FinO/ProQ-family proteins: an evolutionary perspective

Abstract

RNA-binding proteins are key actors of post-transcriptional networks. Almost exclusively studied in the light of their interactions with RNA ligands and the associated functional events, they are still poorly understood as evolutionary units. In this review, we discuss the FinO/ProQ family of bacterial RNA chaperones, how they evolve and spread across bacterial populations and what properties and opportunities they provide to their host cells. We reflect on major conserved and divergent themes within the family, trying to understand how the same ancestral RNA-binding fold, augmented with additional structural elements, could yield either highly specialised proteins or, on the contrary, globally acting regulatory hubs with a pervasive impact on gene expression. We also consider dominant convergent evolutionary trends that shaped their RNA chaperone activity and recurrently implicated the FinO/ProQ-like proteins in bacterial DNA metabolism, translation and virulence. Finally, we offer a new perspective in which FinO/ProQ-family regulators emerge as active evolutionary players with both negative and positive roles, significantly impacting the evolutionary modes and trajectories of their bacterial hosts.

Keywords: FinO; ProQ; RNA chaperone; RNA-binding proteins; evolution.

Figure 1. Characterised plasmid-encoded FinO/ProQ-family proteins

For each protein, schematic structures of its main RNA ligands and a representative molecular mechanism of translational repression are shown (see the main text for detailed descriptions). Note that fine structural details of the shown interactions are currently unknown. The FinP-traJ and Inc-repZ duplexes are likely partial, even though the interacting RNAs are fully complementary to each other. FinO and FopA are primarily associated with the cognate sRNAs and may dissociate upon duplex formation. The conserved elements of the FinO/ProQ domain in the crystal structure of FinO (amino acids 33–184) [22] are coloured in the same way as for other proteins shown in Figure 2 (see also Figure 3B,C for their annotation). The structure is shown from the RNA-binding concave face. The FinO protein also has a disordered N-terminal extension, not shown here. The structures of FopA and PcnR have not yet been solved.

Figure 2. Characterised chromosome-encoded FinO/ProQ-family proteins

For each protein, schematic structures of its select main RNA ligands and a representative molecular mechanism of translational repression are shown, wherever known (see the main text for detailed descriptions). As in the case of plasmid-encoded FinO-like proteins, structural details of the shown interactions are only partially understood. The conserved elements of the FinO/ProQ domain in the crystal structures of L. pneumophila RocC [63] (amino acids 11–125; in complex with the terminator domain of the RocR sRNA, magenta) and N. meningitidis ProQ (amino acids 1–124) [23] and in the NMR structures of Lpp1668 [25] and E. coli ProQ (amino acids 1–133 and 180–232) [24] are coloured in the same way for FinO shown in Figure 1 (see also Figure 3B,C for their annotation and a zoomed-in view of the RocC–RocR complex). The structures are shown from the concave face. RocC and N. meningitidis ProQ also possess unstructured C-terminal extensions, not shown here.

Figure 3. Genealogy of the FinO/ProQ family

(A) Schematic tree showing the diversity and phylogenetic relationships between known FinO/ProQ homologues (adapted and modified from [3,33,50]). Grey arrows show major extra domain acquisition events. (B) Sequence alignment of core domains of the FinO/ProQ homologues reported in literature so-far (COBALT [110]). Dark grey shadowing corresponds to highly conserved residues, light grey, to moderately conserved ones. Structural elements are annotated above the alignment in the same colours as in Figures 1 and 2. The size of extensions is given in parentheses. Magenta arrows point at the residues which were repeatedly found to be required for RNA binding and/or stabilisation [24,25,33,42,43,59,61,64]. (C) Zoom-in view of the RNA-binding site of L. pneumophila RocC [63]. The 3′-end of the RocR sRNA is bound in a pocket formed by several conserved residues labelled in panel (B).

Figure 4. Mobile extensions of FinO/ProQ-like proteins

(A) The crystal structure of N. meningitidis ProQ contains 6 chains in the crystallographic asymmetric unit [23]. Comparison of these individual chains permits to assess the conformational heterogeneity in this protein. The folded core of the protein (formed by the helices α2, α3 and α4, the β-sheet, and the connecting loops) is invariant and likely rigid. By contrast, the helix α1 (red and grey) shows high flexibility, permitting it to sample a variety of conformations. In the first chain (top left), the flexibility of both helices α1 and α5 (blue) is so high that it does not permit to see their extremities at all. (B) Examples of highly complex FinO/ProQ-like proteins with additional folded and/or disordered domains (as predicted by AlphaFold [111]), mined from genomes of understudied proteobacterial groups.

Figure 5. Replicons and FinO/ProQ-family proteins of Salmonella Typhimurium SL1344

Colour code for the RNA species and proteins corresponds to their replicon of origin. Examples of RNA ligands bound by one or several FinO/ProQ-like proteins are provided based on genome-wide interactomic studies [3,4,72]. Prevalent interactions are shown with full lines, whereas lowly populated, occasional binding is rendered in dotted lines.

Figure 6. Evolutionary implications of FinO/ProQ-family proteins

Both negative and positive molecular mechanisms mediated by FinO/ProQ-like proteins contribute in various ways to the evolution of their bacterial hosts. By repressing the replication or conjugation of their own plasmids, FinO-, FopA- and PcnR-like proteins seemingly limit their propagation in bacterial populations, but at the same time they maximise the chances of their maintenance by mitigating the fitness cost to the host. This may have far-reaching ecological and medical consequences, since such mechanisms ensure the spread of associated antibiotic resistances and virulence genes. Chromosome-encoded ProQ homologues can also be associated with significant fitness costs as they support energetically expensive processes (e.g. flagella, T3SS synthesis, translation). However, under some conditions (exposure to antibiotics, infection), they ameliorate the survival chances of bacteria, by contributing to antibiotic persistence and pathogenicity. FinO/ProQ family proteins also play important roles in genomic innovation. Eventually, plasmids and other mobile elements get ‘domesticated’ and their genes, including FinO-like proteins, integrated into the regulatory circuitry of the host. The acquisition of new genes is also regulated by RocC-like systems through the competence control. While this process can drive genome evolution, the failure to limit foreign DNA uptake may impact on the genome stability. Endogenously, ProQ proteins in several species positively regulate proteins involved in genome maintenance and repair and limit the expression of selfish DNA elements, thereby also contributing to the genome stability. In a long-term perspective, FinO/ProQ-like proteins create molecular niches that enable the recruitment of new structured RNAs into post-transcriptional regulatory pathways of the host bacterium. Such new RNAs can be obtained through horizontal transfer, captured from transcriptional noise, or exapted from pre-existing core genome- or genetic element-encoded functional transcripts.