Blasi, U. | bioRxiv Science

bioRxiv2022

Polymorphic ribonucleoprotein folding as a basis for translational regulation

The widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes in Pseudomonas aeruginosa. How this broadly acting protein can contribute to the regulation requirements of so many different genes remains puzzling. Here, we describe the structures of higher-order assemblies formed on control regions of different P. aeruginosa target mRNAs by Hfq and its partner protein Crc. Our results show that these assemblies have mRNA-specific quaternary architectures resulting from the combination of multivalent protein-protein interfaces and recognition of patterns in the RNA sequence. The structural polymorphism of the ribonucleoprotein assemblies enables selective translational repression of many different target mRNAs. This system suggests how highly complex regulatory pathways can evolve and be rewired with a simple economy of proteinogenic components. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/480102v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1b34242org.highwire.dtl.DTLVardef@1c31071org.highwire.dtl.DTLVardef@16c8750org.highwire.dtl.DTLVardef@27ca3c_HPS_FORMAT_FIGEXP M_FIG C_FIG The RNA chaperone Hfq, in conjunction with the co-repressor Crc, forms higher order assemblies on nascent mRNAs. These complexes impact on translation of hundreds of transcripts in the pathogen Pseudomonas aeruginosa. Assemblies with different quaternary structures result from the interactions of the proteins with sequence motifs and structural elements in different mRNA targets, as well as from a repertoire of protein-to-protein interfaces. In this way, the combination of RNA sequence and two proteins can generate the diversity required to regulate many genes. It is proposed that the multi-step assembly process is highly cooperative and most likely competes kinetically with translation initiation to silence the targeted transcripts.

molecular biology↗

bioRxiv2018

Architectural principles for Hfq/Crc-mediated regulation of gene expression

The global regulator Hfq facilitates the action of regulatory RNAs in post-transcription gene regulation in many Gram-negative bacteria. In Pseudomonas aeruginosa, Hfq, in conjunction with the catabolite repression protein Crc, was shown to form a complex that directly inhibits translation of target transcripts during carbon catabolite repression. Here, we describe and validate high-resolution cryo-EM structures of the cooperative assembly of Hfq and Crc bound to a translation initiation site. The core assembly is formed through interactions of two cognate RNAs, two Hfq hexamers and a Crc pair. Additional Crc protomers can be recruited to form higher-order assemblies with demonstrated in vivo activity. The structures indicate a distinctive RNA conformation and a pattern of repeating motifs that confer regulatory function. This study not only reveals for the first time how Hfq cooperates with a partner protein to regulate translation but also provides a novel structural basis to explain how an RNA code can guide global regulators to interact cooperatively and regulate many different RNA targets.

biophysics↗