Methods for screening bacteria, archaea, algae, and yeast using CRISPR nucleic acids

A method of killing a wild-type bacterial cell having a functional endogenous Cascade-Cas3 CRISPR system within a population of bacterial cells, comprising:

• introducing into the population of bacterial cells a heterologous nucleic acid construct comprising a Cascade-Cas3 CRISPR array (crRNA, crDNA) comprising (5′ to 3′) a repeat-spacer-repeat sequence or a repeat-spacer sequence,
• wherein the spacer of said repeat-spacer-repeat sequence or said repeat-spacer sequence comprises a nucleotide sequence that is 100% complementary to a target sequence of the wild-type bacterial cell, the target sequence having at least 10 consecutive nucleotides adjacent to a protospacer-adjacent motif (PAM) recognized by the functional endogenous Cascade-Cas3 CRISPR system,
• thereby killing the wild-type bacterial cell within the population of bacterial cells;
• provided that the following are not introduced into the population of bacterial cells:
• (a) an exogenous Cas3 polypeptide that recognizes a complex of Cascade and the Cascade-Cas3 CRISPR array, and an exogenous nucleic acid construct encoding said exogenous Cas3 polypeptide;
• and
• (b) an exogenous Cascade polypeptide that recognizes the Cascade-Cas3 CRISPR array, and an exogenous nucleic acid construct encoding said Cascade polypeptide.