Myths and mechanisms: RecBCD and Chi hotspots as determinants of self vs. non-self

Abstract

Bacteria face a challenge when DNA enters their cells by transformation, mating, or phage infection. Should they treat this DNA as an invasive foreigner and destroy it, or consider it one of their own and potentially benefit from incorporating new genes or alleles to gain useful functions? It is frequently stated that the short nucleotide sequence Chi (5 GCTGGTGG 3) recognized by RecBCD helicase-nuclease allows Escherichia coli to distinguish self (i.e., E. coli) DNA from non-self (i.e., any other) DNA and to destroy non-self DNA, and that Chi is "over-represented" in the E. coli genome. We show here that these dogmas are incorrect and apparently based on false assumptions. We note Chis wide-spread occurrence and activity in distantly related species. We illustrate multiple, highly non-random features of the genomes of coli and coliphage P1 that account for Chis high frequency and genomic position, leading us to propose that P1 selects for Chis enhancement of recombination, whereas E. coli selects for the preferred codons in Chi. We discuss other, substantiated mechanisms for self vs. non-self determination involving RecBCD and for RecBCDs destruction of DNA that cannot recombine, whether foreign or domestic.