Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
2000-11-09
2004-03-09
Brusca, John S. (Department: 1631)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C435S252300, C435S320100, C435S325000, C536S023100, C536S024100
Reexamination Certificate
active
06703492
ABSTRACT:
FIELD OF THE INVENTION
The present invention provides nucleic acids, and peptides, polypeptides and proteins encoded by the nucleic acids, isolated from
Staphylococcus epidermidis.
BACKGROUND OF THE INVENTION
Staphylococcus epidermidis
is a gram-positive bacteria present in the normal flora of humans, and is typically present on the skin. It is catalase positive, and grows aerobically. It is inplicated in various human conditions and diseases, including subacute bacterial endocarditis (Baddour L M et al., Production of experimental endocarditis by coagulase-negative staphylococci: variability in species virulence, J. Infect. Dis. 150: 721-727, 1984; Karchmer A W, Archer G L, Dismukes W E,
Staphylococcus epidermidis
causing prosthetic valve endocarditis: microbiologic and clinical observations as guides to therapy, Ann Intern Med. 1983;98:447-455.) and septicemia (Christensen G D et al., Nosocomial septicemia due to multiply antibiotic-resistant
Staphylococcus epidermidis
, Ann. Intern. Med. 96: 1-10, 1982).
S. epidermidis
is estimated to be responsible for about 12% of all hospital patient infections. Because of the organism's peculiar ability to colonize polymer and metallic surfaces, there is a correlation of infection with the insertion of intravenous lines or catheters or implantation of prosthetic devices. Treatment can be difficult since different isolates of
S. epidermidis
show a broad spectrum of antibiotic resistance. The organism also produces a polysaccharide biofilm which helps to protect the bacteria from the human immune system (Tojo M et al., Isolation and characterization of a capsular polysaccharide adhesin from
Staphylococcus epidermidis
, J. Infect. Dis. 157: 713-722, 1988).
The present invention advantageously provides isolated nucleic acids and their encoded peptides, polypeptides and proteins from the genome of
S. epidermidis
, as well as the genomic map of
S. epidermidis
. Thus, the present invention fulfils a a widely-felt need for
S. epidermidis
diagnostics, antigens, and products useful in procedures for preparing antibodies and for identifying compounds effective against
S. epidermidis
infection. Selected nucleic acids and/or polypeptides of the present invention can be advantageously utilized as targets in screenings assays for antibiotics, as diagnostics of infections, and as means to identify
S epidermidis
in any given sample and distinguish it from other bacteria.
SUMMARY OF THE INVENTION
The present invention provides an isolated polynucleotide comprising a member selected from the group consisting of:
(a) a polynucleotide encoding a polypeptide having at least a 70% identity to a polypeptide set forth in the Sequence Listing;
(b) a polynucleotide which is complementary to the polynucleotide of (a); and
(c) a polynucleotide comprising at least 15 sequential bases of the polynucleotide of (a) or (b). The present invention further provides polypeptides encoded by these polynucleotides and methods of using the polynucleotides and polypeptides.
DETAILED DESCRIPTION OF THE INVENTION
Glossary
The following illustrative explanations are provided to facilitate understandirg of certain terms used frequently herein, particularly in the Examples. The explanations are provided as a convenience and are not limitative of the invention.
BINDING MOLECULE refers to a molecule or ion which binds or interacts specifically with polypeptides or polynucleotides of the present invention, including, for example enzyme substrates, cell membrane components and classical receptors. Binding between polypeptides (or polynucleotides) of the invention and such molecules may be exclusive to polypeptides of the invention, which is preferred, or it may be highly specific for polypeptides of the invention, which is also preferred, or it may be highly specific to a group of proteins that includes polypeptides of the invention, which is preferred, or it may be specific to several groups of proteins at least one of which includes a polypeptide of the invention. Binding molecules also include antibodies and antibody-derived reagents that bind specifically to polypeptides of the invention.
GENETIC ELEMENT generally means a polynucleotide comprising a region that encodes a polypeptide or a polynucleotide region that regulates replication, transcription or translation or other processes important to expression of the polypeptide in a host cell, or a polynucleotide comprising both a region that encodes a polypeptide and a region operably linked thereto that regulates expression. Genetic elements may be comprised within a vector that replicates as anepisomal element; that is, as a molecule physically independent of the host cell genome. They may be comprised within plasmids. Genetic elements also may be comprised within a host cell genome; not in their natural state but, rather, following manipulation such as isolation, cloning and introduction into a host cell in the form of purified DNA or in a vector, among others.
HOST CELL is a cell which has been transformed or transfected, or is capable of transformation or transfection by an exogenous polynucleotide sequence.
IDENTITY, as known in the art, is the relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, identity alsomeans the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. Identity can be readily calculated (
Computational Molecular Biology
, Lesk, A. M., ed., Oxford University Press, New York, 1988
; Biocomputing: Informatics and Genome Projects
, Smith, D. W., ed., Academic Press, New York, 1993
; Computer Analysis of Sequence Data
, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994
; Sequence Analysis in Molecular Biology
, von Heinje, G., Academic Press, 1987; and
Sequence Analysis Primer
, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991). While there exist a number of methods to measure identity between two polynucleotide or two polypeptide sequences, the term is well known to skilled artisans (
Sequence Analysis in Molecular Biology
, von Heinje, G., Academic Press, 1987
; Sequence Analysis Primer
, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., SIAM
J. Applied Math
., 48:1073 (1988)). Methods commonly employed to determine identity between sequences include, but are not limited to those disclosed in Carillo, H., and Lipman, D., SIAM
J. Applied Math
., 48:1073 (1988). Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity are codified in computer programs. Preferred computer program methods to determine identity between two sequences include, but are not limited to, GCG program package (Devereux, J., et al.,
Nucleic Acids Research
12(1):387 (1984)), BLASTP, BLASTN, and FASTA (Atschul, S. F. et al.,
J. Molec. Biol
. 215:403 (1990)).
ISOLATED means separated “by the hand of man” from its natural state; i.e., that, if it occurs in nature, it has been changed or removed from its original environment, or both. For example, a naturally occurring polynucleotide or a polypeptide naturally present in a living organism in its natural state is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein. As part of or following isolation, such polynucleotides can be joined to other polynucleotides, such as DNAs, for mutagenesis, to form fusion proteins, and for propagation or expression in a host, for instance. The isolated polynucleotides, alone or joined to other polynucleotides such as vectors, can be introduced into host cells, in culture or in whole organisms. Introduced into host cells in culture or in whole organisms, such DNAs still would be isolated, as the term is used herein, because they would not
Brusca John S.
Conger Michael M.
SmithKline Beecham Corporation
Zhou Shubo (Joe)
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