WO2009106532A2

WO2009106532A2 - Use of prokaryotic tir-domain containing proteins as therapeutic and diagnostic agents

Info

Publication number: WO2009106532A2
Application number: PCT/EP2009/052203
Authority: WO
Inventors: Hermann Wagner; Christine Cirl; Thomas Miethke
Original assignee: Technische Universität München
Priority date: 2008-02-27
Filing date: 2009-02-25
Publication date: 2009-09-03
Also published as: EP2271355A2; WO2009106532A3

Abstract

The present invention relates inter alia to nucleic acid molecules encoding prokaryotic TIR-domain containing polypeptides as well as fragments and functional homologues thereof for diagnostic and therapeutic purposes.

Description

USE OF PROKARYOTIC TIR-DOMAIN CONTAINING PROTEINS AS THERAPEUTIC AND DIAGNOSTIC AGENTS

FIELD OF THE INVENTION

The present invention relates inter alia to nucleic acid molecules encoding prokaryotic TIR-domain containing polypeptides as well as fragments and functional homologues thereof for diagnostic and therapeutic purposes.

BACKGROUND OF THE INVENTION

Microbial infections continue to cause diseases in humans as well as animals.

Humans in particular have developed complementary immune systems, namely the innate and the adaptive immune system to cope inter alia with such infections.

The adaptive immune system is designed to mediate highly sophisticated and specific responses to invading agents by way of B and T cells. This part of the immune system also provides a memory function to prevent repetitive infections.

In evolutionary terms, the innate immune system is older than the adaptive immune system and provides a pre-existing response to categorise the invading infectious agent as well as to launch an immune defence appropriate for the pathogen. A hallmark of the innate immune systems is the detection and categorisation of the infectious agents by so-called pattern-recognition receptors (PRR' s) of which the best understood family are the Toll-like receptors (TLR's).

Up to now approximately ten TLR's have been identified which have been named, e.g. TLRl, TLR2, TLR3, TLR5, etc. The different TLR's are found at different locations of the host cells, are activated by different ligands and lead to different cellular responses. For example, TLR3, TLR7/8 and TLR9 localise to the intracellular endosomal compartment whilst TLR4, TLRl and TLR2 are predominantly found on the cytoplasmic membrane.

TLR3 recognises dsRNA, TLR7/8 recognises ssRNA and TLR9 is believed to be activated dependent on unmethylated CpG motifs of DNA. TLR4 in turn is activated by lipopolysaccharides as they are commonly found on the outer membrane of bacteria.

The selective and orchestrated activation of TLR's activity leads to a response of the innate immune system that is rather specific for the e.g. invading infectious agents and helps the human or animal body to keep the infection under control. It is to be mentioned that the precise nature of ligand- specificity and the orchestration of TLR's mediated signalling is far from being completely understood.

The advent of modern medicine is commonly associated with the development of the first antibiotics, which allowed effective control of diseases that until then were hardly manageable. However, in view of the increasing resistances of pathogenic bacteria and other microorganisms against established antibiotics, there is a continuing need and call for other therapeutic approaches that allow to effectively fight e.g. microbial infections. There is also a continuing need for diagnostic methods and kits that allow to precisely determine the type of microorganism that is responsible for a pathogenic infection as this should allow a selective use of possible medications. OBJECTIVE AND SUMMARY OF THE INVENTION

It is one objective of the present invention to provide molecules that can be used to treat microbial pathogenic infections. It is a further objective of the present invention to provide diagnostic methods and kits that can be used for the diagnosis of microbial infections. Another objective of the present application is to provide methods for treating microbial infections.

These and other objectives as they will become apparent from the ensuing description and claims are attained by the subject matter of the independent claims. Some of the preferred embodiments are defined by the dependent claims.

The inventors of the present invention have surprisingly found that bacterial proteins comprising a Toll/Interleukin-1 receptor (TIR) domain are capable of interfering with Toll-like receptor (TLR) signalling through the MyD88 adaptor molecule.

These findings can be used for a multitude of different applications as will be set out hereinafter.

One embodiment of the present invention relates to an isolated recombinant nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; c) Nucleic acid sequences that specifically hybridize with any of the nucleic acid sequences of a) or b) under stringent conditions. - A -

Preferably, the above mentioned group a) comprises nucleic acid sequences encoding polypeptides comprising SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5.

If the above mentioned group a) also comprises nucleic acid sequences encoding polypeptides of SEQ IDs No.1 and No.2, it is preferred that said nucleic acid sequences do not correspond to the genomic sequences in E. coli encoding a polypeptide of SEQ ID No.1 and in Brucella melitensis encoding a polypeptide of SEQ ID No.2, respectively.

The nucleic acids mentioned in items a) and b) may be used for example in the production of recombinant isolated polypeptides encoded by these nucleic acids. These polypeptides may in turn be used for therapeutic purposes as will be set out hereinafter. Nucleic acid sequences referred to item c) may be used for example as diagnostic markers or therapeutically active molecules in e.g. an antisense approach.

In another embodiment, the present invention relates to a vector comprising at least one of the aforementioned nucleic acid molecules. Such vectors may be a plasmid, a cosmid, a minichromosome, a bacterial artificial chromosome, a viral vector or the like.

Another embodiment relates to a host cell comprising at least one of the aforementioned nucleic acid molecules and/or at least one vector as mentioned above.

Depending on the area of applications, the host cells may be prokaryotic or eukaryotic host cell. Typical prokaryotic host cells include bacterial cells such as Escherichia coli (E. coli). Typical eukaryotic host cells include yeast cells such as Saccharomyces cerevisiae (S. cerevisiae), insect cells such as SF9 cells, plant cells and mammalian cells such as COS or CHO cells.

The present invention further relates to a transgenic animal comprising and preferably expressing at least one of the aforementioned nucleic acid molecules and/or at least one of the aforementioned vectors. Those transgenic animals will typically be made from rodents and preferably from mice and/or rats.

In another embodiment the present invention relates to an isolated recombinant polypeptide encoded by an isolated recombinant nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2.

Thus, in preferred embodiment relating to the isolated recombinant polypeptides, the present invention relates to an isolated recombinant polypeptide encoded by an isolated recombinant nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 3,

SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2.

Such recombinant polypeptides may be used for therapeutic applications, e.g. for treating diseases that are characterized in increased TLR-mediated signaling.

Preferably such recombinant polypeptides may be used for treating diseases which are characterized in aberrantly high levels of interferons, chemokines, proinflammatory cytokines as a result of TLR or MyD88 signaling. Such diseases include autoimmune disease and/or chronic inflammatory diseases including but not limited to rheumatoid arthritis, inflammatory bowel disease, ankylosing spondylitis, psoriasis, juvenile rheumatoid arthritis, lupus erythematodes and other such diseases set forth hereinafter.

The afore-described polypeptides may also be used as diagnostic markers. The person skilled in the art is aware that for this latter area of application, the polypeptides need not be of a recombinant nature. Rather the presence of polypeptides comprising the aforementioned amino acid sequences may be sufficient to detect the infection of a human or animal being with pathogenic prokaryotic organisms such as bacteria including pathogenic strains of e.g. E.coli, Brucella, S. aureus, Salmonella or the like.

In yet another embodiment the present invention relates to an isolated recombinant nucleic acid molecule comprising at least a nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody or fragment thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2.

The present invention also relates to recombinant isolated polypeptides encoded by an isolated recombinant nucleic acid molecule comprising at least a nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2.

In one aspect of this aspect of the invention, the antibody may be a monoclonal or polyclonal antibody. Monoclonal antibodies may be of murine origin. However, preferably monoclonal antibodies or fragments thereof in accordance with the invention will be chimeric, humanized or human antibodies.

Functional analogues of an antibody or fragments thereof are polypeptides that recognize the same type of polypeptides, as do antibodies and fragments thereof in accordance with the invention without necessarily having the typical architecture and amino acid sequence arrangement found for antibodies. Such functional analogues thus e.g. relate to single chain antibodies, scFv, Fab, Fab2', etc. Antibodies, fragments thereof and functional analogues thereof may be used e.g. as therapeutic agents or as diagnostic tools. If they are used as therapeutic agents, they may be applied e.g. to treat infections of humans and/or animals being infected with pathogenic prokaryotic organisms expressing a TIR domain that interferes with TLR- signaling through eukaryotic TIR-domains. Such diseases particularly include urinary tract infections with pathogenic strains of bacteria such as e.g. E. coli, infections caused by Brucella, S. aureus, Salmonella or the like.

If such antibodies, fragments thereof or functional analogues thereof are used for diagnostic purposes, one area of application may reside in the detection of prokaryotic TIR-domain containing polypeptides being present in pathogenic prokaryotic microorganisms.

Another aspect of the present invention relates to vectors comprising the aforementioned nucleic acid molecules encoding for antibodies, fragments thereof and/or functional homologues thereof. The vectors may be the same as those mentioned above.

Yet another aspect of the present invention relates to host cells comprising the aforementioned nucleic acid molecules encoding for antibodies, fragments thereof or functional homologues thereof in accordance with the invention and/or vectors as mentioned above.

Further, the present invention may relate to transgenic animals comprising the aforementioned nucleic acid molecules and/or vectors that comprise nucleic acid sequences encoding for antibodies, functional fragments thereof and/or functional homologues thereof. Yet another embodiment of the present invention relates to pharmaceutical compositions comprising either any of the aforementioned nucleic acid molecules or any of the aforementioned recombinant polypeptides.

These pharmaceutical compositions may comprise optionally at least one pharmaceutically acceptable excipient.

Depending on the nature of the nucleic acid molecule and/or polypeptide that is present within pharmaceutical compositions in accordance with the invention, the present invention relates to pharmaceutical compositions for treating a disease or condition that is characterized and/or caused by increased activity of TLR-mediated and MyD88- dependent signaling. Such diseases include autoimmune disease and/or chronic inflammatory diseases including but not limited to rheumatoid arthritis, inflammatory bowel disease, ankylosing spondylitis, psoriasis, juvenile rheumatoid arthritis, lupus erythematodes and other such diseases set forth hereinafter.

In another embodiment the present invention relates to pharmaceutical compositions for treating a disease or condition caused by pathogenic prokaryotic microorganisms expressing a polypeptide comprising a TIR domain. Diseases which can be treated with the aforementioned pharmaceutical composition and which result from a microbial infection that is caused by pathogenic prokaryotic microorganisms expressing a polypeptide comprising a TIR-domain comprise e.g. infections pathogenic bacteria such as E.coli, Brucella, S. aureus, Salmonella or the like. The diseases caused by such microorganisms include urinary tract infections, acute pyelonephritis, bladder infections such as acute cystitis, asymptomatic bacterial carriage such as asymptomatic bacteriuria (ABU), sepsis and pneumonia.

In yet another embodiment, the present invention relates to a pharmaceutical composition comprising at least one efflux pump inhibitor molecule for treating a disease or condition caused by pathogenic prokaryotic microorganisms expressing a polypeptide comprising a TIR domain. Such efflux pump inhibitor molecules may be selected from the group comprising e.g. Phe-Arg-beta-naphthylamide (PAβN), 1- (l-Naphthylmethyl)-piperazine (NMP) or the like. The disease includes the aforementioned ailments.

In some of the preferred embodiments, the pharmaceutical compositions use such efflux pump inhibitors without antibiotics being present.

The present invention further relates to diagnostic compositions comprising at least one of the aforementioned nucleic acid molecules or at least one of the aforementioned polypeptides and optionally one diagnostically acceptable excipient.

The present invention further relates to the use of a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1,

SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; c) Nucleic acid sequences that specifically hybridize with any of the nucleic acid sequences of a) or b) under stringent conditions as a diagnostic marker as a diagnostic and/or therapeutic agent.

The present invention also relates to the use of a polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; as a diagnostic and/or therapeutic agent.

The present invention further relates to the use of a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2. as a diagnostic and/or therapeutic agent.

The present invention also relates to the use of a polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ

ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2. as a diagnostic and/or therapeutic agent.

Further, the present invention relates to a method of diagnosing diseases or conditions characterized in and/or caused by an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide comprising at least the following steps: a) obtaining a sample from a human or animal individual suspected of suffering from an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide; b) detecting the presence or absence of said microorganism expressing a TIR-domain containing polypeptide; c) deciding on the presence and/or likely occurrence of a pathogenic microbial infection by comparing the results obtained in step b) with appropriate negative and positive controls.

Preferably step b) is performed outside the human or animal body.

The present invention further relates to a method of data acquisition in the context of diagnosing diseases or conditions characterized in and/or caused by an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide comprising at least the steps of: a) detecting a prokaryotic microorganism with a TIR-domain containing polypeptide in a human or animal being.

The present invention further relates to a method of treating a human or animal suffering from a disease or condition that is characterized in and/or caused by increased activity of TLR- signaling through MyD88 by administering at least one nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ

ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2.

The present invention further relates to a method of treating a human or animal being suffering from a disease characterized in and/or caused by increased activity of TLR- signaling through MyD88 by administering at least one polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1,

SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2.

The present invention also relates to a method of treating a human or animal being suffering from an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide by administering a nucleic acid molecule comprising at least one nucleic acid sequence that specifically hybridizes under stringent conditions with any nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2.

The present invention further relates to a method of treating a human or animal being suffering from an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide by administering at least one nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2.

The present invention further relates to a method of treating a human or animal being suffering from an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide by administering at least one polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2.

The present invention further relates to a method of identifying molecules that are capable of interfering with the inhibitory effect of any of the polypeptides described herein on MyD 88 -mediated signaling comprising at least the following steps: a) Providing at least one polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: aa) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; ba) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; b) Determining the effect of said polypeptide on the activity of MyD88; c) Providing a molecule other than said polypeptide or MyD88; d) Determining the influence of said molecule on the effect of said polypeptide on the activity of MyD88.

FIGURE LEGENDS:

Fig. 1 Genomic localization and protein structure of TcpC and TcpB

(A) Operon structure of CFT073 serU and Brucella phe t-RNA islands. (B) Comparison of the tertiary structure of the TIR-domain of human TLRl and the predicted tertiary structure of TcpC and TcpB (composed using PyMOL). (C) Amino acid sequence comparison of TcpC and TcpB. Identical residues are underlined. (D) Amino acid sequence comparison within boxes 1-3 of the TIR-domain of TLR2, TLR4, MyD88, TIRAP, TcpB and TcpC. Identical residues found in at least two sequences are underlined.

Fig. 2 Tcps reduce cytokine secretion and increase accumulation of intracellular bacteria

(A) TNF-secretion by RAW264.7 macrophages (2x10⁶ cells/well) or (B) IL-6 secretion by HCV29 uroepithelial cells (2x10⁶ cells/well), which were either not infected (hatched bar) or infected with CFT073 (white bars), or the mutant tcpC::kan (black bars), or the complemented mutant tcpC: : kan+TpT CTpC (gray bars) with the indicated MOIs. Cytokine levels were determined 5 hours after infection. Error bars indicate SDs of three individual cultures. (C) RAW264.7 macrophages (2xlO⁶ cells/well) were either not infected (white bars) or infected with the complemented mutant tcpC: :kan+pΥ cpB with indicated MOIs. TcpB protein expression was induced 2.5h before tcpC: :kan+pΥ cpB was added to the culture (black bars).

Non-induced bacteria harboring pTcpB served as control (gray bars). TNF- secretion was determined 5.Oh after infection. (D) The experiment in (C) was repeated using the E. coli strain BL21-CodonPlus® RIL as host for the plasmid pTcpB. Error bars indicate SD of three individual cultures. (E) Intracellular bacteria in RAW264.7 macrophages (2x10⁶ cells/well) or (F)

HCV29 cells (2x10⁶ cells/well) 5 hours after infection. Extracellular bacteria were killed with gentamicin (50 μg/ml). (G) Total number of bacteria per well, determined 5 hours after infection of RAW264.7 macrophages (2x10⁶ cells/well) or (H) HCV29 cells (2x10⁶ cells/well). Error bars indicate SD of three individual experiments. *p<0.05, ANOVA on Ranks.

Fig. 3 Tcps impair TLR-signaling and interact with MyD88

(A) HEK293 cells (3x10⁴ cells/well) were transfected with a NF-κB- luciferase reporter construct (50 ng/ml), TLR4- (2.5 ng/ml), MD2- (2.5 ng/ml) and TcpC-encoding plasmids as indicated in the graph. At 24h post transfection cells were stimulated with endotoxin (100 ng/ml, white bars) or TNF (10 ng/ml, black bars) for 24h. Unstimulated cells served as controls (gray bars). (B) The experiment was performed as in (A) except that cells were transfected with a plasmid encoding for TLR2 (4 ng/ml) and stimulated with HSP60 (20 μg/ml, white bars). The TcpB-encoding plasmid was used at a concentration of 8 ng/ml. Unstimulated cells served as controls (black bars). Luciferase activity was normalized to cells transfected with empty vector (e.v.). Error bars depict SDs from three individual cultures. (C) Streptavidin agarose was coated with TIR-T cpC as described in Methods. Cell lysates were prepared from HEK293 cells which were not (-) or were transfected (+) with myc-tagged MyD88 as indicated. Pull-down assays of the cellular lysates were performed with TIR-TcpC agarose (+) or empty agarose (-). Bound proteins were washed three times with 0.03 or 0.5 M NaCl, eluted under acidic conditions and analyzed by Western blotting using a MyD88 anti-serum or an anti-myc mAb. An anti-serum specific for GFP was used as isotype control for the MyD88 anti-serum. (D) RAW264.7 cells were stimulated for the indicated period of time with the tcpC::kan mutant. Pulldown assays were performed with the concentrated cell lysates and analyzed by Western blotting using a MyD88 anti-serum. In addition, expression levels of MyD88 were analyzed in cellular lysates. β-actin expression was used as loading control. (E) HEK293 cells were transfected with MyD88-myc, IRAKI -flag and IRAK4-flag. Pull-down assays were performed in the absence (-) or presence (+) of TIR-TcpC or EGFP. Bound proteins were analyzed by Western blotting using an anti-myc and anti-flag mAb simultaneously. N-oc: lysates were treated with N-octylglucoside. (F)

HEK293 cells were transfected with MyD88-myc, or TRIF-flag, or the flag- labeled intracellular domain of TLR2 (ICD-TLR2). Pull-down assays were performed in the absence (-) or presence (+) of TIR-TcpC. Bound proteins were analyzed by Western blotting using an anti-myc or anti-flag mAb. (G) The experiment was performed as described in (C) with the exception that pull-down assays were performed in the absence (-) or presence (+) of TcpB. (H) BMMs (2xlO⁶ cell/well) from wild type and MyD88-deficient mice were not infected (black bar) or infected with the mutant tcpCr.kan (gray bars) or CFT073 (white bars) with MOIs indicated in the graph. TNF-secretion was analyzed 5.Oh post infection. Error bars represent SD from three individual cultures. (I) Wild type and (J) MyD88-deficient BMM were infected with tcpCr.kan or CFT073 with MOIs indicated in the graph. 5.Oh after infection extracellular bacteria were killed with gentamicin (50 μg/ml) and the number of intracellular bacteria was determined. Error bars indicate SD of three individual experiments. *p<0.05, ANOVA on Ranks.

Fig. 4 TcpC is a virulence factor that promotes bacterial burden in the urinary tract and renal tissue damage. (A and B) Bacterial burden in urine and kidneys after infection of C57BL/6 mice (8-10 mice/time point) with CFT073 or the tcpCr.kan mutant (1x10⁸

CFU/mouse). (C) Bacterial numbers in the kidneys, 24h after infection with CFT073, tcpCr.kan or tcpC::kan+pTcpC (*p<0.05, for CFT073 and tcpC: :kan+pΥ cpC vs tcpCr.kan, Fishers exact test). (D) Macroscopic abscesses (dotted line) in cross sections of mouse kidneys after infection with CFT073 or (E) tcpCr.kan mutant. (F) Histology of kidney tissue stained with htx-eosin after paraformaldehyde fixation or (G) with specific antibodies to neutrophil granulocytes (green, Rb68C5) and the PapG adhesin (red, antiserum to a synthetic PapG peptide). The abscess is indicated by the white dotted line. (H) TcpC is common in the most virulent uropathogenic E. coli strains from children with acute pyelonephritis (n=101) less common in acute cystitis (n=58) and ABU (n=77) and rare in fecal E. coli strains (FN, n=39). tcpC was detected by PCR (TcpC for: 5'-GGC AAC AAT ATG TAT AAT ATC CT-3', SEQ ID No.6; TcpC rev: 5'- GCC CAG TCT ATT TCT GCT AAA GA -3', SEQ ID No.31). *p=0.016, ^#p=0-001, Fishers exact test. Fig. 5 TcpC is secreted by CFT073 and subsequently taken up by host cells (A) Spontaneous and induced TcpC expression by CFT073 (1x10⁷ bacteria/well) upon culture in medium, medium at pH5 or upon co-culture with RAW264.7 (2xlO⁶ cells/well) for 5.Oh. The mutant tcpC::kan was used as negative control. (B) BMMs (2x10⁶ cells/well) were co-cultured in transwell plates with the mutant tcpC::kan (gray bars) or CFT073 (white bars) with MOIs indicated in the graph. BMM cultured in the absence of bacteria served as control (black bar). TNF-secretion was analyzed 5.Oh post infection. Error bars represent SD from three individual cultures. (C) Detection of intracellular levels of TcpC by Western blot after co-culture of

RAW264.7 cells (2xlO⁶ cells/well) with CFT073 (MOI 1) or with the mutant tcpCr.kan (MOI 1) in normal (left lanes) or transwell plates (right lanes). Uninfected cells (mock) served as negative control. BMM were trypsinized after 5h of culture, washed and lysed with RIPA-buffer. (D) RAW264.7 cells (5x10⁴ cells/well) were cultured in transwell plates with the mutant tcpCr.kan complemented (left graph) or not complemented (right graph) with pFlAsH- TcpC at an MOI of 5. Immediately before infection FlAsH-EDT₂ reagent was added to the culture and TcpC-accumulation in macrophages was monitored by confocal microscopy 90 min. after infection. (E) BMMs (2x10⁶ cells/well) were incubated with different doses of TIR-T cpC in the presence or absence of methyl-β-cyclodextrin (10 mM, MβCD) as indicated in the graph. Intra- and extracellular TIR-TcpC was detected by Western blot after 2.5h of culture in the cell lysate and concentrated culture supernatant, respectively.

Fig. 6 TNF-secretion is reduced by the purified TIR-domain of TcpC and use of PAβN as therapeutic compound

(A) RAW264.7 macrophages (2x10⁶ cells/well) were stimulated with Pam3Cys (lμg/ml), poly(LC) (2.5 μg/ml), ultrapure LPS from £. coli K12 (100 ng/ml), flagellin from S. typhimurium (1 μg/ml) and CpG 1826 (2 μM) in the presence of titrated amounts of the purified TIR-domain of TcpC (TIR- TcpC) as indicated in the graph. TNF secretion was analyzed 3h after stimulation. (B) To control for non-specific suppressive effects, cells were stimulated with ultrapure LPS from E.coli K12 (100 ng/ml) in the presence of titrated amounts of recombinant EGFP expressed and purified by the same method as used for TIR-T cpC. TNF was determined after 5.Oh of culture. All error bars depict SD from three individual cultures. (C) BMMs (2x10⁶ cells/well) were stimulated with ultrapure LPS from E. coli Kl 2 (100 ng/ml) in the presence of absence of MβCD (10 mM) and different doses of TIR- TcpC as indicated in the graph. TNF was determined after 2.5h of culture. (D) RAW264.7 cells (2xlO⁶ cells/well) were infected with CFT073 (white bars) or the mutant tcpC::kan (black bars) for 5.Oh at MOIs indicated in the absence or presence of the efflux pump inhibitor PAβN (52 μM). Error bars indicate SD of three individual cultures. (E) RAW264.7 cells (2x10⁶ cells/well) were infected with CFT073 (MOI 1) or with the mutant tcpCr.kan (MOI 1) or were not infected (mock) in the presence or absence of PAβN (52 μM) as indicated in the graph. TcpC was detected by Western blot after 5.Oh of culture.

Fig.7 Sequence alignment of prokaryotic TIR domain containing proteins using CLUSTAL W 2.0 multiple sequence alignment. Boxes I to III are in bold.

Fig. 8 Sequence alignment of the amino acid sequences of TcpC and TcpB using CLUSTAL W 2.0 multiple sequence alignment. Boxes I to III are in bold.

Fig. 9 Sequence alignment of the nucleic acid sequences of TcpC and TcpB using CLUSTAL W 2.0 multiple sequence alignment. DETAILED DESCRIPTION OF THE INVENTION

Before some of the embodiments of the present invention are described in more detail, the following definitions are introduced.

As used in this specification and in the intended claims, the singular forms of "a" and "an" also include the respective plurals unless the context clearly dictates otherwise.

The terms "about" and "approximately" in the context of the present invention denote an level or interval of accuracy that a person skilled in the art will understand to still ensure the technical effect of the feature in question. The term typically indicates a deviation from the indicated numerical value of ±10 % and preferably of

±5 %.

It is to be understood that the term "comprising" is not limiting. For the purposes of the present invention the term "consisting of is considered to be a preferred embodiment of the term "comprising of. If hereinafter a group is defined to comprise at least a certain number of embodiments, this is meant to also encompass a group which preferably consists substantially of these embodiments only.

Other definitions will be introduced in the context of the respective terms.

As mentioned above, the present invention is based on the surprising discovery that pathogenic prokaryotic microorganisms express TIR-domain containing polypeptides that contribute to the pathogenicity of these microorganisms.

As will be set out hereinafter the uropathogenic E.coli strain CFT073 expresses the protein TcpC (SEQ ID No. 1) which comprises a TIR-domain. A similar protein, namely TcpB is found in Brucella melitensis (B. melitensis) (SEQ ID No. 2). The experimental results explained hereinafter show that these TIR-domain containing prokaryotic polypeptides obviously undertake a kind of molecular mimicry that allows the pathogenic invader to down-regulate at least MyD88 mediated TLR- dependent signal transduction pathways of the innate immune system.

Without wanting to be bound to a particular scientific theory, it is considered justified assuming that other pathogenic prokaryotic microorganisms will undertake a similar approach for down-regulating MyD88 mediated signaling of the innate immune system.

The present invention in one embodiment thus relates to a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; c) Nucleic acid sequences that specifically hybridize with any of the nucleic acid sequences of a) or b) under stringent conditions.

If the above mentioned group a) also comprises nucleic acid sequences encoding polypeptides of SEQ IDs No.1 and No.2, it is preferred that said nucleic acid sequences do not correspond to the genomic sequences in E. coli encoding a polypeptide of SEQ ID No.1 and in Brucella melitensis encoding a polypeptide of SEQ ID No.2, respectively. In one preferred embodiment such nucleic acid molecules will be isolated recombinant nucleic acid molecules.

The term "isolated" indicates that a nucleic acid molecule or a polypeptide has been isolated from its natural environment and is presented in a form in which it is not found in nature.

The nucleic acid sequences according to items a) and b) will typically be used to produce polypeptides that can act as a therapeutically active agent as will be set out hereinafter. However, the polypeptides encoded by nucleic acid sequences a) and b) may also be used to express polypeptides for raising antibodies, functional fragments thereof and/or functional analogues thereof that can then be applied as diagnostic or therapeutic agents.

The nucleic acid sequences according to item c) may be used directly for diagnostic purposes, e.g. as a probe molecule in a diagnostic assay or as a therapeutically active agent, e.g. in an antisense approach.

If the nucleic acid molecules according to items a) and c) are used for the aforementioned purposes they will be typically isolated and preferably recombinant nucleic acid molecules. If they are used for diagnostic approaches as described hereinafter, they may, however, also be of natural origin.

The present invention also relates to a polypeptide encoded by any of the aforementioned nucleic acid molecules of items a) and b).

If the polypeptide is selected from the group referred to under item a) above, it can be preferred to select it from the group of polypeptides comprising SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5. In one embodiment these polypeptides may be isolated and preferably recombinant polypeptides. In yet another embodiment, these polypeptides may be synthetic polypeptides.

The polypeptides as encoded by nucleic acid sequences of item a) may be used as therapeutically active agents.

As will be set out hereinafter, the polypeptide TcpC (SEQ ID No. 1) is found in the pathogenic E.coli strain E.coli CFT073 and contributes to the uropathogenicity of this microorganism. The mode of action of TcpC seems to include that, after secretion by the microorganism, it is taken up by the eukaryotic host cells and subsequently interferes with MyD 88 mediated TLR-related signaling of the innate immune system.

The influence of TcpC on MyD88 signaling seems to be that by directly or indirectly interacting with MyD88, activation of downstream effectors of MyD88 such as NF- KB is down regulated. As a consequence, genes are down regulated on which effectors such as NF-κB usually act. In case of NF-κB, down regulated genes include TNFα, IL-6, IL-I, IL-2, G-CSF, GM-CSF, adhesion molecules, acute phase response proteins and others. Thus, it seems that TcpC acts via a molecular mimicry, i.e. it seems to be capable of entering an interaction with MyD88. But instead of activating MyD88 as would TLR's such as TLR2 or TLR4, TcpC actually constitutively down regulates MyD88 and the other downstream signaling effects that are mediated by MyD88.

Consequently, TcpC may be used as a therapeutic agent for treating diseases and/or conditions that are characterized in and/or caused by an increase of the activity of TLRs that signal through MyD88, preferably of MyD88 itself or of cellular factors the activity of which is regulated by MyD 88 such as NF -KB and its downstream target TNF-α. Such diseases will be described in further detail below. However, a person skilled in the art knows that diseases that are characterized by a constitutively increased activation of TNF-α include inter alia rheumatoid arthritis and juvenile rheumatoid arthritis.

The inventors have found that the effect of TcpC on MyD 88 -mediated signaling seems to result from the TIR-domain that is found within the amino acid sequence of TcpC.

The inventors of the present invention have further found that, while the TIR-domain within TcpC and TcpB shares some structural homology with the TIR-domain as found in eukaryotic TLR' s such as TLRl, the amino acid sequences of TcpC and TcpB seem to be rather unrelated to those of classical eukaryotic TIR-domain containing proteins.

For example, TcpC and MyD88 show a sequence identity of 20% when undertaking a standard blast homology search at the NCBI (http: //www.ncbi.nlm.nih.gov/). When undertaking the same blast homology search, TcpB shows a sequence identity to its eukaryotic homologue (TLRl) being 14 %. TcpC and TcpB in contrast share a sequence identity of 28 % (see Figure 8).

It was also found that TcpC and TcpB seem to comprise three conserved amino acid sequence motives which are designated herein as Box 1, Box 2 and Box 3.

A similar motive structure is also found within the TIR-domain of eukaryotic TIR- domain containing proteins, however, the consensus sequences deduced from the TIR-domain of TcpC and TcpB for Box 1, Box 2, and Box 3 seems to differ considerably in comparison to the respective consensus sequence motives for eukaryotic TIR-domains. Nevertheless, in view of the comparable architecture of TIR-domains within eukaryotic and prokaryotic proteins, it seems justified to assume that TcpC and TcpB excert their inhibitory effect on MyD88 signaling in their eukaryotic hosts by either any of these conserved sequences noticed and/or a combination thereof.

The consensus sequence of Box 1 as deduced from Figure 7 and an alignment with other prokaryotic TIR-domain containing proteins (see Figure 8) comprises in a first aspect of this embodiment the sequence

Y-D-X₁-F (SEQ ID No. 3)

with Xi being F or V. In a preferred embodiment of this first aspect relating to the consensus sequence of Box 1, Xi = F (SEQ ID No. 7).

In a second aspect of the embodiment relating to the consensus sequence of Box 1, the consensus sequence is

Y-D-Xi-F-X₂-S-H-X₃ (SEQ ID No. 8)

with Xi being F, V; X₂ being I, L and X₃ being A, S. A preferred embodiment of this second aspect relating to the consensus sequence of Box 1 relates to the sequence

YDVFISHA (SEQ ID No. 9).

The consensus sequence of Box 2 of prokaryotic TIR-domain containing proteins in a first aspect relates to the sequence

G-XI-X₂-X₃-X₄-X₅-D-X₆-X₇-X₈-X₉-XIO-XI I-G-XI₂ (SEQ ID NO. 4) with X₁ being A, I, V, L; X₂ being K, N, I; X₃ being I, V; X₄ being W, F; X₅ being Y, E; X₆ being A, E, V; X₇ being Y, F, Q, K; X₈ being T, S, V; X₉ being L, F; X₁₀ being K, G, E; Xii being W, V, I; and Xi₂ being D, K.

In a preferred embodiment of this first aspect relating to the consensus sequence of Box 2, the sequence comprises

GAKIFYDAYTLKVGD (SEQ ID NO. 10)

or

GVIIVYDEQTLEVGD (SEQ ID NO. 11).

The consensus sequence of Box 3 in a first aspect comprises

S-Xi-X₂-I-I-X₃-X₄ (SEQ ID No. 5)

with Xi being V, I; X₂ being K, E; X₃ being A, V, F; and X₄ being K, D, R, E.

In a preferred embodiment of this first aspect relating to Box 3, the consensus sequence of Box 3 comprises

SVEEIAK (SEQ ID No. 12)

or

SVKEIAR (SEQ ID No. 13).

Without wanting to be bound to a particular scientific theory it is assumed that polypeptides comprising any of the aforementioned consensus sequence motives of Box 1, Box 2 or Box 3 may also be capable of having the same effect on MyD88 related signaling in eukaryotic host cells as does TcpC.

In preferred embodiments, proteins which have the same type of effect on MyD88 related signaling in eukaryotic host cells may comprise the consensus sequences of Boxes 1, 2 and 3, preferably in the order of numbering.

Thus, in one embodiment, the polypeptides will comprise the sequence

Y-D-X_I-F-X₂-G-X_S-X₄-X_S-Xg-X_V-D-Xg-Xg-X_IO-X_{I I}-Xi₂-Xi_S-G-Xi₄-Xi_S- S-X₁₆-X₁₇-I-

1-X_{I 8}-X_I9 (SEQ ID NO. 14)

with Xi being F or V, with X₃ being A, I, V, L; X₄ being K, N, I; X₅ being I, V; X₆ being W, F; X₇ being Y, E; X₈ being A, E, V; X₉ being Y, F, Q, K; Xi₀ being T, S, V; Xn being L, F; Xi₂ being K, G, E; X₁₃ being W, V, I; Xi₄ being D, K; and with Xi6 being V, I; Xi₇ being K, E; Xi₈ being A, V, F; and Xi₉ being K, D, R, E. X₂ and X₁₅ (in the following also referred to "Si" for the X [here X₂] in the position between Box 1 and Box 2 and "S₂" for the X [here Xi 5] in the position between Box 2 and Box 3) may be amino acid stretches of arbitrary sequence that act as spacers between Boxes 1,2 and 3. These stretches may be of a length as found in e.g. TcpB and TcpC. Typically, Si will have a length of about 5 to about 40 amino acids, with about 10 to about 20 amino acids being preferred and S₂ will have a length of about 50 to about 120 amino acids, with about 80 to 90 amino acids being preferred. In a preferred embodiment, such polypeptides will comprise the preferred consensus sequences of Box 1, Box 2 and Box 3 as mentioned above.

Thus, the invention relates inter alia to polypeptides comprising the sequence:

YDFF-X₁-GVIIVYDEQTLEVGD-X₂-SVKEIAR (SEQ ID No. 15); YDFF-Xi- GAKIFYDAYTLKVGD-X₂-SVEEIAK (SEQ ID NO. 16); YDFF-X₁- GVIIVYDEQTLEVGD-X₂- SVEEIAK (SEQ ID NO. 17); or YDFF-Xi- GAKIFYDAYTLKVGD-X₂-SVKEIAR (SEQ ID NO. 18).

Xi and X₂ may be the spacer regions between the Boxes as defined above, also referred to as Si and S₂.

Thus, in one embodiment, the polypeptides will comprise the sequence

Y-D-XI-F-X₂-S-H-XS-X₄-G-XS-Xe-XV-XS-Xg-D-XIO-XII-Xi₂-XiS-Xi₄-XiS-G-XIe- Xi₇- S-Xi₈-Xi₉-I-I-X₂₀-X₂I (SEQ ID No. 19)

with Xi being F, V; X₂ being I,L; and X₃ being A, S; with X₅ being A, I, V, L; X₆ being K, N, I; X₇ being I, V; X₈ being W, F; X₉ being Y, E; Xi₀ being A, E, V; Xn being Y, F, Q, K; X₁₂ being T, S, V; X₁₃ being L, F; X₁₄ being K, G, E; Xi₅ being W, V, I; Xi6 being D, K; and with Xi₈ being V, I; Xi₉ being K, E; X₂₀ being A, V, F; and X₂i being K, D, R, E. X₄ and X₁₇ (in the following also referred to "Si" for the X [here X₄] in the position between Box 1 and Box 2 and "S₂" for the X [here Xi₇] in the position between Box 2 and Box 3) may be amino acid stretches of arbitrary sequence that act as spacers between Boxes 1,2 and 3. These stretches may be of a length as found in e.g. TcpB and TcpC. Typically, Si will have a length of about 5 to about 40 amino acids, with about 10 to about 20 amino acids being preferred and S₂ will have a length of about 50 to about 120 amino acids, with about 80 to 90 amino acids being preferred. In a preferred embodiment, such polypeptides will comprise the preferred consensus sequences of Box 1, Box 2 and Box 3 as mentioned above.

Thus, the invention relates inter alia to polypeptides comprising the sequence:

YDFFISHA-Xi-GVnVYDEQTLEVGD-X₂-SVKEIAR (SEQ ID No. 20); YDFFISHA-Xi- GAKIFYDAYTLKVGD-X₂-SVEEIAK (SEQ ID NO. 21); YDFFISHA-Xi- GVIIVYDEQTLEVGD-X2- SVEEIAK (SEQ ID NO. 22); or YDFFISHA-X₁- GAKIFYDAYTLKVGD-X₂-SVKEIAR (SEQ ID NO. 23).

The present invention also relates to nucleic acid sequences that encode functional fragments and/or functional homologues of prokaryotic polypeptides comprising a TIR-domain that have a comparable effect on MyD88 mediated signaling, as does TcpC.

The person skilled in the art will understand that a fragment of TcpC that lacks e.g. 5 to 10 amino acids at the N- and/or C-terminus may nevertheless have the same physiological affect as does the full length sequence of TcpC.

The term "functional fragment" in the context of the present invention is therefore to be understood as a polypeptide that comprises part of the native full length sequence of a prokaryotic protein comprising a TIR-domain having substantially the same effect on MyD 88 -mediated signaling as does TcpC. Typically fragments will comprise amino acid deletions at the N- and/or C-terminus of the full-length protein such as TcpC or TcpB. The deletions may make up to about 30 amino acids, up to about 20 amino acids, up to about 10 amino acids, up to about 5 amino acids, etc.

The person skilled in the art is also aware that functional homologues of the aforementioned prokaryotic proteins that comprise a TIR-domain and which have essentially the same effect on MyD88 mediated signaling as TcpC form an aspect of the present invention.

For example, the person skilled in the art will understand that for TcpC, one may replace amino acids that are located without or, in some embodiments even within the conserved regions of Box 1, Box 2 and Box 3 by conservative amino acid substitutions without substantially changing the functional properties of the protein.

Similarly, the person skilled in the art will be aware that one may delete short stretches within the amino acid sequence of TcpC and/or insert short amino acid stretches within TcpC without interfering with this protein's effect on MyD88- mediated signaling.

The term "functional homologue" in the context of the present invention thus relates to polypeptide sequences that have essentially the same effect on MyD 88 -mediated signaling as TcpC and which in comparison to TcpC comprise amino acid mutations, i.e. deletions, insertions and point mutations. "Insertion", "deletion" and "point mutations" are terms well known to the person skilled in the art and are used in their common sense.

The person skilled in the art will be aware that typically a so-called conservative amino acid substitution may not have an effect on the activity of a protein as long as it does not occur in a part of the protein that is essential for its function. A conservative amino acid substitution refers to an exchange by one amino acid for another wherein both amino acids share essentially the same structure and/or physico-chemical properties. For example, one may replace a positively charged amino acid such as glutamate with a positively charged amino acid such as aspartate or a hydrophobic amino acid with a hydrophobic amino acid etc. A non-conservative amino acid substitution typically refers to a substitution where one exchanges one amino acid for another wherein both amino acids differ with respect to their structure and/or physico-chemical properties. In a non-conservative amino acid substitution one may for example replace a positively charged amino acid such as lysine with a negatively charged amino acid such as glutamate. The term "functional homologue" also comprises non-conservative amino acid substitutions as long as they do not have a substantial effect on the protein's activity meaning that the protein carrying the substituted amino acid is still capable of interfering with MyD88- mediated signaling, as does TcpC.

Typically, a polypeptide will be considered to be a functional homologue of TcpC and/or TcpB if the amino acid sequence of said functional homologue displays at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% or at least about 98% sequence identity over a length of about 50 amino acids, over a length of about 100 amino acids, over a length of about 150 amino acids, over a length of about 200 amino acids, over a length of about 250 amino acids, over a length of about 300 amino acids or over the entire length of TcpC (or TcpB).

In an embodiment which can be preferred, a polypeptide will be considered to be a functional homologue of TcpC if the amino acid sequence of said functional homologue displays at least about 35%, at least about 30%, at least about 40%, preferably at least about 50%, at least about 60%, more preferably at least about 70%, at least about 80%, and even more preferably at least about 90%, at least about 95% or at least about 98% sequence identity over a length of about 50 amino acids, over a length of about 100 amino acids, over a length of about 150 amino acids, over a length of about 200 amino acids, over a length of about 250 amino acids, over a length of about 300 amino acids or over the entire length of TcpC.

The person skilled in the art is well acquainted with determining sequence identities. This may be done either visually or by using computer-based algorithms. One particularly suitable programme package for this purpose is the so-called "BLAST Package" being available at NCBI (http: //www.ncbi.nlm.nih.gov/blast/BLAST.cge) Typically similarity analysis will be performed with the standard parameters of the respective programme package, with the standard parameters of the blastp program being preferred.

Thus, for the general parameters, the "Max Target Sequences" box can be set to "100". The "Short Queries" box can be ticked. The "Expect Threshhold" can be set to "10" and the "Word Size" box can be set to "3".

For the scoring parameters, the "Matrix" box can be set to "BLOSUM62". The "Match/Mismatch" box can be set to "1,-2". The "Gap Costs" Box can be set to "Existence: 11 Extension: 1". The "Compositional adjustments" box can be set to "Conditional compositional score matrix adjustment".

For the Filters and Masking parameters, the "Filter" box does not need to be ticked. The "Species specific repeats" box does not need to be ticked. The "Mask for look up table only" Box does not need to be ticked. The "Mask lower case letters" box does not need to be ticked.

For the Discontiguous Word Options, the "Template length" box can be set to "none". The "Template type" box can be set to "Coding"

A polypeptide may be considered to be a functional homologue of e.g. TcpC if it shares the above mentioned identity grades and has a comparable effect on MyD88- mediated signaling in eukaryotic cells as TcpC.

In accordance with the invention, nucleic acid sequences which encode for functional homologues of the aforementioned proteins TcpC and TcpB may also relate to yet unknown sequences encoding proteins as they are expressed by pathogenic prokaryotic microorganisms wherein these proteins carry a TIR-domain. Such proteins may be found e.g. particularly in pathogenic bacteria including pathogenic strains of Escherichia coli, Staphylococcus aureus, Brucella and Salmonella. The person skilled in the art will understand that peptides in accordance with the invention may be further modified to provide additional functionalities. Thus, peptides may be modified at their N- and/or C-terminus as well as within the sequence with chemical functional groups that allow to couple these peptides to other molecular entities.

Such linking molecules which can be used to modify the peptides in accordance with the invention are well known to the person skilled in the art and include without being limited thereto attachment chemistries selected from the group of anhydrides, epoxides, aldehydes, hydrazides, acylazides, arylazides, diazo compounds, benzophenones, carbodiimiz, imidoesters, isothiocyanats, NHS esters, CNBr, maleimiz, tosylates, tresylchlorid, maleic acid anhydrides and carbonyldiimidazole.

In a further embodiment, polypeptides in accordance with the invention are functionally associated with molecules that allow improved penetration of the polypeptides into a cell, tissue or the like. Various target sequences for such purposes are known to the skilled person.

To this end, polypeptides in accordance with the invention may for example be linked to the Tat-peptide from human immunodeficiency virus. Typically, the Tat- peptide will have the sequence:

YGRKKRRQRRR (SEQ ID NO. : 28)

The person skilled in the art will also consider to use polypeptides in accordance with the invention which may or may be linked to the Tat-peptide that are associated with the carrier particles that also allow improved entrance of polypeptides into a cell, a tissue and the like. For example, polypeptides, which may or may not be linked to the Tat-sequence, can be formulated as liposomes or other lipid-based carrier particles that are known to enhance penetration of a compound into cells.

In one embodiment polypeptides in accordance with the invention, which may or may not be linked to the Tat-peptide, and/or nucleic acids in accordance with the invention can thus be associated with cationic lipids.

Cationic lipids, which carry a net positive charge at physiological pH, can readily be incorporated into liposomes for use in the present invention. Such lipids include, but are not limited to, N,N-dioleyl-N,N-dimethylammonium chloride ("DODAC"); N- (2,3-dioleyloxy) propyl-N, N-N-triethylammonium chloride ("DOTMA"); N ,N- distearyl-N,N-dimethylammonium bromide ("DDAB"); N-(2,3-dioleoyloxy)propyl)- N,N,N-trimethylammonium chloride ("DOTAP"); 3p-(N-(N',N'-dimethylamino- ethane)-carbamoyl)cholesterol ("DC-Chol"), N-(l-(2,3-dioleyloxy)propyl)-N-2- (sperminecarboxamido)ethyl)-N,N-dimethylammonium trifluoracetate ("DOSPA"), dioctadecylamidoglycyl carboxyspermine ("DOGS"), l,2-dileoyi-sn-3-phospho- ethanolamine ("DOPE"), l,2-dioleoyl-3-dimethylammonium propane ("DODAP"), and N-(1 ,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxy ethyl ammonium bromide ("DMRIE"). Additionally, a number of commercial preparations of cationic lipids can be used, such as LIPOFECTIN (including DOTMA and DOPE, available from GIBCO/BRL), LIPOFECT AMINE (comprising DOSPA and DOPE, available from GIBCO/BRL), and TRANSFECTAM (comprising DOGS, in ethanol, from Promega Corp.).

In one embodiment the polypeptides or nucleic acid sequences in accordance with the invention are combined with a cationic lipid. In one embodiment the cationic lipid is DOTAP (N-[l-(2,3-dioleoyloxy)propy- l]-N,N,N-trimethylammonium methyl-sulfate). DOTAP is believed to transport polypeptides and nucleic acids into cells and specifically traffic to the endosomal compartment, where it can release the polypeptides and nucleic acids in a pH-dependent fashion. Once in the endosomal compartment, the polypeptides and nucleic acids can interact with certain intracellular TLRs, triggering TLR-mediated signal transduction pathways involved in generating an immune response. Other agents with similar properties including trafficking to the endosomal compartment can be used in place of or in addition to DOTAP.

Other lipid formulations include, for example, EFFECTENE® (a non-liposomal lipid with a special DNA condensing enhancer) and SUPERFECT® (a novel acting dendrimeric technology), SMARTICLES® (charge reversible particles that become positively charged when they cross cell membranes) and Stable Nucleic Acid Lipid Particles (SNALPs) which employ a lipid bilayer. Liposomes are commercially available from Gibco BRL, for example, as LIPOFECTIN® and LIPOFECT ACE™, which are formed of cationic lipids such as N-[l-(2, 3 dioleyloxy)-propyl]-N, N, N- trimethylammonium chloride (DOTMA) and dimethyl dioctadecylammonium bromide (DDAB). Methods for making liposomes are well known in the art and have been described in many publications. Liposomes also have been reviewed by Gregoriadis G (1985) Trends Biotechnol 3:235-241. In other embodiments the immunostimulatory polymers of the invention are combined with microparticles, cyclodextrins, nanoparticles, niosomes, dendrimers, polycytionic peptides, virosomes and virus-like particles, or ISCOMS®.

A preferred chemical/physical carrier particle or vehicle of the invention is a colloidal dispersion system. Colloidal dispersion systems include lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. A preferred colloidal system of the invention is a liposome. Liposomes are artificial membrane vessels which are useful as a delivery vector in vivo or in vitro. It has been shown that large unilamellar vesicles (LUVs), which range in size from 0.2 - 4.0 μm can encapsulate large macromolecules. RNA, DNA and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (Fraley et al. (1981) Trends Biochem Sci 6:77). Liposomes may be targeted to a particular tissue by coupling the liposome to a specific ligand such as a monoclonal antibody, sugar, glycolipid, or protein. Ligands which may be useful for targeting a liposome to an immune cell include, but are not limited to: intact or fragments of molecules which interact with immune cell specific receptors and molecules, such as antibodies, which interact with the cell surface markers of immune cells. Such ligands may easily be identified by binding assays well known to those of skill in the art. In still other embodiments, the liposome may be targeted to the site of infection by coupling it to e.g. an immunotherapeutic antibody as discussed earlier.

Lipid formulations for transfection are commercially available from QIAGEN, for example, as EFFECTENE™ (a non-liposomal lipid with a special DNA condensing enhancer) and SUPERFECT™ (a novel acting dendrimeric technology).

Liposomes are commercially available from Gibco BRL, for example, as

LIPOFECTIN™ and LIPOFECTACE™, which are formed of cationic lipids such as N-[l-(2, 3 dioleyloxy)-propyl]-N, N, N-trimethylammonium chloride (DOTMA) and dimethyl dioctadecylammonium bromide (DDAB). Methods for making liposomes are well known in the art and have been described in many publications. Liposomes also have been reviewed by Gregoriadis G (1985) Trends Biotechnol 3:235-241. Certain cationic lipids, including in particular N-[l-(2, 3 dioleoyloxy)-propyl]- N,N,N-trimethylammonium methyl-sulfate (DOTAP), appear to be especially advantageous when combined with the modified oligoribonucleotide analogs of the invention.

In one embodiment, the carrier particle or vehicle is a biocompatible microparticle or implant that is suitable for implantation or administration to the mammalian recipient. Exemplary bioerodible implants that are useful in accordance with this method are described in PCT International application no. PCT/US/03307 (Publication No. WO95/24929, entitled "Polymeric Gene Delivery System"). PCT/US/0307 describes a biocompatible, preferably biodegradable polymeric matrix for containing an exogenous gene under the control of an appropriate promoter. The polymeric matrix can be used to achieve sustained release of the therapeutic agent in the subject.

The polymeric matrix preferably is in the form of a microparticle such as a microsphere (wherein the nucleic acid and/or the other therapeutic agent is dispersed throughout a solid polymeric matrix) or a microcapsule (wherein the nucleic acid and/or the other therapeutic agent is stored in the core of a polymeric shell). Other forms of the polymeric matrix for containing the therapeutic agent include films, coatings, gels, implants, and stents. The size and composition of the polymeric matrix device is selected to result in favorable release kinetics in the tissue into which the matrix is introduced. The size of the polymeric matrix further is selected according to the method of delivery which is to be used, typically injection into a tissue or administration of a suspension by aerosol into the nasal and/or pulmonary areas. Preferably when an aerosol route is used the polymeric matrix and the nucleic acid and/or polypeptides are encompassed in a surfactant carrier particle. The polymeric matrix composition can be selected to have both favourable degradation rates and also to be formed of a material which is bioadhesive, to further increase the effectiveness of transfer when the matrix is administered to a nasal and/or pulmonary surface that has sustained an injury. The matrix composition also can be selected not to degrade, but rather, to release by diffusion over an extended period of time. In some preferred embodiments, the nucleic acids or polypeptides are administered to the subject via an implant. Biocompatible microspheres that are suitable for delivery, such as oral or mucosal delivery, are disclosed in Chickering et al. (1996) Biotech Bioeng 52:96-101 and Mathiowitz E et al. (1997) Nature 386:410-414 and PCT Pat. Application WO97/03702.

Both non-biodegradable and biodegradable polymeric matrices can be used to deliver the nucleic acid and/or the polypeptides to the subject. Biodegradable matrices are preferred. Such polymers may be natural or synthetic polymers. The polymer is selected based on the period of time over which release is desired, generally in the order of a few hours to days.

Bioadhesive polymers of particular interest include bioerodible hydrogels described by H.S. Sawhney, CP. Pathak and J.A. Hubell in Macromolecules, (1993) 26:581- 587, the teachings of which are incorporated herein. These include polyhyaluronic acids, casein, gelatin, glutin, polyanhydrides, polyacrylic acid, alginate, chitosan, poly(methyl methacrylates), poly(ethyl methacrylates), poly(butylmethacrylate), poly(isobutyl methacrylate), poly(hexylmethacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), and poly(octadecyl acrylate).

Other approaches for facilitating entry of polypeptides and nucleic acids in accordance with the invention into a cell will be obvious to a person skilled in the art.

Polypeptides in accordance with the invention which may or may not be linked to the Tat-peptide and which may or not be associated with particulate carriers as described above, may be used to treat diseases resulting from prokaryotic microorganisms expressing TIR domain-containing proteins.

In general, prokaryotic microorganisms for which pathogenic variants thereof may express TIR-domain containing proteins can be selected from different phylae of bacteria. These phylae may comprise proteo bacteria, gram-positive bacteria, cyanobacteria and prochlorophytes, chlamydia, planctomyces/perellula, verrucomicrobia, flavobacteria, cytophaga, green sulphur bacteria, spirochetes, deinococci, green non-sulphur bacteria, deeply branching hyperthermophyllic bacteria and nitrospira/defferibacter. Typically, one will consider microorganisms causing infectious diseases. Such diseases include airborne transmitted diseases, diseases that are transmitted by person-to-person contact as well as sexually transmitted diseases.

Examples of the aforementioned types of airborne diseases that result from microbial infections are e.g. streptococcal diseases, induced by streptococci, diphtheria, which is induced by Corynebacterium diptheriae, whooping cough, which is a consequence of Bordetella pertussis, tuberculosis resulting from Mycobacterium tuberculosis, meningitis resulting from Neissereria meningitides.

Examples of diseases resulting from person-to-person contact are diseases provoked by staphylococci, gastric ulcers resulting from Helicobacter pylori. Examples of sexually transmitted diseases being a consequence of microbial infection include e.g. gonorrhea and syphilis.

Diseases other than those mentioned previously, include animal-transmitted diseases, arthropod-transmitted diseases and soil-borne diseases. Examples of the aforementioned diseases include Lyme disease, malaria, Rickettsial disease.

Other diseases in the context of the present invention include water-borne microbial diseases such as cholera, giardiasis, legionellosis and typhoid fever as well as food- borne diseases such as staphylococcal food poisoning, clostridial food poisoning, salmonellosis and listeriosis.

A particular focus may be on organisms that cause diseases of the urinary tract such as pathogenic strains of E. coli, Proteus spp., Klebsiella spp., Enterococci and Pseudomonas spp..

Other organisms of particular interest include Brucella, Staphylococcus aureus, Salmonella, Listeria and Mycobacterium tuberculosis. As mentioned above, the present invention also relates to an isolated recombinant nucleic acid molecule comprising at least one nucleic acid sequence that specifically hybridizes under stringent conditions with a nucleic acid sequence selected from the group of a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1,

SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2.

Such nucleic acid sequences may be used as diagnostic markers. Thus, one may e.g. use such nucleic acid sequences in the form of a molecular probe for detecting the presence of pathogenic prokaryotic microorganisms in a eukaryotic host.

The person skilled in the art understands that the term "specific hybridization under stringent conditions" means under conditions that are typically considered to be stringent, these nucleic acid sequences will hybridize only with sequences that encode prokaryotic proteins comprising a TIR-domain but not or at least not to a substantial degree with eukaryotic TIR-domain-comprising proteins, let alone with other proteins, be it of prokaryotic or eukaryotic origin that do not contain any TIR- domain at all.

Typical examples of stringent conditions for hybridization experiments can be found e.g. in Sambrook et. al. Molecular Cloning: A Laboratory Handbook, Cold Spring Harbor Laboratory Press, 3^rd edition, 2001).

Stringent conditions are dependent on the circumstances. Longer sequences hybridize specifically at higher temperatures. In general, stringent conditions are selected in such a way that the hybridization temperature is about 5°C below the melting point (T_m) for the specific sequence at a defined ionic strength and a defined pH value. T_m is the temperature (at a defined pH value, a defined ionic strength, and a defined nucleic acid concentration), at which 50% of the molecules, which are complementary to a target sequence, hybridize with said target sequence. Typically, stringent conditions comprise salt concentrations between 0.01 and 1.0 M sodium ions (or ions of another salt) and/or a pH between 7.0 and 8.3. The temperature is at least 30⁰C for shorter molecules, for example for those comprising between 10 and 50 nucleotides. In addition, stringent conditions may comprise the addition of destabilizing agents, like for example formamide.

Typical hybridization and washing buffers are of the following composition.

Pre-hybridization solution:

0.5% SDS

5 x SSC

50 mM NaPO₄, pH 6.8

0.1% Na pyrophosphate

5 x Denhardt's Reagent

100 μg/ml salmon sperm

Hybridization solution: Pre-hybridization solution

1 x 10⁶ cpm/ml probe (5-10 min, 95°C)

20 x SSC: 3 M NaCl

0.3 M sodium citrate ad pH 7 with HCl

50 x Denhardt's Reagent: 5 g Ficoll

5 g polyvinyl pyrrolidone

5 g Bovine Serum Albumin ad 500 ml with A. dist.

Hybridization is conventionally conducted as follows:

Optional: washing the blot for 30 min in 1 x SSC / 0.1% SDS at 65°C

Pre hybridization: at least 2 h at 50 to 55°C

Hybridization: overnight at 55 to 60^c ⁵C

Washing: 5 min 2 x SSC / 0.1% SDS hybridization temp

30 min 2 x SSC / 0.1% SDS hybridization temp

30 min 1 x SSC / 0.1% SDS hybridization temp

45 min 0 .2 x SSC / 0.1% SDS 65°C

5 min 0. I x SSC room temp.

Another example of stringent conditions includes a wash for 30 minutes at room temperature in a buffer comprising 15OmM NaCl, 20 mM Tris hydrochloride, pH 7.8, 1 mM Na₂EDTA, 0.5% SDS, followed by a 30 minute wash in fresh buffer.

As mentioned above, the nucleic acid sequences that can be used for diagnostic purposes may also be used in a therapeutic approach, i.e. they may be used as antisense sequences to fight infections with a pathogenic prokaryote expressing prokaryotic proteins comprising a TIR-domain.

The person skilled in the art is familiar with such antisense approaches and is well aware what specific means have to be used in order to achieve an efficient antisense effect. If the aforementioned nucleic acid sequences are to be used in an antisense approach they will typically have a length of about 10 to about 500 nucleotides, of about 11 to about 200 nucleotides, of about 12 to about 100 nucleotides, about 13 to about 75 nucleotides or of about 14 to about 50 nucleotides, of about 15 to about 40 nucleotides, of about 16 to about 30 nucleotides or of about 17 to about 25 nucleotides.

Nucleic acid sequences that specifically hybridize in the way it has been described above with nucleic acid sequences encoding prokaryotic proteins having a TIR- domain or functional homologues and/or fragments thereof may not only be antisense sequences but also so-called ribozyme sequences. A ribozyme is a catalytically active sequence that shows complementarity to a target sequence and moreover has sequence motifs that actively cleave the target sequence.

The person skilled in the art will know that such antisense nucleic acid sequence may comprise a modified backbone that still allows the nucleic acid sequence to bind to its target sequence but conveys improved stability to the nucleic acid sequence.

The term "nucleic acid sequence" typically refers to DNA, RNA including mRNA etc.

However, in certain aspects such as an antisense approach, the term "nucleic acid sequence" may also relate to nucleic acid sequences, which carry certain modifications that do not interfere with the respective function of the nucleic acid sequence. For example, if a nucleic acid sequence is to be used as an antisense sequence, one may replace the phosphate backbone by other groups that are known to not interfere with the hybridizing properties of such nucleic acid sequences but convey improved stability to the nucleic acid sequences.

Such backbone modifications may be considered as "analogues of a phosphate bridging groups" and refer to bridging groups other than the known phosphate bridging group but still allowing to connect the cyclic pentose units from the Cs position of one cyclic pentose unit to the C3 position of another cyclic pentose unit. A preferred analogue of a phosphate bridging group is a phosphorothioate bridging group of formula:

O

S— P— O — OH

Other analogues of a phosphate bridging group include without being limited thereto alkylphosponate, arylphosphonate, alkylphosphorothioate, arylphosphorothioate, methylphosphonate, methylphosphorothioate, phosphorodithioate, p-ethoxy, morpholino, and combinations thereof.

Modified backbones such as phosphorothioates may be synthesized using automated techniques employing either phosphoramidate or H-phosphonate chemistries. Aryl- and alkyl-phosphonates can be made, e.g., as described in U.S. Pat. No. 4,469,863; and alkylphosphotriesters (in which the charged oxygen moiety is alkylated as described in U.S. Pat. No. 5,023,243 and European Pat. No. 092,574) can be prepared by automated solid phase synthesis using commercially available reagents. Methods for making other DNA backbone modifications and substitutions have been described.

For use in vivo, the compounds having analogues of phosphate bridging groups in their backbone may have the advantage of being relatively resistant to degradation (e.g., are stabilized). A "stabilized compound" shall mean a compound of the present invention that is relatively resistant to in vivo degradation (e.g., via an exo- or endo- nuclease). Stabilization can also be a function of length or secondary structure.

The person skilled in the art will also understand that antisense sequences may comprise non-natural bases as long as hybridisation with target sequences is not impaired. Analogues of natural bases can include other naturally occurring or non- naturally occurring synthetic bases such as inosine, N⁶-methyl-dA, 5-Methyl-dC, hypoxanthine, dihydrouracil, pseudouracil, 2-thiouracil, 4-thiouracil, 5-aminouracil, 5-(Ci-C₆)-alkyluracil, 5-(C₂-C₆)-alkenyluracil, 5-(C₂-C₆)-alkinyluracil, 5- (hydroxymethyl)uracil, 5-chlorouracil, 5-fluorouracil, 5-bromouracil, 5- hydroxycytosine, 5-(Ci-C6)-alkylcytosine, 5-(C₂-C6)-alkenylcytosine, 5 -(C₂-C₆)- alkinylcytosine, 5-chlorocytosine, 5-fluorocytosine, 5-bromocytosine, N² - dimethylguanine, 2,4-diamino-purine, 8-azapurine (including, in particular, 8- azaguanine), a substituted 7-deazapurine (including, in particular, 7-deazaguanine), including 7-deaza-7-substituted and/or 7-deaza-8-substituted purine, or other modifications of a natural bases. This list is meant to be exemplary and is not to be interpreted to be limiting. In particular, the guanine base can be a substituted or modified guanine such as 7-deazaguanine, 8-azaguanine, 7-deaza-7-substituted guanine (such as 7-deaza-7-(C₂-C₆)alkynylguanine), 7-deaza-8-substituted guanine, hypoxanthine, 2,6-diaminopurine, 2-aminopurine, 8-substituted guanine such as 8- hydroxyguanine and 6-thioguanine.

As has been mentioned above, polypeptides in accordance with the invention such as TcpC, TcpB and/or functional homologues thereof as well as polypeptides comprising the sequence motives of the aforementioned consensus sequence boxes I, II and/or III are typically found as TIR-domain containing polypeptides in pathogenic prokaryotic microorganisms.

These polypeptides may themselves be used as therapeutically active agents in diseases of humans and animals that result from an aberrantly up-regulated MyD88- mediated signaling as can be inferred from e.g. increased NF-κB and TNF-α levels. However, these polypeptides may of course also present interesting targets for identifying compounds that specifically can interact with these polypeptides and interfere with their inhibitory effect on MyD 88 -mediated signaling in a eukaryotic host cell. Such molecules that specifically recognize polypeptides in accordance with the invention may be attractive for different purposes. For example, molecules that specifically recognize polypeptides as described above could be used as diagnostic tools. Such diagnostic tools may for example allow detection of infections with prokaryotic pathogenic microorganisms.

If these compounds in addition or alternatively are capable of specifically interfering with the inhibitory effect of polypeptides in accordance with the invention on MyD 88 -mediated signaling in eukaryotic host cells, they may moreover be attractive therapeutically active compounds that allow to actively fight those diseases and/or conditions that are characterized in and/or caused by pathogenic prokaryotic microorganisms expressing a polypeptide with a TIR-domain.

The person skilled in the art will understand that a compound that specifically recognizes a polypeptide in accordance with the invention does not necessarily have to have the capacity of interfering with this polypeptide's inhibitory effect on MyD 88 -mediated signaling even though it may be preferred that such compounds possess both characteristics, i.e. specifically recognize polypeptides in accordance with the invention and interfere with the inhibitory effect of these polypeptides on MyD 88 -mediated signaling.

A particularly attractive class of molecules that may be capable of specifically recognizing polypeptides obtained from pathogenic prokaryotic microorganisms that express a polypeptide with a TIR-domain are antibodies, functional fragments thereof or functional analogues thereof.

The present invention therefore in one embodiment relates to an isolated recombinant nucleic acid molecule comprising at least a nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. lor SEQ ID No. 2.

The present invention further relates to a recombinant isolated polypeptide encoded by an isolated recombinant nucleic acid molecule comprising at least a nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2.

The term "specific recognition" and its grammatical variations and synonyms describes that antibodies, functional fragments thereof, or functional analogues thereof will be capable of differentiating between a polypeptide with a TIR-domain obtained from a pathogenic prokaryotic microorganism and TIR-domain containing polypeptides of eukaryotic origin. In the context of the present invention, the term "functional fragment of an antibody" describes that one may delete certain portions of an antibody without interfering with the specificity of the resulting fragment for the epitope that is recognized by the antibody. For example, one may delete certain portions of the constant region of an antibody without interfering with the antibody's capability of specifically recognizing its target molecule.

The term "functional analogue of an antibody" refers to the fact that there are various variations of antibodies known that are polypeptides having substantially the same or at least a comparable affinity to an epitope as an antibody from which they are derived even though they do not have an antibody's general structure which typically consists of two heavy and two light chains with each of the heavy and light chains containing three complementary determining regions (CDR' s).

A person skilled in the art is familiar as to how to obtain antibodies against the aforementioned polypeptides such as TcpC and TcpB and how to select antibodies that specifically recognize only prokaryotic proteins with a TIR-domain from a pathogenic prokaryotic microorganism.

In general, antibodies in accordance with the invention may be polyclonal or monoclonal antibodies. Monoclonal antibodies may be preferred. As regards monoclonal antibodies, the present invention considers monoclonal mouse antibodies, but also monoclonal antibodies from other sources such as chimeric antibodies, humanized antibodies or human antibodies. Chimeric antibodies, humanized antibodies and particularly human antibodies are preferred over mice antibodies given that these antibodies are known to have less toxicity problems compared to monoclonal mouse antibodies. Antibodies of the present invention can include IgG, IgM, IgE, IgA and IgD antibodies. However, as mentioned above, the present invention contemplates not only antibodies that recognize the aforementioned polypeptides, but also functional fragments and/or functional analogues thereof.

Functional fragments and/or functional analogues of antibodies in accordance with the invention include antigen binding fragments of these antibodies which may be Fab, Fab'-, F(ab)₂ and Fv antibody fragments. Such antigen binding fragments may also only consist of the complimentary determining region with or without non-CDR framework regions.

Antibodies, functional fragments or functional analogues thereof may comprise all or a portion of the constant region for any of the aforementioned isotypes. If the constant region is present it may be of the γl, γ2, γ3, γ4, μ, β, δ, ε-type. As far as the light chain is concerned, the constant part may be of the K or λ-type. Functional fragments and/or functional analogues of antibodies in accordance with the invention also include e.g. single chain antibodies such as scFv. Such antibodies may be so- called "heavy chain antibodies" (HCAbs) as they are know from Cameldae. Such heavy chain antibodies comprise V_HH antibodies. Further, the present invention considers the use of bispecifϊc or trispecifϊc antibodies such as Fab-scFv (bibody) or Fab-(scFv)(2) (tribody). The aforementioned terms are used as they are known in the art and have been described in various publications.

The person skilled in the art is also aware how to produce the aforementioned antibodies given that there has been extensive documentation of how to create and produce e.g. humanized antibodies, chimeric antibodies, single chain antibodies etc. As mentioned above antibodies, functional fragments and/or functional analogues thereof in accordance with the present invention may be characterized in that they specifically recognize prokaryotic proteins comprising a TIR-domain as they occur in pathogenic prokaryotic microorganisms. The antibodies, functional fragments and/or functional analogues thereof may preferably recognize an epitope located within SEQ ID Nos. 3 to 23.

By way of their specific recognition the antibodies, functional fragments and/or functional analogues thereof may be used as diagnostic markers. For example, these antibodies may be used in ELISA-based assays or other common detection assays to allow determination of the presence of a pathogenic microorganism.

However, the antibodies, fragments and/or functional analogues thereof may of course e.g. by way of their capacity to specifically recognize the aforementioned polypeptides also interfere with the inhibitory influence of prokaryotic polypeptides with a TIR domain on MyD 88 -mediated signaling in eukaryotic host cells.

Antibodies, fragments and/or functional analogues with such dual properties, i.e. specific recognition and release of inhibitory action of the antigen on MyD88- mediated signaling, may not only be used as diagnostic markers, but also as a therapeutically active agent as they allow to fight those conditions that are caused by the pathogenic prokaryotic microorganisms that express a polypeptide with a TIR- domain.

The present invention in one embodiment further relates to vectors comprising any of the aforementioned nucleic acid sequences. The nature and type of the vector may vary depending on which specific nucleic acid sequence it comprises and for what purposes it is needed. If for example a vector is constructed that uses a nucleic acid sequence encoding for a polypeptide comprising the sequences for consensus boxes I, II and III for producing a therapeutically active protein that can be used in a disease caused by increased MyD88 mediated signaling, the vector will typically be an expression vector that allows to obtain large amounts of properly folded protein. Depending on whether expression is to be achieved in a prokaryotic or eukaryotic host cell, the vectors may be prokaryotic and/or eukaryotic expression vectors such as plasmids, cosmids, minichromosomes, bacterial phages etc. The person skilled in the art will be familiar how to select an appropriate vector depending on the specific need.

In this context, the person skilled in the art will realize that depending on whether one wants to use the vector to express a polypeptide or to transcribe an antisense sequence, the nature of the vectors will differ.

However, typically these vectors will as functional elements comprise a promoter that is operatively linked to the nucleic acid sequence to be transcribed and/or potentially translated, a termination sequence that allows proper termination of transcription and translation and a selectable marker that allows those host cells that have taken up the vector and allow for functional expression of e.g. the polypeptide of interest to be identified. The person skilled in the art will be aware that the nature of the promoters for example will depend on whether the vector is going to be used in a prokaryotic or eukaryotic host cell. The choice as to whether one will for example attempt expression in a prokaryotic or eukaryotic host cell will in turn depend on the nature of the nucleic acid sequence and/or amino acid sequence to be expressed. For example, if TcpC or a fragment thereof is going to be expressed, expression in a prokaryotic host cell such as E.coli may be aprimafacie choice which may lead the skilled person to select common expression vectors such as pGEX, pQE etc. If on the other hand, the vector is used to express antibodies, fragments and/or functional analogues thereof, one may choose to express these antibodies in prokaryotic host cells or in a eukaryotic host cell if glycosylation is suspected to have a beneficial effect on either the e.g. stability and/or activity of the antibody. Depending on these aspects, the person skilled in the art will decide whether to use a vector that can be used for protein expression in prokaryotic host cells or a vector that can be used in eukaryotic host cells. The present invention also relates to host cells comprising any of the aforementioned nucleic acid sequences and/or vectors. It follows from what has been said above that the host cells may be prokaryotic host cells or eukaryotic host cells. Prokaryotic host cells may be any type of prokaryotic microorganism as it is commonly used for expression of e.g. polypeptides such as E. coli, Corynebacterium glutamicum, etc.

If, however, protein expression is attempted in eukaryotic host cells, one may use eukaryotic microorganisms such as yeast, such as S. cerevisiae, S. pombe, Pichia pastoris.

One may also use eukaryotic mammalian cells such as COS cells, CHO cells, NIH3T3 cells, HEK293 cells etc. Eukaryotic or prokaryotic host cells in accordance with the invention not only relate to host cells that express nucleic acid sequences and/or vectors in accordance with the invention for production purposes.

One could for example also envisage creating a cell line which either constitutively or in a controlled fashion expresses any of the aforementioned polypeptides in accordance with the invention that are derived from prokaryotic pathogenic microorganisms expressing proteins with a TIR-domain. Such host cells should be upon expression of e.g. TcpC be hampered as to TLRs-dependent signal transduction. Thus, cell lines which upon usual stimulation with compounds such as LPS or oligonucleotides would activate TLRs and up-regulate MyD88 activity would be down regulated with respect to these signal transduction pathways if e.g. TcpC is expressed in these eukaryotic cells. These cell lines may then be used as a model to screen for e.g. small molecules that release this inhibitory effect.

The present invention also relates to transgenic animals that harbor any of the aforementioned nucleic acid sequences, vectors and/or host cells. Such transgenic animals may be interesting model organisms to simulate the effects of pathogenic prokaryotic microorganisms by either constitutive or controllable expression of prokaryotic polypeptides comprising a TIR-domain such as TcpC. The person skilled in the art is familiar as to how to produce such transgenic animals. Typically preferred species for such transgenic animals will be rodents such as mice and rats.

It has been mentioned above that the present invention discloses various molecules such as nucleic acid molecules and/or polypeptides that may be used as therapeutically active agents.

The present invention in one embodiment therefore relates to pharmaceutical compositions comprising any of the aforementioned nucleic acid molecules and/or polypeptides and optionally at least one pharmaceutically acceptable excipient.

The person skilled in the art will be aware that the specific composition of the various pharmaceutical compositions may differ depending on the exact nature of the pharmaceutically active agent that is present.

If for example a pharmaceutical composition is used that comprises an antisense nucleic acid sequence as described above, the requirements as to the specific excipients that may be present within the formulation may differ from the situation where the pharmaceutical composition comprises an antibody as the pharmaceutically active agent.

Currently different pharmaceutical compositions are preferred. One of the preferred type of pharmaceutical compositions is one that comprises an antisense nucleic acid sequence as described above.

Another presently preferred pharmaceutical composition comprises a polypeptide derived from a prokaryotic protein with a TIR-domain that is present within a pathogenic prokaryotic microorganism as described above as the pharmaceutically active agent. Such polypeptides may be e.g. the aforementioned TcpC, TcpB, functional homologues thereof or polypeptides that comprise the consensus sequences of consensus Box I, II and/or III.

Other preferred embodiments relate to pharmaceutical compositions comprising antibodies, functional fragments and/or functional analogues thereof as described above as pharmaceutically active agent.

Another preferred group of pharmaceutical compositions relates to compositions comprising a pharmaceutically effective amount of an efflux pump inhibitor. As will be described hereinafter it has been found that prokaryotic proteins comprising a

TIR-domain which are derived from pathogenic prokaryotic microorganisms seem to be secreted by the pathogenic prokaryotic microorganisms. More specifically, these proteins seem to be secreted by multi drug efflux pumps of prokaryotic microorganisms .

Thus, in a preferred embodiment the present invention relates to pharmaceutical preparations that comprise a pharmaceutically effective amount of an efflux pump inhibitor as the pharmaceutically active agent. Such efflux inhibitors may interfere with the secretion of prokaryotic proteins comprising a TIR-domain from pathogenic prokaryotic microorganisms. Efflux pump inhibitors acting on type 1 secretion systems may be preferred.

Such efflux pump inhibitors include e.g. Phe-Arg-beta-naphthylamide (PAβN), 1-(1- Naphthylmethyl)-piperazine (NMP) and the like. A preferred efflux pump inhibitor is the efflux pump inhibitor PaβN. Such pharmaceutical preparations may comprise the efflux pump inhibitor as the sole pharmaceutically active agent. However, such pharmaceutical preparations may comprise in one embodiment other pharmaceutically active agents as long as these pharmaceutically active agents are not antibiotics. In another embodiment, such pharmaceutical preparations may comprise antibiotics aside from the efflux pump inhibitor. The person skilled in the art will realize that the afore-mentioned different types of pharmaceutical composition may be used for different areas of application as will be set out hereinafter. However, before the specific indications for which these pharmaceutical compositions can be inter alia used are described in further detail, it may be pointed out that the pharmaceutical compositions may be formulated for e.g. oral, rectal, nasal, intramuscular, intravenous, subcutaneous application and other routes of administration.

The specific composition will depend on what form the actual pharmaceutical dosage form comprising the pharmaceutical composition in accordance with the invention should take. If for example the pharmaceutical dosage form is to be administered as a tablet, the requirements will be different from a situation where it is administered as liquid.

Pharmaceutical compositions in accordance with the invention may take the form of a tablet, a capsule, granules, spheroids, liquids, gels, ointments etc.

The pharmaceutical dosage forms in accordance with the present invention may be used for different therapeutic purposes. The therapeutic purposes may be roughly divided into two categories.

One category relates to pharmaceutical preparations that are used for treating infections with prokaryotic microorganisms that express prokaryotic proteins with a TIR-domain. Such infections by pathogenic prokaryotic microorganisms may be caused by bacteria including E.coli, Staphylococcus aureus, Brucella spp.,

Salmonella spp., Mycobacterium tuberculosis, Neisseria gonorrhoeae, Listeria monocytogenes or Chlamydophila pneumonia. An example of a pathogenic strain is E. coli CFT073 which causes urinary infections. The specific diseases may e.g. be urinary tract infections, acute pyelonephritis, bladder infections such as acute cystitis, asymptomatic bacterial carriage such as asymptomatic bacteriuria (ABU) sepsis, tuberculosis and pneumonia.

The pharmaceutical preparations that are used for these purposes may comprise, e.g. the aforementioned antisense nucleic acid sequences, the aforementioned antibodies, functional fragments and/or functional analogues thereof and/or efflux pump inhibitors such as PaβN.

The present invention thus also relates to the use of these compounds in the manufacture of medicaments for treating infections by pathogenic prokaryotic microorganisms such as bacteria including E.coli, Staphylococcus aureus, Brucella spp., Salmonella spp., Mycobacterium tuberculosis, Listeria monocytogenes or Chlamydophila pneumonia. The diseases may be the same as mentioned above.

Pharmaceutical preparations in accordance with the invention may however also be used to treat diseases and/or conditions that are characterized in and/or caused by an apparently high activity of TLR- and particularly MyD88 mediated signaling. As is well known to the person skilled in the art, increased signaling via eukaryotic TIR- domains may lead to increased activity of NF-κB, activation of M AP -kinases, IRF7 or e.g. IRF3 leading ultimately to increased expression of factors such as TNFα, IL-6 and proinflammatory cytokines, chemokines and interferons.

Such pharmaceutical preparations can be used for treating autoimmune diseases and/or chronic inflammatory diseases.

In the context of the present invention, the terms "autoimmune disease" and equivalently, "autoimmune disorder" and "autoimmunity", refer to immunologically mediated acute or chronic injury to a tissue or organ derived from the host. The terms encompass both cellular and antibody-mediated autoimmune phenomena, as well as organ-specifϊc and organ-nonspecific autoimmunity. Autoimmune diseases include insulin-dependent diabetes mellitus, rheumatiod arthritis, systemic lupus erythematodes, multiple sclerosis, athero-sclerosis, and inflammatory bowel disease. Autoimmune diseases also include, without limitation, ankylosing spondylitis, autoimmune hemolytic anemia, Behget's syndrome, Goodpasture's syndrome, Grave's disease, Guillian-Barre syndrome, Hashimoto's thyroiditis, idiopathic thrombocytopenia, myasthenia gravis, pernicious anemia, polyarteritis nodosa, polymyositis/dermatomyositis, primary biliary sclerosis, psoriasis, sarcoidosis, sclerosing cholangitis, Sjogren's syndrome, systemic sclerosis (scleroderma and CREST syndrome), Takayasu's arteritis, temporal arteritis, and Wegener's granulomatosis. Autoimmune diseases also include certain immune complex- associated diseases.

Diseases mediated from TNFα and other cytokines include inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease, ankylosing spondylitis, psoriasis.

Increased TNFα levels also contribute to diseases of the central nervous system such as ischemia and traumatic injury. Some cardiovascular diseases may also be characterized by increased levels of TNFα with specific diseases being atherosclerosis, myocardial infection, heart failure, myocarditis and cardiac allograft rejection as well as vascular endothelial cell responses.

Yet another type of disease that is mediated by TNFα includes respiratory diseases such as chronic bronchitis, chronic obstructive pulmonary disease, acute respiratory distress syndrome and asthma.

TNFα may also be implicated in renal diseases such as ischemic renal injury, renal transplant rejection and glomerulonephretes. Other inflammatory diseases in which TNFα is involved include juvenile rheumatoid arthritis, therapy-resistant sarcoidosis, inflammatory myopathies, Behcet disease and inflammatory eye disease.

The treatment of rheumatoid arthritis and juvenile rheumatoid arthritis is currently preferred.

All of these aforementioned diseases may be treated by pharmaceutical compositions comprising polypeptides that are derived from prokaryotic TIR-domain containing polypeptides as they are found in pathogenic prokaryotic microorganisms such as bacteria and as have been described above.

The present invention in one embodiment also relates to the use of a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; c) Nucleic acid sequences that specifically hybridize with any of the nucleic acid sequences of a) or b) under stringent conditions as a diagnostic marker as a diagnostic and/or therapeutic agent.

The person skilled in the art understands that these nucleic acid molecules do not have to be made from recombinant isolated nucleic acid molecules, but that diagnostic approaches may rely on the detection of these nucleic acid molecules in a sample as obtained from the patient suffering from a urinary tract infection by pathogenic bacteria such as E. coli.

As mentioned above, the present invention also relates to a method of diagnosing diseases and/or conditions characterized in and/or caused by an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide comprising at least the following steps: a) obtaining a sample from a human or animal individual suspected of suffering from an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide; b) detecting the presence or absence of said microorganism expressing a TIR-domain containing polypeptide; c) deciding on the presence and/or likely occurrence of a pathogenic microbial infection by comparing the results obtained in step b) with appropriate negative and positive controls.

Preferably step b) is performed outside the human or animal body.

The person skilled in the art is familiar how to detect pathogenic prokaryotic microorganism in samples. To this end, one may use the antisense sequences described herein in hybridization approaches or one may use e.g. the antibodies described herein.

The present invention further relates to a method of data acquisition in the context of diagnosing diseases or conditions characterized in and/or caused by an infection with a pathogenic prokaryotic microorganism expressing a TIR-domain containing polypeptide comprising at least the steps of: a) detecting a prokaryotic microorganism with a TIR-domain containing polypeptide in a human or animal being. Yet another aspect of the present invention relates to the use of prokaryotic TIR- domain containing polypeptides that are isolated from pathogenic prokaryotic microorganisms as a target for searching small molecules that are capable of interfering with the inhibitory action of these polypeptides on MyD 88 -mediated signaling in eukaryotic host cells.

The present invention further relates to a method of identifying molecules that are capable of interfering with the inhibitory effect of any of the polypeptides described herein on MyD 88 -mediated signaling comprising at least the following steps: a) Providing at least one polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: aa) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; bb) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; b) Determining the effect of said polypeptide on the activity of MyD88; c) Providing a molecule other than said polypeptide or MyD88; d) Determining the influence of said molecule on the effect of said polypeptide on the activity of MyD88.

The person skilled in the art will be aware how the various steps a) to d) of the screening methods may be performed.

Polypeptides may be produced by e.g. recombinant protein expression in prokaryotic host cells. The person skilled in the art is familiar how to recombinantly express such proteins and how to purify and enrich them. The person skilled in the art is also familiar how to determine the effect of such polypeptides on the activity of MyD88 in eukaryotic host cells. This may e.g. be done as is described in the experimental section hereinafter. For example, one way of determining the inhibitory effect of such a polypeptide on the activity of MyD88 mediated signaling may be to determine whether the activity of NF-κB is down- regulated. A down-regulation of NF-κB activity may be determined by e.g. decreased levels of transcription which are influenced by NF -KB such as TNF-α, IL- 6, IL-I, IL-2, G-CSF, GM-CSF, adhesion molecules, acute phase response proteins. To this end one may use for example cell lines such as RAW264.7 macrophage cell, uropethelial cell line HCV29, HEK293 cells, HeIa cells and stimulate these cells with agents that are known to induce MyD88 activity via TLR induced activity. Such stimulating compounds include LPS, nucleic acids such as single stranded or double stranded DNA and RNA, flagellin, lipopeptides, peptidoglycan, zymosan, poly(LC), synthetic imidazoquinolone-like molecules, hemozoin and profilin. In general, one may use any type of compound that is known to activate the activity of TLR' s such as TLR4, TLR7, TLR8 and TLR9. Increased levels of factors such as TNF-α, IL-6, IL-I, IL-2, G-CSF, GM-CSF, adhesion molecules and acute phase response proteins can be determined by ELISA, Westernblot and RT-PCR.

Subsequently, one can add the polypeptides in accordance with the invention and determine whether MyD88 activity as reflected by TNF-α levels is decreased.

Once one has established an assay that allows determination of the effect of a polypeptide as described above on the activity of MyD88 signaling, one can then test molecule libraries for compounds that release the inhibitory activity of the polypeptides on MyD88 mediated signaling. This may be achieved by adding compounds from libraries to these assays and analyzing whether MyD88 activity is restored as can be measured by e.g. increased TNF-α levels. For screening molecule libraries one may rely on small molecules libraries, nucleic acid libraries, antibody libraries, phage display libraries, etc. Further preferred embodiments of the invention relate to:

1. An isolated recombinant nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1,

SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; c) Nucleic acid sequences that specifically hybridize with any of the nucleic acid sequences of a) or b) under stringent conditions.

2. An isolated recombinant nucleic acid molecule comprising at least a nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. lor SEQ ID No. 2.

3. A vector comprising at least one nucleic acid molecule in accordance with 1 or 2.

4. A vector according to 3 wherein the vector is a plasmid, a cosmid, a minichromosome or a viral vector. 5. A host cell comprising at least one nucleic acid molecule in accordance with any of 1 or 2 and/or at least one vector in accordance with 3 or 4.

6. A host cell in accordance with 5 wherein the host cell is a prokaryotic host cell.

7. A host cell in accordance with 6 wherein the host cell is a eukaryotic host cell.

8. A transgenic animal comprising at least one nucleic acid molecule in accordance with any of 1 or 2 and/or at least one vector in accordance with any of 3 or 4 and/or at least one host cell in accordance with any of 5 to 7.

9. An isolated recombinant polypeptide encoded by any of the nucleic acid molecules of 1 a) to b).

10. An isolated recombinant polypeptide encoded by any of the nucleic acid molecules of 2 a) to b).

11. A pharmaceutical composition comprising at least one nucleic acid molecule of 1 or 2 and optionally a pharmaceutically acceptable excipient.

12. A pharmaceutical composition comprising at least one polypeptide of 9 or 10 and optionally a pharmaceutically acceptable excipient.

13. A pharmaceutical composition comprising at least one nucleic acid molecule of 1 a)-b) and/or at least one polypeptide of 9 for treating a disease and/or condition that is characterized in and/or caused by increased activation via TIR-domain containing eukaryotic molecules. 14. A pharmaceutical composition according to 13 wherein the disease to be treated is an autoimmune diseases and/or chronic inflammatory diseases.

15. A pharmaceutical composition according to any of 13 or 14 wherein the disease to be treated is selected from the group comprising rheumatoid arthritis, juvenile rheumatoid arthritis, inflammatory bowel disease, Ankylosing spondylitis, psoriasis, therapy-resistant sarcoidosis, inflammatory myopathies, Behcet disease, inflammatory eye disease, diseases of the central nervous system such as ischemia and traumatic injury, cardiovascular such as atherosclerosis, myocardial infection, heart failure, myocarditis, cardiac allograft rejection and vascular endothelial cell responses, respiratory diseases such as chronic bronchitis, chronic obstructive pulmonary disease, acute respiratory distress syndrome and asthma, renal diseases such as ischemic renal injury, renal transplant rejection and glomerulonephritis, lupus erythematodes, lupus erythematosus or diabetes Sjόrgens syndrome.

16. A pharmaceutical composition comprising at least one nucleic acid molecule of Ic), 2 and/or at least one polypeptide of 10 for treating a disease and/or condition characterized in and/or caused by pathogenic prokaryotic microorganisms expressing a polypeptide comprising a TIR domain.

17. A pharmaceutical composition comprising at least one efflux pump inhibitor molecule treating a disease and/or condition that is characterized in and/or caused by pathogenic prokaryotic microorganisms expressing a polypeptide comprising a TIR domain.

18. A pharmaceutical composition according to any of 16 or 17 wherein the disease to be treated is selected from the group comprising urinary tract infections, acute pyelonephritis, bladder infections such as acute cystitis, asymptomatic bacterial carriage such as asymptomatic bacteriuria (ABU)sepsis, tuberculosis, pneumonia or infections induced by E. coli, Staphylococcus aureus, Brucella spp. or Salmonella spp..

19. A pharmaceutical composition according to any of 16 or 17 wherein said disease is caused by microorganisms selected from the group comprising Escherichia coli, Staphylococcus aureus, Brucella spp., Salmonella spp., Mycobacterium tuberculosis, Listeria monocytogenes or Chlamydophila pneumonia.

The present invention will now be described with respect to some of its specific examples. These examples are however not to be construed in a limiting way.

EXAMPLES

Material and Methods

Patients and E. coli strains

E. coli isolates were obtained from children with their first defined episode of acute pyelonephritis or acute cystitis. Isolates from asymptomatic carriers were obtained after screening for bacteriuria in school-girls and fecal isolates from healthy children without a history of UTI. The strains were maintained as deep agar stabs and subcultured on TSA plates for DNA extraction.

Murine UTI infection model

Female C57BL/6 mice were used at an age of 8-16 weeks. E. coli were injected into the urinary tract as described previously (Hagberg et al.). In brief, 0.1 ml of the bacterial suspension (1x10⁹ CFU/ml) was installed into the bladder of anesthetized mice through a soft polyethylene catheter (0.61 mm outer diameter; Clay Adams). Urine samples were obtained daily and the mice were sacrificed after seven days. Bacterial tissue counts were obtained after homogenisation and plating. Tissues were fixed in paraformaldehyde and stained with htx-eosin for histology. Immunohistochemistry used antibodies to neutrophils (Rb6-8C5) with DAPI counterstaining to visualise cell nuclei. P-fimbriated E. coli were detected using an anti-serum to a synthetic peptide within the PapG adhesin.

Cell lines and generation of bone marrow derived macrophages

Murine RAW 264.7 macrophages and HEK293 cells were obtained from ATCC. The human uroepithelial cell line HCV29 cells was provided by Dr. Sόren Schubert (Bean et al.). Murine bone marrow was prepared from femora and tibiae, which were rinsed with cell culture medium. Bone marrow cells were cultured at a density of 5x10⁶ cells/dish in the presence of 1000 U/ml M-CSF which was added a second time on day 3. The medium used was VLE (very low endotoxin) DMEM (PAA Laboratories, Cόlbe, Germany) supplemented with 10% fetal bovine serum (Biochrom KG, Berlin, Germany), 1% penicillin-streptomycin (PAA Laboratories) and 2-mercaptoethanol (50 μM, GibcoBRL Lifetechnologies GmbH, Karlsruhe, Germany).

Anti-sera, monoclonal antibodies, cytokine ELISAs An anti-serum against TcpC was generated by immunizing rabbits with the peptides H₂N-EQTLEVGDSLRRNIDL-CONH₂ (SEQ ID NO. 24) and H₂N- FLNKKWTQYELDSLIC-CONH₂ (SEQ ID NO. 25) (Eurogentec SA, Seraing, Belgium). To quantify TNF and IL-6 in culture supernatants, ELISA Duo sets (R&D Systems, Wiesbaden-Nordenstadt, Germany) were applied as described by the manufacturer. The anti-DnaK antibody came from Stressgen, Germany, anti-myc antibody is a product of Invitrogen, MyD88 (N19), and GFP antibody (116) was purchased from Santa Cruz Biotechnology. Mouse anti β-actin and anti-flag antibodies came from Sigma, strep-Tactin HRP-conjugate from IBA (Gόttingen, Germany). HRP-labeled anti-mouse and anti-rabbit secondary antibodies were bought from Dianova (Germany). Plasmids

MyD88-, the intracellular domain of TLR2 (ICD-TLR2)- and IRAKI -expression plasmids were kindly provided by Dr. Carsten Kirschning (Munich, Germany), IRAK4 expression plasmid was a kind gift of Dr. Klaus Rϋckdeschel (Hamburg, Germany), whereas the plasmid encoding human TRIF came from Dr. Shizuo Akira (Osaka, Japan).

Cloning, production and purification of TcpB and TcpC constructs, construction of the CFT073 tcυCr.kan mutant TcpB and tcpC were amplified by PCR from genomic DNA of B. melitensis or the E. coli strain CFT073, respectively, and cloned into different eukaryotic and prokaryotic expression plasmids (described in supplemental methods). The E. coli CFT073 ectcp::kan mutant strain was constructed as described in supplemental methods using the lambda red recombinase system (Datsenko et al).

Creation of tetracysteine-tagged TcpC fusion proteins

For studying TcpC-secretion by CFT073, a C-terminal tetracysteine (TC) tag was introduced to visualize the protein during macrophage infection. TC-tagged fusion proteins were generated based on pTcpC carrying a C-terminal Cys-Cys-Pro-Gly- Cys-Cys³³ TC-tag. Insertion mutagenesis was performed using the primer pair FlAsH-TcpC for:

5'-GCATACAGGAGAAGATGCTGCCCGGGCTGTTGTATGGACCGTTCTCG-S' (SEQ ID No.26) and FlAsH-TcpC rev: 5'- CGAGAACGGTCCATACAACAGCCCGGGCAGCATCTTCTCCT-GTATGC-S' (SEQ ID No. 27) yielding pFlAsH-TcpC. The tcpCr.kan mutant was then complemented with this plasmid, and protein production was verified using the Lumio™ detection kit provided by Invitrogen following the manufacturer's instructions.

Confocal microscopy of fcpC.vfcα/7+pFlAsH-TcpC-infected RAW264.7 macrophages RAW264.7 macrophages (5xlO⁴ cells/well) were seeded into a μ-Slide (ibidi, Munich, Germany) in Opti-MEM medium (Invitrogen) to avoid nonspecific binding to serum proteins by the FlAsH-EDT₂-reagent (3 μM, Invitrogen). To reduce background staining, cells were incubated twice with the blocking reagent 2,3- dimercaptopropanol (BAL, 250 μM, Invitrogen). Immediately before infection with fc/?C.v£α/?+pFlAsH-TcpC or tcpCr.kan mutant (MOI of 5), RAW cells were stained with the FlAsH-EDT₂ reagent (Invitrogen) as described by the manufacturer. 0.4 μm filter inlays (Corning) were used to separate bacteria from cells. Live cell confocal microscopy was performed on a Leica SP5 instrument monitoring TC-tagged protein production for 90 min.

Inhibition of TIR-TcpC uptake by MβCD

BMM were incubated with methyl-β-cyclodextrin (10 mM, MβCD, Sigma) for 30 min. before adding different amounts of recombinant TIR-TcpC. Cells were treated with trypsin (15 min., 50 μg/ml), washed three times with PBS and subsequently lysed with RIPA-buffer. Intra- and extracellular TIR-TcpC was detected by Western blot. MβCD-pre-treated or untreated BMM were also stimulated with ultrapure endotoxin (100 ng/ml) in the presence or absence of recombinant TIR-TcpC to analyze how uptake inhibition of TIR-TcpC influenced TNF-secretion.

Induction of TcpC-expression by CFT073

To induce expression of TcpC the E. coli CFT073 strain was grown in LB-medium at 30⁰C to an optical density of OD6oo=0.5. Bacteria (IxIO⁷) were transferred to a 6 well plate and cultured in the presence of RPMI, or RPMI acidified to pH5, or cocultured with RAW264.7 (2xlO⁶ cells/well) at 37°C. After 5.Oh supernatants were harvested, centrifuged and concentrated 50-fold using a Nanosep 3K Omega (PALL). Concentrated supernatants were separated by SDS-PAGE and analyzed by Western blot. Infection and stimulation assays

BMM, RAW264.7 and HCV29 cells were seeded in 6-well plates at concentrations between 1.5 x 10⁶ and 2.0 x 10⁶/well in DMEM (primary cells) or RPMI-1640 supplemented with 5% FCS, 1% penicillin-streptomycin and 0.1 % 2- mercaptoethanol. Immediately before each assay, cells were washed and new antibiotic free medium (1-5% FCS) was added. Cells were then either infected with varying amounts of bacteria (usually for 5h) or were stimulated with TLR-ligands in the absence or presence of the purified recombinant TIR-domain of TcpC (TIR- TcpC) for 2h. Culture supernatants were used for quantification of TNF by ELISA or concentrated 20-fold to detect TIR-TcpC by Western blotting. In case cells were infected with bacteria, extracellular bacteria were killed after collection of the supernatant by addition of 50 μg/ml gentamicin in PBS. In case cells were co- cultured with TIR-TcpC, they were washed with PBS and collected after trypsination (250 μg/well, 10 min.) to avoid the possibility that TIR-TcpC could still stick to the cell surface. After two additional wash steps in PBS, cells were lysed with 1ml NP- 40 (1% Igepal) or RIPA buffer supplemented with protease inhibitors (Roche). For analysis of TcpC secretion, transwell plates (Corning Inc., USA) were used to separate bacteria from the cultured cells via a 0.4 μM pore size filter. In some experiments 52 μM of the efflux pump inhibitor phenylalanine-arginine-β- naphtylamide (Sigma) was added during infection.

Pull-down experiments

Purified TcpC-TIR, TcpB or EGFP (see supplemental methods) carrying each a C- terminal Strep-tag II was used as as "bait" protein using a biotinylated- protein :protein interaction kit (Pierce, Perbio Science GmbH, Germany). 100 μg of purified TIR-TcpC, TcpB or EGFP was bound to the agarose-coupled streptavidin as recommended by the manufacturer for Ih at 4°C. After two blocking steps, lysates from HEK293 cells either transfected or non-transfected with MyD88-myc, IRAKl- flag, IRAK4-flag, TRIF-flag, or ICD-TLR2-flag plasmids were added to the column (Ih, 4°C, followed by 30 min. RT). To prepare the lysates cells were solubilized by intensive homogenization in PBS-buffer followed by a final sonifϊcation step. In some experiments HEK293 lysates were treated with 0.125% (w/v) N- octylglucoside. Lysates of RAW264.7 cells were solubilized using NP -40 buffer provided with 0.125% (w/v) N-octylglucoside followed by dialysis against PBS. Three wash steps were performed using an actetate buffer with 0.025M or 0.5M NaCl. Elution of the bound "prey" proteins was accomplished by three consecutive steps using an elution buffer with pH 2.8 and subsequently collected in neutralization buffer (2M Tris/Cl pH 8.0) before being analyzed by SDS-PAGE or Western blot.

Luciferase reporter assays to analyze the function of TcpB and TcpC

HEK293 cells (3x10⁴ cells/well) were transfected using Geneporter® (Peqlab, Erlangen, Germany) or Lipofectamin®2000 (Invitrogen) in 96 well plates with NF- KB- (50 ng/ml), or IFN-β promoter (50 ng/ml) luciferase reporter constructs as well as plasmids encoding TLR2 (4 or 5 ng/ml), TLR3 (5 ng/ml), TLR4 (1 or 2.5 ng/ml), MD2 (2.5 ng/ml), MyD88 (5 ng/ml), IRAKI (5 or 50 ng/ml), IRAK4 (5 or 50 ng/ml), TcpB-flag (1 to 500 ng/ml), or TcpC-flag (5 ng/ml), which were used either alone or in various combinations as described in figure legends. Total amount of plasmids was kept constant by transfection of empty vector. HEK293 cells were seeded on 96-well plates one day before transfection in DMEM containing 10% FCS. Plasmids were mixed with Geneporter® (2 μl/well) in serum free medium or with Lipofectamine® (0.5 μl/well) in Opti-MEM®-I medium (Invitrogen). After a short incubation, lipoplexes were added to the cells. Depending on the experiments, cells were stimulated 24h later with endotoxin (100 ng/ml), HSP60 from C. pneumoniae (20 μg/ml), poly(LC) (30 μg/ml) or TNF (10 or 50 ng/ml). 24h later, cells were lysed to quantify luciferase activities using reagents from Promega (Madison, WI) and PJK GmbH (Kleinblittersdorf, Germany).

Detection of TcpC by SDS-PAGE and Western blot.

TcpC-detection upon CFT073 infection was accomplished by a rabbit polyclonal antiserum (diluted 1.1000) on 15% SDS-gels (under reducing conditions). Anti- rabbit IgG coupled with peroxidase (Jackson Immunoresearch) served as secondary antibody (diluted 1 :7000).

Blots were washed two times with TBST and once with TBS and visualized using the ECL-reagent (NEN Life Science Products, Boston, MA) as described by the manufacturer.

Software and statistic

The complete genomic sequences of the E. coli strain CFT073 (AEO 14075) and B. melitensis (NC_003317) were downloaded from http://www.ncbi.nlm.nih.gov/genomes/static/eub.html at NCBI. The operon structure of the CFT073 serif island aaάphe island of B. melitensis was depicted using Vector NTI 10 (Invitrogen Corp.). Pattern searches for TIR domains were performed using PFAM HMM search (http://pfam.janelia.org/) or SMART (http://smart.embl- heidelberg.de/). Prediction of tertiary structures of TcpB and TcpC were calculated using ESyPred3D (Lampert et al.) and the HMMSTR/Rosetta Prediction Server

(http://www.bioinfo.rpi.edu/~bystrc/hmmstr/about.html). Fishers exact test was used to statistically evaluate the fcpC-frequency of E. coli isolates, whereas ANOVA on Ranks, Dunn's method, was used for the statistical analysis of bacterial counts.

Results

Genomic location and structure of TcpB and TcpC

Two genes encoding putative homologues of the human TLR/TIR-domains were identified in a database search of bacterial genomes (Fig. IA). A subsequent in silico analysis of their tertiary structure predicted significant similarity to the TIR-domain of human TLRl (Fig. IB). TcpB was found in B. melitensis, located close to the 5' attachment site of a putative phe t-RNA island (Fig. IA), consisting of several operons. One gene close to the 3' attachment site of the island encodes an integrase, but most remaining genes have unknown functions. TcpC was found in the uropathogenic E. coli strain CFT073, located within a ser£/-island, in an operon containing two genes in the middle of the island and an integrase gene next to the 5' attachment site. Amino acid sequence analysis of TcpB and TcpC revealed that the TIR-domain is located in the C-terminal half of each protein, where both proteins share a certain degree of sequence homology (Fig. 1C). The N-terminal half contains no other annotated domain except for a putative transmembrane segment in the case of TcpC. TLR homologous sequences within the TIR-domains of the Tcps include a Box 1 motif, which is present in eukaryotic TIR-domains and which is essential for signaling (Fig. lD)(Radons et al).

TcpC and TcpB reduce proinflammatory responses during infection of macrophages and epithelial cells

To analyze the function of TcpC during infection, a fcpC-deletion mutant of CFT073 (tcpC::kan) as well as the tcpC: :kan+pΥ cpC mutant, which was complemented with a plasmid containing the tcpC operon controlled by its endogenous promoter, were constructed. The innate response was studied in the murine RAW264.7 macrophage cell line and the uroepithelial cell line HCV29. Infection with the tcpC::kan mutant stimulated a much higher TNF (Fig. 2A) or IL-6 response (Fig. 2B) in macrophages or HCV29 cells, respectively, than the wild type CFT073 strain or the complemented tcpC: : kan+TpT CTpC mutant. In analogy, TcpB reduced TNF secretion in RAW264.7 macrophages using the mutant tcpCr.kan and a BL21 Kl 2 strain, each complemented with an inducible plasmid encoding tcpB (Fig. 2C, D).

TcpC was subsequently shown to facilitate the intracellular survival of CFT073. The wild type and the complemented mutant tcpC: :kan+pΥ cpC had accumulated in higher numbers than the mutant tcpCr.kan 5 hours after infection of RAW264.7 cells and HCV29 cells (Fig. 2E and F), while total bacterial numbers were similar (Fig. 2G, H).

Bacterial-Tcps affect TLR-signaling

TcpC and TcpB were shown to suppress TLR-mediated signaling in nuclear factor (NF)-κB reporter assays. HEK293 cells were transfected with TLR4, MD2, a NF-κB reporter construct and with the TcpC or TcpB plasmid. Transfected cells were stimulated with endotoxin or TNF. TcpC and TcpB inhibited the TLR4-mediated NF-κB response to LPS but the response to TNF was not affected (Fig. 3A, supplementary Fig. SlA). Both proteins also impaired the NF -KB response to the potent TLR2 agonist HSP60 from C. pneumoniae (Costa et al). in cells transfected with TLR2 (Fig. 3B, Fig. SlB). These results showed that the Tcps interfere with TLR-signaling.

Then MyD88 was over-expressed in HEK293 cells and the influence of TcpB on NF- KB activation was quantified. TcpB efficiently blocked MyD 88 -induced activation of NF -KB (Fig. SlC). Furthermore, TcpB inhibited NF -KB activation induced by co- expression of IRAKI and IRAK4 or by co-expression of MyD88, IRAKI and IRAK4 (Fig. SlC). TcpB did not impair poly(I:C)-stimulated and TLR3/TRIF- mediated activation of the IFN-β promoter, however, as shown in HEK293 cells transfected with an IFN-β promoter reporter construct, TLR3 and TcpB (Fig. SlD).

TcpC was subsequently shown to bind to MyD88 in pull-down assays using the purified TIR-domain of TcpC (TIR-TcpC). TIR-TcpC interacted with transfected and endogenous MyD88 of HEK293 cells (Fig. 3C). Furthermore, endogenous MyD88 of RAW264.7 cells bound to TIR-TcpC when pre-stimulated with the tcpC::kan mutant for at least 15 min. (Fig. 3D). Pre-stimulation of RAW264.7 cells was required to raise endogenous MyD 88 -levels (Fig. 3D). TIR-TcpC did not interact with other components of the TLR-signaling cascade, as shown by pull-down assays with IRAKI, IRAK4 (Fig. 3E), TRIF and the intracellular domain of TLR2 (Fig. 3F). TcpB shared the ability of TIR-TcpC to bind endogenous and transfected MyD88 (Fig. 3G).

Subsequent experiments addressed if MyD88 is required for the function of TcpC using wild type or MyD 88 -deficient bone marrow-derived macrophages (BMM) infected with E. coli CFT073 or the tcpC::kan mutant. While TcpC suppressed TNF- secretion by MyD88-positive BMMs it failed to do so in MyD88-defϊcient BMMs (Fig. 3H). Furthermore, the difference in intracellular accumulation between the tcpCr.kan mutant and E. coli CFT073 or the complemented tcp::kan+pΥcpC mutant was seen in wild type but not in MyD88-deficient BMMs (Fig. 31, J). Taken together, these results show that TcpC interacts and interferes with MyD88-dependent effector functions of innate immunity.

TcpC increases bacterial burden and renal tissue damage

A direct effect of TcpC on the pathogenesis of acute pyelonephritis was demonstrated by comparing the wild type or mutant tcpCr.kan strain in the murine urinary tract infection (UTI) model. A difference in bacterial burden and tissue damage was observed. The wild type multiplied to much higher levels, as shown by cultures of urine and kidney homogenates (Fig. 4A, B). The complemented tcpC: :kan+pΥ cpC mutant, in contrast, reached similar bacterial numbers in the kidneys as CFT073 after 24 hours (Fig. 4C). Furthermore, kidney abscesses were detected in mice after infection with CFT073 but not with the tcpCr.kan mutant (Fig. 4D-F). By staining for P fimbriae, we detected bacteria in the center of the abscesses, which contained numerous neutrophils (Fig. 4G).

TcpC is common in isolates causing severe urinary tract infection

The molecular epidemiology of tcpC in human UTI was examined. E. coli strains were isolated from the urine of patients with severe kidney infections (acute pyelonephritis), bladder infections (acute cystitis) or asymptomatic bacterial carriage (asymptomatic bacteriuria, ABU). Isolates from the fecal flora of individuals without UTI were used as commensal E. coli controls. TcpC homologous sequences were present in about 40% of acute pyelonephritis isolates but were less common in cystitis (21%) or asymptomatic bacteriuria (16%) strains, or commensal E. coli strains (8%) (Fig. 4H). The results suggested that the fcpC-sequences enhance virulence, based on the association with the clinical severity of UTI. TcpC is secreted by CFT073

A polyclonal TcpC anti-serum was generated, which detected TcpC in CFT073 lysates, but not in lysates of the tcpCr.kan mutant strain (Fig. 5A). TcpC production was enhanced by lowering the pH of the culture medium or by co-incubation of CFT073 with RAW264.7 cells (Fig. 5A). TcpC was also detected in the culture supernatant of CFT073 -infected HCV29 and RAW264.7 cell (Fig. S2A), but failed to detect DnaK (Fig. S2B) making it unlikely, that TcpC was released in the course of bacterial lysis. Using a transwell system it was then shown that physically separated CFT073 suppressed TNF-induction in BMM compared to the tcpCr.kan mutant (Fig. 5B). Bacteria did not cross the membrane of the transwell as verified by cultivation. In addition, TcpC was present in equal amounts intracellularly compared to a non-separated co-culture as determined by Western blotting (Fig. 5C). Confocal microscopy confirmed this finding and showed that TcpC was clearly detectable within host cells using a FlAsH -tagged variant of TcpC (Fig. 5D). The cholesterol extracting agent methyl-β-cyclodextrin (MβCD) (Lafont et al.) was used for blocking the cellular uptake of TcpC. As shown in Fig. 5E the compound impaired the uptake of recombinant TIR-TcpC and extracellular TcpC was only detectable in the presence of MβCD. Taken together, the results show that CFT073 secretes TcpC and that the secreted and recombinant protein is taken up by host cells.

Recombinant TIR-T cpC is sufficient to impair the macrophage response The data above suggested that secreted TcpC is sufficient to impair the cytokine response of innate immune cells. This was confirmed as recombinant TIR-TcpC inhibited TNF -release by RAW264.7 cells stimulated with a variety of TLR-ligands in a dose-dependent manner (Fig. 6A). There was efficient inhibition of the MyD88- dependent TNF-response to LPS but not of poly(I:C)-stimulated TNF-secretion, which involves TRIF rather than MyD88. Again, recombinant TIR-TpcC was found intracellularly (Fig. S3). Recombinant EGFP purified like TIR-TcpC did not interfere with endotoxin-induced TNF-secretion (Fig. 6B). These results confirmed the previous observation that TcpB impaired TLR2- and TLR4-induced activation of NF-κB but not TLR3-driven activation of the IFN-β promoter (Fig. Sl). MβCD reversed the inhibition of LPS-induced signaling by TIR-TcpC, indicating that uptake of TIR-T cpC was required for its function (Fig. 6C). The efflux pump inhibitor PAβN neutralizes the activity of TcpC The efflux pump inhibitor phenylalanine-arginine-β-naphtylamide (PAβN) (Pannek et al.) was tested as to its effect on TcpC secretion. As shown in Fig. 6D PAβN blocked the ability of CFT073 to inhibit TNF-production by RAW264.7 cells but TNF-secretion induced by the tcpr.kan mutant was not influenced. Furthermore, the compound impaired the secretion of TcpC by CFT073 (Fig. 6E). Thus, PAβN could be envisaged as an additional treatment strategy accompanying antibiotics in severe UTI.

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Claims

3. A vector comprising at least one nucleic acid molecule in accordance with claim 1 or 2.

4. A vector according to claim 3 wherein the vector is a plasmid, a cosmid, a minichromosome or a viral vector.

5. A host cell comprising at least one nucleic acid molecule in accordance with any of claims 1 or 2 and/or at least one vector in accordance with claims 3 or 4.

6. A host cell in accordance with claim 5 wherein the host cell is a prokaryotic host cell.

7. A host cell in accordance with claim 6 wherein the host cell is a eukaryotic host cell.

8. A transgenic animal comprising at least one nucleic acid molecule in accordance with any of claims 1 or 2 and/or at least one vector in accordance with any of claims 3 or 4 and/or at least one host cell in accordance with any of claims 5 to 7.

9. An isolated recombinant polypeptide encoded by any of the nucleic acid molecules selected from the group consisting of: a. Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.

8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b. Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2.

10. An isolated recombinant polypeptide encoded by any of the nucleic acid molecules of claim 2 a) to b).

11. A pharmaceutical composition comprising at least one nucleic acid molecule of claim 1 or claim 2 and optionally a pharmaceutically acceptable excipient.

12. A pharmaceutical composition comprising at least one isolated recombinant polypeptide encoded by any of the nucleic acid molecules of claim 1 a) to b) or of claim 2 a) to b) and optionally a pharmaceutically acceptable excipient.

13. A pharmaceutical composition comprising at least one nucleic acid molecule of claim 1 a)-b) and/or at least one isolated recombinant polypeptide encoded by any of the nucleic acid molecules of claim 1 a) to b) for treating a disease and/or condition that is characterized in and/or caused by increased activation via TIR-domain containing eukaryotic molecules.

14. A pharmaceutical composition according to claim 13 wherein the disease to be treated is an autoimmune diseases and/or chronic inflammatory diseases.

15. A pharmaceutical composition according to any of claim 13 or 14 wherein the disease to be treated is selected from the group comprising rheumatoid arthritis, juvenile rheumatoid arthritis, inflammatory bowel disease, Ankylosing spondylitis, psoriasis, therapy-resistant sarcoidosis, inflammatory myopathies, Behcet disease, inflammatory eye disease, diseases of the central nervous system such as ischemia and traumatic injury, cardiovascular such as atherosclerosis, myocardial infection, heart failure, myocarditis, cardiac allograft rejection and vascular endothelial cell responses, respiratory diseases such as chronic bronchitis, chronic obstructive pulmonary disease, acute respiratory distress syndrome and asthma, renal diseases such as ischemic renal injury, renal transplant rejection and glomerulonephritis, lupus erythematosus, lupus erythematodes or diabetes Sjόrgens syndrome.

16. A pharmaceutical composition comprising at least one nucleic acid molecule of claim Ic), claim 2 and/or at least one polypeptide of claim 10 for treating a disease and/or condition characterized in and/or caused by pathogenic prokaryotic microorganisms expressing a polypeptide comprising a TIR domain.

18. A pharmaceutical composition according to any of claim 16 or 17 wherein the disease to be treated is selected from the group comprising urinary tract infections, acute pyelonephritis, bladder infections such as acute cystitis, asymptomatic bacterial carriage such as asymptomatic bacteriuria (ABU)sepsis, tuberculosis, pneumonia or infections induced by E. coli, Staphylococcus aureus, Brucella spp. or Salmonella spp..

19. A pharmaceutical composition according to any of claim 16 or 17 wherein said disease is caused by microorganisms selected from the group comprising Escherichia coli, Staphylococcus aureus, Brucella spp., Salmonella spp., Mycobacterium tuberculosis, Listeria monocytogenes or Chlamydophila pneumonia.

20. Use of a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No.

8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; c) Nucleic acid sequences that specifically hybridize with any of the nucleic acid sequences of a) or b) under stringent conditions as a diagnostic marker as a diagnostic and/or therapeutic agent.

21. Use of a polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) Nucleic acid sequences encoding polypeptides comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID

Nos. 8,4 and 5; b) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; as a diagnostic and/or therapeutic agent.

22. Use of a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ

ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8,4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2. as a diagnostic and/or therapeutic agent.

23. Use of a polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: a) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes polypeptides comprising amino acid sequences of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; b) A nucleic acid sequence encoding an antibody, functional fragment or functional analogue thereof that specifically recognizes functional homologues and/or fragments of polypeptides comprising amino acid sequences of SEQ ID No. 1 or SEQ ID No. 2. as a diagnostic and/or therapeutic agent.

24. Method of identifying molecules which are capable of interfering with the inhibitory effect of any of the polypeptides in accordance with claim 6 on MyD 88 activity comprising at least the following steps: a) Providing at least one polypeptide encoded by a nucleic acid molecule comprising at least one nucleic acid sequence selected from the group consisting of: aa) Nucleic acid sequences encoding polypeptides comprising SEQ ID

No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 8, a combination of SEQ ID Nos. 3, 4 and 5 or a combination of SEQ ID Nos. 8, 4 and 5; ba) Nucleic acid sequences coding for functional homologues and/or fragments of SEQ IDs No. 1 or 2; b) Determining the effect of said polypeptide on the activity of MyD88; c) Providing a molecule other than said polypeptide or MyD88; d) Determining the influence of said molecule on the effect of said polypeptide on the activity of MyD88.