Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region

Park

Proc. Natl. Acad. Sci. U.S.A.

et al. 2020

Self Cite

Many proteins are refractory to targeting because they lack small-molecule binding pockets. An alternative to drugging these proteins directly is to target the messenger (m)RNA that encodes them, thereby reducing protein levels. We describe such an approach for the difficult-to-target protein α-synuclein encoded by the SNCA gene. Multiplication of the SNCA gene locus causes dominantly inherited Parkinson’s disease (PD), and α-synuclein protein aggregates in Lewy bodies and Lewy neurites in sporadic PD. Thus, reducing the expression of α-synuclein protein is expected to have therapeutic value. Fortuitously, the SNCA mRNA has a structured iron-responsive element (IRE) in its 5′ untranslated region (5′ UTR) that controls its translation. Using sequence-based design, we discovered small molecules that target the IRE structure and inhibit SNCA translation in cells, the most potent of which is named Synucleozid. Both in vitro and cellular profiling studies showed Synucleozid directly targets the α-synuclein mRNA 5′ UTR at the designed site. Mechanistic studies revealed that Synucleozid reduces α-synuclein protein levels by decreasing the amount of SNCA mRNA loaded into polysomes, mechanistically providing a cytoprotective effect in cells. Proteome- and transcriptome-wide studies showed that the compound’s selectivity makes Synucleozid suitable for further development. Importantly, transcriptome-wide analysis of mRNAs that encode intrinsically disordered proteins revealed that each has structured regions that could be targeted with small molecules. These findings demonstrate the potential for targeting undruggable proteins at the level of their coding mRNAs. This approach, as applied to SNCA, is a promising disease-modifying therapeutic strategy for PD and other α-synucleinopathies.

Section: Proteome-and Transcriptome-wide Studies To Evaluate Synucleozidsupporting

confidence: 74%

Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA

Park

Proc. Natl. Acad. Sci. U.S.A.

et al. 2020

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Cold Spring Harb Symp Quant Biol

“…re-sults). It is critical that a miRNA binding site be exposed in an unstructured region of the TDMD target RNA (Pawlica et al 2016). However, the great majority of transcripts fulfilling these criteria does not induce TDMD.…”

Section: Outstanding Questionsmentioning

confidence: 99%

How Complementary Targets Expose the microRNA 3′ End for Tailing and Trimming during Target-Directed microRNA Degradation

Pawlica

Sheu‐Gruttadauria

MacRae

et al. 2019

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microRNAs (miRNAs) are crucial for posttranscriptional regulation of messenger RNAs. "Classical" miRNA targets predominantly interact with the miRNA seed sequence located near the miRNA 5 0 end. Interestingly, certain transcripts that exhibit extensive complementarity to the miRNAs 3 0 region, instead of being subjected to regulation, induce miRNA decay in a process termed target-directed miRNA degradation (TDMD). Here, we review recent advances in understanding the molecular mechanisms of TDMD. Specifically, we discuss how extensive miRNA complementarity to TDMD-inducing targets results in displacement of the miRNA 3 0 end from its protective pocket in the Argonaute protein. Unprotected miRNA 3 0 ends are then available for enzymatic attack by still-unidentified cellular enzymes. Identification of these cellular enzymes and discovery of additional TDMD-inducing transcripts are subjects for future research.

“…In addition to the highly complementary binding required for TDMD, proximal auxiliary sequences can boost its activity, as described for the 3′ additional motif in UL144-145 mRNA ( Lee et al, 2013 ). Similarly, the HSUR-1 miR-27-binding region must be available in a conformationally flexible region for TDMD to be active, being evidenced by the fact that HSUR-1 mutants with an intact miR-27 binding site that is artificially sequestered in predicted helices lose their ability to trigger TDMD ( Pawlica et al, 2016 ). The same may be true for more distal sequences within endogenous transcripts.…”

Section: Mechanism Of Tdmdmentioning

confidence: 99%

Target RNAs Strike Back on MicroRNAs

et al. 2018

MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell- or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3′-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3′ end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.