DbpB

Details DbpB DbpB

1999-07-12

2001-11-06

Schwartzman, Robert A. (Department: 1636)

Chemistry: natural resins or derivatives; peptides or proteins;

Proteins, i.e., more than 100 amino acid residues

C530S324000

Reexamination Certificate

active

06313270

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 dbp (DEAD box proteins, ATP-dependent RNA helicase) family, hereinafter referred to as “dbpB”.
BACKGROUND OF THE INVENTION
It is particularly preferred to employ Staphylococcal genes and gene products as targets for the development of antibiotics. The Staphylococci make up a medically important genera of microbes. They are known to produce two types of disease, invasive and toxigenic. Invasive infections are characterized generally by abscess formation effecting both skin surfaces and deep tissues.
S. aureus
is the second leading cause of bacteremia in cancer patients. Osteomyelitis, septic arthritis, septic thrombophlebitis and acute bacterial endocarditis are also relatively common. There are at least three clinical conditions resulting from the toxigenic properties of Staphylococci. The manifestation of these diseases result from the actions of exotoxins as opposed to tissue invasion and bacteremia. These conditions include: Staphylococcal food poisoning, scalded skin syndrome and toxic shock syndrome.
The frequency of
Staphylococcus aureus
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
Staphylococcus aureus
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.
DbpA of
E. coli
is a member of the DEAD-type ATP-dependent RNA helicases. Both ATPase and RNA helicase activities of DbpA have been demonstrated in
E. coli
. Since DbpA hydrolyzes ATP only in the presence of bacterial 23S rRNA and it is able to unwind 16S and 23S rRNA hybrids, it has been strongly implicated in the important biological process of ribosomal assembly. Two other
E. coli
DbpA homologues, SrmB and DeaD (CsdA), are also implicated in ribosomal biogenesis since overexpression of deaD and srmB can suppress the effect of a temperature-sensitive mutation in L24, a protein that is necessary for the assembly of the large ribosomal subunit, and in the rpsB gene encoding the ribosomal protein S2, respectively. RhlB of
E. coli
, another DbpA homologue, is a major component of RNA degradosome which is important in RNA processing and messenger RNA degradation. The eIF4A, the eukaryotic homologue of DbpA, is involved in initiation of translation. There are eight conserved domains in the DEAD box proteins and all these are also found in the DbpB of
S. aureus
. Therefore, it is very likely that the DbpB of
S. aureus
could play an important role in the ribosomal assembly, translation, or RNA processing and mRNA turnover.
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.
The polypeptides of the invention have amino acid sequence homology to a known
E. coli
dbpA protein. See Iggo, R., Picksley, S., Southgate, J., McPheat, J., Lane, D. P. 1990, Nucleic Acids Res., 18:5413-5417; EMBL Accession Number: X52647. Also see Fuller-Pace, F. V., et al 1993, EMBO J. 12, 3619-3626.; Nicol, S. M., and Fuller-Pace, F. V. 1995. Proc. Natl. Acad. Sci. USA. 92, 11681-11685; and Boddeker N., et al. 1997. Nucleic Acids Res. 25, 537-545.
SUMMARY OF THE INVENTION
It is an object of the invention to provide polypeptides that have been identified as novel dbpB polypeptides by homology between the amino acid sequence set out in Table 1 [SEQ ID NO: 2] and a known amino acid sequence or sequences of other proteins such as
E. coli
dbpA protein.
It is a further object of the invention to provide polynucleotides that encode dbpB polypeptides, particularly polynucleotides that encode the polypeptide herein designated dbpB.
In a particularly preferred embodiment of the invention the polynucleotide comprises a region encoding dbpB polpeptides comprising the sequence set out in Table 1 [SEQ ID NO:1] which includes, for example, a full length gene, or a variant thereof.
In another particularly preferred embodiment of the invention there is a novel dbpB protein from
Staphylococcus aureus
comprising the amino acid sequence of Table 1 [SEQ ID NO:2], or a variant thereof.
In accordance with another aspect of the invention there is provided an isolated nucleic acid molecule encoding a mature polypeptide expressible by the
Staphylococcus aures
WCUH 29 strain contained in the deposited strain.
A further aspect of the invention there are provided isolated nucleic acid molecules encoding dbpB, particularly
Staphylococcus aures
dbpB, including mRNAs, cDNAs, genomic DNAs. Further embodiments of the invention include biologically, diagnostically, prophylactically, clinically or therapeutically useful variants thereof, and compositions comprising the same.
In accordance with another aspect of the invention, there is provided the use of a polynucleotide of the invention for therapeutic or prophylactic purposes, in particular genetic immunization. Among the particularly preferred embodiments of the invention are naturally occurring allelic variants of dbpB and polypeptides encoded thereby.
Another aspect of the invention there are provided novel polypeptides of
Staphylococcus aureus
referred to herein as dbpB as well as biologically, diagnostically, prophylactically, clinically or therapeutically useful variants thereof and compositions comprising the same.
Among the particularly preferred embodiments of the invention are variants of dbpB polypeptide encoded by naturally occurring alleles of the dbpB gene.
In a preferred embodiment of the invention there are provided methods for producing the aforementioned dbpB polypeptides.
In accordance with yet another aspect of the invention, there are provided inhibitors to such polypeptides, useful as antibacterial agents, including, for example, antibodies.
In accordance with certain preferred embodiments of the invention, there are provided products, compositions and methods for assessing dbpB expression, treating disease, for example, disease, such as, infections of the upper respiratory tract (e.g., otitis media, bacterial tracheitis, acute epiglottitis, thyroiditis), lower respiratory (e.g., empyema, lung abscess), cardiac (e.g., infective endocarditis), gastrointestinal (e.g., secretory diarrhoea, splenic absces, retroperitoneal abscess), CNS (eg., cerebral abscess), eye (e.g., blepharitis, conjunctivitis, keratitis, endophthalmitis, preseptal and orbital cellulitis, darcryocystitis), kidney and urinary tract (e.g., epididymitis, intrarenal and perinephric absces, toxic shock syndrome), skin (e.g., impetigo, folliculitis, cutaneous abscesses, cellulitis, wound infection, bacterial myositis) bone and joint (e.g., septic arthritis, osteomyelitis), assaying genetic variation, and administering a dbpB polypeptide or polynucleotide to an organism to raise an immunological response against a bacteria, especially a
Staphylococcus
aureus bacteria.
In accordance with certain preferred embodiments of this and other aspects of the invention there are provided polynucleotides that hybridize to dbpB polynucleotide sequences, particularly under stringent conditions.
In certain preferred embodiments of the invention there are provided antibodies against dbpB polypeptides.
In other embodiments of the invention there are pro

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