Structure and RNA-binding properties of the bacterial LSm protein Hfq

Abstract

Over the past years, small non-coding RNAs (sRNAs) emerged as important modulators of gene expression in bacteria. Guided by partial sequence complementarity, these sRNAs interact with target mRNAs and eventually affect transcript stability and translation. The physiological function of sRNAs depends on the protein Hfq, which binds sRNAs in the cell and promotes the interaction with their mRNA targets. This important physiological function of Hfq as a central hub of sRNA-mediated regulation made it one of the most intensely studied proteins in bacteria. Recently, a new model for sRNA binding by Hfq has been proposed that involves the direct recognition of the sRNA 3' end and interactions of the sRNA body with the lateral RNA-binding surface of Hfq. This review summarizes the current understanding of the RNA binding properties of Hfq and its (s)RNA complexes. Moreover, the implications of the new binding model for sRNA-mediated regulation are discussed.

Structural model of an mRNA in complex with the bacterial chaperone Hfq

“…4B, open circles). The smallest R g value of 58 ± 1 Å was reached at 1:1 rpoS:Hfq 6 (Fig. S4 E and F), at which concentration 95% of the RNA is expected to be bound with Hfq (24).…”

“…3B, red bars). When the (AAN) 4 , A 6 , and U 5 motifs were all mutated, expression of rpoS:: lacZ fusions was reduced a further 50% (compare Δ2 and Δ3 in Fig. S2 A and B), showing that the (AAN) 4 , A 6 , and U 5 motifs not only interact with different surfaces of Hfq, but also make distinct contributions to the regulation of rpoS translation by sRNAs and Hfq.…”

“…If the distal face of Hfq binds the upstream (AAN) 4 motif while the lateral rim interacts with the downstream U 5 motif, Hfq binding likely alters the tertiary conformation of the rpoS mRNA. To test that hypothesis, we used SAXS to compare the global shape of free rpoS RNA and the rpoS•Hfq complex in solution, at molar ratios from 1:0.5 to 1:3 RNA:Hfq 6 (Fig. 4).…”

“…Hfq belongs to the Sm/Lsm protein family (5) and recognizes diverse RNA targets by three distinct RNA binding surfaces (6). The distal face of the Sm ring binds AAN triplets (7,8) present in many mRNA targets of sRNA regulation (9).…”

Inhibition of Phagocytic Killing of Escherichia coli in Drosophila Hemocytes by RNA Chaperone Hfq

“…A protein called the host factor required for phage Qb RNA replication (Hfq) forms a complex with a variety of small noncoding RNAs and facilitates their binding to target mRNAs (7)(8)(9)(10)(11)(12)(13). Hfq of Escherichia coli is a protein of 102 aa residues, and its orthologs exist in a number of Gram-negative and -positive bacteria constituting the Hfq family of proteins (14)(15)(16)(17). Hfq has been shown to play a role in the virulence of uropathogenic E. coli (18) and other bacterial species (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35).…”