An evolutionary perspective on gene regulation in bacteria

Genome-wide measurements of transcriptional activity in bacteria
indicate that the transcription of successive genes is strongly
correlated beyond the scale of operons. I will present an analysis of
hundreds of bacterial genomes to identify supra-operonic segments of
genes that are proximal in a large number of genomes. The synteny
segments that it yields correspond to genomic units of strong
transcriptional co-expression. Structurally, the segments contain
operons with specific relative orientations (co-directional or
divergent) and nucleoid-associated proteins are found to bind at their
boundaries. Functionally, operons inside a same segment are highly
co-expressed even in the absence of regulatory factors at their
promoter regions. Remote operons along DNA can also be co-expressed if
their segments share a transcriptional or sigma factor, without
requiring these factors to bind directly to the promoters of the
operons. As evidence that these results apply across the bacterial
kingdom, I will demonstrate them both in the Gram-negative bacterium
Escherichia coli and in the Gram-positive bacterium Bacillus subtilis.
The underlying process that we propose involves only RNA-polymerases
and DNA: it implies that the transcription of an operon mechanically
enhances the transcription of adjacent operons. In support for a
primary role of this regulation by facilitated co-transcription, I
will show that transcriptional read-through, the transcription of
successive operons in one go, is strongly and specifically enhanced in
synteny segments. Finally, the analysis indicates that facilitated
co-transcription may be evolutionary primitive and may apply beyond
bacteria.