The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment

Abstract

The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.

The Amyloid Region of Hfq Riboregulator Promotes DsrA:rpoS RNAs Annealing

“…We also chose to avoid the addition of salts (except those already present in RNA, protein, and peptide solutions) in order to allow a better investigation in deep-UV [ 45 ]. When the complex is analyzed in the presence of salts (or far-UV absorbing buffers), the spectral bandwidth accessible is limited, reducing the spectral information obtained [ 67 ]. We checked that presence of salts (NaCl 50 mM) does not change significantly the kinetics of annealing.…”

Apomorphine Targets the Pleiotropic Bacterial Regulator Hfq

“…Hfq-CTR peptide (SRPVSHHSNNAGGGTSSNYHHGSSAQNTSAQQDSEETE) was chemically synthetized and prepared as described previously in Partouche et al [ 28 ]. DNA-induced fibrillation was described previously in [ 32 , 50 , 51 ]. As salts, pH and temperature may influence the stability of amyloid self-assembly [ 52 ], we first check if our fibers are stable in our experimental conditions.…”

Probing amyloid fibril secondary structures by infrared nanospectroscopy: experimental and theoretical considerations

“…45 This region is required for Hfq to form a membrane-associated coiled structure. 46 Unfortunately there is no high-resolution structure of this part of Hfq, only information based on infrared analysis of a solution that contains different aggregated species (from oligomers to fibrils). Unlike pathologic amyloid fibrils, Hfq amyloid structures appear only in vitro at a high concentration and the concentration of Hfq amyloid fibrils decreases with dilution.…”