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
1997-08-22
2003-01-07
Ketter, James (Department: 1632)
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Recombinant dna technique included in method of making a...
C435S252300, C435S320100, C435S325000, C536S023100, C536S023500
Reexamination Certificate
active
06503729
ABSTRACT:
BACKGROUND OF THE INVENTION
1. Field of the Invention
The present application discloses the complete 1.66-megabase pair genome sequence of an autotrophic archaeon,
Methanococcus jannaschii,
and its 58- and 16-kilobase pair extrachromosomal elements. Also identified are 1738 predicted protein-coding genes.
2. Related Background Art
The view of evolution in which all cellular organisms are in the first instance either prokaryotic or eukaryotic was challenged in 1977 by the finding that on the molecular level life comprises three primary groupings (Fox, G. E., et al.,
Proc. Natl. Acad. Sci. USA
74:4537 (1977); Woese, C. R. & Fox, G. E.,
Proc. Natl. Acad. Sci. USA
74:5088 (1977); Woese, C. R., et al.,
Proc. Natl.,Acad. Sci. USA
87:4576 (1990)): the eukaryotes (Eukarya) and two unrelated groups of prokaryotes, Bacteria and a new group now called the Archaea. Although Bacteria and Archaea are both prokaryotes in a cytological sense, they differ profoundly in their molecular makeup (Fox, G. E., et al.,
Proc. Natl. Acad. Sci. USA
74:4537 (1977); Woese, C. R. & Fox, G. E.,
Proc. Natl. Acad. Sci. USA
74:5088 (1977); Woese, C. R., et al.,
Proc. Natl.,Acad. Sci. USA
87:4576 (1990)). Several lines of molecular evidence even suggest a specific relationship between Archaea and Eukarya (Iwabe, N., et al.,
Proc. Natl. Acad. Sci. USA
86:9355 (1989); Gogarten J. P., et al.,
Proc. Natl. Acad; Sci. USA
86:6661 (1989); Brown, J. R. and Doolittle, W. F.,
Proc. Natl. Acad. Sci. USA
92:2441 (1995)).
The era of true comparative genomics has been ushered in by complete genome sequencing and analysis. We recently described the first two complete bacterial genome sequences, those of
Haemophilus influenzae
and
Mycoplasma genitalium
(Fleischmann, R. D., et al.,
Science
269:496 (1995); Fraser, C. M., et al.,
Science
270:397 (1995)). Large scale DNA sequencing efforts also have produced an extensive collection of sequence data from eukaryotes, including
Homo sapiens
(Adams, M. D., et al.,
Nature
377:3 (1995)) and
Saccharomyces cerevisiae
(Levy, J.,
Yeast
10:1689 (1994)).
M. jannaschii
was originally isolated by J. A. Leigh from a sediment sample collected from the sea floor surface at the base of a 2600 m deep “white smoker” chimney located at 21
o
N on the East Pacific Rise (Jones, W., et al.,
Arch. Microbiol.
136:254 (1983)).
M. jannaschii
grows at pressures of up to more than 500 atm and over a temperature range of 48-94° C., with an optimum temperature near 85° C. (Jones, W., et al.,
Arch. Microbiol.
136:254 (1983)). The organism is autotrophic and a strict anaerobe; and, as the name implies, it produces methane. The dearth of archaeal nucleotide sequence data has hampered attempts to begin constructing a comprehensive comparative evolutionary framework for assessing the molecular basis of the origin and diversification of cellular life.
SUMMARY OF THE INVENTION
The present invention is based on whole-genome random sequencing of an autotrophic archaeon,
Methanococcus jannaschii
. The
M. jannaschii
genome consists of three physically distinct elements: (i) a large circular chromosome; (ii) a large circular extrachromosomal element (ECE); and (iii) a small circular extrachromosomal element (ECE). The nucleotide sequences generated, the
M. jannaschii
chromosome, the large ECE, and the small ECE, are respectively provided as SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3.
The present invention is further directed to isolated nucleic acid molecules comprising open reading frames (ORFs) encoding
M. jannaschii
proteins. The present invention also relates to variants of the nucleic acid molecules of the present invention, which encode portions, analogs or derivatives of
M. jannaschii
proteins. Further embodiments include isolated nucleic acid molecules comprising a polynucleotide having a nucleotide sequence at least 90% identical, and more preferably at least 95%, 96%, 97%, 98% or 99% identical, to the nucleotide sequence of a
M. jannaschii
ORF described herein.
The present invention also relates to recombinant vectors, which include the isolated nucleic acid molecules of the present invention, host cells containing the recombinant vectors, as well as methods for making such vectors and host cells for
M. jannaschii
protein production by recombinant techniques.
The invention further provides isolated polypeptides encoded by the
M. jannaschii
ORFs. It will be recognized that some amino acid sequences of the polypeptides described herein can be varied without significant effect on the structure or function of the protein. If such differences in sequence are contemplated, it should be remembered that there will be critical areas on the protein which determine activity. In general, it is possible to replace residues which form the tertiary structure, provided that residues performing a similar function are used. In other instances, the type of residue may be completely unimportant if the alteration occurs at a non-critical region of the protein.
In another aspect, the invention provides a peptide or polypeptide comprising an epitope-bearing portion of a polypeptide of the invention. The epitope-bearing portion is an immunogenic or antigenic epitope useful for raising antibodies.
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Brown, J.R., and Doolittle, W.F., “Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications,”Proc. Natl. Acad. Sci. USA 92:2441-2445 (Mar. 1995).
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Eberhart, C.G., and Wasserman, S.A., “The pelota locus encodes a protein required for meiotic cell division: an analysis of G2/M arrest in Drosophila spermatogenesis,”Development 121:3477-3486 (Oct. 1995).
Faguy, D.M., et al, “Molecular analysis of archaeal flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria,”Can. J. Microbiol. 40:67-71 (1994).
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Gogarten, J.P., et al., “Evaluation of the vacuolar H+-ATPase: Implications for the origin of eukaryotes,”Proc. Natl. Acad. Sci. USA 86:6661-6665 (1989).
Hamilton, P.T., and Reeve, J.N., “Structure of genes and an insertion element in the methane producing archaebacteriumMethanobrevibacter smithii,” Mol. Gen. Genet. 200:47-59 (1985).
Hartmann, E., and König, H., “Uridine and dolichyl diphosphate oligosaccharides are intermediates in the biosythesis of the S-layer glycoprotein ofMethanothermus fervidus,” Arch. Microbiol. 151:274-282 (1989).
Hirta, R., et al., “Molecular Structure of a Gene, VMA1, Encoding the Catalytic Subunit of H+-Translocating Adenosine Triphosphate from Vacuolar Membranes ofSaccharomyces cerevisiae,” J. Biol. Chem. 265(12):6726-6733 (1990).
Iwabe, N., et al., “Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated gen
Bult Carol J.
Smith Hamilton O.
Venter J. Craig
White Owen R.
Woese Carl R.
Ketter James
Schnizer Richard
The Board of Trustees of the University of Illinois
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