GnT VI), mannosidase II, fucosyltransferase, galactosyl tranferase (GalT) or sialyltransferases (ST).
• N-acetylglucosamine transferase GnT I
• the host organism is transformed two or more times with D ⁇ A libraries including sequences encoding glycosylation activities. Selection of desired phenotypes may be performed after each round of transformation or alternatively after several transformations have occurred. Complex glycosylation pathways can be rapidly engineered in this manner.
• each library construct includes at least two exogenous genes encoding glycosylation enzymes.
• promoters include, for example, the AOX1, AOX2, DAS, and P40 promoters.
• selectable marker such as a gene to impart drug resistance or to complement a host metabolic lesion. The presence of the marker is useful in the subsequent selection of transformants; for example, in yeast the URA3, HIS4, SUC2, G418, BLA, or SHBLE genes may be used.
• the library may be assembled directly from existing or wild-type genes.
• the D ⁇ A library is assembled from the fusion of two or more sub-libraries.
• one useful sub-library includes D ⁇ A sequences encoding any combination of enzymes such as sialyltransferases, mannosidases, fucosyltransferases, galactosyltransferases, glucosyltransferases, and GlcNAc transferases.
• the enzymes are of human origin, although other mammalian, animal, or fungal enzymes are also useful.
• genes are truncated to give fragments encoding the catalytic domains of the enzymes.
• the enzymes may then be redirected and expressed in other cellular loci.
• the choice of such catalytic domains may be guided by the knowledge of the particular environment in which the catalytic domain is subsequently to be active. For example, if a particular glycosylation enzyme is to be active in the late Golgi, and all known enzymes of the host organism in the late Golgi have a certain pH optimum, then a catalytic domain is chosen which exhibits adequate activity at that pH.
• Another useful sub-library includes DNA sequences encoding signal peptides that result in localization of a protein to a particular location within the ER, Golgi, or trans Golgi network. These signal sequences may be selected from the host organism as well as from other related or unrelated organisms.
• Membrane-bound proteins of the ER or Golgi typically may include, for example, N-terminal sequences encoding a cytosolic tail (ct), a transmembrane domain (tmd), and a stem region (sr). The ct, tmd, and sr sequences are sufficient individually or in combination to anchor proteins to the inner (lumenal) membrane of the organelle.
• a preferred embodiment of the sub-library of signal sequences includes ct, tmd, and/or sr sequences from these proteins.
• Still other useful sources of signal sequences include retrieval signal peptides, e.g. the tetrapeptides HDEL or KDEL, which are typically found at the C-terminus of proteins that are transported retrograde into the ER or Golgi.
• Still other sources of signal sequences include (a) type II membrane proteins, (b) the enzymes listed in Table 3, (c) membrane spanning nucleotide sugar transporters that are localized in the Golgi, and (d) sequences referenced in Table 5.
• MNN1 S. 1,3- Golgi (trans) cerevisiae mannosyltransferase
• signal sequences are selected which are appropriate for the enzymatic activity or activities which are to be engineered into the host.
• signal sequences are selected which are appropriate for the enzymatic activity or activities which are to be engineered into the host.
• a modified microorganism capable of terminal sialylation of nascent N-glycans a process which occurs in the late Golgi in humans, it is desirable to utilize a sub-library of signal sequences derived from late Golgi proteins.
• the trimming of Man 8 Glc ⁇ Ac 2 by an ⁇ -l,2-mannosidase to give
• Man 5 GlcNAc 2 is an early step in complex N-glycan formation in humans. It is therefore desirable to have this reaction occur in the ER or early Golgi of an engineered host microorganism. A sub-library encoding ER and early Golgi retention signals is used.
• a DNA library is then constructed by the in-frame ligation of a sub-library including DNA encoding signal sequences with a sub-library including DNA encoding glycosylation enzymes or catalytically active fragments thereof.
• the resulting library includes synthetic genes encoding fusion proteins.
• signal sequences may be inserted within the open reading frame of an enzyme, provided the protein structure of individual folded domains is not disrupted.
• a DNA library transformed into the host contains a large diversity of sequences, thereby increasing the probability that at least one transformant will exhibit the desired phenotype. Accordingly, prior to transformation, a DNA library or a constituent sub- library may be subjected to one or more rounds of gene shuffling, error prone PCR, or in vitro mutagenesis.
• the DNA library is then transformed into the host organism.
• yeast any convenient method of DNA transfer may be used, such as electroporation, the lithium chloride method, or the spheroplast method.
• integration occurs via homologous recombination, using techniques known in the art.
• DNA library elements are provided with flanking sequences homologous to sequences of the host organism. In this manner integration occurs at a defined site in the host genome, without disruption of desirable or essential genes.
• library DNA is integrated into the site of an undesired gene in a host chromosome, effecting the disruption or deletion of the gene.
• library DNA may be introduced into the host via a chromosome, plasmid, retroviral vector, or random integration into the host genome.
• Recyclable marker genes such as ura3, which can be selected for or against, are especially suitable.
• transformants displaying the desired glycosylation phenotype are selected. Selection may be performed in a single step or by a series of phenotypic enrichment and/or depletion steps using any of a variety of assays or detection methods. Phenotypic characterization may be carried out manually or using automated high-throughput screening equipment. Commonly a host microorganism displays protein N-glycans on the cell surface, where various glycoproteins are localized. Accordingly intact cells may be screened for a desired glycosylation phenotype by exposing the cells to a lectin or antibody that binds specifically to the desired N-glycan. A wide variety of oligosaccharide-specific lectins are available commercially (EY).
• antibodies to specific human or animal N-glycans are available commercially or may be produced using standard techniques.
• An appropriate lectin or antibody may be conjugated to a reporter molecule, such as a chromophore, fluorophore, radioisotope, or an enzyme having a chromogenic substrate (Guillen et al., 1998. Proc.
• Screening may then be performed using analytical methods such as spectrophotometry, fluorimetry, fluorescence activated cell sorting, or scintillation counting.
• analytical methods such as spectrophotometry, fluorimetry, fluorescence activated cell sorting, or scintillation counting.
• Protein isolation may be carried out by techniques known in the art.
• an enzyme such as endo- ⁇ -N-acetylglucosaminidase (Genzyme Co., Boston, MA) may be used to cleave the N-glycans from glycoproteins. Isolated proteins or N-glycans may then be analyzed by liquid chromatography (e.g.
• U.S. Patent No. 5,595,900 teaches several methods by which cells with desired extracellular carbohydrate structures may be identified. Prior to selection of a desired transformant, it may be desirable to deplete the transformed population of cells having undesired phenotypes. For example, when the method is used to engineer a functional mannosidase activity into cells, the desired transformants will have lower levels of mannose in cellular glycoprotein. Exposing the transformed population to a lethal radioisotope of mannose in the medium depletes the population of transformants having the undesired phenotype, i.e. high levels of incorporated mannose.
• cytotoxic lectin or antibody directed against an undesirable N-glycan, may be used to deplete a transformed population of undesired phenotypes.
• the enzyme For a glycosyltransferase to function satisfactorily in the Golgi, it is necessary for the enzyme to be provided with a sufficient concentration of an appropriate nucleotide sugar, which is the high-energy donor of the sugar moiety added to a nascent glycoprotein.
• nucleotide sugars to the appropriate compartments are provided by expressing an exogenous gene encoding a sugar nucleotide transporter in the host microorganism.
• the choice of transporter enzyme is influenced by the nature of the exogenous glycosyltransferase being used.
• a GlcNAc transferase may require a UDP-GlcNAc transporter
• a fucosyltransferase may require a GDP- fucose transporter
• a galactosyltransferase may require a UDP-galactose transporter
• a sialyltransferase may require a CMP-sialic acid transporter.
• the added transporter protein conveys a nucleotide sugar from the cytosol into the Golgi apparatus, where the nucleotide sugar may be reacted by the glycosyltransferase, e.g. to elongate an N-glycan.
• the reaction liberates a nucleoside diphosphate or monophosphate, e.g. UDP, GDP, or
• nucleoside diphosphate As accumulation of a nucleoside diphosphate inhibits the further activity of a glycosyltransferase, it is frequently also desirable to provide an expressed copy of a gene encoding a nucleotide diphosphatase.
• the diphosphatase (specific for UDP or GDP as appropriate) hydrolyzes the diphosphonucleoside to yield a nucleoside monosphosphate and inorganic phosphate.
• the nucleoside monophosphate does not inhibit the glycotransferase and in any case is exported from the Golgi by an endogenous cellular system.
• Suitable transporter enzymes which are typically of mammalian origin, are described below. Examples The use of the above general method may be understood by reference to the following non-limiting examples. Examples of preferred embodiments are also summarized in Table 6.
• Example 1 Engineering of P. pastoris with -l,2-Mannosidase to produce insulin.
• An -l,2-mannosidase is required for the trimming of Man 8 GlcNAc 2 to yield Man 5 GlcNAc 2 , an essential intermediate for complex N-glycan formation.
• An OCH1 mutant of P. pastoris is engineered to express secreted human interferon- ⁇ under the control of an aox promoter.
• a D ⁇ A library is constructed by the in-frame ligation of the catalytic domain of human mannosidase IB (an ⁇ -l,2-mannosidase) with a sub-library including sequences encoding early Golgi localization peptides.
• the D ⁇ A library is then transformed into the host organism, resulting in a genetically mixed population wherein individual transformants each express interferon- ⁇ as well as a synthetic mannosidase gene from the library. Individual transformant colonies are cultured and the production of interferon is induced by addition of methanol. Under these conditions, over 90% of the secreted protein includes interferon- ⁇ . Supernatants are purified to remove salts and low-molecular weight contaminants by C 18 silica reversed-phase chromatography.
• Desired transformants expressing appropriately targeted, active ⁇ -l,2-mannosidase produce interferon- ⁇ including N-glycans of the structure Man 5 Glc ⁇ Ac 2 , which has a reduced molecular mass compared to the interferon of the parent strain.
• the purified supernatants including interferon- ⁇ are analyzed by MALDI-TOF mass spectroscopy and colonies expressing the desired form of interferon- ⁇ are identified.
• GlcNAc Transferase I activity is required for the maturation of complex N-glycans.
• Man 5 Glc ⁇ Ac 2 may only be trimmed by mannosidase II, a necessary step in the formation of human glycoforms, after the addition of GlcNAc to the terminal ⁇ -1,3 mannose residue by GlcNAc Transferase I (Schachter, 1991 Glycobiology 1(5):453-461).
• a library is prepared including DNA fragments encoding suitably targeted GlcNAc Transferase I genes.
• the host organism is a strain, e.g. a yeast, that is deficient in hypermannosylation (e.g.
• an OCH1 mutant provides the substrate UDP-GlcNAc in the Golgi and/or ER, and provides N-glycans of the structure Man 5 Glc ⁇ Ac 2 in the Golgi and/or ER.
• the transformants are screened for those having the highest concentration of terminal GlcNAc on the cell surface, or alternatively secrete the protein having the highest terminal GlcNAc content.
• a visual method e.g. a staining procedure
• a specific terminal GlcNAc binding antibody e.g. a specific terminal GlcNAc binding antibody
• a lectin e.g. a lectin.
• the desired transformants exhibit reduced binding of certain lectins specific for terminal mannose residues.
• a human glycoform in a microorganism it is desirable in order to generate a human glycoform in a microorganism to remove the two remaining terminal mannoses from the structure GlcNAcMan 5 GlcNAc 2 by action of a mannosidase II.
• a DNA library including sequences encoding cis and medial Golgi localization signals is fused in-frame to a library encoding mannosidase II catalytic domains.
• the host organism is a strain, e.g. a yeast, that is deficient in hypermannosylation (e.g. an OCH1 mutant) and provides N-glycans having the structure Glc ⁇ AcMan 5 Glc ⁇ Ac2 in the Golgi and/or ER.
• the enzymes ⁇ 2,3 -sialyltransferase and ⁇ 2,6-sialyltransferase add terminal sialic acid to galactose residues in nascent human N-glycans, leading to mature glycoproteins. In human the reactions occur in the trans Golgi or TG ⁇ . Accordingly a D ⁇ A library is constructed by the in-frame fusion of sequences encoding sialyltransferase catalytic domains with sequences encoding trans Golgi or TG ⁇ localization signals.
• the host organism is a strain, e.g. a yeast, that is deficient in hypermannosylation (e.g.
• Example 6 Method of engineering strains to express GDP-Fucose Transporter.
• the rat liver Golgi membrane GDP-fucose transporter has been identified and purified by Puglielli, L. and C. B. Hirschberg 1999 J Biol. Chem. 274(50):35596-35600.
• the corresponding gene can be identified using standard techniques, such as N-terminal sequencing and Southern blotting using a degenerate D ⁇ A probe.
• the intact gene can is then be expressed in a host microorganism that also expresses a fucosyltransferase.
• Example 7 Method of engineering strains to express UDP-Galactose Transporter
• UDP-galactose (UDP-Gal) transporter has been cloned and shown to be active in S. cerevisiae. (Kainuma, M., et al. 1999 Glycobiology 9(2): 133-141).
• a second human UDP-galactose transporter (hUGTl) has been cloned and functionally expressed in Chinese Hamster Ovary Cells. Aoki, K., et al. 1999 J.Biochem. 126(5): 940-950.
• Segawa and coworkers have cloned a UDP-galactose transporter from Schizosaccharomyces pombe (Segawa, H., et al. 1999 Febs Letters 451(3): 295-298).
• CMP-Sialic Acid Transporter Human CMP-sialic acid transporter (hCST) has been cloned and expressed in Lee 8 CHO cells by Aoki and coworkers (1999). Molecular cloning of the hamster CMP-sialic acid transporter has also been achieved (Eckhardt and Gerardy Schahn 1997 Eur. J. Biochem. 248(1): 187-192). The functional expression of the murine CMP-sialic acid transporter was achieved in Saccharomyces cerevisiae by Berninsone, P., et al. 1997 J
• EBI European Bioinformatics Institute
• bovine cDNA (partial), Narimatsu et al (1986) Proc. Natl. Acad. Sci. USA 83:4720-4724
• human cDNA (partial) Uejima et al (1992) Cancer Res. 52:6158- 6163 29.
• human cDNA (carcinoma) Appert et al (1986) Biochem. Biophys.
• human gene (partial), Wang et al (1993) J. Biol. Chem. 268:4355- 4361 45. human gene (5 1 flank), Aasheim et al (1993) Eur. J. Biochem.
• yeast expression systems can be obtained from sources such as the American Type Culture Collection, Rockville, MD. Vectors are commercially available from a variety of sources.

Landscapes

• Health & Medical Sciences (AREA)
• Life Sciences & Earth Sciences (AREA)
• Chemical & Material Sciences (AREA)
• Engineering & Computer Science (AREA)
• Organic Chemistry (AREA)
• Genetics & Genomics (AREA)
• Zoology (AREA)
• Wood Science & Technology (AREA)
• Bioinformatics & Cheminformatics (AREA)
• Biotechnology (AREA)
• General Engineering & Computer Science (AREA)
• General Health & Medical Sciences (AREA)
• Biochemistry (AREA)
• Biomedical Technology (AREA)
• Microbiology (AREA)
• Molecular Biology (AREA)
• Medicinal Chemistry (AREA)
• Chemical Kinetics & Catalysis (AREA)
• General Chemical & Material Sciences (AREA)
• Mycology (AREA)
• Plant Pathology (AREA)
• Biophysics (AREA)
• Physics & Mathematics (AREA)
• Animal Behavior & Ethology (AREA)
• Diabetes (AREA)
• Pharmacology & Pharmacy (AREA)
• Public Health (AREA)
• Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
• Veterinary Medicine (AREA)
• Virology (AREA)
• Tropical Medicine & Parasitology (AREA)
• Botany (AREA)
• Immunology (AREA)
• Proteomics, Peptides & Aminoacids (AREA)
• Endocrinology (AREA)
• Hematology (AREA)
• Obesity (AREA)
• Pain & Pain Management (AREA)
• Rheumatology (AREA)
• Emergency Medicine (AREA)

Priority Applications (11)

Applications Claiming Priority (6)

Publications (2)

Family

ID=27395978

Family Applications (1)

Country Status (15)

Cited By (60)

Families Citing this family (446)

Family Cites Families (124)