Staphylococcal GTPase obg nucleotide sequence encoding Staphylococcal GTP-binding protein

Abstract

The present invention provides an isolated Staphylococcal GTPase obg gene and a Staphylococcal GTP-binding protein encoded thereby. A recombinant expression vector and an engineered host cell are also provided that include a polynucleotide encoding a Staphylococcal GTP-binding protein. The present invention further relates to a method of producing Staphylococcal GTP-binding protein and a method for high throughput screening to identify potential antimicrobial compounds useful against Staphylococcal bacterial strains.

Description

FIELD OF THE INVENTION

[0002] The present invention generally relates to nucleotide sequences that encode proteins which are essential for bacterial growth. More particularly, the present invention is directed to a GTPase obg gene encoding a GTP-binding protein in Staphylococcal bacterial strains. Specifically, the present invention is directed to a Staphylococcus aureus (“S. aureus”) obg gene that is capable of expression in a host cell to produce enzymatically functional S. aureus GTP-binding protein. Additionally, the present invention pertains to recombinant expression vectors incorporating the GTPase obg gene of the present invention. The present invention is further directed to Staphylococcal GTP-binding protein, methods for producing GTP-binding protein, and methods for using GTP-binding protein as a novel thereapeutic target in affinity-based pharmacological screening procedures for the discovery of antibiotics active against S. aureus and other Staphylococcal bacteria.

BACKGROUND OF THE INVENTION

[0003] Numerous pathogenic organisms are responsible for infectious disease and health-related problems in humans and other animals throughout the United States and the world. As treatments are developed for combating a particular organism, such as treatments incorporating newly developed antibiotics and chemical compounds effective at eliminating existing strains of a particular organism, newer strains of such organisms emerge which are resistant to the existing treatments. Accordingly, there remains a continual need for the development of new ways for pharmaceutically combating pathogenic organisms.

[0004] One particular organism of concern is the bacterium S. aureus, which is an opportunistic human pathogen both in the community and in hospitals, and is the primary cause of nosocomial bacterial infections in the United States. S. aureus has a highly invasive nature and is associated with a number of life threatening systemic illnesses, such as bacteremia/sepsis, toxic shock syndrome and toxic epidermal necrolysis, as well as common bacterial infections of the skin. Once the organism enters the bloodstream, patients are at risk of developing serious diseases such as endocarditis, osteomyelitis, and septic shock.

[0005] Despite the development and use of newer antimicrobial agents to combat S. aureus infections, the morbidity and mortality from serious S. aureus infections remain high. One reason is that S. aureus is adept in developing resistance to multiple antibiotics. The recent emergence of methicillin-resistant and vancomycin-resistant strains of S. aureus in Japan, and subsequently in the United States, has further highlighted the importance of finding alternative approaches to the prevention and treatment of Staphylococcal infections, and has focused renewed attention on the need for development of new classes of antibiotics to combat such bacterial strains. Despite the imminent crisis in S. aureus antibiotic resistance, the identification of novel targets for the development of novel antimicrobial agents remains elusive.

[0006] One promising way of pharmaceutically combating bacterial strains, including S. aureus and other Staphylococcal strains, is to interfere with genetic processes relating to growth and/or viability of the bacteria. Methods for combating organisms by interfering with genetic processes essential to survival and growth of the organism are becoming of increasing interest. In particular, researchers are directing their attention to chemical compounds that interfere with such processes.

[0007] A potential target for use with screening processes to identify chemical compounds that are useful in combating pathogenic organisms is a GTPase superfamily of GTP(guanosinetriphosphate)-binding proteins that includes G-proteins, elongation factors in E. coli, mammalian Ras, and procaryotic proteins such as Era, FtsZ, and Fth, etc. These GTPase regulatory molecules are classified as belonging to the GTPase superfamily due to a common ability to bind guanine nucleotides and hydrolyse GTP. March, “Membrane-Associated GTPases in Bacteria”, Molec. Microbiol., Vol. 6, pp. 1253-57, 1992.

[0008] GTP-binding proteins are important signaling molecules in bacteria as well as in eukaryotic cells. GTP-binding proteins have been recognized for many years as components of signal transduction pathways in eukaryotes. Only recently, however, has it been discovered that prokaryotes contain GTP-binding proteins that are essential for growth and/or viability of the organism. The involvement of these bacterial proteins in signal transduction in prokaryotes, however, is still not entirely clear.

[0009] One member of this superfamily of GTP-binding proteins which is of particular interest is the protein expressed by the obg gene (short for spoOB-associated GTP-binding protein). The obg gene specifically encodes a GTP-binding protein which is essential for bacterial growth and which is structurally conserved across an extraordinarily wide range of bacterial species. Obg was initially identified as a gene dowstream of the stage 0 sporulation gene spoOB in Bacillus subtilis in 1989. Trach et al., “The Bacillus subtilis spoOB Stage 0 Sporulation Operon Encodes An Essential GTP-Binding Protein” J. Bacteriol., Vol. 171, pp. 1362-71, 1989. Transcription analysis of this operon revealed that spoOB and obg are cotranscribed.

[0010] Various observations have been made about the Obg protein in certain organisms. Obg in Bacillus subtilis has been shown to bind GTP by the cross-linking method. Trach et al., supra. Bacillus subtilis Obg has also been characterized by its enzymatic activity with respect to GTP hydrolysis. Welsh et al., “Biochemical Characterization of the Essential GTP-Binding Protein Obg of Bacillus subtilis”, J. Bacteriol., Vol. 176, pp. 7161-68, 1994. It has also been demonstrated that Obg plays a crucial role in sporulation induction in Bacillus subtilis and Streptomyces griseus. Kok et al., “Effects on Bacillus subtilis of a Conditional Lethal Mutation in the Essential GTP-Binding Protein Obg”, J. Bacteriol., Vol. 176, pp. 7155-60, 1994; Okamoto et al., “Molecular Cloning and Characterization of the obg Gene of Streptomyces griseus in Relation to the Onset of Morphological Differentiation”, J. Bacteriol., Vol. 179, pp. 170-79, 1997.

[0011] Very little is known, however, about the physiological function of Obg. Obg homologs have recently been discovered in a diverse range of organisms ranging from bacteria to archaea to humans, and the evolutionary conservation between distantly related species suggests that this family of GTP-binding proteins has a fundamental, but unknown, cellular function. It has been proposed that, by monitoring the intracellular GTP pool size, Obg is involved in sensing changes in the nutritional environment leading ultimately to morphological differentiation. Okamoto et al., supra.

[0012] Obg is a unique GTPase in that it possesses an extended N-terminal glycine-rich domain not found in eukaryotic or archaeal homologs. An isolated Bacillus subtilus temperature-sensitive obg mutant was found to carry two closely linked missense mutations in the N-terminal domain, suggesting that this portion of obg is essential for cellular function. Kok et al., supra.

[0013] Very little is known about the essential functions of Obg, however. To date, Obg has been validated to be essential for growth in both Gram-negative bacteria (E. coli, Caulobacter crescentus) and Gram-positive bacteria (Bacillus subtilis). Maddock et al., “Identification of an Essential Caulobacter crescentus Gene Encoding a Member of the Obg Family of GTP-Binding Proteins”, J. Bacteriol., Vol. 179, pp. 6426-31, 1997; Arigoni et al., “A Genome-Based Approach for the Identification of Essential Bacterial Genes”, Nature Biotechnology, Vol. 16, pp. 851-56, 1998; Trach et al., supra. In addition, depletion of Obg has been shown to cause cessation of Bacillus subtilis cell growth. Vidwans et al., “Possible Role for the Essential GTP-Binding Protein Obg in Regulating the Initiation of Sporulation in Bacillus subtilis”, J. Bacteriol., Vol. 177, pp. 3308-11, 1995. Because the Obg protein appears to be essential for cell growth and/or viability, compounds that interfere with Obg functionality, such as compounds which bind with and inhibit Obg, are of interest as potential antimicrobial agents.

[0014] The Obg family is attractive as a potential target for antibacterial drug discovery for several reasons. First, the obg gene is a novel target because it is a hypothetical open reading frame (ORF) and its function is essentially unknown. Further, Obg homologs are highly conserved among bacteria. Additionally, there is a low toxicity potential because the obg gene is distinguishable from its nearest human homologs. Furthermore, the obg gene encodes essential cell function, to the extent that mutation is detrimental for cell growth. Finally, Obg protein GTPase activity can be assayed in vitro, in light of functional similarity with in vivo activity, and assays are relatively simple for target development.

[0015] U.S. Pat. Nos. 5,585,277 and 5,679,582 to Bowie et al. disclose methods for screening chemical compounds for potential pharmaceutical or antimicrobial effectiveness. Among other things, these patents teach methods for identifying possible ligands which bind to target proteins. The methods of these patents may be useful in affinity-based assays for the initial identification of chemical compounds that interfere in vitro with protein function by binding with and inhibiting the protein of interest.

[0016] To date, however, the obg gene sequence and the encoded protein have not been identified in Staphylococcal bacterial strains, such as S. aureus. Accordingly, it can be seen that there remains a need in the art for the identification of GTPase obg gene DNA sequences that encode GTP-binding protein in Staphylococcal bacterial strains, such as S. aureus. Further, there remains a need in the art for the identification of a Staphylococcal obg gene that is capable of expression in a host cell to produce functional Staphylococcal GTP-binding protein for use in screening procedures for antimicrobial compounds. Additionally, there remains a need for recombinant expression vectors incorporating a Staphylococcal GTPase obg gene. Further, there remains a need for methods for producing GTP-binding protein and for using GTP-binding protein as a novel therapeutic target in screening procedures directed toward the discovery of antimicrobial agents active against Staphylococcal bacteria, and S. aureus in particular. The present invention is directed to meeting these needs.

SUMMARY OF THE INVENTION

[0017] It is an object of the present invention to provide a new and useful nucleotide sequence encoding Staphylococcal GTP-binding protein.

[0018] It is another object of the present invention to provide a Staphylococcal GTPase obg gene sequence.

[0019] It is a further object of the present invention to provide a novel S. aureus GTPase obg DNA sequence

[0020] It is yet another object of the present invention to provide a Staphylococcal GTPase Obg protein for use with antimicrobial compound screening methods.

[0021] A still further object is to provide a S. aureus GTP-binding protein amino acid sequence for use as a novel therapeutic target in affinity-based pharmacological screening procedures.

[0022] Yet another object of the present invention is to provide recombinant expression vectors incorporating the Staphylococcal GTPase obg gene of the present invention.

[0023] Still a further object of the present invention is to provide recombinant expression vectors that are useful in host cells, such as E. coli, for producing Staphylococcal GTP-binding protein.

[0024] It is still a further object of the present invention to provide methods for producing Staphylococcal GTP-binding protein that is functional in in vitro assays for identifying antimicrobial compounds active against Staphylococcal bacteria.

[0025] It is yet another object of the present invention to provide methods for using GTP-binding protein in affinity-based screening procedures for the identification of antimicrobial agents effective against Staphylococcal bacteria such as S. aureus.

[0026] According to the present invention, an isolated polynucleotide that encodes a Staphylococcal GTP-binding protein is provided. More particularly, the polynucleotide encodes a Staphylococcus aureus GTP-binding protein. The isolated polynucleotide may particularly comprise a nucleotide sequence as set forth in SEQ ID NO:1, and may encode a polypeptide comprising an amino acid sequence as set forth in SEQ ID NO:2. The isolated polynucleotide may comprise a Staphylococcal, and particularly a Staphylococcus aureus, GTPase obg gene. Variations of polynucleotides are contemplated, such as those comprising a complementary DNA strand, or which encode a fragment, derivative or analog of the polypeptide.

[0027] The present invention is also directed to an isolated and purified polypeptide comprising a Staphylococcal GTP-binding protein, and particularly a Staphylococcus aureus GTP-binding protein, such as a polypeptide encoded by an obg gene. In particular, the polypeptide may comprise an amino acid sequence as set forth in SEQ ID NO:2. The polypeptide may alternatively be a fragment, derivative or analog of a polypeptide.

[0028] The present invention additionally provides a recombinant expression vector comprising a polynucleotide that encodes a Staphylococcal GTP-binding protein, which may particularly be a Staphylococcus aureus GTP-binding protein. The expression vector may be a plasmid, and specifically a pET14b plasmid.

[0029] The present invention additionally pertains to an engineered host cell for use in producing Staphylococcal GTP-binding protein. The engineered host cell comprises an isolated polynucleotide that encodes a Staphylococcal GTP-binding protein, and particularly Staphylococcus aureus GTP-binding protein. The host cell may specifically be an E. coli bacterial cell, and the isolated polynucleotide may be introduced into the host cell by a vector, which may further include a regulatory sequence operatively linked to the isolated polynucleotide, such that expression of the isolated polynucleotide may be induced by addition of an inducing agent appropriate to the regulatory sequence.

[0030] The present invention further relates to a method of producing Staphylococcal GTP-binding protein, such as Staphylococcus aureus GTP-binding protein. The method broadly comprises the steps of introducing into suitable host cells a polynucleotide that encodes Staphylococcal GTP-binding protein, and culturing the host cells under conditions in which the host cells express the polynucleotide to produce Staphylococcal GTP-binding protein. The method may include the further step of recovering the Staphylococcal GTP-binding protein. The polynucleotide may be introduced into the host cells with a suitable expression vector, such as a plasmid. The host cells are preferably E. coli bacterial cells, such as E. coli BL21 (DE3).pLys.S cells. The method may include contacting the host cells with an inducing agent, such as isopropylthiogalactoside (IPTG), thereby to induce expression of the polynucleotide.

[0031] Finally, the present invention provides a method for high throughput screening to identify potential antimicrobial compounds useful against Staphylococcal bacterial strains. The steps of this method include providing a selected amount of Staphylococcal GTP-binding protein, contacting the Staphylococcal GTP-binding protein with a test compound to form a test combination, and determining whether the test compound binds with the Staphylococcal GTP-binding protein. A test compound that binds with the Staphylococcal GTP-binding protein is identified as a potential antimicrobial compound useful against Staphylococcal bacterial strains. The Staphylococcal GTP-binding protein may be a polypeptide having the sequence set forth in SEQ ID NO:2, or may be a fragment, derivative or analog thereof. The step of determining whether the test compound binds with the Staphylococcal GTP-binding protein may be accomplished by the steps of providing a control group of Staphylococcal GTP-binding protein, subjecting the test combination and control group to increasing temperature, and measuring the temperature at which biophysical catalyzation unfolding of the Staphylococcal GTP-binding protein occurs in each of the test combination and the control group. When unfolding of the Staphylococcal GTP-binding protein in the test combination occurs at a higher temperature than unfolding of the Staphylococcal GTP-binding protein in the control group, the test compound is, identified as a compound that binds with Staphylococcal GTP-binding protein.

[0032] These and other objects of the present invention will become more readily appreciated and understood from a consideration of the following detailed description of the exemplary embodiments of the present invention when taken together with the accompanying drawings, in which:

BRIEF DESCRIPTION OF THE DRAWINGS

[0033] FIG. 1 shows the nucleotide and deduced amino acid sequences (SEQ ID NO:1 and SEQ ID NO:2, respectively) of the S. aureus obg gene identified by the present invention;

[0034] FIG. 2 is a graphical illustration comparing the alignment of the inferred amino acid sequence (SEQ ID NO:2) of the S. aureus obg gene fragment identified by the present invention relative to corresponding regions of various bacterial strains (SEQ ID NO:5-SEQ ID NO:9);

[0035] FIG. 3 is a diagrammatic illustration of the unrooted phylogenetic tree for Obg amino acid sequences for various species, including the Obg protein of S. aureus identified by the present invention;

[0036] FIG. 4A is a photographic illustration of an SDS-polyacrylamide gel electropherogram depicting total soluble proteins and purified Obg proteins from E. coli overexpression of recombinant S. aureus Obg according to the present invention;

[0037] FIG. 4B is a photographic illustration of Western blots showing the reactions of anti-His-Tag antibody and anti-Caulobacter Obg antibody to the purified Obg protein of the present invention; and

[0038] FIG. 5 shows the far UV CD spectra of purified bacterially expressed S. aureus Obg protein according to the present invention.

DETAILED DESCRIPTION OF THE EXEMPLARY EMBODIMENTS

[0039] The present invention concerns the isolation and purification of the obg gene from Staphylococcal bacterial strains, and particularly from an important pathogenic bacterium, Staphylococcus aureus (“S. aureus”). The present invention also concerns engineered expression of Staphylococcal (and particularly S. aureus) Obg protein in a host cell, such as E. coli. Additionally, the present invention concerns the use of Obg protein in high-throughput screening to identify potential antimicrobial agents active against Staphylococcal bacterial strains as inhibitors of Obg function.

[0040] I. DNA Sequencing and Analysis of the S. aureus obg Gene

[0041] A. Cloning and Sequencing of the obg Gene from S. aureus

[0042] A DNA fragment expected to include the full-length obg gene was isolated and amplified from S. aureus by polymerase chain reaction (PCR). The PCR process used degenerate oligonucleotides derived from conserved amino acid segments of known obg homologs from other bacteria (MFVDQVK and EFEFID; amino acid 1-7 and 423-428, respectively, of the Bacillus subtilis obg). In particular, the oligonucleotide primers used had the following nucleotide sequences:

[0043] (1) 5′-CGCCATATGTTYGTNGAYCARGTNAA-3′ (SEQ ID NO:3)

[0044] (2) 5′-CCGCTCGAGTTATTCNACRAAYTCRAAYTC-3′ (SEQ ID NO:4)

[0045] To confirm that the resulting PCR amplified S. aureus DNA contained obg, the nucleotide sequence of the entire fragment was determined. Plasmid templates for nucleotide sequencing were purified using Qiagen miniprep kits, manufactured by Qiagen, located in Valencia, Calif. PCR cycle sequencing was carried out with an APPlied Biosystems automated sequencer, at the Massachusetts General Hospital DNA Sequencing Core Facility, Department of Molecular Biology, Boston, Mass. The S. aureus obg nucleotide sequence encodes a 1290 base pair (bp) open reading frame (ORF) which has an overall G+C composition of 36.6% as illustrated in FIG. 1 and as set forth as SEQ ID NO:1. The putative start and stop codons are underlined in FIG. 1.

[0046] The deduced amino acid sequence of the PCR product showed significant homology to obg from other bacteria, suggesting that the PCR product comprised S. aureus obg. The ORF encodes a polypeptide of 430 amino acids long with a predicted molecular mass of 45.8 kDa. The amino acid sequence of this polypeptide is set forth as SEQ ID NO:2. The S. aureus Obg is an acidic protein with an estimated pl value of 4.9.

[0047] The alignment of the inferred amino acid sequence (SEQ ID NO:2) of the S. aureus obg gene of the present invention is illustrated in FIG. 2 along with corresponding regions of Enterococcus faecalis (SEQ ID NO: 5), Enterococcus faecium (SEQ ID NO: 6), Streptococcus pyogenes (SEQ ID NO: 7), Bacillus subtilis (SEQ ID NO: 8), and Clostridium acetobutylicum (SEQ ID NO: 9). The consensus GTP-binding motifs are indicated by overlying bars. Analysis of the amino acid sequence shows that key structural elements are highly conserved in the inferred amino acid sequence of S. aureus Obg, as seen in FIG. 2. Amino acid residues in the N-terminal region are particularly well conserved compared to Obg from other bacterial species, while those in the C-terminal side are far less conserved. Consistent with other GTP-binding proteins, S. aureus Obg protein possesses three consensus sequence motifs (FIG. 2) which confer GTP-binding activity.

[0048] B. Phylogenetic Analysis of S. aureus obg

[0049] Referring to FIG. 3, a more in-depth evolutionary examination of the S. aureus Obg was carried out using the PHYLIP phylogenetic analysis package. Felsenstein, “Phylogenetic Inference Program (PHYLIP) Manual Version 3.5c”, University of Washington, Seattle, 1993. FIG. 3 shows the unrooted tree for obg amino acid sequences analyzed by using the PROTDIST and FITCH programs from the PHYLIP phylogenetic package: Abbreviated species are as follows:

[0050] A. thaliana=Arabidopsis thaliana;

[0051] H. influenza=Haemophilus influenza;

[0052] E. coli=Escherichia coli;

[0053] C. trachomatis=Chlamydia trachomatis;

[0054] M. tuberculosis=Mycobacterium tuberculosis;

[0055] C. acetobutylicum=Clostridium acetobutylicum;

[0056] S. aureus=Staphylococcus aureus;

[0057] E. faecium=Enterococcus faecium;

[0058] S. pyogenes=Streptococcus pyogenes;

[0059] B. subtilis=Bacillus subtilis;

[0060] H. pylon=Helicobacter pylon;

[0061] M. pneumonia=Mycoplasma pneumonia; and

[0062] C. crescentus=Caulobacter crescentus.

[0063] Amino acid sequences obtained from the combined GenBank/Swissprot/PIR database were used in the phylogenetic analyses, instead of DNA sequences, to eliminate biases due to different G+C ratios. Normand et al., “Nucleotide Sequence of nifD from Frankia alni Strain ARI3: Phylogenetic Inference”, Mol. Biol. Evol., Vol. 9, pp. 495-506, 1992. Sequences were aligned using ClustalW. Swofford et al., “Phylogenetic Inference”, Molecular Systematics, Sinauer Associates, Inc., pp. 407-514, 1996. The PHYLIP 3.5c phylogenetic inference software package, in the form of compiled executable programs for Macintosh computers, was used for comparison of the protein sequences.

[0064] The primary sequence analysis was carried out using the PROTDIST program using a Dayhoff amino acid comparison matrix, manufactured by Dayhoff. This program produced distances expressed in expected changes per amino acid position, including back mutations. The distance matrices produced were converted to phylogenetic trees using the FITCH program which uses the Fitch-Margoliash least-squares distance matrix. TREEDRAW was used to generate the unrooted phylogenetic trees presented.

[0065] As shown in the unrooted phylogenetic tree, Obg is highly conserved among a wide range of bacterial species. Notably, S. aureus Obg forms a distinct cluster with other Gram-positive bacteria, while the closest homolog in humans is only distantly related to bacterially-derived proteins.

[0066] C. Polynucleotides Encoding Staphylococcal GTP-binding Protein

[0067] The present invention provides an isolated nucleic acid (polynucleotide) having the nucleotide sequence as set forth in SEQ ID NO:1, which encodes for the polypeptide having the deduced amino acid sequence as set forth in SEQ ID NO:2. Additionally, it should be understood that the present invention generally contemplates polynucleotides encoding Staphylococcal GTP-binding protein, as well as polynucleotides specifically encoding the S. aureus GTP-binding protein.

[0068] It should be understood that polynucleotides according to the present invention may be in the form of RNA or in the form of DNA, including cDNA, genomic DNA, and synthetic DNA. The DNA may be double-stranded or single-stranded. If single stranded, the DNA may be the coding strand or non-coding (anti-sense) strand. The coding sequence which encodes the polypeptide may be identical to the coding sequence as set forth in SEQ ID NO:1 or may be a different coding sequence which, as a result of the redundancy or degeneracy of the genetic code, encodes the same polypeptide as does the polynucleotide set forth in SEQ ID NO:1.

[0069] The polynucleotide that encodes the polypeptide as set forth in SEQ ID NO:2 may include, without limitation: (a) only the coding sequence for the polypeptide; (b) the coding sequence for the polypeptide and additional coding sequence(s) such as a leader sequence; and (c) the coding sequence for the polypeptide, optionally including additional coding sequence(s), and further including non-coding sequence(s), such as introns. Accordingly, it should be understood that polynucleotides according to the present invention may include only coding sequence for the polypeptide, or may include additional coding and/or non-coding sequences.

[0070] The present invention further contemplates variations of the herein described polynucleotides that encode for fragments, analogs and derivatives of the polypeptide having the deduced amino acid sequence as set forth in SEQ ID NO:2. A “fragment”, “derivative” or “analog” of the polypeptide should be understood to encompass a polypeptide which retains essentially the same biological function or activity as such polypeptide. These polynucleotide variations may be naturally occurring allelic variants of the polynucleotide or nonnaturally occurring variants of the polynucleotide, and include deletion variants, substitution variants and addition or insertion variants. An allelic variant should be understood to mean an alternate form of a polynucleotide sequence which may have a substitution, deletion or addition of one or more nucleotides, which does not substantially alter the function of the encoded polypeptide.

[0071] II. Construction, Expression and Purification of Enzymatically Active S. aureus Obg GTP-binding Protein.

[0072] The present invention additionally relates to the GTP-binding protein encoded by the obg gene in Staphylococcal bacterial strains, and S. aureus in particular. Additionally, the present invention is directed to expression vectors, host cells and methods for producing the GTP-binding protein using such expression vectors and host cells. In particular, the obg gene from the Gram-positive pathogenic bacterium, S. aureus, was expressed in E. coli. Purified S. aureus Obg protein recovered therefrom showed enzymatic activity in vitro and its far ultraviolet circular dichroism spectra suggested alpha-helical secondary structure, consistent with Obg.

[0073] A. Construction of a Suitable Expression Vector and Host Cell

[0074] A 1290 bp DNA fragment encoding the S. aureus obg gene was amplified by PCR using the following oligonucleotide primers:

[0075] (1) 5′-CGC(CATATG)TTTGTGGATCAAGTCAA-3′ (SEQ ID NO:1 0)

[0076] (2) 5′-CCG(CTCGAG)TTATTCAACGAATTCAAATTC-3′ (SEQ ID NO: 11)

[0077] The S. aureus obg coding sequence was cloned into vector pET14b for high-level expression in E. coli (Novagen, Madison, Wis.). Here, the isolated and amplified PCR product was digested with NdeI and BamHI (restriction sites are shown in parentheses in the above primers), ligated into the expression vector pET14b (Novagen) and transformed into E. coli BL21 (DE3).pLys.S. Recombinant Obg contained an additional twenty amino acid residues: six histidines for rapid affinity purification purposes and a thrombin cleavage site to remove extra N-terminal sequences if so required (recombinant 6× his-tagged Obg was therefore 49,368 Da). The resulting construct specified an N-terminal 6× his-tag fused to the entire Obg coding region.

[0078] It should be understood that, in addition to the particular example above, the present invention contemplates various vectors that include polynucleotides of the present invention, host cells which are genetically engineered with vectors of the invention and the production of polypeptides of the invention by recombinant techniques.

[0079] The present invention generally contemplates that host cells, such as E. coli, may be genetically engineered (transduced or transformed or transfected) with the vectors of this invention which may be, for example, expression vectors or integrative vectors. It should be understood that the polynucleotide may be included in any one of a variety of expression vectors for expressing a polypeptide. The vectors contemplated by the present invention may be, for example, in the form of plasmids, viral particles, phages, etc. It should be appreciated that any form of vector may be used provided that it is replicable and viable in the host. The engineered host cells can be cultured in conventional nutrient media, where the culture conditions, such as temperature, pH and the like, are those generally known for culturing the host cell selected for expression, as apparent to the ordinarily skilled artisan.

[0080] The appropriate DNA sequence may be inserted into the vector by a variety of procedures as known in the art. In general, the DNA sequence is inserted into an appropriate restriction endonuclease site(s) by procedures as understood by those ordinarily skilled in the art. It is preferred that the DNA sequence in the expression vector is operatively linked to an appropriate control sequence, such as a promoter sequence, such that expression of the DNA sequence may be induced upon addition of an appropriate inducing agent, such as IPTG in the case of the pET14b plasmid vector. The expression vector thus formed may be employed to transform an appropriate host with the DNA sequence of interest, thereby to permit the host to overexpress the protein upon addition of suitable quantities of the inducing agent.

[0081] The present invention is also directed to host cells containing the polynucleotide sequence of the present invention, such as host cells into which the polynucleotide sequence has been introduced, such as by an expression vector as described above. Various types of host cells are contemplated, such as prokaryotic cells, bacterial cells, lower eukaryotic cells such as yeast cells, and higher eukaryotic cells such as mammalian cells. It should further be understood that the expressed polypeptides of the present invention may be recovered from the host cells by conventional techniques as known in the art.

[0082] B. Expression and Purification of GTP-binding Protein

[0083] Here, protein expression was induced by adding IPTG (final concentration 1 mM) to a growing culture (30° C.) at OD600=0.7. Three hours after induction, the cells were harvested, resuspended in binding buffer (5 mM imidazole, 0.5 M NaCl, 20 mM Tris-HCl, pH 7.9) and sonicated on ice. Cell debris was removed by centrifugation at 15,000 rpm for 15 minutes, and the clarified supernatant was purified on an Ni++ affinity column manufactured by Novagen, according to the manufacturer's instructions. Here, soluble recombinant Obg was purified by Ni++ affinity chromatography to produce a protein of high purity (FIG. 4A, lanes 4 & 5) which was used in preliminary GTPase assays. The yield per liter of culture of the purified protein was approximately 5 mg. The protein eluted from the column with the following buffer, 1 M imidazole, 0.5 M NaCl, 20 mM Tris-HCl, pH 7.9, was essentially homogeneous.

[0084] As shown in FIG. 4A, the E. coli BL21 (DE3).pLys.S containing the pET-Obg construct expressed a soluble protein with an apparent molecular size of 55 kDa. This value is higher than the molecular weight calculated from the protein's primary sequence. The difference may be due to an imperfect spherical shape or presence of highly charged amino acids. FIG. 4A illustrates SDS-PAGE showing total soluble proteins and purified Obg proteins, where the size of the Obg protein is indicated by an arrow. Lane 1 shows molecular weight standards (SeeBlue, Novex): 250, 98, 64, 50, 36 kDa; lane 2 shows extract prepared from cells harboring vector pET14b alone; lane 3 shows extract prepared from cells containing pET14b vector with the obg gene; and lanes 4 and 5 show purified Obg protein. As illustrated in FIG. 4A, recombinant Obg was not detectable either in extract from cells not treated with IPTG nor in cells harboring vector pET14b alone (FIG. 4A, lane 2).

[0085] The identity of the overexpressed protein as Obg was confirmed by Western blots using anti-6× his antibody as well as polyclonal anti-Caulobacter Obg antibody. Western blots are illustrated in FIG. 4B, showing the reactions of anti-His-Tag antibody (Novagen) and anti-Caulobacter Obg antibody to the purified Obg protein. Here, purified S. aureus Obg was resolved by SDS-PAGE and transferred to a PVDF membrane. The membrane was incubated overnight in TBST buffer (50 mM Tris/HCl, 150 mM NaCl, 0.1% (v/v) Tween 20, pH 7.5) containing 5% (w/v) BSA. After blocking, the membranes were incubated with anti-6xhis-antibody or anti-Caulobacter Obg antibody (diluted 1:1000 in TBST buffer) for 30 min, washed with TBST buffer and incubated with gentle shaking at room temperature for 30 min in TBST containing a 1:5,000 dilution of alkaline phosphatase-coupled goat anti-rabbit antibody (Promega, Middletown, Wis.). The membrane was washed again and the immunoreactive bands visualized by soaking the membrane in 10 ml alkaline phosphatase substrate (Promega) containing nitroblue tetrazolium (NBT) and 5-bromo-4-chloro-3-indolylphosphate (BCIP). Color development was stopped by rinsing the membrane with water. A set of prestained SDS-PAGE standard proteins (SeeBlue, Novex) were used for molecular weight estimation.

[0086] Analysis of the primary sequence of Obg revealed a central portion of the protein which contained sequences identified as the GTP-binding domain (FIG. 1). Obg has been shown to hydrolyze GTP in B. subtilis. Welsh et al., “Biochemical Characterization of the Essential GTP-Binding Protein Obg of Bacillus subtilis”, J. Bacteriol., Vol. 176, pp. 7161-68, 1994. Accordingly, we examined the ability of purified S. aureus Obg to hydrolyze GTP. Following incubation with γ32P-GTP under standard conditions, purified Obg was shown to catalyze release of labeled inorganic phoshate (Pi). The hydrolysis of GTP by S. aureus Obg was found to be linear with respect to protein concentration (data not shown). Further kinetic analysis of the GTPase activity of Obg is currently being investigated.

[0087] The far ultraviolet CD spectra of purified bacterially expressed S. aureus Obg protein was also investigated. A highly purified preparation of Obg protein was eluted from a Ni++ affinity column. Far ultraviolet circular dichroism spectra were determined on an AVIV 62DS circular dichroism spectrometer (Aviv Associates, Inc., Lakewood, N.J.) at 4° C. using a 1 cm optical path length cuvette. Protein concentration was determined by the Bradford method, as understood in the art. Concentration of Obg was adjusted to 0.05 mg/ml in 10 mM NaPi, 0.5 M NaCl and 10% glycerol, pH 8.0. As shown in FIG. 5, the far ultraviolet CD spectra (200-260nm) of purified Obg showed distinctive double minima at 222 and 208 nm characteristic of alpha-helical secondary structure.

[0088] It should be understood that the present invention contemplates various polypeptides, such as the polypeptide having the deduced amino acid sequence as set forth in SEQ ID NO:2, as well as fragments, derivatives and analogs of such polypeptide, as previously defined. The polypeptides of the present invention may be recombinant polypeptides, natural polypeptides or synthetic polypeptides, such as those produced by conventional peptide synthesizers. The polypeptides, as well as polynucleotides, of the present invention are preferably purified to homogeneity and are provided in an isolated form, meaning that the material is removed from its original environment (e.g. the polypeptide is separated from coexisting materials in a natural system, or incorporated in a vector or composition that is not part of its natural environment). It should further be understood that the present invention contemplates polypeptides comprising Staphylococcal GTP-binding protein generally, as well as S. aureus GTP-binding protein in particular.

[0089] III. Methods for Using Staphylococcal Obg protein in High-throughput Screening Assays

[0090] The present invention also contemplates the use of the polypeptides according to the present invention with screening procedures to identify antimicrobial agents effective against Staphylococcal bacterial strains, such as S. aureus. While the preferred embodiments of the invention utilize the S. aureus bacterial strain, it should be understood that the present invention is contemplated for use with other types of Staphylococcal bacterial strains.

[0091] In particular, the present invention contemplates the use of Staphylococcal GTP-binding protein as a novel therapeutic target in affinity-based pharmacological screening procedures for the discovery of antibiotics active against S. aureus and other Staphylococcal bacterial strains. Exemplary screening procedures known in the art are recited in U.S. Pat. Nos. 5,585,277 and 5,679,582 to Bowie et al., and are incorporated herein by reference.

[0092] The present invention provides methods for identifying pharmaceutically suitable antimicrobial compounds that act by inhibiting the function of the GTP-binding protein encoded by the Staphylococcal obg gene. One method for high-throughput screening involves identifying target compounds which bind to Obg protein thereby to inhibit GTP-binding function that is essential for cell growth and/or viability. Such compounds which bind with Obg are potential candidates for investigation as antimicrobial agents.

[0093] In particular, the present invention contemplates a method wherein a test compound is incubated with Staphylococcal GTP-binding protein to form a test combination. A control group of GTP-binding protein may be provided for comparison with the test combination. The method includes determining whether the test compound binds with Staphylococcal GTP-binding protein, which may be accomplished by various methods as known in the art for identifying ligands of target proteins. A test compound which binds with Staphylococcal GTP-binding protein is identified as a potential inhibitor of Obg protein function in a Staphylococcal bacterial strain, and therefore is a potential antimicrobial candidate.

[0094] One particular method for determining whether a test compound binds with Staphylococcal GTP-binding protein involves the step of increasing the temperature of a test combination wherein GTP-binding protein and test compound are present and increasing the temperature of a control group wherein GTP-binding protein is present, but the test compound is absent. A test compound which binds with GTP-binding protein is identified when protein unfolding due to denaturation from increasing temperature, e.g., biophysical catalization unfolding, occurs at a higher measured temperature in the test combination compared to the control group. Stated differently, a test compound which binds the Obg protein will increase the temperature at which the protein unfolding occurs, as a result of the binding test compound preventing or retarding the protein unfolding process at a given temperature. Accordingly, identifying those test compounds for which protein unfolding occurs at a higher temperature in the presence of test compound relative to the absence of test compound provides a method for screening test compounds to identify potential antimicrobial agents.

[0095] Preferably, the screening methods of the present invention are adapted to a high-throughput format, allowing a multiplicity of compounds to be analyzed in a single assay. Such inhibitory test compounds may be found in, for example, naturally occurring libraries, fermentation libraries encompassing plants and microorganisms, compound files, and synthetic compound libraries. Such compound libraries are commercially available from a number of known sources. The compounds identified using the methods of the present invention discussed above may be modified to enhance potency, efficacy, uptake, stability and suitability for use in pharmaceutical formulations and the like. These modifications are achieved and tested using methods well-known in the art.

[0096] Accordingly, the present invention has been described with some degree of particularity directed to the exemplary embodiments of the present invention. It should be appreciated, though, that the present invention is defined by the following claims construed in light of the prior art so that modifications or changes may be made to the exemplary embodiments of the present invention without departing from the inventive concepts contained herein.

Claims

1. An isolated polynucleotide that encodes a Staphylococcal GTP-binding protein.

2. An isolated polynucleotide according to claim 1 wherein said polynucleotide encodes a Staphylococcus aureus GTP-binding protein.

3. An isolated polynucleotide according to claim 1 wherein said polynucleotide comprises a nucleotide sequence as set forth in SEQ ID NO:1.

4. An isolated polynucleotide according to claim 1 wherein said polynucleotide encodes a polypeptide comprising an amino acid sequence as set forth in SEQ ID NO:2.

5. An isolated polynucleotide according to claim 1 wherein said polynucleotide comprises a Staphylococcal GTPase obg gene.

6. An isolated polynucleotide according to claim 1 wherein said polynucleotide comprises a Staphylococcus aureus GTPase obg gene.

7. An isolated polynucleotide according to claim 1 wherein said polynucleotide comprises a complementary DNA strand of a nucleotide sequence as set forth in SEQ ID NO:1.

8. An isolated polynucleotide according to claim 1 wherein said polynucleotide encodes a polypeptide selected from the group consisting of a fragment, a derivative and an analog of an amino acid sequence as set forth in SEQ ID NO:2.

9. An isolated and purified polypeptide comprising a Staphylococcal GTP-binding protein.

10. An isolated and purified polypeptide according to claim 9 wherein said polypeptide comprises a Staphylococcus aureus GTP-binding protein.

11. An isolated and purified polypeptide according to claim 9 wherein said polypeptide comprises an amino acid sequence as set forth in SEQ ID NO:2.

12. An isolated and purified polypeptide according to claim 9 wherein said polypeptide is selected from the group consisting of a fragment, a derivative and an analog of a polypeptide comprising an amino acid sequence as set forth in SEQ ID NO:2.

13. An isolated and purified polypeptide according to claim 9 wherein said polypeptide is encoded by a Staphylococcal GTPase obg gene.

14. An isolated and purified polypeptide according to claim 9 wherein said polypeptide is encoded by a Staphylococcus aureus GTPase obg gene.

15. An isolated and purified polypeptide according to claim 9 wherein said polypeptide is an expression product of a transformed host cell containing a polynucleotide that encodes a Staphylococcal GTP-binding protein.

16. An isolated and purified polypeptide according to claim 15 wherein said polynucleotide encodes an amino acid sequence as set forth in SEQ ID NO:2.

17. A recombinant expression vector comprising a polynucleotide that encodes a Staphylococcal GTP-binding protein.

18. A recombinant expression vector according to claim 17 wherein said polynucleotide encodes a Staphylococcus aureus GTP-binding protein.

19. A recombinant expression vector according to claim 17 wherein said polynucleotide comprises a nucleotide sequence as set forth in SEQ ID NO:1.

20. A recombinant expression vector according to claim 17 wherein said polynucleotide encodes a polypeptide comprising an amino acid sequence as set forth in SEQ ID NO:2.

21. A recombinant expression vector according to claim 17 wherein said expression vector is a plasmid.

22. A recombinant expression vector according to claim 21 wherein said plasmid is a pET14b plasmid.

23. A recombinant expression vector according to claim 22 wherein said pET14b plasmid comprises a nucleotide sequence as set forth in SEQ ID NO:1.

24. A recombinant expression vector according to claim 17 wherein said polynucleotide is a recombinant Staphylococcus aureus obg gene.

25. A recombinant expression vector according to claim 24 wherein said polynucleotide includes at least one histidine.

26. A recombinant expression vector according to claim 24 wherein said polynucleotide includes a thrombin cleavage site.

27. An engineered host cell for use in producing Staphylococcal GTP-binding protein, wherein said engineered host cell comprises an isolated polynucleotide that encodes a Staphylococcal GTP-binding protein.

28. An engineered host cell according to claim 27 wherein said isolated polynucleotide encodes Staphylococcus aureus GTP-binding protein.

29. An engineered host cell according to claim 27 wherein said isolated polynucleotide comprises a nucleotide sequence as set forth in SEQ ID NO:1.

30. An engineered host cell according to claim 27 wherein said host cell is a bacterial cell.

31. An engineered host cell according to claim 30 wherein said bacterial cell is an E. coli bacterial cell.

32. An engineered host cell according to claim 27 wherein said isolated polynucleotide is introduced into said host cell by a vector.

33. An engineered host cell according to claim 32 wherein said vector comprises a polynucleotide sequence as set forth in SEQ ID NO:1.

34. An engineered host cell according to claim 32 wherein said vector includes a regulatory sequence operatively linked to said isolated polynucleotide.

35. An engineered host cell according to claim 34 wherein expression in said host cell of said isolated polynucleotide is inducible by addition of an inducing agent appropriate to said regulatory sequence.

36. A method of producing Staphylococcal GTP-binding protein comprising the steps of: (a) introducing into suitable host cells a polynucleotide that encodes Staphylococcal GTP-binding protein; and (b) culturing said host cells under conditions in which said host cells express said polynucleotide to produce Staphylococcal GTP-binding protein.

37. A method according to claim 36 including the step of recovering said Staphylococcal GTP-binding protein.

38. A method according to claim 36 wherein said polynucleotide encodes Staphylococcus aureus GTP-binding protein.

39. A method according to claim 36 wherein the step of introducing is accomplished with a suitable expression vector.

40. A method according to claim 39 wherein said expression vector is a pET14b plasmid.

41. A method according to claim 40 wherein said pET14b plasmid includes a Staphylococcal obg coding sequence.

42. A method according to claim 41 wherein said Staphylococcal obg coding sequence comprises the nucleotide sequence set forth in SEQ ID NO:1.

43. A method according to claim 36 wherein said host cells are E. coli bacterial cells.

44. A method according to claim 43 wherein said E. coli bacterial cells are E. coli BL21 (DE3)pLysS cells.

45. A method according to claim 36 wherein the step of culturing includes contacting said host cells with an inducing agent, thereby to induce expression of said polynucleotide.

46. A method according to claim 45 wherein said inducing agent is isopropylthiogalactoside (IPTG).

47. A method for high throughput screening to identify potential antimicrobial compounds useful against Staphylococcal bacterial strains, said method comprising the steps of: (a) providing a selected amount of Staphylococcal GTP-binding protein; (b) contacting said Staphylococcal GTP-binding protein with a test compound to form a test combination; and (c) determining whether said test compound binds with said Staphylococcal GTP-binding protein, whereby a test compound that binds with said Staphylococcal GTP-binding protein is identified as a potential antimicrobial compound useful against Staphylococcal bacterial strains.

48. A method according to claim 47 wherein step (a) thereof is accomplished by providing a selected amount of a polypeptide comprising an amino acid sequence as set forth in SEQ ID NO:2.

49. A method according to claim 47 wherein step (a) thereof is accomplished by providing a selected amount of a polypeptide selected from the group consisting of a fragment, a derivative and an analog of a polypeptide comprising an amino acid sequence as set forth in SEQ ID NO:2.

50. A method according to claim 47 wherein the step of determining whether said test compound binds with said Staphylococcal GTP-binding protein is accomplished by the steps of: (a) providing a control group of Staphylococcal GTP-binding protein; (b) subjecting the test combination and control group to increasing temperature; (c) measuring the temperature at which biophysical catalyzation unfolding of said Staphylococcal GTP-binding protein occurs in each of said test combination and said control group, whereby when unfolding of said Staphylococcal GTP-binding protein in said test combination occurs at a higher temperature than unfolding of said Staphylococcal GTP-binding protein in said control group, the test compound is identified as a compound that binds with Staphylococcal GTP-binding protein.