US 2005O1534O2A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0153402 A1 Pompeius et al. (43) Pub. Date: Jul. 14, 2005 (54) CORYNEBACTERIUM GLUTAMICUM Jul. 8, 1999 (DE)........................................ 1993.1420.9 GENES ENCODING REGULATORY Jul. 9, 1999 (DE). ... 199321. 22.1 PROTEINS Jul. 9, 1999 (DE) 19932.128.0 Jul. 9, 1999 (DE) 19932.134.5 (75) Inventors: Markus Pompeius, Waldsee (DE); Jul. 9, 1999 (DE). ... 19932206.6 Burkhard Kroger, Limburgerhof (DE); Jul. 9, 1999 (DE) 199322O7.4 Hartwig Schroder, Nubloch (DE); Jul. 14, 1999 (DE) 1993.30O3.4 Oskar Zelder, Speyer (DE); Gregor Aug. 31, 1999 (DE). ... 1994.1390.8 Haberhauer, Limburgerhof (DE) Sep. 3, 1999 (DE). 19942O882 Sep. 3, 1999 (DE)........................................ 19942124.2 Correspondence Address: LAHIVE & COCKFIELD, LLP. Publication Classification 28 STATE STREET BOSTON, MA 02109 (US) (51) Int. Cl. ............................ C12P 13/04; C12O 1/68; C07H 21/04; C12N 9/00; (73) Assignee: BASF AG, Ludwigshafen (DE) C12N 1/21; C12N 15/74 (21) Appl. No.: 11/006,098 (52) U.S. Cl. ............................. 435/106; 435/6; 435/69.1; 435/183; 435/320.1; 435/252.3; (22) Filed: Dec. 6, 2004 536/23.2 Related U.S. Application Data (57) ABSTRACT (63) Continuation of application No. 09/602,874, filed on Jun. 23, 2000, now abandoned. Isolated nucleic acid molecules, designated MR nucleic acid molecules, which encode novel MR proteins from Coryne (60) Provisional application No. 60/141,031, filed on Jun. bacterium glutamicum are described. The invention also 25, 1999. Provisional application No. 60/142,690, provides antisense nucleic acid molecules, recombinant filed on Jul. 1, 1999. Provisional application No. expression vectors containing MR nucleic acid molecules, 60/151,251, filed on Aug. 27, 1999. and host cells into which the expression vectors have been introduced. The invention still further provides isolated MR (30) Foreign Application Priority Data proteins, mutated MR proteins, fusion proteins, antigenic peptides and methods for the improvement of production of Jul. 1, 1999 (DE)........................................ 19930476.9 a desired compound from C. glutamicum based on genetic Jul. 8, 1999 (DE)........................................ 19931419.5 engineering of MR genes in this organism. US 2005/O153402 A1 Jul. 14, 2005 CORYNEBACTERIUM GLUTAMICUM GENES molecules of the invention, therefore, can be used to identify ENCODING REGULATORY PROTEINS microorganisms which can be used to produce fine chemi cals, e.g., by fermentation processes. Modulation of the RELATED APPLICATIONS expression of the MR nucleic acids of the invention, or modification of the sequence of the MR nucleic acid mol 0001. This application claims priority to U.S. Provisional ecules of the invention, can be used to modulate the pro Patent Application No. 60/141,031, filed Jun. 25, 1999, U.S. duction of one or more fine chemicals from a microorganism Provisional Patent Application No. 60/142,690, filed Jul. 1, (e.g., to improve the yield or production of one or more fine 1999, and also to U.S. Provisional Patent Application No. chemicals from a Corynebacterium or Brevibacterium spe 60/151,251, filed Aug. 27, 1999. This application also claims priority to German Patent Application No. 19930476.9, filed cies). Jul. 1, 1999, German Patent Application No. 19931419.5, 0005. The MR nucleic acids of the invention may also be filed Jul. 8, 1999, German Patent Application No. 1993 used to identify an organism as being Corynebacterium 1420.9, filed Jul. 8, 1999, German Patent Application No. glutamicum or a close relative thereof, or to identify the 19932122.1, filed Jul. 9, 1999, German Patent Application presence of C. glutamicum or a relative thereof in a mixed No. 19932128.0, filed Jul. 9, 1999, German Patent Appli population of microorganisms. The invention provides the cation No. 19932.134.5, filed Jul. 9, 1999, German Patent nucleic acid Sequences of a number of C. glutamicum genes, Application No. 19932206.6, filed Jul. 9, 1999, German by probing the extracted genomic DNA of a culture of a Patent Application No. 199322074, filed Jul. 9, 1999, unique or mixed population of microorganisms under Strin German Patent Application No. 19933003.4, filed Jul. 14, gent conditions with a probe Spanning a region of a C. 1999, German Patent Application No. 1994.1390.8, filed glutamicum gene which is unique to this organism, one can Aug. 31, 1999, German Patent Application No. 19942088.2, ascertain whether this organism is present. Although filed Sep. 3, 1999, and German Patent Application No. Corynebacterium glutamicum itself is nonpathogenic, it is 199421242, filed Sep. 3, 1999. The entire contents of all of related to species pathogenic in humans, Such as Coryne the aforementioned applications are hereby expressly incor bacterium diphtheriae (the causative agent of diphtheria); porated herein by this reference. the detection of Such organisms is of Significant clinical relevance. BACKGROUND OF THE INVENTION 0006. The MR nucleic acid molecules of the invention 0002 Certain products and by-products of naturally-oc may also serve as reference points for mapping of the C. curring metabolic processes in cells have utility in a wide glutamicum genome, or of genomes of related organisms. array of industries, including the food, feed, cosmetics, and Similarly, these molecules, or variants or portions thereof, pharmaceutical industries. These molecules, collectively may serve as markers for genetically engineered Coryne termed fine chemicals, include organic acids, both protei bacterium or Brevibacterium species. e.g. The MR proteins nogenic and non-proteinogenic amino acids, nucleotides and encoded by the novel nucleic acid molecules of the inven nucleosides, lipids and fatty acids, diols, carbohydrates, tion are capable of, for example, performing a function aromatic compounds, Vitamins and cofactors, and enzymes. involved in the transcriptional, translational, or posttransla Their production is most conveniently performed through tional regulation of proteins important for the normal meta the large-scale culture of bacteria developed to produce and bolic functioning of cells. Given the availability of cloning Secrete large quantities of one or more desired molecules. vectors for use in Corynebacterium glutamicum, Such as One particularly useful organism for this purpose is Coryne those disclosed in Sinskey et al., U.S. Pat. No. 4,649,119, bacterium glutamicum, a gram positive, nonpathogenic bac and techniques for genetic manipulation of C. glutamicum terium. Through Strain Selection, a number of mutant Strains and the related Brevibacterium species (e.g., lactofermen have been developed which produce an array of desirable tum) (Yoshihama et al., J. Bacteriol. 162: 591-597 (1985); compounds. However, Selection of Strains improved for the Katsumata et al., J. Bacteriol. 159: 306-311 (1984); and production of a particular molecule is a time-consuming and Santamaria et al., J. Gen. Microbiol. 130: 2237-2246 difficult process. (1984)), the nucleic acid molecules of the invention may be utilized in the genetic engineering of this organism to make SUMMARY OF THE INVENTION it a better or more efficient producer of one or more fine chemicals. 0003. The invention provides novel bacterial nucleic acid 0007. This improved yield, production and/or efficiency molecules which have a variety of uses. These uses include of production of a fine chemical may be due to a direct effect the identification of microorganisms which can be used to of manipulation of a gene of the invention, or it may be due produce fine chemicals, the modulation of fine chemical to an indirect effect of Such manipulation. Specifically, production in C. glutamicum or related bacteria, the typing alterations in C. glutamicum MR proteins which normally or identification of C. glutamicum or related bacteria, as regulate the yield, production and/or efficiency of produc reference points for mapping the C. glutamicum genome, tion of a fine chemical metabolic pathways may have a direct and as markers for transformation. These novel nucleic acid impact on the overall production or rate of production of one molecules encode proteins, referred to herein as metabolic or more of these desired compounds from this organism. regulatory (MR) proteins. Alterations in the proteins involved in these metabolic 0004 C. glutamicum is a gram positive, aerobic bacte pathways may also have an indirect impact on the yield, rium which is commonly used in industry for the large-scale production and/or efficiency of production of a desired fine production of a variety of fine chemicals, and also for the chemical. Regulation of metabolism is necessarily complex, degradation of hydrocarbons (Such as in petroleum spills) and the regulatory mechanisms governing different path and for the oxidation of terpenoids. The MR nucleic acid ways may interSect at multiple points Such that more than US 2005/O153402 A1 Jul. 14, 2005 one pathway can be rapidly adjusted in accordance with a bolic pathway proteins (MR), which are capable of, for particular cellular event. This enables the modification of a example, performing an enzymatic Step involved in the regulatory protein for one pathway to have an impact on the transcriptional, translational, or posttranslational regulation regulation of many other pathways as well, Some of which of metabolic pathways in C. glutamicum. Nucleic acid may be involved in the biosynthesis or degradation of a molecules