Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Recombinant dna technique included in method of making a...
Reexamination Certificate
1998-11-12
2002-03-26
Clark, Deborah J. R. (Department: 1633)
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Recombinant dna technique included in method of making a...
C536S023200, C536S023700, C536S023100, C435S320100, C435S325000, C435S455000
Reexamination Certificate
active
06361965
ABSTRACT:
FIELD OF THE INVENTION
This invention relates to newly idenified 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 YabO family, as well as their variants, hereinafter referred to as “YfiI pseudouridine synthase,” “YfiI pseudouridine synthase polynucleotide(s),” and “YfiI pseudouridine synthase 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 which 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 charactetize 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 YfiI pseudouridine synthase embodiments of the invention, that have a present benefit of, among other thrings, 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 YfiI pseudouridine synthase, in particular YfiI pseudouridine synthase polypeptides and YfiI pseudouridine synthase 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 farther 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 YfiI pseudouridine synthase 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 YfiI pseudouridine synthase polypeptides and polynucleotides as described in greater detail below. In particular, the invention relates to polypeptides and polynucleotides of a YfiI pseudouridine synthase of
Streptococcus pneumoniae
, which is related by amino acid sequence homology to
B.subtilis
YlyB,
E. coli
YfiI polypeptide. The invention relates especially to YfiI pseudouridine synthase having the 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.
TABLE 1
YfiI pseudouridine synthase Polynucleotide and Polypeptide Sequences
(A)
Streptococcus pneumoniae
YfiI pseudouridine synthase polynucleotide sequence
[SEQ ID NO:1].
5′-
TGACTTTATCAACTTTGNCAATTTTCAATGTGGCAGATAGCTATCTGACGGTTGGAGTGATTATTTTATTGA
TTGCAATGCTAAAAGAGGAAATAA
ATGGAAATTAAAATTGAAACTGGTGGTCTGCGTTTGGATAAGGCTTTGTCAGATTTGTCAGAATTATCACGT
AGTCTCGCGAATGAACAAATTAAATCAGGCCAGGTCTTGGTCAATGGTCAAGTCAAGAAAGCTAAATACACA
GTCCAAGAGGGTGATGTCGTCACTTACCATGTGCCAGAACCAGAGGTATTAGAGTATGTGGCTGAGGATCTT
CCGCTAGAAATAGTCTACCAAGATGAGGATGTGGCTGTCGTTAACAAACCTCAGGGAATGGTTGTGCACCCG
AGTGCTGGTCATACCAGTGGAACCCTAGTAAATGCCCTCATGTATCATATTAAGGACTTGTCGGGTATCAAT
GGGGTTCTGCGTCCAGGGATTGTTCACCGTATTGATAAGGATACGTCAGGTCTTCTCATGATTGCTAAAAAC
GATGATGCGCATCTAGCACTTGCCCAAGAACTCAAAGATAAAAAGTCTCTCCGCAAATATTGGGCGATTGTT
CATGGAAATCTGCCTAATGATCGTGGTGTAATTGAAGCGCCGATTGGCCGGAGTGAAAAAGACCGTAAGAAA
CAGGCTGTAACTGCTAAAGGGAAGCCTGCAGTGACGCGTTTTCACGTCTTGGAACGCTTTGGCGATTATAGC
TTAGTAGAGTTGCAACTGGAGACAGGGCGCACTCATCAAATCCGTGTCCACATGGCTTATATCGGCCATTCA
GTCGCTGGTGATGAGGTCTATGGTCCTCGCAAGACTTTGAAAGGACATGGACAATTTCTTCATGCCAAGACT
TTAGGTTTTACTCATCCGAGAACAGGTAAGACCTTGGAATTTAAAGCAGATATCCCAGAGATTTTTAAGGAA
CCTTGGAGAGAT
TGAGAAAAGTAAGAATGAAAAAGGGAATTAACTAGTTTAGCACTTGTAGGCGCTTTTTTAGGTTTGTCATGG
NATGGGGATGTTCCAGG-3′
(B)
Streptococcus pneumoniae
YfiI pseudouridine synthase polypeptide sequence
deduced from a polynucleotide sequence in this table [SEQ ID NO:2].
NH
2
-
MEIKIETGGLRLDKALSDLSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVTYHVFEPEVLEYVAEDL
PLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKN
DDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAKGKPAVTRFHVLERFGDYS
LVELQLETGRTHQIRVHMAYIGHSVAGDEVYGPRKTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFKE
PWRD-COOH
Deposited materials
A deposit containing a
Streptococcus pneumoniae
0100993 strain has been deposited with the National Collections of Industrial and Marine Bacteria Ltd. (herein “NCIMB”), 23 St. Machar Drive, Aberdeen AB2 1RY, Scotland on 11 April 1996 and assigned deposit number 40794. The deposit was described as
Streptococcus pneumoniae
0100993 on deposit.
On 17 April 1996 a
Streptococcus pneumoniae
0100993 DNA library in
E. coli
was similarly deposited with the NCIMB and assigned deposit number 40800. The
Streptococcus pneumoniae
strain deposit is referred to herein as “the deposited strain” or as “the DNA of the deposited strain.”
The deposited strain contains a full length YfiI pseudouridine synthase gene. The sequence of the polynucleotides contained in the deposited strain, as well as the amino acid sequence of any polypeptide encoded thereby, are controlling in the event of any conflict with any description of sequences herein
The deposit of the deposited strain has been made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Mi
Chen Shin-Lin
Clark Deborah J. R.
Deibert Thomas S.
Gimmi Edward R.
King William T.
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