Polyphosphate drives bacterial heterochromatin formation.

Area of Science:

• Bacterial epigenetics
• Chromatin structure
• Molecular biology

Background:

• Heterochromatin, typically found in eukaryotes, also exists in bacteria as densely protein-occupied DNA regions that silence genes.
• The nucleoid-associated protein Hfq is a known silencing factor, though its DNA binding appears nonspecific.
• Hfq is notably enriched in AT-rich regions, common in prophages and mobile genetic elements.

Purpose of the Study:

• To investigate the role of polyphosphate (polyP) in the DNA binding specificity of bacterial Hfq.
• To understand how polyP influences gene silencing and genome stability in bacteria.

Main Methods:

• In vitro reconstitution of Hfq-polyP-DNA interactions.
• Analysis of Hfq DNA binding profiles in the presence and absence of polyP.
• Assessment of prophage/transposon mobilization, mutagenesis rates, and cell death.

Main Results:

• Polyphosphate (polyP) is essential for Hfq's site-specific DNA binding to AT-rich sequences.
• Absence of polyP leads to altered Hfq DNA binding, increased prophage and transposon mobilization, higher mutagenesis, and enhanced DNA damage-induced cell death.
• Hfq and polyP form phase-separated condensates on AT-rich DNA, mediated by Hfq's disordered C-terminal extensions.

Conclusions:

• Polyphosphate (polyP) is a critical factor in bacterial heterochromatin formation.
• PolyP directs Hfq to specific DNA sites, influencing genome stability and gene expression in bacteria.