  The formation mechanism of operons remains controversial despite the proposal
of many models. Although acquisition of genes from other species, horizontal
gene transfer, is considered to occur, definitive concrete cases have been
unavailable. It is desirable to select horizontally transferred genes reliably
and examine their relationship to operons. We here developed a method to
identify candidates of horizontally transferred genes based on minimization of
gene cluster insertions/deletions. To select a benchmark set of positively
horizontally transferred genes against which the candidate set can be
appraised, we devised another procedure using intergenetic alignments.
Comparison with the benchmark set of horizontally transferred genes
demonstrated the absence of a significant number of false positives in the
candidates, showing that the method identifies horizontally transferred genes
with a high degree of confidence. Horizontally transferred genes constitute at
least 5.5% of the genes in Escherichia, Shigella, and Salmonella and ~46% of
which originate from other gamma-proteobacteria. Not only informational genes,
but also operational genes (those involved in housekeeping) are horizontally
transferred less frequently than expected. A gene-cluster analysis of
Escherichia coli K-12 operons revealed that horizontal transfer produced four
entire operons and expanded two operons, but deletion of intervening genes
accounts for the formation of no operons. We propose that operons generally
form by horizontal gene transfer. We further suggest that genes with related
essential functions tend to reside in conserved operons, while genes in
nonconserved operons generally confer slight advantage to the organisms and
frequently undergo horizontal transfer and decay.
