Corynebacterium glutamicum genes encoding novel proteins

Abstract

Isolated nucleic acid molecules, designated MCP nucleic acid molecules, which encode novel MCP proteins from Corynebacterium glutamicum are described. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing MCP nucleic acid molecules, and host cells into which the expression vectors have been introduced. The invention still further provides isolated MCP proteins, mutated MCP proteins, fusion proteins, antigenic peptides and methods for the improvement of production of a desired compound from C. glutamicum based on genetic engineering of MCP genes in this organism.

1 . An isolated nucleic acid molecule selected from the group consisting of
 a) an isolated nucleic acid molecule encoding an MCP protein, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1, or a complement thereof;   b) an isolated  Corynebacterium glutamicum  nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of those sequences set forth in Appendix A, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1, or a complement thereof;   c) an isolated nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence selected from the group consisting of those sequences set forth in Appendix B, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1, or a complement thereof;   d) an isolated nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising an amino acid sequence selected from the group consisting of those sequences set forth in Appendix B, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1, or a complement thereof;   e) an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 50% identical to an entire nucleotide sequence selected from the group consisting of those sequences set forth in Appendix A, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1, or a complement thereof;   f) an isolated nucleic acid molecule comprising a fragment of at least 15 contiguous nucleotides of a nucleotide sequence selected from the group consisting of those sequences set forth in Appendix A, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1, or a complement thereof; and   g) an isolated nucleic acid molecule which hybridizes in 6× sodium chloride/sodium citrate (SSC) at 65° C. to the complement of a nucleotide sequence selected from the group consisting of those sequences set forth in Appendix A, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1, or a complement thereof.   
     
     
         2 . An isolated nucleic acid molecule comprising the nucleic acid molecule of  claim 1  and a nucleotide sequence encoding a heterologous polypeptide. 
     
     
         3 . A vector comprising the nucleic acid molecule of  claim 1 . 
     
     
         4 . The vector of  claim 3 , which is an expression vector. 
     
     
         5 . A host cell transfected with the expression vector of  claim 4 . 
     
     
         6 . The host cell of  claim 5 , wherein said cell is a microorganism. 
     
     
         7 . The host cell of  claim 6 , wherein said cell belongs to the genus  Corynebacterium  or  Brevibacterium.    
     
     
         8 . A method of producing a polypeptide comprising culturing the host cell of  claim 7  in an appropriate culture medium to, thereby, produce the polypeptide. 
     
     
         9 . A method for producing a fine chemical, comprising culturing the cell of  claim 7  such that the fine chemical is produced. 
     
     
         10 . The method of  claim 9 , wherein said method further comprises the step of recovering the fine chemical from said culture. 
     
     
         11 . The method of  claim 9 , wherein said cell belongs to the genus  Corynebacterium  or  Brevibacterium.    
     
     
         12 . The method of  claim 9 , wherein said cell is selected from the group consisting of  Corynebacterium glutamicum, Corynebacterium herculis, Corynebacterium lilium, Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Corynebacterium acetophilum, Corynebacterium ammoniagenes, Corynebacterium fujiokense, Corynebacterium nitrilophilus, Brevibacterium ammoniagenes, Brevibacterium butanicum, Brevibacterium divaricatum, Brevibacteriumflavum, Brevibacterium healii, Brevibacterium ketoglutamicum, Brevibacterium ketosoreductum, Brevibacterium lactofermentum, Brevibacterium linens, Brevibacterium paraffinolyticum , and those strains set forth in Table 3. 
     
     
         13 . The method of  claim 9 , wherein expression of the nucleic acid molecule from said vector results in modulation of production of said fine chemical. 
     
     
         14 . The method of  claim 9 , wherein said fine chemical is selected from the group consisting of organic acids, proteinogenic and nonproteinogenic amino acids, purine and pyrimidine bases, nucleosides, nucleotides, lipids, saturated and unsaturated fatty acids, diols, carbohydrates, aromatic compounds, vitamins, cofactors, polyketides, and enzymes. 
     
     
         15 . The method of  claim 9 , wherein said fine chemical is an amino acid selected from the group consisting of lysine, glutamate, glutamine, alanine, aspartate, glycine, serine, threonine, methionine, cysteine, valine, leucine, isoleucine, arginine, proline, histidine, tyrosine, phenylalanine, and tryptophan. 
     
     
         16 . An isolated polypeptide selected from the group consisting of
 a) an isolated MCP polypeptide;   b) an isolated polypeptide comprising an amino acid sequence selected from the group consisting of those sequences set forth in Appendix B, provided that the amino acid sequence is not encoded by any of the F-designated genes set forth in Table 1;   c) an isolated polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of those sequences set forth in Appendix A, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1;   d) an isolated polypeptide comprising a naturally occurring allelic variant of a polypeptide comprising an amino acid sequence selected from the group consisting of those sequences set forth in Appendix B, provided that the amino acid sequence is not encoded by any of the F-designated genes set forth in Table 1;   e) an isolated polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence which is at least 50% identical to an entire nucleotide sequence selected from the group consisting of those sequences set forth in Appendix A, provided that the nucleic acid molecule does not consist of any of the F-designated genes set forth in Table 1;   f) an isolated polypeptide comprising an amino acid sequence which is at least 50% identical to an entire amino acid sequence selected from the group consisting of those sequences set forth in Appendix B, provided that the amino acid sequence is not encoded by any of the F-designated genes set forth in Table 1; and   g) an isolated polypeptide comprising a fragment of a polypeptide comprising an amino acid sequence selected from the group consisting of those sequences set forth in Appendix B, provided that the amino acid sequence is not encoded by any of the F-designated genes set forth in Table 1, wherein said polypeptide fragment maintains a biological activity of the polypeptide comprising the amino sequence.   
     
     
         17 . The isolated polypeptide of  claim 16 , further comprising a heterologous amino acid sequence. 
     
     
         18 . A method for diagnosing the presence or activity of  Corynebacterium diphtheriae  in a subject, comprising detecting the presence of at least one of the nucleic acid molecules of  claim 1 , thereby diagnosing the presence or activity of  Corynebacterium diphtheriae  in the subject. 
     
     
         19 . A method for diagnosing the presence or activity of  Corynebacterium diphtheriae  in a subject, comprising detecting the presence of at least one of the polypeptide molecules of  claim 16 , thereby diagnosing the presence or activity of  Corynebacterium diphtheriae  in the subject. 
     
     
         20 . A host cell comprising a nucleic acid molecule selected from the group consisting of
 a) a nucleic acid molecule set forth in Appendix A, wherein the nucleic acid molecule is disrupted by at least one technique selected from the group consisting of a point mutation, a truncation, an inversion, a deletion, an addition, a substitution and homologous recombination;   b) a nucleic acid molecule set forth in Appendix A, wherein the nucleic acid molecule comprises one or more nucleic acid modifications as compared to the sequence set forth in Appendix A, wherein the modification is selected from the group consisting of a point mutation, a truncation, an inversion, a deletion, an addition and a substitution; and   c) a nucleic acid molecule set forth in Appendix A, wherein the regulatory region of the nucleic acid molecule is modified relative to the wild-type regulatory region of the molecule by at least one technique selected from the group consisting of a point mutation, a truncation, an inversion, a deletion, an addition, a substitution and homologous recombination.