Genes identified as required for proliferation in Escherichia coli
First Claim
1. A method of screening a candidate compound for the ability to reduce the activity or level of a gene product required for cell proliferation, said method comprising the steps of:
- expressing an antisense nucleic acid against a nucleic acid encoding said gene product in a cell to reduce the activity or amount of said gene product in said cell, thereby producing a sensitized cell;
contacting said sensitized cell with a candidate compound, wherein said candidate compound is not previously known to possess the ability to reduce cell proliferation; and
determining whether said candidate compound inhibits the growth of said sensitized cell to a greater content than said candidate compound inhibits the growth of a nonsensitized cell.
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Accused Products
Abstract
The sequences of nucleic acids encoding proteins required for E. coli proliferation are disclosed. The nucleic acids can be used to express proteins or portions thereof, to obtain antibodies capable of specifically binding to the expressed proteins, and to use those expressed proteins as a screen to isolate candidate molecules for rational drug discovery programs. The nucleic acids can also be used to screen for homologous genes that are required for proliferation in microorganisms other than E. coli. The nucleic acids can also be used to design expression vectors and secretion vectors. The nucleic acids of the present invention can also be used in various assay systems to screen for proliferation required genes in other organisms as well as to screen for antimicrobial agents.
81 Citations
49 Claims
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1. A method of screening a candidate compound for the ability to reduce the activity or level of a gene product required for cell proliferation, said method comprising the steps of:
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expressing an antisense nucleic acid against a nucleic acid encoding said gene product in a cell to reduce the activity or amount of said gene product in said cell, thereby producing a sensitized cell;
contacting said sensitized cell with a candidate compound, wherein said candidate compound is not previously known to possess the ability to reduce cell proliferation; and
determining whether said candidate compound inhibits the growth of said sensitized cell to a greater content than said candidate compound inhibits the growth of a nonsensitized cell. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A method of screening a candidate compound for the ability to inhibit proliferation of a microorganism said method comprising:
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(a) identifying a gene or gene product required for proliferation in a first microorganism;
(b) identifying a homolog of said gene or gene product in a second microorganism;
(c) identifying an inhibitory nucleic acid sequence which inhibits the activity of said homolog in said second microorganism;
(d) contacting said second microorganism with a proliferation-inhibiting amount of said inhibitory nucleic acid, thus sensitizing said second microorganism, (e) contacting the sensitized microorganism of step (d) with a candidate compound; and
(f) determining whether said candidate compound inhibits proliferation of said sensitized microorganism to a greater extent than said candidate compound inhibits proliferation of a nonsensitized microorganism. - View Dependent Claims (15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25)
introducing a nucleic acid comprising a random genomic fragment from said first microorganism operably linked to a promoter wherein said random genomic fragment is in the antisense orientation; and
comparing the proliferation of said first microorganism transcribing a first level of said random genomic fragment to the proliferation of said first microorganism transcribing a lower level of said random genomic fragment, wherein a difference in proliferation indicates that said random genomic fragment comprises a gene involved in proliferation.
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16. The method of claim 15, wherein said step of identifying a homolog of said gene is a second microorganism comprises identifying a homologous nucleic acid or a nucleic acid encoding a homologous polypeptide in a database using an algorithm selected from the group consisting of BLASTN version 2.0 with the default parameters and FASTA version 3.0t78 algorithm with the default parameters.
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17. The method of claim 15, wherein said step of identifying a homolog of said gene in a second microorganism comprises identifying a homologous nucleic acid or a nucleic acid encoding a homologous polypeptide by identifying nucleic acids which hybridize to said first gene.
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18. The method of claim 15, wherein the step of identifying a homolog of said gene in a second microorganism comprises expressing a nucleic acid which inhibits the proliferation of said first microorganism in said second microorganism.
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19. The method of claim 15, wherein said inhibitory nucleic acid is an antisense nucleic acid.
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20. The method of claim 15, wherein said inhibitory nucleic acid comprises an antisense nucleic acid to a portion of said homolog.
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21. The method of claim 15, wherein said inhibitory nucleic acid comprises an antisense nucleic acid to a portion of the operon encoding said homolog.
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22. The method of claim 15, wherein the step or contacting the second microorganism with a proliferation-inhibiting amount of said nucleic acid sequence comprises directly contacting said second microorganism with said nucleic acid.
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23. The method of claim 15, wherein the step of contacting the second microorganism with a proliferation-inhibiting amount of said nucleic acid sequence comprises expressing all antisense nucleic acid to said homolog in said second microorganism.
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24. The method of claim 14, wherein said candidate compound is a compound not previously known to possess the ability to inhibit cellular proliferation.
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25. The method of claim 14, wherein said candidate compound is a natural product.
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26. A method of screening a candidate compound for the ability to inhibit proliferation said method comprising:
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(a) identifying an inhibitory nucleic acid sequence which inhibits the activity of a gene or gene product required for proliferation in a first microorganism;
(b) contacting a second microorganism with a proliferation-inhibiting amount of said inhibitory nucleic acid, thus sensitizing said second microorganism;
(c) contacting the proliferation-inhibited microorganism of step (b) with a candidate compound; and
(d) determining whether said candidate compound inhibits proliferation of said sensitized second microorganism to a greater extent than said candidate compound inhibits proliferation of a nonsensitized second microorganism. - View Dependent Claims (27, 28, 29, 30, 31, 32)
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33. A method of screening a candidate compound for activity against a biological pathway required for proliferation, said method comprising:
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sensitizing a cell by expressing an antisense nucleic acid against a nucleic acid encoding a gene product required for proliferation in a cell to reduce the activity or amount of said gene product;
contacting the sensitized cell with a candidate compound, wherein said candidate compound is not previously known to possess the ability to reduce proliferation; and
determining whether said candidate compound inhibits the growth of said sensitized cell to a greater extent than said candidate compound inhibits the growth of an nonsensitized cell. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41, 42, 43)
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44. A method of screening a candidate compound for the ability to inhibit cellular proliferation, said method comprising:
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contacting a cell with an agent which reduces the activity or level of a gene product required for proliferation of said cell;
contacting said cell with a candidate compound, wherein said candidate compound is not previously known to possess the ability to reduce cell proliferation; and
determining whether said candidate compound reduces proliferation to a greater extent than said candidate compound reduces proliferation of a cell which has not been contacted with said agent. - View Dependent Claims (45, 46, 47, 48, 49)
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Specification