Chemistry: molecular biology and microbiology – Micro-organism – per se ; compositions thereof; proces of... – Bacteria or actinomycetales; media therefor
Reexamination Certificate
1998-05-06
2003-05-06
Ponnaluri, Padmashri (Department: 1627)
Chemistry: molecular biology and microbiology
Micro-organism, per se ; compositions thereof; proces of...
Bacteria or actinomycetales; media therefor
C435S041000, C435S076000, C435S004000, C514S029000, C536S007100
Reexamination Certificate
active
06558942
ABSTRACT:
TECHNICAL FIELD
The invention relates to the field of combinatorial libraries, to novel polyketides and antibiotics and to methods to prepare them. More particularly, it concerns construction of new polyketides and to libraries of polyketides synthesized by polyketide synthases derived from a naturally occurring PKS, as illustrated by the erythromycin gene cluster.
BACKGROUND ART
Polyketides represent a large family of diverse compounds ultimately synthesized from 2-carbon units through a series of Claisen-type condensations and subsequent modifications. Members of this group include antibiotics such as tetracyclines, anticancer agents such as daunomycin, and immunosuppressants such as FK506 and rapamycin. Polyketides occur in many types of organisms including fungi and mycelial bacteria, in particular, the actinomycetes.
A number of lactones of keto acids have been synthesized using standard organic chemistry. These include a series of unsaturated ketolactones synthesized by Vedejes et al.,
J. Am Chem Soc
(1987) 109:5437-5446, shown as formulas 201, 202 and 203 in
FIG. 11
herein. Additional compounds of formulas 204 and 205, also shown in
FIG. 11
were synthesized as reported by Vedejes et al.
J Am Chem Soc
(1989) 111:8430-8438. In addition, compounds 206-208 (
FIG. 11
) were synthesized by Borowitz, 1975, Mass spectra of 6-ketononanolides and related ketolactones,
J. Heterocyclic. Chem.
12(1): 101-106, compound 209 has been synthesized by Ireland et al.,
J Org Chem
(1980) 45:1868-1880.
The polyketides are synthesized in vivo by polyketide synthases (PKS). This group of enzymatically active proteins is considered in a different category from the fatty acid synthases which also catalyze condensation of 2-carbon units to result in, for example, fatty acids and prostaglandins. Two major types of PKS are known which are vastly different in their construction and mode of synthesis. These are commonly referred to as Type I or “modular” and Type II, “aromatic.”
The PKS scaffold that is the subject of the present invention is a member of the group designated Type I or “modular” PKS. In this type, a set of separate active sites exists for each step of carbon chain assembly and modification, but the individual proteins contain a multiplicity of such separate active sites. There may be only one multifunctional protein of this type, such as that required for the biosynthesis of 6-methyl salicylic acid (Beck, J. et al.,
Eur J Biochem
(1990) 192:487-498; Davis, R. et al.,
Abstracts of Genetics of Industrial Microorganism Meeting
, Montreal, Abstract P288 (1994)). More commonly, and in bacterial-derived Type I PKS assemblies, there are several such multifunctional proteins assembled to result in the end product polyketide. (Cortes, J. et al.,
Nature
(1990) 348:176; Donadio, S. et al.,
Science
(1991) 252:675; MacNeil, D. J. et al.,
Gene
(1992) 115:119.)
A number of modular PKS genes have been cloned. U.S. Pat. No. 5,252,474 describes cloning of genes encoding the synthase for avermectin; U.S. Pat. No. 5,098,837 describes the cloning of genes encoding the synthase for spiramycin; European application 791,655 and European application 791,656 describe the genes encoding the synthases for tylosin and platenolide respectively.
The PKS for erythromycin, used as an illustrative system is a modular PKS. Erythromycin was originally isolated from
S. erythraeus
(since reclassified as
Saccharopolyspora erythraea
) which was found in a soil sample from the Philippine archipelago. Cloning the genes was described by Donadio, S. et al.,
Science
(1991) 252:675. The particulars have been reviewed by Perun, T. J. in
Drug Action and Drug Resistance in Bacteria
, Vol. 1, S. Mitsuhashi (ed.) University Park Press, Baltimore, 1977. The antibiotic occurs in various glycosylated forms, designated A, B, C and D during various stages of fermentation. The entire erythromycin biosynthetic gene cluster from
S. erythraeus
has been mapped and sequenced by Donadio et al. in
Industrial Microorganisms: Basic and Applied Molecular Genetics
(1993) R. H. Baltz, G. D. Hegeman, and P. L. Skatrud (eds.) (
Amer Soc Microbiol
) and the entire PKS is an assembly of three such multifunctional proteins usually designated DEBS-1, DEBS-2, and DEBS-3, encoded by three separate genes.
Expression of the genes encoding the PKS complex may not be sufficient to permit the production by the synthase enzymes of polyketides when the genes are transformed into host cells that do not have the required auxiliary phosphopantetheinyl transferase enzymes which posttranslationally modify the ACP domains of the PKS. Genes encoding some of these transferases are described in WO97/13845. In addition, enzymes that mediate glycosylation of the polyketides synthesized are described in WO97/23630. U.S. Ser. No. 08/989,332 filed Dec. 11, 1997 now allowed describes the production of polyketides in hosts that normally do not produce them by supplying appropriate phosphopantetheinyl transferase expression systems. The contents of this application are incorporated herein by reference.
There have been attempts to alter the polyketide synthase pathway of modular PKS clusters. For example, European application 238,323 describes a process for enhancing production of polyketides by introducing a rate-limiting synthase gene and U.S. Pat. No. 5,514,544 describes use of an activator protein for the synthase in order to enhance production. U.S. Pat. Nos. 4,874,748 and 5,149,639 describe shuttle vectors that are useful in cloning modular PKS genes in general. Methods of introducing an altered gene into a microorganism chromosome are described in WO93/13663. Modification of the loading module for the DEBS-1 protein of the erythromycin-producing polyketide synthase to substitute the loading module for the avermectin-producing polyketide synthase in order to vary the starter unit was described by Marsden, Andrew F. A. et al.
Science
(1998) 279:199-202 and Oliynyk, M. et al.
Chemistry and Biology
(1996) 3:833-839. WO 98/01571, published Jan. 15, 1998, describes manipulation of the erythromycin PKS and polyketides resulting from such manipulation. In addition, WO 98/01546, also published Jan. 15, 1998 describes a hybrid modular PKS gene for varying the nature of the starter and extender units to synthesize polyketides.
In addition, U.S. Pat. Nos. 5,063,155 and 5,168,052 describe preparation of antibiotics using modular PKS systems. A number of modular PKS have been cloned. See, e.g., U.S. Pat. No. 5,098,837, EP 791,655, EP 791,656 and U.S. Pat. No. 5,252,474.
Type II PKS, in contrast to modular PKS, include several proteins, each of which is simpler than those found in Type I polyketide synthases. The active sites in these enzymes are used iteratively so that the proteins themselves are generally monofunctional or bifunctional. For example, the aromatic PKS complexes derived from Streptomyces have so far been found to contain three proteins encoded in three open reading frames. One protein provides ketosynthase (KS) and acyltransferase (AT) activities, a second provides a chain length determining factor (CLDF) and a third is an acyl carrier protein (ACP).
The present invention is concerned with PKS systems derived from modular PKS gene clusters. The nature of these clusters and their manipulation are further described below.
DISCLOSURE OF THE INVENTION
The invention provides recombinant materials for the production of combinatorial libraries of polyketides wherein the polyketide members of the library are synthesized by various PKS systems derived from naturally occurring PKS systems by using these systems as scaffolds. Generally, many members of these libraries may themselves be novel compounds, and the invention further includes novel polyketide members of these libraries. The invention methods may thus be directed to the preparation of an individual polyketide. The polyketide may or may not be novel, but the method of preparation permits a more convenient method of preparing it. The resulting polyketides may be further modified to convert them
Kao Camilla M.
Khosla Chaitan
Ponnaluri Padmashri
The Leland Stanford Junior University
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