Methods for attenuation of virulence in bacteria

A method of identifying a putative target for attenuation of pathogen virulence, the method comprising:

• (a) determining a codon usage frequency of one or more codon of a pathogen;
• (b) identifying at least one gene comprising one or more over-represented codon or one or more under-represented codon;
• (c) identifying a set of tRNA molecules responsible for interacting with the one or more over-represented codon or under-represented codon in the at least one gene during translation;
• (d) providing a population of nucleic acid sequences encoding a putative target for attenuation of pathogenic virulence and an in vitro or in vivo translation system;
• (e) altering a translation process involving one or more member of the set of tRNA molecules and the in vitro or in vivo translation system, thereby altering expression of at least one member of the population in (d);
• and,
• (f) testing for one or more effect of the altering, thereby identifying one or more putative target for attenuation of pathogen virulence.

A method of identifying virulence-related nucleic acid sequences in a pathogenic organism, the method comprising:

• (a) analyzing a population of nucleic acid sequences derived from the pathogenic organism and identifying one or more over-represented codons or under represented codons as compared to a nonpathogenic organism;
• (b) determining a distribution for at least one member of the one or more over-represented codons or under-represented codons;
• (c) selecting a subset of nucleic acid sequences from the population of nucleic acid sequences based upon the distribution of the over-represented or under-represented codons;
• and,
• (d) analyzing the subset of nucleic acid sequences for virulence activity, thereby identifying one or more virulence-related nucleic acid sequence in a pathogenic organism.

A method of regulating gene expression in a bacterial organism, the method comprising:

• (a) identifying one or more over-represented codons or under-represented codons within a set of nucleic acid sequences from a bacterial organism;
• (b) identifying at least one tRNA species responsible for encoding at least one of the one or more over-represented codons or under-represented codons;
• and,
• (c) modulating an expression or activity of the at least one tRNA species in the bacterial organism;
• thus, altering a translation of a nucleic acid sequence comprising the one or more over-represented or under-represented codons, thereby regulating the expression of one or more gene in the bacterial organism.

A method for selectively affecting one or more pathogenic organism in a population, the method comprising:

• (a) providing a first population comprising nucleic acid sequences from a pathogenic organism;
• (b) providing a second population comprising nucleic acid sequences from a nonpathogenic organism, which nonpathogenic organism comprises a same species as the pathogenic organism;
• (c) determining a distribution of codon usage in the pathogenic organism as compared to a distribution of a codon usage in the nonpathogenic organism;
• and,
• (d) selecting one or more codons that are over-represented or under-represented in the nucleic acid sequences of the pathogenic organism based upon the distribution of codon usage in the pathogenic organism and the nonpathogenic organism,
• (e) identifying at least one tRNA species responsible for encoding at least one selected codon, which selected codon comprises a codon that is over-represented or under-represented in the pathogenic organism relative to the nonpathogenic organism;
• and,
• (f) altering the expression or activity of the identified tRNA species, thereby selectively affecting the pathogenic organisms in the population.