trmD

Details trmD trmD

2000-07-28

2002-02-26

Achutamurthy, Ponnathapu (Department: 1652)

Chemistry: molecular biology and microbiology

Enzyme , proenzyme; compositions thereof; process for...

C514S012200

Reexamination Certificate

active

06350600

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 trmD (tRNA methyl transferases) family, as well as their variants, herein referred to as “trmD,” “trmD polynucleotide(s),” and “trmD 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,
Steptococcus 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 Streptococcus 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
Steptococcus pneumoniae
strains that are resistant to some or all of the standard antibiotics. This phenonenon has created an unmet medical need and demand for new antimicrobial agents, vaccines, drug screening methods, and diagnostic tests for this organism.
Moreover, the drug discovery process is curreny undergoing a fundamental revolution as it embraces “functional genomics,” that is, high throughput genome- or gene-based biology. This approach is rapidiy soperseding earlier approaches based on “positional cloning” and other methods. Functional genomics relies heavily on the various tools of bioinformatics to identify gene sequences of interest from the many molecular biology databases now available as well as from other sources. The is a continuing an 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 trmD 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 charaction of such factors and their antagonist and agonist to find ways to prevent, ameliorate or correct such infection, dysfunction and disease.
SUMMARY OF THE INVENTION
The present invention relates to trmD, in particular trmD polypeptides and trmD 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 trmD expression or activity.
Various changes and modifications with in 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 trmD polypeptides and polynucleotides as described in greater detail below. In particular, the invention relates to polypeptides and polynucleotides of a trmD of
Streptococcus pneumoniae
, that is related by amino acid sequence homology to
B. subtilis
trmD polypeptide. The invention relates especially to trmD 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.
TABLE 1
trmD Polynucleotide and Polypeptide Sequences
(A)
Streptococcus pneumoniae
trmD polynucleotide sequence
[SEQ ID NO:1].
5′-
atgaagattgatattttaaccctctttccagagatgttttctccactggagcactcaatcgttggaaaggct
cgagaaaa
agggctcttggatatccagtatcataattttcgagaaaatgctgaaaaggcccgtcatgtagatgatgagcc
ctacggag
gcggtcagggcatgttgctcagagcacaacctattttcaattcctttgatgctattgaaaagaaaaatccgc
gcgttatt
ctcctcgatcctgctggaaagcagtttgatcaggcttatgctgaagatttggctcaagaggaagagctaatc
tttatctg
tgggcactatgagggttatgatgagcgcattaagaccttggtaacagatgagatttccctaggcgactatgt
cctcactg
gtggagaattggcagctatgaccatgattgatgctacagttcgcctgattccagaagtgattggcaaggagt
ctagccac
caagatgatagtttttcttcaggtcttttagaatatcctcagtacacacgtccctatgattatcgaggcatg
gtcgtgcc
agatgtattgatgagtggccaccatgaaaagattcgtcagtggcgattgtacgagagtttaaagaaaaccta
cgagcgca
gaccagatttacttgaacattatcaactgacagtagaagaagaaaaaatgctggcagaaatcaaagaaaaca
aagaataa
-3′

(B)
Streptococcus pneumoniae
trmD polypeptide sequence deduced from a
polynucleotide sequence in this table[SEQ ID NO:2].

NH
2
-
MKIDILTLFPEMFSPLEHSIVGKAREKGLLDIQYHNFRENAEVDDEPYGGGQGMLL
RAQPIFNSFDAIEKKNPRVI
LLDPAGKQFDQAYAEDLAQEEELIFICGHYEGYDERIKTLVTDEISLGDYVLTGGELAAM
TMIDATVRLIPEVIGKESSH
QDDSFSSGLLEYPQYTRPYDYRGMVVPDVLMSGHHEKIRQWRLYESLKKTYERRPDLLEH
YQLTVEEEKMLAEIKENKE
-COOH
Deposited Materials
A deposit comprising 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 Apr. 11, 1996 and assigned deposit number 40794. The deposit was described as
Streptococcus pneumoniae
0100993 on deposit.
On Apr. 17, 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 comprises a full length trmD gene. The sequence of the polynucleotides comprised 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 Micro-oganism for Purposes of Patent Procedure. The deposited strain will be irrevocably and without restriction or condition released to the public upon the issuance of a patent. The deposited strain is provided merely as convenience to those of skill in the art and is not an admission that a deposit is required for enablement, such as that required under 35 U.S.C. §112. A license may be required to make, use or sell the deposited strain, and compounds derived therefrom, and no such license is hereby granted.
In one aspect of the invention there is provided an isolated nucleic acid molecule encoding a mature polypeptide expressible by the
Streptococcus pneumoniae
0100993 stain, which polypeptide is comprised in the deposited strain. Further provided by the invention are trmD polynucleotide

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