INHIBITION OF BIOFILM FORMATION

Abstract

The present invention relates to compositions and methods for reducing or inhibiting biofilm comprising modulating expression of a cysB gene in a cell. The invention also provides methods for modulating the expression of a cysB, cysD, cysI, cysJ, cysK, and ybiK. The invention further provides methods for identifying gene(s) involved in biofilm formation and for identifying biofilm inhibitors.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority from U.S. provisional patent application Ser. No. 60/587,680, filed on Jul. 14, 2004, and U.S. provisional patent application Ser. No. 60/609,763, filed on Sep. 14, 2004.

FIELD OF THE INVENTION

The invention relates to methods for reducing or inhibiting biofilm formation. The invention also relates to methods for modulating the expression of a cysB gene. Further, the present invention relates to methods for identifying genes involved in biofilm formation and for identifying biofilm inhibitors.

BACKGROUND OF THE INVENTION

Bacterial biofilms exist in natural, medical, and engineering environments. The biofilm may offer a selective advantage to a microorganism to ensure its survival, or allow it a certain amount of time to exist in a dormant state until suitable growth conditions arise. This selective advantage could pose serious threats to human health. For example, biofilms are involved in 65% of human bacterial infections. Biofilms are also involved in prostatitis, biliary tract infections, urinary tract infections, cystitis, pyelonephritis, lung infections, sinus infections, ear infections, acne, and chronic wounds.

Biofilms contribute to a variety of medical conditions. Each year in the United States alone, over 7 million patients receive medical device implants, including central venous catheters, endotracheal tubes, mechanical heart valves, pacemakers, and prosthetic joints. Approximately one-half of these patients develop nosocomial infections, and approximately 80,000 deaths per year are attributed to nosocomial infections. Biofilms provide a structural matrix that facilitates bacterial adhesion to the inert surfaces of medical device implants and venous catheters. Microscopic studies confirm that central venous catheters are coated by bacteria embedded in biofilms. Unfortunately, more than 1 million patients develop urinary tract infections from such catheters.

Some diseased tissues, such as tumors, are susceptible to bacterial colonization. Bacterial colonization has been identified in calcified human aneurysms, carotid plaques, femoral arterial plaques, and cardiac valves. Arterial calcification resembles infectious lesion formation in animal models of atherosclerosis. A toxin produced by Cag-A positive Helicobacter pylori colonization of the stomach could lead to tissue inflammation and lesions in the arterial walls resulting in atherosclerosis. Bacterial colonization could also lead to the formation of kidney stones. Eradication of bacteria, and the biofilms that protect them, from the diseased tissue enables the host's immune system and/or a pharmaceutical agent to reach the diseased tissue. For example, clostridia spores and attenuated Salmonella typhimurium, used to deliver therapeutic proteins to tumors, may be more effective if the biofilm did not exist or is removed.

Biofilms may also cause diseases, such as cystic fibrosis, or contribute to chronic symptoms. Chronic bacterial infections represent a serious medical problem in the United States. Antibiotics are typically used to treat both acute and chronic infections. In chronic bacterial infections, biofilms protect the bacteria from the antibiotics and the host's immune system, thus increasing the rates of recurring symptoms and resistance to the antibiotics. Researchers theorized that a biofilm gives bacteria a selective advantage by reducing the penetration of an antibiotic to the extent necessary to eradicate the bacteria. Through biofilms, the microbes can resist antibiotics at high concentrations, about 1 to 1.5 thousand times higher than necessary in the absence of biofilms. Not surprisingly, during an infection, bacteria surrounded by biofilms are rarely resolved by the host's immune defense mechanisms.

As discussed above, biofilms provide a protective barrier for bacteria, thus, allowing the bacteria to resist antibiotic treatments. Developers of antibiotics must face the continuous challenge of antibiotic resistance. Antibiotic resistance significantly hinders treatment of the medical condition. For example, microbial resistance to minocycline and rifampin, which are widely used to treat infections, is emerging. A 1998 study of an intensive care unit revealed that 6 out of 7 vancomycin-resistant enterococci were resistant to rifampin.

Biofilm inhibition offers numerous advantages. Bacteria have no known resistance to biofilm inhibitors. Thus, unlike antibiotics, biofilm inhibitors can be used repeatedly and effectively in the same patient and for the same medical condition. For example, biofilm inhibitors may be employed to treat, cure, or prevent acute or chronic infections. They may be used to control microorganisms residing on living tissues. They may also be used to cure, treat, or prevent arterial damage, gastritis, urinary tract infections, cystitis, otitis media, leprosy, tuberculosis, benign prostatic hyperplasia, chronic prostatitis, chronic infections of humans with cystic fibrosis, osteomyelitis, bloodstream infections, skin infections, open wound infections, and any acute or chronic infection that involves or possesses a biofilm.

Biofilm inhibitors can act specifically on the biological mechanisms that provide bacteria protection from antibiotics and from a host's immune system. In one study of urinary catheters, rifampin was able to clear planktonic or suspended methicillin-resistant Staphylococcus aureus, but was unable to eradicate the bacteria in a biofilm. Current treatment of infections, e.g. nosocomial infections, often requires sequential or simultaneous administration of a combination of products, such as amoxicillin/clavulanate and quinupristin/dalfopristin. A direct inhibition of the bacterial mechanisms used to form biofilms may help reduce blood stream infections (BSI).

In addition, a direct inhibition of the bacterial mechanisms used to form biofilms delays the onset of microbial resistance to antibiotics, and possibly, reduces the emergence of multi-resistant bacteria. Another approach to reducing or inhibiting biofilm formation is to apply evolutionary pressure to the bacterial growth mechanisms. Accordingly, extensive research are devoted to elucidating the genes, especially the critical players, that are involved in controlling biofilm formation.

Accordingly, for the reasons discussed above and others, there continues to be a need for a means to control biofilm and its formation.

SUMMARY OF INVENTION

The present invention provides a method for reducing or inhibiting a biofilm comprising modulating expression of a cysB gene in a cell capable of biofilm formation.

Further, the present invention provides a method for modulating the expression of a cysB gene comprises contacting a cell capable of biofilm formation with a composition comprising a compound selected from the group consisting of ursolic acid or asiatic acid, or a pharmaceutically acceptable salt of such compound, a hydrate of such compound, a solvate of such compound, an N-oxide of such compound, or a combination thereof.

The present invention further provides a method for identifying a gene or genes involved in biofilm formation comprising a) mutating a gene, wherein the gene is a cysB gene or a gene related to cysB in at least one cell capable of biofilm formation; b) contacting the cell with a compound selected from the group consisting of ursolic acid or asiatic acid or an analog of such compound; c) contacting at least one wild-type cell with the compound chosen in step b); and d) measuring the biofilm formation by the cell and the biofilm formation by the wild-type cell, wherein a modulation of the biofilm formation by the cell compared to the biofilm formation by the wild-type cell indicates the involvement of the gene in biofilm formation.

The present invention provides a method for identifying an agent that reduces or inhibits biofilm formation comprising contacting a cell capable of biofilm formation with the agent; providing a reporter marker linked to a gene, wherein the gene is a cysB gene or a gene related to cysB, wherein the reporter marker allows detection of the expression of the gene; and detecting modulation of the expression of the gene or of its gene product.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the inhibition of biofilm formation in E. coli K12, P. aeruginosa PAO1, and V. harveyi BB120 with ursolic acid.

FIG. 2 shows the inhibition of air-liquid interface biofilm with ursolic acid.

FIG. 3 shows a comparison of the inhibition of biofilm formation by wild-type E. coli and mutant E. coli (cys B mutation) with ursolic acid.

FIGS. 4-8 show analogs of ursolic acid and asiatic acid.

FIG. 9 shows the chemical structures of ursolic acid and asiatic acid.

DESCRIPTION OF THE INVENTION

Definitions

“Acceptable carrier” refers to a carrier that is compatible with the other ingredients of the formulation and is not deleterious to the recipient thereof.

“Reducing or inhibiting” in reference to a biofilm refers to the prevention of biofilm formation or growth, reduction in the rate of biofilm formation or growth, partial or complete inhibition of biofilm formation or growth.

“Modulates” or “modulating” refers to up-regulation or down-regulation of a gene's replication or expression.

Description

The present invention provides a method for reducing or inhibiting a biofilm comprising modulating the expression of a cysB gene in a cell capable of biofilm formation.

Biofilm inhibitors can be used to treat diseases caused by bacteria existing in biofilms. For example, the inhibitors can contribute to the treatment of cystic fibrosis. In cystic fibrosis, Pseudomonas aeroginosa reside on the lungs of cystic fibrosis patients. The inhibitors can prevent, reduce, or eradicate the biofilm of Pseudomonas aeroginosa. In addition, biofilm inhibitors can prevent the attachment of Helicobactor pylori to gastric epithelial cells in patients with gastritis. This prevents the bacteria's invasion into these epithelial cells. By preventing H. pylori attachment to gastric epithelial cells, biofilm inhibitors also prevent or reduce the risks associated with subsequent virulence factors, such as arterial damage which may lead to a stroke. Moreover, biofilm inhibitors can also be used to treat urinary tract infections. E. coli reside intracellularly in bladder cells. The E. coli resist conventional antibiotics and evade the host's immune systems. The biofilm inhibitors can prevent, control, reduce, or eradicate the E. coli. The biofilm inhibitors prevent or disrupt the attachment of E. coli to uroplakin or the proteins of the tight junctions of umbrella cells of the bladder, thereby potentially controlling the re-occurrence of urinary tract infections.

Biofilm formation involves biological pathways conserved among different species of bacteria. For example, different species of bacteria share a common global regulator in the formation and maintenance of biofilms. Jackson et. al. showed catabolite repression induced by glucose caused 30% to 95% reduction in biofilms among E. coli, Citrobacter freundii, Klebsiella pneumoniae, and Salmonella enterica Typhimurium. (Jackson, et al. J. Bacteriol. 2002, 184, 3406-3410). A bacterial autoinducer signal, AI-2, has been shown to be involved in the formation of biofilms. AI-2 and genes responsive to this signal have been identified in a variety of bacteria. Preferably, in an embodiment of the present invention, the biofilm is reduced or inhibited by modulating expression of cysB in Escherichia coli, Proteus mirablis, Francisella tularensis, Vibrio sp., Pseudomonas aeruginosa, V harveyi, Pseudomonas sp., Salmonella sp., Haemophilus influenzae, Borrelia sp., Neisseria sp., Bacillus sp., Burkholderia sp., Klebsiella sp., or Yersinia pestis. Still, preferably, the biofilm is reduced or inhibited by modulating expression of cysB in a Gram-negative bacteria.

CysB may be modulated in a number of ways. For example, N-acetyl-serine and sulfur limitation up-regulate cysB. Lochowska, A. et al., Functional Dissection of the LysR-type CysB Transcriptional Regulator. J. Biol. Chem. 2001, 276, 2098-2107. In addition, like other LysR type regulators, cysB can repress itself. Lilic, M. et al., Identification of the CysB-regulated gene, hslJ, related to the Escherichia coli novobiocin resistance phenotype. FEMS Micro. Letters. 2003, 224, 239-246.

The disclosure herein describes another means to modulate cysB. The present invention, therefore, also provides a method for modulating the expression of a cysB gene comprising contacting the cell with a composition comprising a compound selected from the group consisting of ursolic acid or asiatic acid, or a pharmaceutically acceptable salt of such compound, a hydrate of such compound, a solvate of such compound, an N-oxide of such compound, or a combination thereof.

The disclosure herein describes the discovery that the cysB gene, a transcriptional regulator of the biosynthesis of cysteine, is involved in biofilm formation. (Verschueren, K. H. G., Crystallization of full-length CysB of Klebsiella aerogenes, a LysR-type transcriptional regulator, BIOLOGICAL CRYSTALLOGRAPHY D57:260-262, 2001). As demonstrated in the examples herein, the removal of cysB from E. coli results in a significant reduction of biofilm formation in E. coli as compared to wild-type E. coli. The cysB protein is a transcriptional regulator of the LysR family of genes. The transcriptional regulators of this family have helix-turn-helix DNA binding motifs at their amino-terminus. The cysB protein is required for the full expression of the cys genes, which is involved in the biosynthesis of cysteine.

The cysB gene is genetically conserved among different species of bacteria, and more specifically Gram-negative bacteria. Verschueren, et al., Acta Cryst. (2001) D57, 260-262; Byrne et al., J. Bacteriol. 1988 170 (7), p. 3150-3157. In fact, cysB is conserved among Pseudomonas sp. including, but not limited to, P. aeruginosa, P. putida, and P. syringae. (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi. Blast search of the cysB gene at the Microbial Genomics database at the National Center for Biotechnology Information (NCBI) of the National Institutes of Health (NIH)). The cysB gene is also genetically conserved among the following species of bacteria: Vibrio sp. (e.g. V. harveyi and V. cholera), Proteus mirablis, Burkholderia sp. (e.g. B. fongorum, B. mallei, and B. cepacia), Klebsiella sp., Haemophilus influenza, Neisseria meningitides, Bordetella pertussis, Yersinia pestis, Salmonella typhimurium, and Acinetobacter sp. (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi. Blast search of the cysB gene at the Microbial Genomics database at NCBI of NIH). The cysB gene is also genetically conserved among the Gram-positive bacteria of Bacillus sp. including, but not limited to, B. subtilis, B. cereus, and B. anthracis. (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi. Blast search of the cysB gene at the Microbial Genomics database at NCBI of NIH; van der Ploeg, J. R.; FEMS Microbiol. Lett. 2001, 201, p. 29-35).

In one embodiment of the present invention, the cell is selected from a group consisting of Gram-negative bacteria. In another embodiment of the invention, the cell is selected from a group consisting of Escherichia coli, Proteus mirablis, Francisella tularensis, Vibrio sp., Pseudomonas aeruginosa, V. harveyi, Pseudomonas sp., Salmonella sp., Haemophilus influenzae, Borrelia sp., Neisseria sp., Bacillus sp., Burkholderia sp., Klebsiella sp., and Yersinia pestis. Preferably, the cell is E. coli, Pseudomonas aeruginosa, or V. harveyi. As demonstrated in Example 2, ursolic acid reduces or inhibits the formation of biofilms in E. coli, P. aeruginosa, and V. harveyi. Using a similar method described in Example 2, asiatic acid was shown in Example 6 to reduce or inhibit biofilm formation in E. coli.

Another embodiment of the present invention is a method for modulating the expression of cysD, cysI, cysJ, and/or cysK. Cys B controls the cysDIJK family of genes at the transcriptional level. Leyh, T., et al. J. Biol. Chem. 1992, 267(15), p. 10405-10410. Administration of ursolic acid down-regulates the expression of cysB and certain genes under its transcriptional control, such as cysDIJK, while administration of asiatic acid up-regulates the expression of cysB and certain genes under its transcriptional control. By modulating the expression of cysB, ursolic acid and asiatic acid reduce or inhibit biofilm formation.

Members of the family of LysR transcriptional regulators have been demonstrated to regulate diverse metabolic processes. cysB exhibits direct control of the biosynthesis of cysteine. Verschueren et al., at p. 260. The cysB gene is involved, directly or indirectly, in glutathione intracellular transport, carbon source utilization, alanine dehydrogenases, and the arginine dependent system. YbiK is under the direct control of cysB and participates in glutathione intracellular transport. The data in example 1 demonstrates the down-regulation of ybiK by contacting a bacterial cell with ursolic acid. The down-regulation of ybiK in Example 1 of the specification further supports that ursolic acid down-regulates cysB. In an embodiment of the invention, ursolic acid or asiatic acid modulates the expression of ybiK.

FIG. 9 shows the chemical structures of ursolic acid (C110) and asiatic acid (C255). Ursolic acid (UA) is a pentacyclic triterpene compound isolated from many type of medicinal plants and is present in the human diet. It has been reported to possess a wide range of pharmacological benefits, including anti-cancer and anti-aging therapies. See e.g. Hsu et al., Life Sci. 75(19):2303-2316, Sep. 24, 2004 and Both et al., Arch Dermatol. Res. 293(11):569-575, January 2002. Ursolic acid has also been identified as an antagonist for transforming growth factor (TGFβ1). Murakami et al., FEBS Lett. 566(1-3):55-59, May 21, 2004. However, before the disclosure herein, neither ursolic acid nor asiatic acid has been reported to modulate the expression of the cysB gene. Neither have ursolic acid nor asiatic acid been reported to reduce or inhibit biofilm formations. Analogs of ursolic acid (C110) and asiatic acid (C255) are expected to also modulate the expression of the cysB gene. FIGS. 4-8 show examples of analogs of ursolic acid and asiatic acid.

While any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of this invention, the type of carrier will vary depending on the mode of administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactic galactide) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268 and 5,075,109.

Another means to control biofilm formation is to understand the underlying genetics involved. As it turns out, a complex web of genes regulates the formation and maintenance of biofilms by bacteria. For instance, Sauer et al. demonstrated that approximately 525 proteins are differentially regulated during the different stages of biofilm development in Pseudomonas aeruginosa. Sauer et al., J. Bacteriol. November 2004; 186(21):7312-26. Stanley et al. demonstrated that approximately 519 proteins are differentially regulated during the first 24 hours of biofilm formation in Bacillus subtilis. Stanley, N. R. et al. J. Bacteriol. 2003, 185, 1951-1957. While numerous genes may be involved in a variety of biological pathways, only a few genes play critical roles. Researchers spend considerable amount of effort determining which gene(s) are critical or essential in the biological pathways involved in various stages of biofilm formation and maintenance. The disclosure herein describes the discovery of the genes involved in biofilm formation, such as cysB, cysD, cysI cysJ, cysK gene(s), and ybiK and the compounds that modulate these genes and reduce or inhibit biofilm formation.

Prior to the present invention, researchers look for genes involved in biofilm formation by manipulating various factors, such as media condition, experimental temperature, random gene knock-out, and glucose level. These processes can be tedious, time-consuming, and costly. See e.g. Sauer et al., J. Bacteriol. November 2004; 186(21):7312-26; Ren et al., Applied and Environmental Microbiology, April 2004, 70(4):2038-2043; Verschueren et al., Biological Crystallography, 2001, D57:260-262; Pratt, L. A. and Roberto Kolter, Molecular Microbiology, October 1998, 30(2):285-293. The present invention provides a method for identifying a gene or genes involved in biofilm formation comprising a) mutating a gene, wherein the gene is a cysB gene or a gene related to cysB in at least one cell capable of biofilm formation; b) contacting the cell with a compound selected from the group consisting of ursolic acid or asiatic acid or an analog of such compound; c) contacting at least one wild-type cell with the compound chosen in step b); and d) measuring the biofilm formation by the cell and the biofilm formation by the wild-type cell, wherein a modulation of the biofilm formation by the cell compared to the biofilm formation by the wild-type cell indicates the involvement of the gene in biofilm formation.

As described herein, cysB is involved in biofilm formation. It controls the biosynthesis of cysteine. Verschureren et al., at p. 260. Using cysB, standard methods can be used to identify other genes or gene products under its control that are involved in biofilm formation. For example, expression of cysB may be modulated while either modulating or monitoring the expressions of the other genes suspected of being involved in biofilm formation. This method identifies a gene's (or its gene product) involvement in biofilm formation. A person of ordinary skill in the art may perform additional tests to confirm the gene's (or its gene product) involvement in biofilm formation. Expressions of either cysB or genes under its control, such as cysDIJK family of genes, can be modulated, and using DNA microarrays (as demonstrated in the examples) to determine direct or indirect effects as a result of the modulation. An inhibitor can also be used during these experiments to promote modulation of specific genes or gene products.

The present invention also provides a method for identifying novel agents that reduce or inhibit the formation of biofilms. As described in the specification, the modulation of the expression of cysB inhibits the formation of biofilms. cysB is the global regulator of the biosynthesis of cysteine which directly controls the expression of the genes involved in this process. The invention allows one skilled in the art of screening compounds in drug discovery to measure the modulation of a gene, wherein the gene is a cysB gene or a gene related to cysB, during the screening of compounds as a novel detection method for the reduction or inhibition of biofilms. This method provides various advantages over current screening strategies. Traditionally, the process of identifying biofilm inhibitors involves exposing at least one bacterial cell to a compound and then measuring the decrease in the formation of biofilms 24 to 72 hours after exposure. The reduction in biofilm formation is quantified using crystal violet stain, which can be problematic. As described in the literature, after the bacteria are exposed to the compounds, they are rinsed for a variable amount of time, stained for a certain amount of time with crystal violet stain, rinsed with solvents or combinations of solvents, and analyzed by determining optical densities of the crystal violet solutions compared to the controls. (Pratt, L. A. et al. Mol. Micro. 1998, 30(2), p. 285-298.). Therefore, measurement of the inhibition of biofilm formation can be laborious and can yield unreliable results. Taking advantage of the discovery described herein that modulation of a cysB gene is involved in biofilm formation, the present inventions provides a simple, fast, and inexpensive method of detecting the inhibition of biofilms. The method involves the detection of the modulation of a gene, wherein the gene is a cysB gene or a gene related to cysB involved in biofilm formation. A reporter system is linked to the gene or its gene product. Specifically, the modulation of the cysB gene, a gene related to a cysB gene or its gene product can be detected with a reporter, e.g., a green fluorescent protein, antibiotic, radioactive isotope, or fluorescent dye. Accordingly, the present invention provides a superior method to identify novel biofilm inhibitors than presently available in the art.

Biofilms may also adhere to surfaces, such as pipes and filters. Deleterious biofilms are problematic in industrial settings because they cause fouling and corrosion in systems such as heat exchangers, oil pipelines, and water systems. Elvers et al., Biofilms and Biofouling, 2^nd ed., vol. 1, Academic Press, San Diego, Calif. Biofilm inhibitors can be employed to prevent microorganisms from adhering to surfaces which may be porous, soft, hard, semi-soft, semi-hard, regenerating, or non-regenerating. These surfaces include, but are not limited to, polyurethane, metal, alloy, or polymeric surfaces in medical devices, enamel of teeth, and cellular membranes in animals, preferably, mammals, more preferably, humans. The surfaces may be coated or impregnated with the biofilm inhibitors prior to use. Alternatively, the surfaces may be treated with biofilm inhibitors to control, reduce, or eradicate the microorganisms adhering to these surfaces.

The descriptions herein is not intended to limit the scope of the present invention, but only to demonstrate the far reaching utility of the invention to those skilled in the art. All references cited herein are hereby incorporated by reference in their entirety.

EXAMPLES

Example 1

Inhibition of biofilm formation by E. coli K12 [R1drd19], P. aeruginosa PAO1, and V. harveyi BB120 by the addition of 10 μg/mL ursolic acid. For E. coli K12 [R1drd19], data were collected 16 hours after addition of ursolic acid to a 24 hour biofilm in LB medium; for P. aeruginosa PAO1, data were collected 18 hours after addition of ursolic acid with inoculation in LB medium plus 1% sodium citrate; and for V. harveyi BB 120, data were collected 18 hours after addition of ursolic acid with inoculation in M9 medium. All biofilm mass readings at OD540 were normalized based on the reading of wild type without ursolic acid which was normalized to 1. One standard deviation is shown. The results are shown in FIG. 1.

Example 2

Example 1 was repeated, except ursolic acid was added with inoculation in E. coli JM109 grown in LB 0.2% glucose. Ursolic acid inhibited air-liquid interface biofilm. The results are shown in FIG. 2.

Example 3

To identify the genes controlled by ursolic acid, E. coli K12 was grown in LB medium overnight, diluted 1:100 in fresh LB supplemented with 0, 10, or 30 μg/mL ursolic acid. The same amount of ethanol was supplemented to eliminate solvent effects. The cultures were grown to an OD₆₀₀ of 0.9. The cells were centrifuged in a microcentrifuge for 15 seconds at 20,000×g in mini bead beater tubes (Biospec, Bartlesville, Okla.) that were cooled to −80° C. before sampling. The cell pellets were flash frozen in a dry ice-ethanol bath and stored at −80° C. until RNA isolation.

To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, Calif.) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 30 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen). OD₂₆₀ was used to quantify the RNA yield. OD₂₆₀/OD₂₈₀ and 23S/16S rRNA were measured using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.) to check the purity and integrity of RNA (RNeasy Mini handbook, Qiagen).

The E. coli DNA microarrays were prepared as described previously by Wei, Y. et al (Journal of Bacteriology, 2001, 183 (2) p. 545-556). Each gene probe was synthesized by PCR and has the size of the full open reading frame (200-2000 nt). The double-strand PCR products were denatured in 50% dimethyl sulfoxide and spotted onto aminosilane slides (Full Moon Biosystems, Sunnyvale, Calif.) as probes to hybridize with the mRNA-derived cDNA samples. It has been shown that each array can detect 4228 of the 4290 E. coli ORFs. Each gene has two spots per slide.

Briefly, the total RNA from the E. coli K12 samples grown with and without ursolic acid was first converted into labeled cDNA. Then the cDNA samples (6 μg of each) were each labeled with both Cy3 and Cy5 dyes to remove artifacts related to different labeling efficiencies; hence, each experiment needed at least two slides. The Cy3-labeled sample without ursolic acid and the Cy5-labeled ursolic acid sample (with 10 or 30 μg/mL ursolic acid) were hybridized on the first slide. Similarly, the Cy5-labeled sample without ursolic acid and the Cy3-labeled ursolic acid sample were hybridized on the second slide. Since each gene has two spots on a slide, the two hybridizations generated eight data points for each gene (four points for the sample without ursolic acid and four points for the ursolic acid sample). The microarray experiments with dye-swapping were repeated for both concentrations of ursolic acid.

The cDNA samples of E. coli DH5α treated with FCM or 0.5× LB (6 μg of each) were each labeled with both Cy3 and Cy5 dyes to remove artifacts related to different labeling efficiencies; hence, each experiment required at least two slides. The Cy3-labeled FCM sample and Cy5-labeled 0.5× LB sample were hybridized on the first slide. Similarly, the Cy5-labeled FCM sample and Cy3-labeled 0.5× LB sample were hybridized on the second slide. Since each gene has two spots on a slide, the two hybridizations generated eight data points for each gene (four points for the FCM sample and four points for the 0.5× LB sample). DNA microarrays for the E. coli DH5α treated with ACM or 0.5× LB were performed in an analogous manner.

The DNA microarrays were incubated in prehybridization solution (3.5×SSC [1×SSC is 0.15 M NaCl plus 0.015 M sodium citrate] [Invitrogen], 0.1% sodium dodecyl sulfate [SDS] [Invitrogen], and 0.1% bovine serum albumin [Invitrogen]) at 45° C. for 20 min. The arrays were rinsed with double-distilled water and were spun dry by centrifugation. Labeled cDNA (6 μg) was concentrated to 10 μl of total volume and was mixed with 10 μl of 4× cDNA hybridization solution (Full Moon Biosystems) and 20 μl of formamide (EM Science, Gibbstown, N.J.). The hybridization mix was heated to 95° C. for 2 min and was added to the DNA microarrays; each array was covered with a coverslip (Corning, Big Flats, N.Y.) and was incubated overnight at 37° C. for hybridization. When the hybridization was finished, the coverslips were removed in 1×SSC-0.1% SDS at room temperature, and the arrays were washed once for 5 min in 1×SSC-0.1% SDS at 40° C., twice for 10 min in 0.1×SSC-0.1% SDS at 40° C., and twice for 1 min in 0.1×SSC at 40° C. The arrays were quickly rinsed by dipping in room-temperature double-distilled water and were then spun dry by centrifugation. The hybridized slides were scanned with the Generation III Array Scanner (Molecular Dynamics Corp.). Readings at 570 and 670 nm was used to quantify the probes labeled with Cy3 and Cy5 separately. The signal was quantified with Array Vision 4.0 or 6.0 software (Imaging Research, St. Catherines, Ontario, Canada). Genes were identified as differentially expressed if the expression ratio was greater than 1.4 and the p-value (t-test) is less than 0.05. P-values were calculated on log-transformed, normalized intensities. Including the p-value criterion ensures the reliability of the induced/repressed gene list. Normalization was relative to the median total fluorescent intensity per slide per channel.

TABLE 1
E. coli K12 genes repressed by 10 and 30 μg/mL ursolic acid. The
underlined ratios indicate the corresponding genes were significantly repressed by ursolic acid.
The highlighted genes were repressed both by 10 and 30 μg/mL ursolic acid. ER is expression
ratio and Pv is p-value.
	10 μg/mL	30 μg/mL
	ursolic acid	ursolic acid
Gene	b#	ER	Pv	ER	Pv	Description
arsC	b3503	−1.5	0.045	1.4	0.014	enzyme, drug/analog sensitivity
b2789	b2789	−1.9	0.056	−2.5	0.038	putative D-glucarate permease (MFS family)
cspF	b1558	−1.6	0.003	−1.1	0.357	cold shock-like protein
cspG	b0990	−2.5	0.009	−1.7	0.017	homolog of Salmonella cold shock protein
cysB	b1275	−1.7	0.038	−1.4	0.018	positive transcriptional regulator for cysteine regulon
cysD	b2752	−2.5	9E−04	−2.5	0.024	central intermediary metabolism: sulfur metabolism
cysI	b2763	−1.5	0.069	−1.7	2E−04	central intermediary metabolism: sulfur metabolism
cysJ	b2764	−3.6	0.015	−3.3	0.009	central intermediary metabolism: sulfur metabolism
cysK	b2414	−3.6	0.003	−3.3	0.008	amino acid biosynthesis: cysteine
frvR	b3897	−5.4	0.006	−2	0.175	putative frv operon regulatory protein
gntU_1	b3436	−1.5	0.026	−1.4	0.043	transport of small molecules: carbohydrates, organic acids, alcohols
narH	b1225	−1.6	0.002	−1.4	0.028	energy metabolism, carbon: anaerobic respiration
pheM	b1715	−1.6	0.011	1	0.762	aminoacyl tRNA synthetases, tRNA modification
pheP	b0576	−1.5	0.021	−1.1	0.499	transport of small molecules: amino acids, amines
rimL	b1427	−1.5	0.022	1	0.719	enzyme, ribosomes - maturation and modification
rmf	b0953	−1.5	0.003	1	0.662	factor; ribosomes - maturation and modification
rpmI	b1717	−1.6	0.007	1	0.708	structural component, ribosomal proteins - synthesis, modification
slp	b3506	−1.5	0.006	−1.6	0.002	outer membrane constituents
ugpB	b3453	−1.4	0.045	−1.5	0.021	transport of small molecules: carbohydrates, organic acids, alcohols
ybiK	b0828	−2.4	7E−04	−2.2	0.005	putative asparaginase
yhaD	b3124	−1.6	0.025	−2.6	0.009	glycerate kinase I
yhaF	b3126	−1.5	0.009	−2.4	0.002	alpha-dehydro-beta-deoxy-D-glucarate aldolase
yhaG	b3128	−2	0.004	−2.2	0.008	(D)-galactarate dehydrogenase
b0309	b0309	−1.7	0.042	−1.3	0.155	orf, hypothetical protein
b0484	b0484	−1.5	0.044	−1.1	0.425	putative enzyme, not classified
b0485	b0485	−1.8	0.009	−1.3	0.019	putative enzyme, not classified
b0829	b0829	−1.5	0.032	−1.5	0.09	putative transport; not classified
b1729	b1729	−5.6	0.003	−2	0.133	putative enzyme, not classified
b2379	b2379	−1.5	0.011	1	0.325	putative enzyme, not classified
hdeA	b3510	−1.7	0.008	−1.4	0.008	orf, hypothetical protein
hdeB	b3509	−1.8	6E−04	−1.4	0.01	orf, hypothetical protein
yeeD	b2012	−2.3	0.025	−1.4	0.228	orf, hypothetical protein
yeeE	b2013	−13	0.006	−2	0.182	putative transport, not classified
yjeB	b4178	−1.4	0.005	1	0.833	orf, hypothetical protein
ybhG	b0795	−1.4	0.013	−1.4	0.002	putative membrane, not classified
yhaU	b3127	−1.9	0.074	−4.2	0.003	putative transport protein

Example 4

Effect of adding 30 μg/mL ursolic acid on biofilm formation in LB medium in the presence the cysB mutation (E. coli K12 [R1drd19] vs. E. coli K12 cysB[R1drd19], data collected 16 hours after addition of ursolic acid. All biofilm mass readings at OD540 were normalized based on the reading of wild type without ursolic acid which was normalized to 1. One standard deviation shown. The results are shown in FIG. 3.

Example 5

Example 1 was repeated, except asiatic acid was added with inoculation in E. coli JM109 in MC9 glucose media. Asiatic acid demonstrated approximately 75%, 80%, and 85% biofilm inhibition when tested at 5 μg/ml, 10 μg/ml, and 15 μg/ml, respectively.

Example 6

Example 3 was repeated, except asiatic acid (C255) was added instead of ursolic acid. The results are shown in Table 2.

TABLE 2
E. coli JM109 genes induced by 10 μg/ml and 30 μg/ml asiatic acid in
M9C glucose media. The underlying ratios indicate the corresponding genes were significantly
induced by asiatic acid. ER is expression ratio and Pv is p-value.
	10 ug/ml	30 ug/ml
	Asiatic Acid	Asiatic Acid
Gene	b#	Pv	ER	Pv	ER	Descriptions
b0829	b0829	0.000001	2.83	0.000001	2.46	putative ATP-binding component of a transport system
b1729	b1729	0.000001	2.64	0.000001	2.30	part of a kinase
b1963	b1963	0.000838	2.14	0.000007	2.30	orf, hypothetical protein
b2332	b2332	0.000002	2.14	0.000002	2.30	orf, hypothetical protein
b2420	b2420	0.000006	4.29	0.004108	2.14	orf, hypothetical protein
b2531	b2531	0.000002	2.46	0.000002	2.14	orf, hypothetical protein
b2670	b2670	0.000001	3.25	0.002057	2.64	orf, hypothetical protein
b2834	b2834	0.000063	2.30	0.000121	2.00	orf, hypothetical protein
bolA	b0435	0.000001	2.30	0.000001	2.64	possible regulator of murein genes
cbl	b1987	0.000001	13.93	0.000001	13.00	transcriptional regulator cys regulon; accessory regulatory
						circuit affecting cysM
cysA	b2422	0.000002	4.00	0.000002	3.48	ATP-binding component of sulfate permease A protein;
						chromate resistance
cysB	b1275	0.000001	6.06	0.000001	4.29	positive transcriptional regulator for cysteine regulon
cysC	b2750	0.000001	10.56	0.000001	6.96	adenosine 5-phosphosulfate kinase
cysD	b2752	0.000001	6.96	0.000001	6.50	ATP: sulfurylase (ATP: sulfate adenylyltransferase), subunit 2
cysH	b2762	0.000001	4.59	0.000001	3.03	3-phosphoadenosine 5-phosphosulfate reductase
cysI	b2763	0.000002	4.29	0.000002	3.25	sulfite reductase, alpha subunit
cysJ	b2764	0.000002	3.73	0.000002	4.00	sulfite reductase (NADPH), flavoprotein beta subunit
cysK	b2414	0.000001	4.59	0.000001	3.48	cysteine synthase A, O-acetylserine sulfhydrolase A
cysM	b2421	0.000001	3.73	0.000004	3.25	cysteine synthase B, O-acetylserine sulfhydrolase B
cysN	b2751	0.000001	11.31	0.000001	7.46	ATP-sulfurylase (ATP: sulfate adenylyltransferase),
						subunit 1, probably a GTPase
cysP	b2425	0.000001	4.29	0.000001	4.92	thiosulfate binding protein
cysU	b2424	0.000002	4.92	0.000002	4.92	sulfate, thiosulfate transport system permease T protein
cysW	b2423	0.000002	4.59	0.000002	4.00	sulfate transport system permease W protein
dgt	b0160	0.000002	2.14	0.000057	2.30	deoxyguanosine triphosphate triphosphohydrolase
fliY	b1920	0.000002	4.00	0.000002	3.25	putative periplasmic binding transport protein
ftn	b1905	0.000001	3.25	0.000001	3.03	cytoplasmic ferritin (an iron storage protein)
glgS	b3049	0.000001	2.14	0.000001	2.30	glycogen biosynthesis, rpoS dependent
ilvG_1	b3767	0.000005	2.83	0.000059	2.00	acetolactate synthase II, large subunit, cryptic, interrupted
ilvL	b3766	0.000003	2.30	0.000005	3.48	ilvGEDA operon leader peptide
msrA	b4219	0.000001	2.30	0.000001	2.64	peptide methionine sulfoxide reductase
nlpA	b3661	0.000001	18.38	0.000001	9.85	lipoprotein-28
pssR	b3763	0.001336	2.46	0.001832	2.14	regulator of pssA
pstS	b3728	0.000002	2.64	0.000002	2.00	high-affinity phosphate-specific transport system;
						periplasmic phosphate-binding protein
sbp	b3917	0.000001	18.38	0.000001	12.13	periplasmic sulfate-binding protein
tauA	b3065	0.000001	2.46	0.000001	2.00	taurine transport system periplasmic protein
yaeG	b0162	0.007398	4.59	0.042948	4.00	orf, hypothetical protein
yaiB	b0382	0.000001	2.30	0.000014	2.64	orf, hypothetical protein
ybgR	b0752	0.000002	2.46	0.000002	2.46	putative transport system permease protein
ybiK	b0828	0.000001	6.50	0.000001	5.66	putative asparaginase
yciW	b1287	0.000002	3.03	0.000002	3.73	putative oxidoreductase
yedO	b1919	0.000002	3.73	0.000002	2.83	putative 1-aminocyclopropane-1-carboxylate deaminase
yeeD	b2012	0.000002	3.73	0.000002	2.30	orf, hypothetical protein
yeeE	b2013	0.000002	3.25	0.000002	2.14	putative transport system permease protein
ygbE	b2749	0.000002	6.96	0.000004	5.28	putative cytochrome oxidase subunit
yicG	b3646	0.000001	2.83	0.000001	2.30	orf, hypothetical protein
yicL	b3660	0.000001	6.50	0.000057	2.83	putative permease transporter
yjaE	b3995	0.000002	2.00	0.000002	2.14	putative transcriptional regulator
yjiD	b4326	0.000001	7.46	0.000001	9.85	orf, hypothetical protein
yrbL	b3207	0.000001	2.64	0.000001	2.46	orf, hypothetical protein

Claims

1. A method for reducing or inhibiting a biofilm comprising modulating expression of a gene present in a Gram-negative bacteria cell capable of biofilm formation, the gene being a cysD, cysI, cysJ, cysK or ybiK gene, thereby to reduce or inhibit the biofilm formation.

2. The method of claim 1, wherein modulation of the gene comprises contacting the cell with a composition comprising a compound selected from the group consisting of ursolic acid and asiatic acid, or a pharmaceutically acceptable salt of such compound, a hydrate of such compound, a solvate of such compound, an N-oxide of such compound, or a combination thereof.

3. The method of claim 2, wherein the compound is ursolic acid.

4. The method of claim 2, wherein the compound is asiatic acid.

5. The method of claim 1, wherein the cell is selected from a group consisting of Escherichia coli, Proteus mirablis, Francisella tularensis, Vibrio sp., Pseudomonas aeruginosa, V. harveyi, Pseudomonas sp., Salmonella sp., Haemophilus influenzae, Borrelia sp., Neisseria sp., Bacillus sp., Burkholderia sp., Klebsiella sp., and Yersinia pestis.

6. The method of claim 5, wherein the cell is Escherichia coli.

7. The method of claim 5, wherein the cell is Pseudomonas aeruginosa.

8. The method of claim 5, wherein the cell is V. harveyi.

9. (canceled)

10. The method of claim 2, wherein the gene is cysD.

11. The method of claim 2, wherein the gene is cysI.

12. The method of claim 2, wherein the gene is cysJ.

13. The method of claim 2, wherein the gene is cysK.

14. The method of claim 2, wherein the gene is ybiK.

15. A method for modulating the expression of a gene selected from the group consisting of cysD, cysI, cysK or ybiK, comprising contacting a Gram-negative bacteria cell capable of biofilm formation with a composition comprising a compound selected from the group consisting of ursolic acid and asiatic acid, or a pharmaceutically acceptable salt of such compound, a hydrate of such compound, a solvate of such compound, a N-oxide of such compound, or a combination thereof.

16. The method of claim 15, wherein the compound is ursolic acid.

17. The method of claim 15, wherein the compound is asiatic acid.

18. The method of claim 15, wherein the gene is cysD.

19. The method of claim 15, wherein the gene is cysI.

20. The method of claim 15, wherein gene is cysJ.

21. The method of claim 15, wherein the gene is cysK.

22. The method of claim 15, wherein the gene is ybiK.

23. The method of claim 15, wherein the cell is selected from a group consisting of Escherichia coli, Proteus mirablis, Francisella tularensis, Vibrio sp., Pseudomonas aeruginosa, V. harveyi, Pseudomonas sp., Salmonella sp., Haemophilus influenzae, Borrelia sp., Neisseria sp., Bacillus sp., Burkholderia sp., Klebsiella sp., and Yersinia pestis.

24. The method of claim 23, wherein the cell is Escherichia coli.

25. The method of claim 23, wherein the cell is Pseudomonas aeruginosa.

26. The method of claim 23, wherein the cell is V. harveyi.

27. The method of claim 15, wherein the cell is selected from a group consisting of Gram-negative bacteria.

28.-38. (canceled)