Process for the Production of Fine Chemicals

Abstract

The present invention relates to a process for the production of fine chemicals in a microorganism, a plant cell, a plant, a plant tissue or parts thereof. The invention furthermore relates to nucleic acid molecules, polypeptides, nucleic acid constructs, vectors, antisense molecules, antibodies, host cells, plant tissue, propagtion material, harvested material, plants, microorganisms as well as agricultural compositions and to their use.

1 . A process for the production of fine chemical, comprising increasing or generating in an organism or a part thereof the expression of at least one nucleic acid molecule comprising a nucleic acid molecule selected from the group consisting of:
 a) a nucleic acid molecule encoding of the polypeptide as depicted in SEQ ID NO: 376 or a fragment thereof, which confers an increase in the amount of fine chemical in an organism or a part thereof;   b) a nucleic acid molecule comprising of the nucleic acid molecule as depicted in SEQ ID NO: 375;   c) a nucleic acid molecule whose sequence can be deduced from a polypeptide sequence encoded by a nucleic acid molecule of (a) or (b) as a result of the degeneracy of the genetic code and conferring an increase in the amount of fine chemical in an organism or a part thereof;   d) a nucleic acid molecule which encodes a polypeptide which has at least 50% identity with the amino acid sequence of the polypeptide encoded by the nucleic acid molecule of (a) to (c) and conferring an increase in the amount of fine chemical in an organism or a part thereof; and   e) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (a) to (c) under stringent hybridization conditions and conferring an increase in the amount of fine chemical in an organism or a part thereof;   
       or a nucleotide sequence complementary thereto. 
     
     
         2 . The process of  claim 1 , further comprising growing the organism under conditions which permit the production of the fine chemical in said organism. 
     
     
         3 . The process of  claim 1 , further comprising recovering the free or bound fine chemical. 
     
     
         4 . The process of  claim 1 , further comprising:
 a) selecting an organism or part thereof expressing the polypeptide encoded by the nucleic acid molecule;   b) mutagenizing the selected organism or part thereof;   c) comparing the activity or the expression level of said polypeptide in the mutated organism or part thereof with the activity or the expression of said polypeptide of the selected organism or part thereof;   d) selecting a mutated organism or part thereof having an increased activity or expression level of said polypeptide compared to the selected organism or part thereof;   e) optionally, growing and cultivating the organism or part thereof; and   f) recovering, and optionally isolating, the free or bound fine chemical produced by the selected mutated organism or part thereof.   
     
     
         5 . The process of  claim 1 , wherein the activity of said protein or the expression of said nucleic acid molecule is increased or generated transiently or stably. 
     
     
         6 . An isolated nucleic acid molecule comprising a nucleic acid molecule selected from the group consisting of:
 a) a nucleic acid molecule encoding of the polypeptide as depicted in SEQ ID NO: 376 or a fragment thereof, which confers an increase in the amount of fine chemical in an organism or a part thereof;   b) a nucleic acid molecule comprising of the nucleic acid molecule as depicted in SEQ ID NO: 375 or a fragment thereof, which confers an increase in the amount of fine chemical in an organism or a part thereof;   c) a nucleic acid molecule whose sequence can be deduced from a polypeptide sequence encoded by a nucleic acid molecule of (a) or (b) as a result of the degeneracy of the genetic code and conferring an increase in the amount of fine chemical in an organism or a part thereof;   d) a nucleic acid molecule which encodes a polypeptide which has at least 50% identity with the amino acid sequence of the polypeptide encoded by the nucleic acid molecule of (a) to (c) and conferring an increase in the amount of fine chemical in an organism or a part thereof; and   e) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (a) to (c) under stringent hybridization conditions and conferring an increase in the amount of fine chemical in an organism or a part thereof;   
       whereby the nucleic acid molecule distinguishes over the sequence as depicted in SEQ ID NO: 375 by one or more nucleotides. 
     
     
         7 . A nucleic acid construct comprising one or more regulatory elements which confers the expression of the nucleic acid molecule of  claim 6 . 
     
     
         8 . A vector comprising the nucleic acid molecule of  claim 6 . 
     
     
         9 . The vector of  claim 8 , wherein the nucleic acid molecule is in operable linkage with regulatory sequences for the expression in a prokaryotic or eukaryotic host. 
     
     
         10 . A host cell transformed stably or transiently with the nucleic acid molecule of  claim 6 . 
     
     
         11 . The host cell of  claim 10 , wherein the host cell is a plant cell, an animal cell, a microorganism, a yeast cell, a fungus cell, a prokaryotic cell, an eukaryotic cell or an archaebacterium. 
     
     
         12 . A process for producing a polypeptide, wherein the process comprises stably or transiently transforming the nucleic acid molecule of  claim 6  into a host cell, and expressing the polypeptide encoded by said nucleic acid molecule in the host cell. 
     
     
         13 . The polypeptide produced by the process of  claim 12  wherein the polypeptide distinguishes over the sequence as depicted in SEQ ID NO: 376 by one or more amino acids. 
     
     
         14 . A plant, or plant tissue, propagation material, or harvested material thereof comprising the host cell of  claim 11 , wherein the host cell is a plant cell or an  Agrobacterium.    
     
     
         15 . A method for screening for agonists and antagonists of the activity of a polypeptide encoded by the nucleic acid molecule of  claim 6  conferring an increase in the amount of fine chemical in an organism or a part thereof comprising:
 a) contacting cells, tissues, plants or microorganisms which express a polypeptide encoded by the nucleic acid molecule of  claim 6  conferring an increase in the amount of the fine chemical in an organism or a part thereof with a candidate compound or a sample comprising a plurality of compounds under conditions which permit the expression of the polypeptide; 
 b) assaying the fine chemical level or the polypeptide expression level in the cells, tissues, plants or microorganisms or a media wherein the cells, tissues, plants or microorganisms are cultured or maintained; and 
 c) identifying the agonist or antagonist by comparing the measured fine chemical level or polypeptide expression level with a standard fine chemical or polypeptide expression level measured in the absence of said candidate compound or said sample comprising said plurality of compounds, wherein an increased level over the standard indicates that the compound or the sample comprising said plurality of compounds is an agonist and a decreased level over the standard indicates that the compound or the sample comprising said plurality of compounds is an antagonist. 
 
     
     
         16 . A process for the identification of a compound conferring increased fine chemical production in a plant or microorganism, comprising the steps:
 a) culturing a plant cell or tissue or microorganism or maintaining a plant expressing the polypeptide encoded by the nucleic acid molecule of  claim 6  conferring an increase in the amount of the fine chemical in an organism or a part thereof, and utilizing a readout system which is capable of interacting with the polypeptide under suitable conditions which permit the interaction of the polypeptide with said readout system in the presence of a compound or a sample comprising a plurality of compounds, and said readout system is capable of providing a detectable signal in response to the binding of a compound to said polypeptide under conditions which permit the expression of said readout system and the expression of the polypeptide encoded by the nucleic acid molecule of  claim 6  conferring an increase in the amount of the fine chemical in an organism or a part thereof;   b) identifying if the compound is an effective agonist by detecting the presence or absence or increase of a signal produced by said readout system.   
     
     
         17 . A method for the identification of a gene product conferring an increase in the fine chemical production in a cell, comprising the following steps:
 a) contacting the nucleic acid molecules of a sample, which can contain a candidate gene encoding a gene product conferring an increase in fine chemical after expression with the nucleic acid molecule of  claim 6 ;   b) identifying the nucleic acid molecules, which hybridize under relaxed stringent conditions with the nucleic acid molecule of  claim 6 ;   c) introducing the candidate nucleic acid molecules in host cells appropriate for producing the fine chemical;   d) expressing the identified nucleic acid molecules in the host cells;   e) assaying the fine chemical level in the host cells; and   f) identifying nucleic acid molecule and its gene product which expression confers an increase in the fine chemical level in the host cell after expression compared to the wild type.   
     
     
         18 . A method for the identification of a gene product conferring an increase in fine chemical production in a cell, comprising the following steps:
 a) identifying in a data bank nucleic acid molecules of an organism; which can contain a candidate gene encoding a gene product conferring an increase in the fine chemical amount or level in an organism or a part thereof after expression, and which are at least 30% homolog to the nucleic acid molecule of  claim 6 ;   b) introducing the candidate nucleic acid molecules in host cells appropriate for producing the fine chemical;   c) expressing the identified nucleic acid molecules in the host cells;   d) assaying the fine chemical level in the host cells; and   e) identifying the nucleic acid molecule and its gene product which expression confers an increase in the fine chemical level in the host cell after expression compared to the wild type.   
     
     
         19 . A method for the production of an agricultural composition comprising identifying a compound according to the method of  claim 16 , and formulating the identified compound in a form acceptable for an application in agriculture. 
     
     
         20 . Food or feed composition comprising the nucleic acid molecule of  claim 6 , a nucleic acid construct or a vector thereof, a polypeptide encoded thereby or an antibody which specifically binds to said polypeptide, a plant, plant tissue or harvested material thereof, or a host cell containing said nucleic acid molecule. 
     
     
         21 . A composition comprising the nucleic acid molecule of  claim 6 , a polypeptide encoded thereby, or an antibody which specifically binds to said polypeptide, or a nucleic acid construct or a vector thereof, and optionally an agricultural acceptable carrier. 
     
     
         22 . A composition comprising an antagonist or agonist of the activity of a polypeptide encoded by the nucleic acid molecule of  claim 6  conferring an increase in the amount of fine chemical in an organism or a part thereof. 
     
     
         23 . Food or feed composition comprising the antagonist or agonist identified according to  claim 15 . 
     
     
         24 . A method for identifying plant varieties having increased capacity for production of a fine chemical, wherein the method comprises using the nucleic acid molecules of  claim 6  in mapping and/or breeding processes, and identifying plant varieties which have increased production of said fine chemical.