Chemistry: molecular biology and microbiology – Enzyme – proenzyme; compositions thereof; process for... – Transferase other than ribonuclease
Reexamination Certificate
1999-08-31
2001-08-28
Prouty, Rebecca E. (Department: 1652)
Chemistry: molecular biology and microbiology
Enzyme , proenzyme; compositions thereof; process for...
Transferase other than ribonuclease
C435S069100, C435S183000, C435S252300, C435S320100, C536S023700
Reexamination Certificate
active
06280990
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, the invention relates to polynucleotides and polypeptides of the DNA Polymerase family, as well as their variants, herein referred to as “dnaE,” and “dnaE polynucleotide(s),” and “dnaE polypeptide(s)” as the case may be.
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 pneumoniae
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. pneumoniae
, 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 few decades. 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 that are resistant to some or all of the standard antibiotics. This phenomenon has created an unmet medical need and demand for new anti-microbial agents, vaccines, drug screening methods, and diagnostic tests for this organism.
Moreover, the drug discovery process is currently undergoing a fundamental revolution as it embraces “functional genomics,” that is, high throughput genome- or gene-based biology. This approach is rapidly superseding earlier approaches based on “positional cloning” and other methods. Functional genomics relies heavily on the various tools of bioinformatics to identify gene sequences of potential interest from the many molecular biology databases now available as well as from other sources. There is a continuing and significant need to identify and characterize further genes and other polynucleotides sequences and their related polypeptides, as targets for drug discovery.
Clearly, there exists a need for polynucleotides and polypeptides, such as the dnaE embodiments of the invention, that have a present benefit of, among other things, being useful to screen compounds for antimicrobial 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 to find ways to prevent, ameliorate or correct such infection, dysfunction and disease.
SUMMARY OF THE INVENTION
The present invention relates to dnaE, in particular dnaE polypeptides and dnaE polynucleotides, recombinant materials and methods for their production. In another aspect, the invention relates to methods for using such polypeptides and polynucleotides, including treatment of microbial diseases, amongst others. In a further aspect, the invention relates to methods for identifying agonists and antagonists using the materials provided by the invention, and for treating microbial infections and conditions associated with such infections with the identified agonist or antagonist compounds. In a still further aspect, the invention relates to diagnostic assays for detecting diseases associated with microbial infections and conditions associated with such infections, such as assays for detecting dnaE expression or activity.
Various changes and modifications within the spirit and scope of the disclosed invention will become readily apparent to those skilled in the art from reading the following descriptions and from reading the other parts of the present disclosure.
DESCRIPTION OF THE INVENTION
The invention relates to dnaE polypeptides and polynucleotides as described in greater detail below. In particular, the invention relates to polypeptides and polynucleotides of a dnaE of
Streptococcus pneumoniae
, that is related by amino acid sequence homology to dnaE polypeptide. The invention relates especially to dnaE having a nucleotide and amino acid sequences set out in Table 1 as SEQ ID NO:1 and SEQ ID NO:2 respectively. Note that sequences recited in the Sequence Listing below as “DNA” represent an exemplification of the invention, since those of ordinary skill will recognize that such sequences can be usefully employed in polynucleotides in general, including ribopolynucleotides. The initial amino acid encoded by the codon “GTG” is indicated in SEQ ID NO:2 as valine. However, in one embodiment of the invention, this initial amino acid of a polypeptide of the invention is methionine.
TABLE 1
dnaE Polynucleotide and Polypeptide Sequences
(A)
Streptococcus pneumoniae
dnaE polynucleotide sequence [SEQ ID NO:1].
5′-
GTGAGAAGGATAGAGGAGAAGTGTAAATTGATCGCACAACTAGATACAAAAACAGTCTATAGTTTTATGGAA
AGCGTCAT
TTCGATCGAAAAGTATGTGAGAGCAGCTAAAGAATACGGCTACACTCATTTGGCTATGATGGATATTGACAA
TCTTTATG
GCGCTTTCGACTTTCTAGAGATTACAAAAAATAACGGCATTCATCCTTTGCTAGGGCTTGAAATGACAGTGT
TTGTAGAT
GATCAGGAAGTGAATTTGCGCTTTTTAGCTCTATCTAGTGTGGGCTATCAGCAGTTGATGAAGCTTTCGACA
GCCAAGAT
GCAGGGGGAGAAAACTTGGTCAGTCCTGTCCCAGTACCTGGAGGATATCGCGGTCATTGTGCCTTATTTTGA
TAGAGTTG
AGTCGTTAGAACTAGGCTGTGATTACTATATAGGGGTTTATCCAGAAACACTAGCAAGCGAATTTCATCATC
CTATCTTA
CCTCTTTATCGGGTCAACGCTTTTGAAAGCAGGGATAGAGAAGTTCTTCAAGTTTTAACAGCGATTAAAGAA
AATCTACC
GCTCAGAGAAGTTCCCTTGCGTTCGAGACAAGATGTCTTTATATCAGCAAGTTCTTTAGAGAAACTATTCCA
AGAGCGTT
TTCCGCAAGCTTTGGACAATTTAGAAAAGCTTATTTCAGGCATTTCTTACGACTTGGATATTAGTCTGAAAC
TGCCTCGT
TTTAATCCAGCTAGACCAGCAGTAGAGGAGTTGAGAGAGCGTGCTGAACTGGGGTTTGTTCAGAAGGGGTTG
ACTAGTAA
AGAATATCAAGATAGACTAGACCAAGAATTGTCTGTTATTCATGATATGGGCTTTGATGATTATTTCTTGGT
TGTTTGGG
ATTTGTTGCGTTTTGGACGATCGAATGGCTATTATATGGGAATGGGAAGGGGTTCTGCAGTAGGCAGTTTGG
TTTCTTAT
GCCTTAGACATCACGGGGATTGACCCAGTAGAGAAAAATCTGATTTTTGAACGCTTTCTTAATCGTGAACGC
TATACCAT
GCCTGATATTGATATTGATATCCCAGATATTTATCGTCCAGATTTTATCAGATATGTTGGTAATAAATATGG
TAGTAAAC
ATGCGGCACAAATCGTTACTTTTTCAACCTTTGGAGCCAAGCAAGCTCTTCGAGATGTCTTGAAACGCTTTG
GTGTGCCA
GAGTATGAATTATCTGCAATTACTAAGAAAATCAGTTTTCGTGACAATCTTAAGTCGGCCTATGAGGGCAAT
CTCCAGTT
TCGTCAGCAAATCAATAGTAAGTTAGAATACCAAAAAGCTTTTGAGATTGCTTGCAAGATAGAGGGCTATCC
AAGGCAAA
CCTCTGTCCATGCGGCTGGTGTTGTAATTAGTGACCAAGATTTAACCAACTACATTCCTCTAAAGTATGGTG
ATGAAATT
CCACTGACTCAGTATGATGCTCATGGAGTTGAGGCTAGCGGACTTTTGAAGATGGACTTTCTGGGACTACGA
AATTTGAC
CTTTGTCCAGAAGATGCAAGAGTTGCTTGCTGAAACAGAAGGTATTCACCTTAAAATTGAAGAAATAGATTT
GGAAGACA
AAGAAACGTTAGATTTATTTGCCTCTGGAAATACAAAAGGTATCTTTCAATTTGAGCAACCTGGTGCCATTC
GCTTGCTC
AAACGTGTTCAACCAGTCTGTTTTGAAGATGTCGTCGCAACTACTTCTCTAAATCGACCAGGTGCAAGTGAC
TACATCAA
TAATTTTGTGGCAAGGAAGCATGGGCAGGAAGAAGTGACTGTTCTAGATTCAGCTCTGGAGGATATTTTGGC
TCCAACTT
ATGGCATTATGCTCTATCAGGAGCAGGTTATGCAGGTTGCTCAGCGATTTGCTGGATTTAGTCTTGGGAAGG
CCGATATT
TTGCGTCGAGCTATGGGTAAAAAGGATGCCTCTGCTATGCATGAGATGAGGGCTTCCTTTATTCAAGGCTCC
ATAGAAGC
AGGCCATACTGCGGAAAAATCAGAGCAGGTTTTTGATGTTATGGAGAAGTTTGCAGGTTATGGATTTAATAG
ATCTCATG
CCTACGCCTACTCAGCCTTGGCCTTCCAGTTGGCTTATTTCAAAACGCATTATCCAGCCATTTTTTATCAGG
TCATTGTTA
AATTATTCCAACAGTGATTACTTAATAGATGCACTTGAAGCAGGTTTTGAAGTAGCCTCTCTATCCATCAAT
ACTATTCC
CTATCACGATAAAATTGCCAACAAGTCTATCTATATAGGTTTGAAATCGATTAAGGGGCTCAGCAAGGACTT
GGCGCTTT
GGATTATTGAACATAGACCTTATTCTAACATTGAAGATTTTATAGCTAAATTACCTGAGAATTATCTGAAAC
TTCCTCTG
CTAGAACCTTTGGTAAAAGTTGGTCTTTTCGATTCATTTGAAAAAAATCGTCAAAAAGTATTTAATAACTTA
GCAATCT
ATTTGAATTTGTGAAAGAGTTGGGAAGTTTGTTTGGAGATGCTATTTATAGTTGGCAGGAATCGGAAGATTG
GACGGAAC
AAGAAAAATTTTATATGGAACAAGAGCTTTTAGGGATAGGTGTCAGCAAACATCCACTACAAGCTATTGCAA
GTAAGGCT
ATTTACCCGATTACCCCAATCGGAAATTTGTCAGAAAATAGCTA
Horn Stephanie Van
May Earl
Warren Patrick V
Warren Richard L
Deibert Thomas S.
Gimmi Edward R.
King William T.
Prouty Rebecca E.
Rao Manjunath N.
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