An Hfq-like protein in archaea: Crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii

Abstract

The Sm and Sm-like proteins are conserved in all three domains of life and have emerged as important players in many different RNA-processing reactions. Their proposed role is to mediate RNA-RNA and/or RNA-protein interactions. In marked contrast to eukaryotes, bacteria appear to contain only one distinct Sm-like protein belonging to the Hfq family of proteins. Similarly, there are generally only one or two subtypes of Sm-related proteins in archaea, but at least one archaeon, Methanococcus jannaschii, encodes a protein that is related to Hfq. This archaeon does not contain any gene encoding a conventional archaeal Sm-type protein, suggesting that Hfq proteins and archaeal Sm-homologs can complement each other functionally. Here, we report the functional characterization of M. jannaschii Hfq and its crystal structure at 2.5 Å resolution. The protein forms a hexameric ring. The monomer fold, as well as the overall structure of the complex is similar to that found for the bacterial Hfq proteins. However, clear differences are seen in the charge distribution on the distal face of the ring, which is unusually negative in M. jannaschii Hfq. Moreover, owing to a very short N-terminal a-helix, the overall diameter of the archaeal Hfq hexamer is significantly smaller than its bacterial counterparts. Functional analysis reveals that Escherichia coli and M. jannaschii Hfqs display very similar biochemical and biological properties. It thus appears that the archaeal and bacterial Hfq proteins are largely functionally interchangeable.

The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp. PCC 6803

“…In contrast, no apparent phenotype emerged from an hfq knockout in Staphylococcus aureus (Bohn et al, 2007). Although not all eubacterial genomes encode an Hfq protein, an Hfq-like protein has recently been identified in Archaea (Nielsen et al, 2007). Importantly, although this Methanocaldococcus jannaschii protein differs from the well-characterized eubacterial Hfq proteins in length and amino acid sequence, it does restore complex phenotypes to an E. coli hfq deletion strain (Nielsen et al, 2007).…”

The Sinorhizobium meliloti RNA Chaperone Hfq Mediates Symbiosis of S. meliloti and Alfalfa

“…Hfq is a member of the Sm and Sm-like family of proteins found in all three domains of life (45) and forms a homohexameric structure that binds preferentially to A/U-rich RNAs (reviewed in references 6 and 67). Hfq serves as posttranscriptional regulator that binds small RNAs (sRNA) and mRNAs and facilitates their interaction (1,22,37,60).…”

Structure of anEscherichia coliHfq:RNA complex at 0.97 Å resolution

“…Since A-rich sequences are common in mRNAs while U-rich sequences are present at the 3 0 -end of most sRNAs, it is believed that Hfq binds simultaneously to an sRNA and an mRNA and thereby facilitates their pairing. Crystal structures of Hfq from several Gram-positive and Gram-negative bacteria, including Escherichia coli, have already been presented in the literature (Schumacher et al, 2002;Sauter et al, 2003;Nikulin et al, 2005;Nielsen et al, 2007;Bøggild et al, 2009;Link et al, 2009;Baba et al, 2010;Moskaleva et al, 2010;Beich-Frandsen, Večerek, Konarev et al, 2011;Sauer & Weichenrieder, 2011;Kadowaki et al, 2012;Someya et al, 2012;Wang et al, 2013;Yonekura et al, 2013;Robinson et al, 2014). Recent structural studies on Salmonella typhimurium Hfq also revealed RNA binding to the proximal binding site of Hfq and demonstrated that the free 3 0 -hydroxyl group at the end of the RNA is critical for RNA binding and 3 0 -end recognition (Sauer & Weichenrieder, 2011).…”