Bacteria with reduced genome

Chemistry: molecular biology and microbiology – Micro-organism – per se ; compositions thereof; proces of... – Bacteria or actinomycetales; media therefor

Reexamination Certificate

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C435S440000

Reexamination Certificate

active

08043842

ABSTRACT:
The present invention provides a bacterium having a genome that is genetically engineered to be at least 2 to 14% smaller than the genome of its native parent strain. A bacterium with a smaller genome can produce a commercial product more efficiently. The present invention also provides methods for deleting genes and other DNA sequences from a bacterial genome. The methods provide precise deletions and seldom introduces mutations to the genomic DNA sequences around the deletion sites. Thus, the methods can be used to generate a series of deletions in a bacterium without increasing the possibility of undesired homologous recombination within the genome. In addition, some of the methods provided by the present invention can also be used for replacing a region of a bacterial genome with a desired DNA sequence.

REFERENCES:
patent: 4851348 (1989-07-01), Hanahan
patent: 4981797 (1991-01-01), Jessee et al.
patent: 5578464 (1996-11-01), Lunn et al.
patent: 5747662 (1998-05-01), Simmons et al.
patent: 5824502 (1998-10-01), Honjo et al.
patent: 5962327 (1999-10-01), Dujon et al.
patent: 6015709 (2000-01-01), Natesan
patent: 6022952 (2000-02-01), Weiner et al.
patent: 6117680 (2000-09-01), Natesan et al.
patent: 6238924 (2001-05-01), Dujon et al.
patent: 6335178 (2002-01-01), Weiner et al.
patent: 6372476 (2002-04-01), Belguith et al.
patent: 6410273 (2002-06-01), Crouzet et al.
patent: 6509156 (2003-01-01), Stewart et al.
patent: 6989265 (2006-01-01), Blattner et al.
patent: 2003/0138937 (2003-07-01), Blattner et al.
patent: 2005/0032225 (2005-02-01), Blattner et al.
patent: 0177343 (1986-04-01), None
patent: 0283726 (1988-09-01), None
patent: WO 96/14408 (1976-05-01), None
patent: WO 88/05821 (1988-08-01), None
patent: WO 01/27258 (2001-04-01), None
patent: WO 02/14495 (2002-02-01), None
patent: WO 03/048374 (2003-06-01), None
patent: WO 03/070880 (2003-08-01), None
patent: WO 2005/087940 (2005-08-01), None
Smalley et al, Trends in Microbiology, 11, (1), 6-8, 2003).
Asai et al., “AnEscherichia colistrain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria,”Proc. Natl. Acad. Sci., USA, 96:1971-1976, 1999.
Balbas, “Understanding the art of producing protein and non-protein molecules inE. coli,”Molec Biotechnol., 19:251-267, 2001.
Baneyx, “Recombinant protein expression inE. coli,”Curr Opin Biotech, 10:411-421, 1999.
Bass et al., “Multicopy suppressors of Prc mutangEscherichia coliinclude two HtrA (DegP) protease homologs (HhoAB), DksA, and a truncated RlpA,”Journal of Bacteriology, 178(4):1154-1164, 1996.
Beaulieu et al., “Pathogenic behavior of pectinase-defectiveErwinia chrysanthemimutants on different plants,”MPMI, 6(2):197-202, 1993.
Berry et al., “Application of metabolic engineering to improve both production and use of biotech indigo,”J Indust Micro&Biotech, 22:127-133, 2002.
Blattner et al., “The complete genome sequence ofEscherichia coliK-12,”Science, 277:1453-1474, 1997.
Blaudeck et al., “Specificity of single peptide recognition in TAT-dependent bacterial protein translocation,”J. Bacteriology, 183:604-610, 2001.
Court et al., “Genetic engineering using homologous recombination,”Annu Rev Genet, 36:361-388, 2002.
Current Protocols in Molecular Biology, 16.6.1-16.6.14, John Wiley and Sons, 1994.
Danese et al., “Targeting and assembly of periplasmic and outer-membrane proteins inEscherichia coli,”Annu Rev Genet, 32:59-64, 1998.
Datsenko et al., “One-step inactivation of chromosomal genes inEscherichis coliK-12 using PCR products,”Proc. Natl. Acad. Sci., USA, 97:6640-6649, 2000.
Degryse, “Evaluation ofEscherichia colirecBC sbcBC mutants for cloning by recombination in vivo,”J. Biotechnology, 39:181-187, 1995.
DeLisa et al., “Quorum sensing cia AI-2 communicates the metabolic burden associated with heterologous protein production inE. coli,”Biotech Bioeng, 75(4):439-450, 2001.
Dykstra and Kushner, “Physical characterization of the cloned protease III gene fromEscherichia coliK-12,”Journal of Bacteriology, 163(3): 1055-1059, 1985.
Eichhorn et al., “Deletion analysis of theEscherichia colitaurine and alkanesulfonate transport systems,”Journal of Bacteriology, 182(10)2687-2695, 2000.
Feher et al., “Engineering a reducedEscherichia coligenome,” Conference Abstract, Sep. 11, 2002.
Fekkes et al., “Protein targeting to the bacterial cytoplasmic membrane,”Microbiol. Mol. Biol. Rev., 63:161-193, 1999.
Gill et al., “A comparative study of global stress gene regulation in response to overexpression of recombinant proteins inE. coli,”Metabolic Engineering, 2:178-189, 2000.
Hanahan et al., “Studies on Transformation ofEscherichia coliwith plasmids,”J. Mol. Biol., 166(4):557-580, 1983.
Hannig, “Strategies for optimizing heterologous protein expression inEscherichia coli,”Trends Biotechnol., 16(2):54-60, 1998.
Hayashi et al., “Construction of a genetic linkage map of the model legumLotus japonicususing an intraspecific F2 population,”DNA Research, 8:11-22, 2001.
Hockney, “Recent developments in heterologous protein production inEscherichia coli,” Trends Biotechnol., 12(11):456-632, 1994.
Hynds et al., “The sec-independent twin-arginine translocation system can transport both tightly folded and malfolded proteins across the thylakoid membrane,”J. Biol. Chem., 273:34868-34874, 1998.
Kitamura, “DNA sequence changes in mutations in the ton B gene on the chromosome ofEscherichia coliK-12: insertion elements dominate the spontaneous spectra,,”Jpn J. Genet, 70:35-46, 1995.
Kolisnychenko et al., “Engineering a reducedEscherichia coligenome,”Genome Research, 12:640-647, 2002.
Koob et al., “Minimizing the genome ofEscherichia coli,” Ann NY Acad Science, 745:1-3, 1994.
Koonin, “How many genes can make a cell: the minimal-gene-set concept,”Ann Rev Genome Hum Genet, 1:99-116, 2000.
Lee, “High cell-density culture ofEscherichia coli,”TIBTECH, 14:98-103, 1996.
Murphy, “Use of bacteriophage λ recombination functions to promote gene replacement inEscherichia coli,” J. Bacteriol., 180:2063-2071, 1998.
Muyrers et al., “Rapid modification of bacterial artifical chromosomes by ET-recombination,”Nucleic Acids Research, 27:1555-1557, 1999.
Neidhardt et al., “Culture medium for Enterobacteria,”J. Bacteriol., 119:736-747, 1974.
Oliner et al., “In vivo cloning of PCR products inE. coli,” Nucleic Acids Research, 2(22):5192-5197, 1993.
Otto et al., “Surface sensing and adhesion ofE. colicontrolled by the Cpx-signaling pathway,”Proc. Natl. Acad. Sci., USA, 99(4):2287-2292, 2002.
Park et al., “MppA, a perplasmic binding protein essential for import of the bacterial cell wall peptide L-Ananyl-γ-D-glutamyl-meso-diaminopimelate,”Journal of Bacteriology, 180(5):1215-1223, 1998.
Perna et al., “Genome sequence of enterhemorrhagicEscherichia coliO157:H7,”Nature, 409:529-533, 2001.
Perna et al., “The genomes ofEscherichia coliK-12 and pathogenicE. coli,” Pathogenic E. coli Paradigm for Bacterial Pathogenesis, M.S. Donnenberg, Editor, Academmic Press, 2002.
Pfeifer et al., “Biosynthesis of complex polyketides in metabolically engineered strain ofE. coli,” 291:1790-1792, 2001.
Posfai et al., “In vivo excision and amplification of large segments of theEscherichis coligenome,”Nucleic Acids Research, 22(12):2392-2398, 1994.
Posfai et al., “Markerless gene replacement inEscherichia colistimulated by a double-strand break in the chromosome,”Nucleic Acids Research, 27:4409-4415, 1999.
Posfai et al., “Versatile insertion plasmids for targeted genome manipulations in bacteria: isolation, deletion, and rescue of the pathogenicity island LEE

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