Katharina Semrad

RNA chaperones, RNA annealers and RNA helicases.

RNA molecules face difficulties when folding into their native structures. In the cell, proteins can assist RNAs in reaching their functionally active states by binding and stabilizing a specific structure or, in a quite opposite way, by interacting in a non-specific manner. These proteins can either facilitate RNA-RNA interactions in a reaction termed RNA annealing, or they can resolve non-functional inhibitory structures. The latter is defined as “RNA chaperone activity” and is the main topic of this review. Here we define RNA chaperone activity in a stringent way and we review those proteins for which RNA chaperone activity has been clearly demonstrated. These proteins belong to quite diverse families such as hnRNPs, histone-like proteins, ribosomal proteins, cold shock domain proteins and viral nucleocapsid proteins. DExD/H-box containing RNA helicases are discussed as a special family of enzymes that restructure RNA or RNPs in an ATP-dependent manner. We further address the different mechanisms RNA chaperones might use to promote folding including the recently proposed theory of protein disorder as a key element in triggering RNA-protein interactions. Finally, we present a new website for proteins with RNA chaperone activity which compiles all the information on these proteins with the perspective to promote the understanding of their activity.

Assaying RNA chaperone activity in vivo using a novel RNA folding trap.

In the absence of proteins, RNAs often misfold in vitro due to alternative base pairings which result from the molecule being trapped in inactive conformations. We identify an in vivo folding trap in the T4 phage td gene, caused by nine base pairs between a sequence element in the upstream exon of the td gene and another at the 3′ end of the intron. During translation, the ribosome resolves this interaction; consequently the intron folds correctly and splicing occurs. The introduction of a stop codon upstream of this base pairing prevents resolution of the inactive structure so that splicing cannot proceed. We have used this folding trap to probe for RNA binding proteins which, when overexpressed, either resolve the misfolded structure or impede its formation in vivo. We distinguish between proteins which recognize the intron structure and those which bind non‐specifically and apparently ignore the intron. The first class, e.g. Neurospora crassa CYT‐18, can rescue the exonic trap and intron mutants which cause a structural defect. However, known RNA chaperones such as Escherichia coli StpA and S12 and the HIV protein NCp7, only resolve the exonic trap without suppressing intron mutations. Thus, this structural trap enables detection of RNA chaperone activity in vivo.

Osmolytes stimulate the reconstitution of functional 50S ribosomes from in vitro transcripts of Escherichia coli 23S rRNA

Functional Escherichia coli 50S ribosomal subunits can be reconstituted from their natural rRNA and protein components. However, when the assembly is performed with in vitro-transcribed 23S rRNA, the reconstitution efficiency is diminished by four orders of magnitude. We tested a variety of chemical chaperones (compounds that are typically used for protein folding), putative RNA chaperones (proteins) and ribosome-targeted antibiotics (small-molecule ligands) that might be reasoned to aid in folding and assembly. Addition of the osmolyte trimethylamine-oxide (TMAO) and the ketolide antibiotic telithromycin (HMR3647) to the reconstitution stimulates its efficiency up to 100-fold yielding a substantially improved system for the in vitro analysis of mutant ribosomes.

RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition

RNA chaperone activity is defined as the ability of proteins to either prevent RNA from misfolding or to open up misfolded RNA conformations. One-third of all large ribosomal subunit proteins from E. coli display this activity, with L1 exhibiting one of the highest activities. Here, we demonstrate via the use of in vitro trans- and cis-splicing assays that the RNA chaperone activity of L1 is conserved in all three domains of life. However, thermophilic archaeal L1 proteins do not display RNA chaperone activity under the experimental conditions tested here. Furthermore, L1 does not exhibit RNA chaperone activity when in complexes with its cognate rRNA or mRNA substrates. The evolutionary conservation of the RNA chaperone activity among L1 proteins suggests a functional requirement during ribosome assembly, at least in bacteria, mesophilic archaea and eukarya. Surprisingly, rather than facilitating catalysis, the thermophilic archaeal L1 protein from Methanococcus jannaschii (MjaL1) completely inhibits splicing of the group I thymidylate synthase intron from phage T4. Mutational analysis of MjaL1 excludes the possibility that the inhibitory effect is due to stronger RNA binding. To our knowledge, MjaL1 is the first example of a protein that inhibits group I intron splicing.