Drug – bio-affecting and body treating compositions – Enzyme or coenzyme containing
Reexamination Certificate
1999-06-29
2001-04-17
Navarro, Albert (Department: 1645)
Drug, bio-affecting and body treating compositions
Enzyme or coenzyme containing
C424S190100, C424S193100, C424S197110, C424S234100, C424S244100, C530S350000
Reexamination Certificate
active
06217861
ABSTRACT:
FIELD OF THE INVENTION
This invention relates to newly identified polynucleotides and polypeptides, and their production and uses, as well as their variants, agonists and antagonists, and their uses. In particular, in these and in other regards, the invention relates to novel polynucleotides and polypeptides of the response regulator family, hereinafter referred to as “Response Regulator” and cognate molecules of the histidine kinase family, hereinafter referred to as “Histidine Kinase”.
BACKGROUND OF THE INVENTION
The Streptococci make up a medically important genera of microbes known to cause several types of disease in humans, including, for example, otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospinal fluid. Since its isolation more than 100 years ago,
Streptococcus pneunoniae
has been one of the more intensively studied microbes. For example, much of our early understanding that DNA is, in fact, the genetic material was predicated on the work of Griffith and of Avery, Macleod and McCarty using this microbe. Despite the vast amount of research with
S. pneunoniae
, many questions concerning the virulence of this microbe remain. It is particularly preferred to employ Streptococcal genes and gene products as targets for the development of antibiotics.
The frequency of
Streptococcus pneumoniae
infections has risen dramatically in the past 20 years. This has been attributed to the emergence of multiply antibiotic resistant strains and an increasing population of people with weakened immune systems. It is no longer uncommon to isolate
Streptococcus pneumoniae
strains which are resistant to some or all of the standard antibiotics. This has created a demand for both new anti-microbial agents and diagnostic tests for this organism.
While certain Streptococcal factors associated with pathogenicity have been identified, e.g., capsule polysaccharides, peptidoglycans, pneumolysins, PspA Complement factor H binding component, autolysin, neuramininidase, peptide permeases, hydrogen peroxide, IgA1 protease, the list is certainly not complete. Further very little is known concerning the temporal expression of such genes during infection and disease progression in a mammalian host. Discovering the sets of genes the bacterium is likely to be expressing at the different stages of infection, particularly when an infection is established, provides critical information for the screening and characterization of novel antibacterials which can interrupt pathogenesis. In addition to providing a filler understanding of known proteins, such an approach will identify previously unrecognised targets.
Many two component signal transduction systems (TCSTS) have been identified in bacteria (Stock, J. B., Ninfa, A. J. & Stock, A. M.(1989) Microbiol. Rev. 53, 450-490). These are involved in the bacterium's ability to monitor its surroundings and adapt to changes in its environment. Several of these bacterial TCSTS are involved in virulence and bacterial pathogenesis within the host.
Response regulators are components of the TCSTS. These proteins are phosphorylated by histidine kinases and in tuni once phosphorylated effect the response, often through a DNA binding domain becoming activated. The response regulators are characterized by a conserved N-terminal domain of approximately 100 amino acids. The N-terminal domains of response regulators as well as retaining five functionally important residues, corresponding to the residues D12, D13, D57, T87, K109 in CheY (Matsumura, P., Rydel, J. J., Linzmeier, R. & Vacante, D. (1984) J. Bacteriol. 160, 36-41), have conserved structural features (Volz, K. (1993) Biochemistry 32, 11741-11753). The 3-dimensional structures of CheY from
Salmonella typhimurium
(Stock, A. M., Mottonen, J. M., Stock, J. B. & Schutt, C. E. (1989) Nature, 337, 745-749) and
Escherichia coli
(Volz, K. & Matsumura, P. (1991) J. Biol. Chem. 266, 15511-15519) and the N-terminal domain of nitrogen regulatory protein C from
S. typhimuriumn
(Volkman, B. F., Nohaile, M. J., Amy, N. K., Kustu, S. & Wemmrer, D. E. (1995) Biochemistry, 34 1413-1424), are available, as well as the secondary structure of SpoOF from
Bacillus subtilis
(Feher, V. A., Zapf, J. W., Hoch, J. A., Dahlquist, F. W., Whiteley, J. M. & Cavanagh, J. (1995) Protein Science, 4, 1801-1814). These structures have a (a/b)5 fold. Several structural residues are conserved between different response regulator sequences, specifically hydrophobic residues within the &bgr;-sheet hydrophobic core and sites from the a-helices. This family of response regulators includes PhoP protein from
Bacillus subtilis
. PhoP is the response regulator of the TCSTS which controls the regulation of the alkaline phosphatase genes in
B. subtilis
(Seki, T., Yoshikawa, H., Takahashi, H. & Saito, H., 1987, J. Bacteriol. 169, 2913-2916).
Histidine kinases are components of the TCSTS which autophosphorylate a histidine residue. The phosphate group is then transferred to the cognate response regulator. The Histidine kinases have five short conserved amino acid sequences (Stock, J. B., Ninfa, A. J. & Stock, A. M.(1989) Microbiol. Rev. 53, 450-490, Swanson, R. V., Alex, L. A. & Simon, M. I. (1994) TIBS 19 485-491). These are the histidine residue, which is phosphorylated, followed after approximately 100 residues by a conserved asparagine residue. After another 15 to 45 residues a DXGXG motif is found, followed by a FXXF motif after another 10-20 residues. 10-20 residues further on another glycine motif, GXG is found. The two glycine motifs are thought to be involved in nucleotide binding.
Among the processes regulated by TCSTS are production of virulence factors, motility, antibiotic resistance and cell replication. Inhibitors of TCSTS proteins would prevent the bacterium from establishing and maintaining infection of the host by preventing it from producing the necessary factors for pathogenesis and thereby have utility in anti-bacterial therapy.
Clearly, there is a need for factors, such as the novel compounds of the invention, that have a present benefit of being useful to screen compounds for antibiotic activity. Such factors are also useful to determine their role in pathogenesis of infection, dysfunction and disease. There is also a need for identification and characterization of such factors and their antagonists and agonists which can play a role in preventing, ameliorating or correcting infections, dysfunctions or diseases.
Response Regulator polypeptides of the invention have amino acid sequence homology to a known
Shigella dysenteriae
PhoB protein.
SUMMARY OF THE INVENTION
It is an object of the invention to provide polypeptides that have been identified as novel Response Regulator or Histidine Kinase polypeptides by homology between the amino acid sequence set out in Table 1 [SEQ ID NOS: 2, 4 and 6] and a known amino acid sequence or sequences of other proteins such as
Shigella dysenteriae
PhoB or ResE protein.
It is a further object of the invention to provide polynucleotides that encode Response Regulator or Histidine Kinase polypeptides, particularly polynucleotides that encode the polypeptide herein designated Response Regulator or Histidine Kinase respectively.
In a particularly preferred embodiment of the invention the polynucleotide comprises a region encoding Response Regulator polypeptides comprising a sequence set out in Table 1 [SEQ ID NO:1 and 3] which includes a full length gene, or a variant thereof.
In another particularly preferred embodiment of the invention the polynucleotide comprises a region encoding Histidine Kinase polypeptides comprising a sequence set out in Table 1 [SEQ ID NO:5], or a variant thereof.
In another particularly preferred embodiment of the invention there is a novel Response Regulator or Histidine Kinase protein from
Streptococcus pneumoniae
comprising the amino acid sequence of Table 1 [SEQ ID NO:2 or 6 respectively&rsqb
Deibert Thomas S.
Gimmi Edward R.
King William T.
Navarro Albert
SmithKline Beecham Corporation
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