Chemistry: molecular biology and microbiology – Process of mutation – cell fusion – or genetic modification – Introduction of a polynucleotide molecule into or...
Reexamination Certificate
2000-10-03
2003-11-11
Ketter, James (Department: 1636)
Chemistry: molecular biology and microbiology
Process of mutation, cell fusion, or genetic modification
Introduction of a polynucleotide molecule into or...
C435S254200, C435S254210, C435S320100, C435S255200, C568S833000
Reexamination Certificate
active
06645767
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates generally to materials and methods for engineering microorganisms such as yeast and bacteria whereby single or multiple copies of endogenous or exogenous genes of interest may be added to the microorganism without adding drug resistance gene markers by using a novel suite of recombinant yeast integration plasmids. Specifically, the methods and materials of this invention may be used to produce new strains of yeast which overproduce inositol but which lack drug resistance gene markers. The resulting recombinant microorganism does not contain any drug resistance gene markers and in the case of yeast the genetically modified organism could be considered “generally recognized as safe” (“GRAS”) if only endogenous
Saccharomyces cerevisiae
or other GRAS organism genes are introduced.
BACKGROUND
Biosafety of genetically modified microorganisms for uses in human food, animal feed or plant fertilizers is a major issue to be considered in the development and application of emerging biotechnologies. The United States, Europe, and Japan are especially sensitive to the potential biohazards from foods and additives from biotechnological sources. Most of the current recombinant DNA processes use circular DNA molecules called plasmids as cloning vectors to introduce homologous or heterologous genetic information into microorganisms such as bacteria, yeast, plant, and animal cells. Plasmids have the advantage that they exist normally in prokaryotic and lower eukaryotic cells in single or multimeric forms, which means that a certain gene located on such a plasmid could exist in the cell in multicopy form, which may result in a higher expression of the proteins encoded by these genes. In such instances plasmids serve as vectors on which the new genetic property or properties can be engineered and then be subsequently transferred into a host cell. In order to detect whether such a transfer has been successful and also to maintain the plasmid in the transformed cell, the plasmids must also contain a so-called selection gene marker. A selection gene marker is typically a gene that confers resistance to an antibiotic or another substance that kills or prevents the growth of cells that do not contain such a plasmid. A selection marker can also confer other phenotypic traits that can be selected such as the color of colonies, a new enzymatic activity, as well as others.
Plasmid vectors can be replicated in the host cell if they contain autonomous replication sequences recognized by the host DNA synthesis machinery, or if they are able to integrate in the genome of the host cell. The first type of such plasmids, also known as episomal plasmids, can be amplified in large numbers inside a single host cell and their replication is independent of the host chromosomal replication during the cell cycle. The other type of such plasmids, also known as integrative plasmids, can only be replicated and maintained if they are integrated into the host cell genome. Many plasmid vectors used to transform eukaryotic host cells are known as shuttle episomal vectors, meaning that they contain prokaryotic and eukaryotic DNA sequences that allow their episomal amplification in either type of host cells. There are also combinations of prokaryotic-episomal/eukaryotic-integrative shuttle vectors.
The DNA amplification step of all episomal plasmid vectors required to transform eukaryotic cells is preferably carried out in bacterial hosts due to their faster growth rate and ease of purification of the plasmidic DNA. Most plasmids used in molecular biology (such as pBR and pUC-derived plasmids) contain as a selection marker the bacterial drug resistance marker for the amp
r
or bla gene (See, Sutcliffe, J. G., et al.,
Proc. Natl. Acad. Sci. U.S.A
. 75:3737 (1978), the disclosure of which is incorporated herein by reference). The bla gene encodes an enzyme named TEM-1, which is a widespread plasmidic &bgr;-lactamase for narrow-spectrum cephalosporins, cefamandole, and cefoperazone and all the anti-gram-negative-bacterium penicillins except temocillin.
Unfortunately, when using the most common recombinant DNA plasmid vectors to transform microorganisms these drug resistance gene markers are inherently transferred along with the gene or genes that are of interest to the host microorganism. Consequently there is potential for the transfer of bacterial drug resistance genes from a genetically modified organism (“GMO”) used as a feed additive to a wild or pathogenic bacteria that is present in the normal intestinal flora of the animal being fed, thereby transforming the normal microbial flora of the animal into new and potentially dangerous antibiotic resistant strains. For example, the TEM-1 enzyme was first reported in 1965 from an
E. coli
isolate and is now the most common &bgr;-lactamase found in enterobacteria. Resistance in more than 50% of Amp
r
E. coli
clinical isolates is due to TEM-1.
The world is currently facing similar problems due to indiscriminant overuse or misuse of antibiotics to treat common human and animal illnesses. This overuse/misuse has created drug resistance in bacterial strains that are no longer responsive to available antibiotics. See, Levy, S. B.,
Scientific American
, March 1998, pp. 46-53, the disclosure of which is incorporated herein by reference. The FDA as well as the World Health Organization (WHO) and European regulatory agencies are concerned about biotechnology-derived products that could lead to the uncontrolled dissemination of drug resistance genes into the environment, hence posing a potential health problem. Therefore, genetically engineered organisms, for example, recombinant yeast containing bacterial drug resistance gene markers are considered potentially biohazardous and could not be used as food or as a feed additive without carrying out a comprehensive health and environmental risk assessment for its use.
Another disadvantage of plasmids that contain bacterial antibiotic selection gene markers for use in human or animal food fermentation is that antibiotics are costly and they must be present in the medium in which the bacterial host has to be cultivated. In response to this problem “food-grade” vectors have been developed. See, for example, U.S. Pat. No. 5,627,072, the disclosure of which is incorporated herein by reference.
In the specific case of yeast, and in particular those of the genus Saccharomvces, a recombinant molecule containing a drug resistance gene marker would not be considered “generally recognized as safe” (“GRAS”) by the Food and Drug Administration and would be considered to be a potential biohazard unless a risk assessment is performed on the recombinant yeast. The GRAS classification is important when choosing a microorganism to industrially manufacture a product such as inositol that is also GRAS (see, 21 C.F.R. 184.1370(c)), since a byproduct of the fermentation is the yeast biomass itself or its extract. Therefore, if the yeast biomass is biohazard-free, it can itself be sold for profit as a valuable feed or food additive, which is the case for the genus Saccharomyces. Conversely, a non-GRAS biomass, such as certain yeasts of the genus Candida, for example,
Candida boidinii
, can be considered biohazardous waste, and therefore such biomass has to be disposed of by costly procedures which add to the production cost and which could potentially impact the environment. Currently, biohazardous biomass has to be either incinerated or disposed of according to the NIH guidelines for the treatment of biohazardous waste. Therefore, having a “GRAS” regulatory status is an important aspect to be considered for a successful industrial biotechnology process.
Fermentation technology can produce many compounds at a lower manufacturing cost than the present chemical technologies, with the added advantage of being environmentally safe. Such an example is the production of inositol and inositol-containing metabolites. Industrial methods to produce inositol have been based on chemical conversion of phytic acid (inosi
Henry Susan A.
Villa Manuel J.
Carnegie Mellon University
Katcheves Konstantina
Ketter James
Reed Smith LLP
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