Structure of the Escherichia coli ProQ RNA-binding protein

Abstract

The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.

ProQ/FinO‐domain proteins: another ubiquitous family of RNA matchmakers?

“…For E. coli ProQ, the structure of the N-terminal 121amino acid FinO-like domain was initially modeled based on that of FinO (Smith et al, 2004(Smith et al, , 2007. A recent NMR solution structure of the isolated N-terminal domain (residues 1-119) confirmed that its fold is similar to that of the central domain of FinO, again with multiple positively charged residues on the concave surface (Gonzalez et al, 2017). However, the convex side is more highly charged with distinct positive and negative patches (Fig.…”

“…Later it was compared with the Sm-like domain, and hence was termed Hfq-like, despite little sequence homology and the lack of the a-helix motif characteristic of Sm folds (Smith et al, 2007). Most recently, the NMR structure determined for the isolated C-terminal domain (residues 180-232) shows the tertiary structure is most similar to Tudor domains, which promote binding to proteins with modified amino acids (Gonzalez et al, 2017). Overall the surface of this domain is mostly electrostatically neutral.…”

“…Overall the surface of this domain is mostly electrostatically neutral. Given that the Tudor-like C-terminal domain is only shared among a subset of FinO-domain proteins, it has been suggested that it was acquired by horizontal gene transfer (Gonzalez et al, 2017). Alternatively, proQ might have arisen by gene duplication followed by independent domain evolution.…”

“…However, recent hydrogen deuterium exchange (HDX) studies indicated that most of the E. coli ProQ surface, including the FinO domain, linker and C-terminal domain, is involved in contacts with two RNAs, the sRNA SraB and the mRNA cspE. Interestingly, however, only certain locations on the FinO domain contributed to binding of both these RNAs (Gonzalez et al, 2017). The FinO domain of L. pneumophila RocC also bound the RocR sRNA more tightly than the intact RocC, consistent with a limited contribution of the C-terminal domain to RNA binding (Attaiech et al, 2016).…”

“…Glover and colleagues summarized much of what is known about FinO (reviewed in (Glover et al, 2015)). However, recent discoveries (Attaiech et al, 2016;Smirnov et al, 2016Smirnov et al, , 2017Gonzalez et al, 2017) have increased our understanding of the structure and functions of FinO-domain proteins, suggested broader contributions of these proteins to bacterial physiology and raised new questions about FinO-domain proteins, which we discuss here. While a unified nomenclature would simplify description of this family of proteins in the future, for now we will refer to the individual names resulting from the genetic screens.…”