Alladi Ramakrishnan Hall

Xenogene silencing, stress response and chromosome architecture in E. coli

Aswin Sai Narain Seshasayee

NCBS Bangalore

A significant proportion of a bacterial genome is predicted to have been acquired horizontally. In E.

coli and its relatives, these are under pressure to be maintained in a transcriptionally silent state in

standard growth conditions by a global gene regulatory system centred around a protein called H-
NS; de-silencing of these genes could lead to a strong disruption of gene expression homoeostasis.

This talk will discuss the effect of horizontal gene transfer on gene expression states, and whether

and how a bacterium can adapt to the disruption of their physiological regulation, as follows.

H-NS, a global transcription repressor, binds to A+T-rich sequence tracts, many of which are

horizontally-acquired, and keeps them transcriptionally silent. The talk will discuss genomic-scale

analysis showing that the A+T-rich sequences bound by H-NS are intrinsically capable of high gene

expression, which, as a cumulative increase in gene expression over ~20% of the genome, could

impose a high metabolic cost on the organism. The gene silencing function of H-NS is directed

towards the silencing of highly-transcribable genes at two intertwined levels: (a) sequence

specificity – H-NS binding motifs are more enriched in highly transcribable sequences; (b) co-
regulatory network structure – partial backup of H-NS function by StpA is directed towards highly

transcribable genes.

An indirect consequence of the disruption of the H-NS-centred gene silencing mechanism is the

down-regulation of transcription from a large number (10-12% of all genes) of otherwise highly-
expressed genes. Thus, de-silencing horizontally-acquired genes results in a global disruption of the

gene expression state of the cell. How does the cell adapt to such a circumstance, short of re-
acquiring the silencing system? This is an important consideration: as a regulator of horizontally-
acquired genes, H-NS targets different gene functions even across closely-related bacteria, making

its regulatory network dynamic, and subject to disruption by rampant horizontal gene acquisition.

Genome-scale experimental work in our laboratory has shown that two distinct evolutionary

strategies – inactivation of a replaceable component of the RNA polymerase (the σ38 σ-factor for

general stress response), as well as a well-structured duplication of ~40% of the genome centred

around the origin of replication – converge in partially redressing the transcriptional imbalance of a

strain lacking the gene silencing system. The direct effects and the indirect consequences of these

mutations appear to target distinct coordinates of the chromosome: stress-responsive and

horizontally-acquired genes are encoded around the terminus of replication, and the consequence of

their up-regulation being felt closer to the origin of replication, and vice-versa. This work

immediately presents an intriguing connection between the contrasting direct and indirect effects of

two distinct global regulatory systems and chromosome architecture.